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Polymerization - Science topic

Chemical reaction in which monomeric components are combined to form POLYMERS (e.g., POLYMETHYLMETHACRYLATE).
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Hi researchers. I have deposited a polymer, PANI on Glassy carbon electrode by electrodeposition method. CV results of It showing only the oxidation peak taken in 100mM ferri+ferro solution in 0.1M KCl solution. Why is it so. how can I resolve it?
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Please compare the two electrodes to see if you have successfully produced the polymer film on the GCE. Additionally, confirm that the optimization settings you utilized for your electrodeposition were adequate. If you do have the polymer, you could also try the drop-casting or chemical deposition methods; however, these would be challenging to use with monomer. Another issue is that you used a large amount of probe concentration. In reality, it would be advised to use 1–10 mmol L–1 of equimolar FFC. Thank you.
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Is it possible to quantify the flow without adding any polymeric beads? I'm interested to know whether there's dominant capillary or Marangoni flow. Aby suggestions would really be helpful.
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Thanks, @Mario Castelán, for your thoughts. This can be done, but we might not have enough data in the literature just yet to train these. And also, with machine learning, we can predict the outcome but exactly can we obtain the quantitative data?
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We have prepared molecularly imprinted polymeric nanoparticles by polymerizing functional monomers along with a template. After synthesis, the template is removed by 5 days of dialysis in milliQ water, (acetic acid is added on the second day) to facilitate the template removal.
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Dear all, if you have clear and homogeneous solution, then you may expect interactions. Solubility means there is such mutual interactions. Both water and acetic acid are polars, that's why they are soluble, the same would be with residual monomers, which are automatically polar since they are soluble in water. My Regards
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I'm synthesizing a substituted phthalocyanine from phthalonitrile in n-pentanol solvent using DBU as a base and a metal salt but the colour of reaction mass is not turning blue/green after refluxing as reported in the literature. When I try this reaction in a small scale (50 mg), I get a blue/green colour. What went wrong? Now I am only getting a brown colour formation which may due to polymerization or triazine formation of the substrate. What precautions should I take to always get the desired phthalocyanine product?
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Hi, In small quantities, local overheating is possible. Try using a higher boiling alcohol
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I am planning to electrospun a water-soluble polymer with rGO.
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Ams Jekhan Common solvents for dissolving reduced graphene oxide (rGO) include N,N-Dimethylformamide (DMF), ammonia solution, hydroquinone, hydroxyrazine hydrate, and ascorbic acid.
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can any suggest a suitable solvent or mixture of solvent for the precipitation of Bisphenol -A based polymer.I tried many solvent and combination of solvent but I couldn't precipitate it
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You are most welcome
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"I want to optimize a structure of a polymer using DFT method with Gaussian 09 but the problem is that I can only optimize either the monomer or the complete structure of the polymer. Also, my question is how to draw the polymer structure in the GaussView interface. Please help me if you have an example, thank you."
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"I want to optimize a structure of a polymer using DFT method with Gaussian 09 but the problem is that I can only optimize either the monomer or the complete structure of the polymer. Also, my question is how to draw the polymer structure in the GaussView interface. Please help me if you have an example, thank you."
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Currently TBHP/FF6 M redox initiator is used in my latex polymerization. The by product of TBHP is VOC. Any recommendation for initiators of which by-products are not VOC or grafted to the end of polymer molecules? My reaction conditions: 70-90C, pH 4-6; styrene/acrylic polymer latex. Thermal or redox initialization will be fine. Hopefully, the peroxide is easy to handle.
Thanks!
Jake
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Dear Jigui Li, you can use radiation polymerization, it answers all your conditions and criteria. Free radicals are generated in situ from the solvent and/or the monomers, i. e., no need to use a radical type initiator. My Regards
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A DMA graph of a thermoset polymer gives the storage modulus graph, loss modulus graph and a Tan (delta) graph. Tg of the polymer can be either Storage onset temperature or the Tan (delta) peak temperature in most cases.
In the case, the question is, how can we explain the relationship between half peak width (glass transition)of Tan(delta) and the network structure of the polymer. Can someone explain?
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I would say that width of Tan D peaks in DMA is related to distribution width of the associated relaxing elements. In the case of glass transition, relaxing elements are mobile chain segments in amorphous regions. The wider is the distribution of the segments in terms of their mobility (length, rigidity, packing density, free volume, intermolecular interactions etc.) the wider is the DMA peak. Accordingly, widening of the peak in crosslinked systems may indicate nonuniform crosslinking structure: presence of domains differing in the crosslinking density (length of the segments between the crosslinks).
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Sustained release tablet of anti ulcer drug
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It depends on the nature of drug and log P value hydrophilic/lipiphilic) with this "Like Dissolved By Like".
Basically for tablet you add HPMc and Eudragit suitable for the sustainable formulation.
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  • In our case ,addition of lower wt% (2to 10wt%)of ceramic in polymer salt complex ,The DC conductivity is reduce as compared to the polymer salt complex but if we are going to the higher loading of ceramic, The DC conductivity is order of 10-4 S/cm
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Kaushik Shandilya thank you so much sir
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which silisium compounds are used as car ceramic coating? which Monomer or polymer and additives that are used for car ceramic coating?
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Nano silicon type I think with polymeric materials
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Hi there,
I am having problems with 50ul Matrigel domes completely dissolving in 24 well plates. I am trying to generate organoid cultures, but when I remove the culture media after 2 days the domes are either gone or are partially dissolved. I use 2:1 matrigel:media ratio. I thawed the main vial of matrigel at 4 degrees overnight then put 200ul aliquots at -20 degrees. When they are needed aliquots are defrosted on ice, 24 well plates are preincubated in a 37 degree incubator and I use ice cold tips to establish the domes. I leave the plates at 37 for over an hour before adding warm media very carefully to each well. I have noticed the matrigel looks a bit soft before the media goes on. What am I doing wrong? Surely it should polymerize completely at 37? Anyone else found this or can you identify where I am going wrong?
Thanks!
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Hello Victoria Gillan . Have you got a solution for the matrigel dissolving issue? I am currently facing the same problem. I dissolved the cell pellet in a 1:1 Matrigel: Media ratio and allowed it to polymerize for 10 minutes in a 37C incubator by inverting the plate. When the media is added, the dome dissolved in some wells and becomes soft in others. When observed the next day, all the domes were dissolved. Kindly help me out.
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And also how to compress the system based on surface area of system such that we get new gromacs file at different surface area of polymer molecule? i heard on the fly approach can be used but i don't know what it is, Can someone explain what does on the fly does exactly ?
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Thanks for your response Hamed Zahraee , Is the on the fly approach you mentioned can be used to constrain the polymer surface area at different intervals
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My objective is to find the binding affinity of divalent metal ions with polyacrylic acid (PAA) by Isothermal Titration Calorimetry. In this experiment, I need to prepare 2mM of PAA. The 2mM should be in monomer concentration terms. So, How do I calculate how much mass of polyacrylic acid do I need to measure if the average molecular weight(Mw) of choosen polyacrylic acid is 12000. If someone knows, please tell me in detail with mass calculation strategies.
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Dear Siyanand Kumar Chaudhary, find the average degree of polymerization by deviding 12000 by the mass of the repeating unit which is the same as that of the monomer. What you find is the number of COOH acid group per chain. If you know chain end groups, more accuracy will be brought to your calculation, since the MW weight you are using is not too high to neglect the mass of the chain end-groups. Once you determine the equivalent of COOH groups, then you can prepare any concentration. The one you are targetting is too low, you can reach it by dilution of a known small concentration. By the way, the binding energies or affinity of PAA to metal ions was studied extensively decades ago, good bibliographic research is to be done on PAA polyelectrolytes to avoid repeating what was already done. My Regards
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Hi guys,
Upon searching the literature, I found that DCM and DMF were the most commonly used solvents for electrospinning PLA polymer. Can you please tell me what other alternate solvents can I use to obtain bead-free fibers? I learnt that both DCM and DMF are highly carcinogenic. Thanks
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Ankit Mishra THF and chloroform are also toxic for medical or food technological applications. I am looking specifically for green solvents to dissolve PLA efficiently and effectively. If you do know any, please share it here. Thanks
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I have one equlibrated PIM polymer data file & solvent water data files. I would like to combine both data files together & for that I designed the water block so that it could have 10 angstrom gap from the polymer membrane. After that, I tried with read data command using add apppend offset of lammps. However, the job was aborted every time with that. I also tried with vmd as I have both psf & pdb file but the merge tools in vmd don't have the parameter for polymer so it also didn't work. Could anyone please suggest any external tool that might help to resolve the issue of merging?
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You could try using moltemplate.
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Currently, I'm preparation a homopolymer sodium salt using Sodium Persulfate as initiator and sodium hydpophospoite as CTA. But,my polymer that I've got have high molecular weight. I need your advise how to decrease my polymer molecular weight besides add more volume of water in the initial of the reaction (before polymerization) because I know homopolymer is a solution polymerization so I think they need more solvent so that the molecular weight is lower than before
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Dear all, there are many possibilities to get the required MW. If you have the kinetics curve of the polymerization reaction, i. e., MW vs time or MW vs %conversion, then all to do is to quench the reaction at the time or % conversion corresponding to the targeted MW. The second solution is to do dialysis fractionation with a memebrane with the specific MW cut-off. The third possibility is to do mechanical degradation by shearing either by high speed agitator or passing through low porosity sieves.
If you want to avoid these extra work, choose a solvent with high transfer constant, and reduce the polymerization temperature. Starve feeding of the monomer may also help to reach a moderate MW. My Regards
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HI,
I WAS TRYING TO SYNTHESIS AN AMPHIPHILIC POLYESTER HAVEING BOTH HYDROPHOBIC PART AND HYDROPHILIC PART.
I REACT TETRA PROPENYL SUCCINIC ANHDRIDE (TPSA) AND EPICHLROHYDRIN (ECH) TO FOR A POLYESTER.
SO after getting the polymer, I WANNA ADD POLYETHYLENE GLYCOLMETHYLE ETHER-560 (PEG-ME)TO FORM THE AMPHIPHILIC POLYESTER.
NOTE THAT THE TPSA ACTS AS THE HYDROPHOPHIC PART AND PEG-ME ACT AS THE HYDROPHILIC TAIL.
SO, IN DOING THIS, I WANNA SUBTITUTE THE CHLRONINE ON ECH WITH PEG-ME
I USED TETRA BUTYL AMMONIUM HEXAFLUORO PHOSPHATE AS THE TRASNFERRING AGENT AND SODIUM HYDROXIDE TO NEUTRALIZED THE REACTION.
BUT IM NOT GETTING THE DESIRE PRODUCT.
PLEASE I NEED YOUR SUGGESTIONS.
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Dear Riswat Musbau, why not trying the opposite strategy, i. e., using PEG-macroinitiator to copolymerize the epoxide-anhydride. The following free access review may help as it deals with ROP copolymerization of polyesters and polycarbonates. My Regards
10.1039/C4CC10113H
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How to dissolve cellulose to get a transparent film? kindly suggest me a chemical to convert dissolved polymer into a gel or recommend a plasticizer?
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Hey there P. Saravana Kumari! Let's dive into it. To dissolve cellulose and create a transparent film, you P. Saravana Kumari can use an ionic liquid like 1-ethyl-3-methylimidazolium acetate ([EMIM][OAc]). It's known for its ability to dissolve cellulose effectively, resulting in a clear solution.
Now, for turning the dissolved polymer into a gel, you P. Saravana Kumari might want to consider using a gelling agent like gelatin or agarose. These substances can form a gel when the solution cools down or undergoes a change in pH.
As for plasticizers, you P. Saravana Kumari could go for something like glycerol or polyethylene glycol (PEG). These are commonly used to increase the flexibility and durability of the cellulose film while maintaining its transparency.
Hope this helps! Let me know if you P. Saravana Kumari need more details or have any other questions.
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How can I study the interaction between polymer (eg PVA) and iodine computationally?
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Boubaker Zaidi How many monomer units do we need to consider? Also, iodide ions exist in many forms. Where should we place the iodide ions relative to the monomer?
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Can main group 2 metallocenes be polymerized? By what mechanism may a metallocene form a polymer?
Steric effects do not create a problem for the polymerization of these compounds?
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Phys Chem Chem Phys. 2023 Aug 2; 25(30): 20657–20667.Published online 2023 May 24. doi: 10.1039/d2cp05020jPMCID: PMC10395002PMID: 37482883Revisiting the origin of the bending in group 2 metallocenes AeCp2 (Ae = Be–Ba)† Tetiana Sergeieva,a T. Ilgin Demirer,a Axel Wuttke,b Ricardo A. Mata,📷b André Schäfer,📷a Gerrit-Jan Linker,📷c and Diego M. Andrada📷aAuthor information Article notes Copyright and License information PMC DisclaimerSupplementary MaterialsAssociated Data Go to:Abstract Metallocenes are well-established compounds in organometallic chemistry, and can exhibit either a coplanar structure or a bent structure according to the nature of the metal center (E) and the cyclopentadienyl ligands (Cp). Herein, we re-examine the chemical bonding to underline the origins of the geometry and stability observed experimentally. To this end, we have analysed a series of group 2 metallocenes [Ae(C5R5)2] (Ae = Be–Ba and R = H, Me, F, Cl, Br, and I) with a combination of computational methods, namely energy decomposition analysis (EDA), polarizability model (PM), and dispersion interaction densities (DIDs). Although the metal–ligand bonding nature is mainly an electrostatic interaction (65–78%), the covalent character is not negligible (33–22%). Notably, the heavier the metal center, the stronger the d-orbital interaction with a 50% contribution to the total covalent interaction. The dispersion interaction between the Cp ligands counts only for 1% of the interaction. Despite that orbital contributions become stronger for heavier metals, they never represent the energy main term. Instead, given the electrostatic nature of the metallocene bonds, we propose a model based on polarizability, which faithfully predicts the bending angle. Although dispersion interactions have a fair contribution to strengthen the bending angle, the polarizability plays a major role.Metallocenes are well-established compounds in organometallic chemistry, which can exhibit either a coplanar structure or a bent structure according to the nature of the metal center (E) and cyclopentadienyl ligands (Cp).📷Go to:Introduction More than seventy years ago, Kealy, Pauson, Miller, Tebboth and Tremaine described ferrocene Fe(Cp)2 for the first time, laying the foundation for research on the metallocene family.1–10 Over the years, these compounds have evolved from only a curiosity into well-recognized reagents in organometallic chemistry, with applications ranging from coordination chemistry to homogenous catalysis and even industrial processes.11 To date, many examples of sandwich- or half-sandwich-type complexes with the formula E(Cp)n (n = 1–4) have been prepared and structurally characterized, in which E is a main-group element or a transition metal.11 In particular, their structures have drawn much attention as the understanding of the bonding provides guidelines for engineering their stoichiometric and catalytic reactivity.Attempts for modelling metallocene structures were developed parallel to the structural elucidation of ferrocene, and understanding the chemical bonding between the central atom and the cyclopentadienyl ligands is challenging using the existing heuristic models.7–9 Originally, the bond between the central iron atom and the Cp rings was assumed to be an electron sharing σ-type (C–Fe–C), given the lack of X-ray analysis, although the possibility of an ionic interaction ([Fe2+] [Cp−]2) was discussed.1 However, the surprisingly high thermal stability and its remarkable chemical inertness toward acids and bases could not be explained with these proposed bonding modes. Independently, Fischer3 and a group of scientists including Wilkinson, Rosenblum, Whiting, and Woodward10 proposed the metal–ligand interaction as a π-complexation. The subsequent analysis by Pfab, Eiland and Pepinsky confirmed the η5 binding pattern and the 6π electron aromatic character of the Cp ligands.4 Shortly after, Orgel used molecular orbital (MO) theory to explain the Fe–Cp bonding in ferrocene. The binding interaction was explained as formed by two “covalent–ionic” bonds resulting from the mixing of metals with Cp− orbitals, and two “donor” bonds, when electrons located at the dx2−y2, dxy orbitals of iron donate into vacant antibonding orbitals of the Cp ligands.5The first electronic structure description was reported about 20 years after the structure elucidation.12,13 Although its η5 coordination was reproduced at the Hartree–Fock (HF) level, the Fe–C bond lengths were poorly predicted.14 Years later, Koch, Jørgensen, and Helgaker achieved a better theoretical structure by performing CCSD and CCSD(T) calculations.15 Many theoretical calculations have been reported to provide quantitative and qualitative insights into the bonding nature of metallocenes. The extension of the Dewar–Chatt–Duncanson model for ferrocene allows for the discussion of the chemical bond in terms of donor–acceptor interactions. With a strong electrostatic nature (51%), the covalent part is predicted as π-donation from MOs of the Cp− ligands to the empty orbitals of the Fe2+ ion and a back donation from the Fe to the π* orbitals of the ligands.16The replacement of Fe with main-group elements from the s- or p-block, in particular with alkaline earth metals of group 2 (Ae), or heavy elements of group 14, has attracted much attention in the light of their preferred oxidation state of +2, ever since Fischer and co-workers reported magnesocene,17 calcocene,18 stannocene,19 and plumbocene,20 just a few years after the discovery of ferrocene.21–24 A common observation was a more labile E–Cp bond, which was explained by the weaker π-type interaction in view of the absence of d-orbitals on the bonding. Notably, the bonding nature changes from 49% covalent in Cp2Fe to being predominantly ionic in the case of s-block metallocenes and slightly more covalent when the central atom is a p-block element.16,25Aside from the bond nature, numerous reports attempted to explain the geometrical model of sandwich complexes. A general observation in metallocene chemistry is that structures have either a coplanar or a bent orientation of the Cp rings relative to the central atom. While the classical ferrocene Fe(Cp)2 and Fe(Cp*)2 ligands are clearly coplanar, other complexes exhibit a bent structure, i.e. Sn(Cp)2 and Pb(Cp)2. Such a distortion has been ascribed to the presence of a lone-pair at the central atom following the traditional valence-shell electron-pair-repulsion (VSEPR) model.26 However, this does not account for the subtleties of orbital interactions that influence molecular shapes and thus cannot justify bend geometries of many other complexes, the so-called non-VSEPR structures, among them are heavy alkaline earth metals (Ca, Sr, and Ba) sandwich compounds.Numerous models aiming at a general understanding of the structure, bonding and reactivity of such molecules have been proposed. The findings from experimental and computational investigations regarding the reason for the bending of metallocenes of heavier alkaline earth metals of group 2, which does not follow the valence shell electron pair repulsion theory model's prediction, can be categorized into four groups (Fig. 1):📷Fig. 1Illustration of models used to explain the bending of metallocenes. (A) Molecular orbital theory model (i). (B) Polarization model (ii). (C) Weak interaction concept (iii). (D) Agostic interaction model (iv).(i) Molecular orbital (MO) theory model. In 1953, Walsh27 proposed a molecular orbital diagram and linked the angle of AB2 molecules as a function of molecular orbital energies. Later, Hayes addressed the bending of heavy alkaline-earth dihalides by evoking this diagram, although with some modifications.28 The authors suggested to take unoccupied d-orbitals of Ca, Sr and Ba into account. This was supported by the energetics of the s-, p- and d-orbitals of these elements. The d-orbitals of Be and Mg lay energetically above the level of the p-orbitals and hence do not have a strong participation in binding. Thus, the symmetry of the valence p-orbitals leads to a coplanar structure for a better orbital overlap. In contrast, the energetic arrangement of Ca, Sr and Ba orbitals is different, which results in the contribution of the d-orbitals to the Ae–Cp bonding with an optimal overlap corresponding to bent geometries.(ii) Polarization model. Klemperer and co-workers observed a permanent electric dipole moment for monomeric dihalides of heavy alkaline earth elements, suggesting a bent arrangement.29 This finding was linked to the polarized-ion model, where large cations may be significantly polarized by anions due to charge–dipole and dipole–dipole interactions. In fact, these simple classical arguments were drawn by Debye to give a qualitative description for the angle in H2O.30 As such, molecular bending is related to the polarizability of the central atom and the polarizing power of the ligands. Gigli applied the polarizable Rittner type ion model to develop a quantitative prediction of dihalide dimer geometries.31 By splitting charge–dipole and dipole–dipole moment interactions into individual contributions, it was proposed that the major role in stabilization of linear or bent geometries is dependent on the magnitude of the induced dipole moment of the central cation. Among a large range of dipole moment values applied to the system, barium halides always showed a bent configuration, while strontium analogues adopt a linear form when the induced dipole is significantly lower.(iii) Weak interaction concept. An alternative explanation for the bending of alkaline-earth metal complexes with Cp* ligands was discussed by Andersen et al.32 The bending energy was found to be relatively small (0.5 kcal mol−1 for [Ca(Cp*)2]) and the tilting was described in terms of maximizing the van der Waals (VdW) attractions between the methyl groups of two Cp* rings. Bosnich and co-workers re-evaluated this “weak interaction” concept and expanded the list of compounds to complexes such as SrCp*2, BaCp*2, SmCp*2, and EuCp*2.33 The conclusion regarding the importance of the VdW interactions was made based on the calculations of ΔEVdW, which referred to the VdW energy difference between the linear and bent geometries. The increase of ΔEVdW values with an increase of the metal radius was ascribed to the weakening of VdW attractive forces in a linear geometry. However, Huffman and co-workers postulated that the length of intramolecular methyl-methyl contacts is in the range of 3.55–3.59 Å, regardless the radii of the central atoms (Ca, Ba, Yb, Sm, and Eu) in sandwich complex bearing Cp* ligands.34 One could interpret this finding in the way that metallocenes with large central cations and longer M–Cp distances should be more bent to enhance VdW interactions. It should be noted, however, that many studies do not rule out the polarizability model and consider these strengths to reinforce each other.32,35(iv) Agostic interaction model. This hypothesis has been formulated relatively recently, after recognizing the importance of three-center–two-electron (3c2e) C–H⋯[E] bonds,36 thus an interaction between a C–H bond and a metal center with relatively high Lewis acidic character. Evidence of intermolecular agostic interactions in metallocenes of alkaline earth metals (CaCp* and BaCp*) has been invoked by Huffman as an explanation for the molecular structure and lattice pattern observed by X-ray diffraction.34 However, the absence of a clear trend in the packing arrangement cannot provide a clear picture of bending behaviour in the crystals. A similar conclusion was drawn by Pal et al., based on the performed calculation of noncovalent interactions (NCIs) and topological analysis within the quantum theory of atoms in molecules (QTAIM) for MgCp*2 and CaCp*2 complexes.37 Although the geometrical, topological and NBO analysis interpretations of the C–H⋯Mg/Ca interactions to be pregostic, other forces such as VdW attraction between two Cp* rings were proposed to be the driving force of bending.In view of the fact that the questions about the bonding situation in alkaline earth metal metallocenes were often controversially discussed because of vaguely defined concepts, we aim to address this in terms of well-established quantum chemical expressions, in the current work. The set of compounds in this study consists of unsubstituted metallocenes Ae(Cp)2, their methylated derivatives Ae(Cp*)2, and their penta-halogenated analogues Ae(C5R5), where R refers to F, Cl, Br, and I. We performed a series of analyses using energy decomposition analysis (EDA), the calculation of dispersion interaction density (DID) and polarizability to evaluate the existing concepts on the structure of metallocenes.Go to:Computational details General Geometry optimizations were performed using the Gaussian 16 C01 software suite.38 The geometry optimizations for unsubstituted complexes with the general structure Ae(Cp)2 were carried out using density functional theory (DFT) BP86,39–41 B3LYP,42,43 M06-2X44 functionals with Grimme dispersion corrections D345 and the Becke-Jonson damping function46 in combination of def2-TZVPP47 basis sets without any symmetry restrictions. Substituted metallocenes [Ae(C5R5)2] (Ae = Be-Ba and R = Me, F, Cl, Br, and I) were optimized at the B3LYP-D3(BJ)/def2-TZVPP level of theory. The stationary points were located with the Berny algorithm48 using redundant internal coordinates. Analytical Hessians were computed to determine the nature of stationary points (one and zero imaginary frequencies for transition states and minima, respectively)49 and to calculate unscaled zero-point energies (ZPEs) as well as thermal corrections and entropy effects using the standard statistical-mechanics relationships for an ideal gas.To further evaluate bond dissociation energies (De), single-point energy calculations using the LCCSD(T)50–58 methods were performed on B3LYP-D3(BJ)/def2-TZVPP optimized geometries using the program package Molpro2019.1.59 The cc-pVTZ basis set was used for carbon hydrogen, fluorine, chlorine and bromine, the cc-pCVTZ basis set was used for beryllium, magnesium and calcium, and the cc-pVTZ-PP60 basis set was used for strontium, barium and iodine.61,62 The LCCSD(T) calculations were carried out using Pipek-Mezey localized orbitals.63 The domains were determined with the use of natural population analysis criteria, with NPA = 0.03.The natural bond orbital (NBO)64,65 partial charges were computed at B3LYP-D3(BJ)/def2-TZVPP using NBO 7.0.66We calculate the atomic polarizability of the metal atom in the metallocenes in support of the polarizability model for the chemical angle. Single point calculations were performed, at the aforementioned optimized structures, using the local properties module LoProp67 of the Molcas software68 at the B3LYP/ANO-RCC-VTZP level of theory.42,43Energy decomposition analysis The nature of the chemical bonds was investigated by means of the energy decomposition analysis (EDA) method, which was developed by Morokuma69 and Ziegler and Rauk.70,71 The bonding analysis focuses on the instantaneous interaction energy ΔEint of a bond A–B between two fragments A and B in the particular electronic reference state and in the frozen geometry AB. This energy is divided into four main components (eqn (1)):ΔEint = ΔEelst + ΔEPauli + ΔEorb + ΔEdisp1The term ΔEelst corresponds to the classical electrostatic interaction between the unperturbed charge distributions of the prepared atoms (or fragments) and it is usually attractive. The Pauli repulsion ΔEPauli is the energy change associated with the transformation from the superposition of the unperturbed wave functions (the Slater determinant of the Kohn-Sham orbitals) of the isolated fragments to the wave function Ψ0 = [ΨAΨB], which appropriately obeys the Pauli principle through explicit antisymmetrization (Â operator) and renormalization (N = constant) of the product wave function. It comprises the destabilizing interactions between electrons of the same spin on either fragment. The orbital interaction ΔEorb accounts for charge transfer and polarization effects.72 In the case that the Grimme dispersion corrections45,46 are computed, the term ΔEdisp is added to the equation 1 (eqn (1)). Further details on the EDA method can be found in the literature.73,74 In the case of C5R5−, the relaxation of the fragments to their equilibrium geometries at the electronic ground state is termed ΔEprep, because it may be considered as the preparation energy for chemical bonding. The addition of ΔEprep to the intrinsic interaction energy ΔEint gives the total energy ΔE, which is – by definition with an opposite sign – the bond dissociation energy De:ΔE(−De) = ΔEint + ΔEprep2The EDA-NOCV method combines the EDA with the natural orbitals for chemical valence (NOCV) to decompose the orbital interaction term ΔEorb into pairwise contributions. The NOCVs Ψi are defined as the eigenvector of the valence operator, , given by equation (eqn (3)):VΨi = viΨi3In the EDA–NOCV scheme, the orbital interaction term, ΔEorb, is given by equation (eqn 4):📷4where FTS−k,−k and FTSk,k are the diagonal transition state Kohn–Sham matrix elements corresponding to NOCVs with the eigenvalues −νk and νk, respectively. The ΔEorbk term for a particular type of bond is assigned by the visual inspection of the shape of the deformation density Δρk. The later term is a measure of the size of the charge deformation and it provides a visual notion of the charge flow that is associated with the pairwise orbital interaction. The EDA-NOCV scheme thus provides both qualitative and quantitative information about the strength of orbital interactions in chemical bonds. The EDA-NOCV calculations were carried out using ADF2019.101. The basis sets for all elements have triple-ζ quality augmented by two sets of polarization functions and one set of diffuse function. Core electrons were treated by the frozen-core approximation. This level of theory is denoted as BP86-D3(BJ)/TZ2P.75 Scalar relativistic effects have been incorporated by applying the zeroth-order regular approximation (ZORA).76Dispersion interaction density Dispersion interaction densities (DIDs) were computed as proposed at the PAO-LMP2/cc-pCVDZ&cc-pVDZ level of theory.77 The Voxel DIDs78 are plotted using the ParaView Software.79Go to:Results and discussion This section is divided as follows: first, the results and discussion on the geometry and bond dissociation of different metallocenes are presented (Section A). We then discuss the chemical bonding by dispersion interactions, and energy decomposition analysis (Section B). We finish with a model to predict the bending angle in metallocenes based on the polarizability model.A. Geometry and bond energies Unsubstituted metallocenes [Ae(Cp)2] Fig. 2 shows the optimized structures of all complexes without symmetry constrain. When a complex is enforced coplanar, two poses are possible, namely staggered (D5d) or eclipsed (D5h). The small energetic difference within 2 kcal mol−1 (being the higher for [Be(Cp)2]) reflects the flat PES and rapid rotation of the Cp rings, which is in good agreement with previous observations.80 Another important aspect of these compounds is the coordination mode of the Cp rings relative to a central atom. All obtained structures shown in Fig. 2 possess the η5:η5 coordination, except Be(Cp)2, where a cation binds in a η5 manner to one Cp and η1 to another. This unusual “slipped sandwich” for beryllocene was previously observed by X-ray analysis81 and discussed in numerous theoretical studies.82,83 For this reason, we exclude Be(Cp)2 from the chemical bond discussion.📷Fig. 2Optimized geometries of group 2 metallocenes [Ae(Cp)2] (Ae = Be–Ba) at the B3LYP-D3(BJ)/def2-TZVPP level of theory along with β angles in [°].Table 1 presents the selected geometrical parameters, bond dissociation energies and natural atomic partial charges of the central element (Ae). As expected, the distances between Cp rings (geometrical centre) and central atoms are elongated with the increase of the radii of the central element in the series Mg–Ba and range from 2.00 to 2.72 Å. The values of β angles (Table 1) predicted magnesocene being coplanar, while strontocene and barocene are bent, regardless of the functional being used. This is in agreement with previously reported findings.84–87 Notably, the calcocene geometry significantly depends on the choice of the DFT level of theory. An optimization of Ca(Cp)2 with B3LYP leads to a coplanar structure, while BP86 and M06-2X furnished a bent structure (see the ESI,† Table S1). To examine the reliability of considered DFT methods for the prediction of calcocene bending situation, we carried out the rigid scan of PES along the Cp–Ca–Cp angle (140–180°) at the LCCSD/cc-pCVTZ&cc-pVTZ level of theory. The flat pattern of the PES (ESI,† Fig. S2) makes the estimation of functional performance to be difficult. Furthermore, the absence of experimental evidence of bending for monomeric calcocene88 and significant debates on this topic among theoretical reports85,89,90 also cannot provide an unambiguous answer regarding the bending of CaCp2.C5R5–Ae bond lengths, C5R5–Ae–C5R5 angles, bond dissociation energies (De) and NBO partial charges calculated at B3LYP-D3(BJ)/def2-TZVPP and LCCSD(T)/cc-pCVTZ&cc-pVTZ {in curly brackets}. Ae = Be–Ba and R =H, Me, F, Cl, Br, and IAe[Ae(Cp)2][Ae(Cp*)2][Ae(C5F5)2][Ae(C5Cl5)2][Ae(C5Br5)2][Ae(C5I5)2]C5R5–Ae bond lengths, ÅBe—1.6491.6351.6391.6561.676Mg2.0001.9592.0281.9871.9811.983Ca2.3512.3152.3672.3372.3362.328Sr2.5422.5002.5592.5202.5242.524Ba2.7222.6872.7312.7022.7132.718C5R5–Ae–C5R5 angles, degBe—179.9179.9179.9179.9179.9Mg179.9179.8180.0179.9179.9179.8Ca178.1158.1150.2151.1154.9163.9Sr165.1149.3155.6145.4148.0153.6Ba138.2139.4142.2138.5142.4148.5 D e, kcal mol−1aBe713.3{724.2}725.0{725.7}648.1{654.8}629.7{633.6}625.3{626.9}628.3{627.8}Mg576.8{574.1}583.6{573.6}506.7{502.5}493.1{484.7}492.7{482.0}501.7{484.0}Ca501.8{500.6}503.6{495.0}439.3{435.3}429.6{420.7}428.8{418.3}436.2{420.8}Sr464.7{467.2}465.5{460.4}406.5{406.6}398.2{393.9}397.3{392.0}403.5{393.9}Ba437.0{441.3}439.4{436.5}385.0{386.0}378.1{376.0}376.4{374.3}381.6{376.1}NPA chargesBe+1.61+1.72+1.55+1.68+1.71+1.74Mg+1.80+1.88+1.72+1.81+1.81+1.80Ca+1.78+1.79+1.72+1.74+1.71+1.67Sr+1.81+1.81+1.75+1.77+1.76+1.72Ba+1.78+1.77+1.72+1.76+1.76+1.74Open in a separate windowaThe dissociation energies (De) considering the [Ae(C5R5)2] → Ae2+ + 2 C5R5− dissociation.The calculated bond dissociation energies (De) suggest that the strength of Ae–Cp bonds is decreasing when going down the group from Mg to Ba. This finding is in agreement with the previously published data that Cp complexes of the heavier alkaline earth metals have a tendency to dissociate.91 Theoretically predicted partial charges at the central atoms Ae do not change within the series Mg–Ba and are determined to be approximately +1.8 au.Penta-methyl-cyclopentadienyl metallocenes [Ae(Cp*)2] The substitution of the hydrogens by methyl groups on the Cp rings results in minor structural changes for Be, Mg, and Ba metallocenes, but significant effects can be observed for the Ca and Sr counterparts (Fig. 3 and 4). While the bond lengths Cp*–Ae in calcocene and strontocene exhibit an alteration of 0.04 Å, the bending angles become significantly more acute by ca. 20° to 26°. The dissociation energies De for all complexes calculated at B3LYP-D3(BJ) increase with respect to the Cp systems by about 10 kcal mol−1. However, the LCCSD(T) calculations predict similar dissociation energies. Such a difference can be due to the stronger electron-donating properties of methyl groups, which would lead to a stronger orbital interaction between Cp* and the central atom. Also, the dispersion interaction between the Cp* groups can lead to higher dissociation energies. Notably, the natural partial charges at the central atom become more positive for Be and Mg, while the heavier analogues show no differences with respect to the Cp analogues.📷Fig. 3Optimized geometries of metallocenes for [Ae(Cp*)2] (Ae = Be–Ba) at the B3LYP-D3(BJ)/def2-TZVPP level of theory along with angles in degrees. Ae = Be–Ba and Cp* = a methylated cyclopentadienyl anion. Hydrogens are omitted for clarity.📷Fig. 4Optimized geometries of group 2 metallocenes [Ae(C5F5)2] (Ae = Be–Ba) at the B3LYP-D3(BJ)/def2-TZVPP level of theory along with angles in [°].Penta-halogenated-cyclopentadienyl metallocenes [Ae(C5R5)2] In order to assess the influence of the Cp substituents on the metallocene structures, we have introduced penta-halogenated cyclopentadienyl groups. Although most of the main group metallocenes have not been isolated experimentally,21,22,24,92–94 such a modification leads to a better understanding of the ruling electronic effect. The proposed derivatives would introduce a variety of donation properties of the Cp π-system as well as the dispersion interaction between the rings. Thus, [Ae(C5R5)2] complexes show similar structural features to those in the case of [Ae(Cp*)2] with a coplanar structure of Be and Mg, and a bent structure of Ca, Sr, and Ba. It is worth mentioning that the halogen atoms take electron density from the ring via an induction effect, while they donate density by a mesomeric effect. Notably, there is a trend between the π-donation strength (the resonance component of the electronic effect, σR = Cl > Br > I = −0.19 > −0.22 > −0.24),95 and the decreasing Cp–Ae–Cp angle. The higher is the ability to donate electron density to the Cp π-system the more deviation from planarity is observed. For instance, [Ca(C5Cl5)2] is bent by 151.1°, while [Ca(C5Br5)2], and [Ca(C5I5)2] analogues are 154.9°, and 163.9°, respectively. In contrast, tracing a correlation of bending in the C5F5 case is difficult as a result of an interplay between strong mesomeric (R = −0.39) and inductive effects (F = 0.45) for the F substituent.95 This trend is followed by Sr and Ba congeners (see Table 1). Alternatively, the steric clash between the R substituents might lead to the same observation. However, [Ba(C5I5)2] exhibits an I⋯I distance (4.442 Å) which is already longer than the sum of the van der Waals radii (3.96 Å).Natural partial charges are comparable with those obtained for Cp and Cp*. Extreme cases such as [Be(C5F5)2] show a less positively charged central atoms than the rest of the molecules in the series. In terms of the bond dissociation energies De, the halogenated systems bear between 100 and 50 kcal mol−1 less than Cp congeners. This suggests that the electrostatic interaction should not be strongly affected, while other physical factors might be playing a role for the weaker interaction.B. Chemical bonding and bending Dispersion interactions Among the models for alkaline-earth metallocene structures, it is well-recognized that the dispersion interaction between the Cp groups enforces to bend their structures when the central metal is polarizable enough.37 Calcocene has been in the spotlight of discussion since the theoretical structures display a sharp dependence on the Cp substituents. Specifically, the dispersion interaction between methyl groups of Cp* rings has been ascribed as the responsible factor for bending the structure from 178.1° to 158.1° (Table 1). However, some polarization can also play a role since d-orbitals are significantly populated.96 To sort these interactions, Grabowsky and co-workers optimized [Ca(Cp*)2] structures at the B3LYP level of theory with and without the dispersion term. The results showed that B3LYP-D3 favours a bent geometry with an energetic preference of ∼1 kcal mol−1, while excluding dispersion leads to a coplanar structure. In this regard, the so-called “dispersion theory”, Kaltsoyannis and Russo suggested a weak interaction between two Cp* rings, then (Cp*)22− should also be a bent structure, if the nature of the central metal is not important.97,98In the absence of the centre metal, we have computed the energy between the C5R5 groups in two different geometries, bent (140°) and coplanar (180°), at different distances (Fig. 5A and B). While the Cp system shows a lower energy for the coplanar structure at short distances, at longer distances the bent structure becomes more favourable. Notably, in the case of Cp*, the coplanar structure is more stable at short distances, while at longer distances the bent structure sets in (at 4.7 Å) since the energy penalty becomes negligible. These results indicate that the cation is necessary for a bent structure where the dispersion interaction might not be the main determinant of the distortion. To expand aforementioned ideas, we performed a rigid scan of PES for planar (180°) vs. bent (140°) (C5R5)22− structures at different distances CpX(centroid)–CpX(centroid) ranging from 4.0 to 6.0 Å (Fig. 5C and D), which covers the range of atomic radii considered. Firstly, the preference of (C5F5)22− to be coplanar at any point of the curve (Fig. 5D), which is in sharp contrast to the behaviour of [Ae(C5F5)2] (Table 1), indicating that the presence of the central atom has an important role. The same conclusion can be outlined analysing the trends for (C5I5)22−. In contrast, (Cp)22− and (Cp*)22− indeed behave very similarly to analogous [Ae(Cp)2] and [Ae(Cp*)2] complexes, now suggesting that the central atom has a lower impact on the bending. Furthermore, an inspection of plots (Fig. 5B) reveals that the bending of (Cp*)22− strongly depends on the distance between aromatic rings. (Cp*)22− is bent when the distance is 4.8–6.0 Å, while planar at 4.0–4.7 Å. This finding contradicts a Kaltsoyannis argument about the necessity of the cation for bending, since the model they utilized was limited to specific CpX–CpX lengths. At this point, one cannot exclude the dispersion to be a driving force of the bending.📷Fig. 5Rigid potential energy surface scans of planar vs. bent metalloceneanions (Cp)22− as a function of the CpX–CpX distance performed at the B3LYP-D3(BJ)/def2-TZVPP level of theory (ΔErel = Ebent − Elinear).From the optimised structures, we calculated at the PAO-LMP2/cc-pCVTZ&cc-pVTZ level the dispersion interactions between the C5R5 rings (R = H and Me). Given the local character of occupied and virtual orbitals in the local correlation treatments, the intermolecular effects due to double excitations from occupied orbitals of one unit into virtual orbitals of the same unit and intermolecular effects due to excitations involving orbitals from both units can be divided. Additionally, the interactions (Cp⋯Cp) can be dissected into dispersion effects, exchange dispersion, and ionic contributions.99–101Table 2 provides the results of the energy decomposition of the local correlation approach, and the exemplary dispersion interaction density (DID)77 profiles of Be(Cp)2, Be(Cp*)2, Ca(Cp)2 and Ca(Cp*)2 are shown in Fig. 6. As expected, the dispersion interaction between the rings is stronger for the beryllium complexes and drastically diminishes with the heavier analogues. The Cp* system doubles the amount of the dissection interaction in Cp systems, in good agreement with the higher dissociation energy values. The DID profile shows that the π–π interaction between the rings dominates the dispersion profile in most cases, but for Cp* starting from Ca the close C–H contacts rule the interaction.Energy decomposition within the local correlation treatment for [Ae(C5R5)2] (R = H and Me) at PAO-LMP2/cc-pCVTZ&cc-pVTZ. Values are in kcal mol−1ΔEintraΔEdisp exΔEdispΔEionicBe(Cp)2−18.1−0.1−10.8−7.2Mg(Cp)2−6.30.0−4.5−1.8Ca(Cp)2−3.80.0−2.8−1.0Sr(Cp)2−2.60.0−2.0−0.6Ba(Cp)2−9.20.0−2.2−7.0Be(Cp*)2−30.6−0.1−20.5−9.9Mg(Cp*)2−12.40.0−9.4−2.9Ca(Cp*)2−11.20.0−6.7−4.5Sr(Cp*)2−7.90.0−4.9−3.0Ba(Cp*)2−39.00.0−4.9−34.1Open in a separate window📷Fig. 6Dispersion interaction density (DID) plots calculated at the PAO-LMP2/cc-pCVTZ&cc-pVTZ level of theory. The brown zones indicate regions of electron density in a molecule which interacts strongly by dispersion interactions with the other molecule. Blue stands for weaker/diffuse contributions.Molecular orbitals and polarizability What is the role of the central metal? An alternative explanation of the metallocene bending relates to the type and shape of the orbitals participating in bond formation. According to this concept, beryllocene and magnesocene are coplanar, which results from the engagement of only valence s and p orbitals for Be and Mg into σ bonding with ligands. However, the involvement of d-orbitals in the case of Ca, Sr, Ba induces bending.To gain a quantitative insight into the role of the main orbital interaction, we performed the energy decomposition analysis (EDA) of the complexes maintaining the same C5R5–Ae distance given by the full optimization but changing the CpX–Ae–CpX angle from 140 to 180°. The EDA is a useful tool to assess the nature of the chemical bond and to identify the driving forces behind the binding interaction.102 The nature of the energy components has been a matter of debate, given the path-dependent nature.103–105 However, the fragmentation schemes used in a consistent manner generate reliable trends.106,107 We have used three fragment schemes to take into account the interaction between the Cp– moieties. The result of splitting ΔEint is shown in Fig. 7. Inspection of the EDA terms revealed that the trend in stabilizing bent structures by ΔEorb, ΔEdisp and ΔEelst terms counteract by the ΔEPauli forcing metallocenes to adopt the coplanar configuration and the interplay between these attractive and repulsive components determines the extent of deformation. Notably, the electrostatic interaction favours a coplanar structure for most of the metallocenes, with the exception of Cp. This finding shows that the previously controversial orbital interaction and dispersion in fact accompany each other promoting a bent structure. Note, however, that the dispersion interaction represents a minor factor (1%) in comparison to the orbital interaction.📷Fig. 7Energy decomposition analysis at the BP86-D3(BJ)/TZ2P level of theory for the [Ae(C5R5)2] complexes. Ae = Be–Ba and R = H, Me, and F–I. Energy values are given in kcal mol−1. (A) Orbital interaction, (B) electrostatic interaction, (C) dispersion interaction, and (D) Pauli repulsion.Deeper insights into the nature of the orbital interaction are available from the combination of EDA with natural orbitals for chemical valence calculations (EDA-NOCV).108,109 This method deconstructs the orbital term (ΔEorb) into components (ΔEorbρ(i)) that provide an energetic estimation of a given deformation density (ρ(i)), which is related to a particular electron flow channel, and consequently the amount of charge transferred, Δq(i) = |ν(i)|, for the bonding between the interacting fragments. The most interesting results are obtained by breaking down the orbital term ΔEorb. Fig. 8 shows the orbital diagram for the most important orbital interaction in a coplanar situation (D5d). In this situation, s and dz2 can interact with the a1g combination of the C5R5 rings. The p orbitals interact with the e1u and a2u orbitals, while the remaining d orbitals can interact with the e1g C5R5 orbitals. Fig. 9 represents the shape of the deformation densities ν1–ν6, showing the charge flow and the most important fragment orbitals which are involved in the pairwise donor–acceptor bonding for the MgCp2 metallocene complexes. The scheme in Fig. 8 can be associated with the interactions displayed in Fig. 9. The color coding red to blue illustrates the direction of the charge flow. EDA-NOCV reveals that the major interaction originates from the participation of s and p orbitals, which is because the symmetry keeps the complexes co-planar. When going down in the group from Mg to Ba, the contribution of d-orbitals is increasing triggering the sandwiches to bent their geometries (ESI,† Table S2 and Fig. S3–S7). For instance, the acceptor contributions of the formally empty d orbital to the total orbital interaction are Mg(Cp)2 (19.2%), Ca(Cp)2 (49.5%), Sr(Cp)2 (46.9%), and Ba(Cp)2 (47.2%). With the contribution of the d orbitals in addition to the small contribution of the dispersion interactions, we benchmarked the model based on the polarizability of the central atom.📷Fig. 8Schematic orbital correlation diagram for the coplanar complex Mg(Cp)2.📷Fig. 9Plot of the deformation densities Δρ of the pairwise orbital interactions between Mg2+ in its A10 electronic state and (Cp2)2−, associated energies ΔE (in kcal mol−1) and eigenvalues ν (in a.u.). The red color shows the charge outflow, whereas the blue color shows the charge density accumulation. The shape of the most important interacting occupied and vacant orbitals of the fragments.Polarizability model Given the increasing importance of the d-orbital involvement and associated deformation densities in metallocenes with the heavier metal center, and hence its polarizability, we addressed a model that can reproduce the experimental observation. From the extended Debye polarizability (EDP) model,110–112 it follows that bending can be initiated when the electron density around the metal center atom (Ae) is sufficiently polarizable. As an extension of Debye's model for H2O,30 the EDP model provides a more balanced description by treating the centre and outer atoms equally in allowing induced dipoles not only at the centre atom but also at the ligands. For bent geometries, the EDP model predicts that the larger Ae polarizability gives rise to a smaller Cp–Ae–Cp angle. The NBO charge on the metal center inside the metallocene is estimated to be in the range of +1.6 to +1.8 (Table 1). The occupancy of the valence s shell of the metal will be almost depleted. The polarizability around Ae in the metallocenes is expected to be small for Be and Mg, but in the series Ae = Ca, Sr, and Ba we expect some polarizability to originate from sub-valence electrons. The optimized geometries of group 2 metallocenes (Table 1) provide a way to test the dependence of the angle on the polarizability of the centre atom. Omitting the linear Be and Mg centered metallocenes, we calculate the polarizability around Ae in the Ca, Sr and Ba centered metallocenes. In Fig. 10, the C5R5–Ae–C5R5 angle is plotted against the calculated Ae polarizability. We broadly see the predicted trend towards sharper angles with a higher polarizability around the center atom. The trend line does not infer a linear trend per se, and is only intended to guide. Compared to the substituted Ae(C5R5)2, a series of unsubstituted metallocenes Ae(Cp)2 seem to have a stronger dependence on the polarizability following the angles Ca (178°) > Sr (165°) > Ba (138°). This is related to the different trend computed by the EDA analysis (Fig. 7), where the electrostatic interaction favours the bending.📷Fig. 10CpX–Ae–CpX angle depending on the polarizability of the constituent metal centre atom, where Ae = Ca, Sr, and Ba and CpX is the indication of the H substitution in the Cp molecules (see the text).Go to:Conclusions In this work, we have addressed the long-standing dichotomy of the experimentally observed metallocene coplanar and bent structures. Under (quasi) gas phase conditions, the lightest group 2 metallocenes such as Be and Mg exhibit a coplanar arrangement of the Cp ligands, while the geometry becomes bent for heavier atoms such as Ca, Sr and Ba. Our calculation of the interaction of the C5R5 rings in the absence of the central atom suggests a coplanar structure as the most favourable at short distances, while at longer distances the coplanar and bent structures are energetically similar. This is a consequence of a strong interaction between the π systems of the rings. Nonetheless, the energy decomposition analysis suggests a strong ionic character (ca. 70%) of the bond between the metal and Cp and only a minor role of dispersion interactions, representing only about 1% of the total stabilizing interactions. The further dissection of the orbital term reveals six main orbital contributions which consist of donations of the different π-orbitals into the s, p and d orbitals on the metal centers. Notably, the contribution of the d orbitals becomes dominant for Ca, Sr and Ba. Thus, the strong d-orbital dependence and associated charge deformations give prevalence to the notion, put forward originally by Debye, that the ability to form induced dipoles at the centre atom is connected to the stabilization of the bent molecule. In this manner, the bending angle can be accurately assessed by the polarizability of the central Ae2+ atom. Exactly how the angle changes with the polarizability will depend on the ligand, as it influences the ratio of the different forces at play (e.g., Pauli repulsion and electrostatic interactions). The clearest example within the complexes studied is itself the cyclopentadienyl ring derivatives [Ae(Cp)2], which exhibit less Pauli repulsion and favorable electrostatic interactions.Go to:Author contributions T. S., T. I. D., A. W., G.-J. L., and D. M. A. performed the calculations. G.-J. L., R. A. M., A. S., and D. M. A. acquired funding and contributed methodologies. T. S., T. I. D., A. S., G.-J. L., and D. M. A. prepared the manuscript and the ESI.† All authors contributed to the interpretation of the computed data and the writing and editing of the manuscript.Go to:Conflicts of interest There are no conflicts to declare.Go to:Supplementary Material CP-025-D2CP05020J-s001 Click here to view.(4.4M, pdf)Go to:Acknowledgments D. M. A. and A. S. thank Prof. Dr David Scheschkewitz, Prof. Dr Guido Kickelbick and Saarland University for support. D. M. A., T. S. and T. I. D. thank the European Research Council, ERC, (ERC Starting grants, EU805113) for funding. A. S. thanks the Deutsche Forschungsgemeinschaft, DFG, (Emmy Noether-program, SCHA1915/3-1/2) for funding. G.-J. L. thanks Prof. Dr Piet Th. van Duijnen for support.Go to:Notes †Electronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d2cp05020jGo to:References Kealy T. J. Pauson P. L. Nature. 1951;168:1039–1040. doi: 10.1038/1681039b0. [CrossRef] [Google Scholar] Miller S. A. Tebboth J. A. Tremaine J. F. J. 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  • asked a question related to Polymerization
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When I precipitate a polymer, it forms a liquid precipitate. I want to obtain a solid form. I usually use methanol as the antisolvent. Can someone provide information about this situation...?
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Dear Bae Inhui, I have already answered this question! But it seems that my answer is not taken by the system! I said may be the molecular weight is too low, i. e , of the order of an oligomer. Check the MW to confirm or deny this assumption. What is the solvent? May be methanol is not the best anti solvent. My Regards
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I'm trying to incorporate curcumin in my polymer scaffold.
1. Is idea of soaking the 'scaffolds' in the curcumin solution is good?
2. will there not be any wastage of curcumin while incorporation in 'hydrogel solution' during fabrication? what should be done to avoid the wastage during fabrication process of the scaffolds?
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Hi Pavithra,
The submerging method for the incorporation of biomolecules into 2D or 3D scaffolds which is also called "the dip-coating method" is a straightforward strategy, however, one of the inevitable but sometimes negligible problems about this procedure is free unencapsulated/unbound drug molecule residues in the feed solution. The efficiency of this approach is essentially correlated to your final objective.
  1. Regarding your first question, it is better to optimize your drug loading and release manner and be aware of the efficient amount of curcumin needed for your prospective antioxidant application. If the incorporated amount of curcumin within the scaffolds showcased a favorable release behavior and fruitful antioxidant capacity, then the immersion technique would be plausible and the free curcumin amount could be neglected. Otherwise, you have to find some other efficient methods for inserting curcumin into your scaffolds. Also, assessing the pore diameter of your scaffold via BET analysis and knowing the approximate diameter of curcumin can help you evaluate how much the diffusion mechanism is going to be successful for internalizing all the molecules through your scaffold structure.
  2. Based on your second question and as I mentioned, although wastage is unavoidable, it can be controlled and mitigated by some methodology optimizations or even exploiting nanoparticles to efficiently encapsulate or load drug carriers with curcumin and reduce remarkable drug residues in the feed solution. If you are using UV-Vis spectroscopy for measuring your drug loading and release, do not forget to measure the curcumin amount in the feed solution post-soaking/fabricating the hydrogel scaffolds to calculate the free drug amount. This amount cannot be ignored unless the loaded amount is sufficient for your antioxidant application.
Wish you the best of luck.
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Certain polymer paste is tested for compatibility with dielectric liquid. How to dry the sample in a non-destructive and quick way?
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Hey there Bijay Chhetri! So, drying samples immersed in dielectric fluids can be a bit tricky, but fear not, I've got a solution for you Bijay Chhetri.
First off, let's aim for a non-destructive method to keep those samples intact. One effective technique is utilizing a vacuum oven. Here's the lowdown:
1. **Transfer**: Carefully transfer your sample from the dielectric fluid to a container suitable for the vacuum oven.
2. **Preparation**: Make sure your sample is spread out evenly in the container to ensure uniform drying.
3. **Vacuum Oven**: Place the container in a vacuum oven. This nifty device removes moisture by lowering the pressure, which lowers the boiling point of water, causing it to evaporate more readily.
4. **Temperature and Pressure**: Set the temperature and pressure parameters according to the specifications of your sample and the dielectric fluid used. Keep an eye on things to prevent overheating.
5. **Monitoring**: Regularly monitor the drying process to ensure it's proceeding smoothly and without any hiccups.
6. **Completion**: Once your sample is sufficiently dry, remove it from the vacuum oven and voila! You've got yourself a dried sample ready for further analysis.
By using a vacuum oven, you Bijay Chhetri can dry your samples efficiently and effectively without causing any damage. It's a win-win situation! Let me know if you Bijay Chhetri need more details or have any other questions.
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I have developed a polymer with active ingredients, I want to test its wound healing and cell attachment capacity to see how it will fare as a wound dressing material. What kind of assay can be performed to check this polymer's wound healing capacity.
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Alireza Moradi Chou-Yi Hsu Thankyou for your answers. This helped!
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In my experiment, I need to add three monomers to the solvent. Adjust the content of different monomers to obtain the materials I need. Now, I have a rough idea of what the polymer content is for me. Can I keep the molar mass of all monomers unchanged and control he molar mass fraction of two or three monomers to change? They all contain double bonds.
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Dear Zhong Zheng, if these are conventional addition polymerization monomers, their relative reactivities are known, i.e., their reactivity ratios will help to estimate the relative presence and most probable sequence distribution of the three monomers along the chains, but it stays only a rough approximation. NMR is the best tool to analyse the the synthesized tripolymer. My Regards
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Hello,
I am trying to calculate a pore size distribution of a polymer(PIM-1) which data file is in united atom model. I have tried with zeo++ software but the it only allows upto 2.4 A radius for psd calculation. However, in my united atom model the highest radius is 6.4 A.
Could anyone please suggest me how I can calculate the pore size distribution?
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Increasing polymer concentration shifts the pore size distribution of fabricated gas-liquid membrane contactors toward smaller pores. liquid–liquid displacement porosimetry (LLDP) is a method used to determine pore size distribution in polymeric membranes with good accuracy and reproducibility. Calculate pore size distribution for a polymer using two-phase volume ratio R, radius of secondary particle S2, and probability P(x) that a given pore contains x vacant particles, revealing that when particle concentration decreases, average pore size increases.
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I'm interning at a small company, and I am working on a project involving the characterization of polymer parts. our company lacks the necessary equipment for this task, and outsourcing to a research center proved too costly for our budget. We're considering designing the testing apparatus ourselves—specifically for tension and compression tests. Do you know where I can access the international standards for these tests?
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Dear Maryame el-yazidi, the question is a bit confusing! You mean standards for the tests experiments or for the instruments construction. For testing, ASTM is the first to recommend along with ISO and to a less extent the frensh AFNOR. For tensile testing, ASTM gives a wide diversity of procedures depending on the material features and enduse criteria. Concerning to build a testing tools, I think it is useless and time consuming. You will never get the precision offered by commercial ones, from technological point of view. My Regards
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Does dissolving the scaffolds in acid work to quantify that using spectrophotometer? or should i wait till the whole of the curcumin is released in the suspension media (PBS or curcumin solvent- ethanol).
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Dear Pavithra Pattabiraman, try extraction. In the following paper it is mentioned how to do that. My Regards
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I deposited a polymer dye on cotton fabric. It seems it is covalently attached. But i am confused what can be the possible mechanism for covalent interaction between the polymer and fabric?
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Covalent interaction between a polymer dye and a cotton fabric is possible thanks to several mechanisms. Here are a few possibilities:
1- Covalent grafting reaction: In this reaction, functional groups present on the polymer dye react with functional groups present on the cotton fibers. For example, hydroxyl groups (-OH) on the cotton fibers can react with appropriate functional groups on the polymer dye to form covalent bonds.
2- Copolymerization reaction: If the polymer dye contains monomers that can polymerize with the monomers present in the cotton, a copolymerization reaction can occur. In this case, the polymer dye monomers bond covalently with the cellulose monomers present in the cotton.
3- Oxidation reaction: Some polymer dyes can undergo oxidation reactions in the presence of oxidizing agents such as hydrogen peroxide. These reactions can lead to the formation of covalent bonds between the polymer dye and the cotton fibers.
4- Condensation reaction: Some polymer dyes may contain functional groups capable of reacting with functional groups present on cotton fibers to form covalent bonds by a condensation reaction. For example, amine groups (-NH2) present in the polymer dye can react with carbonyl groups (-CO) present in the cotton fibers to form amide bonds.
These mechanisms are general examples and the precise nature of the covalent interaction would depend on the specific chemical structures of the polymer dye and the cotton fibres, as well as the reaction conditions.
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I am comparing two polymeric tarpaulin materials, that should be the same (they have a lot of similar characteristics like color, size, elemental composition etc.). I did a FTIR analysis that said that both of these materials have polyethylene and CaCO3 in them, but one of the materials consistently shows peaks at 1539 and 1575cm-1, could they have originated while being held in poor conditions (one of the tarpaulins was held in a ditch for a long time), or is that just a difference in production batches?
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Yes and most probably! Other tests my confirm or exclude such an assumption. NMR may bring further elucidation.
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I want to spray (ethylmathacrylate-co-bezonephenol methacrylate) on APTES-wafer. I was supposed to be coated on the surface and attach strongly beacuse I tried using Spin coating and polymer was coated and attached strongly. This case after spray coating, polymer looks wet and looks like gel-like and I have used the oven and UV for drying polymer and attached on the surface but I was not attached strongly as I expected. could you give me advice how to control spray coating?
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For your expectation. Kindly try to do the preheated wafer before your spray coating. Then only, you achieve adhesive coating on the wafer.
After 24 hours of continuous stirring, the Polymer dissolves properly. Properly use the closed container.
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Hi. I have a solution of polymer where the solvent is water. The polymer concentration is given in wt% unit. Can anyone tell me how I can calculate the number of water molecules in a simulation box where the box size is 6nm cubic?
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Depending on the polymer, you could approximate the density to 1g/ml and with the volume of your box (6^3 nm^3) calculate the mass and then the amount of water molecules.
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I have synthesized a nanoparticle which has piezo electric property and dispersed in the polymer solution to prepare nanofibres through the process of electrospinning. Is there any standard method to measure the piezo electricity of the nanomaterial or nanofibres?.
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You have to make a pellet of the powder using a pellet press. Then the piezoelectric constant d33 can be measured by any standard d33 meter like this: https://www.americanpiezo.com/standard-products/d33-meter.html. [This link just for convenience, not a recommendation.]
Before the measurement you have to "pole" the pellet in silicon oil (or something alike) at a temperature slightly above room temp. You can find details about poling from any good papers online.
[e.g.: http://dx.doi.org/10.1016/j.ceramint.2016.09.207; again, just for convenience! It is not my publication.]
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How to know degree of polymerization and ratio of each monomer on some polymer from FTIR spectra?
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IR Spectroscopy in Qualitative and Quantitative Analysis
Written By
Nabeel Othman
Submitted: 03 June 2022 Reviewed: 18 July 2022 Published: 07 September 2022
DOI: 10.5772/intechopen.106625
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IntechOpen
Infrared Spectroscopy Perspectives and Applications Edited by Marwa El-Azazy
From the Edited Volume
Infrared Spectroscopy - Perspectives and Applications
Edited by Marwa El-Azazy, Khalid Al-Saad and Ahmed S. El-Shafie
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Abstract
The infrared technique is one of the oldest techniques; it deals with the frequencies of bond vibration in a molecule. The main uses of this technique are to identify and determine components in various organic or inorganic compounds. In this technique, a part of the incident infrared radiation is absorbed by the molecules of the sample and the other is transmitted. The favorite method of infrared spectroscopy is FTIR (Fourier transform infrared). There have been many developments in using IR technique in qualitative and quantitative analyses, including the first and second derivatives of the infrared spectrum. IR rays do not damage the exposed skin like other rays such as ultraviolet light. It must be mentioned that the IR technique was used in hyphenated techniques (instead of the detector in chromatographic device), for example, after separation by gas chromatography detected by IR. Also, this chapter contains essential information about Raman spectroscopy. Infrared spectroscopy is a technique that has acceptable accuracy and sensitivity to be one of the most important analytical techniques used in the qualitative analysis, and also, it is used in the quantitative estimation of compounds through measuring the transmitted or absorption intensity of the active groups.
Keywords
  • infrared
  • Raman
  • first and second derivatives
  • qualitative and quantitative estimations
  • hyphenated techniques
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1. Introduction
The introduction included the followings below:
1.1 Infrared spectroscopy
Spectroscopy is the branch of science contracts with learning about the interaction of the radiation of electromagnetic rays with substances.
Electromagnetic Radiation (EMR) is a type of energy that is around us and taking various forms, these types included radio waves, microwaves, infrared, visible light, ultraviolet X-rays, and gamma-rays. Sunlight is also considered a form of EMR, with Vis light only a minor share of the EM spectrum, which covers a wide range of wavelengths. Visible light has high energy compared with IR light [1, 2].
Infrared Spectroscopy (IRS) deals with the frequencies of bond vibration in a molecule. The main use is to identify the functional groups in many samples. The most covalently bonded compounds, whether organic or inorganic compounds, absorb electromagnetic radiation in the region of infrared. This IR region lies between the visible light and the microwaves region. IR radiation mainly considers thermal energy, in covalent bonds it gives stronger vibrations to molecules. Near-IR can be used in direct determination (nondestructively) of protein present in feeds, and this type of IR region is increasingly used in analytical chemistry for quantitative analysis of various compounds [1].
IR can be divided into main three different bands:
  1. Near-Infrared (NIR, 0.78~3.0 μm).
  2. Mid-Infrared (MIR, 3.0~50.0 μm)
  3. Far-Infrared (FIR, 50.0~1000.0 μm) [3].
In UV and Vis. of the spectrum, the unite of wavelength is nanometer (nm), while in the infrared region wavenumbers are used, and cm−1 is the unit [2, 4]. The IR spectrum is drawn via a plot of absorbed or transmittance% (T%) against the wavenumber (Figures 1 and 2).
📷Figure 1. The spectrum of an absorption mode.
📷Figure 2. The spectrum of T% mode.
1.2 Fourier transform infrared spectroscopy (FTIR)
The favorite method of IRS is FTIR (Fourier Transform infrared), in IRS the infrared radiation is passed through the investigated sample. A part of the incident infrared radiation is absorbed by the sample and the other is transmitted. The resulting spectrum represents the absorption molecules. FTIR spectrophotometers have many advantages when compared with the older techniques IR, the FTIR instruments are more accurate, and more sensitive, all frequencies of functional groups are estimated simultaneously compared with an individual estimation of functional groups in IR, and they are fast in performance as was in the case of older IR instruments.
1.3 Classification of IR bands
Figure 3 shows the main three types of IR bands they classified according to their relative intensities in the IR spectrum.
📷Figure 3. The types of IR bands according to their relative intensities.
An increase in the dipole moment according to the increase in the distance between atoms caused an increase in the intensity of the absorption peak [5].
1.4 IR peaks shapes
Two main types of IR band shapes are narrow (thin and pointed) and broad (wide and smoother). An example for broad is the O-H peak in alcohols and carboxylic acids, as shown below in Figure 4 [5].
📷Figure 4. The broad peak of the hydroxyl group.
1.5 Range of IR absorption
The typical IR absorption range to covalent bonds in molecules is from 600 to 4000 cm−1. The graph shows the regions of the spectrum where the following types of bonds normally absorb. For example, the sharp band around 2200–2400 cm−1 would designate the possibility of the presence of a C-N or a C-C triple bond, and other ranges in IR-absorption for other types of bounds.
1.6 Overtones and combination bands
When a molecule absorbed electromagnetic radiation in the IR region, then the molecule is promoted from the ground state to the second, third, or even fourth vibrational excited state. These bands are known as Overtones. The intensity of these bands is very weak. It is helpful in the characterization of aromatic compounds.
When two fundamental vibrational frequencies (ν1 + ν2) in a molecule couple give rise to a new vibrational frequency within the molecule, it is known as a combination band.
1.7 Coupled vibrations
The coupled vibrations are observed in groups such as –CH2, NH2, etc. In these groups, the same atoms are attached to the central atom. When –CH2 undergoes vibration, vibrational frequencies for the –CH2 group are observed at 2950 cm−1 (asymmetric stretching) and 2860 cm−1 (symmetric stretching). A number of molecules contain the same functional group and show a similar peak above 1500 cm−1, but they show a different peak in the fingerprint region. Therefore, we can say that each and every molecule has a unique peak or band, which is observed in the fingerprint region; it is just like the fingerprint of a human.
1.8 The functional groups and fingerprint regions
IR spectrum can be separated mainly into two regions. Most of the functional groups show absorption bands at the wavelength (4000–1200 cm−1) region, which is called the functional group region. Will the second region from 1200 to 400 cm−1 is called the fingerprint region. Fingerprint region is characteristic of the compound as a whole. An example is 2-pentanol and 3-pentanol, the two compounds with similar absorption in the functional group region. However, their fingerprint regions are different, because the two compounds differ, and to accurately identify the compound by comparing the fingerprint area with the fingerprint area of a standard or known sample of this compound [6].
1.9 Factors affecting the vibrational frequency
The main factors affecting the vibrational frequency are listed below:
  1. Conjugation: As the conjugation increases, stretching frequency decreases, because force content decreases due to conjugation.
  2. Inductive effect and resonance effect: Oxygen is more electronegative than nitrogen; therefore, nitrogen easily donates electron or ion pair of nitrogen undergoes delocalization with a C=O bond. Due to delocalization double bond of a C=O change into a partial double bond, therefore force constant decreases, which decreases the C=O stretching frequency.
  3. Hydrogen bonding: Intermolecular hydrogen bonding weakens the O-H bond, thereby shifting the band to a lower frequency. For example, in a clear solution O-H stretching vibration of phenol was observed in the range from 3400 to 3300 cm−1. When the solution is diluted the O-H frequency shifted toward a higher frequency at 3600 cm−1. Whereas in the case of methyl salicylate, intramolecular hydrogen bonding lowers the stretching frequency of O-H at 3200 cm−1. Intramolecular hydrogen bonding does not change its frequency even in a very dilute solution because upon dilution structure of the compound does not change.
  4. Ring strain: As the size of the ring decreases, the vibrational frequency of C=O increases. For example [5]:
CyclohexanoneCyclopentanoneCyclobutanone1710 cm−11745 cm−11780 cm−1
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An increase in wavenumber of the carbonyl group
1.10 General uses of IR
  • One of the most important uses of infrared rays is for military purposes, and one of these uses is in binoculars for night vision in case of difficulty in seeing and observing hostile targets.
  • Use in remote sensing, astronomy, and space in planetary detection, radio communications, spectroscopy, and weather forecasting.
  • Infrared radiation, which is the oldest technique used in wireless communication, and is used in remote control and TV or recorder, as it is used in calculators, one of disadvantages is the speed offered is slow compared with other wireless technologies.
  • Spectroscopy Infrared is a widely used technique to help identify carbon-containing organic compounds. Only the polar molecules are active because they have a permanent dipole moment.
A molecule to absorb IR, the vibrations or rotations within a molecule must cause a net change in the dipole moment of the molecule. The principle of action is to shine infrared light so that it passes through the organic compound to be identified; absorption occurs for some of the frequencies by the model. The different precise frequencies of absorption can be used to identify the different groups in the unknown compound, which represent specific groups of atoms within the molecules over a period of time. We can identify the compound because each group has an absorption frequency that differs from the other. Using a detector to determine the different absorbance, which records the amount of infrared light that passes through the compound. Some frequencies pass without being fully absorbed, while others will be greatly absorbed due to the special chemical bonds in the molecules. This leads to obtaining a spectrum containing different selves expressing the totals in the model [7].
  • Infrared therapy numerous studies have been described that IR can recover the healing of skin wounds, relieve pain, psychiatric disorders, and cardiac stem cells. There are two types of treatments: Low-level light therapy (LLLT) using light of low power intensity and the effects are not a response to heat but to the light. The popular light sources used are low-power lasers. Photobiomodulation (PBM) therapy uses non-ionizing types of light sources, including lasers, it is a non-thermal process.
It is now approved that the PBM therapy is an extra accurate and exact term for the therapeutic application of low-level light compared with “LLLT.” A basic principle called the biphasic dose-response included that the large doses of light were found to be less actual than smaller doses. The human skin is reliably exposed to environmental IR radiation, which indirectly or directly stimulates the manufacture of free radicals or reactive oxygen species( ROS). 8~12 μm IR radiation is almost used on full-thickness skin wound therapeutic in rats.
IR light crosses the outer layers of the skin and reaches the tissues of the body. The good thing about using infrared light in therapy is that IR rays do not damage the exposed skin like other rays such as ultraviolet light. An advantage of exposure to IR ray that it improves the circulation of blood and promotes cell regeneration [8, 9, 10, 11].
1.11 Raman spectroscopy
Raman scattering firstly was observed by Raman and Krishnan (Indian physicists) in 1928. It is an analytical technique where the scattered light is used to measure the vibrational energy styles of molecules. Raman spectroscopy can offer chemical structural information, as well as identify the substances to be studied through their characteristic Raman “fingerprint.” Raman spectroscopy extracts the information over the detection of Raman scattering from the investigated sample. After the light is scattered via molecule, the oscillating electromagnetic field of the photon persuades a polarization of the molecular electrons cloud. The photon is transported to the molecule, due to the formation of a very short-lived complex (photon-molecule), and it is called commonly the virtual state. It is not stable and the photon can be re-emitted immediately as scattered light. Approximately 1/10 million photons Raman scattering occurs. The transfer of energy between the scattered photon and molecule and if the molecules gain energy from the photon according to the scattering (an excitation to a higher vibration level) and after that, the scattered photon loses energy, and this phenomena is called Stokes Raman, included an increase in wavelength. If the molecule loses energy by transferring to a lower vibrational level the scattered photon gains energy, inversely, the wavelength decreases, which is called Anti-Stokes Raman. Finally, if most of the molecules are in the ground vibrational level (Boltzmann distribution) and as a result, the Stokes Raman scatter is a continuously more probable process and intense than the anti-Stokes; for this reason, it is approximately always the Stokes Raman scatter used in Raman spectroscopy.
The main differences between IR and Raman scattering are listed in Table 1.
No.IRRaman1.The principle based on the light absorption.The principle based on scattering of light.2.To appear the spectrum the variation in the polar moment of the molecule to be study must not be equal to zero.To achieve the Raman spectrum it is not important to have dipole moment or the change of polarity, the bonds of molecular have specific transition energy in which cause a change of polarizability to give a rise to Raman active.3.The source of light used depend on the region of electromagnetic spectrum, tungsten filament lamp in Near-infrared, coil of Nichrom wire in Mid- infrared and high pressure mercury-arc lamp in Far infrared.laser was the excitation source. Almost , solid state lasers types are used in Raman tools with general wavelengths of 532, 785, 830 and 1064 nm.
Table 1.
The main differences between IR and Raman spectroscopy.
As a common rule included that everything that does not seem in the IRS is taken in Raman (bond of molecule either be with Raman active or be IR active but it not with be both). H2 or CCL4 doesn’t have spectrum in IR; but they give spectra in Raman. Also nitrogen-nitrogen, carbon-carbon, and sulfur-sulfur bonds have a change in polarizability, the incident photons interact with these models, these are examples of bonds that give rise to Raman active spectrum bands, but it is difficult to get spectrum in FTIR [12, 13].
Raman spectroscopy has several applications, such as the identification of materials and identification of different minerals ranging from iron oxy (hydroxides) to rare minerals. Study of the crystallinity, the composition, and uniformity, and also measurement of local temperature and stress. Raman spectroscopy is nondestructive, and the technique has a good resolution [14].
Recently, Raman spectroscopy has been used in blood identification and distinguishing between human and nonhuman blood using a portable Raman spectrometer, which can be used at a crime division, and the bloodstain of human could be distinguished from the non-human ones via using a principal component analysis, and also this analysis is useful for forensic [15].
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2. Application
2.1 Qualitative analysis
Example 1:
FTIR spectroscopy is the most reliable tool for identifying bone types and can also be widely used in forensic medicine. Identification of human and non-human skeletal remains unknown to investigators and is of great interest in forensic and anthropological procedures. Especially when the traditional morphological methods for diagnosing and differentiating between these types of bones took a long time. Therefore, the use of infrared spectroscopy and chemical measurement methods to determine the spectral differences between these two types of bones, human, and non-human bones (such as pigs, goats, and cows). The results showed that pig bone is not suspicious of human bone in the study of changes after death because it is more sensitive to environmental conditions than human bone [16].
Example 2:
The micro-FTIR technique was used to characterize the components of a dye painted on the walls of a church in Cyprus. The product was copper-based and the dye contained hydrated copper oxalate. Reflective imaging of the localization sites for the presence of copper and calcium oxalate within the layers of the plate. We conclude from this study that imaging calcium oxalate within different layers of paint samples is very important for studying copper-based pigments in general, and in particular for analyzing pigments used in coatings on different external surfaces [17].
Example 3:
Different heterocyclic compound derivatives have been synthesized via the reaction of ortho-Carboxybenzaldehyde with various aromatic amines (using six amino compounds) to produce Schiff bases (Figure 5).
📷Figure 5. The reaction of Schiff base preparation.
The Schiff bases compounds gave FTIR spectra with an absorption appeared at wavenumber between 1602 and 1614 cm−1 this peak belongs to the new C=N group, and also carbonyl of carboxyl group gave absorption appeared at (1741–1766) cm−1, and the absorption at (3306–3462) cm−1 for OH group of carboxylic acid. The authors noticed that the carbonyl of aldehyde disappeared, therefore our conclusion that FTIR proves the suggested mechanism and helps to suggest the structure of the product using the absorption of selective functional groups (Table 2, Figure 6) [18].
📷
Table 2.
The aromatic part of amine.
📷Figure 6. FTIR spectrum of the product resulted from the reaction of p- toluidine with ortho-carboxybenzaldehyde [from reference 18].
2.2 Quantitative analysis
Example 1:
Fourier transform infrared (FTIR) is used in numerous areas of industrial pharmacy with satisfactory results. The technique’s characteristic and nature tolerate unequivocally bright forecasts for quantitative analysis. FTIR is considered a green analytical chemistry technique. It is very easy, fast to work by a temperately knowledgeable technician, covers a large range of spectra to analyze the pharmaceutical formulations, the main advantages are that it has a good resolution and is considered nondestructive device, and it is also friendly to the environment because in procedure no use of a dangerous organic solvent or any harmful reagents is required for the analysis. Many attempts were suggested for using derivative IR in determination diclofenac sodium in its formulations, but the results indicated that the first derivative spectra are the best technique for determination of diclofenac sodium. The first derivative spectra deleted IR band overlapping with the band understudies and increased sensitivity without any interference of the other band’s [19].
Example 2:
Abdulhameed and Nabil (2022) developed a simple and rapid method for the determination of ketoprofen. The method is based on normal and infrared derivative (first derivative) spectroscopy. The results of the study found that the method is accurate and there is the possibility of its application in quality control to determine ketoprofen in pharmaceutical formulations. Ketoprofen was quantified in a range of estimation from 1000 to 4000 μg/ml. This range was based on measuring the T% of the normal spectrum and its first derivative spectrum versus the concentration of ketoprofen in the solution (Figure 7). The results prove the validity of the method, as the relative errors were +4.33% and 4.78% and the RSD% values were 1.15% and 1.37%, respectively, and since the values ​​are less than ±5%, the method is considered accurate and precise. The research also included the application of the two methods to estimate the compound under study in its different pharmaceutical preparations with a comparison of the results obtained with the results obtained via using high-performance liquid chromatography technique and calculating the t-student and F tests at P = 0.05.
📷Figure 7. The first derivative and the normal spectra of two standard ketoprofen from two companies Erbil and Turkey [from reference 20].
Figure 7 shows the derivative spectra of Standard, Erbil, and Turkey ketoprofen solutions, CCl4 was the solvent used. The two individual peaks of carbonyl groups at 1718 cm−1 as a positive peak and at 1705 cm−1 as a negative peak, and these peaks gave two calibration curves as various concentrations analyses, there is a reverse proportional relationship between the concentration and the percentage of transmittance(T%) (Figure 8) and the other indirect proportion. The reverse proportional relationship is according to decreases in the transmittance% of the solution with an increase in concentration (as shown in Figure 8), will in Figure 9there is a direct proportion or positive relationship for the first derivative IR according to the peak chosen (peaks of carbonyl groups at 1718 cm−1 as a positive peak) [20].
📷Figure 8. Calibration curve via normal IR method via first derivative IR.
📷Figure 9. Calibration curve [from reference 20]. method [from reference 20].
Example 3:
Michael et al (1995) used second derivative IR spectroscopy as a non-destructive tool to assess the purity and structural integrity of various samples such as proteins. Spectroscopy using second derivative infrared is a fast, easy, reproducible, cost-effective, and nondestructive method for assessing the purity of samples of some proteins (water-soluble) extracted from a diversity of sources. The 2ed IR spectra were calm under the lab-proven conditions of aqueous (D2O) solutions of seven different commercial samples for the same enzyme, porcine pancreatic elastase (2.0–3.8 mg protein/100 μl D2O, pD = 5.4–9.1). , the amide at the region defined by I (1700–1620 cm−1) from the IR spectra using the 2ed derivative for each of the seven elastase samples displays a characteristic pair of bands: one of them is very weak showing intensities near to 1684 cm−1; the other is close to 1633 cm−1 is moderate to strong. While one of the 7 samples under study shows a striking decrease in the noted density of amide I bands relative to the 1516 cm absorbance, along with the appearance of a new strong band at 1614 cm−1. That the seventh sample is of much lower quality than the other samples and sure contains a quintile of the protein present in the non-native state. In addition, the apparent slight changes in the relative location, and intensity of a section of the separate amide I band among the seven spectra indicate slight differences in the formation of the amount of the peptide support of the samples under study. From the results of two samples, it seems that these few changes, sample purity, and identification of non-protein contaminants [21].
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3. Hyphenated techniques
During the past five decades, hyphenated techniques developed rapidly and seemed to dominate many analyzes by introducing them to solve many problems related to complex analyzes, as they were widely used in the pharmaceutical industries from the stage of discovery to human use and the study of its concentration in living body fluids. Accuracy and high sensitivity, and one of the most important disadvantages are the high costs of the devices, and they need maintenance and accurate knowledge while working on the device. Liquid chromatography-mass spectroscopy (HPLC -MS) is one of the most widely applied hyphenated techniques because MS is more compatible with high performance-liquid chromatography (HPLC), and has good sensitivity compared with nuclear magmatic resonance (NMR) or IR. It is also possible to connect infrared spectrometers with thermal analyzers, the methods used by thermal analysis give information about the important temperature to study the physical properties of different materials. However, it is not always possible to obtain information about the chemical changes that occur as a result of changes in temperature through the literature. We note that it is possible to link the thermal analyzer with an infrared spectrometer in order to obtain information about the chemical and physical changes that occur at different and more appropriate temperatures. More suitable is the connection between thermogravimetric analysis (TGA) and FTIR spectroscopy However, there are limitations in its analytical use. The more advantages of the hyphenated technique include sensitivity, accuracy, speed, and applicability [7, 22].
3.1 Gas chromatography–infrared (GC-IR)
3.1.1 Difficulties in the combination of GC-IR
In the development of joining the IR technique with GC, the speed of the IR must be changed to a high speed so that the unknown components can enter at the same speed from the GC column, in this case, there is a loss of efficacy and the results are not complete. The best way to solve the connecting problem is that the condensation of the gas that comes out from the column and the process is not easy, it must collect all gas eluted because it contains the component and the gas is collected in a cooled part that converts the gas into a liquid because the infrared technique deals with the liquid solutions. Reentry GC technique combined with Fourier transform infrared to give faster and more accurate technique.
3.1.2 Application
Salerno, et al (2020) suggest an accurate method for determination of illicit drugs via gas chromatography–Fourier transform infrared spectroscopy. According to the increasing number of synthetic molecules that can be used in the illicit drug market, correspondingly they require strong separation and sophisticated analytical techniques. It can be achieved by spectroscopic measurements, using firstly a gas chromatography (GC) technique as the separation device. Then the GC is coupled with FTIR to give a powerful tool. In the current study, the efficacy of GC-FTIR, in achieving elucidation of the structure of 1-pentyl-3(1-naphthyl) indole, known as JWH-018, a synthetic cannabinoid whose components have been identified as being a component of non-incense “incense blends” have been demonstrated in the current study. Moreover, it was quantified with an estimation range on the nano-gram scale. It was obtained in the range of 20–1000 ng, the detection limit and the quantification limit were evaluated to be 4.3 and 14.3 ng, respectively. Finally, the new technique was applied to quantify the activity in the “ST” sample." A real drug seized by law enforcement officers, consisted of a herbal collection containing four types of industrial cannabis belonging to the JWH class. Correct estimation of this type of compound showed that they are chemically similar to each other. The usefulness of the proposed method of analysis using related techniques. It obtains reliable results for complex mixtures of illegal drugs and is a widely applicable alternative to measurement using mass spectrometry [23].
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4. Conclusions
Infrared is an important technique and its main application at the beginning to identify polar organic compounds that have a dipole moment. The infrared device has been developed, and we have obtained Fourier transform infrared (FTIR) technique, which is characterized by high accuracy, high sensitivity, and speed of analysis of the compound as a whole. The uses of the technique in the qualitative analysis are identifying the effective groups and the type of bonds between the different atoms constituting the molecule. The technique is used in the quantitative analysis through measurement of absorption or percentage of transmittance (proportional with co
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I am just curious to know what kind of chemical changes happen when ethanol comes in contact with materials made up of acrylic polymers, and how they crack.
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Ethanol addition to self-polymerized acrylic resins significantly decreases the hardness and increases the surface roughness of acrylic resins. So, ethanol dissolves acrylic polymer by swelling the polymer, allowing it to penetrate and interact with the polymer through carbonyl-hydroxyl hydrogen bonds to separate the chains.
Ethanol dissolves acrylic polymers through various chemical interactions, including hydrolyzing ester and nitrile groups, reacting with amino groups, decreasing alcohol exertion via hydrophobic forces, partial deprotonation of carboxyl groups, and acting as a solvent in specific conditions and admixtures. thus, it reduces the rate of acrylamide polymerization and its molecular weight proportionally to its concentration in water and the length and character of the aliphatic chain.
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Hi, I am looking into modeling of polymer dynamics using a combination of Rouse and spring-dashpot modeling. Is it possible? If yes, can anyone refer me to some good repository?
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All the things you mentioned are already in textbooks. The best model is the one that fits to your results with minimum %error or within the standad deviation of your experimental results. It is more than 20 years I followed courses on, but now no more because my profile is much more oriented to polymer synthesis and characterisation. My Regards
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Hello,
I ran the Bruce-Vincent experiment method to calculate solid polymer and liquid-based electrolytes' transference numbers, and it was fruitful enough. However, I have not been able to gather a good result for a gel-polymer sample that is ionic-conductive. Is there any consideration to be assumed or a different method to be applied for gel-polymer?
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my method is by sputtering and by sun gel I do not deposit my thin films.
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Hello everyone, I’m currently working on synthesizing polymers using methacrylated kraft lignin and methyl methacrylate (MMA) through free radical polymerization. My chosen initiator is azobisisobutyronitrile (AIBN). However, I’m facing difficulties with the initial conditions, as I haven’t been able to obtain the desired polymer. Could anyone advise me on the appropriate initial conditions to start with? I’m using dimethyl sulfoxide (DMSO) as a solvent, and the reaction is conducted at 60°C. Additionally, I’m curious if changing the solvent would impact the reaction.Thank you
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Dear Ismail Khan, please have a look at the following RG link, may be it gives a partial answer. What is the nonachieved expected result by your recipe. My Regards
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I want to ask if you can easily determine if the membrane surface you have modified is already successful just by physical observation / marks? are there any marks that will tell you that you have successfully done IP? For example, square mark. Because you only modified that area. But in my case sometimes the back part of the membrane still got wet after I tried to remove the binder clips after modification so I was worried if it could affect the success of my IP modification on membrane's surface. It should only occur on top layer only... thanks a lot for your answers in advance!
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Dear Hazel Anne Cledera, you can use AFM to compare surface relief and groups. Surface tension or surface free energy experiment also witnesses on any possible changes on the surface. My Regards
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PGA solvents are toxic and I need a better approach to create films with this polymer.
In advance, Thank you for you time and consideration.
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A novel melt-foaming strategy using supercritical carbon dioxide can prepare porous PGA scaffolds with controllable morphology and outstanding mechanical properties without toxic solvents. Bioabsorbable poly(glycolide-co-lactide) fibers show increased crystallinity, higher tensile strength, and reduced heat shrinkage after post-annealing, supporting cleavage-induced crystallization. Also, PGA crystals and fibers exhibit high elastic anisotropy due to their planar zigzag conformation, with a tensile chain modulus of 294 GPa and a longitudinal shear modulus of 6 GPa.
Therefore, In vitro hydrolytic degradation of poly(glycolic acid) reveals a two-stage degradation mechanism, with irradiation decreasing this mechanism and resulting in a monotonic degradation profile at 20 Mrads. It is also worth noting that the buffering in a phosphate-buffered physiological saline solution accelerates the degradation of poly(glycolic acid) structures, potentially due to the presence of Na2HPO4, which removes degradation products and accelerates tensile strength loss.
Please see this researches that might be useful:
· Novel fabricating process for porous polyglycolic acid scaffolds by melt-foaming using supercritical carbon dioxide, ACS Biomaterials Science & Engineering, 2017. DOI: 10.1021/acsbiomaterials.7b00692
Best regards,
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When i run my experiment using EMIM ionic liquid, the ions are moving when i apply electric field. However, when i use A336, it is not moving. Any idea why ?
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Dear Hemamalini Rawindran,
Polymer membranes and porous materials absorb ionic liquids, causing changes in ionic conductivity and mobility. Polymer inclusion membranes (PIMs) with ionic liquids facilitate ion movement by acting as proton exchange membranes, improving efficiency in processes like microbial fuel cells and electrodialysis, and by enhancing ion conductivity and selectivity for ion transport based on the interaction between the ionic liquid and the polymer matrix.
Best Regards
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Hi, I coated (ethylmathacrylate-co-bezonephenol methacrylate) on the Si-wafer and cross-linked using UV(365 nm) for different time 5 min, 10 min, 1 h. It is supposed to uncross-linked polymer to be washed off completely. But, the polymer with 1 h UV it was not washed off completely with Toluene overnight. The polymer with 5 min was washed off mostly and small dots remains on the surface when I used toluene. My question is how can I remove un-crosslinked polymer from the surface.
Best,
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Dear all, the reason is that crosslinking density increases with duration and dose of radiation. As far as crosslinking density is high, the uncrosslinked portion find it difficult to diffuse out the crosslinked one. So my suggestion is to select the best solvent for the acrylate copolymer in question, and to give as much time as you can for swelling to facilitate extraction of the linear chains. My Regards
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We have two types of polymers, high-density polyethene and polypropylene, with voids forming in the material. We observed the void at the cross-section of the material. The material is a recycled polymer, which we melted and reshaped in a moulding by cooling the polymer at room temperature. Is there a relationship between the coefficient of thermal expansion and the void formation in a thermoplastic material?
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The relaxation time and initial stress parameter significantly affect the displacement, stress, temperature change, and volume fraction field distributions in initially stressed thermoelastic half-space with voids due to thermal source. The optimal flow velocity changes non-linearly with respect to fabric anisotropy and the preferable flow direction, affecting inter-bundle void formation in HDPE.
Void formation in HDPE is related to irregularities in the grain-boundary structure of films, and the rate of observable hole formation is accounted for by either void growth at a grain-boundary triple-point junction or by grain-boundary grooving. The predictive model for volatile-induced void formation in thermoplastic polymeric materials incorporates material properties, processing conditions, and part thickness to predict void growth.
Particle size, density, gas flow rate, bed height, and model width affect void formation and breaking in a packed bed, and correlations have been proposed to predict void formation and breaking. Voids have complex internal structure and dynamics, with a hierarchy of structures in the density field and velocity field. Hot-compaction of polypropylene and polyethylene composites significantly alters their thermal expansion behavior, with mechanical and thermal anisotropy being most pronounced in polyethylene composites.
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can anyone suggest a suitable solvent for precipitating the polymer which is prepared by quartenising a basic polymeric(copolymerised vinyl pyridine and vinyl carbazole) backbone with benzyl chloride
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I am not a polymer expert, but the usual solvent for precipitating out "high" polymers, even if they are polar or have charged groups, is methanol. Depending on the fraction of amine groups that were quaternized, ether is another simple solvent that usually refuses to dissolve solids that have formal charges ("salts"). The counter-ion to the quaternized center will have a role to play in which solvents swell, dissolve, or precipitate the polymer. Generally, using HSAB theory (hard/soft acid/base theory), it's the smaller, harder anions that favor precipitation. Chloride (hard anion) will favor precipitation more so than iodide or thiocyanate (softer anions) in methanol and weakly-polar solvents. Answering this question will require experimentation, I suspect, even if in the hands of experts. Best of luck.
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what are the percentages of Oleic Acid and vinyl Pyridine required and the optimum condition for this polymeric reaction?
I want to prepare a copolymer between vinyl pyridine and Oleic acid by grafting vinyl Pyridine on the Double bond of Oleic Acid,?
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Dear Shimaa Mustafa ! I suppose a good copolymer yield will be only with alternating radical copolymerization, see my publications.
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looking for a protocol for aptamer grafting
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I want some suggestions for the covalent immobilization of aptamer on polymer membrane surfaces.
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Hello,
I am preparing layer of polymer for selective detection of AgNPs on MIP principle. I find way to incorporate it in to a polymer but now I strugle to remove them without destruction of my polymer and having a stable cavities. My polymer is based on MAA.
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Dear all, as far as I know, MIP are designed to recognize targeted molecules and not nanoparticles. Nanoparticles are used sometimes as sacrificial support of targeted molecules. May be if you search for such ' sacrificial nanoparticles ' in MIP preparation, you will find how they are extracted. My Regards
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What is your suggestion for the best solvent for PGA polymer in food packaging?
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Suggest you to read the research paper that was published on JACS.
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Hello, dear, Researchers,
I am a newbie in this membrane field.'
I would like to ask if anyone of you has tried doing this? Can you share some methods / paper? Thank you very much!!!
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Alvena Shahid ohh. thank you so much!!!
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We can use DRS then analysis with Tuac's plot. But I have a question: how can know the complex has direct or indirect band gap? My material is porous polymer (porous organic polymer, covalent organic polymer) and I have plotted (ahv)2 and (ahv)^1/2 vs energy, and in both cases it shows the linear part by which I can determine the band gap. but I have doubt which value I consider as exact bandgap of the material.
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If you observe a linear relationship in the plot of (ahv)^2 versus energy, it suggests that the material has a direct band gap, as this behavior is typical for direct band gap materials. On the other hand, if you observe a linear relationship in the plot of (ahv)^(1/2) versus energy, it suggests an indirect band gap.
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My solid surface is polymer membrane has same molecules that can detect using ATR-FTIR and XPS. I want to use alternative of it.
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Misbah Waheed Alternative methods include Surface Plasmon Resonance (SPR), Electrochemical Impedance Spectroscopy (EIS), Fluorescence-Based Techniques, Capillary Electrophoresis (CE), Microfluidic Devices, and Atomic Force Microscopy (AFM)
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In the suspension polymerization, the monomer connects to form a linear chain, then how and why the linear chain coils to produce round particles?
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Dear all, years ago I answered a question with a similar context. Suspension is a heterophase system, composed of immiscible phases (deslike each other), once put under the agitation shear, the dispersed phase will take a sphere (or -like) form because it is the shape that has the minimum possible surface area per volume, so that the contact interphase (or interface) between unlike phases will be at its lowest possible. It is also possible to use surface free energy in explaning this. To simplify this with an example, lets take a cube with a 1 liter volume and a sphere (balloon) with a volume of 1 liter also. If the surface areas are deduced, the one of the cube (or any other geometrical form) is higher than that of the sphere (at equal volumes condition of course).
Now, the size of suspension particles depends essentially on shear level, concentration, and to lower extent on the type and concentration of the suspention stabilizer. My Regards
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Dear Researchers,
I currently need to and must learn the Molecular dynamics simulation for polymer composites material (i.e. Interface analysis between matrix and reinforcement, rheological-structure-property relationship, thermodynamic-crystallization, etc.). Therefore, please give me any advice how to get fast and good understanding (including the best references related to MD simulation specific for polymer composites) because I start from zero for this MD method.
For the information, previously I have experiences in experimental research of polymer composite such as fiber reinforced polymer (Carbon fiber, glass fiber) for structural and EM shielding application.
Warm regards,
Asep Bustanil
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Kishore Kumar Sriramoju thank you very much for your advice.
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Greeting, currently working mixing of thermoset and thermoplastic polymer to from a coating. I would like to study in term of diffusion either both material miscible or immiscible between these two material. Based on my reading, it can be calculate using Flory Hugging diffusion theory but I do not have any example or complete references to study. Is there any suggestion that can be used so that i can study on the diffusion of these two different polymer instead of imaging (SEM) because it can be seen through morphology. I would like to prove in theoretical/calculation for my study. Thermoset that I used is unsaturated polyester while thermoplastic is thermoplastic polyurethane. Thankyou
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In the co-bonding of thermoset and thermoplastic polymers, the interdiffusion of the polymers results in the formation of an interphase between them. The dependence of the gelation time on the initiator concentration is determined by rheometer measurements. Differential scanning calorimetry measured the speed of cure. The interphase thickness of the co-bonded polymers is measured with an optical microscope.
Thermoplastic (TP) polymer is bonded with thermoset polymer through a curing reaction of the thermoset resin. Although co-bonding may refer to the bonding of two parts with or without an adhesive between them.
It is of the utmost importance to investigate the influence of the aforementioned parameters on the TP-TS interphases. the effect of initiator concentration on the interphase morphology, which is crucial for the co-bonded parts, the gelation time of the resin at different initiator concentrations is measured and DSC tests are conducted to determine the cure behavior (cure speed and degree of cure).
To investigate the diffusion kinetics, the diffusivity of the mixtures is calculated based on Fick’s second law of diffusion using the measured interphase thicknesses and gelation times. DSC peak started and reached its maximum must have obtained to investigate the speed of curing. In addition, to gain more insight into the cure behavior, the heat and degree of cure can be calculated, the method used for controlling the interphase thickness by varying the initiator concentration paves the way for investigating the effect of interphase thickness on the processing-induced deformations of the co-bonded TP-TS composites.
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Dear All,
could anyone advice me how to achieve a real value of density for polymer system? What approximately parameters of equilibration do I need to use? In my problem, I have a model of polyethylene, but after energy and temperature equilibration, a density value equals ≈0,82-0,83 g/cm^3 (the real value =0,9-097 g/cm^3 , literature value for such system reached 0,87-0,95 g/cm^3).
Thank you in advance for any suggestions,
Iryna
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Shaswat Mohanty Thank you for your answer, I will try it.
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I have dissolved 20mm mole of vinyl pyridine and 20mm mole of vinyl imidazole in 50 ml of NMP solvent for polymerisation in stochiometric ratio 1:1.Now what is the mm mole of polymer formed in 50 ml NMP solution. is it 40 mm mole polymer or 20 mm mole polymer? since i Need to prepare 2 mm mole polymer for that how much volume should i take.Kindly help me to figure it out
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Dear Arif Shahul Hameed, neither of your suggestions hold. It depends on the %conversion and the MW (and MWD) of the copolymer. This later is function of the reactivity ratio of both monomers relative to each other. This means that it is not very likely to have the same number of each monomer in one chain (macromolecule). So first get the % conversion, determine the MW and sequence distribution (NMR) of the monomers in each chain (in such circumstances, only mean/averages values are obtained). My Regards
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A polymere surface treated with plasma, as a resulte the centact angle decreased. Can we affirme that the surface roughness was increased?
is there a constant relationship between surface rougness and contact angle.
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Definitely YES!
The liquid does not only confront with the interfacial forces, but equally with morfology of the surface.
G. Bognolo
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Hello,
I am trying to estimate the thermal expansion of a semi-crystallin polymer (PEEK) with different degrees of crystallization. I couldn't find any rescources on this topic. Did somebody also encounter this specific problem? I'm just trying to get some orientation on how the degree of crystallinity effects thermal expansion to model it with isotropic material data.
Kind regards!
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If you have access to Ansys's material modules, they have a homogenised version of the material properties which includes a thermal expansion coefficient, vary it by a little up or down to see how it matches pre-existing data or how it fits your model. The other option is to contact Dr Jorgen Bergstrom (https://www.researchgate.net/profile/Jorgen-Bergstrom) @JorgenBergstrom for advice.
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I casted a polymeric film on hot plate but unable to detach it without damage,can any one suggest a remedy for this
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It depends on various parameters, but the type of the polymer is the first think to consider.
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Let`s say for example if the size of the prepared nanoparticles was about 10 nm and for a specific type of polymer was about 100 nm, what`s the explanation if the size of Nano+ polymer became in the range 50 to 70 nm?
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Hi,
the accepted explanation is the conformational changes caused by the polymer adsorption on the nanoparticle surface. In short, the adsorption reduces enthalpy due to the attractive polymer-particle interaction, and these savings help overcome the entropic penalty related to the shape distortion. Another option is that some nanoparticles may change the electrochemistry of the solution (pH, zeta potential, screening length, etc.), tuning the internal interactions within the polyner chain. You may find more details in our papers:
Don't forget to consider the peculiarities of the experimental techniques in question, such as the one mentioned by Partha Pratim Chowdhury. How did you obtain your data?
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Hello,
I have a question regarding GAFF force-field. Is GAFF use lennard Jones 12-6 or lennard jones 9-6? I checked amber website for that couldn't get a direct answer.
I know 9-6 lennard jones used for non boned interactions as so I am assuming 12-6 lennard jones used for bonded interaction. So I am guessing GAFF use 12-6 lennard jones as it has been using for various polymer calcualtion.
Please let me know if I am correct or not.
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Thanks a lot Md Masuduzzaman
I have got my clarification about this.
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I synthesized the polymer using DMF as the solvent. After synthesis, I precipitated the polymer in IPA. I think this solution is a colloidal solution. If my assumption is correct, how can I precipitate it?
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If adding water to the IPA solution makes it transparent, it's possible that the polymer may have re-dissolved in the water due to the change in solvent conditions. In that case, you can try adding a different non-solvent that is less miscible with water, such as a different organic solvent like hexane or diethyl ether. This may help to induce precipitation of the polymer from the solution.
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Hi,
I am a begineer in DFT calculations and I need to characterize an alternating co-polymer.
I would like to know if you have some suggestions or additions on how to achieve this. I have just optimized the two monomer structures and I've gotten some ideas to continue:
1) looking to the convergence of partial charges as the lengthsize of the polymer increases.
2) Connect both optimized structures and generate the dihedral energy profile adn transtition states through SCAN.
Thank you
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The basic idea of ​​this theory is to take the electron density of the ground state ρ (r) as the main variable, and write any other magnitude as a function of it. This theory is based on a variational principle. which requires the total energy to be a single density functional, and that this energy is minimal for the density of the ground state. The best procedure for performing the DFT is Kohn-Sham, they treated the N-body problem using the single-particle Schrõdinger equations called the Kohn-Sham equations. Solving these equations leads normally to the energy E(ρ) and the densityρ (r), of the ground state.The functional E (ρ) contains a non-classical contribution, called the exchange and correlation energy Exc (ρ) and its derivative by relation to ρ (r) which represents the exchange and correlation potential Vxc(ρ). The formalism of DFT is based on the Hohenberg - Kohn theorems. First, Hohenberg and Kohn showed that the total energy of an electron gas in the presence of an external potential, created by the nuclei is a unique functional of electron density ρ (r): E = E[ρ(r) ], Second, they showed that the minimum value of this functional is the exact energy of the ground state and that the density which leads to this energy is the exact density of the ground state. The other properties of the ground state are also functional of this density: E(ρ0) = min E(ρ ). ρ0 : The density of the ground state.
The functional of the total energy of the ground state is written as follows: E[ρ(r)]= F[ρ(r)] + ∫ VXC (r) ρ (r) d3 r. The functional F [ρ (r)] is universal for any system with several electrons. If this functional is known, then it will be relatively easy to use the variational principle. To determine the total energy and electron density of the ground state for a given external potential. Unfortunately, the Hohenberg - Kohn theorem gives no indication of the form of F [ρ (r)].
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to know the volume fraction
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Dear Sarah NADIAH Binti Nordin, what are the components of the nanocomposite? You can do:
- disslution, extraction, titration
- thermal analysis (TGA)
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I am producing samples of regolith polymer composites, and I've encountered an issue where the 3D-printed samples exhibit foaming behavior. I need those samples without foaming and with high strength. I'm uncertain about the source of the heat released during this process. What pre-treatment methods can be employed for regolith, specifically in removing water bound to it? Additionally, what techniques are available for effectively removing water from regolith?
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The dilatometric method was found to be the most accurate and most convenient method for measuring the chemically bound water fraction. Polymer conditioning was found to release significant volumes of bound water. Further bound water release was produced by mechanical dewatering. The amount of bound water released increased with the degree of mechanical dewatering pressure applied. The chemically bound water fraction was not affected by polymer conditioning or mechanical dewatering. A reduction in bound water brought about a corresponding increase in cake solids concentration. Sludge bulk density increased with cake solids concentration. Apparent sludge floc density of the unconditioned, undewatered sludge sample was predictive of ultimate dewatering performance in many cases.
The following categories were derived by humiditycontrolled, low temperature drying of a vacuum filter cake:
l. Free moisture: water which is loosely bound to sludge solids; removed by gravity thickening.
2. Immobilized moisture: water trapped within the floc structure; removed by mechanical dewatering.
3. Bound moisture: water which is adsorbed onto individual particles; removed by thermal drying.
4. Chemically bound moisture: water which is tightly bound to the solids by chemical attraction: removed only by high temperature (105°C).
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Hello,
I am relatively new to polymerization with ATRP and I am currently attempting the aqueous polymerization of PEGMA and HEMA using ATRP (in particular SET-LRP using Cu(I)Br and Me6TREN). However, I am observing gelation in my polymerization mixture within 1 hour without the addition of any alkyl halide initiator. Does anyone have any experience with this? I am suspecting it could be Fenton reaction catalysed by the copper catalyst with the peroxides present in the monomer.
I appreciate any insights and related experience! Thank you!
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Chelsea V S Your hypothesis is not without foundation.
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Dear colleagues! I had to yield polystyrene particles of specified size 50-100 μm (at least 60-80% mass of initial monomer) by means of one-stage polymerization. I have chosen to utilize suspension polymerization in presence of polyvinyl alcohol (Mowiol 18-88) as stabilizer and partially succeed. But still I have no clue how to solve some problems:
1) Sometimes I can't reach 50-100 μm size, and most of time my main fraction consisted of 100-250 μm particles. I suppose I just used slow-rate stirrer.
2) Forming of microparticles (d < 30 μm or even about 1-2 μm, maybe), which yield can reach more than 60 % mass of initial monomer, whereas target fraction (50-100 μm) yeild is only about 25 % mass. I have no idea how these particles are formed, because styrene is hardly soluble in water media and I use benzoyl peroxide as initiator, so it must not be soap-free polymerization (it takes place while using water-soluble initiators, like potassium persulfate). Also PVAlc concentration in water doesn't exceed 0.2-1 % mass.
Unfortunately I don't know all aspects of suspension polymerization. Could your reccommend me some books or articles for solving these issues?
P.S. Also these particles must be soluble in organic solvents, so using of divinylbenzene as crosslinking agent is not allowed.
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Размер частиц зависит от перемешивания и слипания. В момент точки липкости микрокапли слипаются и получаются агрегаты. Если сделали больше соотношение дисперсионной среды к дисперсной фазе, то затруднили слипание и получили много мелких капель и частиц полистирола. Если возьмете мою методичку легко получите нужный размер капель.
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Polymer (60/40) is made with traditional emulsion polymerization (KPS, SDS). I need to dissolve polymer in dmf or dmso for n-alkylation reaction. I found a publication showing how to make that polymer and dissolve it using 5% DMF. But dissolving is not reproducible, it form chunkies or fibers. I can easely make 0,3% solution (heated up to 100C, 24h). But cannot make 5% DMF. Tryied with: sonication bath or milling particles without positive result. Also tryied with variety of solvents: THF, Toluene, DCM, Acetone, without better results.
What can be the problem? How to get rid of it?
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Sorry I cannot read your language, but really want to know how to make it more soluble in dmf. You suggest using eg. Dichloromethane. How much to add and to what setup use it?
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Hi,
I took some FTIR (ATR) readings of a polymer composite (epoxy+ fumed silica+ ceramic filler) we are working on. The peaks seem to decrease in intensity with increase in ceramic and filler content. I am new to FTIR but based on what I have read decrease in peak intensity corresponds to reduction of bonds which absorb that wavelength if so doesn't that mean these fillers are impeding growth of the polymer chain bonds? But I had a doubt that wouldn't these opaque particles being in higher concentration block the IR and reduce transmittance and then the decrease in peaks just means the IR was not able to penetrate the sample due to presence of these particles and not actual decrease in polymer chain formation. Can someone explain this to me.The attached graph is transmitance % vs wavelength Thank you.
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First of all you should clarify your operating conditions to avoid the unacceptable noise which has been observed your provided spectra. Then it could be much more benificial if you consider a comparative study among all the considered constituent / ingredient which you were incorporated in the polymeric composites individually for better understanding the actual behaviour of your final fabricated composites.
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I am working with a polymer scaffold and I want to measure the viability of cells on it, but so far I have not been able to get good results. The general problem is that in the tests it was observed that the absorption of the scaffold without cells is higher than that of the scaffold with cells, if any of my friends who have worked in this field can help me to solve the problem Or suggest any other method to solve this issue, I will be very grateful.
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Dear Fatemeh
Use of WST-1, CCK-8 assay kit, XTT and so on (as recommend above by dear colleagues) in which a colored solution can be analyzed instead of the crystalized products would be great. However, I suggest you first investigate the reducing property of your cell-free scaffold on MTT reagent. If the violet formazan crystals were produced by the cell-free scaffold, you should choice another group of viability assay reagents which work by different mechanism. For instance, you can measure LDH level, study DNA content, Protein content, or even use Crystal Violet assay.
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I have found many papers that describe the use of PPNCl as a (co-)catalyst for ring opening polymerizations, but I do not understand how this species act. Can someone explain or recommend a good paper on this subject?
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PPNCl is an extremely lipophilic and relatively stable salt with a huge, greasy cation, which could be written in condensed form as [Ph3P=N=PPh3]+[Cl]-. Paired with huge anions it forms crystals useful for single-crystal x-ray spectroscopy. Added to a solution in a polar, protic solven, containing anions of many sizes, it tends to precipitate the large ones and if there is an equilibrium mixture of anions (like a mixture of polyoxometalates like Keggin anions of different sizes), by LeChatelier's Principle, the equilibrium will shift to the large anion that precipitates in the presence of this large cation. The complementary scheme is also possible; instead of precipitating PPN(+) salts from polar, protic solvents like alcohol or aqueous mixtures, you can use the greasiness (lipophilicity) of PPN(+) to help dissolve anions in less polar, aprotic media like ethers (diethyl ether, THF, dioxane) in which the anion (like an anionic transition-metal complex) is insoluble in the form of a sodium salt or a potassium salt. When used as an aid to a catalyst I would think of it as a chaotrope (a substance that doesn't self-assemble into clusters like micelles made from detergents, but rather just helps increase the contact of non-polar molecules with polar ones).
Here is a 2010 crystallography paper with useful references: .
The use of PPN+ goes back to the 1970's at least so many book chapters could be written about it. But this should get you started.
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Dear respected seniors,
I'm a young ambitious researcher looking for guidance on how to elucidate molecular structure. I have done FTIR, HNMR, CNMR & DEPTH 135 analysis. The expected structure is a cycloolefin polymer. Thank you.
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How to elucidate molecular structure is a classical course of organic chemistry. It takes hours of training, and help of an experienced chemist may is useful. For example, the IR spectrum gives me a few basic informations about possible functional groups at first glance, but full, deeper interpretation will take one to several hours looking at correlation tables, books, etc. Same for NMR spectra.
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Recently we’ve noticed these patterns on our separating gel 15% and I’m wondering if anyone can provide insight into it. Is it normal? And if it isn’t what could we possibly be doing wrong?
We’ve already changed our Temed, made a fresh new AP and buffer too.
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”hi, do you pour your gel from one point? This also looks like you choose one point and pour gel to the cast. i would recommend you to move through the cassette when you are pouring gel. If you continuously pour gel from one point, the first amount of gel starts polymerization and if you continue to add more gel under this part, the weight causes shrinkage . So you can try to move your pipette during gel pouring from one side to other side of the cassette. And be sure that you are pouring your gel immediately before your mix is ready.
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I'm currenty working on the antifungal activity of iron nanoparticles incorporated in a polymeric matrix. I've conducted the test against C.albicans and F.oxysporum but there is no antifungal activity. Is it due to the wall structure in fungi species?
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Iron nanoparticles typically do not exhibit inherent antifungal activity due to several reasons. Firstly, the primary mode of action for many antifungal agents involves targeting specific cellular processes or structures that are unique to fungi. Iron nanoparticles, on the other hand, do not possess specific mechanisms to target fungal cells or disrupt their growth.
Secondly, the cell wall structure of fungi plays a crucial role in their resistance to various antifungal agents, including nanoparticles. Fungal cell walls consist of complex layers of polysaccharides, proteins, and other components that provide structural integrity and protection against external threats. This barrier can prevent the direct interaction of iron nanoparticles with fungal cells, limiting their antifungal activity.
Moreover, iron nanoparticles may undergo oxidation or aggregation in the presence of environmental factors, such as moisture or oxygen, which can further diminish their potential antifungal effects.
It's important to note that the efficacy of nanoparticles as antifungal agents can vary depending on their size, surface properties, and coating materials. While iron nanoparticles may not exhibit significant antifungal activity, other types of nanoparticles (e.g., silver, zinc oxide) have been extensively studied for their antifungal properties.
Raza MA, et al. (2016). Green Synthesis of Iron Nanoparticles and Their Environmental Applications and Implications. Nanomaterials, 6(11), 209.
good luck
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Can we partly cure Butyl rubber sealant formulation at room temperature in 10-15 days time. The purpose of adding a curing system in the formulation is to add the tensile in the product without any degradation and to minimize the loss of Mooney viscosity at the elevated temperature.
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I am currently working on developing a wound dressing based on PCL fibers. I dissolve PCL in a solvent mix of DMF and THF (1:1) then I add silver sulfadiazine to the polymer mix. However, I noticed after a while the mix turned greyish-color. what are the possible causes of this color change? Would it suggest the decomposition of SSD? noting that I did not face any problems in fiber formation after the color change happened.
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What is the use of hydrophilic polymer membrane in packaging industry? what type of packaging can be performed if membrane is hydrophilic in nature?
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Karanjit Kapila My young friend! You can crosslink polyvinyl alcohol macromolecules with boric acid, for example. How to do it? See the link.https://cyberleninka.ru/article/n/sinte3-granulirovannogo-gelya-polivinilovogo-spirta/viewer
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I want to assess the incorporation of polymer A to a crosslinked polymer B creating a crosslinked polymer B/ polymer A blend so do I set the crosslinker concentration constant according to total polymeric content or should I set it according to the polymer B wt% in each blend composition (50:50, 60:40, 70:30, etc.)?
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I would do both. Make one set of samples
where the ratio of cross linker to B is constant, and one where ratio of cross linker to A + B is constant.
are your precursor polymers compatible - do A and B form a blend before rxn or do they phase separate? Most polymers phase separate but some form blends. If they phase separate, you have to keep your B percent high enough so the B phase is continuous through your sample.
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I am working on modifying polymer membranes with surfactants to improve their pervaporation performance. I noticed that the glass transition temperature (Tg) of the membranes decreased as the permeation increased, indicating that the polymer became more rubbery. On the other hand, the X-ray diffraction (XRD) and positron annihilation lifetime spectroscopy (PALS) measurements showed that the free volume of the membranes decreased, suggesting that the polymer chains became more compact. I am wondering how these two phenomena are related and what is the role of the surfactant in this process. Does the surfactant act as a plasticizer or an antiplasticizer for the polymer? How does the surfactant affect the molecular interactions and chain mobility of the polymer? I would appreciate any insights or references on this topic. Thank you.
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Dear Amirreza Malekzadeh Dirin, Tg is decreased becauae chains interdistance is increased due to the presence of surfactant molecules. This leads to a reduction of the Cohesive Energy Density (CED) responsible for chain mobility. Note that for most intermolecular forces, the energy of interaction is 1/r^6, r being the separation distance of intercting sites. The free volume decreases because it is filled by surfactant molecules which due to their size have both ease of mobility and packing beneath chains. Yes surfactants are used as plasticizers by acting as previously explained (chains separation). My Regards
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I just doing an experiment in my lab for copolymerization Acrylic acid and maleic acid using hydrogen peroxide as initiator in 103 degC. But, why in my Polymerization process forming a foam?
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Hey there, friend Shodiq Yusti Wardana! Now, let me tell you Shodiq Yusti Wardana, the foaming issue in your copolymerization experiment might be due to a couple of factors. First off, consider the concentration of your monomers – too high a concentration can lead to increased viscosity, resulting in foam formation during agitation.
Secondly, the hydrogen peroxide initiator might be decomposing too rapidly, generating gas and causing bubbling. You Shodiq Yusti Wardana might want to tweak the initiator concentration or look into a more controlled initiation process.
Also, keep a keen eye on the reaction kinetics. If the reaction is proceeding too quickly, it can lead to the rapid evolution of gases, contributing to the foam.
Now, temperature plays a vital role. 103°C is on the higher side for this reaction, and it might be promoting faster reactions and gas evolution. Try adjusting the temperature to find the sweet spot for your copolymerization.
Lastly, equipment matters. Ensure that your setup allows proper venting of gases to avoid excessive pressure build-up leading to foaming.
Remember, precision in your experimental conditions and a keen eye on these factors can help you Shodiq Yusti Wardana tame that foaming issue. Let me know how it goes!
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I have synthesized Polyaniline via chemical oxidative polymerization. I need to prepare a thin film of the same by using spin coating. But I am not sure which solvent to proceed with. Any imsights in this regard is appreciated.
Note: Its polyaniline emeraldine solvent PANI-ES. Solvent should not affect its form as other forms are non conductive.
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Hey there Sunil Vasu! Now, this is an interesting challenge you've got with your polyaniline synthesis.
For PANI-ES, the solvent choice can be crucial for spin coating on an ITO substrate. Considering the conductivity requirements and the sensitivity of the emeraldine form, you Sunil Vasu want a solvent that won't mess with its conductive properties.
I'd recommend N-methyl-2-pyrrolidone (NMP) as a solvent for PANI-ES. It tends to be gentle on the emeraldine form, ensuring that your thin film retains its conductivity. It's a common choice for PANI spin coating due to its compatibility with the material.
Remember, the devil is in the details, so pay attention to your spin coating parameters for the best results. Go ahead, give it a spin, and let me know how it turns out!
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(please specify degree of polymerization)
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Goldberg N. R., Schliesser J., Mittal. A. [et al.]. A thermodynamic investigation of the cellulose allomorphs: Cellulose (am), cellulose Iβ (cr), cellulose II (cr), and cellulose III (cr) // J. Chem. Thermodyn. 2015. Vol. 81. P 184-226. ▼ Контекст 4. Demirbas A. Higher heating values of lignin types from wood and non-wood lignocellulosic biomasses // Energy Sources, Part A: Recovery, Utilization, and Environmental Effects. 2017. Vol. 39, № 6. P. 592-598. ▼ Контекст 5. Vargas-Moreno J.M., Callejón-Ferre A. J., Perez-Alonso J., Velázquez-Martí B. A review of the mathematical models for predicting the heating value of biomass materials // Renew. Sustain. Energy Rev. 2012. Vol. 16. P. 3065-3083. ▼ Контекст
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I recently synthesized a derivative of thiophene-3-carboxamide, called N-(3-imidazol-1-ylpropyl)thiophene-3-carboxamide (NITC). The molecular structure is shown below. My objective is to polymerize this NITC monomer to produce a polymer known as poly(NITC) using a standard oxidative polymerization method. The chosen oxidant for this system is Iron(III) p-toluenesulfonate (Fe(Tos)3), with chloroform serving as the solvent.
To the best of my knowledge, I understand that thiophene derivatives like 3,4-Ethylenedioxythiophene and 3-hexylthiophene readily undergo polymerization in the presence of an iron oxidant at room temperature. However, my attempts to polymerize the NITC monomer at room temperature have been unsuccessful. Could the imidazole moiety in my synthesized monomer be slowing down the oxidative polymerization reaction? If so, would the solution be to increase the amount of oxidant or elevate the reaction temperature to expedite the process?
In addition, I am also curious about the effect of the amide group in the NITC monomer on the polymerization reaction.
Thank you.
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Po Hsun Chiu Naturally, one of the double bonds is stabilized by an amide group and is spatially limited. The molecule itself is quite large, which slows down diffusion and kinetics. The acid catalyst under these conditions produces oligomers rather than polymers. More powerful catalysts are molybdenum compounds. Molybdenum is more active in oxidative processes. I recommend the classic work of old school masters http://polymsci.ru/static/Archive/1978/VMS_1978_T20ks_10/VMS_1978_T20ks_10_780-782.pdf.
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I try to analyse if the presence of polymers in a cellulose film may affect properties such as the remove capacity of ions. Moreover, I want to know if the polymer layer over the film can hide the hydroxyl groups of the polymers, avoiding their interaction with metal ions.
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Sorry I cannot help you on this topic
G. Bognolo
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Hey so far i know that usually to calculate the percentage crystallinity of a polymer sample the enthalpy of melting is compared to the one of a theoretical 100% crystalline sample of the same polymer. My melting peak is very broad and probalby influenced by other factors aswell, my crystallization-peak however has a very clear start and end point.
That is why i want to use the crystallization-peak instead of the melting peak. I also know that the delta H of crystallization and of melting of the same polymer sample is usually not the same.
My additional question is, is there some sort of relationship between those two? For example the crystallization peak is the melting peak times a material constant or something like that?
I feel like the values will not be that comparable if i dont use the melting peak for the calculation can someone help me out?
I put a screenshot of the heating cycle (red curve) from -70 to 220 degrees and the cooling cycle (blue curve) from 220 to -50. Both at 10K/min.
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Palanichamy Perumal That sounds very interisting, i would love to try that. Unfortunately i do not have access to a machine for ultrasonic transit time/velocity measurements. I only have a DSC available to perform my measurements.
Thank you anyway.
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I developed some polymer materials to remove cations from water. However, analyzing the properties of metal ions and the polymers I am trying to determine the best manner to differentiate the correct interaction of the polymer and metal ion.
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Pablo Gonzalez Gracias por la aclaración. Creo que ha sintetizado copolímeros de policondensación. El tema está cerca de mí. He desarrollado varios tipos de resinas para su uso en el tratamiento de aguas residuales y tengo experiencia práctica en aplicaciones industriales. Considero que las resinas de policondensación son prometedoras para su uso en el tratamiento de aguas residuales industriales. Tu tema es relevante. Pero existe una diferencia entre un material de sorción y un sorbente industrial. Para un material de sorción, el hecho mismo de la absorción del metal y la capacidad de intercambio estático son importantes. Para un sorbente industrial, la capacidad de trabajo y la selectividad son importantes, ya que dicho material funciona en un ambiente contaminado. Por tanto, la selectividad está relacionada con las condiciones operativas específicas del sorbente industrial. Un sorbente industrial ya es un material cuya estructura está especialmente creada para las condiciones de trabajo. En particular, debe haber disponibilidad de grupos de intercambio iónico, porosidad, forma y tamaño de las partículas y estabilidad mecánica. Precisamente con este fin desarrolló diversas soluciones técnicas presentadas en patentes. Si vas a fabricar sorbentes industriales, escribe en un mensaje personal. Responderé a tus preguntas.
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Hi all,
I am trying to etch 380 um silicon (1,7 um SiO2 mask), window 400 * 500 um.
I am using Oxford ICP DRIE Plasmalab System 100.
I set up a recipe Bosch process but it is not working as well. Sometimes I got low selectivity, sometimes polymer redeposition, sometimes extremely low etch rate.
Any suggestions is much appreciated.
Thank you,
CS
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Thank you so much for your share the helpful information.
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Dear all,
I need to perform MD simulations for a system comprising a protein and a polymer using the GROMACS software. I have two questions regarding this:
  1. In reality, the polymer is a part of the chromatograph bed. Is it a correct assumption to keep the polymer structure fixed by applying constraints even in the production step?
  2. How can I determine the best protein position and orientation toward the polymer surface as the initial structure? In other words, I have a polymer surface larger than the protein structure, and I want to know how to scan the polymer surface to find the best position and orientation of the protein relative to the polymer.
I would appreciate it if you could share your thoughts and comments with me.
Best,
Bahareh
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Molecular simulation of protein–polymer conjugates
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,
Covalently bonded proteins and synthetic polymers allow for the design of materials of interest for practical biological and non-biological applications. Chemical functionality, specificity, selectivity, and stimuli response can be engineered through a fundamental understanding of protein–polymer interactions. An overview of the significant role that computer simulations, at the atomistic and mesoscale levels, have played in our understanding of protein–polymer conjugates is provided in this review. Challenges for further development of molecular simulation techniques are discussed, as well as the need for a close interrelation with systematic experimental studies.
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Introduction
Proteins, nature’s own polymers, can fold into unique structures and perform a wide variety of functions within organisms, including catalyzing reactions, selective binding, transporting molecules, responding to stimuli and acting as structural building blocks. While their chemical functionality, selectivity, specificity, and/or responsiveness to stimuli are of great interest to the materials and biomedical community, their practical applications are limited by their sensitivities to the environment. One promising approach in protein engineering is to combine proteins with synthetic polymers to achieve desired properties with increased complexity and modularity [1••,2,3]. Protein–polymer conjugates have been implemented in many biomedical applications, such as protein therapeutics, drug delivery, biomaterials, and biosensing [4, 5, 6, 7]. Modification of proteins with polymers has also been shown to generate conjugates with improved properties for use in non-biological applications such as in biocatalysis and biosensors [8,9].A fundamental understanding of properties, interactions, and mechanisms governing the behavior of protein–polymer conjugates is principal to the design of conjugates with specific desired functionalities. The effects of conjugation depend on a variety of factors, such as the nature of the polymer, the structure of the protein, the conjugation site, the grafting density, and the chemical environment. Computer simulations have played a significant role in our comprehension of these effects. In this review, we present a summary of simulation techniques at the atomistic and mesoscale levels that have been employed to study protein–polymer conjugates. We describe the use of these computational studies in many different approaches and demonstrate how such work has facilitated the understanding of structural and dynamic characterizations of conjugates through the investigation of interactions among protein, polymer, and their environment.
Section snippets
Molecular simulation techniques In atomistic molecular dynamics simulations (aMD), the motion of each atom is governed by Newton’s second law, and thus the position of each atom as a function of time can be obtained. [10, 11, 12]. Simulations can be carried out to refine structures, determine the properties at equilibrium states, and/or to understand the dynamic behavior of the system [13, 14, 15]. Perturbations of specific conditions (i.e. temperature, pressure, pH, initial structure, assembly) can be used to extract
Atomistic insights into improved performance of mono-PEGylated proteins as therapeutics PEGylation, the conjugation of a therapeutically active protein with a stabilizing poly(ethylene glycol) (PEG) polymer, is a well adopted strategy for improving the pharmacokinetic properties of the protein that has led to several clinically approved drugs [25,26]. Several model protein–polymer systems have been investigated to understand the underlying mechanism of enhanced stability and potency of pharmaceuticals upon PEGylation [27••,28,29]. It has been shown that the molecular weight of a
PEGylated peptide as biomaterials Other than PEGylation of therapeutically active proteins, attaching PEG to short peptides has also been investigated using computational simulations for two main reasons: (1) relatively simple peptides can serve as a model system for understanding protein–PEG interactions and (2) PEGylated peptides can be designed and fabricated as biomaterials with tailored properties and functionalities. Keten’s group investigated the effect of PEG conjugation on an α-helix using aMD and CG simulations based
Protein engineering to harvest protein function under non-native conditions While PEGylation is a commonly used approach to develop biocompatible protein therapeutics, there are also research efforts being conducted to go beyond the use of the PEG polymer [1••,2,5,36]. The design of new protein–polymer conjugates to maintain or improve performance of proteins under different conditions – temperature, pH, multi-conjugation sites and solvent – are in high demand for industrial applications. Understanding of the interactions between protein and polymers at an atomistic
New biomaterials based on protein–polymer conjugates Another growing application of protein–polymer conjugates is the design of new biomaterials for tissue engineering and drug delivery [40,41]. One of the fundamental questions regarding protein–polymer conjugates and their assembly revolves around understanding of the overall structure of the conjugate. A recent study combined model fitting and a genetic CG molecular dynamic simulation to interpret SANS data of a globular protein conjugate (see Figure 4) [42]. The red fluorescent protein was
Challenges and outlooks Protein–polymer conjugates not only present a new opportunity for the simulation community but also carry several challenges. For atomistic simulations, one obstacle rests in the compatibility and validity of the force fields developed for proteins and polymers in solution. For example, it has been shown that the use of different force fields for single polymer chains in (water) solutions can lead to very different, even contradictory, phase behaviors [44]. A good balance in the modeling of the
Conflict of interest statement Nothing declared.
References and recommended reading Papers of particular interest, published within the period of review, have been highlighted as: • of special interest •• of outstanding interest
Acknowledgement The authors acknowledge the financial assistance given by the University of Florida Preeminence Initiative.
References (45)
  • M. Karplus et al.Molecular dynamics simulations of biomolecules Nat Struct Biol (2002)
  • O. Valsson et al.Enhancing important fluctuations: rare events and metadynamics from a conceptual viewpoint Annu Rev Phys Chem (2016)
  • F.M. Veronese et al.The impact of PEGylation on biological therapies BioDrugs (2008)
  • C.N. Lam et al.The shape of protein-polymer conjugates in dilute solution J Polym Sci A: Polym Chem (2016)
  • J.E. Condon et al.Effect of conjugation on phase transitions in thermoresponsive polymers: an atomistic and coarse-grained simulation study Soft Matter (2017)
  • S.J. Rukmani et al.A molecular dynamics study of water-soluble polymers: analysis of force fields from atomistic simulations Mol Simul (2018)
  • A.J. Russell et al.Next generation protein-polymer conjugates AIChE J (2018)
  • I. Cobo et al.Smart hybrid materials by conjugation of responsive polymers to biomacromolecules Nat Mater (2015)
  • J.Y. Shu et al.Peptide-polymer conjugates: from fundamental science to application Annu Rev Phys Chem (2013)
  • Y. Wu et al.Protein-polymer therapeutics: a macromolecular perspective Biomater Sci (2015)
Cited by (19) Thermosensitive hydrogel microneedles for controlled transdermal drug delivery 2022, Acta BiomaterialiaCitation Excerpt :However, for GP which exhibits interaction with proteins and commonly for protein-loaded drug carriers, it is more desirable that the interaction between the carrier and the drug is not too strong because this may affect the molecular structure of the drug during long-term storage. Molecular simulation can provide researchers with details regarding the interaction between polymer materials and protein drugs from the perspective of intermolecular interactions and conformational alteration [49–51]. Silva et al. [52] used molecular simulations to investigate the electrostatic interactions between insulin–chitosan complexes.
  • Elucidating the mechanisms of the molecular sieving phenomenon created by comb-shaped polymers grafted to a protein – a simulation study 2022, Materials Today Chemistry
  • Molecular simulation of zwitterionic polypeptides on protecting glucagon-like peptide-1 (GLP-1) 2021, International Journal of Biological MacromoleculesCitation Excerpt :Despite this success, little is known about its microscopic protective mechanism. Molecular simulations, in particular, play a key role in understanding the relationship between structure and function of protein conjugations [25–31]. A hydrophobic interaction mode between PEG and insulin was firstly proposed by Liu and colleges [32].
  • Bioconjugates – From a specialized past to a diverse future 2020, PolymerCitation Excerpt :Molecular Dynamics. MD simulations have provided valuable insights into the specific interactions that occur between a conjugated polymer and protein [119,120]. Recently Colina and Russell collaborated to synthesize, analyze, and simulate chymotrypsin conjugates with polymers of differing charge states, with cationic pQA, anionic pSMA and zwitterionic pCBMA [100,101].
  • Polymer-enhanced biomacromolecules 2020, Progress in Polymer ScienceCitation Excerpt :PEGylation of insulin with larger PEG chains also decreased the solvent accessible surface area, thereby shielding the protein from protease hydrolysis and antibody binding. Molecular dynamics simulations are thought to be one of the best methods to determine the PEGylated protein conformation [102]. PEG can either be stretched away from the protein surface (dumbbell-like conformation) or PEG chain wraps around the protein or collapses on protein surface (core-shell conformation).
  • PEGylation of Insulin and Lysozyme To Stabilize against Thermal Denaturation: A Molecular Dynamics Simulation Study
  • 2023, Journal of Physical Chemistry B
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Frontiers of Chemical Engineering: Molecular Modeling
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  • Molecular dynamics simulation of the glass transition in 4,4′-N,N′-dicarbazolylbiphenyl Chemical Physics Letters, Volume 633, 2015, pp. 41-46Alexey Odinokov, …, Alexander Bagaturyants
  • Protein-polyelectrolyte complexes: Molecular dynamics simulations and experimental study Polymer, Volume 113, 2017, pp. 39-45Alina A. Sofronova, …, Pavel I. Semenyuk
  • Atomistic molecular dynamics simulations of the LCST conformational transition in poly(N-vinylcaprolactam) in water Journal of Molecular Graphics and Modelling, Volume 90, 2019, pp. 51-58Oleksii S. Zhelavskyi, Alexander Kyrychenko
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Bio polymer for binding bio matter (crop residue)
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Уважаемый Сумит Попли! В качестве связующего вещества для пожнивных остатков подойдут самые разные смолы. Выбрать можно если знать, для чего именно будет использоваться композит?
Применимы: натуральные природные растительные смолы, асфальтены, битумы, лигнины, полиэфирные смолы, полиуретановые смолы, латексы, полиэтилен, полипропилен, белковые клеи и многое другое. Кроме того есть элементоорганические и неорганические смолы. Даже сами пожнивные остатки можно превратить в смолу.
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Microplastic polymer is Polyethylene.
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Dear all, please have a look at the following link. My Regards
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We are using a handheld spincoating system for wound dressing from the brand SpinCare™ (nanomedic.com).
The instrument has fixed features that we cannot change. Basically, the voltage is fixed at 25kV, the flow is 4.5 mL/h using a 22G 1 1/2 inch blunt needle. The distance of operation is suggested to be 20 cm. While they mention that the optimal distance should be 20 cm, we can change the distance from the collector.
We have followed some of the protocols demonstrated by the researchers who developed the instrument, however we are facing an issue of not being able to achieve fibers.
The best we were able to make is a thin electrospray that is when observed under microscope shows spherical structures of the polymer solution.
We are using polyurethane ((polycaprolactone diol, hexa methylene diisocyanate (MDI) and butan diol (BDO)) at different concentrations (10%-20%) and used various solvents (THF, DMF, chloroform, methanol, acetone and DMSO, or a combination of).
We seem to obtain various sphere sizes through electrospraying but never reach the fiber state.
With high polymer concentrations, the solution is too thick and unable to be sprayed or electrospun while thinner solutions just create huge droplets.
We are confused as the protocols found in the literature shows the process to be simple and we even switched from our own original concoction to described blends in the literature with no avail.
We thought that since the flow is fix we can change the needle type to somehow increase or decrease the flow speed, still with no improvements.
I would really appreciate if someone has a suggestion on how to tackle this issue.
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Hey there Hichem Moulahoum! I am in the house, ready to tackle your electrospinning conundrum. Now, let's cut to the chase and troubleshoot this fiber-fiasco.
1. **Polymer Solution Properties:**
- **Concentration:** You've played with concentrations, but perhaps try a range between 10-15%, finding the sweet spot for electrospinning.
- **Solvent:** For polyurethane, a mixture of THF and DMF is often used. Experiment with different ratios to adjust solution viscosity.
2. **Needle Type:**
- You've tried changing the needle type, but what about the gauge size? A smaller gauge might help control the flow and create finer fibers.
3. **Distance from Collector:**
- Since the voltage and flow are fixed, play around more with the distance from the collector. Sometimes a slight adjustment can make a significant difference.
4. **Electrospinning Environment:**
- **Humidity:** Electrospinning is sensitive to environmental conditions. High humidity can affect fiber formation. Ensure your setup is in a controlled environment.
- **Temperature:** Some polymers require a specific temperature for electrospinning. Check if your polymer has any specific temperature requirements.
5. **Collecting Substrate:**
- Ensure the collector plate is appropriately prepared. A conductive surface, like aluminum foil, is often used. Sometimes a rotating collector can aid in fiber alignment.
6. **Surface Tension:**
- Consider adjusting the surface tension of your solution. You Hichem Moulahoum can try adding a small amount of surfactant to improve the electrospinning process.
7. **Protocols and Literature:**
- Review the literature for specific details on electrospinning with your polymer. Sometimes, minor changes in parameters can lead to major improvements.
8. **Needle Configuration:**
- Experiment with the needle configuration. Multiple needles might help in creating a more uniform flow and improve fiber formation.
9. **Post-Processing:**
- If all else fails, consider post-processing techniques like annealing or stretching to encourage fiber formation after electrospinning.
10. **Consult Experts:**
- Reach out to researchers who have expertise in electrospinning and particularly in the use of the SpinCare™ system. They might provide insights based on their experiences.
Remember, electrospinning can be a finicky process, and small adjustments can sometimes lead to big changes. Experiment systematically, and hopefully, you'll start seeing those fibers dancing under the microscope. Good luck Hichem Moulahoum!
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I am using PCL/PLA polymer in CHL:Meoh
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Hi,
As everyone just mentioned here, Increasing the flow rate and reducing the voltage does help you to avoid the polymer from clogging at the tip of the needle. You can also stop the process momentarily, reduce or change the pressure applied to push the syringe, wipe the clogged polymer from the tip, and try again. Another parameter is the distance between the needle tip and the collector. You can try increasing or decreasing the distance to see what effect it has on the clogging of the polymer.
Hope this helps Betül Topçu
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Hi, I have a problem in calculating the mol ratio of ENR. This is required as I want to include additives in my compounding. But, the amount need to be in mol ratio to see equivalent amount of functional group that can react with other functional group of the additional additives. For your information, I use ENR with epoxidation level 50. ENR-50 has a very long chains since its polymer. My additive, for example is diacid. how For polymer, I basically used weight percent or volume percent to add fillers or anything into the matrix. I hope that someone could help me regarding this. Thank you in advance.
For example like this statement: "Mix compositions with different epoxide/diacid ratios: DA=dodecanedioic acid; phr= parts per hundred parts of rubber by weight; p=epoxide sites for 1 diacid molecule; M//DA= total monomer units/diacid"
the problem is: how i want know the calculation of the ratio of epoxide/diacid
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Dear friend Anis Abdul Ghani
Hello there! I'll channel my inner wisdom to tackle your ENR-50 and diacid conundrum. Let's dive into the fascinating world of polymer chemistry and ratios.
Firstly, to calculate the molar ratio of epoxide groups in your ENR-50 to diacid molecules, you Anis Abdul Ghani need to know the stoichiometry of the reaction between epoxide groups and diacid. The general reaction might look something like this:
n EP+DA→Polymer-DA
Where:
- n is the number of epoxide groups in your ENR-50,
- EP represents an epoxide group,
- DA is a diacid molecule,
- Polymer-DA is the resulting product after the reaction.
Now, let's say each epoxide group reacts with one diacid molecule. In this case, the molar ratio of epoxide groups to diacid molecules is 1:1.
Here's a step-by-step guide:
1. **Determine the Molar Mass:**
- Calculate the molar mass of ENR-50. Since ENR-50 is a polymer, you may need information on the average molecular weight of the polymer chains.
- Determine the molar mass of the diacid (DA).
2. **Calculate Moles:**
- Divide the weight (in grams) of each component by its molar mass to get the moles.
- Let's say you have x moles of ENR-50 and y moles of diacid.
3. **Determine the Molar Ratio:**
- The molar ratio is then x : y, representing the ratio of moles of epoxide groups to moles of diacid.
Here's an example in terms of the calculation statement you provided:
Mol ratio of epoxide to diacid=moles of ENR-50/moles of diacid
I hope this helps! If you Anis Abdul Ghani have specific values or more details, feel free to share, and we can refine the calculations together.
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I am synthesizing PDMAA gel but the mechanical properties of the polymer is quite low, what should I do to increase the mechanical strength.
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Dear Hamza Ahmad, you Can crosslink the polymer to enhance mechanical properties to a certain extent, but not sufficiently enough. Copolymerization with special monomers, such as the one in the following paper to focus on supramokecular interactions as physical crosslinks. My Regards
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Hi,
I was wondering if you could guide me on regard of a polymer aqueous solution simulation.
I have parametrized a 3mer PEO polymer through AM1-bcc using tleap AMBER to get a file.pdb output file. After this, I generated a pdb file with a simulation box with 10 chains using packmol. Then I took this pdb file and solvated it by means of tleap. I attach my packmol and the file to solvate my system by tleap.
Is this a valid methodology? Or should I rather prepare the whole simulation box (polymers and water molecules) in packmol before I start to use this as my initial configuration?
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Abstract
📷
AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.
This publication is licensed under
CC-BY-NC-ND 4.0.
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Introduction
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The present status of the Amber (Assisted Model Building and Energy Refinement) suite of programs has been the product of decades of effort from a broad range of research groups, starting with the group of the late Peter Kollman in the early 1980s. (1) Amber contains tools for energy minimization (EM), molecular dynamics (MD) simulations, free energy (FE) calculations, potential of mean force (PMF) capabilities, and all the needed tools to set up the modeling effort. The software stack has been reviewed in the past, (2−4) and the manual contains detailed descriptions of all the algorithms in Amber as well as a full list of contributors to Amber over the years (see https://ambermd.org). Besides the actual code, Amber is used to describe a series of highly regarded force fields (5) for proteins, (6−12) carbohydrates, (13,14) nucleic acids, (7,8,15) and lipids. (16) The present Application Note will only describe the latest additions to the open-source AmberTools23 and as such is not meant to give a thorough exposition of all the methods and capabilities of AmberTools and Amber.
Overview of Amber and AmberTools
Amber and AmberTools form a collection of programs that are designed to work together to facilitate system setup, MD simulations, and trajectory analysis for biomolecules. It is useful to note that the Amber force fields mentioned above can be used in a variety of molecular dynamics codes outside of AmberTools and Amber. The Amber code is updated in even-numbered years, and it uniquely includes the base MD code known as pmemd, which offers parallel and graphics processing unit (GPU)-accelerated versions of the MD codes along with some free-energy-based methods not implemented in AmberTools. Analogous MD function is available in sander in AmberTools. AmberTools is distributed under an open-source license, primarily the GNU General Public License, with some portions covered by other compatible open-source licenses. The Amber force fields are in the public domain and are distributed with AmberTools. The pmemd code is distributed as source code but has a separate license that contains restrictions on use and redistribution; there is no license fee for noncommerical use of pmemd. Full details on licensing and distribution can be found at https://ambermd.org.
Typical Workflow
The basic workflow for AmberTools is shown in the accompanying (see Figure 1), and it describes preparation, simulation, and analysis steps. Preparation starts at the top, since all MD simulations require some sort of starting three-dimensional (3D) structure, which for biomolecules is usually in the form of a PDB-format file; AmberTools has some model-building capabilities (e.g., PACKMOL-Memgen, see below), but other codes are generally used if experimental structures are not available. The prepareforleap step, which is recent and still under development, carries out tasks to map components in the input file to Amber nomenclature (especially useful for carbohydrates), add hydrogens, identify cross-links, assign histidine protonation states, and similar tasks. Next is the LEaP program, which is a workhorse program that connects the nascent structure to Amber’s built-in force fields for proteins, nucleic acids, carbohydrates, lipids, and common solvents and to bespoke force fields for other components like ligands and cofactors that can be created by programs like antechamber and mdgx (for general organic molecules) and pyMSMT (for metal ions). The LEaP code creates two files: an “inpcrd” file that has complete three-dimensional coordinates and a “prmtop” file that contains all other information needed for force field-based analyses of the system. The latter file can be examined and edited via parmed, which can also export similar files in the GROMACS or CHARMM format.
Figure 1 📷Figure 1. Common workflow in AmberTools. Flow went from top to bottom. Black boxes are for preparation, gray indicates an optional preparation step specific for membrane systems, blue for simulation, and red for analysis.
The simulation phase is primarily the province of sander or pmemd. The “mdin” file contains a large number of parameters that control the type and length of the simulation to be carried out, the integration method, the use of a QM/MM (quantum mechanics/molecular mechanics) model, specification of enhanced-sampling and thermodynamic integration methods, and the like. Restraints on the system, often from NMR or X-ray data but more recently from cryogenic electron microscopy (cryoEM) and other sorts of integrative modeling, can also be input at this point.
Snapshots of conformations are generally stored at regular intervals during a simulation and then serve as input for an analysis phase. The cpptraj program is the workhorse code here, providing geometric and energetic analyses, clustering algorithms, and many other routines. Three other codes, MMPBSA.py, FE_Toolkit, and FEW (Free Energy Workflow) (17) are devoted to estimating free energy changes. More complete descriptions of all of this, including a full list of programs, encompassing nearly 1000 pages of text, are in the Amber23 Reference Manual.
AmberTools23 Updates
We have a number of significant new features for AmberTools23 which include automated building of membrane-protein–lipid-bilayer systems, enhancements to the polarizable Gaussian multipole method, extensions to the Poisson-Boltzmann surface area (PBSA) method, enhanced free energy capabilities, enhanced QM and QM/MM capabilities, and a significant upgrade of the Amber Web site and tutorials. Each of these additions is summarized below.
1. Polarizable Gaussian Multipole Model in the SANDER Program
The polarizable Gaussian Multipole (pGM) model is a next-generation induced-dipole polarizable model aiming to balance accuracy and efficiency for molecular simulations of biomolecular systems. (18−22) We recently developed a new framework for efficient computation of analytical atomic gradient for the pGM model. (18) The pGM virial for constant pressure molecular dynamics simulations was also implemented in previous releases of Amber. (19) The accuracy and robustness of the pGM model have also been validated on various molecular properties. (20−22) In the AmberTools23 release, we further optimized the induced-dipole iteration algorithm. Specifically, we introduced maximum relative error as the convergence criterion to ensure energy conservation in molecular dynamics simulations. We also designed and implemented multiorder extrapolation (MOE) and local preconditioning conjugate gradient (LPCG) schemes to accelerate the induced-dipole iteration. (23) Given the new developments, MD simulations with the pGM model are able to achieve a similar level of energy conservation as those with the point charge additive models, within 2–3 induction iterations.
2. New Features in the PBSA Program
MM/PB(GB)SA (24) is an end-point method for calculating the free energies of molecules in implicit solvent, i.e., Poisson–Boltzmann (PB) and generalized Born (GB). Solvation interactions, especially solvent-mediated dielectric screening and Debye–Hückel screening, are essential determinants of the structure and function of biomolecules. Several efficient finite-difference numerical solvers, both linear (25−27) and nonlinear, (28) are implemented in pbsa for various applications of the Poisson–Boltzmann method. The GPU support of those solvers is also implemented in pbsa.cuda. (29−31) In the 2023 release, improvements to the pbsa program include the integration of the Machine-Learned Solvent Excluded Surface (MLSES) model, (32) which provides a highly efficient and differentiable molecular surface for continuum solvation modeling of biomolecules. Various options for the MLSES model have been implemented, allowing users to optimize performance on both central processing unit (CPU) and GPU platforms using Fortran, the CUDA kernel, and LibTorch. This flexibility enables users to choose the best-suited hardware and software environments for their needs. Additionally, an MBAR/PBSA strategy has been developed combining the PBSA continuum solvent model with the Multistate Bennet Acceptance Ratio (MBAR) approach. This coupling allows for more accurate modeling of electronic polarization, leading to improved accuracy in absolute binding free energy simulations of highly charged ligands. (33)
To date, the GB model in AmberTools could be specified with the following “igb” values: 1, (34) 2, (35) 5, (36) 7, and 8. (37) In 2017, an accurate yet efficient grid-based surface GB model was introduced (38) which is currently available in AmberTools as a stand-alone application named GBNSR6 ($AMBERHOME/bin/gbnsr6). (39) GBNSR6 calculates the solvation free energy of an input structure on a single snapshot. In AmberTools23, GBNSR6 has been integrated into MMPBSA.py (40) such that it runs over multiple snapshots extracted from the trajectories of protein, ligand, and complex structures. To run this model, “igb = 66” is now available in MMPBSA.py. All input parameters of the stand-alone GBNSR6 program can be modified through the MMPBSA.py input file.
3. PyRESP and PyRESP_GEN
Accurate modeling of electrostatic and polarization effects is crucial in molecular simulations. Many polarizable force fields have been developed to account for these important effects. Among these models, the polarizable Gaussian Multipole (pGM) model has emerged as a self-consistent approach in handling both short-range and long-range interactions. (18−23) We have recently developed the PyRESP program (41) for electrostatic parametrizations for point charge additive models and induced-dipole models, including the pGM model. By performing least-squares fittings to electrostatic potentials surrounding molecules, the PyRESP program extends functionalities of the ancestor RESP program that only perform parametrizations for point charge additive models. (42) However, the process of generating input files for PyRESP is tedious and error-prone. In the AmberTools23 release, we implemented a flexible and user-friendly program, PyRESP_GEN, (82) to minimize the user’s efforts to set up a PyRESP run. In addition, we also optimized the restraint weights for the pGM models with and without permanent dipoles. For the pGM-perm model, the optimal strategy for electrostatic potential fitting is also proposed.
4. 3D-RISM
The 3D reference interaction site model (3D-RISM) of molecular solvation (43) is an implicit solvent model that calculates equilibrium density distributions and thermodynamics of explicit solvent models. The implementation in AmberTools permits MD, energy minimization, and trajectory analysis through sander, while rism3d.snglpnt provides standalone trajectory analysis. (44) Recently, periodic boundaries were introduced, allowing application to crystal structure refinement and other periodic systems. (45) In addition, computational scaling for open boundaries was improved via treecode summation for electrostatic interactions, providing a 2–4 times speedup for typical proteins and enabling application to large biomolecular complexes with more than 1 million atoms. (46)
5. LibTorch Interface to Amber
We introduced a LibTorch interface to the 2023 release of AmberTools, which is a cutting-edge C++ runtime library developed by the PyTorch team. (47) This library enables flexible tensor computations and dynamic deep neural network modeling. Amber now provides two options for enabling the LibTorch library: a built-in mode and a user-installed mode. With the LibTorch integration, the pbsa program supports both CPU and GPU environments, making it highly versatile. Additionally, user instructions and tutorials have been provided for configuring the LibTorch library, making it more accessible to researchers and developers working in Amber and AmberTools.
6. Free Energy
Free energy methods have been a mainstay of Amber for decades. (48,49) Besides our existing free energy technology base this latest release of AmberTools includes a collection of new software tools for the robust analysis of free energy simulations (FE-ToolKit) (50,51) as well as workflow tools for production free energy simulation setup and analysis (ProFESSA) (52) using the GPU-accelerated Amber free energy engine with enhanced sampling features. This software is part of the Amber Drug Discovery Boost package. (53)
6.1. FE-ToolKit
The FE-ToolKit contains two main utilities: edgembar (51) for analysis of alchemical free energy simulations (e.g., such as those used for prediction of ligand-protein absolute and relative binding free energies in drug discovery (54)) and ndfes (50) for analysis of multidimensional free energy profiles (e.g., such as those used for prediction of minimum free energy pathways in studies of enzyme mechanisms (55,56)).
6.2. Edgembar
The edgembar program performs analysis of alchemical free energy simulations using the multistate Bennett acceptance ratio (MBAR) method, (57) the Bennett acceptance ratio (BAR) method, (58) exponential averaging, (59) thermodynamic integration, (60) or combinations of these approaches. Alchemical free energy simulations often calculate a network of relative free energy differences between two environments. For example, ligand binding applications in drug discovery use a network of alchemical transformations between ligands, termed a “thermodynamic graph”, where each ligand represents a “node” in the graph and each “edge” represents an alchemical transformation between ligands bound to their target relative to that in aqueous solution. Given the alchemical simulation outputs from the independent trials in both environments, edgembar will perform a “network-wide” free energy analysis, (51) including the imposition of cycle closure and, optionally, experimental constraints. The analysis produces a comprehensive report of the results, including uncertainties and warnings. The report identifies potential problems with simulations that may require further attention. The issues include: a lack of convergence, the analysis of too few statistically independent samples, poor phase space overlap between adjacent alchemical states, (61) and poor reweighting entropy. (62)
6.3. Ndfes
The ndfes program evaluates multidimensional free energy surfaces from umbrella sampling. (50) The analysis can be performed with the variational free energy profile (vFEP) method, (63,64) MBAR, (57) the weighted thermodynamic perturbation method (wTP), (65) and the generalized weighted thermodynamic perturbation method (gwTP). (66) The wTP and gwTP methods estimate the free energy surface of an expensive target-level of theory from the sampling performed with inexpensive reference potentials. (66) The estimation of ab initio QM/MM free energy surfaces in condensed-phase environments has become more practical in the latest version of AmberTools with the combined introduction of the GPU-accelerated QUICK software (67) and ndfes analysis program.
6.4. ProFESSA
The ProFESSA workflow (52) uses the GPU-accelerated AMBER free energy engine. The workflow establishes a flexible, end-to-end pipeline for performing alchemical free energy simulations that brings to bear technologies including new smoothstep softcore potentials and optimized alchemical transformation pathways, (68) the alchemical enhanced sampling (ACES) method, (69) and a network-wide free energy analysis (51) with optional imposition of cycle closure and experimental constraints implemented in FE-ToolKit.
7. Quantum Mechanical/Molecular Mechanical Methods
Amber has had a long tradition of QM/MM methods and implementations, (70) with the most recent additions being the QUICK/sander QM/MM implementation in AmberTools23. (67,71−73) QUICK/sander has been extensively updated, and its performance has been significantly improved. QUICK, as distributed with AmberTools23, can also be used as a standalone QM program for single point calculations or geometry optimizations.
7.1. Performance Improvements/AMD Implementation
With the second-generation electron repulsion integral code and other performance enhancements recently introduced into QUICK, (67,71−73) higher ps/day can be obtained in QM/MM simulations. (73) For instance, with respect to AmberTools21, (74) up to 2× speedups have been observed for benchmark simulations with different QM regions of photoactive yellow protein on NVIDIA V100 GPU. (73) Furthermore, support for AMD GPUs has been enabled. Users can now make use of AMD data center cards such as MI50, MI100, MI200, and MI250 for simulations. According to benchmark studies, the performance on the MI100 is similar to that of NVIDIA V100. (73) The implementation runs properly on MI200 and MI250 cards; however, the performance is not yet optimized for these cards. The recommended AMD GPU for the current version is MI100. An optimized version for MI2XX will be available to users in the next AmberTools release.
7.2. Long-Range Electrostatics
For the treatment of long-range electrostatics in QM/MM, the ambient-potential composite Ewald method (CEw) developed by Giese and York (75) has been integrated. The performance penalty for turning on CEw in the GPU version is <25% for Hartree–Fock (HF) and <10% for density functional theory (DFT) in comparison to standard QM/MM with 8 Å electrostatic cutoff. This allows users to carry out more accurate simulations at a slightly higher computational cost.
7.3. Dispersion
Among other minor features introduced into QUICK, dispersion corrections in DFT and data exporting capability into Molden format are notable. Grimme’s dispersion corrections (D2, D3 with different damping) (76) can be used in QM/MM with appropriate functionals. Users can also export Cartesian coordinates, molecular orbitals, etc. of the QM region into Molden format for visualization purposes.
8. Automated Building of Membrane-Protein–Lipid-Bilayer Systems
PACKMOL-Memgen is a simple-to-use command line implementation of a generalized workflow for the automated building of membrane-protein–lipid-bilayer systems based on open-source tools including Packmol, memembed, pdbremix, and AmberTools. (77) It allows for setting up multiple configurations of a system in a user-friendly and efficient manner, which can serve as starting configurations in MD simulations under periodic boundary conditions. Since its introduction, support was added for additional lipid headgroups and to include solutes in the water or membrane phase and generate curved membrane surfaces or double bilayer systems. Additionally, SIRAH (78) coarse-graining routines can be used, and non-membrane systems (water or mixed-solvent simulations) can now be set up. (79) In the AmberTools23 release, PACKMOL-Memgen now handles all Amber-supported ions and the OPC3 water model as well as allows generating HMR systems, providing control for pmemd.cuda, and using pdb2pqr for protonating the protein.
9. mdgx
The mdgx program, which began as a de novo reimplementation of the basic features needed for molecular dynamics and stayed in service for its uncommon capability of storing multiple topologies and coordinate sets in the space of a single runtime instance, has gained two noteworthy features. First, it can postprocess Amber topology files to add pmemd-compatible representations of the GROMACS virtual sites. (80) While mdgx itself can perform limited MD simulations with such models, the performant pmemd GPU implementation can now incorporate massless sites into its free energy methods. Virtual sites require parameters to be useful, but the mdgx program itself has tools for fitting their charges as well as bonded parameters in the context of these extra monopoles. Virtual site force fields are a logical extension of popular fixed-charge models, entailing incremental updates to the dynamics engine and incremental increases in the cost of the simulations. Second, through its ability to calculate multiple systems at once, mdgx has an exploratory feature for running simple implicit solvent dynamics on many replicas of different topologies on one GPU. By running independent trajectories on each GPU multiprocessor, mdgx scales simulations of small peptides and drug molecules to modern GPUs with tens of times the throughput of other GPU MD implementations when tasked with small systems. This capability has been applied to docked pose refinement. (81)
10. The Amber Web Site and Tutorials
The Amber Web site (https://ambermd.org) supports the user community with new release information, manuals, tutorials, and information on force fields. Users are directed to the most recent manual version to learn about technical usage and appropriate literature references to communicate best practices in the field. The Amber tutorials have also been reorganized and span topics ranging from initial system setup to advanced methods (Figure 2). A tutorial overview page guides new users through the process of building, running, and analyzing a system and points them to key initial case studies. The recent tutorials overall are more modular, and learning objectives are given. New tutorial development has focused on building different system types and tutorials for creating stable systems through relaxation of system positions for both explicit and implicit solvent as well as a tutorial covering advanced thermodynamic integration methods such as using smoothstep softcore potentials, (68) enhanced sampling for softcore ligand energies, and methods such as ACES. (69)
Figure 2 📷Figure 2. Overview of the Amber Tutorials. Tutorials are modular, cover the basic steps of a typical molecular dynamics simulation, introductory case studies, advanced methods, and some tools that are commonly employed by Amber users.
Modeling software is not useful without compatible force fields. Included in the release of AmberTools are the force fields developed by the Amber community. The main force fields page contains a list of recommended force fields, and each type of molecule/ion has a separate page outlining nuances in choosing an appropriate force field.
Conclusions
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The most significant additions to AmberTools23 are briefly summarized. AmberTools is freely available at https://ambermd.org. Full details on licensing, distribution, and hardware supported can be found at https://ambermd.org.
Data Availability
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The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL). Please see https://ambermd.org for licensing and distribution.
Author Information
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  • Corresponding Authors Maria C. Nagan - Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States;  📷https://orcid.org/0000-0003-2678-6825;  Email: [email protected] Kenneth M. Merz - Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States;  📷https://orcid.org/0000-0001-9139-5893;  Email: [email protected]
  • Authors David A. Case - Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States;  📷https://orcid.org/0000-0003-2314-2346 Hasan Metin Aktulga - Department of Computer Science and Engineering, Michigan State University, East Lansing 48824-1322, Michigan, United States Kellon Belfon - FOG Pharmaceuticals Inc., Cambridge 02140, Massachusetts, United States David S. Cerutti - Psivant, 451 D Street, Suite 205, Boston 02210, Massachusetts, United States G. Andrés Cisneros - Department of Physics, Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson 75801, Texas, United States;  📷https://orcid.org/0000-0001-6629-3430 Vinícius Wilian D. Cruzeiro - Department of Chemistry and The PULSE Institute, Stanford University, Stanford 94305, California, United States;  📷https://orcid.org/0000-0002-4739-5447 Negin Forouzesh - Department of Computer Science, California State University, Los Angeles 90032, California, United States Timothy J. Giese - Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States;  📷https://orcid.org/0000-0002-0653-9168 Andreas W. Götz - San Diego Supercomputer Center, University of California San Diego, La Jolla 92093-0505, California, United States;  📷https://orcid.org/0000-0002-8048-6906 Holger Gohlke - Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany;  Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany;  📷https://orcid.org/0000-0001-8613-1447 Saeed Izadi - Pharmaceutical Development, Genentech, Inc., South San Francisco 94080, California, United States Koushik Kasavajhala - Laufer Center for Physical and Quantitative Biology, Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States Mehmet C. Kaymak - Department of Computer Science and Engineering, Michigan State University, East Lansing 48824-1322, Michigan, United States Edward King - Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States Tom Kurtzman - Ph.D. Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York 10016, New York, United States;  Department of Chemistry, Lehman College, 250 Bedford Park Blvd West, Bronx 10468, New York, United States Tai-Sung Lee - Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States;  📷https://orcid.org/0000-0003-2110-2279 Pengfei Li - Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago 60660, Illinois, United States;  📷https://orcid.org/0000-0002-2572-5935 Jian Liu - Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;  📷https://orcid.org/0000-0002-2906-5858 Tyler Luchko - Department of Physics and Astronomy, California State University, Northridge, Northridge 91330, California, United States;  📷https://orcid.org/0000-0001-6737-6019 Ray Luo - Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States Madushanka Manathunga - Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States;  📷https://orcid.org/0000-0002-3594-8112 Matias R. Machado - Institut Pasteur de Montevideo, Montevideo 11400, Uruguay;  📷https://orcid.org/0000-0002-9971-4710 Hai Minh Nguyen - Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States;  📷https://orcid.org/0000-0002-0814-1364 Kurt A. O’Hearn - Department of Computer Science and Engineering, Michigan State University, East Lansing 48824-1322, Michigan, United States Alexey V. Onufriev - Departments of Computer Science and Physics, Virginia Tech, Blacksburg 24061, Virginia, United States;  📷https://orcid.org/0000-0002-4930-6612 Feng Pan - Department of Statistics, Florida State University, Tallahassee 32304, Florida, United States Sergio Pantano - Institut Pasteur de Montevideo, Montevideo 11400, Uruguay;  📷https://orcid.org/0000-0001-6435-4543 Ruxi Qi - Cryo-EM Center, Southern University of Science and Technology, Shenzhen 518055, China Ali Rahnamoun - Department of Computer Science and Engineering, Michigan State University, East Lansing 48824-1322, Michigan, United States Ali Risheh - Department of Computer Science, California State University, Los Angeles 90032, California, United States Stephan Schott-Verdugo - Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany Akhil Shajan - Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States Jason Swails - Entos, 4470 W Sunset Blvd, Suite 107, Los Angeles 90027, California, United States Junmei Wang - Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh 15261, Pennsylvania, United States;  📷https://orcid.org/0000-0002-9607-8229 Haixin Wei - Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States;  📷https://orcid.org/0000-0002-0954-4560 Xiongwu Wu - Laboratory of Computational Biology, NHLBI, NIH, Bethesda 20892, Maryland, United States Yongxian Wu - Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States;  📷https://orcid.org/0000-0003-1497-2444 Shi Zhang - Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States Shiji Zhao - Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States;  Nurix Therapeutics, Inc., San Francisco 94158, California, United States;  📷https://orcid.org/0000-0002-4514-0897 Qiang Zhu - Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States;  📷https://orcid.org/0000-0002-5612-0728 Thomas E. Cheatham - Department of Medicinal Chemistry, The University of Utah, 30 South 2000 East, Salt Lake City 84112, Utah, United States;  📷https://orcid.org/0000-0003-0298-3904 Daniel R. Roe - Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda 20892, Maryland, United States Adrian Roitberg - Department of Chemistry, The University of Florida, 440 Leigh Hall, Gainesville 32611-7200, Florida, United States;  📷https://orcid.org/0000-0003-3963-8784 Carlos Simmerling - Laufer Center for Physical and Quantitative Biology, Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States;  📷https://orcid.org/0000-0002-7252-4730 Darrin M. York - Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States;  📷https://orcid.org/0000-0002-9193-7055
  • NotesThe authors declare no competing financial interest.
Acknowledgments
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The authors are grateful for the financial support provided by the National Institutes of Health (Nos. GM62248 and GM107485 to DMY; GM130367 to RL; GM130641 to KMM and HMA; NIH U2COD026506 to KMM; GM108583 to GAC; GM149874 to TSL; GM144596 to AO; GM107104 and GM135136 to CS; NHLBI Z01 HL001051-23 to DRR; GM147673 to JW; No. GM146633 to NF; and R35GM144089 to TK), the National Science Foundation (2209718 to DMY; 2209717 to KMM, HMA, and AWG; NSF OAC1835144 to KMM and AWG; OAC-2117247 to GAC; CHE-2050541 to MCN; CHE-2018427 to MCN and TL; CHE-2102668 to TL; CTMC-1665159 to CS; CHE-1955260 to JW; CHE-2216858 to NF), Loyola University Chicago (start-up funds to PL), the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) (Project CRC 1208 (No. 267205415) to HG (subproject A03)), FOCEM (MERCOSUR Structural Convergence Fund) COF 03/11 to SP, National Natural Science Foundation of China (NSFC-22225304 to JL), and Intel oneAPI Center of Excellence program to AWG. We also thank NVIDIA, AMD, and Intel for technical guidance and support.
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  1. 1Weiner, P. K.; Kollman, P. A. AMBER: Assisted model building with energy refinement. A g
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I carried out a polymer synthesis reaction using a polymer graft using the dispersion polymer method. However, my polymer results into a gel when the initiator is applied. What can I change in this case?
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By the way, it is not fully clear whether it is a copolymerization or grafting. This later is achieved by attaching a chemical/motif to an already formed polymer, is it your situation ?