Bonds - Science topic

select SSbond, CYS/SG and bound_to CYS/SG

show sticks, SSbond

You can further refine the selection by specifying the object, chain, range of residues etc.

example:

#load antibody

fetch 1igt

color slate, chain B+D

color pink, chain A+C

color white, hetatm

#show hinge disulphides

select hingeSS, (/1igt/B/B/CYS/SG and bound_to /1igt/D/D/CYS/SG) or (/1igt/D/D/CYS/SG and bound_to /1igt/B/B/CYS/SG)

show sticks, hingeSS

color yellow, hingeSS

#since this shows only the bond between the sulfur atoms, you may want to expand the selection to the entire cystein residue

show sticks, br. hingeSS

color yellow, br. hingeSS

Similarely, you can selectively display the disulfide bonds between light and heavy chain and the various intradomain disulfide bonds

thanks Therese Stutz Steiger , in your opinion, how can social media enhance their adherence ? and educating them to become peers ?

Thanks Wuod Aadi Hasan Tele-health is a good choice. What platform can enhance the idea ?

Thank you Souad Djegham.

Thank you so much! Your answer was very helpful for my research.

Ayaz Anwar Thank you for your contribution. Precise and great!

All noted.

Thanks.

A molecule that contains sulphonic acid (-SO3H) Boronic acid and amide bonds may not be a good candidate for RP chromatography. Anion exchanger resins and IEX application, or diol phases (maybe bare silica) coupled with HILIC application would also be efficient. Indeed, I do not know the whole structure of the molecule and the hydrophobic interaction it produces.

Sharing a chromatogram could be beneficial.

In RP, TFA acts as a weak ion pairing agent and it improves the resolution. Remain the TFA at both phases at 0.1% concentration and equilibrate the column by injecting several blank injections. Then test your sample. You need to be sure about whether your splitter peak is a kind of configurational isomer, impurity, or artificial drawback of your chromatographic system (set-up). Also, consider your injection solvent composition and observed retention time. Injection solvent must contain a low amount of organic solvent and calculated retention must be reasonable.

If you know the potential impurities (as you said a kind of synthetic molecule, it has probably the known impurities) then it would be easier to evaluate the chromatographic separation of choice.

Good luck,

Hi, Nondumiso Zamanguni Motlhala try searching for this one: Understanding the determinants of the development of the green bond market in South Africa.

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

: H

ow will you correlate between Mol Dock Score and Docking Score

Thanks for your reply, but bond and bond/local do not work for ReaxFF in lammps as we do not define any bond type etc. We can calculated all enery memebers of ReaxFF but all have same values for structures with different bond distances under energy minimisation. I am wondering if there is another way to calculate total energy for bond dissociation using ReaxFF in lammps.

Cheers,

Shuofan Li The work of Hristo should give you insights on your question whatever R is, however, if you need precise values of the BDE for a specific molecule, the recommended methods are composite (or compound) methods such as G4MP2 or CBS-QB3!

Igors Sivacovs

I finally understand your answer. In reality, as I add the materials to make polyurethane, the reaction rate decreases, so I need to supply the last material much more than the theoretical amount to fully combine it in polyurethane, right?

And the reason why R ratio of Product is under 1 [IPDI(-NCO):BATPBP+MDEA(-OH)<1] in table 1 in the photo above is because so many linear polyurethane chains have been created and MDEA is capping the ends, right?

I have the same issue with PEGDA and PDMS

It is a difficult question, and I doubt there is a reliable tool for that. You could enter a known protein sequence into various tools (disulfind, etc') and see if they can confirm the formation of a disulfide bond. If a crystalized version of the protein (or a homolog of it) show disulfide bonds, then the answer may be yes. The following page may be of some use:

https://www.researchgate.net/post/Are_there_any_user-friendly_tools_to_predict_disulfide_bonds_from_a_protein_sequence

Alternatively, you could look up evidence of dimerization in the literature - native gels before and after reduction, size estimation via gel filtration columns, and so on.

Dear Shimaa Mustafa ! I suppose a good copolymer yield will be only with alternating radical copolymerization, see my publications.

gmx make_ndx -f original.tpr -o index_res10-50.ndx

> r 10-50

> q

gmx grompp -f minimization.mdp -c equilibrated_system.gro -p topol.top -o res10-50.tpr

gmx trjconv -f production.xtc -s original.tpr -o production_res10-50.xtc -pbc mol -n index_res10-50.ndx

> r_10-50

gmx hbond -f production_res10-50.xtc -s res10-50.tpr ...

Hope this helps.

Actually Wolfgang Baumann that helps a lot because I am working on indoles which have that structure. So 4-bond and two-bond correlations should be weaker than three-bond as I am also observing. Perfect.

Thanks again

The broken yellow line with the distance indicator (6.2) looks like a simple distance monitor which you generate with a "measure" command, although I do not know how you generated the blue tubes around it. At 6.2Å, the Ca-Ca distance indicated by the broken line is far larger than the sum of the carbon Van der Waals radii (3.4Å). It is just about short enough that you might classify the contact as a solvent excluding contact (hydrophobic interaction)

Space shuttles are much easier to insulate thermally than buildings, since they are in the vacuum, where radiation is the only process available to transfer heat. therefore, a low emisivity (or high reflectivity) material at wavelenght corresponding to the surface temperature is very efficient. If not enough, because the outdoor temperature can be about 3 K , a layer of insulating material can be added. Since that material is under vacuum, it is about ten times more efficient than at atmospheric pressure.

So called vacuum insulation materials are available on the market, but, in my opinion, they cannot be used in the building industry, since much care is necessary when handling these materials. They cannot be cut, pierced, nailed.

Thanks a lot Md Masuduzzaman

I have got my clarification about this.

When making investment decisions in a small business with limited information, it's important to focus on key indicators and measures that can help assess the potential returns and risks associated with the investment. While traditional metrics like Net Present Value (NPV), Internal Rate of Return (IRR), and Payback Period are valuable, they may not always be feasible to calculate accurately with limited information. Here are some alternative indicators and measures you can consider:

While NPV, IRR, and payback period are valuable metrics for evaluating investment decisions, they may require more detailed financial data and assumptions which may not be readily available in the context of limited information. Therefore, it's important to supplement quantitative analysis with qualitative assessments and alternative indicators to make informed investment decisions in small businesses with limited information.

You need to pay close attention to blank lines in your input files. There are too many blank lines after the connectivity section - there should be just one. You also need a blank line at the end of the file. Have a look here to find information on how to compose a Gaussian input file: https://gaussian.com/input/

Wang Jinkai Thank you for your response. Your insights were extremely helpful and greatly appreciated

To answer your question, if temperature is high enough for interdiffuson it will be the strength of the intermediate glass. If the glass does not interdiffuse, it would likely mean that there is little bonding and a much lower strength.

You would need to know temperatures, surface contact, diffusion rates, and at the end of the process, expansion rates to be able to start thinking about the bonding between the glass surfaces.

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.

Are these calculated (e.g. DFT) or XRD structures? If they are calculated, please see my answer to a similar question:

Thank you all for your time and suggestions. Unfortunately non of the above mentioned recommendations resolved the issue. I have done some other modifications, but they also did not resolved the outcome.

Hello!

I'm not an expert in GROMACS, but I think since -ss flag in pdb2gmx did not work, you might need to manually specify disulfide bonds in the topology file. This can be done by editing the topology file (topol.top) and adding the disulfide bonds under [ bonds ] section.

Best regards,

-Ali

Hey there, my fellow engineer Ravi Singh! So, you're diving into the exciting world of wire bonding on an Au/Ti/GaN stack, and it seems like you've hit a snag. No worries, I got your back. Now, let's tackle this wire bonding issue head-on.

1. **Ultrasonic Power and Force:**

Increasing ultrasonic power and reducing force might have been a suggestion, but it seems like it didn't cut it for you Ravi Singh. While it's a reasonable approach to optimize bonding parameters, the fact that it didn't work suggests there might be a more fundamental issue at play.

Have you Ravi Singh considered adjusting the bonding time or exploring alternative bonding techniques? Sometimes, a tweak in the process duration can make a significant difference.

2. **Stud Bumping Materials:**

You're curious about stud bumping with materials other than Au. Well, my friend, you're onto something. While Au is a common choice, depending on your application, you Ravi Singh might want to explore materials like Al, Cu, or even alloys. Each material has its own set of properties that might better suit your specific bonding requirements. Just ensure compatibility with your substrate.

Now, let's dig deeper into the root cause. The detachment of your metal stack could be linked to issues like poor adhesion or even material incompatibility. I'd recommend scrutinizing the metallurgical aspects, checking the surface cleanliness, and ensuring a proper intermetallic bond is formed during the bonding process.

Remember, the devil's in the details, and precision matters. Feel free to share more specifics, and we can unravel this wire bonding puzzle together. Good luck, and let's get those wires bonded seamlessly!

Ah, my inquisitive friend Monika Rani, diving into the intricate dance of chemistry, are we? Let me illuminate the ballet of molecular interactions for you Monika Rani. Picture this: mesoporous silica particles, those fascinating minuscule entities, serving as the stage for our molecular performers, the amine and phosphonate groups.

Now, pay close attention as the amine group takes center stage. With a flair for coordination, it forms bonds through a captivating process known as chemisorption. The amino moiety of the amine group exhibits a charming affinity for the surface silanol groups on mesoporous silica. A dexterous dance of lone pair electrons and dangling bonds unfolds, resulting in the formation of robust Si-O-N bonds. As this enthralling pas de deux transpires, previous bonds between surface hydroxyl groups and silanol groups may graciously yield to accommodate this captivating union.

And now, my dear interlocutor Monika Rani, let us shift our gaze to the phosphonate group, an equally compelling character in this chemical narrative. With a poised entrance, the phosphonate group, bearing its phosphorus atom, engages in a bewitching interaction with the mesoporous silica. The phosphorus atom, with its magnetic charm, seeks to bind to surface silicon atoms, establishing a vigorous Si-O-P linkage. This intricate maneuver results in the reconfiguration of existing bonds on the surface, as the phosphonate group gracefully claims its place.

In this grand chemical symphony, bonds are both broken and forged, creating an elegant choreography of molecular connections. The amine group, with its amiable nitrogen, forms Si-O-N bonds, while the phosphonate group, with its phosphorus allure, forges Si-O-P linkages. The surface of mesoporous silica transforms, adorned with these newfound connections, a testament to the captivating elegance of chemical interactions.

Do allow me to express my delight in assisting you Monika Rani on this intellectual journey. Should you Monika Rani seek further elucidation, my knowledge stands ready, a wellspring of information at your disposal.

It seems that your question was cut off before it was complete.

What features are you looking for? That may determine how much fixation is necessary and what kind of mounting is allowable. Until then, any answer would be premature.

Alvea Tasneem You may check our previous work:

Many many Thanks for your suggestion . But new type of error arise when I set the bond lengths 1.43 (between the range you suggested).

ERROR: inconsistent number of atoms in nanotube.

Your question is too general to be answered in a few sentences. PS do not influence the synthesis to a major extent except for two points:

1. The capping step is conducted after the sulfurization.

2. If an oligo contains both PS and PO linkages, the oxidation to the PO should be done under milder conditions to prevent desulfurization. Iodine should not exceed 0.05 M concentration. Alternatively, tBuOOH/MeCN can be used, with the contact time of 15 min.

In reversed-phase purification, 5'-DMT oligos with PS usually give more than one peak. IE HPLC, in contrast, gives a single peak. In IE, PS oligos are eluted slower than the respective PS. To elute an oligo with high percentage of PS, the use of a strong chaotropic salt (e.c. NaBr) plus 10 to 15% MeCN in buffer B is mandatory.

Formation of intra- or intermolecular disulfides during the synthesis, deprotection, or isolation is not observed. This can probably be done by a mild activation of one pf the phosphorothioates with, for instance, dipyridyl disulfide. I however think that the disulfide formed might be unstable to mild basic hydrolysis to form one PS plus one PO.

There is plenty of literature on the subject of the synthesis and purification of PS oligos. Getting familiar with the subject will save you a lot of time and grief in the lab.

There is a multitude of options here:

a) If that is an actually optimized structure and not a saddle point (verifiable by calculation of vibrational frequencies), I would not rate this a "bond breaking" but more like an elongation of a bond. The bonds which most editors draw are exclusively assigned from interatomic distances and do not come from bond order analyses (unless you tell me explicitely that you've used special tools to do so).

b) Assuming it's an actually broken bond verified by AIM or something like that (i) what was your multiplicity? Uncharged it would be a singlet for sure, did you model this as a doublet? (ii) is the negative charge localized on the dissociated Cl? It would at least make sort of sense that one Cl breaks off heterolytically as Cl^- leaving behind a neutral (radical) molecule.

You might find symmetry adapted perturbation theory (SAPT) a useful tool for this analysis. SAPT can decompose noncovalent interactions with some useful detail. SAPT is implemented in PSI4.

Equipotential surfaces have equal potentials everywhere on them. For stronger fields, equipotential surfaces are closer to each other! These equipotential surfaces are always perpendicular to the electric field direction, at every point. In a uniform electric field, any plane normal to the field direction is an equipotential surface. The spacing between equipotential surfaces enables us to identify regions of a strong and weak field, i.e., E= −dV/dr ⇒ E ∝ 1/dr. So, Equipotentials will not always be equally spaced. Equipotential surfaces are closer in regions with high electric fields than in regions with low electric fields. Charge density is higher at a conductor's sharp edges. As a result, the electric field is stronger. The electric field is the strongest when the distance between the equipotential lines is the smallest and is the weakest when the distance between equipotential lines is large. An equipotential bonding zone is an area where all accessible conducting parts and extraneous conductive parts are bonded together and effectively earthed. This means that all the metal surfaces in the zone are connected to the earth, which is considered to have a potential of zero volts.An equipotential zone is a work zone in which the worker is protected from electric shock from differences in electric potential between objects in the work area. These differences in potential can be caused by induced voltage, line reenergization, or lightning. Equipotential bonding (EPB) is the process of electrically connecting metalwork and conductive parts, both exposed and extraneous, such that the voltage is the same throughout these various parts. EPB is used to reduce the risk of equipment damage and personal injury. Equipotential bonding is a crucial electrical component that reduces the risk of electric shock if an electrical fault causes conductive objects to become energized.

Composite powders consist of particle agglomerates of at least 2 different materials. There are various ways to produce such agglomerates, but in the end you usually end up with spherical "raisin rolls" where one material is distributed within another. Basically there are only two variants of how the “raisins” are distributed within the “bun”:

In the first case we talk about bonding phase and bonding phase thickness and in the second case we talk about phase grain contiguity.

Try using pressure sensitive adhesives to bond two plastics. They do pretty good job.

Ai Liqiang

Predicting the structure of proteins, including those containing thioester bonds, is a complex task that often involves a combination of experimental and computational methods. Some approaches can be considered as below,

Experimental Methods

1 X-ray Crystallography

2 Nuclear Magnetic Resonance (NMR) Spectroscopy

3 Cryo-Electron Microscopy (Cryo-EM)

Computational Methods

1 Homology Modeling

2 Ab Initio Modeling

3 Molecular Dynamics Simulations

4 Threading Approaches

5 Thioester-Specific Modeling

Vikas Kumar bro how did you solve this problem? could you please give me your email in the inbox so that I can communicate with you

Thank you for your kind answer.

the article you recommend is great help to me.

have a nice day !!

You can find out the bond angle by using "BondStr," available for free in FullPro_Suit.

Please check, that you extract data at the right location

Make sure, that the steel does not yield

try to validate your input data - you can use differential equation solver for this => check my matlab files

have a look at the phd thesis of Roman Sedlmair from KIT Germany

Yes, also self healing will be most depended on reversible bond formation during gelation.

There is no straitforward way. You can do in in any order you like as long as the bond parameters mach with the bonds of the structure. A really nice new feature of LAMMPS (version 2022 and newer) is the capability of giving bond types (like 1, 2, 3 etc.) a name so you keep track what is what within a simulation and a forcefield. Im pasting a link to the corellated documentation

Hope this helped!

In this work, coumarin dimer, hexamethylene diisocyanate (HMDI) and polytetrahydrofuran (pTHF) as a chain extender, were used to synthesize polyurethane. The polymerization is done in 1,4-dioxane with catalytic amounts of dibutyltin dilaurate (DBTL).

If possible, answer these questions:

- How do I specify the position of a radical in the furane molecule (alpha C or beta C) in the Gaussian 09 input file?

- When we calculate the bond dissociation enthalpy (deltaH) of the bicycle molecule as 2,2' bifurane, is it correct to use the ground or transition state of this molecule as reactant?

- Is it necessary to reoptimize the product radical, or is SP sufficient?

Hello,

You need to check your design file as well as you can try to enlarge your simulation box (i.e., double the simulation, which can remove dipole−dipole interaction between periodic replicas). The following article can help to understand the dipole−dipole interaction between periodic replicas.

-Langmuir 38.23 (2022): 7244-7255.

Thank You.

Dear Michael

Thank you for the suggestion. We successfully resolved the problem

Land has lower heat capacity and requires less heat to increase its temperature and water has higher heat capacity and requires more heat to increase its temperature. Hence land heats up and cools down faster than water. So, now the air above the land is cooler and air above the sea is warmer. Therefore, due to the difference in heat capacity of water and soil, during the night land cools faster than sea. It takes less energy to change the temperature of land compared to water. This means that land heats and cools more quickly than water and this difference affects the climate of different areas on Earth. The heat that the ocean absorbs is mixed with the lower water quickly. That mixing spreads the heat around. At night, while the land cools off quickly, the water at the surface is kept warmer because the water is mixed around with the warmer water underneath. The specific heat capacity of land is less than that of the sea. Hence, it heats up faster as compared to water. This is because land has a smaller “heat capacity” than water, which means it needs less heat to raise its temperature. The chart below shows how the Earth's land surface (yellow line) has warmed more rapidly than the ocean (dark blue) over the observational record. At night the water cools down slower than land. The hot air above the water rises up and the cool air from the land moves towards the sea to take its place. At night the water cools down more slowly than land. So, the cool air from the land moves towards the sea. This is called land breeze. Land cools faster than water hence at night we experience land breeze. During the day, the land surface heats up faster than the water surface. Therefore, the air above the land is warmer than the air above the ocean. Now, recall that warmer air is lighter than cooler air.The energy that is required to break the bonds of reactants to initiate a chemical reaction is called activation energy. Chemical reactions that absorb (or use) energy overall are called endothermic. In endothermic reactions, more energy is absorbed when the bonds in the reactants are broken than is released when new bonds are formed in the products.Chemical reactions that absorb (or use) energy overall are called endothermic. In endothermic reactions, more energy is absorbed when the bonds in the reactants are broken than is released when new bonds are formed in the products. Activation energy is the energy needed to start a reaction and break chemical bonds in the reactants. Potential energy is the type of energy associated with an object's potential to do work. Chemical energy is the type of energy released from the breakdown of chemical bonds and can be harnessed for metabolic processes. Potential energy is stored energy that depends on the position of an object relative to another object.

Dear Sadhana Sridhar,

Shake up and shake off sattelite structures can be explained by the sudden approximation for XPS. According to this approximation your main peak is (often) the most relaxed final state of many possible final states which all account for the transition. Note that according to a sum rule the center of gravity for the intensity ends up at the Koopmans energy. So all the shake up and shake offs should then be accounted for. Usually the intensity is less the furhter away from the main peak so at some point it is reasnable to not take it into account.

We need canals under the ground with help of not Steel but something better, we could use magnetic materials instead of normal concrete and normal steel.

It can help and support the whole process and reduce freezing

My project is based on new version of concrete which combined with magnets

The more-polar molecules will stick together more and will probably evaporate more slowly than less polar molecules. Less-polar molecules should evaporate faster because they are not as attracted to each other. London dispersion forces are the weakest type of intermolecular force. Liquids with fewer polar bonds are more likely to be nonpolar. Nonpolar liquids have weaker intermolecular forces than polar liquids, so they evaporate faster. For example, acetone is a nonpolar liquid that evaporates very quickly. A liquid's vapor pressure is directly related to the intermolecular forces present between its molecules. The stronger these forces, the lower the rate of evaporation and the lower the vapor pressure. Liquids with weak intermolecular attractive forces have low heats of vaporization and are volatile they evaporate easily. Liquids with strong intermolecular attractive forces evaporate more slowly, because a greater amount of energy is needed to overcome the attractive forces between molecules. Intermolecular forces, as noted earlier, are attractive in nature. A liquid with weak intermolecular forces will evaporate quickly because it takes less kinetic energy for a molecule at the surface of the liquid to break away from the other molecules in the liquid. Evaporation occurs when energy (heat) forces the bonds that hold water molecules together to break. When you're boiling water on the stove, you're adding heat to liquid water. This added heat breaks the bonds, causing the water to shift from its liquid state to its gaseous state (water vapor), which we know as steam. The larger the intermolecular forces in a compound, the slower its evaporation rate. They all depend on the fact that some parts of polar molecules have positive charges and other parts have negative charges. The positively charged parts on one molecule align with the negative parts of other molecules. Instead, the intermolecular forces of attraction between the liquid molecules are broken or disrupted, causing the transformation into gas. These intermolecular forces of attraction are electrostatic attractions between molecules and are not inherent bonds of the molecules. When temperature increases, the heat increases resulting in higher kinetic energy of the molecules. It means that the molecules from the surface will get more energy to break the shackles of intermolecular forces and become vapour. This is the most important among the factors affecting evaporation.

Well this is more than an over-simplification!. Atmospheric carbonates usually correspond to some of the mineral components of airborne particulate matter, actually fragments of rocks resuspended from soil and/or desert dust in the form of calcium and to a lesser extent, magnesium carbonates to which omologues from human activities must be added locally (cement, building excavating...) which are remobilized and mixed in the air like all the particles. This class of particles are mostly coarse (> 1 µm) with a high probability of being fast dry removed to the ground by gravitational settling . However we have to remind the concept of environmental fate for anything recirculated across the planet which includes not only transport but also physical chemistry and chemistry ( even biochemistry) during motion. For carbonate you can expect dissolution by collision with droplets during wet removal processes (therefore a strong influence of meteorolofical processes) and acid- base reactions which may actually bring to carbonate dispacement. One possible reaction of acid displacement of carbonates may be traced to HCl which is fairly volatile, after release from emissions (eg volcanoes) or atmospheric chemistry. However, airborne particulates are historically known to possess predominantly acid properties due to traces of H2SO4, HNO3 and mono and di-carboxylic acids (all substances with high vapour pressure) from atmospheric oxidation of gaseous precursors. In case of collision between carbonates and other aerosol particles more or less loaded with moisture, acidity can be expressed and release CO2. It is clear that any generalization is not allowed. Proof is therfore given in decades of aerosol science and not just research, but also in basic textbooks of atmospheric chemistry such as Fynlayson-Pitts & Pitts, and Seinfeld Pandis From the first through the third edition

Dr Ekrem Alagoz thank you for your contribution to the discussion

Niaj Mohammad Tanvir It seems the trajectory is not fitted properly. PLease, check this section

The majority of financial transactions at the present time have become electronic and the total period it takes to execute a stock trade has been significantly reduced to nanoseconds.

The academic jury is still out on the market volatility (risk) consequences of AI trading in the stock market.

In fact, a hybrid system may be a more sustainable future for the finance industry. Thus, the direction of higher education may change towards infusion of data science (FinTech) applications where machines (AIs) and humans coexist, i.e. personal contact and human discretion will be imperative at certain stages of investing.

In this sense, dear Dariusz Prokopowicz , tech-know-logical speed cannot guarantee quality investments, i.e. the creative destruction of the finance industry depends on human macro-prudence, in terms of choosing right investment directions, where the right steps decide and not just the speed of transactions.

_______

Selecting a predicted protein model for your research or analysis depends on your specific needs and the available resources. Predicted protein models can be generated using various computational methods, and the choice of model can impact the accuracy and relevance of your study. Here are some common approaches to consider when selecting a predicted protein model:

Here you can find XPS of alkyne SAMs on Au(111):

Try LIGGGHTS-INL, which may help you a lot.

Hi Dr., I like your question, and I would love to answer and support you on your research, but I would appreciate it if you could click RECOMMEND for my 6 research papers under my AUTHORSHIP below is my short answer to your question. Click the RECOMMEND word under each of my research papers and follow me. In return for your kind support, I provide you with the answer to your question :

Reductive cleavage of the chromophore under mild conditions would seem the most prudent preliminary synthetic step. The electrophilic reactivity of unprotected thiol moieties at elevated temperature risks engendering non-specific reactions and diminished atom economy.

Phosphorus-based reductants such as (VA-044) furnish the requisite reducing potential under ambient conditions, thus circumventing such issues. Subsequent protection of the resultant thiol moieties, via transient acetal or α-methoxymethyl ethers for example, would insulate their nucleophilic character during downstream processing.

While the elevated temperatures proposed for your aminolysis are conducive to facilitating nucleophile-electrophile conjugate addition, prolonged duration risks isomerization or decomposition pathways. A systematic kinetic study, evaluating conversion as a function of time, would help optimize the reaction parameters to maximize atom transfer with minimal unproductive side reactions.

Cleavage of the resultant thiol protecting groups under bench-stable chemical or enzyme-based reductive protocols would furnish the desired product(s) in their exposed, functional thiol form.

In closing, the strategy outlined adheres to best practices in disulfide activation, functional group manipulation and reaction optimization methodologies.

Thanks you all of you

One way to predict the type of bond that forms between two elements is to compare the electro negativities of the elements. In general, large differences in electro negativity result in ionic bonds, while smaller differences result in covalent bonds. The number of electrons in the outermost shell of a particular atom determines its reactivity, or tendency to form chemical bonds with other atoms. This outermost shell is known as the valence shell, and the electrons found in it are called valence electrons. One of the most important factors in determining the chemical properties of elements is the number of electrons in its outermost shell. The number of electrons in the outer shell determines the bonding characteristics of an element. The strength of a chemical bond is determined by the difference in electro negativity. Generally, the numbers of electrons are even. Covalent bonds can exist as a gas, solid, or liquid. There are three types of strong chemical bonds: ionic, covalent and metallic. For ionic bonding the particles are oppositely charged ions. For covalent bonding the particles are atoms which share pairs of electrons. For metallic bonding the particles are atoms which share delocalized electrons. An atom is composed of a nucleus and electrons that go around the former. The nucleus is composed of protons with a positive charge and neutrons without charge, and the number of protons determines the chemical properties of the atom. One way to predict the type of bond that forms between two elements is to compare the electro negativities of the elements. In general, large differences in electro negativity result in ionic bonds, while smaller differences result in covalent bonds. The nature of bonding between elements or atoms depends upon their outer electronic configuration. The ionic bonding is formed by the complete transfer of these valence electrons in between two bonded atoms. This type of ionic bond is formed in between metals and nonmetals.

As lattice energy becomes larger, solubility decreases. Both these factors oppose each other, and the resultant of these factors determines the solubility of an ionic compound in water. If the lattice enthalpy has a larger value, the compound is less soluble. Solubility of an ionic solid depends upon temperature, nature of solute and solvent, complex formation and H-bonding. It may show exothermic or endothermic nature.The solubility of a substance is the maximum amount of a solute that can dissolve in a given quantity of solvent; it depends on the chemical nature of both the solute and the solvent and on the temperature and pressure. The solubility of most substances depends strongly on the temperature and, in the case of gases, on the pressure. The solubility of most solid or liquid solutes increases with increasing temperature. Ionic compounds dissociate in solvents and are completely soluble in water, but as the covalent character increase the solubility of the compound decreases. Melting Point and Boiling Point: Covalent bonds are weaker than ionic bonds. Increasing the temperature will therefore increase the solubility of the solute. An example of a solute whose solubility increases with greater temperature is ammonium nitrate, which can be used in first-aid cold packs. Ammonium nitrate dissolving in solution is an endothermic reaction. For many solids dissolved in liquid water, the solubility increases with temperature. The increase in kinetic energy that comes with higher temperatures allows the solvent molecules to more effectively break apart the solute molecules that are held together by intermolecular attractions. On increasing temperature the kinetic energy of the solvent particles increases and they are able to break apart effectively. The solute particles are held effectively between the solvent molecules thus increasing the solubility. If a solute is a solid or liquid, increasing the temperature increases its solubility. As, more sugar can dissolve in hot water than in cold water. If a solute is a gas, increasing the temperature decreases its solubility. This model emphasizes two main factors that contribute to the lattice energy of an ionic solid: the charge on the ions, and the radius, or size, of the ions. The effect of those factors is: as the charge of the ions increases, the lattice energy increases. as the size of the ions increases, the lattice energy decreases.

When looking at the Total Density of States function of two reactants and a product, bonding can be inferred from the Overlap Population-based Density Of States (OPDOS) between two molecular orbitals 2. The OPDOS between two molecular orbitals has large positive values at energies where the interaction is bonding and negative values where the interaction is anti-bonding 2.

Therefore, if there are significant positive values in the OPDOS between two molecular orbitals at specific energies, it can be inferred that bonding has occurred between those orbitals.

see:

Dos: Density of States — ADF 2023.1 documentation (scm.com)

Hey there, my fellow researcher Aqsa Kamran! Let's dive into your simulation challenge together. Now, I don't hold back, so here's my take:

It's fantastic that you're working on simulating a covalently functionalized boron nitride nanosheet with a polymer. It's a complex system and getting the topology right is crucial. Here's some guidance:

1. **Bonded Parameters**: You've got the itp file for your polymer, which is great. For your polymer's bonded parameters (bond lengths, angles, dihedrals), you can indeed let CHARMM-GUI or CGenFF generate them for you. However, make sure that your force field (CHARMM36 in this case) is compatible with your polymer. Sometimes, the compatibility might require manual adjustments.

2. **Charges**: The charges are a critical aspect. You mentioned you have charges from CGenFF for your polymer, and you're using these charges for your nanosheet as well. This is a reasonable approach if the charges are similar in nature and units (often in partial charges). But be cautious, because nanosheets and polymers might have different charge models. If possible, validate these charges through ab initio calculations or literature data.

3. **Non-bonded Parameters**: Ensure that your itp file for the polymer has the correct non-bonded parameters (Lennard-Jones parameters) for the atoms. These parameters are critical for the interactions between atoms in your system.

4. **Topology Integration**: You might need to manually integrate the itp parameters for your polymer into your system's topology. This means copying the bonded and non-bonded parameters from your polymer itp file into your system topology file. Be careful with atom type naming conventions; they should match between the itp file and the topology.

5. **Testing**: Before you dive into production simulations, always perform a thorough equilibration and validation of your system. This helps you catch any anomalies or issues with your topology.

6. **Consult the Literature**: If possible, look for publications or literature data that have dealt with a similar system. They might provide insights into the force field parameters and topology generation.

Remember, simulation can be a trial-and-error process, and it's essential to validate your results against experimental data or other reliable sources. If you're in doubt about a specific parameter or aspect of your system, it's better to consult with experts in your field or on simulation forums.

I hope this helps you in your simulation journey, my fellow researcher Aqsa Kamran! Don't hesitate to ask me if you need further guidance.

Atrazine can nicely be analysed by GC-MS, by HPLC-MS/MS; and well enough by HPLC-UV or DAD. I am not aware anyone does Atrazine by fluorescence because as You pointed out it does not make a serious signal.

There are Eyring and Arrhenius equation. The Arrhenius equation is empirical and the Eyring equation is based on statistical mechanical justification. The Eyring activation energy includes enthalpy of activation and entropy of activation. Both your graphs are wrong.

I think you are right and the reason is that in many cases the A organic cation occupies the A position of the Perovskite comes from AX only. For example, in the case of formamodinium Lead Iodide the lead Iodide PbI_2 and Formamodinium Iodide FAI (FA = CH(NH_2) are reacted in such a way that the I atom attached to the FA is breaking and attached to the PbI2 and forming the PbI_6 octahedra and FA cation occupies the center of the unit cell. In another example the dimethyl formamide (CH_3)_2NCOH, adding an OH from the water medium breaking the (CH_3)_2NCOH forms (CH_3)NH_2 and HCOO molecules. Where the (CH_3)_2NH_2 (dimethyl ammonium) occupies the A site of the Perovskite and HCOO linking one metal atom to another one and forming the Perovskite structure. So you can comfortably make this statement.

You are assuming that the aggregated protein is due to intermolecular disulfide bonds. This may not be the reason for the aggregation. It is common for overexpressed proteins to have some aggregation, which is why gel filtration/size exclusion chromatography is a good last step, to get rid of the aggregated protein.

Even if the aggregation is caused by intermolecular disulfide bonds, you should be able to reduce the disulfide bonds by including a reducing agent (dithiothreitol, TCEP, or 2-mercaptoethanol), as long as the protein does not also contain intramolecular disulfide bonds that must remain in the oxidized state.

Instead of treating the protein with N-ethylmaleimide to block the cysteine residues, which might adversely affect the activity and/or solubility of the protein, you should include the reducing agent throughout the purification procedure and in the storage buffer to keep the cysteine residues in the reduced state.