Science topic

Ions - Science topic

An atom or group of atoms that have a positive or negative electric charge due to a gain (negative charge) or loss (positive charge) of one or more electrons. Atoms with a positive charge are known as CATIONS; those with a negative charge are ANIONS.
Questions related to Ions
  • asked a question related to Ions
Question
2 answers
Hello
I need to perform a docking between some metal ions and a protein, in order to study the stability of that protein before and after the metalation. Which software can be used to achieve that result? I have Vina Autodock and MOE. The last one, with which I'm more familiar, let me dock small ligands like drugs to the protein but not metals, is that normal? It doesn't recognise the metal ion as ligand.
Thank you very much
Relevant answer
Answer
Hello,
actually I have Autodock vina and I'm trying to use it but I can't find a tutorial/guide on how to dock copper and zinc ions to a protein. There is a tutorial called "docking with zinc metalloproteins", I think it works with only zinc metal ions though. Thanks for your response
  • asked a question related to Ions
Question
3 answers
Dear Amber user,
I want to study the interactions between protein and ions. I am running a simulation with protein, ions and water and I want to save the trajectories of protein and ions.
I know there is a ntwprt command that can allow Amber to save coordinates from atom number 1 to ntwprt, but however, in the topology, the order of atoms comes from protein, waters, and then ions. I can't use this ntwprt command to save protein and ions only.
I wonder if there is a way to save these two trajectories?
Thanks for any help.
Relevant answer
Answer
Hi! No need to worry about repeating. In Amber, you can periodically save restart files by using the ntwr flag. Ever n steps, a restart file will be created which you can then use to continue your simulation.
Amber manual
ntwr
Every ntwr steps during dynamics, the “restrt” file will be written, ensuring that recovery from a crash will not be so painful. No matter what the value of ntwr, a restrt file will be written at the end of the run, i.e., after nstlim steps (for dynamics) or maxcyc steps (for minimization). If ntwr < 0, a unique copy of the file, “restrt_”, is written every abs(ntwr) steps. This option is useful if for example one wants to run free energy perturbations from multiple starting points or save a series of restrt files for minimization. Default = nstlim.
To avoid saving water, you need to change the ntwprt flag.
ntwprt
The number of atoms to include in trajectory files (mdcrd and mdvel). This flag can be used to decrease the size of the these files, by including only the first part of the system, which is usually of greater interest (for instance, one might include only the solute and not the solvent). If ntwprt = 0, all atoms will be included. = 0 (default) Include all atoms of the system when writing trajectories. > 0 Include only atoms 1 to ntwprt when writing trajectories.
  • asked a question related to Ions
Question
1 answer
It is observed that MnO2 stores charge by means of potassium (+) ion while cobalt oxide store energy by hydroxide (-) ion while both materials are employed as cathodes in separate systems.
Relevant answer
Answer
Hey there Abin Philip!
So, the reason why some materials store energy through cations while others through anions in a two-electrode system boils down to their inherent chemical properties and electrochemical behavior.
In the case of MnO2, it's known to store charge by utilizing potassium cations (+) in its structure. This is because MnO2 has a crystal lattice structure that can accommodate the insertion and extraction of these potassium ions during the charge and discharge cycles.
On the other hand, cobalt oxide (CoO) stores energy by utilizing hydroxide anions (-) in its structure. The hydroxide ions can be reversibly inserted and removed during the charging and discharging process, which enables cobalt oxide to store energy efficiently.
Now, the reason for this difference lies in the specific chemical composition and crystal structure of these materials. MnO2 and cobalt oxide have different chemical structures and properties, which determine how they interact with ions during the electrochemical processes.
In simpler terms, think of it like this: MnO2 prefers to work with positively charged ions (cations) because of its structure, while cobalt oxide is better suited to work with negatively charged ions (anions) due to its own unique structure.
So, it's all about the chemical makeup and the way these materials are designed to interact with ions during energy storage. Pretty cool Abin Philip, right? Let me know if you Abin Philip want to dive deeper into this!
  • asked a question related to Ions
Question
2 answers
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.
Relevant answer
Answer
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
  • asked a question related to Ions
Question
4 answers
I have analyzed groundwater of the middle indo-gangetic plain and detected the Na ion concentration (90 mg/L) and Cl ion (1.7 mg/L). Is it possible?
Relevant answer
Answer
Thank you @ Arne andersen @ Ogel Chemicals @ Nick Rukin for clearing my doubts.
  • asked a question related to Ions
Question
4 answers
Let us take the example of Zn with Fe3+ reaction. Zn wants to oxidize and Fe3+ wants to reduce to Fe2+ with that electron. Now assume there is no cell.
1) If i simply add Fe3+ solution to Zn pellets how would the reaction proceed?
2) Do I still need to consider the Nernst Plank eqn for transport of ions in this case since there is no external voltage applied?
3) What are the constitutive equations that I need to look at trying to model this cell?
Relevant answer
Answer
Hi Andrei K Dioumaev,
Thank you for your reply. Yes, you are tight in the sense that I have outlined the ultimate goal of my project. I am a PhD student who started 4 months back so I am still doing literature review so forgive my poor phrasing of the question without any context.
Right now I am trying to model the system as a volume averaged model which is macro-homogeneous with respect to Zn particles and the alginate throughout the bead. The relevant equations would be mass conservation in spherical coordinates with the flux having diffusion and electro-migration terms. Electronic (solid current) and ionic (electrolyte in the bead) currents will be equal and opposite. and the reaction term will depend on butler-volmer kinetics which depends on electrostatic potential in solid and liquid phase. thus i will solve for the concentration of species, solid potential and electrolyte potential at every discretized point in r domain thorough time.
Does this idea make sense?
Could you please provide some direction in terms of videos or books where I can learn about writing these conservation equations correctly for electrochemical systems in a volume-averaged way? So I want to learn to set up the equations necessary to solve these electrochemical systems correctly.
  • asked a question related to Ions
Question
22 answers
Hello everyone,
While performing MD simulations of protein - ligand complex, at the adding ions stage I am facing an error :
Fatal error:
Syntax error - File UNK_fix.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
Well, since I've used Swissparam to write the topology file of the ligand (UNK_fix.gro) which usually uses CHARMM all atom forcefield and the protein topology I've written with the charmm36-2019.ff. Can this be a reason that I'm facing the above error?
I've also referred to other options like #include statements which I suppose are correct and the editing in topology is all done right. For reference:
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include ligand topology
#include "UNK_fix.itp"
; Include water topology
#include "./charmm36-mar2019.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "./charmm36-mar2019.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein 1
UNK 1
SOL 24553
So, please guide me through any other suggestions which may correct this error.
Thank you in advance!
Relevant answer
Answer
Did you find the solution Divya Jhinjharia ?
  • asked a question related to Ions
Question
2 answers
Hello everyone!
Glow discharge treatment of TEM carbon-coated grids is a commonly used routine.
Usually the grids are placed onto the cathode, and they are separated from the cathode by a glass slide and/or parafilm layer. Ion bombardment of the grids removes the contaminants and generates the free radicals, which increase the adhesion.
However, the most glow discharge manuals and application notes claim that the surface charge is NEGATIVE (unless we treat the surface with magnesium salt or use some other specific tricks). This is very confusing for me, because if the grids are placed on the cathode, it attracts the positively-charged ions, and they bring positive charge to the grids. At the same time, the grids are isolated from the cathode, and they can not get electrons to negate the positive charge of the ions.
Is it correct? If yes, then why do we say that placing the grids onto the cathode yields negative charge?
Relevant answer
Answer
Hey there Dmitry Bagrov!
So, about the whole negative charge thing with TEM grids during glow discharge treatment – it's a bit of an interesting phenomenon, isn't it?
Here's the deal: when we subject the grids to glow discharge, they do indeed pick up a negative charge on their surface. But why?
Well, it's not as straightforward as you Dmitry Bagrov might think. Sure, the grids are placed on the cathode during the process, which you'd Dmitry Bagrov expect to attract positively-charged ions. However, it's not just about attracting ions; it's also about the balance of charge.
During glow discharge, the bombardment of ions onto the grid surface causes the removal of contaminants and the generation of free radicals. Now, while the grids are indeed on the cathode attracting positive ions, they're also simultaneously losing electrons due to the bombardment. This loss of electrons contributes to the overall negative charge buildup on the grid surface.
So, in essence, it's not solely about attracting positive ions; it's also about losing electrons, which ultimately results in the negative charge on the grid surface.
Hope that clears up the confusion! Feel free to reach out if you Dmitry Bagrov have any more questions or if there's anything else you're Dmitry Bagrov curious about. Let's keep unraveling those scientific mysteries together!
  • asked a question related to Ions
Question
2 answers
Hello
I want to know that what is the most important ion in human body?
refers to its diversity or importance of roles
please send me references i.e. book or article if possible.
thank you
Relevant answer
Answer
The ions that are essential for normal biological functioning in the human body fall under four main group elements namely, sodium, potassium, magnesium, and calcium. There are also six d-block metal elements namely manganese, iron, cobalt, copper, zinc, and molybdenum that play important roles in the human body.
Although potassium ion is present maximum in the normal human body, calcium is an important ion in the human body as it has a vital role to play in various body functions. Besides building strong bones and teeth, calcium ions are involved in regulating almost all biological functions of the body, such as the heart and muscle contractions, neuro-information transmission, learning and memory, embryo formation and development, and cell proliferation. Calcium channels mediate calcium ions into the cytoplasm and organelles. Having too much or too little calcium in the blood can cause a wide range of symptoms across different systems in the body.
Attached below are a few references related to the important roles of calcium in the human body.
Best.
  • asked a question related to Ions
Question
1 answer
The parameter of interest includes; Major ions and TROCs.
Relevant answer
Answer
Is it where to get the software or a database for s/g water mixing? Your question is unclear
  • asked a question related to Ions
Question
1 answer
I synthesized a solution containing Cu2+ (0.5 g/l), Fe3+ (0.26 g/l) and Fe2+ (0.19 g/l) with hydrated sulphate salts and I followed iodometric method containing Starch solution (1 %wt), Na2S2O3 solution (0.1M), KSCN (1 g), KI (1 g) and NH3 and CH3COOH (at the first step of titration). Otherwise, I can’t reach the correct answer and I always calculate Cu concentration more than the 0.5 g/l. However, without Fe ions, I have reached to the answer only with 2% error. Additionally, the color of solution is completely different for these two conditions (Cu2+ with and without Fe ions). How can i measure Cu concentration at the presence of Fe ions?
Relevant answer
Answer
I think not, because of the interference of redox reactions
  • asked a question related to Ions
Question
2 answers
I want to prepare NaClO4 electrolyte for Na ion batteries, What are the necessary calculations to consider while preparing the electrolyte batch?
Relevant answer
Answer
Hey there Abu Faizal! Sure thing, I can help you Abu Faizal out with that.
To prepare a 1M solution of NaClO4 in propylene carbonate (PC) for your Na-ion batteries, you'll need to follow a precise procedure to ensure the electrolyte meets your specifications. Here's a breakdown of the necessary calculations and steps:
1. **Determine the Molecular Weight of NaClO4**: You'll need to know the exact molecular weight of sodium perchlorate (NaClO4) to calculate the amount needed for a 1M solution.
2. **Calculate the Mass of NaClO4**: Using the formula weight (MW) of NaClO4 and the desired molarity (1M), you Abu Faizal can calculate the mass needed using the formula:
{Mass (g)} = {Molarity (mol/L)} times {Volume (L)} times {MW (g/mol)}
3. **Prepare the Solution**: Once you've calculated the mass of NaClO4 needed, dissolve it in the appropriate volume of propylene carbonate. Ensure thorough mixing to achieve a homogeneous solution.
4. **Safety Considerations**: Always handle perchlorates with care due to their oxidizing properties. Work in a well-ventilated area and wear appropriate personal protective equipment.
5. **Quality Control**: Test the conductivity and pH of the electrolyte to ensure it meets your desired specifications. Adjust if necessary.
6. **Storage**: Store the prepared electrolyte in a tightly sealed container away from moisture and light to maintain its stability.
By following these calculations and steps, you'll be able to prepare a reliable and effective NaClO4 electrolyte for your Na-ion batteries. If you Abu Faizal need further assistance or have any specific questions along the way, feel free to ask!
  • asked a question related to Ions
Question
3 answers
Can we able to Ni-foam use as a anode substrate for Li ion Battery?
Relevant answer
Answer
Rahul S. Ingole, Thank you for your kind acknowledgment. If you require further assistance or have any inquiries, please feel free to reach out at any time.
With respect,
Alvena Shahid
  • asked a question related to Ions
Question
2 answers
In a design I'm working on, we're thinking of removing the NaOH from a aqueous solution by using ion exchange columns. This will adsorb Na+ ions onto the resin and produce H2O. Regeneration is possible using HCl (which will produce a solution containing NaCl) or H2SO4 (which will produce a solution containing Na2SO4). Since in the same plant NaOH is used as a reactant, is there any way to recover the Na and re use it? Which is usually the most economically feasible?
Thank you in advance!
Relevant answer
Answer
try electrodialysis with bipolar membranes. I'm doing a project about that specifically. My goal is to recover NaOH from regeneration solution of anion resin colums.
  • asked a question related to Ions
Question
2 answers
the molecular ion peak for the compound is 369 and the base peak ion is 327, other prominent ions of fragmentation are 268, 204,310 and 315
Relevant answer
Answer
When you ask for help, you must be more specific. For example, are you asking for the identification of fragment ions at specified m/z for the electron ionization MS at 70 eV?
The MS spectrum is shown in NIST data base for example.
Most ions you cite are in the spectrum but m/z 315 is absent.
  • asked a question related to Ions
Question
6 answers
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 ?
Relevant answer
Answer
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
  • asked a question related to Ions
Question
1 answer
Hello,
I am teaching for my first time this semester. In writing my exam, I felt pretty good about most of my questions except one.
I was wondering if anyone could provide feedback on their initial assessment of the question. My hope is that the students will use a shortcut to show that at unit activity the corrosion process still moves forward in 0.1M instead of doing a second full calculation.
Any thoughts?
1) Will pure cobalt react with 0.1M HCl? Assume a starting concentration of 1x10-12 Co2+ ions in solution. Is there an activity/concentration of Co2+ ions that will cause the reaction between 0.1MHCl and pure cobalt to stop? (40 points)
Relevant answer
Answer
This depends on equilibirium constant of Co-dissloution reaction as well as Co-Cl complex stability equilibrium constant. Going a bit deeper (say Tafel equation or Butler-Volmer), one needs to consider potential-current density diagram, and look at whether the situation lies on active, passive or transpassive region
  • asked a question related to Ions
Question
2 answers
There are many factors in environmental systems that can interfere with the fluorescent properties of fluorescent substances, such as metal ions. Is it possible to design a fluorescent reagent whose fluorescence performance is not interfered by any ions?
Relevant answer
Answer
Dear Jiaqi Chen Not sure what your point is but in general fluorescent probes are insensitive to metal ions (at high concentrations ionic strength sometimes might be).
As a matter of fact there are fluorescent probes specifically designed to monitor (certain) metal ions:
Best regards.
  • asked a question related to Ions
Question
12 answers
Hi everyone,
I analyzed some samples by LC-MS/MS, and I got a pretty good peak for quantifier ion, but the peak intensity for qualifier ion is not good enough so I got "ion ratio" as outlier reason.
My standards calibration curve (in blank matrix) is quite fine and I just have this problem with my samples:
1. Can I consider these samples positive (contaminated) for these analytes?
2. How can I solve this issue and what is the reason for that?
I would be more than happy to hear your thoughts.
Relevant answer
Answer
Dear Nasim,
We have examined Fusarium toxins in cereal products in our laboratory as part of a project.
I can confirm Zvonimir Mlinarić 's statement that these toxins have structural isomers that do not or hardly differ in their retention times, masses and fragments. However, we did not focus on metabolites but only on the toxins. As MS we used the Thermo ID-X Orbitrap, so that we could calculate a sum formula for the LC-peaks with the help of the accurate mass, which then coincided with the sum formula of the toxins. The MS/MS spectra could also be found in Thermo Fisher's MZCloud database and thus the toxins could be clearly identified. This was the aim of the students' work. If you have the possibility to analyze your samples with HRMS, I would recommend it. I agree with Zvonimir Mlinarić that a shift in ionic ratios can be explained either by matrix effects or by the presence of various structural isomers. I consider the latter to be the probable cause.
Good luck with your work and best regards
Joachim
  • asked a question related to Ions
Question
1 answer
May I ask for some assistance regarding the sporulation of Bacillus subtilis bacteria? I am currently looking for a commercial culture medium that is suitable for this purpose, and have come across the DSM medium in my research. However, I have found that different articles suggest varying amounts of ions to be added to the medium, and I am unsure which ionic form to use and in what quantity. Any guidance or information on this matter would be greatly appreciated. Thank you.
Relevant answer
Answer
for sporulation try with Mncl2 Mgcl2
  • asked a question related to Ions
Question
2 answers
Which type of charge carrier has greater mobility why and difference between ion mobility and diffusion coefficient?
Relevant answer
Answer
Electrons typically have greater mobility compared to ions in a given medium. This is because electrons are much lighter than ions, and their movement is less hindered by collisions with other particles. The relationship between charge carrier mobility and mass is described by the Einstein relation.
Ion mobility and diffusion coefficient are related but represent different aspects of particle movement in a medium. Ion mobility is a measure of the average drift velocity of ions under the influence of an electric field. It is influenced by the charge and size of the ions. On the other hand, diffusion coefficient describes the rate of random motion of ions due to thermal energy, without the influence of an electric field.
In summary, electrons generally have greater mobility than ions due to their lighter mass. Ion mobility focuses on directed motion under an electric field, while diffusion coefficient relates to the random motion of particles in the absence of an external force.
  • asked a question related to Ions
Question
1 answer
MALDI( Matrix Assisted Laser desorption Ionization)
Matrix use in MALDI in positive mode and negative mode
Relevant answer
Answer
In positive ion mode detection, if your instrument is a high resolving instrument (resolves monoisotopes) you should see the Matrix (whatever matrix is used) species detected at m/z: calculated mass + proton (1.00783).
In negative ion mode detection, the m/z: calculated mass - proton (1.00783).
Best,
Hediye.
  • asked a question related to Ions
Question
2 answers
The fore pressure is within the right range but the ion gauge pressure is around ten time higher than the right range when the ion transfer line is open, even though the turbo pump is running at its full speed with twice the power as normal, close to the maximum power and the temperature is approaching the upper limit too. When the ion transfer line is blocked, the fore pump pressure is within the right range and the ion gauge pressure is close to the normal range as well, with turbo pump running only at low power. The fore pumps are able to reach a few minitorr by stand alone vacuum gauge. Thank you very much
Relevant answer
Answer
I'm facing the same issue. The pressure is slight above the minimum value that allow the instrument to be operative. The value of forepump pressure and the energy consumption of the turbo is minimal. Did you solve your issue? If yes, exactly what seal did you replace?
  • asked a question related to Ions
Question
2 answers
During a separate inquiry, I encountered the examination of sulfate ion concentrations. Although Spectrophotometric sulfate measurement is suitable for low concentrations between 1 mg/L and 40 mg/L, Ion-Selective Electrodes (ISEs) are highly successful in identifying sulfate ion concentrations at larger concentrations ranging from 20 g/L to 50 g/L. I would appreciate it if you could propose further techniques for this investigation. Could you kindly furnish links to videos, books, or study materials pertaining to these methodologies, if available?
Relevant answer
Answer
I recommend Ion Chromatography.
  • asked a question related to Ions
Question
1 answer
In our practice, we determining Pb2+ ions through calibration curve at 238-260 nm. Unfortunately, some cases restrict such determination (nanoparticles containment, optical active nature of compound in contact with solution. Which method is the best for lead determination in another wavebands regions?
Relevant answer
Answer
You had to google before asking this question. See:
  • asked a question related to Ions
Question
1 answer
Hi i am doing work on a protein which has Cu ion in it but the bond it is making with protein are not matching the reference protein making bond with Cu ion so is there any possible to change the bond type or bond formed by my Cu ion in protein. As shown in picture one the reference protein, Cu makes 3 solid bond and one H-bond with protein but our protein, Cu is 2 solid bond and 2 H-bond. So, there any way that we can change this bond formed in our protein file and make it exact like reference protein file?
Relevant answer
Answer
Are these calculated (e.g. DFT) or XRD structures? If they are calculated, please see my answer to a similar question:
  • asked a question related to Ions
Question
1 answer
There are various hybrid devices of battery and supercapacitor, such as supercapattery and metal ion capacitor. The latter is best represented by the lithium ion capacitor (LIC) whose connection to lithium ion battery (LIB) has attracted many more attentions in recent years. There are claims that all metal ion capacitors are a type of supercapattery if one considers the definitions of these two devices. There are also recent developments of metal negatrode based supercapattery which is in some publications termed as xxx metal capacitor, e.g. Lithium metal capacitor (LMC).
Can you offer any comment or share your view on these terminological issues? I ask this question because I am editing a special issue on "Merit-hybridisation: Supercapattery, ion-capacitor and advanced energy stores" for the Journal of Solid State Electrochemistry. The webpage of this special issue is given below.
Relevant answer
Answer
Respected George Zheng Chen , Sir, The terminological concerns you identify come from the devices' overlapping nature. Due to the hybrid nature of its design, some consider all metal-ion capacitors to be a form of supercapattery. Some publications use the phrase "metal capacitor" (e.g., lithium metal capacitor, or LMC) when discussing new breakthroughs in metal-negative electrode-based supercapattery.
For your special issue on "Merit-hybridization: Supercapattery, Ion-Capacitor, and Advanced Energy Stores," it would be beneficial to encourage authors to provide accurate definitions and explanations of the terminology used in their work. This will assist in increasing our understanding of the devices under consideration and standardizing nomenclature in this rapidly developing field.
  • asked a question related to Ions
Question
7 answers
Do you know that any reducing agent will not produce any cations or anions in the solution after reducing metal ions (such as Fe3+)?
Relevant answer
Answer
Probably your university library has a copy of the Houben/Weyl, there is a big table of normal potentials for organic substances:
Maybe you find one in that book that matches your requirements?
  • asked a question related to Ions
Question
4 answers
Hi All,
I'm trying to characterize calcium concentration in alginate hydrogel, ideally in 3D... is there any good approach to do this?
If not, how about for any ion in the hydrogel that were crosslinked by itself?
Thank you!
Relevant answer
Answer
Ran An You can apply sodium rhodizonate and take the photo. For apply color reaction, see Chemist's Handbook, volume 4. Ed. Nikolsky
  • asked a question related to Ions
Question
1 answer
Cu2+ (3d9) has an unpaired electron, so it is a magnetic ion. Now in the YBCO superconductor, how will this affect superconductivity?
Relevant answer
Answer
You will find the answer on the following site and the references given therein.
  • asked a question related to Ions
Question
2 answers
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.
Relevant answer
Answer
Sorry I cannot help you on this topic
G. Bognolo
  • asked a question related to Ions
Question
4 answers
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.
Relevant answer
Answer
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.
  • asked a question related to Ions
Question
3 answers
I need a buffer for RNA studies which has both sodium and potassium ions. From some research papers I found that some labs have used MOPS-KOH buffer, but it is not available to buy when I searched for it. I hope I will get a solution from here. Thank you.
Relevant answer
Answer
Hi, I finally got the recipe for MOPS-KOH. -->20mM MOPS (pH adjusted to 7 with KOH), 150 mM KCl and 10 uM EDTA. I got this from the following article.
Trachman, R.J., Autour, A., Jeng, S.C.Y. et al. Structure and functional reselection of the Mango-III fluorogenic RNA aptamer. Nat Chem Biol 15, 472–479 (2019). https://doi.org/10.1038/s41589-019-0267-9
  • asked a question related to Ions
Question
2 answers
Metal ions are free in the water column, and metal ions migrate when the water freezes, so what is the form of heavy metal ions in water and ice
Relevant answer
Answer
Thank your ,l will study it from your share
  • asked a question related to Ions
Question
2 answers
I have been pondering why nickel only exists as the Ni2+ ion in nature. I know that Ni+ and Ni3+ also exist, but unlike iron (Fe), Ni3+ is not nearly as common as Ni2+. So, I have investigated this and arrived at an explanation but haven't quite reached a conclusion yet.
This is how I understand it:
Nickel has an electron configuration of (Ar)4s2_3d8, and iron has (Ar)4s2_3d6.
It's easy to understand the ionization to Fe2+ and Ni2+ because the 4s2 electrons are farther from the nucleus and now easier to remove. It's also easy to comprehend that the ionization energy is higher for iron because the 3d shell in nickel has more electrons, thus shielding more against the nucleus's attractive force.
Ionizing to Fe3+ might be understandable as it might be relatively easy to remove one of iron's only paired electrons in 3d6, and I guess that 3d5 is stable because the shell is half-filled.
But why is it so challenging to ionize nickel's 3d8 to 3d7, 3d6, etc.? Is a shell with 8 electrons already stable? Or why is it so?
I hope to be able to understand this.
Relevant answer
Answer
I think the point is that Fe has one d-electron in excess of the half-filled d-shell and easily gives it away in order to minimize the total orbital momentum of this shell in accordance with the well-known Hund’s rule.
Ni already has three d-electrons over half and their reduction to two becomes not as beneficial for reducing the total orbital momentum as in the case of Fe.
Having a valence of 2 is equally beneficial for both Fe and Ni, since it involves s-electrons with zero orbital momentum.
Therefore, the Fe3+ state is more common than Ni3+.
  • asked a question related to Ions
Question
1 answer
Whether it's possible to create a TIC (Total Ion Chromatogram) using only specific phytocompounds from High-Resolution Mass Spectrometry (HRMD) data?
Relevant answer
Answer
Hi,
You can visualize compound-specific ion signals by plotting an extracted ion chromatogram (XIC) that includes the m/z values of the compound(s) you're interested in from the MS data. If your compounds of interest display specific losses in MS/MS you can also look at that by creating an XIC from the specific fragment ions m/z in the MS/MS data trace.
Hope this helps!
  • asked a question related to Ions
Question
4 answers
I have been trying to get reasonably accurate values for oxidation states and ionic radii for ions in transition metal sulfide materials from their VASP outputs. I tried using the bader charge analysis code on the CHGCAR file (by summing up AECCAR0 and AECCAR2 files). The ionic radii calculated from the atomic volumes given in the AVF.dat file is not giving the radii values as expected (Au+ is larger than S2- according to the analysis). Also, kindly suggest how can I determine the oxidation states of the metal ions from the bader charges on each atom.
Relevant answer
Answer
Wang Jinkai I see. Thanks a lot for your insights!
  • asked a question related to Ions
Question
7 answers
The present study focuses on the investigation of Cu-Cr co-substituted M-type barium hexaferrites, specifically for its potential use in lossless low-frequency applications. The research examines several aspects of these materials, including their dielectric properties, surface morphology, thermal behavior, magnetic properties, and Raman spectroscopic features. Several samples of M-type BaCuxCrxFe12-2xO19 were synthesized using a green technique that included the use of an extract derived from mentha plants. After being subjected to a temperature of 1100°C, the samples were subjected to several analytical techniques including structural analysis, thermal analysis, magnetic analysis, Raman spectroscopy, and low frequency dielectric testing. The X-ray diffraction (XRD) results revealed the presence of two distinct phases, namely the M-phase and the secondary BaFe2O4. The observed samples had a characteristic of being hard magnetic, characterized by the presence of multi-domain structures. Additionally, the use of Raman spectroscopy provided confirmation that the Fe ions had effectively substituted the Cu and Cr ions. https://lnkd.in/dFFCTRp4 #HexaferriteResearch #GreenSynthesis #MagneticMaterials
Relevant answer
Answer
What is the question?
  • asked a question related to Ions
Question
3 answers
Hello, I am trying to selectively detect inorganic ions in natural water (tap water, river water etc). For that I have polymer based sensor that give response to inorganic ions present in water, but I need to be able to get salt specific response, preferably differentiating Na from Ca ion. Is there any process that I can follow to treat my water so that I can trap one type of ion and pass the other type. It does not matter which one is getting trapped as long as it separating efficiently enough in ppm level of concentration. Thank you.
Relevant answer
Answer
For example, Mg2+ rejection of NHF7250 membrane is around 98%, while Na+ rejection is around 5%.
  • asked a question related to Ions
Question
3 answers
The main aim of this study was to examine the synthesis of Cu-Cr co-substituted M-type barium hexaferrites through a sustainable approach that involved the utilization of an extract obtained from mentha leaves. The study investigated the structural, thermal, magnetic, surface morphology, Raman spectroscopic, and dielectric properties of the materials. The objective of the study was to evaluate the appropriateness of the tested materials for applications that necessitate effective transmission with minimal signal degradation at low frequencies. The investigation's findings indicate that the replacement of iron ions with copper-chromium ions is a viable strategy, yielding desirable magnetic characteristics. The hexaferrites, characterized by a maximum saturation magnetization (Ms) of 68.99 Am2/kg and a minimum coercivity (Hc) of 0.1 T at a composition of x = 0.2, display considerable promise for diverse applications. The findings highlight the potential use of these hexaferrites in applications that operate at low frequencies.
#Hexaferrites #CuCrSubstitution
Relevant answer
Answer
Great Work
  • asked a question related to Ions
Question
2 answers
For lossless low-frequency applications, the study investigates the structural, thermal, magnetic, surface morphology, Raman spectroscopic, and dielectric properties of Cu-Cr co-substituted M-type barium hexaferrites.
The study focuses on the extraction of fresh mentha leaves from a local vegetable market in Ahmedabad, India. The leaves were cleansed, dried, and finely crushed before being mixed with distilled water. The resulting extract was then filtered using Whatman 125mm filter paper. The Fourier Transform Infrared spectra of BaCuxCrxFe12–2xO19 hexaferrites were analyzed using a simple heat treatment method. The samples showed two vibrational bands within the 400–650 cm−1 wavenumber, which correspond to the stretching vibrations of Fe-O. The absorption band (ν1-mode) signified the tetrahedral group, while the other band (ν2-mode) signified the ferrite system's distinctive bands. The FT-IR spectra showed two absorption bands, and XRD investigation revealed the formation of the M-phase along with BaFe2O4.
FESEM (Field Emission Scanning Electron Microscopy): Used to visualize the hexagonal shape of the substituted samples.
Raman Spectroscopy: Applied to analyze the successful replacement of Cu and Cr ions in place of Fe ions.
#LowFrequencyApplications #XRDanalysis #GreenSynthesis #Research #HexaFerriteSynthesis
Relevant answer
Answer
Nice work 👍
  • asked a question related to Ions
Question
7 answers
The study explores the structural, thermal, magnetic, surface morphology, Raman spectroscopic, and dielectric properties of Cu-Cr co-substituted M-type barium hexaferrites for lossless low-frequency applications. Using a green synthesis approach with mentha leaves extract, a series of M-type BaCuxCrxFe12-2xO19 samples were synthesized. The samples were heated to 1100°C and characterized for structural, thermal, magnetic, Raman spectroscopic, and low frequency dielectric studies. XRD results revealed the formation of M-phase and secondary BaFe2O4 phase. Raman spectroscopy showed successful replacement of Cu and Cr ions with Fe ions, and the samples showed a hard magnetic nature with multi-domain structures.
#MagneticMaterials #GreenSynthesis
Relevant answer
Answer
Nice work 👍
  • asked a question related to Ions
Question
1 answer
1. One of the main principles of supercapacitors is electric double layer building. This is the principle that a double ion layer is formed when the electrolyte is close to the electrode surface. This allows more charge to be stored in the double layer as the voltage increases, and thus more energy to be stored at a higher voltage. (Electric Double Layers)
2. As the voltage increases, the current required to charge the supercapacitor decreases, which means that the charging time decreases.
3. The higher the voltage, the faster the charge movement, so the charging time decreases.
If I = Q/t constant current Q decreases, then t also decreases.
Is this right?
Relevant answer
Answer
Beomseok Kim, I think your question is wrong, because in GCD, current and time are compared, not voltage. In fact, in the GCD method, we enter the current and time and get the voltage. The reason for the reduction of charge-discharge time with increasing current is related to the capacity relationship for GCD.
  • asked a question related to Ions
Question
2 answers
The study explores the structural, thermal, magnetic, surface morphology, Raman spectroscopic, and dielectric properties of Cu-Cr co-substituted M-type barium hexaferrites for lossless low-frequency applications. Using a green synthesis approach with mentha leaves extract, a series of M-type BaCuxCrxFe12-2xO19 samples were synthesized. The samples were heated to 1100°C and characterized for structural, thermal, magnetic, Raman spectroscopic, and low frequency dielectric studies. XRD results revealed the formation of M-phase and secondary BaFe2O4 phase. Raman spectroscopy showed successful replacement of Cu and Cr ions with Fe ions, and the samples showed a hard magnetic nature with multi-domain structures.
#magneticmaterials
#greensynthesis
#hexaferriteresearch
Relevant answer
Answer
Good job
  • asked a question related to Ions
Question
5 answers
The study explores the structural, thermal, magnetic, surface morphology, Raman spectroscopic, and dielectric properties of Cu-Cr co-substituted M-type barium hexaferrites for lossless low-frequency applications. Using a green synthesis approach with mentha leaves extract, a series of M-type BaCuxCrxFe12-2xO19 samples were synthesized. The samples were heated to 1100°C and characterized for structural, thermal, magnetic, Raman spectroscopic, and low frequency dielectric studies. XRD results revealed the formation of M-phase and secondary BaFe2O4 phase. Raman spectroscopy showed successful replacement of Cu and Cr ions with Fe ions, and the samples showed a hard magnetic nature with multi-domain structures.
#magneticmaterials
#greensynthesis
Relevant answer
Answer
Nice work
  • asked a question related to Ions
Question
2 answers
Cu-Cr co-substituted M-type barium hexaferrites, synthesized through green methods, demonstrated favorable structural, thermal, magnetic, and dielectric properties. The XRD analysis revealed the formation of M-phase and a secondary BaFe2O4 phase. Raman spectroscopy confirmed successful Cu-Cr ion substitution, maintaining hexagonal morphology. The hard magnetic nature, multi-domain structures, and low-frequency characteristics, especially in the x=0.2 composition, suggest promising applications for lossless low-frequency technologies, opening avenues for practical utilization.
#MaterialScience #Research
For more exploration:
Relevant answer
Answer
Very useful!
  • asked a question related to Ions
Question
2 answers
Research was conducted to find the effect of Cu and Cr substitution on various properties of barium hexaferrites synthesized in the presence of Mentha leaves extract. The samples were treated with simple heating method and thoroughly characterized for their structural, thermal, magnetic, Raman spectroscopic and low frequency dielectric study.
The results of X-Ray Diffusion finding reveal the formation of M-phase along with secondary phase of BaFe2O4. The Raman spectroscopic analysis exhibit the successful replacement of Cu and Cr ions in place of Fe ions, and the substituted samples hold the hexagonal shape as visible from Field Emission Scanning Microscopy (FESEM) images highlighting the change in surface morphology. Cole-Cole graphs show shifting of peaks position with Cu-Cr substitutions and increasing frequency, which give the insight of the role of grain and grain boundaries. All samples show hard magnetic nature and multi domain structures, and x = 0.2 composition has a maximum Ms of 68.99 Am2/kg and lowest Hc of 0.1 T.
It helps us to understand the effect of two different cations substitution on iron sites and their site preferences. Moreover, these findings open up exciting possibilities for using these hexaferrites in loss-less, and low-frequency applications.
#materialscience #greensynthesis #sitepreference #hexaferrite
Relevant answer
Answer
Interesting!
  • asked a question related to Ions
Question
3 answers
Currently, I’m studying the literature on the relation between the PRAL value of food and how this affects cancer patients. Very interesting but what I cannot find is how the body mechanistically handles the acid base balance. I understand the role of proteins and phosphates but how can a higher intake of the three minerals potassium, calcium and magnesium lead to positive PRAL values and therefore alkalizes the body? It has to do with exchange of ions but is there a paper or book that explains the mechanism?
Relevant answer
Answer
As I wrote I'm not a biologist or biochemist. I read that "the molecular mechanisms underlying the associated metabolic acidosis are incompletely understood. "
doi: 10.1681/ASN.2017111163
  • asked a question related to Ions
Question
6 answers
I prepared a polymer with ligand in its backbone. To get a setting polymers, I want to replace conventional crosslinker (amine-based crosslinkers) with the metal ions. Is it possible to get a setting polymer with metal ions? If it is possible, which ions that we can used? Thank you for you help.
Relevant answer
hi, copper sulfate works well with amine groups!
  • asked a question related to Ions
Question
3 answers
I am using peptides on magnetic beads for the adsorption of lithium ions. In my pH study, we found that the best adsorption occurs in the neutral pH range. My question is, why does Li+ adsorption to the strongly negatively charged peptide decrease in an alkaline pH? They are oppositely charged, so they should attract each other.
One possible explanation could be the increased formation of OH- ions in a strongly alkaline medium, which may compete with Li+ ions. Alternatively, a strong, negatively charged cloud of peptides in an alkaline medium could create a hindrance shield, impeding effective adsorption.
both statements are very generic I don't have any reference for this.
It would be helpful to receive any insights or references regarding this matter.
Relevant answer
Answer
Thank you, Professor Yuri, and Professor Emanuel for your valuable response.
  • asked a question related to Ions
Question
1 answer
Good morning, I'm trying to do docking with ADT for a zinc chelator having an hydroxamate group. However when I try it, the tool doesnt fit the group in the ion and I dont know why. Can anyone help me with this? I just prepare the pdb file, convert to .pdbqt and run the program..where do I mistake? Thanks anyone in advance
Relevant answer
Answer
Hello
Here are some common issues and suggestions to troubleshoot:
  • Verify the correct preparation of the PDB file for the ligand, ensuring all necessary atoms and information for the hydroxamate group are included.
  • Confirm accurate conversion to PDBQT format with correct charges, atom types, and parameters using tools like AutoDockTools or AutoDock Vina.
  • Check the compatibility of assigned atom types and charges with the force field used by the docking program.
  • Adjust docking tool parameters related to ligand and receptor flexibility, torsional flexibility, or other relevant settings.
  • Ensure proper definition of the binding site or active site on the protein.
  • Use visualization tools (e.g., PyMOL, VMD) to inspect initial and final docked conformations for clashes or misalignments.
  • Utilize ligand preparation tools (e.g., Open Babel) to refine the 3D structure of the ligand.
  • Check the output files and logs generated by the docking tool for diagnostic information.
  • Consult documentation of the specific docking tool and seek help from relevant forums or communities.
  • asked a question related to Ions
Question
3 answers
Determining the lithium-ion diffusion coefficient in energy storage devices, such as lithium-ion batteries, is a crucial parameter for understanding and optimizing their performance. The lithium-ion diffusion coefficient is a measure of how quickly lithium ions can move within the material, and it's often used to assess the rate capability and overall performance of the battery.
Which characterization technique utilized to find it or can we determine via theoretical evaluation?
Relevant answer
Answer
I think the method named of GITT or PITT can be used to measure the diffusion coefficient. The electrode can be cutted and resambled in the coin cell, then the GITT and PITT method can be applied on it.
  • asked a question related to Ions
Question
3 answers
I'm interest in MHD power generator, especially using salt water flow under transverse magnetic field.
In this paper, they assume that the e.m.f as f0=4w(B_0)(V_E) constant value independent of the hall current. However I think that if we connect the electrode, the ions are eliminated by reduction and oxidation on the electrode surface. So the removing charge effect will decrease the e.m.f value.
So I want to know my guess is reasonable and way how to get the maximum power produced by the device.
Relevant answer
Answer
Power factor mainly depending on load ….
  • asked a question related to Ions
Question
2 answers
Dear all, I am looking for advice on plotting the trajectory of Li ions in a lithium-ion conductor. I have performed AIMD simulations (say for LiCoO2) in VASP and have found VMD could be a way to serve my purpose but I am unable to find steps to do it.
Please help.
Relevant answer
Answer
Hi..
I have made these two videos for VASP AIMD calculations. First video i have explined how to convert XDATCAR to .pdb file and next one I explained how to make movie from XDATCAR.pdb file. If you discover this information to be beneficial, kindly express your support by giving it a thumbs up, leaving a comment, and sharing it with others. We appreciate your viewership.
  1. How to Convert AIMD XDATCAR file into a pdb file using VASPKIT: https://youtu.be/zYopurMg0Ac?si=vgaAjQCxJ72_G6p3
  2. How to create a movie from XDATCAR file: https://youtu.be/x987ZKr5GB4?si=dFHf0Usq4wItNQ1q
Thank you
Best
SB
  • asked a question related to Ions
Question
2 answers
Dear All,
I am trying to simulate a dimer and would like to restrain a part of it on both chains. not a problem and the error is commonşy reported. so i tried all teh suggestions but none is working as grompp is accepting one of the posres files but throws the error for the other one. my toplogy file looks like this.
---------------
; Include chain topologies
#include "topol_Protein_chain_A.itp"
;; Include CRD Position restraint file for Chain A
#ifdef POSRES_CRD_A
#include "posre_crd_chain_A.itp"
#endif
#include "topol_Protein_chain_B.itp"
; Include CRD Position restraint file for Chain B
#ifdef POSRES_CRD_B
#include "posre_crd_chain_B.itp"
#endif
#include "topol_Ion_chain_A2.itp"
#include "topol_Ion_chain_B2.itp"
#include "topol_Protein_chain_A3.itp"
#include "topol_Protein_chain_B3.itp"
; Include water topology
#include "./charmm36-jul2022.ff/spce.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "./charmm36-jul2022.ff/ions.itp"
[ system ]
; Name
2 Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
Ion_chain_A2 1
Ion_chain_B2 1
Protein_chain_A3 1
Protein_chain_B3 1
SOL 111424
NA 48
--------------------
any suggestions are appreciated.
thank you
ayesha
Relevant answer
Answer
Dear Ayaz
Thank you for your answer. I was able to resolve the issue with the help from answers on GROMACS forum. the problem was in preparing the position restraint files using the original pdb files and using their atom indices.
Thank you so much for taking time to read my question
Best
Ayesha
  • asked a question related to Ions
Question
2 answers
Hai everyone....
I have a medium with added Na2CO3 for algal growth...after somedays algal cells will utilize the Carbonate for its growth...i need to find out how much carbonate ion is consumed by algae after 15 days of growth...Any one kindly tell me the titration procedure for this...
Relevant answer
Answer
Hi Divya, you'll most likely want to do a simple acid-base titration, using a standardized concentration of sulfuric acid (maybe starting in the range of 0.01 M H2SO4) and use a pH meter for the end point (can be 4.5 or down to 4.2 depending on composition of ions and expected alkalinity result. Results below 20 ppm CaCO3 usually would use an endpoint of 4.2). You can also use a dye as an indicator for pH endpoint, such as bromocresol green. You can find more information in Standard Methods for Water and Wastewater, "2320 Alkalinity". I would assume some of your carbonate would convert to bicarbonate with atmospheric CO2.
  • asked a question related to Ions
Question
2 answers
What do experts in HiPIMS sputtering think about a possible definition of HiPIMS? Definition: HiPIMS is a high-power density P-DCMS sputtering process with an amount of self-sputtering of target ions, where C < Ysetm/(Yseng+Yserg) < ∞, based on a critical ionization threshold of sputtered target atoms. To reach the critical threshold the -power density (current density multiplied by the discharge voltage) at the target within the pulse has to be about one order of magnitude higher than for conventional DCMS and P-DCMS. Yse secondary emission yields, tm means ions from the target material, ng noble gas, rg reactive gas. Classical (traditional) DCMS and P-DCMS are low-power density processes, gas-ion dominated discharges. If Ysetm is about 0 then target-materiel ionization is almost neglectable. If Ysetm/(Yseng+Yserg) goes to infinity, then self-sustained sputtering, SS-DCMS, a high-power density DCMS as a target-ion dominated discharge is ignited. C is a process and material specific value. C > 0 is describing the onset of LE-HiPIMS (low-energy HiPIMS). This C values have to be highlighted in future scientific investigations. Please study the model of A. Anders: Anders et al., J. Appl. Phys. 121, 171101 (2017). Thanks for your comments!
Take care.
J. Vetter
Relevant answer
Answer
Rajesh, yes indeed, it's a look at the classical pulsed process. However, it is possible to get target atom ionization also without pulsing? Yes its possible!
  • asked a question related to Ions
Question
2 answers
Hello,
I'm struggling to comprehend how the current measured in a double voltage clamp experiment corresponds to the entry of ammonium ions while investigating an ammonium transporter. Is the current primarily driven by ammonium ions, and would this current be absent without their presence? I'm seeking a clearer understanding of the origin of the current and how the transport of ammonium ions across the membrane via the transporter influences the observed current.
Thanks
Relevant answer
Answer
Dear Ahmed,
perhaps the following study, their references and publications that cite this study are helpful for your question:
Good luck.
Martijn
  • asked a question related to Ions
Question
2 answers
I would like to try chelate natrium ions from my medium.
Relevant answer
Answer
Hello Jürgen! Thank you for your answer. My point is, that I would like to lower osmolality for my experimental design, and chelating sodium seems like the best option for our experiment. I found for example sodium gluconate, which should work well probably. However have no experience with it yet.
  • asked a question related to Ions
Question
1 answer
Hello Scholars,
I am performing compositional analysis (using ICP-OES) of electroplated Nickel with mild steel (MS) as base substrate. I want to strip Nickel from MS without contaminating the solution with Fe ions. Nitric acid can not be used as it produces iron nitrate. What solution should I use to strip Nickel?
What are the methods to perform compositional analysis of electroplated metal other than ICP-OES and XRF?
Any thought on EDS?
Relevant answer
Answer
TXRF, or total reflection XRF technique, can be used for such a purpose.
  • asked a question related to Ions
Question
1 answer
hello everyone,
I am doing a VASP calculation, and I encounter the error code "Error EDDDAV: Call to ZHEGV failed. Returncode = 11 1 12". I do not know how to solve it. here is my INCAR file .
Global Parameters
ISTART = 0 # 0= initialize the orbitals,1 =if wavecar file exists 2 = continuation job/restart with constant basis set
ICHARG = 2
LREAL = .FALSE. # (Projection operators: automatic)
ENCUT = 520 #(Cut-off energy for plane wave basis set, in eV)
PREC = Accurate #(Precision level: Normal or Accurate, set Accurate when perform structure lattice relaxation calculation)
LWAVE = .FALSE. #(Write WAVECAR or not)
LCHARG = .TRUE. #(Write CHGCAR or not)
!Electronic Relaxation
ISMEAR = 2 #(Gaussian smearing, metals:1)
SIGMA = 0.2 #(Smearing value in eV, metals:0.2)
NELM = 90 #(Max electronic SCF steps)
NELMIN = 6 #(Min electronic SCF steps)
EDIFF = 1E-08 #(SCF energy convergence, in eV)
!Ionic Relaxation
NSW = 1000 #(Max ionic steps)
IBRION = 2 #(Algorithm: 0-MD, 1-Quasi-New, 2-CG)
ISIF = 3 #(Stress/relaxation: 2-Ions, 3-Shape/Ions/V, 4-Shape/Ions)
EDIFFG = -2E-02 #(Ionic convergence, eV/AA)
#ISYM = 0 #(Symmetry: 0=none, 2=GGA, 3=hybrids)
ISPIN = 2
Relevant answer
Answer
Honestly, this is a very, very common VASP error during a diagonalisation procedure, and there a lot of possible origin. First, have you checked your initial geometry to see if there's no issue (overlapping atoms for example)?
Then, a few notes:
- ISMEAR = 2 is not Gaussian, it's the second order Methfessel-Paxton smearing so be careful
- NELM = 90 is extremely low, you can safely put it at 1000 (or even beyond) to be sure that the electronic loop does converge before proceeding to the Ionic loop otherwise you are going to have weird results, especially considering the next note.
- EDIFF = 1E-08 is a very, very, strict energy convergence tolerance. Usually, the only cases where you would need such a value is for GW/CRPA calculations, which is not your case here. A value of 1e-5 (or 1e-6 in the worst cases) should be sufficient for this calculation. In fact, coupled with your very low NELM value, I'm pretty sure this could lead to spurious results.
- ISPIN = 2 without initializing MAGMOM leads to a ferromagnetic state initialization with +1 on each atom, which could lead to the error you see if the system has no such ground state.
  • asked a question related to Ions
Question
3 answers
when we using the energy of batteries During discharge these ion move back to the cathode through the electrolyte releasing. But when we are not using the li-ion slowly lose their charge how and why ?
Relevant answer
Answer
Hi dear friend
According to these conditions, the battery is self-discharged and this issue is related to factors such as: non-formation of the SEI film, high ambient temperature, poor packaging against moisture, side reactions of electrolyte and active materials, as well as conditions related to physical micro-short circuit.
If you explain a little more about the conditions of battery assembly, it will be possible to provide a better explanation.
  • asked a question related to Ions
Question
2 answers
In what solvent does ammonia exist as NH3 type rather than as NH4+ ions (Except under strongly alkaline aqueous conditions.)? What can be done to increase the nucleophilic attack of NH3?
Relevant answer
Answer
There was no ammonia removal in water without at least some NaCl in solution, suggesting that the device works by converting chloride ions into chlorine and hypochlorous acid, which then react with ammonia to form nitrogen gas.
In isolation, NH3 and HCl do not react to form the ionic salt, using anion photoelectron spectroscopy and ab initio theory found that an excess electron induces the hydrogen-bonded complex NH3···HCl to form the negative ion of ionic ammonium chloride, a deformed Rydberg radical, NH4, polarized by a chloride anion, Cl–.
  • asked a question related to Ions
Question
4 answers
Hello everyone,
I docked the inhibitor to the metalloenzyme and the next step was the minimization of the complex. Unfortunately, during the minimization protocol, I got the error as below:
>Solvent file: XXX\bin\Windows-x64\..\..\data\water.slv
>Block specifies desired NFIELD -- accepting block
>RDSOLV: missing params for atom number 36261 (type n2) in .slv file, solvation model 3
>MINI: Error generating interactions
>Problem in minimization of distinct structures.
>Skipping input structure due to forcefield interaction errors.
>BatchMin: normal termination
The atom number 36261 is the Nickel 2+ ion. I've tried to change for the one without charge, but still the OPLSe do not operate with it.
My question is about: how to add the nickel ions to the FF with proper parameters.
Thank you!
Michal
Relevant answer
Answer
Try with Schrodinger Q/A
  • asked a question related to Ions
Question
5 answers
As per the literature, NiO thin films can be etched in an RIE system using Cl2- based gas. Will there be any contamination issues if I use an RIE system dedicated to III-V group material (e.g.-GaN, GaAs)?
Any kind of suggestions would be a great help for my research work.
Thanks,
Relevant answer
Answer
Netaji Suvachintak thank you for the clarification.
  • asked a question related to Ions
Question
1 answer
To prepare lithium battery cathode precursor material by hydrothermal method, a certain amount of nickel, manganese and cobalt metal salt with precipitant was poured into the reactor, after the process, the amount of nickel in the precursor material was lower than the amount that entered the reactor , what is the reason?
Relevant answer
Answer
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 :
Here are some potential reasons why the amount of nickel in the hydrothermally synthesized lithium battery cathode precursor material could be lower than the initial amount added:
Nickel metal salt precipitation/insolubility during the hydrothermal process - The high temperature and pressure hydrothermal conditions could have caused some of the nickel salt to precipitate out of solution prematurely before being incorporated into the crystal structure. This precipitated nickel would not be included in the final product analysis.
Nickel salt adsorption onto reactor wall/surfaces - Hydrothermal reactions are often carried out in Teflon-lined stainless steel reactors. Some of the nickel ions could have adsorbed or adhered to these surfaces during the long reaction time, being removed from the final product.
Preferential crystallization of other metals over nickel - Depending on factors like temperature, pH, concentrations etc., it's possible the manganese and cobalt salts were preferentially incorporated into the crystal lattice over nickel during nucleation and growth stages. This could explain lower final nickel content.
Nickel leaching during washing/workup - Without proper control of pH during washing, a small amount of nickel ions may have leached or dissolved out of the precursor material crystals, leading to a lower overall nickel content after drying.
The final nickel content is lower than intended due to inadequately controlled reaction/washing parameters. Further optimization of temperature, time, concentrations, pH etc. would be needed to fully incorporate the stoichiometric nickel amount
  • asked a question related to Ions
Question
1 answer
We have been optimizing the method for determination of five (5) pesticides including 2 4-dichlorophenoxyacetic acid (221.04 g/mol), Metalaxyl (279.33 g/mol), Tebuconazole (307.82 g/mol), 4,4'-Dichlorodiphenyltrichloroethane (DDT) 354.48 g·mol−1, and Cypermethrin (416.3 g/mol) using the Agilent 1100 HPLC coupled with the Waters tandem Mass spectrometry with electrospray ionization. We are using masslynx software.
For Mass spectrometry we are using the cone voltage (v) range 10-30; Source temp 80°C; desolvation temp 150°C; desolvation gas flow 650 L/hr; cone gas flow 110 L/hr; and cappilary voltage 3.0 kv.
The stock standard solution was prepared in pure Acetonitrile. For direct infusion, the working standard solution was diluted in 90:10 (HPLC water: acetonitrile). We managed to get the precursor ion and daughter ions of Tebuconazole (308.23 ►56.4, 69.4, 124.7) and Metalaxyl (280.15 ►192, 220.1, 248.1) in positive mode. But for 2 4-dichlorophenoxyacetic acid, 4,4'-Dichlorodiphenyltrichloroethane, and Cypermethrin nothing was observed.
We tried to run LC for two pesticides using a gradient method with a mobile phase composition of HPLC water with 0.1% formic acid (A) and Acetonitrile (B). The gradient was 0.00 min (50% B); 10 min (90% B); 13 min (90% B); 13.10 min (50% B) and 15 min (50% B) at a flow rate of 0.25 mL/min and 400 Bar. The good separation was observed.
For the three pesticides, the literature suggests the use of ammonium acetate. We prepared 2 mM NH4CH2COO in water and used in dilution of the three standards. It worked on Cypermethrin (in positive mode 433.12 ►104.3, 186.6, 268.6) and 2 4-dichlorophenoxyacetic acid (in negative mode 223.02 ►58.4, 94.3, 140.9,) but for 4,4'-Dichlorodiphenyltrichloroethane the precipitate formed. However, we left it.
We tried to run LC using the same gradient method with a mobile phase composition of 2 mM NH4CH2COO HPLC water with 0.1% formic acid (A) and Acetonitrile (B) for all four pesticides. There were no separation observed.
Because the Cypermethrin and 2 4-dichlorophenoxyacetic acid work in the presence of ammonium acetate, we were forced to repeat optimization of Tebuconazole and Metalaxyl with the same dilution solvent. Unfortunately, we didn’t succeed.
We tried to change the cone voltage of 5, to 35 but still no any significant precursor ion observed for the two pesticides.
Please can you assist me on how to optimize it so that the LC method can accommodate all five pesticides?
Relevant answer
Answer
Hi Anna, maybe this application will be helpful to you: 06-ADC-F-03-EN Method for the determination of 346 Residual Pesticides in Milk using LCMS-8045 and GCMS-TQ8040 NX (shimadzu.com)
  • asked a question related to Ions
Question
3 answers
I want to perform MD Simulation of Ionic compounds in Gromacs but facing problems at various points.
One of my approaches of the work is submitting the pdb files of the cations and anions to ATB server to obtain the .itp files and Gromos 54a7.ff. I build the topology from these files.
I use packmol to pack 500 anions and cations pdb files in one box and then change them to .gro.
When I proceed to minimization with this .gro file and topolgy file, Gromacs prompt fatal error of mismatch of all the atoms in topology and .gro file.
I use charmm-gui to model the cation and anion with charmm forcefield in the topology but face the same problem.
Cgenff method as in protein-ligand complex simulation gave me broken cation_ini.pdb (since the number of atoms is correct I neglect this ) but when I proceed to combine the .gro files of the ions, like proten-ligand complex to get one structure file, they appear covalently bonded or scattered in the space which is not the correct chemistry of ionic compounds.
Ligpargen, Polypargen, Acpype, and TppMkTOP servers returns error whenever I submit either of the ions to get the topology file from them.
When I use AmberTools23, I got error at the step of packing the ions together and saving the prmtop and rst7/inpcrd files of the system.
I do appreciate your patience and guiding replies.
Relevant answer
Answer
You can ask always your questions in the GROMACS forum and get your answer directly from gmx experts: https://gromacs.bioexcel.eu/
  • asked a question related to Ions
Question
2 answers
Solid state electrical conductivity.
Relevant answer
Answer
I feel like the question is quite vague. Which metal complex, with which other metal complex? Or what class of complexes with what other class of complexes? It's not at all clear if you are referring to metalation, substitution, doping, counterions, auxilary ligands or what?
The way the question reads you have a metal complex and you are unhappy with it's solid state properties. So make another, and test it's properties. Or specify in more detail what it is that you are trying to accomplish.
  • asked a question related to Ions
Question
1 answer
when we do DFT calculations for Li ion battery in ATK, then li ions or li atoms are intercalated???
Relevant answer
Answer
Hey there, Sunita Saharan researcher friend! I am here to assist you.
In Atomistic Tool Kit (ATK), which is a popular software for performing Density Functional Theory (DFT) calculations, you generally work with ions rather than isolated atoms. When simulating a lithium-ion battery, you are typically interested in the behavior of lithium ions, not just isolated lithium atoms.
To set up your simulation in ATK for a lithium-ion battery, you would typically create a supercell that includes the lithium ions within a crystal lattice structure (e.g., a cathode material). This allows you to study the behavior of lithium ions as they move in and out of the host material during charging and discharging cycles, simulating the electrochemical processes in a battery.
So, in ATK, you would work with lithium ions that are part of a larger structure, and you can model their movement and interactions with other components of the battery, such as the anode and electrolyte.
To convert lithium atoms to lithium ions within your simulation, you can use appropriate charge states and boundary conditions that mimic the electrochemical environment of a battery.
Remember that ATK provides a versatile platform for modeling complex materials and systems, and you can customize your simulation settings to suit your specific research needs in the realm of lithium-ion batteries. Good luck with your research!
  • asked a question related to Ions
Question
3 answers
I have hydrolyzed my protein in 5 ml of 6N HCL and diluted the hydrolysate in 100 ml. Now, i have to run my sample on LC-MS. Therefore, i have to remove Cl ion from my samples before injecting it in LC-Ms. If i remove HCL through vacuum dryer then do i get rid off from HCL completely with no chlorine ion in residues?
or any other suggestion for running the samples in LC-MS hydrolyzed with 6N HCL?
Relevant answer
Answer
Assuming the analysis target here is amino acids, after hydrolysis to get rid of Cl and other interferences, it is advisable to perform a cation exchange treatment. Protonated amino acids will retain on resin while most of the neutral and anionic species flow through. After elution, you can analyze AAs either by HILIC or derivatization followed by RP chromatography...chloride removal by forming CuCl, AgCl, BiOCl, and Friedel's salt (complexation-induced precipitation) is an alternative strategy but not necessary for this case...
  • asked a question related to Ions
Question
8 answers
Hello,
I am not familiar with different analysis modes of mass spectrometry so I seek your help.
I wish to understand the difference between DIA and DDA analysis.
I understand that DDA searches the top N number of the highest-intensity precursor ion peaks to go through MSMS, then after a certain amount of time, it selects the next N number of peaks and so on.
I also know that DIA is not top N but rather chooses an isolation window and fragments EVERY ion in that window.
Heres my question, if DDA keeps selecting top N and the next and the next, doesn't that also mean that eventually every ion will be fragmented? like DIA? am I completely missing something?
To me this sounds like tomato tomato so I appreciate all the help I can get
Thanks
Andrew
Relevant answer
Answer
Hi Andrew,
Your basic assumptions are first of all correct. However, there are some further details to consider. For DIA the preset of precuser ions applies, here also the minimum intensity and the fragmentation energy must be preset. This form of acquisition is usually very selective, only the given masses are fragmented. If additional peaks occur, they may not be seen or they will not be fragmented, because the system has no parameters. With the DDA all masses are fragmented, which correspond to given parameters. These are mainly the intensity of the peak, by which the user can specify how small the signal may be. The fragmentation energy is then used to generate the fragmentation. Usually a dynamic exclusion is then used. First the most intense mass is fragmented, then excluded, so the next mass becomes the most intense mass and fragmented and so on until the last signal is smaller than the specified intensity. This fragmentation ends with that. After a predefined time n the excluded masses are removed from the exclusion list again, because at a later time a further PEAK with this mass can occur, which means however another compound and in order to ensure that then also MS-MS spectra is messured. This dynamic exclusion also prevents that only the most intense mass is selected and thus no MS-MS spectra of the other masses are measured.
Many greetings
Joachim Horst
  • asked a question related to Ions
Question
1 answer
I have an idea that explains consciousness. About 8 years ago, Professor Donald Hoffman asked a very important question to help us understand consciousness. He asked, "How is it possible for calcium and potassium ions that enter and exit through neuronal membranes to give rise to our conscious experience of, for example, the color green, or a smell, or a sound?"
So, my idea that answers this question is that the color green, for example, has a specific frequency associated with it, and the same goes for the color red or any other stimuli around us. When these frequencies enter the brain, they can be considered as inputs.
The frequency of the color green,
for example, has a specific code or pattern in the brain. This code represents the way that nerve cells communicate with each other through the exchange of calcium and potassium ions across neuronal membranes.
We can call this process that occurs in the brain "processing," and the brain, because it translates these frequencies, can be thought of as a compiler in a computer.
A compiler takes human-readable code and converts it into machine-readable code, known as machine language.
Then, somehow, our conscious experience of the color green emerges.
We can consider the formation of conscious experiences as outputs.
To me, this topic feels similar to programming. In programming, we have outputs, compilers, processing, and inputs. So, could it be possible that the brain is programmed to understand all these frequencies, decode their patterns, and create consciousness? I'm not saying that we are
programmers, but rather, it's the brain itself.
What I'm trying to say is that everything in the universe has its own frequency and its own specific code.
The brain decodes these codes through the electrical activity that occurs with the entry and exit of ions across neuronal membranes, and then consciousness is formed.
Is it possible that this could be true?
"I believe that we can prove this through experiments on animals."
Relevant answer
Answer
Hi,
Yes, it's possible that your theory might have elements of truth. Nonetheless, the real validation would come through rigorous experimentation, as you've proposed, using animals to discern if there's a consistent correlation between specific external frequencies and resultant neural patterns contributing to consciousness. However, based on current scientific understanding, your theory would require substantial empirical evidence to gain wide acceptance.
Hope this helps.
  • asked a question related to Ions
Question
6 answers
both are gives same optical properties or not ?
Relevant answer
Answer
metal ion is a type of atom compound that has an electric charge. Such atoms loose electron(s) very easily to form cations.The metal ions can be formed by any of the metals in the Periodic Table. The rare earth ions consists of ions of the lanthanide series.
  • asked a question related to Ions
Question
1 answer
Water purification
Relevant answer
Answer
Yes, Schiff bases can be utilized for the removal of heavy metal ions from water due to their chelating properties. A Schiff base is a compound formed by the condensation of an aldehyde or ketone with a primary amine. Schiff bases have functional groups that can bind with metal ions, forming stable complexes. This ability to form complexes makes Schiff bases suitable for various applications, including heavy metal ion removal.
Here's a general approach on how Schiff bases can be used for heavy metal ion removal from water:
  1. Synthesis of Schiff Base Ligands: Schiff base ligands can be synthesized by reacting aldehydes or ketones with primary amines. These ligands can be designed to have specific functional groups that exhibit high affinity for binding metal ions.
  2. Complexation with Metal Ions: Once synthesized, the Schiff base ligands are introduced into the water containing heavy metal ions. The functional groups on the Schiff bases can coordinate with the metal ions, forming complexes through chelation. This leads to the removal of metal ions from the water.
  3. Adsorption or Precipitation: The formed metal-Schiff base complexes can either adsorb onto surfaces or precipitate out of solution, depending on the specific properties of the complex. This process effectively removes the metal ions from the water.
  4. Filtration or Separation: The water is then subjected to filtration or separation processes to remove the formed complexes, which may be in the form of solid precipitates or attached to adsorbent materials.
  5. Regeneration: In some cases, the metal-Schiff base complexes can be regenerated for further use. This might involve changing the pH or using appropriate chemical treatments to break the metal-ligand bonds and release the metal ions.
It's important to note that while Schiff bases can be effective in heavy metal ion removal, the practical application can depend on factors such as the type of metal ions present, the specific ligand used, pH conditions, and the concentration of metal ions in the water. Additionally, the stability and reusability of the Schiff base complexes, as well as any potential environmental impact of the removal process, need to be considered.
Research in this area is ongoing, and scientists are continually exploring and optimizing the use of Schiff bases and other chelating agents for heavy metal ion removal from water to address environmental pollution and water quality issues.
  • asked a question related to Ions
Question
4 answers
Hi everyone
I have a problem with Histag protein purification. I have this construct with his tag on N-terminal. I went for small-scale expression and I had some good bands. However, on a large scale, the protein didn't bind with the HiTrap TALON cobalt. My protein contains an Mg2+ ion coordinated by the side chains of Asp, His. How to overcome this metal ion issue, or Should I change the column to a Ni-Trap?
I appreciate your help
Relevant answer
Answer
I doubt the Mg2+ in the active site is relevant here. Do you have any chelators or metal ions in the sample before it goes onto the column? When you say the protein does not bind, do you really mean it doesn’t bind or are you saying you didn’t manage to elute anything? I think it’s important to know whether you have a binding or elution issue. Either way you’ll end up with no protein. Do you have confirmation of successful expression on SDS gels?
  • asked a question related to Ions
Question
1 answer
Hello all - I am new to learning MS and don't have a lot of guidance. I am having a really hard time finding information on what criteria is used to choose the optimal CE for an MRM transition. I have found multiple resources online showing how to do edit ramp functions in my software (Analyst) to obtain an "optimal" CE, but it doesn't explain why that CE was chosen as optimal, so I have no way of knowing for sure that the function worked correctly and that I am choosing the best CE. I have been looking up and down, left and right and cannot get a clear answer. I've also asked multiple people who have all told me different things. I've been told to choose a CE where the parent and daughter ion are about the same intensity; I've been told to choose a CE where the parent ion is 20% the intensity of the daughter ion, and so on. If someone could tell me how they choose their optimal CE I would really appreciate it.
Relevant answer
Answer
Hello Grace - The usual approach is to choose the CE that gives the highest abundance for maximum sensitivity. With Analyst you can either do this manually by doing a ramp of the CE on the MRM transition or you can use the Compound Optimization app to do this automatically. Don't forget that the CE is only 1 parameter that needs to be optimised. For best sensitivity and repeatability you need to optimise everything including the source parameters.
  • asked a question related to Ions
Question
2 answers
what are differences between mechanism of heavy metal ions adsorption on activated carbon and mechanism of ion adsorption on volatege connected types of carbon electrodes?
Electrical field or functional group? Which factor really acts?
may a supercapacitor electrode without voltage absorbe ions?
Valence of ions are effective?
Relevant answer
Answer
@yuri_morgorod
Thank you professor
  • asked a question related to Ions
Question
3 answers
Recently, I looking for the information about graphene oxide (GO) especially the common problem or disadvantages when applied ion the membrane. Why GO is more special in some researchers so used as nanoparticle or catalyst in membrane modification. I am sure if every material have a weaknesses. So anyone please tell me. Give me some references to my email: [email protected]
Relevant answer
Answer
Graphene oxide (GO ) is a promising hydrophilic nanoparticle that has been successfully investigated in membranes to improve polymers' mechanical, electrical, thermal, and chemical properties. However, some of the identified limitations of GO in membrane applications include:
1. Challenges of attaining their cost-efficient and scalable manufacturing process: https://doi.org/10.1016/j.envint.2019.03.029
2. High water solubility hence prone to solubility (leaching): https://doi.org/10.1016/j.envint.2019.03.029 and https://doi.org/10.1039/C7CP02303K
3. Highly susceptible to agglomeration within polymer: https://doi.org/10.1016/j.surfin.2023.102747
  • asked a question related to Ions
Question
1 answer
I heard that the electronic structure of the precursor is changed and the valence state difference occurs due to metal ion doping, so I wonder how this improves structural stability.
Relevant answer
Answer
Dear Hyowon Jang.
I think it is a principal of least action known from mechanics.
If we assume that space is discrete on fundamental level and consists of action quanta h (recall the formula for the photon energy ε=hν), and the outer electrons in an atom distort the surrounding space the most, then there will be nothing surprising in the fact that the valence electrons of neighboring atoms combine to distort the surrounding space together in a minimal way. This enhances the interaction of atoms with each other, makes the crystalline structure of the substance more ordered and strong.
You can better understand what was said if you get acquainted with my last year's report on how the thermal expansion of the elements of the periodic table in the solid state occurs and depends on:
Yours sincerely, Dulin Mikhail.
  • asked a question related to Ions
Question
2 answers
What easy methods are availablefor coating of active materials like WS2 on Cu foil used in Li-Ion batteris ?
Relevant answer
Answer
Typically, we use the slurry casting method. Please refer to any publication in my profile for more information
  • asked a question related to Ions
Question
4 answers
Hello, I am trying to quantify some very low abundance peptides and need to squeeze every last bit of sensitivity out of my instrument (Waters Xevo tq-s). Is it possible to collect SRM data and then combine the signal from multiple product ions? Would this actually lead to a useful increase in sensitivity? Thank you for your help
Relevant answer
Answer
As noted by Taban, using 'MRM' mode accomplishes this and maintains selectivity (which TIC may not). Additionally, time should be spend OPTIMIZING the HPLC analysis method, detector settings (gas flow, temp, voltages etc), reducing the use of any additives which may contribute to higher background noise signals, cleaning and servicing the instruments.
  • Improvements to S/N translate to improvements to sensitivity. Never rely on "area" or "ion" counts alone. You must measure S/N for each peak (sample) to determine detection levels.
  • asked a question related to Ions
Question
3 answers
Hi Everyone
I need to improve the solubility of Potassium Humates in hard water. Generally, potassium humates are soluble in hard water but within a few minutes, it has precipitated due to the complexation of humates with Ca & Mg ions. Can anyone help me to avoid this precipitation or sedimentation?
Relevant answer
Answer
I suggest doing the dilution little by little under agitation and heating and doing a treatment to reduce the hard water salts. You could decalcify using ion exchange resins to capture calcium and magnesium from hard water.
  • asked a question related to Ions
Question
1 answer
  • I want to make a unit cell of NiO. We know that NiO is an antiferromagnetic material meaning the magnetic moments of the neighbouring Ni ions align in an alternating manner (one spin up and then down). So what should be the coordinates of the Ni and O ions, so that if I want to make a unit cell/supercell, the program can understand the location of spin up and down of Ni and the non-magnetic ion O?
Relevant answer
Answer
Can you specify the editor / package you are using?
If you generate input for a quantum chemistry package, all you have are the positions of the atom nuclei forming an NaCl structure in this case, while the electrons don't know yet where they are and what spin they will get. If you run the program with a suitable method for magnetic properties (which means that basic DFT might not be enough), the electron distribution and spin densities should come out correctly after the calculation.
  • asked a question related to Ions
Question
1 answer
I am starting research about zinc ion batteries and looking for standard commercial material for zinc-ion battery cathode, but I can't find any publication about commercial material of MnO2 as cathode zinc-ion batteries. Do you have any suggestions or papers about other cathode materials for zinc-ion batteries? (using commercial vanadium or PBA).
Relevant answer
Answer
Some of the cathode materials that have shown promise in research studies include:
  1. Manganese dioxide (MnO2): MnO2 has been investigated as a cathode material for zinc-ion batteries. It has good electrochemical properties and a high theoretical capacity, making it a potential candidate.
  2. Prussian blue analogs (PBAs): PBAs, such as Prussian blue (Fe4[Fe(CN)6]3) and its derivatives, have been explored for zinc-ion battery cathodes. PBAs offer advantages such as good electrochemical stability, high capacity, and the ability to reversibly intercalate zinc ions.
  3. Vanadium oxide (V2O5): V2O5 has been studied as a cathode material for zinc-ion batteries. It exhibits high capacity and good electrochemical performance, making it a potential candidate.
  • asked a question related to Ions
Question
2 answers
I am having trouble understanding calcium ion fatigue,, I always have seen papers go over the idea that it's the sodium ions that inhibit calcium ion release which would then limit the muscle to contract. I have been seeing some people write about calcium ion fatigue and how an excessive amount of calcium ions can cause higher muscle damage and this occurs through higher rep training as well as training a muscle at longer lengths because the stretch activated ion channel will open allowing calcium ions to flow in. I am confused in the sense if all that is true or if the idea of fatigue is more complicated?
Relevant answer
Answer
The concept of calcium ion fatigue and muscle fatigue, in general, can be complex and multifactorial. While the involvement of calcium ions in muscle contraction and relaxation is well established, the exact mechanisms underlying muscle fatigue are still an area of active research. I'll try to provide some insights into the topic:
  1. Role of Calcium Ions in Muscle Contraction: Calcium ions play a crucial role in initiating muscle contraction. When a muscle is stimulated, an action potential triggers the release of calcium ions from the sarcoplasmic reticulum (a specialized structure within muscle cells). These calcium ions bind to troponin, leading to a conformational change that allows the interaction between actin and myosin filaments, resulting in muscle contraction.
  2. Sodium Ions and Calcium Ion Release: The role of sodium ions in inhibiting calcium ion release you mentioned is related to the process of muscle relaxation. After muscle contraction, the sarcoplasmic reticulum actively pumps calcium ions back into its storage sites. This process requires energy, and sodium ions play a role in maintaining the electrochemical gradient necessary for calcium ion uptake. If the concentration of sodium ions is disrupted (e.g., due to excessive muscle activity or fatigue), it can impair the ability of the sarcoplasmic reticulum to take up calcium ions, affecting muscle relaxation.
  3. Calcium Ion Fatigue: Excessive calcium ion influx into the muscle cell can lead to various detrimental effects, potentially contributing to muscle fatigue. It is suggested that elevated levels of calcium ions can activate enzymes called proteases, which can degrade proteins within the muscle cell, leading to muscle damage. Additionally, high calcium ion levels may also impair the muscle's ability to generate force efficiently, affecting muscle performance during contraction.
  4. Stretch-Activated Ion Channels: Stretch-activated ion channels are a group of ion channels that respond to mechanical stress or stretching of the muscle cell membrane. These channels can allow calcium ions to enter the cell when the muscle is stretched or under tension. It has been proposed that during eccentric (lengthening) contractions or exercises performed at longer muscle lengths, the activation of stretch-activated ion channels may lead to an increased influx of calcium ions, potentially contributing to muscle damage and fatigue.
It is important to note that muscle fatigue is a complex phenomenon influenced by various factors, including metabolic processes, energy depletion, accumulation of metabolites (e.g., lactate), neural factors, and others. The interplay between these factors and the specific mechanisms involved in muscle fatigue are still being investigated.
To gain a more comprehensive understanding of muscle fatigue and the role of calcium ions, it is recommended to refer to scientific literature and research papers in the field of muscle physiology and exercise science. These studies provide detailed insights into the mechanisms of muscle fatigue and the role of calcium ions in muscle function and fatigue.
  • asked a question related to Ions
Question
2 answers
There are plenty of analytical techniques in measuring these analyte. I want to know which works best in terms of accuracy, ease of use, and turnaround time.
Relevant answer
Answer
ion selective electrode for electrolyte and ion chromatography for inorganic ions
  • asked a question related to Ions
Question
2 answers
I am analyzing UPLC-MS data, where I don't have standards and performing a non-target screening of small-molecule compounds. How can I convert the mass ion intensity which is in percentage to ppm or ppb?
Relevant answer
Answer
You can not do so, that would be unscientific.
LC-MS analysis is not a "universal" detection method and/or analytical technique. - - LC-MS analysis is far more complex a technique than you realize. A proper method of LC-MS (or LC-MS/MS) analysis with a full set of standards (calibration tables for each compound) would be needed to make any type qualitative statements about possible concentrations present (to express in units, such as ppm). "Mass ion intensity" is only an arbitrary signal intensity, as depending on: the HPLC method used, solution chemistry, detector type and settings, operator's experience, instrument type and IF the compound(s) present will or will not ionize under the analysis conditions selected etc, the signal values obtained will be different.
  • asked a question related to Ions
Question
3 answers
Hi, I'm going to study the binding affinity of my protein with calcium ions. I'm looking for a buffer that can control the pH around 8.5 or more. I heard that Tris is not really good for ITC so I'm looking for another buffer that can control pH at 8.5 or more. May I have some advice on this? Thank you in advance.
  • asked a question related to Ions
Question
2 answers
like Pb(NO3)2
Relevant answer
Answer
Without additional additives, solid Pb(OH)2 will form, that's just determined by thermodynamics. Therefore, you have to introduce an additional equilibrium in order to counteract the precipitation. Chelate complexes, e.g. with EDTA, would be the first idea, but of course you will have EDTA in your solution in that case.
  • asked a question related to Ions
Question
1 answer
Dear researchers
I am working on the activated carbon, which synthesized by sulfuric acid impregnation. From EDS , 3% sulfur content attached to the AC. I studied the this material for Pb2+ uptake, and it can remove up to 100 mg/L initial concentration of lead solution. But, when studied, the selectivity by mixing Pb 2+ with Mg2+. Cu2+ and Zn2+ the material was not selective. May I know the reason.
Here is the supporting data related to the coexisting ions :
Ion Ionic radius Type of acid
Cu2+ 73 Borderline
Mg2+ 79 Hard
Pb2+ 119 borderline
Zn2+ 74 borderline
Thank you all. :)
Relevant answer
Answer
If the sulfate or sulfonate anion is the active site on carbon treated by H2SO4, these anions would prefer hard cations. This may be an over simplification, but you suggest that line of reasoning by giving the HASB class of cations.
  • asked a question related to Ions
Question
4 answers
Dear colleagues
we are working with ISFET measurement technology to detect NO3-, H2PO4 and K+ as well as pH.
I am looking for a comprehensive publication with the subject: conditioning of ion sensitive ISFET. So, how is the ionophore optimally conditioned or made sensitive to the corresponding ion. Is there any indication for different approach when different concentrations are to be analyzed?
Who has researched different conditioning procedures and published the results?
Many thanks and best regards from Osnabrück / Germany, Stefan
Relevant answer
Answer
Hello Stefan,
I wanted to share with you that we are using ion-selective electrodes from Van London, available at http://www.vl-pc.com/default/index.cfm/ion-selective/laboratory/ise-potassium/. According to the data sheets provided by Van London, they recommend immersing the electrode in deionized water for thirty minutes prior to its first usage or after long-term storage. Once this procedure is followed, the electrode is ready for use. We have been using this procedure and it has been successful for us.
In most cases, the ionophore used in ion-selective electrodes is similar to the ISFET ionophore. However, it's worth noting that different sensor providers may have their own conditioning recommendations. For example, Hach sensors suggest conditioning the sensors in a low concentration solution, typically around 10ppm, for a duration of 10-30 minutes(https://support.hach.com/myhach/s/article/KA-en-US-TE6932-1009127?language=en_US).
Please feel free to contact me if you have any additional questions
Best Regards, Mohamed
  • asked a question related to Ions
Question
4 answers
I have tried using Autodock to dock the Tio2 complex to a protein. However, a few of the web-based properties of this metal ion need to be validated. The computer algorithm identifies it as a carbon atom in the final findings.
Zn paratmeter: Non-H-bonding Zinc for the ZN atom_par 1.48 0.550 1.7000 -0.00110 0.0 0.0 0 -1 -1 4 #
Likewise, I need the parameter for Tio2. Kindly help me to solve this issue.
Thank you in advance!
Relevant answer
Answer
Thank you for the insightful remarks and suggestions. In this project, we investigate anatase titanium dioxide.
  • asked a question related to Ions
Question
3 answers
Calcium is a metal ion and am getting difficulty in molecular docking calcium ion with protein. Most of the docking tools are not able to process metal ion as ligand.
Relevant answer
Answer
This is a experience I would share; you can simply find a pdb file from a database which has a calcium ion and copy-past its atom types and coordinates into your pdf file. However, the ion may not be resides within the appropriate site within the protein. For fixing such complication you can manually change x y z coordination by changing 1.000, 2.000, and 3.000 values in the following line of CA structure in a pdb file;
HETATM 1 CA CAL A 1 1.000 2.000 3.000 1.00 0.00 CA
For docking you may use DOCK Blaster server, but bling docking dose not determine the correct binding site.
  • asked a question related to Ions
Question
4 answers
Which water is in a state of downward movement in the gravity and type of stream load comes from groundwater seepage and ions are in solution?
Relevant answer
Answer
Stream load is composed of dissolved or solution load, suspended load, and bed load. The dissolved load comes primarily from groundwater seepage into the stream. Ions in solution also come from the solution of materials that line the channel. The majority of a stream's sediment load is carried in solution or in suspension. The remainder is the bed load. Earth material that has been dissolved into ions and carried in solution is the dissolved load. Flowing streams pick up and transport weathered materials by eroding sediments from their banks. Streams also carry ions and ionic compounds that dissolve easily in the water. Sediments are carried as the following loads: dissolved, suspended, and bed. A dissolved load is composed of ions in solution. The suspended load is the fine‐grained sediment that remains in the water during transportation. As flooding river is muddy and discolored from the large amounts of sediment suspended in the water. Gravity and pressure move water downward and sideways underground through spaces between rocks.
  • asked a question related to Ions
Question
2 answers
Hi
I am using Gromacs 2018 version. I ran the MD simulation for 400 ns at 300K (I didn't change the classic tutorial md.mdp except for nstep). While watching the .xtc file, I noticed that the water molecules were coming out of the simulation box, but I ignored it (image 1 is the figure I saw in frame 0, while image two further frames). I thought it wouldn't be a problem because of PBC, but I still couldn't understand why it was like this. What surprised me was that at 400 ns, there were no ions left in the unit cell and ions were visible outside the unit cell. According to PBC, if an ion was leaving the unit cell (it must have left since I saw ions around it), wouldn't the ions have to come back in to balance the number of molecules inside? It's as if there are no ions in my unit cell but there are ions in the display cells. How is this interpreted? Any idea what is the problem?
Relevant answer
Answer
Try the trajconv (gromacs knife) for centring the macromolecule and then analyze for RMSD and RMSF for molecule of interest i.e. protein or ligand.
I hope that might work for you.
  • asked a question related to Ions
Question
1 answer
I am trying to dock a ligand to an active site with a metal ion. The docking is successful but there are no bonds to the metal ion and the metal ion is not shown in the ligand interaction diagram.
The problem is when my supervisor runs the same ligand with the same protein, he is getting bonds to the metal ion and the metal ion shows up in the ligand interaction diagram.
I believe it's due to some settings like excluding metal ions in some setting but cannot figure out what. Any insight into this is highly appreciated.
Relevant answer
Answer
Glide is a popular molecular docking program used to predict the binding mode and affinity of ligands with a protein target. However, its default settings and scoring functions are primarily designed for small organic molecules and may not explicitly account for metal ions.
First, we should know that metal ions have a unique coordination geometries and bonding characteristics compared to organic ligands. Their interactions with proteins involve coordination bonds and electrostatic interactions, which requires specialized treatment in docking algorithms.
Secondly, if glide algorithm was used. In some cases, the Glide docking approach may not adequately model the binding of metal ions due to limitations in the force fields or scoring functions used. These computational methods are typically optimized for organic ligands and may not accurately capture the metal-ligand interactions. Consequently, the docking program may fail to recognize or inaccurately consider the presence of metal ions during the docking process, leading to potential errors in the subsequent visualization and analysis of ligand-metal interactions.
Addressing this issues, specialized docking programs or modified protocols can be employed that are specifically designed to handle metal-ligand interactions. These programs may utilize for instance custom force fields, scoring functions, and algorithms build to accurately model the coordination chemistry of metal ions.
You may want to explore Auto-Dock, MOE or GOLD. I hope this would help!!!!!!!!!!!
  • asked a question related to Ions
Question
3 answers
For example why Tricine - Tris gives better resolution than Glycine - Tris in this papper?
I know it is related to the ion fronts but I don't truly understand why that changes the resolution of the assay.
Thanks for your help.
Relevant answer
Answer
In gel electrophoresis, the choice of buffer can significantly influence the resolution of proteins on the gel. The buffer composition affects several factors, such as pH, conductivity, and buffering capacity, which in turn impact the movement and separation of proteins during electrophoresis.
In the paper you mentioned, the comparison between Tricine-Tris and Glycine-Tris buffers highlights the differences in resolution. Tricine is a zwitterionic buffer with a lower pKa value compared to glycine. Here are a few factors that contribute to the improved resolution with Tricine-Tris compared to Glycine-Tris:
  1. pH Range: The choice of buffer affects the pH range over which the electrophoresis is performed. Tricine has a lower pKa (around pH 8.2) compared to glycine (around pH 9.6). This means that at a given pH, Tricine has a better buffering capacity and can maintain a stable pH throughout the electrophoresis process. This stability helps to separate proteins with better resolution.
  2. Stacking and Resolution: Tricine buffer has a lower conductivity compared to glycine buffer. This lower conductivity reduces the magnitude of ion fronts formed during electrophoresis, resulting in improved stacking of proteins at the sample application site. Enhanced stacking concentrates the proteins into narrow, well-defined bands, leading to better resolution during separation.
  3. Buffer Composition: Tricine buffer contains a different counterion compared to glycine buffer. Tricine uses bis-tris propane as a counterion, while glycine uses sodium hydroxide. The counterions can affect the migration of proteins due to their charge and ionic interactions. The specific interactions of Tricine with proteins might facilitate better resolution in certain cases.
These video playlists might be helpful to you:
  • asked a question related to Ions
Question
2 answers
I need to purify a metalloprotein in its apo form. During heterologous expression of protein, there are chances that the protein binds to metal ions from E coli. How can I get recombinant protein from E. coli without the metal?
Relevant answer
Answer
in general is it difficult to predict if a metallo protein will be produced in metallated state or not, since it depends from many factors as its metal specificity and affiinity, its expression level, the media composition and the purification protocol, since for example if you are using IMAC, it is also possible that the protein during the elution step will strip some metal from the coloumn.
in general while, if you would like to produce fully metallated protein, media supplementation with metal could be a possible solution, if the metal is not structural and your can remove it with-out induce protein unfolding, aggregation and precipitation, you can try to prepare the apo form by incubating the purified protein with a metal chelant (eg EDTA for bipositive metals as zinc, nickel, copper, BCS for monopositive metal as Cu+) and subsequentelly remove the complexed metal with a buffer exchange (by desalting of dialisys) in a metal free buffer.
In some cases if the affinity of the protein for the metal is high, reduction of pH could to protonate binding residues could be necessary to obtain the apo form.
In the past i applied the following protocol:
O/N incubation in 50 mM sodium acetate, 20 mM EDTA, pH 5.0, at 4°C, followed by protein concentration by ultrafiltration and buffer excnahge by desalting with PD10 coloumn in metal -free Tris20mM, NaCl150mM pH=8 buffer) for the production of the 2 following Zn binding protein
- apo Zmp1 ( ) a bacterial metallo protease
N.B To be sure that you buffer is metal free, you can pass it though a metal chelating coloumn (eg chelex) or you can just add to it low EDTA (or a different chelant) concentration, if it do not affect your downtream applications.
Of course this approach work only if your protein is stable in the apo-form.
The first time, I suggest to you to perfom the metal depletion at low concentrations (max 10-20uM) so you will minimize possible aggregation propensityi in case the lost of the metal expose some hydrofobic regions.
good luck
Manuele
  • asked a question related to Ions
Question
1 answer
There is no clear explanation for the formation of triiodide anion from the reaction of iodine molecule with iodide ion.
Relevant answer
Answer
In the simplest FMO/NBO approximation, you just have three pz orbitals as depicted here:
Of course, there will also be some interaction between the px and py orbitals, but pi bonds as known for L-shell elements aren't formed for elements in the lower periods.