Science topic

Hydrogen Bonding - Science topic

A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.
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Water is an important component that affects the properties of DES. The addition of appropriate amount of water can effectively reduce the viscosity of DES, however, the addition of excessive water may destroy the hydrogen bond system of DES. So, I would like to know how to detect whether DES is still DES in the process of adding water to DES, or is converted into an aqueous solution. Thank you!
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My understanding is that the exact definition of "proper" DES's is still in flux. However, even when formulated with a significant concentration of water they typically have very low water activity compared to what you would expect for an ideal solution (negative Raoult law deviation). But not everyone is fond of measuring vapor pressures.
One alternate technique that should give you an idea about the state of hydrogen bonding is density measurements of a series of DES solutions containing an increasing % of water. You need one or two pycnometers. Plot the difference between the actual results and the "ideal" density - what you expect for a weighted average of the "two" components (DES and water). Large positive numbers suggest stronger hydrogen bonding than for the separate components. Then you can verify it with FTIR etc.
But the main question is compatibility with your DES applications. Sometimes (like in some electrochemical processes) water has to be rigorously excluded. At other times (like for dissolution of polar organics) a certain amount of water is acceptable or even desirable.
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Hello,
I am running a VMD simulation and using VMD software to analyze hydrogen bonds, but I want to study electrostatic interaction. I would like to have a graph number of bonds through time. I don't know if I'm in the right place to ask, but would you know how to obtain this graph for the electrostatic bond? I tried to find answers on the internet but couldn't find any.
Thank you so much for your help.
Alix
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Hi Alix! I suspect that you use a trajectory from another MD engine to analyze with VMD, right? Because VMD is mainly a visualization tool. So if you want to analyze electrostatics with PME then you have to open Extensions-> Analysis and there you find PME electrostatics. In the same section you may find hydrogen bonds analysis. If you want to know if two particles with positive and negative charges can associate with each other then you might need to compute RDFs between chosen pairs of atoms. Otherwise, for looking for bonds I would probably suggest you to use another tool for analyzing your trajectory or to write your own customized.
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Hello everyone,
I tried to dock a ligand to a molecule using AutoDock software with a blind docking method. My ligand is an under-investigated small-drug molecule and the protein interactions of the ligand is not known. From my docking results the binding energy for the molecules I investigated was found as -5.78, however there was no hydrogen bonds formed between these molecules. Can I assume that these molecules are docked or how can I check the reason why hydrogen bonds weren't formed?
Additionally, is there any way anyone can recommend to screen the proteins interacted with a ligand whose proteins interactions weren't studied?
Sorry for the inconvenience,
Thanks in advance.
Mervenur
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Hi mervenur
Please paste the coordination of the best pose of docked molecule to the pdb structure of protein (without water molecules) and open it BIOVA discovey studio Visualizer. It can be downloaded from following address:
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Polymer Flooding
1. For a reservoir with formation damage, if we go ahead with polymer flooding, won’t the polymer molecules get blocked – particularly – by the smaller pore sizes?
2. If the polymer molecules get blocked in smaller pore sizes, where and when will it happen from the injection well or the core-inlet?
3. If the polymer molecules get blocked in smaller pore sizes, to what extent, further transportation of polymer molecules – into the reservoir – horizontally – away from the injection well – gets influenced?
4. If the polymer molecules get blocked in smaller pore sizes, to what extent, polymer molecules get dispersed and diffused (on top of its expected advective transport) as a function of pore-sizes – during its transportation – away from the injection well?
5. Whether the shear and pull forces associated with the polymers will get influenced/altered – nearer to the injection well itself?
In such cases, will it lead to the partial or full destruction of polymer structures?
In case, if the polymer structure gets destructed, then, how will it do the intended job of enhancing the water viscosity?
Further, whether, viscosity reduction - would lead - to an enhanced adsorption (and sometimes absorption as well) of polymer molecules to the grain surfaces and thereby further making the polymer flooding process weaker?
OR
would it require an enhanced water saturation as well – for the polymers to retain their enhanced viscosity?
6. Feasible to get the details of reduction in water-phase permeability – resulting from polymer retention in pores – at the field-scale?
7. In a real field scenario, whether polymer molecules retain to have a strong hydrogen bonding with water molecules – particularly – away from the injection well or the local pore-size distribution play a crucial role?
8. Whether the adsorption of polymer molecules onto the surfaces of the solid rock grains would really aid the flow of oil comfortably in the absence of significant frictional resistance?
If it is so, then, polymer flooding enhances the sweeping not only volumetrically or macroscopically but also microscopically?
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Dear Suresh Kumar Govindarajan, you have asked many questions at once. A complete answer requires reviews papers. I resume my modest experience in polymer flooding. Before choosing the right polymer candidate, a succint study of reservoir chemistry and permeability are done. The structure and molecular weight of the polymer are taken to lessen to a great deal both adsorption and degradation. If the polymer loose these features (filtration), fingering problem arises and water gets out leaving the oil behind. Available and complete studies on 'daqing' field in China are free access via google search, please take profit. My Regards
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Respected Sir/ Madam,
Actually I have performed DFT calculation for an ESIPT probe molecule. I made a 1:1 complex of this probe with a water molecule where one H atom of water molecule involve in intermolecular H-bonding with carbonyl Oxygen of this probe. The energy calculation of different forms (enol and keto) of this complex in ground and excited state has been done. Now I want calculate Hydrogen bond energies. Can anyone please tell me the procedure of Hydrogen bond energy calculation ?
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Dear Riya,
The hydrogen bond energy of a complex can be calculated by using the usual definition where the energies of the isolated molecules EA and EB are subtracted from the total energy EAB of the complex, EHB = EAB−EA−EB. You can have a look at these papers.
It can also be calculated using the V(rc) value obtained at BCP employing atoms-in-molecule (AIM) analysis.
Thanks,
Dr. Dipankar Sutradhar
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Dear All,
In vasp, I would like to calculate the non-covalent interactions (NCI), more precisely the amount of hydrogen bonding, van-der waals interactions, and steric repulsions in which the H2O molecules are involved. I need to see their magnitude. Could you recommend any tools/program?
In advance, thanks a lot for all help.
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Dear Martin,
Sorry for the late answer and thanks a lot for the answer. It is quite helpful.
Best wishes
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I am trying to calculate hydrogen bonds between protein and ligand but i am unable to calculate per-residue hydrogen bonds using gmx hbond command of gromacs.
Please suggest me a way to do so.
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if i understand your question correctly, you were trying to calculate each residue's hydrogen bonding to ligand with respect to time, by using gmx hbond. You could create index file of each amino acid in the general area of the ligand, and one by one do gmx hbond.
hope it answered your question
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I'm doing molecular dynamics simulation to study the effect of mutation towards thermostability of an enzyme. After doing some analyses using VMD, I found that mutant is more stable than wild type, new hydrogen bonds and salt bridges are formed. VMD told me that new hydrogen bond are formed at the residue that I have mutated before, with % occupancy higher than 50 %. I've read that the higher % occupancy of hydrogen bond means higher stability of hydrogen bond during simulation. I also read some articles, websites and journals, but none of them make me understand about hydrogen bond occupancy. Would you like to tell me, or suggest me, where I can read about hydrogen bond occupancy ? Thank You
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Basically, as atom-atom distances and atom-atom-atom angles fluctuate in the course of a molecular dynamics simulations, in some snapshot structures along the trajectory, a hydrogen bond can be observed , while in others the distance between acceptor and donor is too large or the angle wrong to count as a hydrogen bond. The hydrogen bond occupancy tells you in what fraction of the structures the specific hydrogen bond can be detected. A high occupancy signifies that no matter how the protein structure wiggles and shakes, the hydrogen bon is there most of the time. A low occupancy means that in a large fraction of the structures, the hydrogen bond appears to be broken.
See https://ctlee.github.io/BioChemCoRe-2018/h-bond/ "Hydrogen Bond Analysis Tutorial"
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Dear Gromacs users,
I want to know the Hbond occupancy .Now I can only use VMD to calculate the final hydrogen bond occupancy rate of the simulated environment, but I want to understand the change of this hydrogen bond occupancy rate over time. What should I do? Please help me to provide some methods。
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𝐒𝐀𝐌𝐄𝐄 𝐔𝐋𝐋𝐀𝐇 Thank you! But i want calculat this occpancy with time, not hbonds number with time. such as my first picture.
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I am interrogating the rmsd and the extent of hydrogen bonding of compounds relative to a protein backbone and I want to correlate.
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Hello Aaron,
in general a higher RMSD value is correlated with a lower number of (intramolecular, backbone) hydrogen bonds.
Why this makes sense? because the RMSD (root mean square deviation) is a measure for the average distance between (usually backbone) atoms and thus a measure of stability of a protein. The more backbone hydrogen bonds, the higher the stability and the lower the RMSD.
to visualize, you can plot the rmsd values vs. the h-bond count at every nth timestep of your protein simulation. you should get a correlation (but don't expect a perfectly linear one)
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Hello everyone,
I docked a protein with a ligand that contains bromine "Br", I got a very good result of binding energy, inhibition constant and number of hydrogen bonds (5H bonds) but I could not visualize the 2D diagram of interactions with the discovery studio, knowing that I have no problem with the autodock vina or with discovery studio. Is there anyone who can help me please!?.
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Thank you so very much Sutanu Mukhopadhyay . I particularly like
I used it as a web tool: it works online without having to download the application.
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Hello I did 100 ns simulation using GROMACS a protein protein complex ( chain A for antigen - chain B & C for antibody) now I want to calculate the number of hydrogen bonds. I select chain A and chain B, but it shows nothing. What i should select for selection 1 and selection 2?
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Magnus Bertelsen yes, I tried but it shows nothing.
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I am optimizing the method of developing natural deep eutectic solvent by using different methods, molar ratio and water content. For heating and stirring method, I used 1:1 Choline chloride:1,2 propanediol. The combination does not form liquid either direct heating or in water bath up-to 2 hours. The temperature is below 100 degree C. I tried to add minimal amount of water (less than 50%). However, the combination does not form homogeneous solution. It only form clear homogeneous solution when I put more water (160%) and its stable at room temperature. My concern is some journals mention the excessive water content may disturb the hydrogen bonds between Choline chloride and 1,2 propanediol. I tried to rotavap to remove water content and it starts recrystallising again. I repeated the experiment by using total dried Choline chloride (freeze dried) after reading some suggestions from previous researchers that had similar issue that caused by wet Choline chloride. However, I obtained similar results 😢. May I have some other suggestions or opinions that may solve the problem? Thanks in advance
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For those arriving at this question: to properly answer this question you have to measure the solid-liquid phase diagram. It will tell you the maximum solubility of choline chloride in 1,2-propanediol at a certain temperature (e.g. 30 ºC). Probably a choline chloride mole fraction of 0.5 (1:1) is higher than the maximum composition at the temperatures you work.
Adding water increases the solubility (lowers the melting point) and can be a solution. Of course also within the thermodynamic limits.
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Hi researchers,
I have used Amber16 to run a molecular dynamics simulation of my protein system for 50 ns. After the production run was completed, I have generated an MD trajectory with 2500 snapshots which I further analysed using the Cpptraj program. The issue is, after doing a few analyses using cpptraj, the results were generated in the .DAT extension which I can only open in Excel. I analysed the dynamic cross-correlation of all atoms (DCCM), hydrogen bond analysis, Radius of gyration and all the results were generated in the .DAT extension (file format). Therefore, can anyone suggest to me how to change the result file format or what are the software, can be used to view the results generated by AMBER 16? If there is an option in AMBER to visualise this file format, then kindly do let me know as it will help me to progress my research.
Thanks, regards
~Priya
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Hi. You can use Gnuplot, MATLAB, Xmgrace etc. for plotting .dat files.
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Is OH bending IR band in PVA is related to inter/intermolecular hydrogen bond? why does it disappear on blending with another polymer?
Can anyone suggest a suitable reference?
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Hi all, I have used the below code for analyzing hbonds in my protein, but I am facing the error below. Please provide solution for this error?
python3 readHBmap.py -hbm hbmap.xpm -hbn rg.ndx -f md_0_1.gro -o occupancy.xvg -op pairs.dat -t 80 -dt 100
ERROR: Traceback (most recent call last):   File "readHBmap.py", line 295, in <module>     startingLine,framesLine,numberFrames,numberHbonds=readFiles().hbmap(hbmap,inputHbmap)   File "readHBmap.py", line 208, in hbmap     numberFrames=int,framesLine[0] TypeError: 'map' object is not subscriptable
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Hi, I resolved this. This error was because of using '-n' function for calling index (.ndx) instead of '-hbn' in gmx hbond command . After changing, when I used readhbmap.py command, it worked.
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I search for the forces acting on the adsorption from water of an insoluble particle onto polymer surface. I found that the intermolecular forces that governs the adsorption in water are the hydrogen bonding and van der waals forces. My question is about the effect of the hydrogen bonding (in water medium) on insoluble particles in water?
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OK, that is of course a different deal. In an ionic oxide compound, of course there will be some sort of surface saturation, so the oxide ions will be coordinated by the water hydrogen via hydrogen bridges while the lead atoms will be coordinated by the water oxygen, that's a complexation process (https://en.wikipedia.org/wiki/Coordination_complex).
The reason for the insolubility in such a case is that the lattice energy of the solid is much stronger than the solubilization energy would be. The associated concept would be the HSAB principle (https://en.wikipedia.org/wiki/HSAB_theory).
However, I should mention that I have never heard the term "polymer" being applied to PbO2, that does not match the bonding situation in that material at all.
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Hello,
I'm currently making a life cycle assessment for a liquid hydrogen tank.
One of the materials considered is a carbon fibre reinforced PEEK.
However, there is not a lot of data about the environmental impact of the polymer. Indeed, the only article I have found is the one from Daniel GARRAIN (which served as a reference for the Idemat database).
(PDF) The environmental behaviour of PEEK as an innovative material in a new portable hydrogen fuel cell (researchgate.net)
If any of you have data about it, I would be interested in exchanging with you.
Regards,
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I'm currently looking at the rheological properties of the polymer Xanthan Gum. focusing on its dynamic viscosity to be more specific. I'm assessing the effects of pH (ranging from 3.6 to 5.6, 0.4 increment, total of 6 pH's) on the dynamic viscosity of xanthan gum solution (dissolving xanthan gum powder into acetic buffer with equal ionic strength, concentration is kept at 0.04%).
Firstly, my viscosity data collected shows that, as pH increases from 3.6 to 4.0 then 4.4, the viscosity increases; but as I bring up the pH from 4.4 to 4.8, 4.8 to 5.2, then lastly 5.2 to 5.6, the increasing viscosity trend plateaus and the increase in viscosity is less significant compared to the 3.6-4.4 jump. At this range, does pH has an effect on the viscosity of xanthan gum based on its molecular configuration? Though some sources states that xanthan gum's viscosity remains stable and unchanged within the range of pH 3-12 at a high concentration like 1% not 0.04%, yet some suggest pH still plays an effect, though I'm not sure how on the chemical and molecular aspect.
A possible conjecture I can think of is the xanthan gum's order-disorder and helix-coil transition is affected by protonation. In figure 2, it demonstrates how electrolytes affect the structure of the polymer; in figure 3, it shows how at a state of a helical rod and no longer a random coil, it is capable to hydrogen bonds among each other. Hence, I'm wondering of pH plays an effect on it's structural transition, such that the increased intermolecular forces at the form of a helical rod would make it more viscous in solution.
Here are the resources I have used so far:
Brunchi, CE., Bercea, M., Morariu, S. et al. Some properties of xanthan gum in aqueous solutions: effect of temperature and pH. J Polym Res 23, 123 (2016). https://doi.org/10.1007/s10965-016-1015-4
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Dear Ryan Lo, you may find various stufies on this topic. Please have a look at the following free access RG fille. My Regards
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Hi all,
I am wondering if there are any good benchmarking studies out there testing the accuracy of B3LYP, DSD-PBEP86, or M06-2X functionals for NMR determination of intramolecular H-bonding. (My compound/drug is somewhat large: 4-anilino-6,7-ethylenedioxy-5-fluoroquinazoline. And I am looking at the rather rare NH---F bonding. (I must use DefT2ZVP basis set, as one of the R group constituents will eventually be Iodine. We are going through a series of halogens with increasing electron-withdrawing properties (σp>0).)
Thus far, I have read that B3LYP is rather ubiquitous, and very accurate for geometrical parameters. M0 functionals, however, appear to be good for non-covalent bonding determination.
"Experimental and theoretical DFT (B3LYP, X3LYP, CAM-B3LYP and M06-2X) study on electronic structure, spectral features, hydrogen bonding and solvent effects of 4-methylthiadiazole-5-carboxylic acid"
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Dear Corentin Lefebvre , I am highly optimistic its old version of DFT-poll
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I need to know a way to calculate the hydrophobic interactions between the protein and the ligand. in addition, I also need to do the same for the electrostatic interactions and hydrogen bonds. but the hydrogen bonds i can get from VMD easily. the goal is to make a graph like the attached one. any help is appreciated.
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Run MD simulation, store van der Waals and Coulombic interactions between entities of interest, and calculate the ensemble average. (Interaction energies calculated from a single configuration are almost meaningless because of the strong distance-dependence.)
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Hello!
I have a few questions related to molecular docking and its analysis. I used Ligplot+ to analyse my docking results.
  1. When a mutation occurs for a Ser residue (S188F, Mediterranean variant of G6PD), I noticed that the active site residue (His263) shifts from hydrogen bond interaction to hydrophobic interaction. Is there a reason for this?
  2. Apart from that, while performing molecular docking, is it important to include all important residues inside the grid box? (when I did that, the ligand did not bind to its active site but when I made my grid box smaller and included the active site residue, it bound to the active site.)
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the effect at the structural level can be seen in the non-covalent interactions. The hydrogen bonds can be analyzed since the amino acid serine that has a hydroxyl group is lost with the mutation to phenylalanine. Furthermore, there is also an effect on the polarity of the active site and it can be calculated with the hydropathic index.
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To visualize hydrogen bonds in Pymol between a protein and the surrounding water molecules, I tried using "Action -> Find -> Polar Contacts -> Involving solvents", which shows hydrogen bonding between solvent molecules and protein and hydrogen bonding between different solvent molecules, making visualizing hbonds between just the solvent and protein very messy. Is there a way (that preferably does not involve writing a script) to display only the hydrogen bonding between the solvent and protein?
I encounter a similar problem in VMD, where I tried to create an HBond representation with the selected atoms as "protein or (water and within 3 of protein)"
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In Pymol, the appropriate command would be
show_contacts sel1, sel2, result="contacts", cutoff=3.6, bigcutoff=4.0
https://pymolwiki.org/index.php/Show_contacts for link to the appropriate plugin
with sel1 replaced by "polymer" and sel2 by "solvent"
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Hi there,
I am a little confused about a few concepts that I would like elucidated. An article states, "This phenomenon can be rationalized by the fact that the NH proton becomes more acidic with increasing electron-withdrawing character of the 4’ substituent and thus more strongly hydrogen bonding."
Meanwhile, the process of determining if intra-HBs exist is given by another article, which uses hydrogen bond acidity and the formula:
Δδ = δ(DMSO) − δ(CDCl3)
and
A= 0.0065 + 0.133Δδ
"For NH compounds, if A > 0.16 the NH group is not part of an intramolecular hydrogen bond, and if A < 0.05 the NH group is part of an intramolecular hydrogen bond."
So, in this case, a LOWER value is indicative of stronger HBs.
I believe my confusion may be down to the fact that the first instance is looking at the NH proton, whilst the second is looking at the bond itself.
Indeed:
"...the overall hydrogen bond acidity of a molecule, A, and does not relate to any specific acidic group in a molecule. It is only a measure of the hydrogen bond acidity of a particular NH group if this is the sole acidic group in the molecule."
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The two papers you cite adopt two different approaches to get an insight into HB of different compounds.
The former considers implicitly HB from a MO point of view. In this case, the interaction is - at least partially - due to a CT from a Lewis base X into an empty sigma* MO located on Ar-NH. Thus an electron-withdrawing effect from one hand stabilises the deprotonated form (Ar-N(-): acidity), and on the other increases the CT Ar-N–H <-- X (HB). Thus, it concludes that acidity is paralleled by HB. This seems a case of resonance-assisted H-bond.
The latter paper considers HB depending on the polarity of the NH bond. The larger the polarity, the larger the difference in chemical shift in solvents of different polarity, such as chloroform and dimethylsulfoxide. In this case an electrostatic explanation is implicitly mentioned to account for HB.
Indeed, HB as long as other sigma-hole sister interactions, is currently considered a non-covalent interactions depending on different contributions, such as a CT term, a (often prevailing) electrostatic contribution, and a dispersion term. The weight of each of contribution varies from case to case, so it would be not fair to adopt a single criterion to evaluate HB. Therefore, the two papers are not necessary conflicting, since they refer to different chemical systems, one with a prevailing CT contribution, and the other with a prevailing electrostatic contribution.
Nowadays, theoretical calculations (MP2 / DFT/ CCSD / ... ) are of great help in evaluating the nature of HB in specific case of study, so a help from computational chemistry may be seeked for depending on your need.
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Let's say I take a snapshot from a GROMACS molecular dynamics trajectory and want to visualize which residues of the protein forms hydrogen bonds with the surrounding water molecules. I know this can be done using Pymol's "find polar contacts" tool, but since there's so many other water molecules in the solvent box, it's hard to visualize just the water molecules involved with hydrogen bonding with the protein. Is there any way I can remove water molecules not involved in hydrogen bonding with the protein and keep the ones that do? Thank you!
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Measure distances and angles between polar groups of the protein and water (cmd.distance, cmd.angle) and hide or delete water molecules that do not satisfy geometrical criteria for hydrogen bond with any polar group of the protein. Loop over all water molecules and all polar groups of the protein. Put it into a python script and run it with pymol:
a) $ pymol script.py
b) $ pymol ... run script.py
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Hi all,
just reading through an article regarding intrabmolecular N-H...F bonding. This articles serves as one of the teaching pieces for my internship.
Just wondering how to calculate the ΔEint, as I cannot find it in my optimisation file. Do I need to perform NMR at this stage?
Cheers,
Joshua
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The aforementioned methods are useful for INTERmolecular interaction energies. However, for that particular paper, the INTRAmolecular hydrogen bond interaction energies you're referring to were calculated through NBO analysis in Gaussian 16. You can look into further details of how exactly they did it in their supporting information's Computational details section: (https://chemistry-europe.onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fchem.202103135&file=chem202103135-sup-0001-misc_information.pdf).
If you want to perform your own NBO analyses I'd suggest looking into the appropriate section of the Gaussian documentation.
Additionally, Joaquin Barroso-Flores has a blog with some nice entries discussing Gaussian's NBO module (https://joaquinbarroso.com/2009/11/11/nbo/)
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As hydrogen bonding is one of the important parameter for shale hydration inhibition with water, what happens after this bonding?
like when clay mineral charges are neutralized by hydrogen bonds and cation exchange reactions between inhibitor and minerals, does the adsorption of inhibitor layer on shale surface count as swelling? Because it will somehow increase the size of original formation due to adsorption.
How to address this issue.
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Let's imagine a piece of shale . This porous material in the pores is oil (you are interested in it), water, all shale minerals are hydrated. If there are ions, they are bound to water by an ion / dipole interaction; to molecules with a covalent bond, water is bound by a dipole / dipole interaction. Water molecules are hydrogen bonded to each other. If you add water to a piece of shale, it will swell due to the diffusion of water until equilibrium is established. The absorbed water will be distributed over all internal equilibrium states.
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Assuming a molecule forms an intramolecular hydrogen bond, can the extent of the intramolecular hydrogen bond be estimated using UV-Vis spectroscopy?
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Dear Bright Emenike
I think the following link will be useful for you
Best regards
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What are the differences between the hydrogen bonds formed in an alpha helix and those formed in beta shears?
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Hi, I can tell you some of my articles that deal with this subject. If you can't download please contact me. Thanks.
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I have docked the compound and got free energy _9kcal, however, no hydrogen bonds seemed to be formed with protein .can anyone guide the compound is docked?
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Thankyou for your prompt reply,i mean to say that I have one transporter protein and three ligands.I adopted multiligand simultaneos docking method.I know the active site where the drug should bind
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I had followed the jerkwin tutorial for MD trajectory analysis, and i want to calculate the hydrogen bonds distance between each residues of my protein.
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You can use gaussian 09 package. Optimised the structures and then check the H-bonds distance from the output file using Gauss view
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Hello.
which one have more hydrogenic bond,alpha helix or beta sheet?
iappreciate your comments.
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Here is the video on the topic that explains hydrogen bounding in Alpha helix https://youtu.be/wM06U0IAv5c
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Dear colleagues researchers,
Could you help me with a problem in MD analysis using Gromacs?
I'm using Gromacs version 2021.4 now, and trying to analyze hydrogen bonds (using HbMap2Grace) with the command:
gmx hbond -f ../md_center.xtc -s ../md.tpr -n ../index.ndx -num hbond-lig -r -0.4 -hbm hbmap-lig -g hb-lig -life hblife -tu us
The program gives me the following error:
Fatal error:
Not enough memory. Failed to calloc -79 elements of size 4 for rdist
(called from file /home/priscila/Documents/gromacs-2021.4/src/gromacs/gmx_hbond.cpp,
line 2856)
I've also tried it with version 5.1, 2018, 2019, 2019.6 and 2020, but all with the same problem.
P.S.: I don't think it's a lack of physical memory on my computer, cause there is enough storage space.
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Some options of hbond tool requires a lot of RAM.
At the end of the "gmx hbond -h" command:
"Note: options -ac, -life, -hbn and -hbm require an amount of memory proportional to the total numbers of donors times the total number of acceptors in the selected group(s)."
You can try to analyze a smaller number of frames or restrict the selection of donors/acceptors.
Best,
Felippe
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I mean for example
the hydrogen bonds formed in aspartic acid between the amino group and the carboxyl group are two hydrogen bonds?
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Dear Ekram, for more information about the hydrogen bonding in amino acids please have a look at the following potentially useful links which might help you in your analysis:
Comparison of Various Types of Hydrogen Bonds Involving Aromatic Amino Acids
This paper has not yet been posted as public full text on RG. However, all three authors have RG profiles. Thus you can easily request the full text from one of the authors directly via RG. In my personal experience most authors respond quite quickly to such full text requests.
Also please see this instructive overview:
Charge, hydrogen donor and acceptor atoms, and polarity of the amino acid side chains
I hope this helps. Good luck with your work!
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I am Working on developing Schiffs Base - Transition metal Complexes Having -OH Group at Terminal Position leading to the formation of Hydrogen bonding ! However I I unable to get the crystal Structure for the same !! Would anyone give me some suggestions Please ? Although I have tried almost all the solvents like MeOH, EtOH, Acetonitrile , etc
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Dear Naseer, many thanks for sharing this very interesting chemical problem with the RG community. My general advice would be to try a different crystallization technique such as the vapor diffusion technique. Depending on the solubility of your compound you can prepare e.g. a solution of the complex in acetonitrile and put the solution in a small vial. Then place the vial in a larger closed glass container in which you put some diethyl ether. Over a few days the diethyl ether will diffuse into the solution and, if you are lucky, crystals will form at the interface layer. Of course this is just one of the different possible methods. For a good overview of different crystallization techniques please find attached three very useful manuals. Good luck with your work and best wishes, Frank Edelmann
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Hi, I'm simulating a box with water and Li+ and Cl- ions and I'm trying to calculate the hydrogen bonds formed by the Cl- anion and the water molecules using the gmx hbond. The command I was using was:
gmx hbond -f .xtc -s .tpr -n .ndx -num -r 0.41 (O-Cl distance taken from Laage & Hynes, PNAS, 104, 11167-11172, 2007)
And the program gets back to me whenever there are no hydrogen bonds, I believe it's because the hbond only sees O and N atoms as acceptors. So I started adding the -contact flag that do not look for hydrogen bonds, but merely for contacts within the cut-off distance, and I use the command:
gmx hbond -f .xtc -s .tpr -n .ndx -num -r2 0.41 -r 0.3 -contact
however the contact values are higher than what I expected and I believe I cannot consider the contacts as hydrogen bonds. I'm not sure what to do and would like to know if anyone has any suggestions.
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The gmx hbond command accepts only the OH and NH groups as donors, and the O and N atoms as acceptors. Felippe Colombari 's suggestion is interesting, but first you must decide if the group you want to calculate hbond is a donor or an acceptor, to classify it correctly according to the gromacs rules.
I have attached the command manual
best regards
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I am trying to correlate the IR spectrum and single crystallography data.
In single crystal IR spectra, I found some inter-molecular hydrogen bonds were stronger (from wavenumber shift), and I think the different hydrogen bond strengths are due to different crystal packing. (At least in single molecule quantum calculations, the -OH wavenumbers are mostly the same)
Is it reasonable that I run QM/MM based on the single crystal molecular geometries (.cif files) and calculate the -OH vibration (freq) to correlate with experimental IR data?
I am not familiar of how single crystal technician actually grab the .cif data, so I am wondering if the cif. files that I received are actually reflecting the molecular packing in real.
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Hello dear RG members,
the strength of hydrogen bonds in solid state structures is indeed strongly influenced by the donor(D)-acceptor(A) distances in a D-H...A bridge.
The D...A distances in strong hydrogen bonds are at 230-250pm and lead to a lengthening of the O-H bond and a shift to smaller frequencies. The D...A distances in weak hydrogen bonds are at 270-300pm.
Thus, it makes sense to look precisely at the chemical environment of the OH groups within the solid state structure and to take it into account for quantum chemical calculations. The .cif file contains the coordinates of all atoms within the unit cell. With appropriate programs, e.g. DIAMOND, the structure can be visualized and distances to neighboring atoms can be determined. However, the .cif file does not contain any direct information about bond lengths and molecular packing, but these result from the atomic coordinates and symmetry encodings.
I hope that my contribution can help.
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We're trying to obtain a computational model of a protein that has not been experimentally solved. There are no homologous proteins, and the best protein structure prediction tools available right now (i.e. RoseTTAFold, AlphaFold 2) failed to predict a folded structure.
However, we believe the protein is likely a beta helix (e.g. similar to PDB: 1EZG) due to its similar chemical properties with other common beta helical proteins, and we have a guess on which residues are involved in hydrogen bonding/beta sheets as well as what the overall beta helical structure of this protein might be like.
Are there any good tools for building a protein from scratch by hand? I tried using Schrodinger's "Build Peptide From Sequence" tool, but that requires specifying the psi and phi angles of each residue not involved in an alpha helix or beta sheet. This makes it extremely difficult to make sure the residues we expect are hydrogen bonding to line up correctly. If there is a tool that can build a protein and adjust each residue by hand, then lining up residues so hydrogen bonding is possible would probably be much easier. Are there any such tools, or are there better ways for building a protein from scratch? Thank you!
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I think the ideal situation is where you know the torsional angles in advance. Most beginners prefer to build a glycine or alanine peptide then mutate it (e.g. FoldX).
If you prefer a user interface method, I recommend chimera (tools>structure editing>build structure), or ascalaph designer.
If you prefer a commandline interface, then Tinker (protein command) or Amber have such capabilities.
Finally, there is a python package that is called peptidebuilder which seems to me the best option out there (but you might have to adjust certain torsions manually).
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CNF is well known to interact with a great number of synthetic or biopolymers via hydrogen bond leading to the hydrogel production. sometimes it directly forms hydrogel without any cross-linker. then, why cant it directly form hydrogen interaction with lignin which is originally linked by hydrogen bond in the natural cell wall ? i am trying to fabricate CNF-lignin directly inspired from natural cell wall. but no succeed. Anyone can give good explanation of it?thanks
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in details?
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i am using auto dock. during the protein preparation i added the add polar hydrogen bond. when i went to save, it is showing error that the protein has 84 non bonded atoms
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Hello,
just ignore it .
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What is the temperature at which hydrogen desorbs from In - polar InN?
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100 degrees centigrade. This is the reason why you denature DNA at 95 degrees centigrade.
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I am interested to know the hydrogen bond strength in ligand docking. Ligand is participating in Sulfur mediated hydrogen bond. I would like to calculate or find out the strength of the same. Kindly suggest me. Note: by using Schrodinger Material software
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You can run a metadynamics simulation (Desmond > Metadynamics) by perturbing the donor-acceptor distance. It will give you a potential energy diagram. The depth of this potential energy diagram is the strength of the hydrogen bond. Here are some examples of metadynamics simulations using Schrodinger Desmond in our previous works:
Note that in these works distance perturbation was done between two entities (ligand/protein), whereas in your study you need to select two atoms (donor and acceptor atoms).
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I want to simulate the vibrational frequencies of a cluster of molecules (2, 3 or 4 molecules) connected by Hydrogen bond in Gaussian Software. But I am getting an the following error message.
"Error in Internal Co-ordinate System".
Then I tried doing simulations in Cartesian co-ordinates giving the required syntax but it gave an error "Error termination request processed by link 9999."
I would be grateful if anyone can tell me how to simulate such Hydrogen bonded clusters using Gaussian. Thanks in advance.  
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Total agreement with the good suggestions of outstanding colleagues. I trust that the question has been solved in the best way. Furthermore, nice to share an outstanding summary about "How to solve the error message in Gaussian" as follow:
Have a good day!!!
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If I have a complex connected with another ligand by a hydrogen bond with coordinated water from that complex; is this H-bond effect on the range of losing the coordinated water until 210 C because I have it? I need references, please.
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Dear dr.
I guess that the answer is not straightforward, first you have to detect the mechanism in each stage of TGA, find the first and second derivatives and try to obtain the product at 210C and do MS (mass Spectroscopy) and IR, i.e. Monitoring the product at different stages, but don't forget removing the water attached to the crystal surface by leaving the product 48hr in a 60C oven
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After using autodock vina,
I analyzed the result that ligand have  a binding energy of -9.5 kcal/mol.
BUT I can't find any hydrogen bonds through the interaction.
What's the problems?
Can i consider this result of docking ?
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There are many factors contributing to favorable inter-molecular interactions. Why do you just focus on hydrogen bonds?
The hydrophobic, vdW, hydrogen bond, conformational terms can all give minus binding energy.
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I am trying to explain the allosteric pathway using molecular dynamics. I have tried to do a contact, correlation and hydrogen bond analysis to determine that path (using holo and apo forms). Is there any software that can help suggest an allosteric path?
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This may not be the best for it worked for us in combining SAXS and molecular dynamics to examine allostery for AIF - see open access paper - Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor. Brosey CA, Ho C, Long WZ, Singh S, Burnett K, Hura GL, Nix JC, Bowman GR, Ellenberger T, Tainer JA. Structure. 2016 Dec 6;24(12):2067-2079. doi: 10.1016/j.str.2016.09.012.
RMSD calculations were generated with the RMSDTT plugin (Luis Gracia, https://github.com/luisico/rmsdtt) of the VMD molecular visualization program.
Electrostatic interactions between residues were quantified based on occupancy using the HBonds plugin (JC Gumbart and Dong Luo http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/) and Salt Bridges (Leonardo Trabuco and Elizabeth Villa http://www.ks.uiuc.edu/Research/vmd/plugins/saltbr/) analysis modules within VMD. Communication between active site residues and the rest of AIF was quantified using Mutual Information (MI) between backbone and side chain dihedral angles. MI measures the dependence between two variables, X and Y, by quantifying probability of knowing the state of X given the state of Y. For each simulation, angles for each residue were extracted using the MDTraj library (Version 1.5.1) (McGibbon et al., 2015).
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Hello, if I perform an FTIR analysis of a polymer mixture in brine? I can still determine whether there is an interaction between polymers? For instance, an ftir analysis for HPAM and Xanthan gum in brine. Can you still determine if a hydrogen bond exists between the polymers in brine? thank you
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Yes, one can.
For films or melts I would prefer IR spectroscopy, for solutions (solvent and solute) I would try Raman spectroscopy, if the solvent absorbs to much of the IR signal.
Of course, you might also see interactions between your polymers and the solvent.
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I have generated a complex of antigen and antibody using haddock and used that cluster for MD run using Gromacs. Now I need to find out the inter hydrogen bonds formed between antigen and antibody complex. what commands do I need to give ?
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ok, thank u, sir, actually these no. of hydrogen bonds are may be individual H - bonds present in each protein 200 and 1600, but I am not sure.
and one more thing is it possible to take one protein as a ligand and run MD as ligand and protein complex ?
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Hello,
In MIP sensors, monomer and target molecules are mixed together, and electropolymerization initiates polymerization to create molecularly imprinted polymers (MIP). The literature says a hydrogen bond is formed between the monomer and target molecule.
Is this hydrogen bond spontaneous or requires incubation time?
I appreciate any help you can provide.
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Dear Sanjida Yeasmin, not an incubation time but an equilibrium time where the interactions reach their maximun, i.e., the perfect arrengements to exploit all sites. My Regards
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· Use of superheated and supercritical water (SW) as a solvent for the ligand-free homogeneous C-C Coupling reactions.
· As the temperature rises, the dielectric constant of water drops significantly from 80.1 (20 °C) to 6 (374 °C) due to the decrease of hydrogen- bond strength.
· At elevated temperatures, water behaves much like diethylether.
· The corresponding yields were often lower than those reported in organic solvents, possibly due to the deactivation of the catalyst
· This drawback of ligandless coupling may be overcome by dispersing the catalytic material in an aqueous hydrotropic medium as it possesses surfactant like properties.
· Advantages :
· low catalyst loadings and rapid reaction times
· ease of reaction (no need for anaerobic conditions)
· Use of a nontoxic, nonflammable solvent.
· The methodology is currently being used in C-C coupling reactions.
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Palladium catalyzed Cross-Coupling Reactions can not be carried out in water due to inactivation of the catalyst in Water. Palladium-Catalyzed reaction needs anhydrous organic solvents.
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I am using Orca 4. What besis set should I used? The molecule contain carbon, nitrogen and hydrogen atom.
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For your system, depending on its size, I could suggest you to use at first glance Pople basis-set with diffuse and polarization orbitals (6-31+G*, 6-31++G** ...). In my opinion, I advise the use of Karlsruhe basis-set (Def2-TZVP, Def2-QZVP...).
I think this article could be of interest for you:
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My question is about the accuracy of DFT based methods in characterising hydrogen bonding. Whether accuracy increases as we go up the Jacob's ladder of DFT functionals?
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Zhaoxi Sun , I mostly agree with the hierarchy of methods you suggested. However, before going down from QZ to TZ level or even further, you should definitely consider using a DFT-based composite method. These are slightly cheaper than (m)GGA/TZ but more accurate and robust (see attached figure). The perhaps best one is r2SCAN-3c (which is better for non-covalent interactions better than most hybrid/QZ approaches but 1000 times faster) but not yet widely available. B97-3c is also very good in many situations.
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There is hydrogen bonding in the glycerol, If we have an IR spectrum of Glycerol then how we will interpret that hydrogen bonding is present there?
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Dear Iqra,
You may indeed be able to see H-bonding of glycerol molecules in condensed phases (solution or solid). They should show as shifts of the position of some IR bands (those implied in H-bonding) with respect to the position of these same IR bands in the spectrum of the isolated glycerol molecule, i.e. in the gas phase, or isolated in a rare gas matrix,... where there is no intermolecular H-bonds.
The attached file may be of help, showing the example of VOCs adsorption on ice, and the formation of surface H-bonds with surface FTIR spectroscopy.
Best wishes
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Dear Researchers,
I am using Chimera 1.15 on PC as well as on Laptop. Both are having Windows10. On PC, the mouse hovering function is not working. When I hover the mouse over the hydrogen bond or bonded protein or any atom, it should show the description. It works fine in laptop but not working on PC.
Though, internet search on forum suggests some settings but its not working.
Can anybody suggest the solution?
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If they both are of same configuration, will work! Else you will need to check for bugs, PC load, and may be after your clean-up of PC reinstall the software. It is compatible for both the systems.
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If two molecules having only hydrogen bond acceptor counts, but not hydrogen bond donor count, is it possible to have a hydrogen bond interaction between these molecules?
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Dear Muniraj Vignesh thank you for your interesting technical question. please have a look at the following useful article which might help you on your analysis:
Hydrogen Bond Donor Acceptor Plugin
I would say that between two molecules having only hydrogen bond acceptor counts you can have very weak van der Waals interactions but no real hydrogen bonds.
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I have performed MD simulation, and have all the results including RMSF, RMSD, PSA etc. Now I want to calculate the Hydrogen bonds made and broken after simulation in the simulated complex on different nano seconds(0, 250,500ns). Can anyone please help me, how I can do that? I have tried Chimera, but it shows there is not any inter HB, although there are several intra HB.
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Look Zumama Khalid exactly what do want ????
Can you please share pic gromacs data file???
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Hello, I am trying to ask which device is the best to determine if there is any intermolecular bonding (i.e. hydrogen bonding) between polymers? Is it FTIR or SEM? If not, what are some good alternatives? Thank you.
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Dear Mohammed Bakir
Polymer scientists define intermolecular forces as the coherent energy density of the material (CED) and FTIR
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I am simulating a peptide in lipid bilayer and wanted to implement hydrogen bonding restraint in my peptide ,I am skeptic about how to do it. Please do help and elaborate on how to implement this.
Thank you in advance
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Look at the contents of the following file:
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Recently I had this problem: to calculate in Gaussian the energy of a hydrogen bond between methyl acetate and heavy water. Am I right that i need to calculate the corresponding thermodynamic quantities for the two systems shown on the slide, taking into account the solvation effects. In addition, I recently have started taking the first steps in quantum chemistry and dont know what is right way to compose an input file (not clear how to add heavy water to the SCRF list and some other aspects).thank you in advance.
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I would suggest you to first learn and carry out some preliminary calculations in Gas Phase Chemistry. After that you can move to QM/MM calculations where you have to introduced hydrogen bonds by dummy atoms by Mechanical Embedding (at the interface of QM and MM). You can refers to Gaussian manual for further help in making QM/MM input file etc.
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I've carried out a 100ns simulation of protein in water and want to calculate hydrogen bond (forward) lifetime between Protein-Water.
 I tried g_trjconv with application of -pbc mol -ur compact options on untruncated(100ns) trajectory. The results came as:
ACF 11303/11303
Normalization for c(t) = 0.0615891 for gh(t) = 1.23179e-06
Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.2#
Hydrogen bond thermodynamics at T = 300 K
Fitting parameters chi^2 =    3.03095
Q =          0
------------------------------ --------------------
Type      Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward         0.001   1793.775      23.259     3.03095
When I tried the same with the original unconverted trajectory(without g_trjconv ,without pbc options), I got a lifetime of 2345.890ps.
Which value should I take, since application of pbc gives a different value than that of the original trajectory value of lifetime.?
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Hey Apramita,
I am trying to find out hydrogen bond lifetime using gmx hbond -ac. But getting the error segmentation fault. Can you help me with this?
How you have calculated H-bond lifetime?
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Hello! Please suggest what techniques can be used for detecting hydrogen-bonded systems in gas phase by mass spectrometry. MW of dimers = 332 Da. The essence of our problem is that we need to evaporate an organic solid (which is a hydrogen-bonded system, a cocrystal), and see whether any dimers or other complexes are formed in the gas phase. Is it possible that the ionizing voltage affects the stability of the dimers in the gas phase? Can one achieve "soft" sublimation conditions by reducing the heating rate and/or it is necessary to use isothermal mode at lower temperature? Are there are reports of such experiments that could allow us to study the dimers (n-mers) in gas phase?
Thanks in advance
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Do you mean proton-bound dimers? Proton-bound dimers, trimers, etc. are very common with soft ionization such as electrospray, APCI, and DART. The relative abundance of species such [2M +H]+ increases with analyte concentration. You can also see anion-bound clusters in negative-ion mode. Very large clusters can be observed under the right conditions. Studies of gas-phase water clusters are a specific example.
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I'm working with iron nanoparticles and it seems that the sedimentation of nanoparticles are enhanced at higher pH (though the zeta potential is high) compaired to pH close to PZC (8.3). Is it possible that the formation of hydrogen bonds enhanced the sedimentation? If possible, How do you provide evidence for formation of hydrogen bonding?
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Sakil Mahmud Thank you.
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I use the calculation for all unique pairs of interacting molecules by CrystalExplorer. But can not find the method ( or way or options) in CrystalExplorer, how to quantify the strength of contacts by calculating the interaction energies. I found many articles with the results of that calculation, but there I could not found in them more detailed instructions on how to make calculated. I would like to correlate this information with the results of the Hirshfeld surface analysis.
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Thank you
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Are nitrogens in the center of porphyrinic ring capable of covalent or hydrogen bonding to carboxylic acid groups?
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Dear Naeimeh Hassanzadeh Goji apparently yes. At least I found this potentially useful article in which reactions of porphyrins with certain halogenated carboxylic acids is reported. The article is entitled
Noncovalent interactions in acid–porphyrin complexes
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I've at my disposal a hydrogel, which upon addition of a reducing agent is degrading, I want to understand this degradation mechanism (My prediction is that the nature of the hydrogen bonding in the hydrogel is undergoing a change). What is the best technique to characterize hydrogen bonding
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Dear Satadru Chakrabarty, different techniques of infra red spectroscopy are used to characterize H-bonds. The fingerprint region is more informative. There are many possible mechanisms to provoke gel degradation, such as disulfide links destruction (if any in your case). Please check the following document. My Regards
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Hello,
I am adding dopamine hydrochloride to my PVA/Chitosan hydrogel to increase adhesion. It is not increasing in adhesion, however.
The catechol groups of the polydopamine should have a strong affinity for hydrophilic surfaces due to their capacity to establish hydrogen bonds. What is the reason that the hydrogel is not increasing in adhesion? Or, are there other ways to increase the adhesion of hydrogel (not through mucoadhesion).
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Dear Ricky Dua, not a simple addition, dopamine should be reacted with the polymer chains, as a substitute side group. My Regards
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I know that the side chain NH2 of asparagine/glutamine and the side chain NH group of tryptophan can donate hydrogen bonds. But why they cannot accpet H-bonds?
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Amines in general are H-bond acceptors (HBAs). In a medium in which they are not protonated, there is no reason why they can't act as HBAs. Primary and secondary amines are also relatively weak H-bond donors (HBDs). The problem of the pyrrole ring in TRP is different: the N atom is involved in an aromatic system and its basicity is largely weakened, but the acidity of the N-H is enhanced. So this pyrrole system will be a poor HBA and a relatively strong HBD.
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one of our hydrogen bonded complex doesn't have proper isosurface region around the hydrogen bond site. The perti. complex have a strong hydrogen bonding interaction which is observed in values of interaction energy and the distance of hydrogen bond (1.55 A). And the QTAIM analysis also shows a larger value of electron density on bcp of the hydrogen bond. But still the NCI analysis doesnt gives a proper isosurface around the hydrogen bonding site.
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This is because in most codes for calculating NCI such as Multiwfn (http://sobereva.com/multiwfn), the RDG is screened in the region with relatively large electron density. For example, in Multiwfn there is a parameter "RDG_maxrho", which is default to 0.05, namely if a point has an electron density > 0.5, the RDG will be automatically set to 100 to avoid showing its isosurface. This design is used to avoid occurrence of RDG isosurface irrelevant to weak interaction.
In your case, you should set RDG_maxrho to a slightly larger value to avoid the screening of the strong H-bond. However, it is strongly suggested to employ the new function defined me, namely Interaction Region Indicator (IRI), this function is able to very clearly exhibit all kinds of interactions in a chemical system. The paper describing this function and comparing it with NCI and AIM has been available in ChemRxiv recently, see DOI: 10.26434/chemrxiv.13591142, you will find IRI extremely useful for you system. IRI has been supported in Multiwfn, the supplmental information of this paper contains a detailed tutorial showing how to perform various kinds of IRI analyses in Multiwfn.
Another choice is using independent gradient model based on Hirshfeld (IGMH) I recently proposed, it is also been supported by Multiwfn. It is able to nicely exhibit interactions between two specific fragment, see Section 4.20.11 of Multiwfn manual. The paper describing IGMH will be prepared soon.
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Definition of physical adsorption process is intermolecular bond(it' s mostly Van der Waals forces) But if the bonding that is hydrogen bond Can be called as physical adsorption process ?
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Hello ... Physical adsorption is a weak adsorption as a result of the bonding strength (van der Waals forces or the hydrogen bond) between molecules, ions, or atoms adsorbed on the adsorbent surface, and is characterized by an enthalpy of less than 40 kJ/mole ..GOOD LUCK@
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I am working on a project for assessing the Antibacterial activity of various chemicals, I was wondering Can i make solution of those components using water as a solvent, depending on the fact that they can form hydrogen bond together which would make them together more likely soluble?
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Dear Youssef Abdelaziz your original question has been asked about six weeks ago. In the meantime, did you give it a try? It would e interesting to learn what you found out.
The following two articles could also be helpful i this respect:
The latter article is freely available as full text in the general internet.
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Hi all,
Im trying to calculate the strength of intramolecular hydrogen bond.
which software do i need to use?
and basic examples please?
I appreciate if you can help me.
Thank you in advance.
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A reliable and very easy way of evaluating H-bond energy is using the relationship based on AIM theory proposed in my recent work J. Comput. Chem., 40, 2868–2881 (2019) DOI: 10.1002/jcc.26068. This analysis can be easily and very quickly realized using Multiwfn (http://sobereva.com/multiwfn). For Gaussian user, one only need to generate .wfn or .wfx or .fch first (see beginning of Chapter 4 of Multiwfn manual on how to generate them), then load the file into Multiwfn, enter topology analysis module, search critical point, then read electron density corresponding to the H-bond you are interested, and finally substitute this value into the formula proposed in the J. Comput. Chem. paper to predict H-bond energy. Please carefully check Section 4.2.1 of Multiwfn manual, this is a very detailed example showing how to use this method to predict H-bond energy between 2-pyridoxine and 2-aminopyridine in their dimer.
By the way, Multiwfn is also able to perform this analysis based on output file of GAMESS-US (you need to change the suffix to .gms), and based on .molden file generated by Molpro, see beginning of Chapter 4 of Multiwfn manual for detail.
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I work with a steroidal ketone and ethylene gylcol (EG). I would like to prove that ethylene glycol forms a hydrogen bond with the carbonyl group of the steroid.
The problem is that so far I have not found a solvent in which both components would dissolve and at the same time the solvent does not affect the hydrogen bonding.
Because of a possible reaction mechanism, it would be important to prove this
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Dear Dávid - You're very welcome. Perhaps, as a compromise so to speak, it might be worth a try to use methylglycol (ethylene glycol monomethyl ether) as a solvent for your steroid ketone. It should be less polar than ethylene glycol itself but it should still be able to form hydrogen bonds.
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Hello everyone,
Please help me to create a CIF with two different molecules which are linked through hydrogen bonding in the same crystal lattice. I am attaching an example to understand what I want to achieve. The attached image and CIF consist of a telmisartan and gentisic acid molecule linked through hydrogen bonding. I want to replace the gentisic molecule with other molecule. Any help would be highly appreciated.
Thank you