Hydrogen Bonding - Science topic

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!

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

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

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?

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.

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.

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

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。

I am interrogating the rmsd and the extent of hydrogen bonding of compounds relative to a protein backbone and I want to correlate.

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!?.

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?

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

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

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?

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

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?

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,

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

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"

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.

Hello!

I have a few questions related to molecular docking and its analysis. I used Ligplot+ to analyse my docking results.

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)"

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."

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!

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

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.

Assuming a molecule forms an intramolecular hydrogen bond, can the extent of the intramolecular hydrogen bond be estimated using UV-Vis spectroscopy?

What are the differences between the hydrogen bonds formed in an alpha helix and those formed in beta shears?

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?

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.

Hello.

which one have more hydrogenic bond,alpha helix or beta sheet?

iappreciate your comments.

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:

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.

I mean for example

the hydrogen bonds formed in aspartic acid between the amino group and the carboxyl group are two hydrogen bonds?

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

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.

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.

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!

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

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

What is the temperature at which hydrogen desorbs from In - polar InN?

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

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.  

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.

After using autodock vina,

I analyzed the result that ligand have  a binding energy of -9.5 kcal/mol.

What's the problems?

Can i consider this result of docking ?

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?

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

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 ?

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.

· 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.

I am using Orca 4. What besis set should I used? The molecule contain carbon, nitrogen and hydrogen atom.

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?

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?

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?

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?

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.

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.

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

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.

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:

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.?

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

It is possible to observe hydrogen-bonded complexes (dimers, trimers, tetramers, etc.) in gas phase with a mass spectrometer?

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?

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.

Are nitrogens in the center of porphyrinic ring capable of covalent or hydrogen bonding to carboxylic acid groups?

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

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).

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?

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.

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 ?

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?

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.

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

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