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Questions tagged [hydrogen-bonds]

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4 votes
0 answers
92 views

Predict if a group will be acceptor/donor of H bonds [closed]

Context: I am a student of cheminformatics, and I am trying to solve a problem in predicting whether atom can be an acceptor/donor of hydrogen bonds, using Python programming language and RDKit ...
Gianmarco Luchetti 's user avatar
6 votes
0 answers
55 views

Is it possible to evaluate rotational and vibrational partition functions for diffusion in the Eyring Theory of Absolute Rates? [closed]

Let us consider the usual expression for Diffusion processes and diffusion coefficients in the Eyring's theory: $$D=\lambda^2k = \lambda^2 \frac{k_BT}{h}\frac{\Omega_\ddagger}{\Omega}e^{-\frac{\...
Giuseppe Basile's user avatar
9 votes
2 answers
699 views

Why are ions in water not paired?

This question is about ions in water, both in reality and as handled by MD (explicit solvent) and QM methods (eg AIMD). Basically the question is this: why are ions not always paired? For a back of ...
Alex I's user avatar
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5 votes
1 answer
331 views

Using DFT to study Hydrogen Evolution Reaction on a surface?

How well can DFT, as implemented in VASP, describe surface reactions? For example, I want to study the hydrogen evolution reaction (HER) on the $(111), (110), (100) \text{ and } (011)$ surface planes ...
thehereandnow's user avatar
9 votes
2 answers
255 views

How to analyze density of states?

I have plotted the density of states (DOS) for my System with Hydrogen-rich and hydrogen lean . When the system is Hydrogen lean, the valence band maximum (HOMO) shifted towards Fermi level and ...
astha's user avatar
  • 1,663
5 votes
0 answers
135 views

What is the relation between enthalpy, ionization potential, internal energy and HOMO/LUMO? [closed]

Is there any relation between enthalpy, ionization potential, internal energy and HOMO/LUMO? I am dehydrogenating a molecule and I need to study the enthalpy of dehydrogenation. If I get any relation ...
astha's user avatar
  • 1,663
7 votes
0 answers
228 views

Collective variable to determine the number of bonds in the shortest Hydrogen bond wire [closed]

I am trying to program a collective variable in PLUMED which is basically the number of bonds in the shortest Hydrogen bond wire in a system of water molecules. I plan to use the HBond_Matrix from ...
fireball.1's user avatar
  • 1,083