All Questions
Tagged with free-energy computational-chemistry
9
questions
4
votes
2
answers
1k
views
How to estimate the temperature needed to overcome an activation energy barrier?
Trying to elucidate a reaction pathway, I calculated the energies for different transition states possible for that reaction (computational chem. DFT). I found activation free energies ranging from 29 ...
3
votes
0
answers
111
views
Gibbs free energy of mixing in a control volume
I'm trying to model the amount of energy lost due to mixing of a $\mathrm{HCl}$ solution using the Gibbs free energy of mixing. However, I really like a second opinion on the model and the results, ...
- 131
6
votes
1
answer
141
views
How does DeepHF (a CRISPR sgRNA design tool) compute binding free energy?
I am looking at the code of DeepHF[1] that computes $\Delta G_\text{binding}$, and I see that it breaks a sequence into overlapping dimers and compute a weighted sum according to a dictionary with 16 ...
- 924
1
vote
0
answers
182
views
Calculating the free energy of separation in AMBER
I am currently busy with my master's research project and I'm trying to calculate the free energy of separation of two cellobiose molecules in ionic liquid, that is, calculate the free energy of ...
1
vote
1
answer
439
views
How can absolute binding free energies be calculated?
In the calculation of binding free energies, such as between a protein and a ligand, I learned that absolute values cannot be obtained from simulation (such as taught in this lecture, slide 2). Rather,...
- 1,118
4
votes
1
answer
322
views
Transition state and intermediate very close to each other
I've been studying a particular reaction with DFT, where a transition state and the following intermediate are very close to each other. The change in geometry is rather small and therefore the ...
- 1,449
19
votes
1
answer
549
views
How to treat pressure in computational chemistry?
I have a reaction where a gas at high pressure and a solution with all kinds of species is involved. How do I take pressure correctly into account to get reasonable values for $G$?
Do I calculate ...
- 1,449
1
vote
0
answers
158
views
Why are non-polar hydrogens neglected in computational protein-drug binding studies?
Why are (non-polar) hydrogen atoms generally neglected in a protein-ligand (or drug) binding energy calculation? They do have charge and mass. Doesn't that affect the free energy calculation?
The ...
- 517
3
votes
1
answer
400
views
Software for chemical reaction simulation in ICE
I want to study what happens in a internal combustion engine in which fossil fuels are mixed along with other chemical additives.
Example:
Acetone drastically reduces surface tension.
Most fuel ...
- 31