All Questions
Tagged with computational-chemistry reference-request
23
questions
3
votes
0
answers
85
views
How does one calculate the electronic difference density in practice?
I am interested in calculating electronic difference density maps. These have been described for quite a long time by Bader and others. For example, below is the fourth of a series of papers which ...
- 13.1k
4
votes
0
answers
83
views
Calculating the energy of a molecule using probability distributions
I wish to calculate the energy for a protein where the position of all the C-alpha atoms is known.
One way is to calculate the pairwise distances between the atoms and then look up a probability ...
- 73
6
votes
0
answers
278
views
Where to find experimental spin-orbit coupling constants?
I am searching for experimental spin-orbit coupling constants, particularly for main group elements and Cr(0) to calculate correlation consistent Composite Approach (ccCA) energetics. This method ...
- 61
4
votes
1
answer
2k
views
Reference on Pople basis set
I need to write reference on 6-311++g(d,p) basis set in my work where I used it on atoms of I-II periods. Does anyone know where it was first published?
- 155
2
votes
0
answers
126
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Antisymmetrized Product of Strongly Orthogonal Geminal (APSG) method
To get a deeper understanding of electronic structure methods, like Hartree-Fock, MP2, and Coupled Cluster method, there are many small programs (codes) available in Python, C++ or Fortran, for ...
- 131
10
votes
3
answers
851
views
What is Nesbet's theorem?
In a talk by Frank Neese there was a slide with title "Nesbet's theorem" and an equation indicating something like "if your wavefunction has the double excitation amplitudes correct, then you can get ...
- 1,452
4
votes
1
answer
414
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Where can I get potential energy surface for simple molecules?
I'm looking for potential energy functions for simple molecules, such as water or hydrogen sulfide. I only need the region around the equilibrium geometry, preferably as a Taylor series expanded in ...
- 1,696
3
votes
0
answers
122
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Error hunting: Guidelines on detecting error cancellation and locating their sources as much as possible?
It is known in computational chemistry, when computing e.g. electronic ground states energy and geometric paramters (bond lengths, angles, torsions etc.) of a given molecule using an ab initio or DFT ...
- 698
18
votes
3
answers
5k
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Modern open-source tools for simulation of NMR spectra
I am interested in predicting the NMR spectrum of small organic compounds. It doesn't matter to me if the prediction is very accurate. I'll eventually be comparing the prediction to experimental ...
- 22k
19
votes
3
answers
736
views
Do modern dispersion-corrected DFT methods give more accurate molecular geometries?
I was discussing with a colleague the use of modern dispersion-corrected density functionals. I take it almost as a given that the methods generally produce "better" (for some definition) geometries, ...
- 27.9k
8
votes
1
answer
402
views
Tunneling corrections in reaction rates
I've studied Transition State Theory since I asked this a while ago, but so far I have not been able to find a detailed explanation of how tunneling corrections are implemented into reaction rates ...
user28429
22
votes
1
answer
970
views
DFT Code for Atoms : Sources
Some time ago I implemented the restricted and unrestricted Hartree-Fock methods. I had a lot of fun and I learned a lot. It goes without saying that Szabo and Ostlund's book "Modern Quantum Chemistry"...
user23061
13
votes
1
answer
1k
views
Why does bond length decrease with increased basis set quality for SCF methods?
From Reviews in Computational Chemistry Vol. 5, for $\ce{H2O}$ using HF, MP2, CCSD, and CCSD(T), all lengths in angstroms:
$$
\small
\begin{array}{rcccc}
\text{Basis} & \text{HF} & \text{MP2}...
- 7,499
10
votes
3
answers
981
views
Free chemical database to search for physical properties?
I am looking for an Open-access tool that can search "backwards", eg. give me all the structures corresponding to a given heat of formation, critical pressure, etc. It would be even better if the ...
user23638
4
votes
1
answer
222
views
Suggestions for simulating transport through membranes with Molecular Dynamics (MD) and Monte Carlo (MC)?
I'm intending to perform a simulation of the transport of simple ions or water through perm-selective membranes, using Molecular Dynamics (MD) and/or Monte Carlo (MC). I've read around that, in ...
- 323
6
votes
1
answer
1k
views
Carbohydrate configurations
I want to study several carbohydrates that includes but not limited to the following molecules:
Glucose
Galactose
Mannose
Fructose
Tagatose
Sorbose
I know that for any carbohydrate, possible list of ...
- 2,487
9
votes
3
answers
2k
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InChIKey generation from InChI
I am trying to find some good resources to understand generation of InChIKeys from the InChI. There seems to be no resource available online. I have gone through the Wikipedia article for InChI, but ...
- 179
8
votes
1
answer
2k
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Difference between single point energy and dimerization energy
I am investigating potential energy surface characteristics of some electrostatic monomeric interactions e.g. $\ce{F-H}$...$\ce{F-H}$.
I'm using DFT and SCS-MP2 to perform the necessary calculations ...
- 683
9
votes
0
answers
898
views
Free Web-Based Orbital Solver to look into the Walsh orbitals of a perturbed cyclopropane
There exists a free online orbital calculator.
When I draw cyclopropane it plots three molecular orbitals, but unfortunately it doesn't use the Walsh orbitals.
Are there any free online tools which ...
- 3,405
8
votes
3
answers
282
views
Is it wise to use ECPs on light atoms for electronic structure calculations?
So, I have a big organic molecule consisting of $\ce{H}$, $\ce{C}$, $\ce{O}$, and $\ce{N}$ atoms and the goal is to find its equilibrium geometry and US/Vis spectrum. The molecule is so big that I was ...
- 19.1k
2
votes
1
answer
118
views
Book recommendations for protein structure refinement
I’m an undergraduate Chemistry student and I’m currently writing my dissertation about semi-empirical methods, particularly PM7, applied to protein structure refinement from X-ray structure. Could you ...
5
votes
1
answer
216
views
Quotable Literature for the Enthalpy of a Proton
A proton obviously has no electronic energy, no vibrational and no rotational degrees of freedom. Therefore I think it is fair to assume, that $$H(\ce{H+})=\frac32\cdot \mathcal{R}\cdot T$$ holds for ...
- 44.3k
11
votes
1
answer
593
views
Database for molecular dipole transition moments?
I'm looking for the dipole transition matrix elements for electronic transitions between the ground and excited states of the carbon dioxide cation, $\text{CO}_2^+$, that is, objects like
$$\langle\...
- 493