Questions tagged [computational-chemistry]
For questions about computational chemistry.
82
questions
5
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0answers
19 views
Confused by NBO output, due to missing bonds
I'm about to do an NBO analysis to evaluate bond characteristics in a novel transition-metal complex.
As I have never done anything like that, I tried to understand the basic output for an octahedral ...
6
votes
1answer
45 views
NBO Calculation failing (ATDIAG DISCRD)
I'm trying to perform NBO calculations on a bimetallic complex to evaluate bond orders. However, while I've previously done NBO calculations to obtain partial charges which worked without problems, ...
5
votes
1answer
43 views
Change in RDKit's encoding of InChi?
Using RDKit (2020.09.5) I would like to assign InChi to molecules expressed as SMILES and fail to replicate this GitHub gist for initial training written about 2 years ago (RDKit 2019.03.2). I would ...
8
votes
2answers
122 views
Why are method developments and new implementations not done much in Gaussian?
While I have seen many papers in which Gaussian is used in calculations, I have not seen any paper in recent times where new methods are implemented in Gaussian. The latest paper I could find ...
8
votes
0answers
56 views
Visualizing wavefunctions in real space
I would like to generate wavefunctions as functions of spatial coordinates (X, Y, Z) using Gaussian G09 and then visualize them. How might I go about doing this? I am using Linux and my preferred ...
5
votes
0answers
48 views
How can I add double bonds to Triazine-derivatives for OpenBabel generation of pdbqt files?
The double bonds are initially present at the sdf file but disappear or are misplaced after .pdbqt conversion. I tried all kinds of combinations using renumbering ...
8
votes
1answer
111 views
Difference between original STO-3G and BSE STO-3G
I am trying to work with the STO-3G basis set, but I noticed that the STO-3G in Basis set exchange is different from the STO-3G originally published, and not only that, the BSE version seem to be ...
6
votes
1answer
91 views
How to extract transition density cube from .fch file in Gaussian?
I have been trying to extract the transition density cube of a simple molecule, $\ce{H_2O}$. I did a regular geometry optimization and then TD-DFT calculation with a keyword ...
6
votes
1answer
161 views
Calculate number of electrons per shell for an atom
Suppose you are given the atomic number of an element, e.g. Technetium, which is 43. Is it possible to return an array which shows the distribution of electrons across different shells of an atom ...
12
votes
3answers
1k views
Why is uncertainty not a big problem in computational chemistry?
The molecular Hamiltonian (or, for simplicity, the Fock operator) contains coulomb potentials as well as momentum operators. To evaluate the coulomb potential, we need to know where the electrons are. ...
4
votes
0answers
36 views
Calculating emission spectrum of organic compounds by DFT. Can someone elaborate in terms of calculating it for aggregatrion induced emission? [closed]
I am planning for the calculation of emission spectra of organic compounds showing the phenomenon of aggregation-induced emission (AIE). Can someone help me get started?
11
votes
1answer
224 views
What units are used in Gaussian 16 for dipole derivatives output?
I ran a frequency analysis employing Gaussian 16 on MP2/6-31+G(d,p) level of theory with the keyword iop(7/33=1) in order to have access to dipole derivatives with ...
8
votes
1answer
72 views
Excited states using ORMAS flag in GAMESS
I am trying to calculate the excited states using single reference CISD on $\ce{CH3OH},$ using ORMAS' CI-X option in GAMESS. As a test example I am using the $\ce{CH3OH}$ that has 2 core, 7 occ. ...
10
votes
3answers
547 views
Which DFT functional should I use to simulate spectra of pesticides?
I am mainly searching for functionals to calculate spectra of pesticides. I found the benchmark test from Goerigk and Grimme$^1$, but don't understand which of the functionals suits my purpose the ...
8
votes
1answer
67 views
Calculation of dispersion energies for organometallic complexes with Gaussian
I've tried to calculate dispersion energies of some organometallic complexes with the Gaussian software using WB97XD/Gen (...
25
votes
3answers
1k views
What does B3LYP do well? What does it do badly?
I have seen a general criticism of B3LYP in computational chemistry (especially with the 6-31G* basis set). I would like to know some of the more/less obvious problems that occur when using it and ...
10
votes
2answers
86 views
How to create a differential spectrum from two simulated spectra, calculated by two different basis sets?
In my bachelor thesis, I compare simulated IR-spectra computed by different basis sets. The simulated spectra from sets like cc-pVTZ and cc-pVQZ are too similar to compare them by plotting them next ...
8
votes
1answer
180 views
Problem obtaining a Raman spectra of a graphene structure
I am trying to obtain the Raman spectra of a graphene structure using Gaussian. I used the input below, but when I did it, I got this error:
...
7
votes
1answer
64 views
What does "Test job not archived" mean?
I am running frequency computation with geom=connectivity in Gaussian. It all converges now but at the very end of the last convergence it says:
...
10
votes
1answer
129 views
How to generate accurate displacements along normal modes?
How can i displace my structure along a particular normal mode, without coupling to other modes ? Rather than a exact mathematical procedure, I am more interested in a software/script/package that can ...
11
votes
2answers
62 views
What is the most appropriate (and easy-to-use) all-atoms force field for liquid electrolytes?
I need to simulate a salt diluted in a liquid electrolyte. My experience is with LAMMPS, but so far I only had coarse grained toy models, and setting up the force field was straightforward. Now I have ...
6
votes
1answer
45 views
Vibrational frequency analysis for NEB result through Maestro
I have ran a Nudged Elastic Band (NEB) calculation using QuantumEspresso through Maestro to find the potential transition state. Within Maestro there is an option where you can select for NEB type ...
10
votes
1answer
121 views
Computing optimized 3D structures in python that take solvent into account
I have been using RDKit to generate 3D coordinates, cleaning-up the structures using a general-purpose force field as follows:
...
10
votes
1answer
147 views
What novel drugs are developed via CADD?
Virtual screening , protein ligand docking, MD simulation, FEP free energy calculations and the QM/MM approach have all been widely applied in optimization for drug discovery.
Which drugs that have ...
12
votes
1answer
76 views
Excited state energy gradient during geometry optimization of a target excited state
During the geometry optimization of the ground state of a molecule, we try to optimize the energy
gradient with respect to the nuclear positions such that the system remains in its lowest energy
state....
6
votes
0answers
65 views
Two-stage unbinding & binding energies with DFT
I'm trying to calculate the stability of the product of a coordinate bonding process of molecules A and B in the polarizable continuum solvent model (PCM, solvent set to water).
I'm getting energies ...
9
votes
1answer
104 views
Understanding emission spectra using TDDFT calculation
I did a TDDFT calculation to get the emission spectra of my molecule. Here are the first five roots for the emission calculation:
...
7
votes
1answer
360 views
Formation energy and Energy above convex hull as indicators of stability
I was trying to understand some indicators about the stability of materials (that basically tell you whether it can be synthesized or not.. right?).
Specifically, I'm trying to link the knowledge of ...
7
votes
1answer
36 views
The number of long-range interaction pairs in Tinker
I tested MM calculation of a benzene molecule with Tinker. The following is the xyz file used for the input.
...
13
votes
1answer
135 views
Are nuclear ab-initio methods related to materials ab-initio methods?
I just read this synopsis in Physics where scientists used first-principles nuclear physics calculations to predict the stability of 700 isotopes up to iron.
I didn't know that this was possible, ...
5
votes
0answers
98 views
What is the relation between enthalpy, ionization potential, internal energy and HOMO/LUMO?
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 ...
8
votes
1answer
94 views
Error running psi4 on charged molecules
I am running a simple energy calculation on a conformer of 3-Sulfopropyl methacrylate, which is given my C=C(C)C(=O)OCCCS(=O)(=O)[O-].
This is my workflow:
...
12
votes
1answer
201 views
How to get more significant digits from OpenBabel?
I am generating conformers from SMILES string using OpenBabel.
The shell script looks something like:
...
9
votes
1answer
311 views
Using OpenBabel or RDKIT Python API to generate conformers from a SMILES string
I have a bunch of monomers in the form of SMILES string and I want to generate conformers from them.
At the moment, I am using RDKit to convert these SMILES strings to .sdf files, then using ...
8
votes
2answers
255 views
How do I figure out how many monomer configurations I need for my simulation?
I am running a quantum mechanical simulation on Psi4 for a certain number of monomers to generate data for a database. Some of these monomers are short, while some are long.
At the moment, I am ...
10
votes
1answer
143 views
Calculating/Visualizing electronic density from orbital information written in the Molden format
I'm trying to obtain an electron density from orbital information written in the Molden format by the formula,
$$
\rho(\mathbf{r}) = \sum_{i}^{occ} |\phi_{i}(\mathbf{r})|^{2}. \tag{1}
$$
Is there any ...
9
votes
3answers
391 views
What is the procedure for constructing an ab initio potential energy surface for CH3Cl + Ar?
I would like to construct a model analytical potential function for collision between CH3Cl and Ar. This would be the sum of CH3Cl intramolecular + CH3Cl---Ar intermolecular potential. First I would ...
9
votes
2answers
353 views
What are Pair Natural Orbitals?
Recently, I came across electron correlation methods that use local pair natural orbitals (LPNOs) or domain-based local pair natural orbitals (DLPNO), such as DLPNO-MP2, DLPNO-CCSD etc. The dynamic ...
9
votes
1answer
93 views
Energy cut-off value for conformer calculations
I want to get familiar with the conformer calculation. I found a paper where they did the conformer calculations already for the molecule I work with. The paper can found here.
In the experimental ...
8
votes
1answer
45 views
Simulation of electronic potential from nanoparticles interacting with molecules
I work with SERS, where the Raman signal gets enhanced by the electric field of the nanoparticles. Now I like to simulate this kind of spectrum with Gaussian. I found a paper[1], where it looks very ...
11
votes
1answer
238 views
What are some of the biggest theoretical and computational challenges in Condensed Phase Chemistry?
What are some of the biggest open-questions / challenges in Condensed Phase theory and computation? What efforts are being done to answer them?
I realize Condensed Phase chemistry is a huge field, but ...
6
votes
1answer
571 views
How to choose starting magnetization while doing spin polarised calculation in Quantum ESPRESSO?
I am trying to run spin polarised DFT calculation in Quantum ESPRESSO on system Co2MnSi. I kept starting magnetization for all these three species as,
...
10
votes
1answer
131 views
What are the trade-offs setting DIRSCF to either .TRUE. or .FALSE. (the default) in GAMESS (US)?
The first software I used to run calculations was Gaussian09. When submitting a input, I used to see a pattern of resource usage where the allocated CPU quickly maxed out, remaining high most of the ...
12
votes
1answer
89 views
How can one computationally determine the flammability of a molecular system?
I can imagine one aspect of flammability (the ability of a substance to ignite on fire) to include calculating the kinetics and thermodynamics of the reaction of the system with oxygen. This is not ...
8
votes
1answer
184 views
Which basis set should be used for a system that contains both anions and cations?
I am trying to model a system that has both anions and cations interacting with each other. (In this case it is calcium ion interacting with two small carboxylic acid molecules). Now, looking through ...
11
votes
0answers
81 views
Bioisosteric replacement using SMARTS (KNIME and RDKit) [closed]
I am trying to create a KNIME workflow that would accept a list of compounds and carry out bioisosteric replacements (we will use the following example here: carboxylic acid to tetrazole) ...
15
votes
2answers
118 views
What is the difference between orbital localisation and NBO?
I am new to computational chemistry, I have used mainly GAMESS and Orca. In GAMESS, there are orbital localisation schemes like Pipek-Mezey, Ruedenberg-Edminston, etc. which generate orbitals that ...
13
votes
2answers
313 views
How to get potential energy surface from GAMESS?
I'm trying to learn GAMESS and performing a simple PES scan of oxygen molecule. After the completion of the calculations I get a .log file with lots of sections like that:
...
8
votes
1answer
1k views
What is the physical meaning of occupations='smearing' in Quantum ESPRESSO?
I want to understand, what is the intuition behind using the occupations='smearing' or 'tetrahedra' in Quantum ESPRESSO input file? I mean how we can interpret what is going to happen inside of ...
9
votes
1answer
563 views
How to do spin polarization calculations using Quantum ESPRESSO?
I am currently new to DFT calculations in Quantum ESPRESSO. Though, I have read some research papers for determining spin polarization and Half-metallicity in certain Heusler alloys. These research ...