Questions tagged [computational-chemistry]

A field which employs computers to model and study chemical systems and chemical behavior, using various models, from approximations of the Schrödinger equation to Monte-Carlo simulations, to modeling with differential equations.

246 questions with no upvoted or accepted answers
Filter by
Sorted by
Tagged with
3
votes
0answers
60 views

The difference between bonding and unpaired single electron radicals

I was wondering as to why would two unpaired single electron radicals form a bond. So, I tried to compute the added ground state energies of two particles in two distinct, yet identical boxes, The ...
3
votes
0answers
158 views

Minimum image convention and the atom “seeing” itself

The minimum image convention in molecular dynamics can be stated as: A particle in the central square must not interact with one of its neighbors in the central square and an image of this neighbor ...
3
votes
0answers
94 views

Precision of non-adiabatic couplings

Let me ask a question about the differentiation of Non-Adiabatic Couplings (NACs), specifically the terms $D_{IJ}$ and $d_{ij}$. According to the Pyxaid paper, the set of $D_{IJ}$ computed via Slater ...
3
votes
0answers
85 views

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 ...
3
votes
0answers
212 views

Transition state search for rotational motion

This question is regarding Gaussian Computational software package. I have a system where one product forms from one conformational arrangement of molecular intermediate (conformational minimum) and ...
3
votes
0answers
135 views

Why is the spin magnetic moment for nickel(II) given as 1.7 Bohr magnetons in some references?

I read some theoretical articles concerning $\ce{Ni-O}$ system, where $\ce{Ni}$ sits at the center of the octahedron formed by $\ce{O}$. The calculated magnetic moment on the $\ce{Ni}$ sites is about $...
3
votes
0answers
67 views

Questions about Genetic algorithm paper of Gilman and Ross

I want to reproduce an (old) biochemistry paper of Gilman and Ross, i.e. " Genetic algorithm selecetion of a regulatory structure that directs flux in a simple metabolic model." ( The following link ...
3
votes
0answers
98 views

Predicting dissociation energy of diatomic iodine computationally

In one of my classes we used ORCA with three different functionals: BP86, B3LYP, and M06-L, all with the basis set def2-SVP. In addition to calculations we did it experimentally by a Deslandres table ...
3
votes
0answers
77 views

Is it possible to “brute-force” material creation through algorithms?

I know its a bit of a soft question, but lately I've wondered what important properties and calculations would a program that iterates through certain types of molecules and atoms need in order to ...
3
votes
0answers
423 views

Are there any free pharmacophore modelling software?

I would like to know if there is any free and relatively updated software to getting started in pharmacophore modelling.
3
votes
0answers
98 views

What closure relations can we use in molecular modelling?

Following my question here about the BBGKY hierarchy I was wondering does anyone have any experience in using the method outlined. In particular how would I take an equation off the page and for some ...
3
votes
0answers
948 views

Are multiple transition states possible? Criteria to choose the correct one?

I am studying a reaction using electronic structure methods using various software packages (ORCA,GAMESS, G09) and have found two possible transition structures between product and reactant. Both have ...
3
votes
1answer
142 views

How are orbitals displayed in computational Chemistry software?

In typical software like Gaussian or GAMESS, the molecular orbitals (or even the basis functions) can be displayed as surfaces. I understand that the surface is probably constructed from a series of ...
2
votes
0answers
47 views

Virtual screening lib

I had a quick question on virtual libraries. I'm hoping to perform a virtual screen using a library that contains very small, soluble compounds - think glycerol and smaller (<100MW). As far as I ...
2
votes
1answer
87 views

Solution of the Roothaan Equations of H2 by Symmetry Arguments

FWIW my background is in physics and maths, but I am just starting a chemistry PhD (the last time I took a chemistry class was high school). I have only some background in representation theory, and ...
2
votes
0answers
38 views

Negative coefficients for DIIS in SCF procedure

I am trying to implement the direct inversion of the iterative subspace (DIIS) algorithm in my simple HF program. After some problems it now seems to work. I can calculate the correct energies in ...
2
votes
0answers
34 views

How to create a Potential Energy Surface in Chemcraft?

The Chemcraft website says that it is possible to create a potential energy surface. Nevertheless, it doesn't work for my Gaussian scan job. ...
2
votes
0answers
37 views

How are class II force field cross-terms derived?

In some class II force fields, there are cross-terms that characterize bond-bond, bond-angle interactions and others. Example of equations below: $$\sum_{bond-bond}^{}k_{bb}(b-b_{0})(b^{'}-b^{'}_{0})$$...
2
votes
0answers
39 views

Bioisosteric replacement using SMARTS (KNIME and RDKit)

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) ...
2
votes
0answers
68 views

What are the alternatives we have to the VEDA 4 vibrational energy distribution analysis software?

Said software is very useful when you need to assign the peaks in vibrational spectra to different vibrational modes found in a hessian calculation for a given molecule, as described in Jamróz, Michał ...
2
votes
0answers
39 views

Energy decomposition analysis. Are there schemes that actually splits up the steric term?

In quantum chemistry, there are many types of energy decomposition analysis (EDA) which partitions the interaction energy between two or more fragments into steric, polarisation, exchange and orbital ...
2
votes
0answers
80 views

Generate Surface with CubeFile from Gaussian in VMD or other free programm

I asked a question before, about how to save a mapped surface from GaussView. I don't get an answer, so I get much deeper in my internet research about it again. Now I want to try to create a mapped ...
2
votes
0answers
53 views

How to extract a image (vector graphic) from a surface EPS plot with GaussView?

I am quiet new to this field of chemistry. I work with GaussView and I created a surface plot for my molecule with the cube and surface generator. This works very well. Now I like to save and copy ...
2
votes
0answers
59 views

Is Tkatchenko's MBD-NL method self-consistent?

I have a question regarding Tkatchenko's [1] new nonlocal many-body dispersion method (MBD-NL). Does anyone know if it's a self-consistent method? I read this paper many times but I'm still not sure. ...
2
votes
0answers
73 views

Grouping QM9 molecules

I have recently been reading a paper, in which given dihedral angles of alanine dipeptide molecule $\psi$ and $\phi$, the conformation is catagorized as either $\beta$-1, $\beta$-2, or $\alpha$. I was ...
2
votes
0answers
257 views

How do I interpret GAMESS thermochemistry output?

In GAMESS's thermochemistry output, which numbers mean what? The gaussian docs have a nice description of how to use thermochemistry data, but for gaussian's output. This appears to be different, eg, ...
2
votes
0answers
707 views

Kinetic Diameter: How to calculate it? Pressure influence?

Wikipedia states: Kinetic diameter is a measure applied to atoms and molecules that expresses the likelihood that a molecule in a gas will collide with another molecule. It is an indication of the ...
2
votes
0answers
30 views

Order of features in chemical descriptors

ECFP are small-molecule descriptors, which are usually represented as a bit vector. I wonder if order of elements of this vector matters, in other words, if this vector encodes any positional ...
2
votes
0answers
27 views

Is there a way to extract the diamagnetic and paramagentic components from NMR output from Gaussian16?

I'd like to be able to split the NMR value in Gaussian16 into its diamagnetic and paramagnetic terms. I'm coming over from ADF, where this can be done easily. Is there a straightforward command to ...
2
votes
0answers
68 views

Available datasets to study using Hückel theory

I'm trying to do some tests using graph Laplacians based on Hückel theory. This, however, is said to be only applicable for conjugated hydrocarbons. My questions are: I have been working with QM9 ...
2
votes
0answers
70 views

How do computational chemistry programs determine the irreducible representation of a molecular orbital?

I was coding a simple RHF code to test my understanding of computational chemistry when I stumbled upon this question. How exactly do computer programs like Gaussian, GAMESS-US etc. know which ...
2
votes
0answers
38 views

What kind of algorithm does computational software use to process molecular symmetry?

Background I'm forced into using GAMESS-UK for an older software package. Using a cs-symmetry molecule, I've noticed that GAMESS will reorient the molecule before running a standard SCF calculation. ...
2
votes
0answers
74 views

Why does a 4-bonded nitrogen atom appears negatively charged after an optimization?

I have a molecule bearing a quaternary ammonium and I optimized it using M062X (also Hartree-Fock) using basis sets 6-31G(d,p) and 6-31G+(d,p) respectively. After optimization, I expect that the ...
2
votes
0answers
52 views

What happens if an orbital has no entry in a point group table?

A while ago I cited a few passages from a book on $f$-orbital contributions in metal complexes. And although usually the $4f$-orbitals are too isolated to really do chemistry and the elctron density ...
2
votes
0answers
45 views

Rotating dihedral and Angles And Generate File For Each Degree

I need to optimize a force field I generated. For this, I should apply Genetic Algorithm (G.A). To apply G.A I should do this for 220 molecules: 1) Find all dihedrals for each molecule ( I did this ...
2
votes
0answers
145 views

DFT Exchange-Correlation Two Electron Integrals

Are there any electronic structure programs that print the exchange-correlation (XC) integrals for a given DFT functional? These integrals are of the form $$\langle pq|w|rs\rangle$$ where $w$ is an XC ...
2
votes
0answers
91 views

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 ...
2
votes
0answers
46 views

Perturbation theory for molecules, chromophore group, dipole approximation,

I am interesting in chromophore group and dipole approximation. For example, i have a molecule (acetone or any other ketone/enol) which is belongs to some symmetry group. Because of the symmetry ...
2
votes
0answers
194 views

Amber Force Field Improper Parameterization Huge Kb Problem

I am trying to parameterize a molecule. I know dihedrals and impropers are the same for Amber Force Field. (Source: http://archive.ambermd.org/201004/0334.html) So, I did PET scan for improper and I ...
2
votes
0answers
39 views

tolerable error, CASSCF simulation of UV/Vis spectrum

Please forgive my ignorance of experimental spectroscopy. I am a computational chemist, not an experimental one. My question is: what would be considered a tolerable or reasonable difference between ...
2
votes
0answers
252 views

Natural orbital population analysis in Gaussian

Within (restricted) density functional theory and Hartree-Fock, respectively the Kohn-Sham orbitals and spin orbitals are the natural orbitals, with occupation numbers either 2 or 0. As I understood, ...
2
votes
0answers
81 views

Generating density matrix of a wavefunction from common quantum chemistry software

I am looking for density matrixes for a couple of closed shell and open-shell systems, and I wonder if there is a trivial way to make e.g. Gaussian just generate an output for me. I may be wrong but ...
2
votes
0answers
49 views

Geometry optimisation in Gaussian09

I have looked at various sources regarding this, including the Gaussian official website. However, I have not managed to understand the geometry optimisation method used by Gaussian, a method known as ...
2
votes
0answers
456 views

Putting high symmetry points labels to a band structure plot

So far I've got this plot using Quantum Espresso. I want to put gamma, X, L, etc labels to the k-path. Quantum Espresso's ouput states the following: ...
2
votes
0answers
129 views

Q-chem equivalent solvent settings for Gaussian NMR ab inito methods

I'm attempting to use Q-Chem 5.0 to replicate CHESHIRE-esque http://cheshirenmr.info/ ab initio calculations of chemical shift values. Unfortunately Gaussian seems to be the predominant tool in this ...
2
votes
0answers
176 views

Implementing the projected atomic orbital (PAO) localization in Gaussian

I am currently attempting to learn how to setup the active space for performing CASSCF calculations. The textbook I am using as a reference is: Roos, Björn O. "Multiconfigurational quantum ...
2
votes
0answers
178 views

Slater Determinant in Python package

Is there any library functions which I could use in python to construct slater determinant? Can someone suggest me something to fix this issue ? Is it really possible to determinant with functions as ...
2
votes
0answers
102 views

Non central chirality in cheminformatics?

What are compact cheminformatics structural representations that allow to deal correctly with axial chirality, such as in binaphthyl compounds or metal complexes?
2
votes
0answers
31 views

How to determine charge of compounds in solution with many amphoteric functional groups?

I am curating a metabolic model that has compounds such as NADH/NADPH/Etc. that have multiple ionize-able hydrogens. Normally with amino acids there are only a few hydrogen with varying pKas that ...
2
votes
0answers
143 views

Creating an IR Spectrum using Gaussian ADMP Calculation

I have a Gaussian 16 trajectory for a small cluster of water molecules carried out with ADMP technique. I was wondering if anyone knows how to compute the IR spectrum from the information in the ...