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.

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34 views

How to control the optimization step size in Gaussian?

I would like to perform a geometry optimization for a weakly bound methane dimer structure with Gaussian 16. During this process, the Newton-Raphson step should be controlled such that its length ...
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1answer
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Aluminium oxide phase diagram

I have been looking for the phase diagram of alumina or Aluminium oxide, could it be that there is not something like that? thank you
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3answers
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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, ...
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1answer
250 views

Calculating Mixing Enthalpy in GROMACS

What is the most reliable way to calculate mixing enthalpy of binary solvent mixture using GROMACS? [EDIT] I have simulated two-component systems of water and organic solvent with GROMACS. In a ...
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1answer
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Existence of Hartree–Fock limit

I'm reading McQuarrie's Physical chemistry textbook [1]. On p. 281, the author explains: If we use a more flexible trial function of the form in which $\psi(\mathbf{r_1},\mathbf{r_2})$ is a product ...
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Mulliken Spin Density

I would like to know if a Mulliken population analysis to calculate spin densities is in general a valid choice. I see that it is made use of, for example here1. So up to-date researches apparently ...
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How to sort and extract multiple structures form a PES-Scan file?

I calculated a PES scan of Propylcyclohexane in gaussian. ...
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128 views

Are there any molecular modeling programs that can build materials made up of three or more elements into a cylindrical shape?

I would like to build a material similar to what is in the image below. I have tried programs such as Material Studio, Quantum ATK, and VNL, but most of them can only do materials with 2 elements.
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1answer
105 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 ...
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How to find bond lengths from .cif files of crystal structure

I am confused about how to calculate the bond lengths within a given structure given its .cif file. I have highlighted the bond of interest in the image below. The atom coordinates are shown in the ...
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2answers
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Coefficients and Parameters for contracted Gaussian basis sets

I'm trying to write a program to calculate fixed-point Hartree-Fock level energies of molecules (for my amusement) and everything makes sense but this. I've been agonizing over this for almost 3 hours ...
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2answers
55 views

How to convert an XYZ file to Z-matrix?

I would like to generate a Z-matrix from the following XYZ file (C2H6dimer.xyz): ...
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2answers
77 views

How to compare three or more molecular structures? [closed]

Let's say you have three or more different geometry files (xyz) for the same structure and you want to compare them. What would be best way for that?
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1answer
53 views

Why does DFT-D finds different optimized geometries for the same structure when using different input geometry files?

When I change c lattice parameter and optimize the structure with DFT-D, every time I get a significantly different geometry with different energy? Why is this happening with DFT-D?
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Why is the water solubility of CO worse than that of CO2?

I tried my best to ask SciFinder, Google, and Google Scholar the wrong questions ... I found many paper on the fitting of the solubility to some equations to be able to calculate the amount of $\ce{CO}...
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1answer
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Are primitive GTOs normalised before contraction, or is the resultant basis function normalised afterwards?

I'm quite curious about this: In a basis set (I'll just use minimal-basis STO-nG basis sets for convenience), the basis functions are written as a linear combination of primitive GTOs. Are the GTOs ...
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What are the signs in `_atom_site_label` in a CIF file mean?

I am trying to write a program that will be able to read CIF files. I am testing on a CIF file like this: ...
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963 views

How can I update a map/mesh and coordinates in a PyMol session file?

I have a PyMol session file I was using to create my figures. It contains a protein and ligand broken into several groups of atoms with a fair bit of overlap. There are also a few meshes built from ...
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2answers
295 views

Search by CAS Registry name to obtain trackable accession: ie InChI?

I'm updating a database and trying to move from CAS Registry names to InChIKeys. I have about ~800 compounds to track. Is there a way to do this mappings programatically? I'm looking for a web service ...
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61 views

What are the rules for constructing Kohn-Sham orbitals?

I just recently began to study quantum chemistry and need some clarification for the construction of Kohn-Sham orbitals. Consider a system of several atoms. Let there be $N$ electrons in this system. ...
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1answer
42 views

Associated occupation numbers of frozen natural orbitals (FNOs) from MP2 method

The paper Frozen Virtual Natural Orbitals for Coupled-Cluster Linear-Response Theory gives the following (simplified) description of frozen natural orbitals (FNOs). In the MP2 method, the unrelaxed ...
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3answers
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Program that simulates basic reactions in organic chemistry

To explain - a friend and I have been working on a program that would allow you to draw organic molecules, indicate the conditions, and predict the products. This would be primarily aimed at basic, ...
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1answer
519 views

What is the reason for including excited states in the wave function in post-Hartree Fock methods?

I'm new to computational chemistry, so perhaps this question has an obvious answer. I'm wondering what the intuitive reason for constructing Slater determinants that involve excited states is, when ...
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49 views

How do I display a potential energy surface with molden?

I calculated a gaussian scan job for propylcyclohexane with two dihedral angles. Now I want to display a potential energy surface for that molecule with molden. I am new to molden and only found the ...
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3answers
668 views

Conversion of Hessian from internal coordinates to cartesian coordinates

I have performed a CASPT2 frequency calculation using the MOLCAS8 program package. I need the full Cartesian Hessian matrix as input for a subsequent program package. MOLCAS8 performs CASPT2 ...
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34 views

Two electron integrals between 1s STO

I am trying to understand SCF cycle by trying to code up solved example from Quantum Chemistry by Levine (page 443, 5th edition). The problem is shown below: One electron integrals are straight ...
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2answers
92 views

High-temperature DFT

Why is it so difficult to perform DFT calculations that consider temperature? I have seen that time-dependent DFT is needed to model systems at high temperature. Why is this the case? What about ...
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1answer
143 views

How to color bonds by the strain?

I need to create a figure of a molecule in which the bonds are colored in a RGB scale according to the values read from a data file. The data file contains, for example, the increase or decrease in ...
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39 views

Illegal valence meaning

I'm using the rdkit package to process some molecules. I noticed that when creating a molecule from a SMILES string the library does some syntactic and some semantic checks. This question regards the ...
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1answer
98 views

Why is the OO-H dissociation is unlikely for the Caro's Acid?

Let us consider the Caro's Acid: $\mathrm{H_2SO_5 \equiv SO_3H-OOH}$. It is widely known that the hydrogen tied with the $\mathrm{-OO-}$ group is pretty much unlikely to dissociate: $$ \text {...
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1answer
48 views

An automated approach to visualize several xyz structures

I have several .xyz files (each composed of several molecules) and I'd like to find an automated way to visualize and save them. I'd appreciate any guidance.
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1answer
122 views

MolView is unable to generate correct 3D structure for hydroxypropadiene

MolView is unable to generate the correct structure of hydroxypropadiene. It instead generates the structure of acrolein (which has the same molecular formula). Why is this so? Is it because ...
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1answer
44 views

Does the amount of solvent interaction energy depend on the absolute gas phase energy?

I've been performing Gaussian 16 DFT optimization and single-point energy calculations on different conformers of a rather large organic molecule. My first series of calculations was without solvent ...
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Covering conformers in a molecular modelling; consider them as a static entity or work with modelling shifts as well?

I am currently working with a molecular docking project, examining potential affinities of a solvent on a protein in an assay to evaluate potential error margin. The solvent is cyclohexanol (referred ...
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MNDO integrals in the global coordinate system

In MNDO and its descendants (Sewart's PMx models, Austin's AM1, MNDO/d, etc.), the nonvanishing two-center two-electron "coulomb integrals" are evaluated via a classical multipole expansion in a local ...
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2answers
810 views

Is hybridization used in ab initio valence bond calculation?

Many general chemistry textbooks introduced the concept "hybridization" to construct a symmetry-adapted VB-type wavefunction. In the textbooks, usually the minimal basis is used and without optimizing ...
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1answer
471 views

Is HF the only method for trying to solve the many-electron Schrödinger equation?

The Schrödinger equation can only be solved analytically for the smallest of "molecular" systems. The Hartree-Fock method is a method of obtaining approximate solutions to the many-electron ...
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29 views

Open source for atomic spectra raw data

Is anyone aware of a open source atomic spectra database? In particular I am looking for high resolution Na atomic emission which can be downloaded in csv or Excel. I am aware of NIST but I could not ...
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1answer
37 views

Determining the torsion energy profile of butadiene by molecular dynamics

Disclaimer: this question is related to my previous question, although it is much more detailed Consider the following rotation of butadiene: I want to determine the relative energy of each dihedral ...
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67 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 ...
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19 views

CHelpG charge calculation vdw radii input

I am running CHelpG charge calculations in Gaussian for complex containing Fe(III). The error message I am getting is that the program cannot find vdw radii. I tried several inputs and non of them ...
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2answers
222 views

Developing Computational Chemistry Software

I want to learn to develop novel methods in computational chemistry (e.g. Grimme's empirical dispersion, DFTB, new DFT functionals, etc.) What is the ideal way to learn this by oneself? I have read ...
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How to create .CIF file from DRX data in a paper, for compound not found in crystallographic database

I tried to recover a .CIF file with the crystal structure for the compound discussed in this 2006 paper, strontium hydroxide octahydrate - $\ce{Sr(OH)2·8H2O}$ - from Cambridge Crystallographic Data ...
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1answer
118 views

What causes energy peaks during a molecular dynamics energy minimization?

I'm minimizing the energy of a protein with NAMD using the fixedatom feature. I put my protein in a water box, and I allow all atoms other than the protein backbone ...
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2answers
524 views

Is there any software that can do geometry optimization using machine learning?

DFT is a computational tool that is used in optimizing and calculating the electronic structure properties of molecules. Are there any machine learning codes that can do something similar in a ...
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0answers
61 views

How do you optimize an organo-metalic compound containing cerium in in Gaussian?

I am trying to perform optimisation of the molecule attached. I need to get partial charges and frequencies. The issue is that it doesn't converge with following input: ...
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1answer
46 views

Why does Chem3D minimize nitrogen dioxide (radical) so badly? [closed]

I build from text O-N+O (the SMILES of this is O=[N+][O-]), I delete the hydrogen atom added automatically on N, then I start MM2 Minimization. Both the bond length ...
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50 views

How to fix 'error: hangup' in Gaussian 16 modredundant scan calcuation?

I have got a problem during my calculations with Gaussian 16. Everytime I start a job to scan the energy about 2 dihydrals I run into the following Error: hangup. I ...
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1answer
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I'd like to model some compounds with DFTB, but some elements don't have parameter files in the official site. Is there a workaround?

I was reading a bit about this technique, Density Functional based Tight binding (DFTB). It's claimed it can provide a speed improvement of several fold when compared to plain DFT, still giving ...
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Constraint optimization of the linear H4 and H6 chain with gaussian [duplicate]

I want to optimize the linear hydrogen chain ($d_{\infty h}$, equal bond lengths) with gaussian 16. Using z-matrix ...

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