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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23 views

How to remove CH3 labels from a molecule's image? [OpenBabel in Python]

I would like to remove CH3 labels from svg images generated in openbabel in Python. I am thinking I should use ...
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metal ion complex with carbon dioxide [closed]

Using ORCA and Avogadro, I stimulated the possible MO orbitals of carbon dioxide complex with lithium ion (Lithium chloride) and cesium ion (cesium chloride) each at a time. i expected that Due to ...
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Evaluation of an element of a basis function and its derivative using some chemistry package [migrated]

Given some element and one of the basic functions of one of the Gaussian basis sets, I'd like to be able to recover the maximum value any of the basis functions can take, as well as their maximum ...
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43 views

Ab initio molecular properties which can be experimentally measured and don't require derivatives/gradients

I'm attempting to teach myself HF and DFT by implementing various algorithms, but I've run into a snag: many molecular properties which are experimentally measurable appear to require taking gradients,...
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Mechanism of decomposition of alkali metal halides in flames

A student recently asked an interesting question What happens when KCl is introduced in the Bunsen flame?. This apparently simply question led me to an interesting debate. We all know that emission of ...
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1answer
43 views

Is there a way to generate SMILES from ChemDraw files? [closed]

I have a set of ChemDraw .cdx files, and I would like to extract smiles strings from it. Can Open Babel do that or maybe the rdkit in Python? Any other suggestions?
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Analytic Hessians for meta-GGA functionals

In many of the free/open-source QM programs like GAMESS, ORCA, NWChem, the calculation of analytic hessians is not possible when a meta-GGA density functional is used, like M06-2X. My first question ...
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QSCAILD (Quantum Self-Consistent Ab Initio Lattice Dynamics)

I made a new scheme of the QSCAILD (Quantum Self-Consistent Ab Initio Lattice Dynamics) method. Above all, I tried to link the QSCAILD with its predecessor method, the SCAILD. If there is anyone ...
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Equilibration of normal modes in water molecule [migrated]

When running a molecular dynamics simulation on a singular water molecule in vacuum to analyze its normal modes of vibration from the NVE (microcanonical) ensemble, the bending mode frequency is ...
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quantum self-consistent ab initio lattice dynamics QSCAILD

I approached the quantum self-consistent ab initio lattice dynamics (QSCAILD) method by referring to the article: https://arxiv.org/abs/2006.12867. I have created a latex text in which I outline the ...
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Normal (Regular) or Inverted Terms?

I have a question on the order of the spin-orbit molecular states. I understand how to find the terms that split from a parent molecular state in a diatomic molecule. But my question is on how to find ...
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39 views

Transition State search

I've been trying to find a transition state for the reaction of Pd + F2 with no luck. Has anyone ever tried a similar reaction, have they managed to get the TS? The reaction proceeds from the ...
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1answer
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Calculating self-diffusion coefficient from MSD programmatically

According to the Einstein relationship, the diffusion coefficient $D$ is $$\lim _{t\rightarrow \infty} \frac{\langle \left(\mathbf{r}(t)-\mathbf{r}(0) \right) ^2\rangle}{6t} = D$$ I have run a MD ...
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Grasping the concept of Electronic Spin, Effective Spin and Fictitious Spin

Trying to learn alone some aspects of quantum mechanics is, sometimes, a struggle. Reading the excellent paper by Piwowarska [1] I was hoping to, finally, understand what is the origin of the so-...
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Can the inner amine groups of Bacteriopheophorbide A become positively charged in aqueous solutions without the use of very strong acids?

In an attempt to calculate the pKa of the carboxylic acid group of Bacteriopheophorbide A (BPheo, Pubchem), I generated the structure in MarvinSketch (ChemAxon product) and I came across an ...
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Software for modelling decomposition reactions

What are some good softwares that can model a decomposition reactions? I have a reaction of H2O2 decomposing on metal exchange hexaaluminate catalyst. The catalyst is present in a packed bed thruster. ...
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Is the Hartree-Fock determinant always the minimum energy single Slater determinant solution to a molecular Hamiltonian?

Is it always true that the Hartree-Fock slater determinant is the minimum energy single slater determinant solution to a given molecular Hamiltonian $H$? By construction, any determinant $|\chi_{i_1}\...
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1answer
41 views

Explanation of terminology in equation used for energy calculation using Hartree–Fock method

I found in the literature that the energy of the Hartree–Fock method is given by the following equation: $$E_\mathrm{HF} = \int (\Psi^* \hat{H}\Psi)\,\mathrm d\tau$$ The term $\Psi$ is the wave ...
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3answers
269 views

How to simulate a Lorentzian broadened spectrum in MATLAB?

I'm trying to simulate the 2nu2 band of HCN in MATLAB. I generate a stick spectrum from the data I have (taken from the HITRAN database) and then use conv() to ...
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52 views

Computational chemistry software to generate files of cartesian coordinates and zmatrix of molecules

Is there any software that I can provide bond lengths, bond angles and torsion dihedrals of a molecule and generate an output file in the format of cartesian coordinates or zmatrix? Example: I would ...
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1answer
284 views

Szabo and Ostlund's calculation of repulsion integral on page 172 via A.41

Returning to Szabo & Ostlund after a hiatus I tried to recreate his STO-3G calculation for HeH+ which begins on p. 168. It all went fine except for the two-electron, two-center integrals. I ...
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1answer
50 views

What is the origin of rotational energy barrier in ethane?

What is the origin of rotational barrier in ethane? In most organic chemistry textbooks, we learned that it's originated from steric repulsion between two methyl groups. But recently I heard that ...
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1answer
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Why should duplicates compounds be removed from compound libraries before screening/activity prediction?

This is one of the first steps to be done while analysing chemical data or applying training models to predict chemical activity. However, I am unclear as to why is this done. Doe sit have a major ...
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What basis set should i use for a molecule like Graphene oxide?

I need to calculer the vibrational frequencies on a graphene oxide structure. Problem is, i am not sure what basis set should i use. Isn`t def-svp used for smaller molecules? Would it work with GO?
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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
29 views

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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63 views

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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113 views

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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119 views

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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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
86 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
57 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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63 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
62 views

Two electron integrals between 1s STO [closed]

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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1answer
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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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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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2answers
125 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
61 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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53 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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1answer
169 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
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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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1answer
67 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
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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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25 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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49 views

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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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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78 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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56 views

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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