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.

Filter by
Sorted by
Tagged with
3 votes
0 answers
80 views

N2 HOMO-LUMO Gap calculation

I am thinking about calculating the HOMO-LUMO energy gap for $\ce{N2}$ molecule. I thought I could model this as a particle in a box problem to find $E_\text{HOMO}$ and $E_\text{LUMO}$. The formula I ...
kevin Tah N.'s user avatar
1 vote
0 answers
29 views

What is the size parameter of the direct red 80 molecule?

Basic information: CAS number: 2610-10-08 Molecular formula: C45H26N10Na6O21S6 Molecular weight: 1373.07 Structural formula: For example: For congo red whose structural formula is demonstrated below, ...
陈永曜's user avatar
1 vote
2 answers
346 views

What is the hydrated diameter of a lithium ion?

When salts dissolve in water, the anions, cations, and strongly polar water molecules undergo hydration reactions, resulting in the formation of hydrated ions with a specific number of coordinated ...
陈永曜's user avatar
0 votes
0 answers
16 views

Model EC50/Kd values using ordinary differential equations

It is my first attempt at using ordinary differential equations to model Kd for antibody binding and help will be much appreciated. To provide some context, I possess binding curve data for the EC50 ...
hypermiler3's user avatar
1 vote
0 answers
50 views

Theoretic (QED) Atomic Ionization Energies Database?

The 2019 paper "QED tests with highly-charged ions" contains a survey of QED-calculated atomic ionization energies. I can manually copy the values of interest therein, but it seem that ...
James Bowery's user avatar
0 votes
0 answers
35 views

15N NMR simulation with orca software

I would like to simulate J(15N-1H) couplings with orca. By default, the software uses the 14N isotope for NMR nitrogen simulation. In the program, in the xyz input, I added M 15 on the line of the N ...
emmanuel C.'s user avatar
0 votes
0 answers
43 views

Energy Decomposition Analysis for SN2 involving ambident nucleophiles and an alkali metal counterion

I am wanting to perform an EDA on transition state structure of the nucleophilic attack of an ambident nucleophile (2 atoms that could be used in nucleophilic attack on the same molecule) on a benzyl ...
MrAmateurChem's user avatar
2 votes
1 answer
45 views

SMARTS: recursive search

i have a question regarding the usage of recursive SMARTS. I'm using python and rdkit for my coding. My goal is to get the substructure of carboxylic acids which are bonded by an ethyl-group to an ...
dideldideldum's user avatar
0 votes
1 answer
67 views

How to compute solvent reorganization energy in Marcus' non-equilibrium approach?

I try to solve the following equations for some system solvated in the water. The goal is to obtain value in kcal/mol. Unfortunately, I cannot reach the desired output. May someone help me? The ...
farmaceut's user avatar
  • 103
1 vote
0 answers
16 views

Matching a Slater-type wavefunction with 6-31G basis set for first and second row atoms Gaussian basis set

I am trying to match the slater wavefunction with 6-31G basis set for first and second row elements. I have matche hydrogen, helium and lithium atom 1s orbital with Slater wavefunction using STO-6G ...
Aparna's user avatar
  • 11
0 votes
0 answers
56 views

HOMO and LUMO energy levels diagrams

Good time of day. I want to draw the same beautiful pictures in my work as I will attach below taking from some articles. Are there any programms or scripts which can do this? I would be glad if ...
UserIn's user avatar
  • 1
0 votes
0 answers
13 views

When optimizing AMBER molecular dynamics parameters for protein-ligand interactions, how do I balance accuracy and efficiency?

Are there established practices for fine-tuning AMBER MD parameters in scenarios like mine, involving specific factors like mutant proteins or non-standard ligands? Has anyone successfully tackled ...
Don Aborah's user avatar
1 vote
0 answers
34 views

Force contribution of image atom using periodic boundary conditions

This is maybe a stupid question but lead to a discussion between me an my colleagues. If we use periodic boundary conditions and an atom has itself as neighbor do we need special care of this ...
g.smith's user avatar
  • 556
2 votes
0 answers
76 views

Gaussian16 optical rotation calculation using a deuterated species

I am running into issues preparing an input file for DFT calculations. Currently, I am trying to submit an optical rotation calculation for an alpha-deuterated benzyl bromide (1 deuterium on the ...
MrAmateurChem's user avatar
0 votes
1 answer
78 views

What is in the output of VeloxChem python based program?

After running SCF optimization with VeloxChem code the output is a lengthy document at the end of which is this section. I am wondering what these numbers mean, more specifically in the parentheses?
Dominik Primožič's user avatar
1 vote
0 answers
37 views

Why is INDO suitable for covalent systems despite neglecting two-center two-electron integral?

I do not have a good basis understanding of basic chemistry so I am hoping to obtain an explanation that is as narrow as possible. My current understanding of the semi-empirical method INDO is that ...
Physkid's user avatar
  • 121
1 vote
0 answers
35 views

Can someone help with GAMESS input files for heavy atom calculations (MoS2, WS2, etc.)?

I'm doing computational research on transition metal dichalcogenides for my chemistry class and I want to calculate a transition state optimization for the reaction $\ce{MoS2 +N^- -> MoSN + S^-}$. ...
Daniel's user avatar
  • 11
0 votes
0 answers
41 views

Coarse-grained algorithms

I am fairly new to the field of oarse-grained molecular systems. I am aware that there are a lot of different already developed CG algorithms. Since there are so many, I struggle to find what I'm ...
Simon Perovnik's user avatar
-2 votes
1 answer
63 views

Is *.xyz a standard file format in computational chemistry?

https://youtu.be/f6K8k0sH2TY The above YouTube tutorial talks about a file format called XYZ. Later, the tutor uses this format to compute the bond length and bond graph of a molecule. Is ...
user avatar
0 votes
0 answers
18 views

Automatically extracting SMILES of sub-group of larger SMILES structure?

Is there any software tool that can automatically extract SMILES of fatty acid legs of phospholipids if the SMILES of the parent lipid is given? Or any tool that can do it in InChI ? Any advice will ...
user1776194's user avatar
0 votes
0 answers
21 views

OOM Error Calculating ESP Charges with Psi4

I'm trying to create a script to generate partial charges for a given .dat file. As an example of my process, I'm currently using gromacs to run minimization on a box of propane. It outputs a min.gro ...
asquith's user avatar
0 votes
0 answers
81 views

What is the difference between zero-point and total energy of a molecule in the output of an ORCA FREQ calculation?

I am trying to find the enthalpies of formation for a couple organometallics in ORCA and as a first time user I am a bit bogged down in the terminology. The Gaussian manual has a section on these ...
Spencer's user avatar
0 votes
0 answers
49 views

Effective Core Potentials and their "corresponding Pople" basis set

Reading through a handout from Yale shows the author correlating the ECP with Pople basis sets. The author of this says the corresponding basis set for SDD is 6-31G, Def2TZV as 6-311G, LANL2MB as STO-...
MrAmateurChem's user avatar
0 votes
0 answers
13 views

Identifying Key Chemical Series, Pharmacophores, and Scaffolds in a Large SDF Dataset

fellow computational chemists! I have encountered a challenge that I'd like to discuss and seek advice on. Suppose I have a substantial dataset in SDF format containing thousands of molecules. My goal ...
Poccia's user avatar
  • 1
0 votes
0 answers
43 views

Reduction of direct product representation

When we do the reduction of the reducible representation generated from the total wavefunction expressed as product of MOs of appropriate symmetry, we can find the direct sum of more than one ...
Chemistry.'s user avatar
0 votes
0 answers
50 views

Group theory and exact Eigenfunctions of Hamiltonian

I think I've understand why the real Eigenfunctions of Hamiltonian belong to a given irreducible representation and I've read that also MOs have to transform as irreducible representation due to the ...
Chemistry.'s user avatar
2 votes
0 answers
37 views

What is the meaning and unit of the integral in the local density approximation (LDA)?

According to Parr and Weitao (1995), the Dirac exchange-energy formula (1930) comes from [I am looking only at the last line of the equation and the rest for completeness] It's an energy, so I'd ...
ste's user avatar
  • 662
2 votes
0 answers
40 views

Commutating operators of angular momenta

I've studied the formal procedure to pass from the uncoupled basis set of individual angular momenta to the coupled basis set of total angular momenta for polyelectronic atoms. I start from an ...
Chemistry.'s user avatar
1 vote
0 answers
43 views

Why do we call STO-nG a basis set?

Why do we call the Hartree Fock basis-set for an atom a "basis set?" In linear algebra, a basis must be linearly independent. Looking at the STO-3G "basis set", the basis functions ...
Frank's user avatar
  • 113
0 votes
1 answer
106 views

How to find the ligand field splitting of d orbitals in a square planar complex?

I am working with a Iron square planar complex with $\ce{NH2-}$ and $\ce{OH-}$ ligands having cis and trans conformation. My question is how to theoretically/computationally calculate the ligand filed ...
Harshdeep Chhabra's user avatar
0 votes
0 answers
85 views

Help with exchange integral interactions!

A single determinant configuration constructed in a basis with 7 spatial orbitals has the following exchange integral interaction energy terms: -2K12 -K13 -K23 -K14 -K24 (i) Draw a configuration that ...
user135298's user avatar
0 votes
1 answer
73 views

Do we know the asymptotic behavior of density functional in DFT?

I was reading a book on DFT the other day, and the author included asymptotic behavior for $E_{xc}[\rho(r)]$. Given that, do we know the asymptotic behavior for kinetic energy and/or total energy in ...
Tensor's user avatar
  • 264
3 votes
1 answer
119 views

Dipole moments of trans and cis nitrous acid

I have a paper due about the isomers of nitrous acid, using various calculations methods to find molecular properties like their dipole moment. I've found the dipole moment of trans isomer to be 1.987 ...
silvermacabre's user avatar
2 votes
0 answers
71 views

Derivation of the conversion of Gaussian type orbitals (in cartesian coordinates) to Gaussian type orbitals (in polar coordinates)

While studying basis sets, I came across Gaussian type orbitals (GTOs), which are used as atomic basis sets. I reviewed the polar form of these orbitals, which are very similar to hydrogen atom ...
MeliodusSama's user avatar
6 votes
0 answers
85 views

Obtaining transition density matrix

I'm trying to assemble a transition density matrix on quantum computer using one-body excitation $\widehat{E}$ operator on 2 active spatial orbitals, i.e. on 4 spin-orbitals. The problem is, I need to ...
Eenoku's user avatar
  • 1,267
5 votes
1 answer
1k views

How to convert SMILES to 3D (with higher accuracy than RDKit)?

I am interested in assigning 3D coordinates to (atoms in) some 10K molecules that I have, currently represented by SMILES. This is because as have been shown by many chemoinformatics papers, 3D and 2D ...
jasperhyp's user avatar
0 votes
1 answer
65 views

G09 how to I prevent Na-O bond formation doing DFT on a sodium carboxylate?

I am trying to determine Gibbs free energy of solvation for a sodium salt of an alkylcarboxylate. B3LYP/6-31g. The minimized structure makes covalent bonds between sodium and carboxylate oxygens. How ...
Nonclassical Carbocation's user avatar
1 vote
0 answers
24 views

Need for AINR-based simulations (vs. laboratory experimentation)

The Results section of this paper related to ab initio molecular dynamics states that "16 $\ce{H_2O}$ and 15 $\ce{HCN}$ molecules were taken together, and the system was allowed to evolve for 750 ...
nightcod3r's user avatar
0 votes
1 answer
243 views

Gaussian simultenous scan with two variables

I am trying to rigid scan two bond distances simultaneously in Gaussian 09/16. For example, I have taken a water molecule and started a rigid scan. Below is my input. # b3lyp/6-31+g(d,p) scan Title ...
Pro's user avatar
  • 181
2 votes
1 answer
79 views

What can visual observations of pi-bonding MOs explain about LCAO expansion coefficients?

For examples of CO and N2, what can their MOs tell us about their expansion coefficients? I've thought that in N2, its symmetric so the expansion coefficients would be equal from the pi-bonding MO due ...
Audrix's user avatar
  • 117
-3 votes
1 answer
117 views

What does the χ (chi) symbol represent in a Slater determinant? [closed]

Context: Computational Chemistry So, I am looking at the molecular orbital approximation, which allows the assumption that the overall wavefunction can be written as individual molecular orbitals Ψ(r1,...
PassionFruitChemistry's user avatar
1 vote
0 answers
103 views

The need for accurcy in constrained molecular dynamics simulations

In constrained molecular dynamics a system of differential algebraic equations $$\begin{align} \dot{q} &= v, \\ M\dot{v} & = f(q) - G(q)^T \lambda, \\ g(q) &= 0 \end{align} $$ is solved. ...
Carl Christian's user avatar
2 votes
0 answers
73 views

How to determine the unitary transformation from atomic orbitals to symmetry-adapted atomic orbitals of Ethylene

I am trying to find the unitary transformation matrix U from the atomic orbitals $|\mathbf{\chi}\rangle$ of ethylene to the symmetry-adapted atomic orbitals $|\mathbf{\chi}'\rangle$ of Ethylene, i.e $|...
curiousrabbit13's user avatar
0 votes
1 answer
36 views

Dependence of the permittivity on solvent mixing ratio

I am doing DFT calculations on an organometalloid compound to assess whether it dissociates into an ion pair in different solvents. I suppose that the more polar the solvent is the more stable this ...
C_Swann22's user avatar
  • 133
3 votes
2 answers
137 views

Why does a symmetric stretch mode not have an imaginary frequency?

Currently studying potential energy systems and our professor asked a question at the end of a lecture and I can't wrap my head around it. He said, "Picture a 2D PES for the simple reaction of H+...
Audrix's user avatar
  • 117
-5 votes
1 answer
101 views

Compound of C+Li+F possible? [closed]

Sorry my chemical knowledge is not very deep so some of what you assume is common knowledge will probably be new to me. For a game i am trying to make i wrote a simple atom / compound simulator where ...
braunbaer's user avatar
1 vote
0 answers
130 views

Gibbs Free Energy for solvation using Gaussian09

I am trying to compute the $\Delta G$ for the solvation of a molecule using the continuum dielectric model in Gaussian09. Following the recomendation in the manual of the software, I am using the SMD (...
AlfredV's user avatar
  • 461
1 vote
1 answer
235 views

QM9 atomization energies

I am doing experiments with the QM9 dataset from http://quantum-machine.org/datasets/ and began with some simple checks on results from the literature. Consistent with what the authors of the paper ...
Arnold Neumaier's user avatar
-1 votes
1 answer
113 views

Difficult in grasping "the extent/limit of conformational space of a compound until it change its stereochemistry"

I have heard that a conformational landscape encompasses all conformers that a compound has for a specific stereoisomer. I think it makes sense verbally, because if all conformers of a stereoisomer ...
Leticia's user avatar
  • 25
3 votes
0 answers
128 views

Derivation of the Hartree-Fock equation

I have to do some tutoring about basic quantum chemistry and the main purpose is to give a deep insight into Hartree-Fock theory. My plan is to start from expressing the many-electron wavefunction as ...
C_Swann22's user avatar
  • 133

1
2 3 4 5
23