Skip to main content

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
0 votes
0 answers
15 views

How to embed multiple molecules with rdkit?

I am new to rdkit and struggle with something I thought would be simple: I want to randomly embed two molecules in 3D space so that the two do not overlap. This is to generate an initial state for ...
harfel's user avatar
  • 101
-2 votes
0 answers
52 views

Number of stable molecules [closed]

Is there are software/freeware (artificial intelligence or whatever) that given some types of atoms and their number how many "stable"/"reliable" molecules we can build involving ...
Vincent ISOZ's user avatar
1 vote
0 answers
36 views

How to interpret molecular orbital (HOMO - LUMO) plots in Chem3D 22.0?

Recently, I have been trying to understand the origin of the difference in reactivity of alkynyl-boron(ate) complexes so I tried to generate a molecular orbital plot on Chem3D (Version 22.0.22 64bit) ...
Swastik's user avatar
  • 1,282
1 vote
0 answers
21 views

Simple tool to estimate molecular dimensions [duplicate]

I would like to know the aproximate dimensions of a given molecule, it does not need to be very accurate. Is there a free and simple tool to do a rough estimation? For example, ChemDraw gives you ...
Brenlla's user avatar
  • 201
6 votes
1 answer
175 views

Where is the negative charge localized in tetrazolate ion?

I am seeing images of tetrazolate ion where the negative charge is placed at different locations: On the nitrogen atom Inside the tetrazole ring or On the carbon atom Is there any electronic ...
Nilay Ghosh's user avatar
  • 26.3k
1 vote
0 answers
67 views

Finding the relative position of the molecule in the adsorbate and adsorbent by minimizing the Hamiltonian

I am trying to model an adsorbing process (or more precisely, Heterogeneous catalysis process between solid catalyst and gas reactants). One of the step is to minimize the Hamiltonian by optimizing ...
Minh Triet's user avatar
1 vote
0 answers
30 views

Is the minimum energy pathway a geodesic in the potential energy surface?

I just finished NEB-TS calculation using Orca 4.2.1. One of the output file is the minimum energy pathway (MEP) data. Am I correct to interpret the MEP as the geodesic (path of minimum length) on the ...
Tensor's user avatar
  • 283
0 votes
0 answers
49 views

Do high-energy conformers allow for more flexibility in ligand binding?

After reading, "High Energy Conformer - Why is it the most stable?" which is at risk of being closed due to lack of detail, I'm curious whether my thoughts on reasons for selecting a high-...
Melanie Shebel's user avatar
0 votes
0 answers
27 views

Incomplete Results and Bond Breaking in Dihedral Angle Scan of Methyl Bithiophene in Excited States Using Gaussian 16

I've been conducting a dihedral angle scan on methyl bithiophene in its excited states using Gaussian 16. Despite following standard procedures, my results appear to be incomplete, and I've observed ...
To'lanboyev Iskandar's user avatar
1 vote
0 answers
41 views

electronic properties simulation from experimental structure, good idea?

Good day to everyone ! I am currently in a physical chemistry internship trying to simulate a Raman spectrum of a molecular crystal using DFTB. Innocently, I directly tried to calculate the normal ...
Nectarion's user avatar
1 vote
0 answers
36 views

How to find the global minima of a supramolecular complex in computational chemistry?

So this is more of a complex problem, and my masters thesis could greatly benefit if I find an answer to this. Essentially, I have a supramolecular inclusion complex. There is this molecule A (the ...
VASUDEVAN K 's user avatar
2 votes
0 answers
94 views

Calculating the enthalpy of formation for ethane in Gaussian

I am attempting to run a benchmarking calculation in Gaussian software to obtain the enthalpy of formation for a series of molecules. I am using the example calculation found here for ethane (C2H6). ...
Zephyr Solabella's user avatar
0 votes
1 answer
54 views

Calculating the Barrier Between Rotamers

There are two stable conformations of a medium-sized organic molecule roughly 5 kcal/mol apart in ground state energies. One is probably the global minimum conformer identified through a conformer ...
quantchem's user avatar
0 votes
0 answers
30 views

FTIR data: Is there a way to obtain stat significant differences observed between groups in LD-PCA?

Besides checking the loadings and choosing peaks of interest, there is a way to point out from the LD-PCA or PCA the differences between groups that are significant? All ideas are very much ...
Microbiologie13's user avatar
2 votes
0 answers
99 views

Can you tell if a HOMO to LUMO transition is allowed just by picturing the MOs?

Someone told me that they said the HOMO to LUMO transition is allowed in benzene and naphthalene just by looking at the MOs and without using the irreps for each orbital and the character tables? How ...
Audrix's user avatar
  • 137
5 votes
0 answers
157 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 ...
cows's user avatar
  • 151
1 vote
0 answers
30 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
452 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
24 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
56 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
47 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
50 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
62 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
95 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
21 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
70 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
17 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
37 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
87 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
87 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
38 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
38 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
45 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
81 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
20 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
24 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
106 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
54 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
46 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
54 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
42 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
41 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
51 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
124 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
101 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
77 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
  • 283
3 votes
1 answer
134 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
80 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
102 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

1
2 3 4 5
23