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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Why Car Parrinello Molecular Dynamics doesn't need an SCF calculation at every time-step?
Reading the various terms of the Lagrangian in CP-MD I'm trying to understand why there is not an SCF procedure hidden there.
In fact, it seems to me like the second term of the Eulero-Lagrange ...
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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 ...
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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 ...
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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) ...
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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 ...
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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 ...
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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 ...
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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 ...
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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-...
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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 ...
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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 ...
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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 ...
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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). ...
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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 ...
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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 ...