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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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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Raman and IR spectra [closed]
Can anybody tell me that how actually the Raman and IR spectrum calculates in DFT calculations?
I am not asking about the keyword. I want to know the principle that how X Y Z cartesian coordinates ...
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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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Adding a molecule in AMBER [migrated]
I'm new to computational chemistry. I want to model the enzyme EGFR and a small molecule Lapatinib. I got a .pdb file of EGFR at the Alphafold website, and got a .sdf file of Lapatinib at the pdb site....
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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 ...
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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 ...
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