A field which implements computers to model and study chemical systems and chemical behavior, using various models, from approximations of the Schrodinger equation to Monte-Carlo simulations to modeling with differential equations.

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Looking for dataset of proteotypic and non-proteotypic peptide [duplicate]

I doing experimentation for peptide prediction using machine learning. I need some data for testing. My background is Computer Science. Any advice how to find proteotypic and non-proteotypic peptides....
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12 views

Meaning of natural orbitals occupation numbers [on hold]

What is the meaning of natural orbitals and occupation numbers? Example of output from Molcas: Natural orbitals and occupation numbers for root 1 sym 1: 1.961698 1.932462 1.972469 1....
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24 views

Spectator mode; what is

I'm reading a paper, found a line: "The other modes have relatively small contributions for the displacements of the heavy atoms and can be considered as spectator modes for the internal conversion". ...
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48 views

(Computationally) finding similarity between two organic compounds

I have been struggling to find an acceptable answer for this question for my purposes. There are many ways to find similarity between two organic compounds - some of which are particularly popular ...
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0answers
12 views

How to make .wrl files from Spartan output?

I am trying to make some 3D printed models of molecular orbitals. I tried using jmol to export the .wrl files, however, when I import the .spardir or any other kind of file exported from Spartan, I ...
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1answer
103 views

Typical runtime for CASSCF calculations

I'm doing single point energy calculations of FeS using ORCA. I originally used DFT with a variety of functionals, and these calculations all took less than a minute. Now I'm attempting to run CASSCF ...
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36 views

Geometry optimization near conical intersection

I have to optimize geometry in S3 state. After running optimization in MOLCAS, it couldn't converge. That was because S3 intersects with S2. I ploted energies during optimization and picked the lowest....
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2answers
53 views

Gaussian scan function help for constructing input file

I have the cartesian coordinates for two molecules that are in a stacked position and I want to be able to calculate the potential energy at 0.2 angstrom steps from when the top molecule is 3.0 ...
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33 views

Calculating Optical Absorption Spectra using Ab Initio Computations

My main question is, How does one compute the optical absorption spectra of a molecule by using say, Configuration Interaction energy and associated transition dipole moments. I am trying to use an ...
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1answer
89 views

Tunneling corrections in reaction rates

I've studied Transition State Theory since I asked this a while ago, but so far I have not been able to find a detailed explanation of how tunneling corrections are implemented into reaction rates ...
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1answer
43 views

Coupling constant (Jab) - Why more unpaired electrons means a smaller coupling?

I hope this is not a "homework" question, but I'm having a bad time trying to figure this out. Available literature proposes 3 equations to calculate the coupling constant during a Broken-Symmetry ...
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1answer
41 views

For what is reaction enthalpy more relevant than reaction free energy?

I know enthalpy is a component of the Gibb's Free Energy (along with entropy). For practical purposes, though, isn't Gibb's Free Energy what a chemist is actually interested in, as that determines the ...
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1answer
42 views

swift API to convert smiles strings to 2D chemical structures

Is there a method or free api written in swift for converting smiles strings to the corresponding 2D structures? I have used babel or ibabel with python, but how do i use it with swift?
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2answers
110 views

Hybrid functional calculations using different approach

In hybrid functional such as B3LYP, PBE0, HSE etc, some part of HF exchange and/or correlation is added to some part of DFT X/C part in order to get better results. My question is if I am adding 1/4 ...
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170 views

Educational practice problems/systems/reactions in computational chemistry

I am not sure if this question is suitable for Chemistry SE, but I think fairly objective answers can be given, and not just I will benefit from them I have almost completed the first year of a MSc ...
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38 views

Extrapolating Properties for Water-Miscible Solutions

I am working with a chemical which has the following properties: The chemical is water-miscible The chemical contains ingredients which have a flashpoint of 200F The chemical is ~80% water (the ...
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21 views

Computational Chemistry Negative Lattice Vectors

This is a computational chemistry question. I've recently been using the Materials Project API to get VASP input data, that I've been processing. The POSCAR format is as so, for those who do not know: ...
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47 views

Car Parinello advantages and disadvantages

A look at wikipedia and some online sources state that Car Parinello is less computationally demanding than self consistent methods. The original journal "Unified approach for Molecular Dynamics and ...
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2answers
95 views

DFT-D3 calculation in Gaussian 09

Can anyone help me to run geometry optimization and frequency calculation using B2PLYPD3 functional including the DFT-D3 dispersion correction? I went through Gaussian manual, however, it was not very ...
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1answer
28 views

Supramolecules in Spartan

Maybe someone here is familiar with supramolecules calculations using Spartan? I am new in this area and trying to figure out some things: First - what's the best way to draw them? I tried to draw one ...
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2answers
92 views

How should I think about potential energy surfaces for reactions of complex systems?

I've recently started doing some computational chemistry, studying the reaction dynamics of some moderately complex organic and inorganic reactions. I'm doing things like finding maxima, minima, TS's, ...
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1answer
42 views

Making sense of J coupling data for Hydronium

I found J coupling data for hydronium using DFT and GIAO but I need help making sense of the data. Can someone with help?
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2answers
130 views

What is the correct way to verify a structure's geometry, for example for benzene?

My goal is to compare a calculated bond length with experimental data. Benzene is obviously common enough to expect sufficient experimental data to be available for it on the internet. I have found ...
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29 views

Considerations when calculating band offsets

I am trying to calculate band offsets of interfaces with the superlattice method: I create a large periodic conventional unit cell. At the bottom of the cell, there are layers of crystal A. At the top ...
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68 views

What are the unsolved problems in quantum chemistry? [closed]

The question is not necessarily limited in quantum, but also computational and theoretical chemistry. Wikipedia listed a few https://en.wikipedia.org/wiki/List_of_unsolved_problems_in_chemistry ...
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72 views

How obtain mass-weighted coordinates used to plot intrinsic reaction coordinates

I have obtained the energies from an IRC calculation. Usually these are plotted in papers vs the mass weighted coordinates; often something like this is labeled on the x axis: $Å \times \sqrt{\mbox{...
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1answer
658 views

There are no wavefunctions in DFT

I have seen this phrase several times across DFT textbooks. However, I am not sure if it still holds. Was there a change or a theorem that proved it otherwise? Several programs display wavefunctions ...
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77 views

Estimating stability and mean life of anomalous tautomers

A pair of bases in the DNA, say, A-T, have a tautomerized form A*-T* (resulting from switching the sides of both protons along the hydrogen bridges). I have studied how, by means of DFT computations, ...
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1answer
79 views

Why is no dynamical correlation recovered in the CASSCF method?

Configuration interaction is the only certain way to get a calculation to converge toward the exact solution of the many-body Schrödinger equation (within the approximations used for the framework of ...
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1answer
101 views

How to find chemical similarity between two compounds using Tanimoto method

I came across a paper named "Chemical Similarity Searching" by Peter Willett John M. Barnard and Geoffrey M. Downs, 1998. At one place, this paper talks of finding chemical structure similarity ...
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1answer
80 views

Why is the CASSCF method multi-configurational, while the CI method is not?

The CASSCF method is perhaps the most commonly used theoretical method for studying difficult chemical systems exhibiting multi-reference character or non-dynamical/static/strong correlation. CASSCF ...
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246 views

DFT Code for Atoms : Sources

Some time ago I implemented the restricted and unrestricted Hartree-Fock methods. I had a lot of fun and I learned a lot. It goes without saying that Szabo and Ostlund's book "Modern Quantum Chemistry"...
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32 views

Compute minimum energy paths from arbitrary positions on the potential energy surface

The minimum energy path is a useful concept in understanding chemical reaction paths. As I understand it, such MEP's are most often computed to verify that a transition state structure connects two ...
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31 views

What should I use as the starting structure for stacking interaction energy calculation using Gaussian?

I have a crystal structure (single crystal, organic molecule- pyranone carboxamide derivative) that shows pi-pi stacking, and I want to do theoretical calculations. I am using Dispersion-correcting ...
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3answers
61 views

How is mean square displacement defined in Brownian motion?

I am trying to calculate mean square displacement (MSD) of water in a simulation to calculate its diffusion coefficient. However I am little confused on its exact form. Can anyone please explain it in ...
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1answer
53 views

Raman Spectrum of carbon chains: How to identify the vibrational modes

So I am using NWChem to calculate the raman spectra of C2H2 and C4H4. For example for the first I obtained the following frequencies: ...
3
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1answer
196 views

What is the purpose of Gaussian, itself?

I have been doing some research into computational chemistry, having never looked into the area before, and have read about a popular, paid-for software "Gaussian", and free alternatives such as "...
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36 views

Conical intersection using GAMESS

I would like to know how to locate conical intersection using a GAMESS calculation. I really appreciate an example alone with this since I am a novice I do not have a clear idea among bunch of ...
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0answers
13 views

Predicting Dissociation Energy in I_2 via orca

In one of my classes we used orca with three different functionals BP86, B3LYP, and M-06L all with the basis set def2-SVP. In addition to predicting via orca we did it experimentally by a deslandres ...
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1answer
200 views

Gaussian: Relaxed scan with modredundant optimization and dummy atoms

I would like to perform a relaxed scan in Gaussian09 on my molecule using the modredundant optimization. Because I want to scan over two bond lengths simultaneously,...
2
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1answer
94 views

Software for visualizing molecular force vectors

I would like to visualize molecular normal modes as vectors sitting on each atom, and not as actual vibrations. I am able to do this, in part, with Molden by copying in the vector into a file readable ...
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2answers
125 views

U- or RO-method for Singlet-Triplet Gap?

When I want to compare the energy between two different spin states of the same molecule, i.e. singlet-triplet-gap, do I better use unrestricted or restricted open formalism to compare the energies ...
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1answer
54 views

How does Gaussian 09 normalize the excitation coefficients?

When I did excited state calculations with Gaussian 09, I was asking me on how those values are normalized because a simple sum over the squared of the coefficients did not yield 1. So ... how are ...
5
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1answer
128 views

How to treat pressure in computational chemistry?

I have a reaction where a gas at high pressure and a solution with all kinds of species is involved. How do I take pressure correctly into account to get reasonable values for $G$? Do I calculate ...
2
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0answers
57 views

Is it possible to “brute-force” material creation through algorithms?

I know its a bit of a soft question, but lately I've wondered what important properties and calculations would a program that iterates through certain types of molecules and atoms need in order to ...
7
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68 views

How dependent are computed charges using the quantum theory of atoms in molecules on the used level of theory?

The quantum theory of atoms in molecules is based on the topology of the electron density. This mathematical analysis allows to find critical points and hence has a unambiguous way of separating a ...
3
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1answer
90 views

Isotropic Fermi Contact Couplings vs. Dipolar Coupling Constant

I need to calculate a Dipolar Coupling Constants for some fancy triplet molecule that has been measured by EPR spectroscopy. My "normal" output from Gaussian gives me the following: Isotropic Fermi ...
8
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2answers
528 views

The time scale of calculations in computational chemistry

Is it possible to determine or get a range of the time required for a specific calculation with knowledge of the type (MM or QM), class (semi-empirical, ab initio or DFT), the degree of theory (MP, CI,...
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1answer
43 views

Determine rate equations for entire kinetic scheme

I am working with the following kinetic scheme that represents pyrolysis of a biomass particle: The paper that discusses this scheme provides the following rate constants: K1 for the pathway of $\...
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2answers
146 views

Single Point Energy in Gaussian software

I used Gaussian software to determine the single point energy (SPE) of 3 molecules namely ethane, ethene and phenol. The SPE for the molecules are -79.83, -78.59 and for phenol it is quite large at -...