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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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Software or methods to predict properties of a substance

There's a very similar question here Software for predicting chemical reactions My question is slightly different. Given a formula for a molecule or a substance consisting of several molecules, is it ...
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21 views

Best level of theory for many CO2 molecule behavior [on hold]

What level of theory is best to use for simulating effects of varying levels of light and magnetic force on a set of closely aligned CO2 molecules (preferably 5 or more). Is there a Windows desktop ...
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Diffuse functions for Ahlrichs/Karlsruhe basis sets in Gaussian?

As the question states, can one use the basis sets of Ahlrichs and coworkers (e.g. def2-SVP, def2-TZVP, ...) with diffuse functions (e.g. def2-TZVPD) in Gaussian? The regular basis sets have been ...
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How to understand MO diagrams for cationic octahedral transition metal complexes

I am having problems understanding the construction of MO diagrams in octahedral transition metal complexes within ligand field theory (LFT) when the metal center is asumed as an cation: I am ...
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1answer
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How to write a cube file?

This is a technical question. I have a real-space representation of a potential in a grid of points, however I have the grid in the format: x y z w v meaning: the coordinates of each point, the ...
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Gaussian Network Model eigenvalues correspondence to mode frequencies

I am in the process of setting up a coarse-grained Gaussian Network Model (Cα-atoms being representative of each residue) for normal mode analysis and would like to obtain the wavenumber/frequency ...
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1answer
36 views

Finding the weighted parameters of the vertex adjacency matrix for a derivative of azulene

In my last question ( Numbering in a derivative of azulene ), I asked about the numbered of a molecule in order to find the Vertex Adjacency Matrix (VAM) of the same molecule. To explain my question ...
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27 views

Vanishing integral rule for two-electron integrals

I understand the vanishing integral rule for a one-electron integral to be: $$\langle i | \hat{O} | j \rangle = 0 \hspace{1cm} \mathrm{if} \hspace{0.2cm} \Gamma_O \neq \Gamma_i \otimes \Gamma_j$$ ...
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How to distribute the heat of reaction in a multiphase system?

I am trying to model the combustion of aluminum particles in air. The first step is to vaporize the particles according to the equation $\mathrm{Δc=(3Φ_sρ_s/τ)(1+0.276*sqrt(Re))}$, which describes the ...
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1answer
32 views

Can Hartree-Fock mix more orbitals than there are electrons?

I'm trying to understand Hartree-Fock well enough to write my own implementation. A point that I seem to be coming to that I'm not sure is correct: the method only produces one-electron orbitals that ...
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1answer
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Maximum metal-metal distance for antiferromagnetic coupling

Imagine a transition metal complex with multiple open-shell transition metal cations. If the metals are relatively close in distance, it is possible that antiferromagnetic coupling will occur between ...
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Link1 and multiple output files in Gaussian: doable?

I have recently started learning Gaussian in my Computational Chemistry class, and I have recently learned how to use the "Link1" option, in order to run multiple calculations from a single input file....
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Q-chem equivalent solvent settings for Gaussian NMR ab inito methods

I'm attempting to use Q-Chem 5.0 to replicate CHESHIRE-esque http://cheshirenmr.info/ ab initio calculations of chemical shift values. Unfortunately Gaussian seems to be the predominant tool in this ...
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1answer
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Multiplication symbol in SMARTS

There is a SMARTS pattern that was published which looks like the following[1] [#6 × 4] and there are actually spaces around the ...
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STO 3G basis expansion of p orbitals

I am expanding $2p_{x},2p_{y},2p_{z}$ (slater type )orbitals in gaussian STO-3G basis as follows, $$|2p_{x}\rangle=C_{1}x\exp(-\alpha_{1}r^{2})+C_{2}x\exp(-\alpha_{2}r^{2})+C_{3}x\exp(-\alpha_{3}r^{2}...
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Implementing the projected atomic orbital (PAO) localization in Gaussian

I am currently attempting to learn how to setup the active space for performing CASSCF calculations. The textbook I am using as a reference is: Roos, Björn O. "Multiconfigurational quantum ...
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1answer
48 views

Can someone tell the me the data bank which has all the STO-3G basis sets for many electron atoms?

I am trying to express the slater orbitals of Helium atom in terms of 3 gaussian functions (STO-3G basis set). Is there any data bank or reference table in which I can find the exponents and ...
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Charge of molecule not conserved upon saving in .pdb or .mol2 format

I optimized my molecule (Gaussian, B3LYP) which has an oxonium ion a few days back. Now I saved it in .pdb and .mol2 file formats. However, the number of electrons, hence charges, hence the ...
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Constructing two body Hamiltonian for Helium atom in hydrogen slater orbitals single particle basis [duplicate]

I am trying to construct a two body states to calculate the matrix elements of electronic Hamiltonian of Helium atom. $$H=-\frac{1}{2}\nabla^{2}_{1}-\frac{1}{2}\nabla^{2}_{2}-\frac{2}{\vec{r}_{1}}-\...
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1answer
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Hartree product and the Slater determinant

I am very new to theoretical chemistry so my question may sound very basic to most. It is known that the Hartree product does not satisfy the antisymmetry principle for electrons while the Slater ...
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Are any other orthonormalizations schemes besides Lowdin normally used when solving SCF equations?

When solving equations of the form: $$F(C)C = SC\epsilon$$ (e.g. Hartree-Fock-Roothan or Kohn-Sham-Roothan) where $F$ is the fock matrix, $C$ is the coefficient matrix and $S$ the overlap matrix, ...
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1answer
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what is the issue in evaluating two electron integral?

What sort of issue is there in two electron integral in quantum chemistry ? Is it a problem of convergence when we do numerically? Can someone suggest any review article or reference articles which ...
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1answer
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Why is the active space for the dinitrogen cation defined this large in my example?

I have a Molpro script which computes $\ce{N2^+}$ potential energies. The significant part is the input for the wave function: ...
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38 views

Slater Determinant in Python package

Is there any library functions which I could use in python to construct slater determinant? Can someone suggest me something to fix this issue ? Is it really possible to determinant with functions as ...
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1answer
83 views

Solving two electron integral numerically

Is there any software package in python or C to evaluate two electron integral repulsion integral in quantum chemistry of atoms. I am trying to solve the helium atom by constructing many body basis....
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1answer
71 views

What exactly is meant by 'multi-configurational' and 'multireference'?

Some topics here have touched on this before (see 1, 2, 3), but I haven't found a clear definition yet. I would like to know what exact property of the wave function these terms refer to. It would ...
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1answer
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How do I have to interpret the input to the OCC flag in Molpro?

I'm trying to understand the occupied orbital specification in Molpro. They're specified by the OCC flag, while it's stated in the documentation, that OCC, m1, m2, ..., mn; where the ...
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Reverse Image Searching a ChemDraw Figure

Is there any image-recognition software out there that can read in a high-resolution image of a ChemDraw-generated figure and back out the structure (such as the SMILES or INChI)? I have a bunch of ...
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How does MP2 level of theory affect the natural orbital picture of the system?

I have performed CASSCF calculations for a series of molecules with varying input orbitals. I have used UNO, UHF, ROHF and MP2 based natural orbitals to perform the CASSCF calculations. For my system ...
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1answer
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Help understanding the equation for Spin Energy in Zero Field

I’m working with a system that experiences spin frustration and for me this is the first time dealing with such a phenomenon. To grasp the concept, I’ve decided to go to the basics and read the ...
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1answer
44 views

Magnetic couplings using DFT in a spin frustrated system

I’m working with a trimeric copper system that have the classic triangular shape and experiences spin frustration. This is my first time dealing with such system and, so far, from what I’m reading, I ...
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1answer
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Why are the calculated NMR values on the DFT & GIAO level of cyclopentane-1,3-dione so far off?

I'm trying to simulate the 13C NMR spectrum of cyclopentane-1,3-dione (PubChem CID: 77466; CAS 3859-41-4; ChemSpider ID: 69875; SDBS No: 15258; SMILES: C1CC(=O)CC1=O...
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1answer
59 views

Eigenvalues of Hessian matrix when the molecule is not at its equilibrium configuration

Given the potential energy surface (PES) of a system, we can calculate the Hessian matrix $H$ of each point $x$ on the PES. $$H_{ij}(x) = \frac{\partial^2 E}{\partial R_i \partial R_j}|_{R = x}$$ ...
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What is the intuition of using “dimer method” for searching transition states?

I learned dimer method for searching transition state in this paper: A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives. However, I still ...
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Restarting a Gaussian partially constrained relaxed surface scan using GICs

I am Using Gaussian 16 rev D.01, and I want to perform relaxed surface scans where I vary a bond distance. At the same time I constrain seven atom coordinates during the entire optimization (this is ...
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1answer
119 views

How to use dispersion correction with TPSSh in Gaussian 16?

A colleague of mine suggested to use TPSSh as a functional. Since I am applying Grimme's D3 dispersion correction by default, I was surprised that it wasn't implemented in the standard density ...
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1answer
165 views

How to sloppy freeze a dihedral angle within a range in a Gaussian modredundant optimization?

I would like to perform an optimization in Gaussian 09 of my molecule with two dihedral angles being frozen. I would like that the values of these dihedral angles are not fixed, but can relax ...
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Visualizing atoms in XYZ file with colors representing partial charges

I have a file containing the atomic coordinates (in XYZ format) of a structure, and I also have a list of the partial atomic charges for each atom. I'd like to create an image of the structure where ...
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Gaussian 09 Geometry Optimization: Identical energies printed in output

This question may be slightly off-topic for this site, but since Gaussian is the "calculator" most often used by computational chemists, perhaps it is relevant still. I have performed a transition ...
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3answers
233 views

What is Nesbet's theorem?

In a talk by Frank Neese there was a slide with title "Nesbet's theorem" and an equation indicating something like "if your wavefunction has the double excitation amplitudes correct, then you can get ...
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1answer
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Is there an algorithm that takes atom coordinates and produces VSEPR geometries?

That is, you would give the coordinates of an atom, the coordinates of four (for example) other atoms, and it would return "tetrahedral" or "square planar" or whatever. I'm currently writing a ...
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Randic's Molecular Connectivity Indices for cis and trans butadiene

Does anyone know how to calculate topographic connectivity indices for cis and trans -butadiene. Randic published the values of 1.9908 for cis and 1.9558 for trans. (Concepts and Applications of ...
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1answer
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GAMESS problem set question [closed]

I am new to GAMESS and I would like to ask for help. I have a problem set in our class but I am having difficulty on how to proceed with GAMESS. The problem is from Shriver and Atkins, Perform energy ...
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51 views

How to interpret Gaussian output for excited states?

I have calculated the excited energies for benzene in Gaussian. The output therefore was: ...
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0answers
77 views

Non central chirality in cheminformatics?

What are compact cheminformatics structural representations that allow to deal correctly with axial chirality, such as in binaphthyl compounds or metal complexes?
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1answer
73 views

What is the difference between non-adiabatic coupling and diabatic coupling?

The diabatic couplings are the off-diagonal terms of wave functions written in a diabatic basis. There is a need to use the diabatic basis when there is a breakdown of the Born-Oppenheimer ...
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Identifying principal quantum numbers in natural population analysis

Following a Hartree-Fock calculation, I would like my program to perform some kind of Natural Bond Orbital (NBO) analysis. Preceding this I would like to output a list of atomic orbitals, along with ...
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1answer
127 views

How do restricted open shell calculations mathematically proceed in the context of the self consistent field iterations?

I'm specifically concerned with HF theory. I understand restricted closed shell calculations use the Roothaan equations. If I understand correctly these equations assume each filled molecule orbital ...
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0answers
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Understanding two-electron integrals in Gaussian 09

I was comparing the two-electron integrals (electron repulsion integrals, ERI) printed by various well-established packages (Gaussian, GAMESS, Molpro etc.) and observed that Gaussian is the oddball in ...
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1answer
59 views

Franck-Condon factors in photoelectron spectroscopy

Franck-Condon factors have been used to predict / assign the vibrational structure of photo-electron spectra. $FCF=|\langle\psi''_{vib}|\psi'_{vib}\rangle|^2 = |\langle\psi''_{vib,1}\psi''_{vib,2},\...