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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 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
15 views

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
30 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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Is it possible to estimate reaction enthalpies in avogadro?

I am trying to roughly-estimate reaction enthalpies in Avogadro, by summing up molecular enthalpies (with the proper sign). There is a tool called calculate energy but, as far as the results ...
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1answer
79 views

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
35 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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28 views

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
22 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 ...
6
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1answer
99 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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5answers
483 views

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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25 views

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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37 views

Lennard Jones Potential - Water

I am trying to code the Lennard Jones potential (LJP) for water (reproducing results in a paper). The paper reports epsilon and sigma values for Oxygen and Hydrogen separately but in the LJP I've been ...
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3answers
217 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
71 views

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
40 views

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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40 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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74 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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0answers
49 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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0answers
49 views

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 ...
6
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1answer
124 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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78 views

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
49 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},\...
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72 views

Why is spin-contamination undesirable?

Why is spin-contamination, introduced by e.g. Unrestricted Hartree Fock, undesirable, and to which problems further on can it lead? The only problem I currently see myself is that spin-contamined ...
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48 views

Does a constrained wave function method exist similar to constrained density functional theory?

I am trying to find out if a constrained wave function method exists for running quantum chemistry calculations. I know that constrained DFT exists and can be used to constrain the charge density to ...
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1answer
151 views

How to calculate the enthalpy of reaction using Gaussian 09?

I'm having a hard time trying to understand what's the correct way to calculate the enthalpy of reaction given that I've already calculated the frequencies of my compounds in Gaussian. Below I show ...
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How can I track the progress / read the output file of an ongoing calculation in GAMESS-LIBCCHEM from NVIDIA? [closed]

That is my question: How can I track the progress / read the output file of an ongoing calculation in GAMESS-LIBCCHEM from NVIDIA? The steps I have followed are in: https://www.nvidia.com/en-us/...
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1answer
199 views

Why is density fitting not used to reduce four-center integrals further down to two-center integrals?

In density fitting, why don't researchers turn all the 4-center integrals into 2-center ones instead of stopping at composing them from 3-center integrals?
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45 views

Calculation Radial distribution function using Potential

I am trying to understand an article where it is describing the accuracy of a potential function obtained via a NN (neural network). To test the ability of the NN potential to describe also ...
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0answers
26 views

How to determine charge of compounds in solution with many amphoteric functional groups?

I am curating a metabolic model that has compounds such as NADH/NADPH/Etc. that have multiple ionize-able hydrogens. Normally with amino acids there are only a few hydrogen with varying pKas that ...
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35 views

Calculating the free energy of separation in AMBER

I am currently busy with my master's research project and I'm trying to calculate the free energy of separation of two cellobiose molecules in ionic liquid, that is, calculate the free energy of ...
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2answers
55 views

Why do we use the word phase and state of matter so interchangeably? [closed]

I would be happy if someone explains me why the word "phase" and "state of matter" is used so interchangeably.Lets say we have HBr and another compound in the system both gases.Then am I to take two ...
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44 views

Creating an IR Spectrum using Gaussian ADMP Calculation

I have a Gaussian 16 trajectory for a small cluster of water molecules carried out with ADMP technique. I was wondering if anyone knows how to compute the IR spectrum from the information in the ...
3
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2answers
126 views

Where can I get potential energy surface for simple molecules?

I'm looking for potential energy functions for simple molecules, such as water or hydrogen sulfide. I only need the region around the equilibrium geometry, preferably as a Taylor series expanded in ...
4
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1answer
94 views

Knowing that CI is variational for any basis set, why is coupled-cluster variational in the full correlation limit?

This is the question asked in Martin's comment to my answer to: Why is Coupled Cluster not variational? In the comment I was also asked to provide a publication as a reference:
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1answer
108 views

Orthogonality of wavefunctions for different normal modes

Vibrational wavefunctions corresponding to different vibrational levels of the same normal mode are orthogonal because they are eigenfunctions of the harmonic oscillator Hamiltonian, which is ...
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2answers
98 views

The difference between CASSCF and MCSCF methods

I'm not sure the exact difference between the MCSCF and CASSCF methods. I know that the CASSCF method proceeds by optimizing both the CSFs and MOs (I mean the coefficients), but I don't know if this ...
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47 views

Total SCF Energy with Pseudopotentials

Is there a physical meaning to the SCF energy of a molecule obtained using pseudopotentials to represent the core electrons of heavy atoms (for example gold)? I've been running calculations in ...
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93 views

Vibrational Self-Consistent Field

There are a few things about VSCF that I don't understand: Which coordinates do you work in? If you work in normal mode coordinates, how do you evaluate the effect of the average of one normal mode ...
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1answer
127 views

Why is Coupled Cluster not variational?

It has been noted in several sources (e.g. J. Romero et al. Strategies for quantum computing molecular energies using the unitary coupled cluster ansatz. arXiv:1701.02691 [quant-ph]) that one of the ...
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2answers
133 views

Are such high oxidation states as reported by Vojovodic et al. possible?

I am a student in theoretical chemistry and I am confused about the paper: Trends in adsorption of electrocatalytic water splitting intermediates on cubic $\ce{ABO3}$ oxides (Montoya, J. H.; Doyle, A. ...
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58 views

Reactivity of carbon-centered radical

I've read this site for a long time but I had never asked a question, so this is my first time :). So, i'm currently working on a computational chemistry project on radical cyclization reactions and ...
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1answer
83 views

The CASSCF orbitals

I have two questions about the orbitals that we get after the CASSCF calculations. First, what are the CASSCF orbitals that we get from these calculations? I mean after optimization, in the CASSCF ...
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1answer
72 views

Maximum required order for the Boys function

I am planning to pretabulate a lookup table in order to evaluate the Boys function. We can expand the Boys function as: $$F_n (x_t + \Delta x) = \sum _{k=0}^\infty \frac{F_{n+k}(x_t)(-\Delta x)^{k}}{...
4
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2answers
143 views

How do I make a ZMAT or XYZ file from scratch?

From a structure representation like the one below for Bacteriochlorophyll A, how do I make the ZMAT or XYZ file? The closest similar question asked here was about converting a PDB entry into XYZ, but ...
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52 views

Bond order analysis in molpro

I'm trying to compute bond orders in a molecule, let's consider S2 as an example. I'm not entirely sure what's the right way to do that, but I assume NBO (Natural Bond Orbital) should give me what I ...
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1answer
60 views

Search by CAS Registry name to obtain trackable accession: ie InChi?

I'm updating a database and trying to move from CAS Registry names to InChiKeys. I have about ~800 compounds to track. Is there a way to do this mappings programatically? I'm looking for a web service ...
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1answer
42 views

Calculating the x, y and z distances between two molecules - AMBER (Molecular Dynamics)

I am interested in calculating the x,y and z distance between two molecules over a given simulation time. I know how to calculate the total (r) distance between them, but I want the distance between ...
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origin of use of differential equations for modeling chemical reactions? [closed]

what are some of the original examples of uses of differential equations for modeling and analyzing chemical reactions, particularly those relevant to biochemistry, involving proteins and enzymes? ...