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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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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
25 views

GAMESS problem set question [on hold]

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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0answers
32 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
15 views

Representative value of interaction energy in docking simulation study [closed]

Interaction energy is calculated as a result of docking simulation in several documents. However, it seems that in the range I saw, I evaluate the minimum value, that is, the energy of the most stable ...
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0answers
65 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
42 views

Web app to immediately look up number of electrons? [closed]

I imagine typing a chemical formula into a web app and having it return information about that molecule, such as how many electrons it has. If I type the chemical formula for FeMoco into WolframAlpha ...
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0answers
31 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
41 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 ...
5
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1answer
111 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
56 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 ...
2
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0answers
29 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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54 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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0answers
45 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 ...
3
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1answer
103 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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0answers
20 views

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
183 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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35 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 ...
2
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0answers
24 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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0answers
29 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
45 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 ...
2
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0answers
37 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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1answer
90 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
87 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
93 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
79 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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0answers
38 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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91 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 ...
6
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1answer
94 views

Why is Coupled Cluster not variational?

It has been noted in several sources (e.g. ref. 1) that one of the disadvantages of the Coupled Cluster method for the description of electron correlation is that, since $e^T$ in $E_{CC} = \langle0|e^{...
9
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2answers
125 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. ...
5
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0answers
51 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 ...
4
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1answer
72 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 ...
4
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1answer
66 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
120 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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49 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 ...
5
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1answer
56 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
41 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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0answers
37 views

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? ...
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40 views

How to develop a Reactive Force Field (ReaxFF)? (Molecular simulation)

Currently, I am working on CO2 capture on Hydrotalcites as solid adsorbents. I want to run molecular simulations to analyse the behaviour of the material under different temperatures, pressures and ...
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1answer
62 views

What causes energy peaks during a molecular dynamics energy minimization?

I'm minimizing the energy of a protein with NAMD using the fixedatom feature. I put my protein in a water box, and I allow all atoms other than the protein backbone ...
6
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1answer
117 views

Relationship between Hartree-Fock and Hückel coefficients

I am new in computational chemistry. I'm studying the Hartree–Fock–Roothaan (HFR) method and have some of questions about the HFR basis function coefficients. Do we have the condition on HFR ...
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1answer
27 views

Separating two sugars according to their heavy atoms - Steered Molecular Dynamics

I am trying to separate two methyl-N,N'-diacetylchitobiose sugars using steered molecular dynamics in AMBER. I have tested out: ...
6
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0answers
160 views

Two-electron integral algorithm

I am writing a molecular integral code from scratch. Right now my code have the following structure: ...
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0answers
26 views

About how long do polymer chains have to be for their physical properties to resemble the polymer more than the monomer? (Or are at least comparable)

For example: According to wikipedia, Styrene is a liquid at room temperature, whereas isotactic Polystyrene does not melt until the 200s celcius. This is a simple property but quite a large change. I ...
2
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1answer
119 views

Write SMILES to SDF in RDKit

I have a file with smiles and I'd like to convert the SMILES to SDF and tag the properties of each molecule, so I can use the SD file in another tool. Here is my code: ...
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0answers
59 views

Failure to Locate Stationary Point in GAMESS

I'm currently trying to optimize the geometry of a complex using GAMESS at the B3LYP level. However, I keep failing to converge the SCF. I've already tried the following: increasing the number of ...
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1answer
29 views

Reading CGTF basis from Basis Set Exchange site

I'm making a simple electronic structure code as an exercise, and I want to confirm that my understanding about basis set data from BSE is correct. The CGTF of H in aug-cc-pVTZ basis is given as: H ...
2
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1answer
60 views

Modeling Belousov-Zhabotinsky reaction using ordinary differential equations

Is it possible to model the BZ reaction using first order ODEs? If so what would these equations be? Or, is there something about the reaction that needs higher orders?
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1answer
38 views

Is it possible to define the coordinates of an atom using other coordinates while optimizing in gaussian 16?

I know it is possible to fix the value of composite expressions using generalized internal coordinates (gic) in gaussian 16. But is it possible to assign that value to the coordinate of another atom. ...
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41 views

Exact meaning, and implications, of the term “adiabatic”? (in the quantum sense, not thermodynamics) [duplicate]

I see the term adiabatic, diabatic, etc in many quantum chemistry and computational chemistry papers thrown around in somewhat inconsistent ways. Example: The Born-Oppenheimer approximation is deeply ...
3
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1answer
70 views

Molecule alignment

I'd like to align ~2000 molecules consisting of 8 atoms of carbon and evaluate their similarity with RMSD (all vs all molecules). What open software can do it in a day or less? I'd like it to work ...