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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20 views

Why aren't the Anton computers used more widely?

The Anton computers are purpose-built by DE Shaw research for molecular dynamics simulations. They achieve performance up to an order of magnitude faster than can be achieved with commodity hardware, ...
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Tight binding model with Extended Huckel Approximation

I've been reading Albright's Orbital Interactions in Chemistry. In the chapter on solids, he provided a general approach to find the band structure of a solid state system Now if we are to model a ...
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Tight binding model for nanoparticles as finite systems

I'm still trying to calculate the band structure ab initio for some hypothetical nanoparticles. It seems that I can directly build a tight-binding model by forming Bloch functions, numerically ...
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32 views

Valency of each atom in a molecule with python

Consider ethanol, where each carbon atom has a valency of 4 and oxygen a valency of -2. I would like to determine these values for many compounds given their SMILES or InChI keys. (For the purpose of ...
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58 views

Simple sandbox software for an interactive molecular dynamics simulation

I'm not sure if this is the right site to ask a such question. But I'm getting to learn the world of the small. I know there is software out there like NAMD, and LAMMPS. But these tools are very ...
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31 views

Overlap matrix for finite sized square lattice of hydrogen atoms

So I'm trying to use the LCAO method to calculate molecular orbitals on a square lattice of hydrogen atoms. To this end, I need to compute the Hamiltonian matrix. With the nearest neighbor interaction ...
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What is the difference between dynamical and non-dynamical correlation and which one is accounted for in Hartree-Fock theory? [duplicate]

It is my understanding that dynamical is related to the movement of individual electrons. I don't fully understand what this means though. Non-dynamical correlation is still very unclear from my ...
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48 views

Why isn't the total energy of an atom the sum of the orbital energies - what is I1 and I2?

We were told that the total energy of a helium atom is not the sum of its orbital energies and that this is Koopman's theorem. This sortof makes sense but I am struggling with contextualizing it. i....
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Radicals in Gaussian [closed]

I want to do a PES scan of a radical structure in Gaussian. However, I'm not completely sure how to prepare an input file. I've figured out that charge and multiplicity are 0 and 2. What I don't know ...
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61 views

How can i convert .gjf or .chk file to .wfn file? [closed]

Please explain to me in details. I can't understand corresponding contents in manual.
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Convert to NASA polynomial format for chemical kinetic calculations

I have calculated thermodynamic properties of a metal oxide through DFT calculations, I want to convert it to NASA polynomial format and use those thermodynamic properties along with rate constants ...
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435 views

Software for generating a lattice from a unit cell for molecular crystals?

I am looking for a software package which can take a unit cell (and lattice parameters, etc.) and from that generate a crystal lattice. Ideally it will have functionality for orthorhombic, hexagonal, ...
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1answer
90 views

High errors in frontier orbital energy calculation using DFT

In a recent paper by Faber et . al., Mean Absolute Error and DFT (B3LYP) error (relative to the experiments) for 9 properties of QM9 dataset molecules has been reported. \begin{equation} \begin{array}...
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151 views

Energies of Virtual Molecular Orbitals (LUMO)

I just had a question about molecular orbitals. I was just wondering if the energies of the LUMO (virtual orbitals) derived from CCSD(T)/cc-pTVZ calculations could be trusted. I remember reading some ...
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33 views

Kinetic Diameter: How to calculate it? Pressure influence?

Wikipedia states: Kinetic diameter is a measure applied to atoms and molecules that expresses the likelihood that a molecule in a gas will collide with another molecule. It is an indication of the ...
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1answer
38 views

Using AutoDock Vina to dock multiple ligands to multiple receptors?

I am trying do that what the title depicts, but I keep running into errors creating the executable script. Is it even possible to automate the docking of multiple ligands to multiple receptors? ...
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27 views

Order of features in chemical descriptors

ECFP are small-molecule descriptors, which are usually represented as a bit vector. I wonder if order of elements of this vector matters, in other words, if this vector encodes any positional ...
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2answers
96 views

Computing force fields using Open Babel

I am trying to use Open Babel (OB) to compute universal force field (UFF) given an xyz file. I read each xyz file and turn it ...
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23 views

Is there a way to extract the diamagnetic and paramagentic components from NMR output from Gaussian16?

I'd like to be able to split the NMR value in Gaussian16 into its diamagnetic and paramagnetic terms. I'm coming over from ADF, where this can be done easily. Is there a straightforward command to ...
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1answer
67 views

Decomposition of total Interaction energy with SAPT or EDA-NOCV

I want to perform energy decomposition analysis for some Hydrogen bonded complexes. I came to know that ORCA and Psi4 allows EDA-NOCV an SAPT(0,2,3) respectively. But I do not know which one would be ...
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1answer
98 views

Generating molecular graph Laplacian based on Hückel theory

While studying graphs and graph Laplacians from "Laplacian eigenvectors of graphs: Perron-Frobenius and Faber-Krahn type theorems.", I encountered a type of graph Laplacians that rise from quantum ...
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Available datasets to study using Hückel theory

I'm trying to do some tests using graph Laplacians based on Hückel theory. This, however, is said to be only applicable for conjugated hydrocarbons. My questions are: I have been working with QM9 ...
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50 views

Is there any publicly available software that can do deterministic CCSDTQP other than MRCC?

MRCC can do arbitrary order coupled cluster but much of the code is computer-generated (not hand-coded by a human) so it can be slow. There are some stochastic codes for high-order coupled cluster, ...
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1answer
71 views

How are orbitals displayed in computational Chemistry software?

In typical software like Gaussian or GAMESS, the molecular orbitals (or even the basis functions) can be displayed as surfaces. I understand that the surface is probably constructed from a series of ...
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1answer
70 views

Confusion about comparing the charge densities of benzene and fluorobenzene

I understand that the functional group $\ce{-F}$ is an electron-withdrawing group. It is expected that the difficulties of an electrophile to attack the carbon atoms are $$\ce{PhH}<\ce{2,4of PhF}&...
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1answer
202 views

Molecular orbital energies prediction with ML algorithms

In the recent years, computational chemistry community has focused on Machine Learning algorithms to predict molecular properties. Unfortunately, many of the authors of such papers are not chemists, ...
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152 views

Is it possible for the kinetic energy integral to be negative?

Is it possible for the kinetic-energy integral, Tij, to be negative? I was messing around with some HF code and found that the integral became negative on some off-diagonal terms. (This could also be ...
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Psi4 gradient calculation with complete basis set? [closed]

I'm trying to set up a gradient calculation for psi4. In my input.dat file, I have tried the following keywords: set basis cc-pVTZ gradient('CCSD(T)') which is ...
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1answer
98 views

QM9 dataset with chirality

I am trying to find chiral centers of molecules in QM9 dataset. Browsing their SMILES representation, I noticed SMILES yield using datasets.get_qm9(GGNNPreprocessor(), return_smiles=True) don't ...
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CNDO/2 clarification

I wrote a piece of code on RHF using Python a while back, and figured I'd extend it to also implement CNDO/2 (yes, I know it's old but I figured it'd be easier for me.) The approximated Fock matrix ...
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60 views

Chirality as atom feature

I have been reading some literature on molecular energy prediction using machine learning techniques and I have noticed that one of the input parameters in many of the available models is "chirality". ...
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1answer
42 views

How to calculate size of a specific cavity in a protein for every frame in trajectory file?

Here is the situation, I have trajecory file of a protein of interest. That protein has 2 main cavities that are participating in interraction with ligands or other proteins and also other cavities. ...
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1answer
75 views

How is the Hessian evaluated?

I was reading about the various ways to optimise the geometry of the system, and found that none of the sources mention how the Hessian matrix is obtained. How does one obtain the Hessian matrix? I’m ...
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Four-electron integrals over GTOs

I was looking through the following presentation: http://folk.uio.no/helgaker/talks/SostrupIntegrals_10.pdf Looking at the section on 4-electron integrals, I couldn't help but notice that the slides ...
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IRC analogue of conical intersections and minimum energy crossing points?

In my project, there are some spin forbidden organometallic reactions that involves both the triplet minima and singlet transition state (TS). Using the penalty method in qchem as well the method of ...
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How to extract force constants for normal modes from ORCA?

I am following the computational method described in Scientific Reports.[1] Where the authors analyze the contribution of each excited state normal-modes to the shift of the transition energy. For ...
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Which DFT functional is best for predicting macroscopic properties of molecular liquids?

Which DFT functional (KS-DFT, to be more specific) performs best at predicting macroscopic properties (density, surface tension, boiling point, relative permittivity etc.) of molecular liquids (...
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What is the dataset with the largest number of molecules?

In computational chemistry we often apply techniques to all molecules of a "dataset". Recently it was asked which dataset contains the largest molecules, and a user accidentally misinterpreted this ...
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3answers
873 views

What are datasets containing molecules with more than 38 heavy atoms?

I have been testing a machine learning approach for molecular energy prediction. The current dataset that I have is QM9, which is consist of molecules with up to 9 heavy atoms. I was wondering if ...
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Does the natural atomic orbital analysis result in natural electron configurations of molecules?

In my understanding, the natural atomic orbital (NAO) analysis is a method of calculation to get occupancy of electrons in center of each atoms. In other words, the result of NAO-occupancy indicates ...
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1answer
300 views

Is it good practise to mix double and triple zeta basis sets?

I need to compute extremely accurate single point energies using the coupled cluster method. The methods to be employed scale largely with the number of basis functions. A few basis functions may have ...
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Applying the constant number of electrons in DFT density optimisation

(Previous related question: Finding mathematically the ground state density in DFT) I am studying the density optimisation procedure (in particular for Orbital-Free DFT) this thesis. The derivative ...
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1answer
94 views

Cauchy-Schwarz integral screening different inequalites

Eq. (9.12.23) in [1] states that: $$\sum_{abcd}c_{ab}c_{cd}g_{abcd}>0\tag{MEST 9.12.23}\label{91223}$$ with $c_{ab}=c_ac_b$ for $c_a$ being some distribution coefficients and $g_{abcd}$ being the ...
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1answer
83 views

Finding mathematically the ground state density in DFT

To find the ground state density in DFT, you set the following Lagrangian: $$L = E[\rho(\vec r)] - \mu\left(\int \rho(\vec r) \mathrm{d}\vec r - N\right)$$ While minimising with respect to the ...
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1answer
172 views

What are Mulliken atomic charges, and how are they computed?

I was reading about the self-consistent extended Hückel method (SC-EHT), and stumbled upon various formulae for the diagonal elements of the Hamiltonian matrix. I noticed that many formulae depend on ...
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1answer
73 views

Are primitive GTOs normalised before contraction, or is the resultant basis function normalised afterwards?

I'm quite curious about this: In a basis set (I'll just use minimal-basis STO-nG basis sets for convenience), the basis functions are written as a linear combination of primitive GTOs. Are the GTOs ...
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1answer
42 views

Extended Hückel method: what are the atomic orbital energies usually used?

I was checking out an extended Hückel (non-iterative) code, and realised that for s-block elements it would be impossible to simply use atomic ionisation energies as an approximation to the orbital ...
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1answer
89 views

Basis sets - negative contraction coefficients?

I was looking through Basis Set Exchange when I noticed quite a few basis sets (STO-3G to STO-6G, for example) have negative contraction coefficients for some primitive Gaussians. As (based on what I ...
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1answer
168 views

When diagonalising the overlap matrix, what happens if the square root of the diagonal matrix does not exist?

I was looking at the code required for a simple RHF computation when I came across the section for the diagonalisation of the Fock Matrix. Based on what I know, the diagonal matrix $\mathbf{s}$ is ...
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1answer
58 views

Which of the free access molecular modelling program apply the B3LYP/G-31G(d,p) level of theory?

Please, let me know which an open free molecular modelling program will apply the B3LYP/G-31G(d,p) density functional level of theory? Thanks. Helen