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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27 views

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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39 views

Application of Hückel theory to different datasets

I have recently been reading about graph Laplacians and apparently there is a specific type of graph Laplacian that comes from quantum chemistry and Hückel theory. This, however, is said to be only ...
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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
51 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
62 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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166 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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141 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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31 views

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 ...
4
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1answer
80 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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50 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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32 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
64 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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29 views

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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61 views

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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37 views

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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126 views

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
829 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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38 views

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
291 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
87 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
79 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
59 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
71 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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33 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
77 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
157 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
56 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
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279 views

Cloud-based molecular modeling software

I’m an IT Acquisitions and Licensing specialist researching well-supported cloud software alternatives to Fujitsu’s molecular modeling SCiGRESS. I am coming in with a tech background, but little to ...
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2answers
145 views

How to convert Gaussian input file .gjf to SMILES?

Is there a way to convert Gaussian input files (.gjf) to SMILES-codes (.smi)? I'm aware of ...
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41 views

How do computational chemistry programs determine the irreducible representation of a molecular orbital?

I was coding a simple RHF code to test my understanding of computational chemistry when I stumbled upon this question. How exactly do computer programs like Gaussian, GAMESS-US etc. know which ...
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113 views

Where to find experimental spin-orbit coupling constants?

I am searching for experimental spin-orbit coupling constants, particularly for main group elements and Cr(0) to calculate correlation consistent Composite Approach (ccCA) energetics. This method ...
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1answer
45 views

Deriving the equations for two-electron integrals in Hartree-Fock theory

In Szabo and Ostlund's Modern Quantum Chemistry, the matrix elements for the hamiltonian of a two-electron system, with an operator $\hat O$, are written on pages 64-66 as $$\langle \Psi_0 | \hat O | ...
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33 views

How to generate Density Functional Tight Binding parameters (Slater-Koster files)?

What is the simplest way (or least complicated way) to generate parameter files (.skf) to be used with DFTB+, for example? Assuming I want to be able to reproduce geometries for a certain type of ...
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1answer
90 views

How to calculate molecular emission spectra?

Is there free software which can calculate the fluorescence emission spectra of organic molecules? Let's say for example: rubrene There is a bunch of quantum free quantum chemistry software: https://...
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Additional example determining Marcus parameters searched

Background / theory: The electron transfer in organic materials was formalized by the Marcus theory, introducing $|H_{ab}|$ to describe the how molecules (or more generally: sites) are coupled with ...
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1answer
86 views

Why does the SCF not converge in a structure optimization with GAMESS of the thiourea molecule at the PM6 level of theory?

I'm using GAMESS to run a geometry optimization on a thiourea molecule, using PM6. However, the output file keeps displaying the error message, "NO FORCE FIELD, SCF DOES NOT CONVERGE." Is there an ...
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1answer
70 views

How do I view a DSN6 file as text?

I am trying to isolate certain pieces of information within a dsn6 file. Specifically, I want to find the electron density around two atoms within a protein. I want to then run a python code to ...
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1answer
60 views

Reference on Pople basis set

I need to write reference on 6-311++g(d,p) basis set in my work where I used it on atoms of I-II periods. Does anyone know where it was first published?
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212 views

DFT vs. MP2 for stacked dimer

Recently, I looked at these two papers analyzing the excited-state properties of modified DNA bases (2-aminopurine and 8-vinyl-A) and how they are influenced by stacking with natural nucleobases: ...
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1answer
72 views

The influence of diffuse functions on electron density calculations

I am not a quantum chemist, but I am (starting to be) a user of electronic structure software. In the picture (screenshot) is the electron density of the same molecule. On the left I calculated the ...
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159 views

Developing Computational Chemistry Software

I want to learn to develop novel methods in computational chemistry (e.g. Grimme's empirical dispersion, DFTB, new DFT functionals, etc.) What is the ideal way to learn this by oneself? I have read ...
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149 views

How to calculate the amount charge transfer from a natural population analysis?

I am trying to reproduce the quantity referred to as the degree of charge transfer reported in this publication by Zhu et al. [Ref. 1] for the F4-TCNQ molecule. I am interested in section 3.2 in the ...
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49 views

What is meaning of LAV2P basis set?

I am working on energy optimization of molecular structure using DFT with Schrödinger software and I found that job is running on LAV2P basis set. I want to know what is the meaning of this basis set ...
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1answer
194 views

Can I compare DFT calculations with different grids?

When doing DFT calculations, some integrations are commonly done numerically on grids. [In fact, more than a single grid may be used at the same time for different integrals, e.g. approximations such ...
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1answer
117 views

How to calculate S² value of a broken-symmetry wave function?

$S$ represents spin, signifies the number of unpaired electrons in the system. For example, if the number of unpaired electrons is $1$, then $S=1/2$. $S^2$ is calculated as $S(S+1)$. From what I have ...
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What kind of algorithm does computational software use to process molecular symmetry?

Background I'm forced into using GAMESS-UK for an older software package. Using a cs-symmetry molecule, I've noticed that GAMESS will reorient the molecule before running a standard SCF calculation. ...
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112 views

Calculating Mixing Enthalpy in GROMACS

What is the most reliable way to calculate mixing enthalpy of binary solvent mixture using GROMACS? [EDIT] I have simulated two-component systems of water and organic solvent with GROMACS. In a ...