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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9 views

extracting parameters from .SKF files ,

I have a question about interpreting .SKF files, I am using these parameters to model defective graphene, when I use parameter set given by dftbBaby/C-C (I think this is from Hotbit) or the ...
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40 views

Computed partial charges for protonated amine: discrepencies between Gasteiger and other methods

Consider the following molecule: SMILES: COC(=O)[C@@H](c1ccccc1)[C@@H]1CCCC[NH2+]1 I would expect the computed partial chage on the amine to be positive, due to ...
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1answer
120 views

What are computed energies in DFT and FF methods relative to?

I am not talking about zero-point energy. I wish to understand how the energy of a system is calculated relative to a zero baseline. This is best explained with an example. From DFT, the energy ...
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157 views

Hartee-Fock vs tight binding and others

I was reviewing many electron computational methods recently and got a bit confused about relation between different approaches. In particular in what is essential elemental difference between Hartree-...
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1answer
49 views

How to perform Mulliken population analysis by hand with GAMESS output?

I did a simple calculation on hydrogen fluoride with GAMESS and I wanted to reproduce the Mulliken population analysis for atomic orbitals. A molecular orbital is a linear combination of atomic ...
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2answers
103 views

GTOs of higher quantum numbers?

I recently realised that the STO-nG basis functions were fit to 1s/2s/3d STOs of various exponents, instead of being fit to STOs of higher principal quantum numbers (such as 2s/3p orbitals etc.). ...
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27 views

Optimization completed on the basis of negligible forces

I am performing relaxed scan in Gaussian and I'm trying to understand the optimization output. Specifically, the line ...
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1answer
117 views

Ab initio method to calculate C-C bond dissociation energy?

I'm trying to review how to calculate bond dissociation energy for C-C in ethane, a very simple calculation (or should be). I get the following Hartree energies for SCF 6-31G(p) for methane, ethane, ...
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1answer
51 views

How to obtain the radial probability distribution function of a given orbital from a quantum chemical calculation?

I know that a very similar question has already been asked here and a very competent and useful answer has been provided (see here). However, that previous question was related to the total electron ...
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1answer
29 views

How to manage complex equilibria when studying a mecanism?

Consider a complex multistep reaction mechanism with several intermediates. There are multiple possible pathways as well as equilibria in solution. One wants to study the reaction mechanism using ...
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42 views

GAMESS(US) Polarizable Continuum Model frequency calculations are giving me what seems to be garbage

I'm trying to run Polarizable Continuum Model (PCM) calculations using the GAMESS(US) software. I'm not that well versed in what exactly these calculations are doing (beyond the whole, 'gas within a ...
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Expected pi-bond properties of aluminum with basic nitrogen and acidic nitrogen

One of the answers to a question that I asked a few hours ago said that "aluminum-nitrogen bonds are not very likely to appear in very stable aromatic rings due to poor orbital overlap and strong ...
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20 views

Roughly guessing stability of a specific molecule from its computed properties

I calculated the properties of the cyclic silicon 2-sulfonatomalonate oxide(2-) anion (IUPAC name: 3, 5-dioxa-4-sila-1-sulfonatocyclohex-1-en-4, 6-dion-2-olate(2-), although, strictly speaking, both ...
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Is there a software that can predict the shape of a custom protein, given its amino acid sequence?

I know that the internet is full of enzyme and protein simulators which can show active site and 3D structure (like bioblender), but the problem with these programs is that they use predefined ...
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1answer
42 views

What are some software packages that allow visualization of molecules in 3D? [closed]

Could anyone suggest a good application or a software that helps visualise molecular structures in 3d? I have tried a few applications like King Draw and molecular constructor but I want to know if ...
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Grouping QM9 molecules

I have recently been reading a paper, in which given dihedral angles of alanine dipeptide molecule $\psi$ and $\phi$, the conformation is catagorized as either $\beta$-1, $\beta$-2, or $\alpha$. I was ...
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109 views

Why we can't see 3-d structures of certain compounds on PubChem?

It's common to read statements like one given below on PubChem: Conformer generation is disallowed since MMFF94s unsupported element. What's the meaning of the statement, and why are certain ...
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How do I interpret GAMESS thermochemistry output?

In GAMESS's thermochemistry output, which numbers mean what? The gaussian docs have a nice description of how to use thermochemistry data, but for gaussian's output. This appears to be different, eg, ...
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86 views

QM9 property based clustering

I have used a machine learning algorithm on QM9 dataset to extract some features. To visualize this feature space, I used a PCA algorithm to project it to a 2D space (in simple words, every point in ...
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118 views

Have IH₃ and IH₅ already been synthesized?

I've seen a paper by Sikalov [1] that says that $\ce{IH3}$ and $\ce{IH5}$ should be observable. Has anyone actually tried to synthesize such molecules? References Sikalov, A. A. Hypervalent Halogen ...
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Is there a rule of thumb to predict when coupled cluster might dip below the variational limit?

Coupled cluster is a non-variational method, meaning that it can give energies that are below the true FCI energy (the "variational limit" for variational methods). Often coupled cluster still gives ...
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112 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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57 views

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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60 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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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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38 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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59 views

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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90 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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24 views

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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2answers
467 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
97 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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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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123 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
67 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? ...
2
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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
100 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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0answers
24 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 ...
2
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1answer
86 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
119 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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62 views

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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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
76 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
218 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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155 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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43 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
121 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 ...