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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16 views

Phase purity using XRD measurements [closed]

I want to know the XRD values in order to calculate the phase purity values of ABO3 perovskites, Is there a database of known XRD measurements or phase purities?
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Number of nodes in Hartree Fock solution

The Hartree Fock equation for atoms is of the form $(\frac{d}{dr^2}+f(r)-\epsilon)P(r)=g(r) \tag1$ Usually algorithms to solve this equation assumes that the number of nodes of $P(r)$,$n_r$,is of ...
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Is this approximate equivalence table between Pople's basis sets and Jensen's DFT attuned polarization consistent basis sets (pcseg-n) correct?

I have some calculations results I runned previously using Pople's basis sets, mostly 6-311+G(d), under Gaussian09. These days I read some texts on Frank Jensen's family of polarization consistent, ...
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Are there Exchange integrals in Semiempirical methods?

One of the major features of semiempirical methods is that they significantly reduce the cost of evaluating 2-electron integrals. In general, they follow the formula for HF, but, introduce many ...
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Meaning of dihedral force constant which is zero [closed]

I am learning on force field parameterization such as CHARMM and I came across the definitions for dihedrals in CHARMM GENERAL FORCE FIELD (CGENFF). For example here: "HGA3 CG331 OG302 CG2O2 0.0000 3 ...
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How much the computation chemistry can predict the stability and properties of the (metallo-)organic molecules? [closed]

I have this vision for the pandemia preparedness platform (aka CERN/ITERA/Mars mission for preparedness) https://biology.stackexchange.com/questions/91025/can-we-prepare-for-pandemics-by-predicting-...
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How does one calculate the electronic difference density in practice?

I am interested in calculating electronic difference density maps. These have been described for quite a long time by Bader and others. For example, below is the fourth of a series of papers which ...
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Gaussview GMMX grid seach: job completed before going through all the structures

I am recently using the GMMX add-on in gaussview to conduct conformer search. I was using the grid search method and the progrom suggested the number of structures is 729 (See picture below). I ...
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Are there any molecular modeling programs that can build materials made up of three or more elements into a cylindrical shape?

I would like to build a material similar to what is in the image below. I have tried programs such as Material Studio, Quantum ATK, and VNL, but most of them can only do materials with 2 elements.
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Are there any semiempirical methods that work with heavy alkaline earth metals?

I did some research. Found some semiempirical methods that work even with heavy lanthanide compounds (RM1). But could not find any references to semiempirical methods compatible with the heavier ...
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How to reproduce the Gaussian 09 SDD basis set in Gamess-US?

I'm trying to migrate away from Gaussian 09, using Gamess-US instead for molecular modelling of some heavy alkaline earth metal complexes, using density functional theory (DFT). In some of my previous ...
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Generating electron density from protein coordinate (PDB)

Normally protein coordinates are generated from electron density, such as that from X-ray scattering experiment. In my case, I want the reverse - PDB to electron density mesh. I thought it was more ...
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Spin Operator algebra

I am trying to teach myself some QM. In Christopher J. Cramers textbook Essentials of Computational Chemistry: theory and models, in Appendix C, he goes over Spin algebra. I am unable to calculate ...
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How to extract a image (vector graphic) from a surface EPS plot with GaussView?

I am quiet new to this field of chemistry. I work with GaussView and I created a surface plot for my molecule with the cube and surface generator. This works very well. Now I like to save and copy ...
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Software recommendations for overlaying molecular structures [closed]

I am looking for a program to overlay the structure of small molecules as an aid for my students in comparing the results of optimization geometries using different optimization methods. At this ...
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1answer
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How to search substructures with explicit hydrogen in RDKit?

For a substructure search I would like to search for structures containing unfused benzyl. The idea was to explicitly add hydrogen. But apparently this does not give the expected results. So, I ...
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1answer
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Tools for Molecular Simulation

I am a high school student and I don't know a whole lot about molecular simulation. I wish to view different conformers of cyclohexane and the changes that occur when substituents are attached (for ...
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Software for simulating NMR spectra [duplicate]

I am wondering is there any open source software that predict NMR spectra by giving the chemical shift? Something like Spinach library http://spindynamics.org/group/?page_id=12 (Matlab is not free, ...
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52 views

Non-trivial cases where the frozen core approximation is bad?

In computational chemistry, it is extremely common to freeze the core electrons after an initial Hartree-Fock calculation, meaning that the core electrons are left out of any treatment of the electron ...
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74 views

How are the parameters of a force field obtained for the bond angle HCH?

In my head, I can't see molecules that I could vary the HCH bond angle without varying other bond lengths, angles and dihedrals to build an energy vs. HCH bond angle curve. If I vary a single HCH ...
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Is Tkatchenko's MBD-NL method self-consistent?

I have a question regarding Tkatchenko's [1] new nonlocal many-body dispersion method (MBD-NL). Does anyone know if it's a self-consistent method? I read this paper many times but I'm still not sure. ...
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1answer
39 views

How to access implicit bond angles that don't appear in Gaussian's z-matrix input?

Suppose I have a Gaussian script to calculate the energy of a relatively large molecule like hexamethyldisiloxane: ...
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1answer
95 views

How are unstable transition states determined? [closed]

The Wikipedia article about the Grignard Reaction says that The addition of the Grignard reagent to the carbonyl typically proceeds through a six-membered ring transition state. This got me ...
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What are the components of Machine learning I have to learn to pursue a project related to computational chemistry? [closed]

I will be going to pursue a project entitled "machine learning and python in Chemistry problems" for my visting student program this August probably. Please help me.
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How do STO-based computer programs implement the STO integral formulae?

In most cases, STO integrals are evaluated assuming that the orbitals are directed towards each other, using spherical harmonics; however, in GTO-based software Cartesian GTOs are used, with the ...
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Curtin-Hammett principle to evaluate alkene insertion

Given an unsymmetrical alkene in a simple non-stereoselective catalytic hydrogenation reaction. If one would want to investigate the nuances in the catalytic cycle of a dihydride complex leading to ...
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52 views

Can density functional approximations including dispersion correction perform worse than without it?

I am trying correlate some experimental properties of a molecule to its calculated equilibrium geometry. To do so, I calculated the geometry and energy of some conformers. Now, I obtain mixed results ...
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140 views

How to obtain curve energy and non-bonded interaction parameters (e.g. Lennard Jones parameters) with Gaussian?

I am parameterizing a force field and would need to obtain non-bonded interaction parameters of atoms (e.g., Lennard-Jones parameters). My primary idea is to obtain a potential energy curve using the ...
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2answers
129 views

Kinetic Energy Evaluation Integral Evaluation Program Ostlund

I'm reading Ostlund's Modern Quantum Chemistry. In Appendix B, the kinetic energy integral is evaluated using the Gaussian Basis functions as ...
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Calculating the energy of a molecule using probability distributions

I wish to calculate the energy for a protein where the position of all the C-alpha atoms is known. One way is to calculate the pairwise distances between the atoms and then look up a probability ...
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1answer
66 views

Computing the bond spring constant from first principles

Given a set of atoms and their positions in space, is there a way to compute the bond spring constant for each pair of atoms that are considered to be bonded (I can already determine the bonds with ...
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1answer
66 views

Kinetic Energy Evaluation Integral Evaluation Program

I'm reading Ostlund's Modern Quantum Chemistry. In Appendix A, the kinetic energy integral is evaluated using the Gaussian Basis functions to be $$ \left(A\left| -\frac{1}{2}\nabla^2 \right| B\...
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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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62 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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138 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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169 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
73 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
111 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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1answer
156 views

Optimization completed on the basis of negligible forces

I am performing relaxed scan in Gaussian (B3LYP/6-31G(d,p)). There are two small organic molecules, one of which is a radical, the other has a benzene ring. I'm trying to understand the optimization ...
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1answer
145 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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63 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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39 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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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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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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41 views

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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49 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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124 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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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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