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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36 views

Constraint optimization of the linear H4 and H6 chain with gaussian [duplicate]

I want to optimize the linear hydrogen chain ($d_{\infty h}$, equal bond lengths) with gaussian 16. Using z-matrix ...
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What are the alternatives we have to the VEDA 4 vibrational energy distribution analysis software?

Said software is very useful when you need to assign the peaks in vibrational spectra to different vibrational modes found in a hessian calculation for a given molecule, as described in Jamróz, Michał ...
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Computational Chemistry Modelling Redox Potentials [closed]

How could I accurately determine the Fe3+/Fe2+ redox potential in an aqueous solution? What would be a good computational model(s) for this?
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MNDO integrals in the global coordinate system

In MNDO and its descendants (Sewart's PMx models, Austin's AM1, MNDO/d, etc.), the nonvanishing two-center two-electron "coulomb integrals" are evaluated via a classical multipole expansion in a local ...
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1answer
46 views

Why does Chem3D minimize nitrogen dioxide (radical) so badly? [closed]

I build from text O-N+O (the SMILES of this is O=[N+][O-]), I delete the hydrogen atom added automatically on N, then I start MM2 Minimization. Both the bond length ...
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1answer
103 views

Computing energy of Guassian basis set

Actually, I'd like to compute decay rate using : $$ \Gamma = 2\pi \ | \langle ab|V|cd \rangle|^2 \delta\ (\epsilon_f-\epsilon_i) $$ where a, b, c, d are the MOs and V is coulomb interaction, and $\...
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2answers
554 views

Is there any software that can do geometry optimization using machine learning?

DFT is a computational tool that is used in optimizing and calculating the electronic structure properties of molecules. Are there any machine learning codes that can do something similar in a ...
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1answer
86 views

Determine and draw planes and axes of symmetry of a molecule using software (VESTA or Mercury)

I designed the $\text{MoS}_2$ molecule (bilayer), with polytype 2H in the VESTA. My goal is to draw the plans and axes of symmetry of the bilayer set. According to the information in the literature, ...
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102 views

Why is the OO-H dissociation is unlikely for the Caro's Acid?

Let us consider the Caro's Acid: $\mathrm{H_2SO_5 \equiv SO_3H-OOH}$. It is widely known that the hydrogen tied with the $\mathrm{-OO-}$ group is pretty much unlikely to dissociate: $$ \text {...
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Energy decomposition analysis. Are there schemes that actually splits up the steric term?

In quantum chemistry, there are many types of energy decomposition analysis (EDA) which partitions the interaction energy between two or more fragments into steric, polarisation, exchange and orbital ...
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Fixing incongruities in PES Scan [closed]

I tried to parameterize a particular x-y-z-t dihedral angle of novel molecule using a Quantum Mechanical scan, but I got the strange result below. The energy changes sharply around 130° and $E_\text{...
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What are the cheapest basis sets able to model intermolecular dipole interactions inside a metal complex and give good relative energies, with DFT?

As a example, If I have a square planar complex of a cation with both a weakly polar ligand (X) and strongly polar ones, like ammonia and water I expect a bit of stabilization due to formation of a ...
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1answer
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Help with molecular dynamics and computational modelling to check validity of hypothesis regarding SN2 reaction mechanisms [closed]

Polar aprotic solvents have a less hindered electronegative atom pointing out, namely oxygen, fluorine, and nitrogen, all of which have lone pairs besides having a partial negative charge. Now, all ...
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Why does exchange integral 1s2p not vanish for Helium excited state?

I am studying first-order perturbation theory applied to the first excited state of Helium. I am facing the following problem: I understand that the Coulomb integral for all 2p functions will not be $...
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Generate Surface with CubeFile from Gaussian in VMD or other free programm

I asked a question before, about how to save a mapped surface from GaussView. I don't get an answer, so I get much deeper in my internet research about it again. Now I want to try to create a mapped ...
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Number of nodes in Hartree-Fock solution

The Hartree-Fock equation for atoms is of the form $\left(\frac{d}{dr^2}+f(r)-\epsilon\right)P(r)=g(r) \tag1$ Usually algorithms to solve this equation assumes that the number of nodes of $P(r)$, ...
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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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1answer
100 views

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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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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34 views

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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1answer
131 views

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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1answer
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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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1answer
228 views

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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2answers
148 views

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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4answers
394 views

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
131 views

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
88 views

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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1answer
54 views

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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1answer
95 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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1answer
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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
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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
104 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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1answer
60 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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1answer
172 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 ...
3
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2answers
134 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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58 views

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 ...
3
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1answer
76 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
72 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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1answer
37 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 ...
7
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1answer
82 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
151 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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176 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
119 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
112 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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