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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Moller Plesset Theory- MP2 correction

I have a molecule LiBH2 with C2V point group. I used 3-21G basis set and obtained RHF coefficients and symmetry of orbitals. I wish to find the set of orbitals (a,b,i,j)( where a and b are occupied ...
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First steps in GAUSSIAN [closed]

For ammonia, I want to obtain the following parameters using GAUSSIAN: Symmetry point group. To do this, I do Tools -> Point group. The program does not do anything. Obviously, I know that it belongs ...
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Two electron integrals between 1s STO

I am trying to understand SCF cycle by trying to code up solved example from Quantum Chemistry by Levine (page 443, 5th edition). The problem is shown below: One electron integrals are straight ...
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Associated occupation numbers of frozen natural orbitals (FNOs) from MP2 method

The paper Frozen Virtual Natural Orbitals for Coupled-Cluster Linear-Response Theory gives the following (simplified) description of frozen natural orbitals (FNOs). In the MP2 method, the unrelaxed ...
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How to solve this error in Gaussian09? UNABLE TO DETERMINE LAMDA IN FmD114 [closed]

I'm doing CCSD(T) and CCSD calculations on a series of small molecules. Several calculations terminated without any problems but one CCSD(T) calculation and one utilizing CCSD gave me this error after ...
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Illegal valence meaning

I'm using the rdkit package to process some molecules. I noticed that when creating a molecule from a SMILES string the library does some syntactic and some semantic checks. This question regards the ...
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2answers
74 views

High-temperature DFT

Why is it so difficult to perform DFT calculations that consider temperature? I have seen that time-dependent DFT is needed to model systems at high temperature. Why is this the case? What about ...
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1answer
42 views

An automated approach to visualize several xyz structures

I have several .xyz files (each composed of several molecules) and I'd like to find an automated way to visualize and save them. I'd appreciate any guidance.
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How do I display a potential energy surface with molden?

I calculated a gaussian scan job for propylcyclohexane with two dihedral angles. Now I want to display a potential energy surface for that molecule with molden. I am new to molden and only found the ...
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1answer
120 views

MolView is unable to generate correct 3D structure for hydroxypropadiene

MolView is unable to generate the correct structure of hydroxypropadiene. It instead generates the structure of acrolein (which has the same molecular formula). Why is this so? Is it because ...
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1answer
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Does the amount of solvent interaction energy depend on the absolute gas phase energy?

I've been performing Gaussian 16 DFT optimization and single-point energy calculations on different conformers of a rather large organic molecule. My first series of calculations was without solvent ...
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Covering conformers in a molecular modelling; consider them as a static entity or work with modelling shifts as well?

I am currently working with a molecular docking project, examining potential affinities of a solvent on a protein in an assay to evaluate potential error margin. The solvent is cyclohexanol (referred ...
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Open source for atomic spectra raw data

Is anyone aware of a open source atomic spectra database? In particular I am looking for high resolution Na atomic emission which can be downloaded in csv or Excel. I am aware of NIST but I could not ...
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Determining the torsion energy profile of butadiene by molecular dynamics

Disclaimer: this question is related to my previous question, although it is much more detailed Consider the following rotation of butadiene: I want to determine the relative energy of each dihedral ...
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CHelpG charge calculation vdw radii input

I am running CHelpG charge calculations in Gaussian for complex containing Fe(III). The error message I am getting is that the program cannot find vdw radii. I tried several inputs and non of them ...
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44 views

How to create .CIF file from DRX data in a paper, for compound not found in crystallographic database

I tried to recover a .CIF file with the crystal structure for the compound discussed in this 2006 paper, strontium hydroxide octahydrate - $\ce{Sr(OH)2·8H2O}$ - from Cambridge Crystallographic Data ...
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How do you optimize an organo-metalic compound containing cerium in in Gaussian?

I am trying to perform optimisation of the molecule attached. I need to get partial charges and frequencies. The issue is that it doesn't converge with following input: ...
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38 views

How to fix 'error: hangup' in Gaussian 16 modredundant scan calcuation?

I have got a problem during my calculations with Gaussian 16. Everytime I start a job to scan the energy about 2 dihydrals I run into the following Error: hangup. I ...
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1answer
56 views

I'd like to model some compounds with DFTB, but some elements don't have parameter files in the official site. Is there a workaround?

I was reading a bit about this technique, Density Functional based Tight binding (DFTB). It's claimed it can provide a speed improvement of several fold when compared to plain DFT, still giving ...
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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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42 views

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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1answer
75 views

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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2answers
86 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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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
69 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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1answer
96 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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1answer
61 views

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
46 views

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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63 views

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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32 views

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
96 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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26 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
115 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
75 views

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
141 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
138 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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2answers
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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
387 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 ...
5
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1answer
86 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
77 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 ...
2
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1answer
40 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
65 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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