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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1answer
142 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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Physical interpreation of coulomb and exchange integral

When trying to solve the Schrodinger equation for the electronic hamiltonian: $$H_{el} = \sum_{i=1}^{N} \bigg( - \frac{1}{2}\nabla_i^2 - \sum_A \frac{Z}{r_{i_A}} \bigg) + \sum_{i>j=1}^{N}\frac{1}{...
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How to retrieve excited state molecular orbital coefficients in Gaussian?

Currently I am doing TD-DFT calculations in Gaussian and want to calculate transition dipole moment for $S_1$ transition manually. However, I do not manage to retrieve molecular orbital coefficients ...
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How much should I scan an aromatic dihedral?

Suppose I have a napthalene-like molecule (attached), and I would like to scan (relaxed) its aromatic dihedral (highlighted atoms). I used CGENFF to obtain its dihedral parameters as follows, HGA4 ...
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1answer
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Aluminum electrodes for NaCl [duplicate]

Upon using aluminium Electrodes for a concentrated solution of NaCl, i conducted electrolysis on the solution for nearly 4-5 hours. There was definitely a gas possibly hydrogen being evolved at the ...
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22 views

How to use dispersion correction with M06-2x in Gaussian 09 or 16?

I would like to perform an optimization calculation using the functional M06-2x using the BJ dispersion correction in Gaussian 0.9. However, I can't find the parameters for this functional as I found ...
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47 views

Virtual screening lib

I had a quick question on virtual libraries. I'm hoping to perform a virtual screen using a library that contains very small, soluble compounds - think glycerol and smaller (<100MW). As far as I ...
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14 views

Sticking coefficents for dissociative adsorption

I am trying to simulate the decomposition of Hydrogen Peroxide ($\ce{H2O2}$) on $\ce{Pt}$ using Chemkin Pro. I am using a two step global reaction model for the reaction which is as follows- $$\ce{...
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1answer
483 views

How to treat pressure in computational chemistry?

I have a reaction where a gas at high pressure and a solution with all kinds of species is involved. How do I take pressure correctly into account to get reasonable values for $G$? Do I calculate ...
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1answer
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Solution of the Roothaan Equations of H2 by Symmetry Arguments

FWIW my background is in physics and maths, but I am just starting a chemistry PhD (the last time I took a chemistry class was high school). I have only some background in representation theory, and ...
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computational methods (gauss view software) optimization in DFT/B3LYP ..Problem in .chk file

After optimization the structure(DFT/B3LYP METHOD) there are 3 files 1).chk file 2).log file 3).gjf file the problem is staring from .chk file. the .chk file is not open by guass view there are some ...
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Clarification on partial charge on atoms in amino acids in protein [closed]

Assignments of partial charges are different in different references for the same amino acid in a protein. For instance, AMBER force fields assign values to all the atoms. However, in the following ...
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2answers
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Non-bonded orbitals in water

General Chemistry perspective: Looking at the molecular orbitals of water, we can see that the oxygen is $sp^3$ hybridized. Oxygen forms two sigma bonds with hydrogens, and there are two lone pair ...
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1answer
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How can I update a map/mesh and coordinates in a PyMol session file?

I have a PyMol session file I was using to create my figures. It contains a protein and ligand broken into several groups of atoms with a fair bit of overlap. There are also a few meshes built from ...
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32 views

How are natural orbitals derived from the electron density matrix?

I have a $4\times4$ electron density matrix in 6-31G for $\ce{H2}$ using psi4 and I am wondering how to get the natural orbitals of the system. I have diagonalised the density matrix $\mathbf{M}$ into ...
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1answer
863 views

Size consistency in computational chemisty methods

I am looking for a clear answer that would explain what exactly size consistency is, why configuration interaction (CI) is not size consistent and how this leads to errors when using CI for large ...
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1answer
204 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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1answer
44 views

Calculating self-diffusion coefficient from MSD programmatically

According to the Einstein relationship, the diffusion coefficient $D$ is $$\lim _{t\rightarrow \infty} \frac{\langle \left(\mathbf{r}(t)-\mathbf{r}(0) \right) ^2\rangle}{6t} = D$$ I have run a MD ...
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4answers
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Boys function for Gaussian integrals in ab-initio calculations

A few days ago I mentioned a problem with an Hartree-Fock program I am writing (HF using cartesian Pople's STO-3G basis set). I can reproduce overlap and kinetic integrals of some references for ($\ce{...
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1answer
491 views

Overlap matrix (H2 molecule, STO-3G) [closed]

I'd want to implement SCF method using Modern Quantum Chemistry (Szabo). But when I want to calculate overlap matrix for H2 (STO-3G basis) my results aren't equal to true overlap matrix that there's ...
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1answer
50 views

SMART string for alkyl group excluding alcohols

I'm quite new to the usage of SMARTS strings. I would like to find all alkyl groups (but no $\ce{CH3})$ in a component, here e.g. cyclohexanol (C1CCC(CC1)O). My ...
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2answers
286 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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0answers
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Obtaining electron density from orbital information in the Molden format [closed]

I'm trying to obtain an electron density from orbital information written in the Molden format by the formula, $$ \rho(\mathbf{r}) = \sum_{i}^{occ} |\phi_{i}(\mathbf{r})|^{2}. $$ Is there any post-...
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37 views

Negative coefficients for DIIS in SCF procedure

I am trying to implement the direct inversion of the iterative subspace (DIIS) algorithm in my simple HF program. After some problems it now seems to work. I can calculate the correct energies in ...
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1answer
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GAMESS problem set question [closed]

I am new to GAMESS and I would like to ask for help. I have a problem set in our class but I am having difficulty on how to proceed with GAMESS. The problem is from Shriver and Atkins, Perform energy ...
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1answer
342 views

Pople Basis Set Abnormality: 3rd row 6-311G

I noticed when looking through the Basis set exchange website that the 6-311 Pople basis sets don't at all match their formulation once you go past the 2nd row of the periodic table. For example, ...
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1answer
3k views

How do the def2-SV, def2-SV(P), and def2-SVP basis sets differ?

I am trying to calculate the energy of complex molecules with DFT and have a question about the Ahlrichs (Karlsruhe) def2 basis sets. What is the difference between the def2-SV, def2-SV(P), and def2-...
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4answers
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DFT Functional Selection Criteria

I have a very very general question: In DFT functional selection , mostly people speak about the most recent ones. For example my professor always asks: " which DFT Functional did you select ? " ...
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0answers
173 views

Total SCF Energy with Pseudopotentials

Is there a physical meaning to the SCF energy of a molecule obtained using pseudopotentials to represent the core electrons of heavy atoms (for example gold)? I've been running calculations in ...
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3answers
7k views

When using Gaussian to calculate NMR, what's the default solvent and frequency?

If I choose GIAO HF/STO-3G, is the default solvent $\ce{CD3Cl}$? Is the default frequency for $\ce{^1H-NMR}$ 500 MHz? What about the frequency for $\ce{^13C-NMR}$?
3
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1answer
218 views

Can someone tell the me the data bank which has all the STO-3G basis sets for many electron atoms?

I am trying to express the slater orbitals of Helium atom in terms of 3 gaussian functions (STO-3G basis set). Is there any data bank or reference table in which I can find the exponents and ...
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22 views

How to perform NBO calculation to get Second Order Perturbation of Fock Matrix from unit to another of meatl complex?

I am doing the NBO calculation of metal complexes but for some system I can fins in the output the Second Order Perturbation Theory Analysis of Fock Matrix in NBO Basis within different units and also ...
3
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1answer
138 views

Is it rigorous enough to change a DFT functional after geometry optimization to calculate excited state properties?

I have done the geometry optimization with the B3LYP functional, however, there is a need to calculate the excited state energy, so the CAM-B3LYP functional should be better suited for that. Do I need ...
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2answers
99 views

How would I make a basic protein folding algorithm? [closed]

On the face of it it doesn't seem especially difficult. Model the amino acids as solid objects linked together. Approximate the 3D force fields around them using a coarse approximation, then set the ...
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0answers
75 views

Stress-Strain Graph Under Uniaxial and Biaxial Strain

I was going through a recently published journal paper by ACS (Applied Nano Materials) about gas separation using nanoporous Graphene. DOI No. - https://dx.doi.org/10.1021/acsanm.0c02340 Supporting ...
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0answers
32 views

Simulation of electronic potential from nanoparticles interacting with molecules

I work with SERS, where the Raman signal gets enhanced by the electric field of the nanoparticles. Now I like to simulate this kind of spectrum with Gaussian. I found a paper[1], where it looks very ...
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0answers
34 views

How to create a Potential Energy Surface in Chemcraft?

The Chemcraft website says that it is possible to create a potential energy surface. Nevertheless, it doesn't work for my Gaussian scan job. ...
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0answers
36 views

What is the definition of energy-independent basis?

I am reading this article by Zatsarinny and Fischer [1]. At some point they span a wave function $\Psi_{E}$ in terms of energy independent basis $$\Psi_{E}=\sum_{k} A_{E k} \Psi_{k}$$ For example, The ...
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1answer
65 views

Do changing opt=modredundant to opt in Gaussian makes geometry optimization not to take into account frozen angles?

I am a newbie to Gaussian and just generated an input for the geometry optimization for some molecules with multi ring system. However, in the article that was a reference for those calculations, some ...
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1answer
105 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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14 views

How do I maintain a charge on one of my species in Quantum Espresso for an NEB calculation?

I am trying to run an NEB calculation that reacts a sulfite anion with an organic molecule. I've gotten it to converge, and I've added necessary the fcp_tot_charge_first = -2 and fcp_tot_charge_last = ...
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0answers
74 views

Why does a 4-bonded nitrogen atom appears negatively charged after an optimization?

I have a molecule bearing a quaternary ammonium and I optimized it using M062X (also Hartree-Fock) using basis sets 6-31G(d,p) and 6-31G+(d,p) respectively. After optimization, I expect that the ...
4
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1answer
123 views

Absorption and Emission at same wavelength?

Is it possible for a molecule to absorb and emit at the same wavelength? What is the reason behind it? I’m working on charged Tin porphyrins and got the excitation and emission (fluorescence) ...
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1answer
63 views

Spin orbital coupling and total angular momentum

The Sodium emission spectrum has 2 bright yellow lines called the Na-D lines. Superficially I understand the cause; there's spin-orbit coupling and the 3p orbital is split into 3p(3/2) and 3p(1/2). ...
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34 views

How to construct spin free coefficient of 2-hole 1-particle configuration?

It is clear that we can expand a cationic state of a molecule in terms of configuration interaction (up to double excitation). It means: $$|I \rangle = \sum_j c^{(I)}_j a_j|\phi_0 \rangle \ + \ \sum_{...
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194 views

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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1answer
66 views

Can we relate approximate Hartree-Fock orbitals to true solutions in the basis-set limit?

Assume that we've "solved" the RHF Hartree-Fock equations in some finite basis, that is, we have arrived at a self-consistent set of coefficients $c_{\mu{}i}$ such that each spatial ...
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25 views

Simulation of Pyridin attached to gold atom

I would like to simulate to get the influence of a gold atom on the oscillation modes of pyridine. I have already carried out simulations in which there is a coordinative bond between nitrogen and ...
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Best way of studying protonation in non-polar solutions with ~100ppm of water present using computational methods?

I am currently looking at the mechanism of the formation of storage deposits in jet fuel. Interestingly, the concentration of acids in the fuel correlates strongly with the total insolubles formed ...

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