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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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 are potential energy curves obtained for diatomic molecules using Hartree-Fock? [closed]

I am looking for a brief explaination on this, or a source that explains this more.
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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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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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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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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
88 views

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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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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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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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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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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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 ...
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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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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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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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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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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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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
66 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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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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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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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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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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How are class II force field cross-terms derived?

In some class II force fields, there are cross-terms that characterize bond-bond, bond-angle interactions and others. Example of equations below: $$\sum_{bond-bond}^{}k_{bb}(b-b_{0})(b^{'}-b^{'}_{0})$$...
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1answer
126 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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Bioisosteric replacement using SMARTS (KNIME and RDKit)

I am trying to create a KNIME workflow that would accept a list of compounds and carry out bioisosteric replacements (we will use the following example here: carboxylic acid to tetrazole) ...
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1answer
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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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Lennard-Jondes cut-off continuity

I am simulating some atoms under the Lennard-Jones potential and I would like to implement a cut-off radius, say at $r_c=2.5\sigma$. It is easy to keep the potential continuous, we can simply shift ...
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1answer
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How to remove CH3 labels from a molecule's image? [OpenBabel in Python]

I would like to remove CH3 labels from svg images generated in openbabel in Python. I am thinking I should use ...
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1answer
49 views

Ab initio molecular properties which can be experimentally measured and don't require derivatives/gradients

I'm attempting to teach myself HF and DFT by implementing various algorithms, but I've run into a snag: many molecular properties which are experimentally measurable appear to require taking gradients,...
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Mechanism of decomposition of alkali metal halides in flames

A student recently asked an interesting question What happens when KCl is introduced in the Bunsen flame?. This apparently simply question led me to an interesting debate. We all know that emission of ...
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1answer
360 views

Is there a way to generate SMILES from ChemDraw files? [closed]

I have a set of ChemDraw .cdx files, and I would like to extract smiles strings from it. Can Open Babel do that or maybe the rdkit in Python? Any other suggestions?
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QSCAILD (Quantum Self-Consistent Ab Initio Lattice Dynamics)

I made a new scheme of the QSCAILD (Quantum Self-Consistent Ab Initio Lattice Dynamics) method. Above all, I tried to link the QSCAILD with its predecessor method, the SCAILD. If there is anyone ...
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quantum self-consistent ab initio lattice dynamics QSCAILD

I approached the quantum self-consistent ab initio lattice dynamics (QSCAILD) method by referring to the article: https://arxiv.org/abs/2006.12867. I have created a latex text in which I outline the ...
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Normal (Regular) or Inverted Terms?

I have a question on the order of the spin-orbit molecular states. I understand how to find the terms that split from a parent molecular state in a diatomic molecule. But my question is on how to find ...
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Transition State search

I've been trying to find a transition state for the reaction of Pd + F2 with no luck. Has anyone ever tried a similar reaction, have they managed to get the TS? The reaction proceeds from the ...
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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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Grasping the concept of Electronic Spin, Effective Spin and Fictitious Spin

Trying to learn alone some aspects of quantum mechanics is, sometimes, a struggle. Reading the excellent paper by Piwowarska [1] I was hoping to, finally, understand what is the origin of the so-...
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Can the inner amine groups of Bacteriopheophorbide A become positively charged in aqueous solutions without the use of very strong acids?

In an attempt to calculate the pKa of the carboxylic acid group of Bacteriopheophorbide A (BPheo, Pubchem), I generated the structure in MarvinSketch (ChemAxon product) and I came across an ...
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Software for modelling decomposition reactions

What are some good softwares that can model a decomposition reactions? I have a reaction of H2O2 decomposing on metal exchange hexaaluminate catalyst. The catalyst is present in a packed bed thruster. ...
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Is the Hartree-Fock determinant always the minimum energy single Slater determinant solution to a molecular Hamiltonian?

Is it always true that the Hartree-Fock slater determinant is the minimum energy single slater determinant solution to a given molecular Hamiltonian $H$? By construction, any determinant $|\chi_{i_1}\...
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Explanation of terminology in equation used for energy calculation using Hartree–Fock method

I found in the literature that the energy of the Hartree–Fock method is given by the following equation: $$E_\mathrm{HF} = \int (\Psi^* \hat{H}\Psi)\,\mathrm d\tau$$ The term $\Psi$ is the wave ...
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How to simulate a Lorentzian broadened spectrum in MATLAB?

I'm trying to simulate the 2nu2 band of HCN in MATLAB. I generate a stick spectrum from the data I have (taken from the HITRAN database) and then use conv() to ...
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1answer
68 views

Computational chemistry software to generate files of cartesian coordinates and zmatrix of molecules

Is there any software that I can provide bond lengths, bond angles and torsion dihedrals of a molecule and generate an output file in the format of cartesian coordinates or zmatrix? Example: I would ...
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306 views

Szabo and Ostlund's calculation of repulsion integral on page 172 via A.41

Returning to Szabo & Ostlund after a hiatus I tried to recreate his STO-3G calculation for HeH+ which begins on p. 168. It all went fine except for the two-electron, two-center integrals. I ...

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