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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How does MP2 level of theory affect the natural orbital picture of the system?

I have performed CASSCF calculations for a series of molecules with varying input orbitals. I have used UNO, UHF, ROHF and MP2 based natural orbitals to perform the CASSCF calculations. For my system ...
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What is the intuition of using “dimer method” for searching transition states?

I learned dimer method for searching transition state in this paper: A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives. However, I still ...
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How to interpret Gaussian output for excited states?

I have calculated the excited energies for benzene in Gaussian. The output therefore was: ...
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Calculating the free energy of separation in AMBER

I am currently busy with my master's research project and I'm trying to calculate the free energy of separation of two cellobiose molecules in ionic liquid, that is, calculate the free energy of ...
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About how long do polymer chains have to be for their physical properties to resemble the polymer more than the monomer? (Or are at least comparable)

For example: According to wikipedia, Styrene is a liquid at room temperature, whereas isotactic Polystyrene does not melt until the 200s celcius. This is a simple property but quite a large change. I ...
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How can I get more information about the Voronoi integral in Gaussian09?

I am working on metal based organic complexes to find out catalytic characters. I am using the B3LYP density functional level of theory in Gaussian09. I need to know the possible keywords for getting ...
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84 views

Should the normal mode of vibration leading to the transition state be removed?

I would like to know whether the normal mode of vibration of the reactant should be deleted when calculating $\Delta ZPE$ and $\delta G_{\text{corr}}(T)$, where $\Delta ZPE$ is the zero-point energy ...
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how to understand to what subshell is related basis function in the Eigenvectors block (GAMESS output)?

So, each subshell of some atom is described by one or combination of few BF's. But I can't find correlation between representation of subshells in eigenvectors block and, say, basis set or something ...
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691 views

Equation or formula for calculating molecular orbital energies

Is there an equation, similar to the Rydberg formula, for calculating the energies of molecular orbitals? For example, with the Rydberg formula, I can work out that the energy of a $1s$ orbital in ...
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57 views

Computational chemistry: is k a quantum number

I am trying to use the natural band offset method to calculate band offsets of junctions. In order to do so, I need to find the core electron eigenstates. I tried using FP-LAPW software Elk. But in ...
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118 views

Calculating Optical Absorption Spectra using Ab Initio Computations

My main question is, How does one compute the optical absorption spectra of a molecule by using say, Configuration Interaction energy and associated transition dipole moments. I am trying to use an ...
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345 views

How obtain mass-weighted coordinates used to plot intrinsic reaction coordinates

I have obtained the energies from an IRC calculation. Usually these are plotted in papers vs the mass weighted coordinates; often something like this is labeled on the x axis: $Å \times \sqrt{\mbox{...
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170 views

Conical intersection using GAMESS

I would like to know how to locate conical intersection using a GAMESS calculation. I really appreciate an example alone with this since I am a novice I do not have a clear idea among bunch of ...
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113 views

Metal Carbonyl Bonding

I am really struggling with this question we have been set in class: Metal-carbonyl bonding: Conceptionally, one can build up $[Fe(CO)_5]$ from the $Fe(CO)_4$ fragment plus free CO in order to ...
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179 views

Creating Molecular Orbital and Walsh Diagrams

Does anyone know of a good website to create your own MO and Walsh diagrams? Could you potentially make them on a software package such as excel? Any advice on this would be greatly appreciated.
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Internal treatments of gas cylinders for toxic gas mixture

The values of toxic components like $\ce{H2S}$, $\ce{NO}$, $\ce{SO2}$, etc. [in ppm level] get decreased after a while due to adsorption phenomenon. Manufacturers design some internal treatments in ...
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101 views

Probablity distribution of bend angle in gromacs

In an analysis I got the probability distribution of a bend angle $P(\theta)$ with respect to time. However, I need to plot $P(\theta)$ with respect to $1- \cos(\theta)$ where $\theta$ refers to the ...
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75 views

Potential energy Surfaces

I am trying to calculate PES for Molecular Oxygen and Atomic Nitrogen Exchange reaction. This is also known as Zeldowich reaction. I found that for asingle reactions, there are many PES's which I ...
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86 views

Basis set in the computational software “Gaussian-03” for studying adsorption of a hydrogen atom on a carbon paste electrode dropcasted with Pt-CNT

What is the basis set in the computational software "Gaussian-03" that can be used to study the interaction of $\ce{H}$-atom with $\ce{Pt-CNT}$ dropcasted electrode? How can we study the energy ...
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141 views

Why are non-polar hydrogens neglected in computational protein-drug binding studies?

Why are (non-polar) hydrogen atoms generally neglected in a protein-ligand (or drug) binding energy calculation? They do have charge and mass. Doesn't that affect the free energy calculation? The ...
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30 views

Simulating enzymatic change rates of Carbonic anhydrase

I'm trying to simulate effects of carbonic anhydrase on cellular pH as caused by changes in bicarbonate. I assume a bicarbonate homeostatic mechanisms which replenishes intracellular concentrations ...
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42 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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26 views

Measuring energy required or generated in gasification

The typical equation used to measure heat is as follows: $q = mcΔT\\ \text{Where, }\\ q = \text{heat} (\pu{J}) \\ m = \text{mass} (\pu{g}) \\ c = \text{specific heat capacity} (\pu{J g^-1 K^-1})\\ ΔT ...
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39 views

TD-DFT transition dipole moment vector does not align with experimental data

I have been modelling excited states of some molecules with similar stucture using TD-DFT theory, however, I have encountered an issue that sometimes transition dipole moment does not align with the ...
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38 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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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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40 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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24 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 ...
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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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35 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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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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17 views

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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50 views

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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41 views

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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59 views

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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462 views

How to find bond lengths from .cif files of crystal structure

I am confused about how to calculate the bond lengths within a given structure given its .cif file. I have highlighted the bond of interest in the image below. The atom coordinates are shown in the ...
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75 views

What are the rules for constructing Kohn-Sham orbitals?

I just recently began to study quantum chemistry and need some clarification for the construction of Kohn-Sham orbitals. Consider a system of several atoms. Let there be $N$ electrons in this system. ...
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41 views

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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171 views

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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46 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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44 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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75 views

Does the natural atomic orbital analysis result in natural electron configurations of molecules?

In my understanding, the natural atomic orbital (NAO) analysis is a method of calculation to get occupancy of electrons in center of each atoms. In other words, the result of NAO-occupancy indicates ...
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150 views

What is meaning of LAV2P basis set?

I am working on energy optimization of molecular structure using DFT with Schrödinger software and I found that job is running on LAV2P basis set. I want to know what is the meaning of this basis set ...
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Getting radial Kohn-Sham orbital from the output of an electronic structure code using gaussian basis sets

As we know that in solving the Schrodinger equation (Kohn-Sham equation), we expand the wavefunction in terms of some basis sets and them optimize the energy (the expectation value of Hamiltonian) by ...
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33 views

NMR Prediction for compounds at variable pH values

Like the title says, I'm looking for any software package that may be able to simulate a variety of NMR at a variety of different pHs. The majority of the software programs that I've found do not have ...
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202 views

Gaussian 09 Geometry Optimization: Identical energies printed in output

This question may be slightly off-topic for this site, but since Gaussian is the "calculator" most often used by computational chemists, perhaps it is relevant still. I have performed a transition ...
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Finding the binding energy iof methylated miRNA to an mRNA

I'm working on a project in biophysics and I need to find if there is a difference in binding of an miRNA to an mRNA when in one case the miRNA is methylated and in the other it isn't. What tools ...
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Using AutoDock Vina to dock multiple ligands to multiple receptors?

I am trying do that what the title depicts, but I keep running into errors creating the executable script. Is it even possible to automate the docking of multiple ligands to multiple receptors? ...
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What computational software is available to simulate drug receptor activity?

Is there any programming software/simulation software that can allow us to see whether a drug/molecule can form interactions with a receptor/enzyme pocket. Does it have anything to do with molecular ...

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