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 to develop a Reactive Force Field (ReaxFF)? (Molecular simulation)

Currently, I am working on CO2 capture on Hydrotalcites as solid adsorbents. I want to run molecular simulations to analyse the behaviour of the material under different temperatures, pressures and ...
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103 views

What is the purpose of the substructure section of a mol2 file?

I'm looking at the tripos mol2 format. (This is the most recent mirror of the specification document that I have found so far: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf). What is the ...
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34 views

QM modelling of charge separation reactions

I have a general question regarding the modelling of reactions in which neutral reactants form charged species/ions (in solution). How can one get the energetics approximately right on reactions like ...
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215 views

Is Argus lab accurate?

I was trying to calculate the resonance energy of benzene by using Argus Lab. These values are weird and very different from the experimental data. I have two questions regarding them. What is the ...
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266 views

How to calculate RESP charges in a system with addition of user-defined extra-point charge in AMBER?

I would like to add in extra point of charge in my molecule system (EP) and calculate the resulting RESP charges. Parameters for the EP has been defined in a separate frcmod file. However, I am not ...
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149 views

Rendering software for publication

Does anyone know how I can render chemical structures of small organic molecules to look like the below images? I have been looking around, and I cannot seem to find an answer. The closest lead I ...
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70 views

Filtering conformation search: redundant elimination or clustering

In my project, I study reaction computationally. The initial step in my workflow involves a conformational search using a constraint to bring the two reactive parts on my molecule together (reaction ...
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66 views

Setting to basis set for electron transfer in type II CdS/TiO2 heterostructre for PYXAID package

I am studying electron injection from $\ce{CdS}$ into $\ce{TiO2}$ using NAMD approach. Now I'm using pyxaid package. Would be possible someone kindly help me with construction of basis set for this ...
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129 views

When two negatively charged molecules are hydrogen bonding with each other, why do the charges increase?

Context [EDIT: As some commentators have suggested, I should conclude that the energy minimize feature is not intended for the purpose of Hydrogen-bonding, and primarily for refining the modelling ...
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99 views

Chain reaction vs single reaction

I am considering the following chain reaction: $$\begin{align} \ce{A_0 + B <=>[$N\cdot k_+$][$k_-$]A_1\\ A_1 + B <=>[$(N-1)\cdot k_+$][$2\cdot k_-$]A_2\\ A_2 + B <=>[$(N-2)\cdot k_+$]...
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182 views

Field Keyword and Molecular Orbitals--Gaussian 09

I am using Gaussian 09 to run calculations. I am applying a 0.1 eV field in the positive Z direction to a molecule. I am also using the %chk keyword so that I may analyze the Molecular Orbitals after ...
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47 views

Langmuir parameters for fixed bed continous column

I have prepared a model of fixed bed adsorption column in MATLAB. I have to insert Langmuir parameter value there, so how can I calculate them in case of continuous fixed bed column. I have calculated ...
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71 views

TINKER molecular modeling extra forces - energy unit

I use the TINKER molecular modeling software package (version 7.1.2) for computational physical chemistry. There is an extra file (extra1.f) included for the user to edit and incorporate their own ...
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111 views

MOLCAS CASPT2 energy

I have calculated all the roots for a specific symmetry and I need to calculate the CASPT2 energy for all the roots. For example: here I have 4 roots and I need to calculate the CASPT2 energy for all ...
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221 views

Cannot optimize transition state

During a Gaussian scan calculation, I got a high negative frequency for a transition state candidate, but it doesn't matter what I do (Berry algorithm, qst methods) I cannot get a stable TS, I always ...
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96 views

Inactive versus frozen orbitals in CASSCF

Does it make any difference if I use the frozen keyword instead of the inactive keyword in MOLCAS CASSCF calculations?
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52 views

Calculate optimal surroundings for given reaction mechanism to lower activation energy?

Let's take a reaction that's fairly well understood, which in this case means that the reaction mechanism is known, maybe something like this from here: If we know the reaction mechanism, we also ...
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50 views

Does higher electron density mean better transport?

In a nano device, do areas with higher electron density necessarily contribute more the to the overall transport compared to areas with lower electron density?
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34 views

Distance weighted interpolation in predictor steps vs corrector steps

I got stuck while reviewing the journal article "Accurate reaction paths using a Hessian based predictor–corrector integrator". Why is the distance weighted interpolation done in the predictor steps, ...
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941 views

Structure of fluoroalkylsilane

I want to use FAS (fluoroalkylsilane) in my molecular dynamics study. How can I find it's real structure? So that I can find proper forcefield for simulating the molecule. It would be very nice if you ...
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103 views

Making a reasonable slab of alpha quartz

I want to perform a molecular dynamics simulation with alpha-quartz as my mineral surface. I want to study adsorption of water on alpha-quartz. The most dominant error that I came up with is the ...
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235 views

How to model iso-surface of molecular orbitals of singlet and triplet excited states

I've modelled the iso-surface of the highest occupied molecular orbital of a molecule with DFT in Gaussian.If I were to model the iso-surface of the molecular orbital of the singlet and triplet ...
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295 views

Spectral analysis of periodic table of elements in time domain

I'm trying to get the spectral analysis data of the periodic table of elements in the time domain format or find a site that has the data in the time domain format. All the sites I know have the data ...
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17 views

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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9 views

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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21 views

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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40 views

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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22 views

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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34 views

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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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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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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150 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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34 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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102 views

Valency of each atom in a molecule with python

Consider ethanol, where each carbon atom has a valency of 4 and oxygen a valency of -2. I would like to determine these values for many compounds given their SMILES or InChI keys. (For the purpose of ...
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39 views

Four-electron integrals over GTOs

I was looking through the following presentation: http://folk.uio.no/helgaker/talks/SostrupIntegrals_10.pdf Looking at the section on 4-electron integrals, I couldn't help but notice that the slides ...
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45 views

Which DFT functional is best for predicting macroscopic properties of molecular liquids?

Which DFT functional (KS-DFT, to be more specific) performs best at predicting macroscopic properties (density, surface tension, boiling point, relative permittivity etc.) of molecular liquids (...
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31 views

Applying the constant number of electrons in DFT density optimisation

(Previous related question: Finding mathematically the ground state density in DFT) I am studying the density optimisation procedure (in particular for Orbital-Free DFT) this thesis. The derivative ...
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117 views

How to generate Density Functional Tight Binding parameters (Slater-Koster files)?

What is the simplest way (or least complicated way) to generate parameter files (.skf) to be used with DFTB+, for example? Assuming I want to be able to reproduce geometries for a certain type of ...
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49 views

Computational chemistry of surface

I would like to simulate the interactions between metal oxides surfaces (TiO2) and a biomolecule, I used AmbersTools (antechamber,parmchk2,leaf) to have the different parameters of my molecule and I ...
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248 views

Hartree Fock for an atom (Beryllium)?

I'm working on solution of Hartree-Fock equation for Beryllium in configuration $1s^2 2s^2$, expanding the orbital with STO-3G basis $$\phi_k=\sum_{p=0}^3 C_{kp}e^{-\alpha_{kp}r^2}$$ I know the values ...
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59 views

Excited state intramolecular proton transfer mechanism

I am trying to explain Excited state intramolecular proton transfer(ESIPT) mechanism through DFT method using Gaussian 09.Generally, in ESIPT mechanism the molecule exist in enol form in its ...
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99 views

GAMESS Gaussian qst2 method alternative

I've heard about the qst2 Gaussian method but I don't have any licence so I use the free GAMESS-US. Nevertheless, I didn't find any Gamess method which allows a TS finding like qst2. Have you heard ...
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42 views

Is the 12-6 Lennard Jones potential a good description of van der Waals interaction energy?

It seems to me that the Lennard Jones potential oversimplifies the more complex nature of van der Waals forces. However, in most of the MD simulation package, this is generally accepted.
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264 views

How do I calculate the full configuration interaction Hamiltonian of H2

I have been trying to follow the paper titled "Towards Quantum Chemistry on a Quantum Computer" (https://arxiv.org/pdf/0905.0887.pdf) by simulating their results on a quantum computer simulator. ...
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16 views

Lipophilicity computational prediction

Is there a web based (or otherwise) computational chemistry tool which is able to calculate lipophilicity of a given compound?
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313 views

How to understand MO diagrams for cationic octahedral transition metal complexes

I am having problems understanding the construction of MO diagrams in octahedral transition metal complexes within ligand field theory (LFT) when the metal center is asumed as an cation: I am ...
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470 views

Link1 and multiple output files in Gaussian: doable?

I have recently started learning Gaussian in my Computational Chemistry class, and I have recently learned how to use the "Link1" option, in order to run multiple calculations from a single input file....
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80 views

STO 3G basis expansion of p orbitals

I am expanding $2p_{x},2p_{y},2p_{z}$ (slater type )orbitals in gaussian STO-3G basis as follows, $$|2p_{x}\rangle=C_{1}x\exp(-\alpha_{1}r^{2})+C_{2}x\exp(-\alpha_{2}r^{2})+C_{3}x\exp(-\alpha_{3}r^{2}...
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70 views

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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46 views

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 ...