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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42
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864 views

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 ...
17
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615 views

Ambimodal transition states in some organic reaction pathways

In many computational studies, mechanisms appear to have so-called ambimodal transition states, i.e. a transition state which can lead to multiple products, in conflict to the common undergraduate ...
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How to Calculate Transition Dipole Moment from Two Known Wavefunctions

I am interested in calculating the transition dipole moment (TDM) from the information from two wavefunctions of different states. This is somewhat similar to calculating the molecular dipole moment ...
13
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1answer
360 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 ...
11
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1answer
153 views

Importance of higher order exchange terms?

The MP2 ground state energy of a molecule or solid can be written as $$E^{(2)} = \frac{1}{2}\sum^{\text{occ.}}_{ij}\sum^{\text{virt.}}_{ab} \frac{\langle ij | ab \rangle [\langle ab|ij \rangle - \...
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270 views

Rotation around CC bond in 1,2-dioxetane: transition states and local minimum structures

TLDR: What: Potential energy surface associated with rotation around CC bond in the ring-opened version of 1,2-dioxetane. How: State average(4)-CASSCF(12,10)/VTZP constrained geometry optimizations ...
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361 views

Understanding two-electron integrals in Gaussian 09

I was comparing the two-electron integrals (electron repulsion integrals, ERI) printed by various well-established packages (Gaussian, GAMESS, Molpro etc.) and observed that Gaussian is the oddball in ...
9
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214 views

What is the largest coupled cluster calculation that has ever been done (as of March 2019)?

I am doing some research and trying to make sure the numbers I am reporting are accurate. I found that the paper by Sylvetsky et. al. says:[1] We were, however, able to complete a ...
9
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115 views

How to color bonds by the strain?

I need to create a figure of a molecule in which the bonds are colored in a RGB scale according to the values read from a data file. The data file contains, for example, the increase or decrease in ...
9
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86 views

Which potentials are suitable for molecular dynamics simulation of simple explicit solvents?

Which potentials (force fields) are suitable for adequately simulating (mixtures of) explicit solvents? Interesting rheological properties include viscosity, surface tension, heat capacity.
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461 views

Free Web-Based Orbital Solver to look into the Walsh orbitals of a perturbed cyclopropane

There exists a free online orbital calculator. When I draw cyclopropane it plots three molecular orbitals, but unfortunately it doesn't use the Walsh orbitals. Are there any free online tools which ...
9
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1answer
193 views

The Krieger-Li-Iafrate Approximation

I am having trouble understanding what KLI approximation is. Could someone explain it to me in an intuitive/simple way?
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160 views

Accuracy of quantum chemistry calculations on iodine neglecting relativistic effects

Triiodothyronine is a molecule with three iodine atoms. If we attempted to calculate its properties with ab initio methods like Hartree-Fock or more complicated ab initio methods which included ...
8
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182 views

Transition state optimisation on the surface of periclase

I want to model a reaction catalysed by periclase ($\ce{MgO}$) using DFT. I have a good guess on the transition state (TS) of the reaction that goes in gas phase/solvent (produced using MOPAC). The ...
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156 views

Computational heat of reation vs. using literature values

My question is I don't understand how to explain why or what I did wrong to have such large differences between my computational heat of reaction and heat of reaction using enthalpies of formation ...
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150 views

Where is bifurcation situated on cyclohexane isomerisation PES?

I am wondering what does PES for cyclohexane isomerisation looks like. I have two possibilities in mind but each has some kind of vagueness. 1) Starting from boat conformation minimum, followed by ...
8
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277 views

Educational practice problems/systems/reactions in computational chemistry

I am not sure if this question is suitable for Chemistry SE, but I think fairly objective answers can be given, and not just I will benefit from them I have almost completed the first year of a MSc ...
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193 views

Quenching rates in nucleation MD simulations

I am trying to perform nucleation simulations with molecular dynamics. To prepare the metastable fluid, I am equilibrating at temperatures about 30 K above the melting temperature, and then "quenching"...
7
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292 views

Cloud-based molecular modeling software

I’m an IT Acquisitions and Licensing specialist researching well-supported cloud software alternatives to Fujitsu’s molecular modeling SCiGRESS. I am coming in with a tech background, but little to ...
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178 views

Vanishing integral rule for two-electron integrals

I understand the vanishing integral rule for a one-electron integral to be: $$\langle i | \hat{O} | j \rangle = 0 \hspace{1cm} \mathrm{if} \hspace{0.2cm} \Gamma_O \neq \Gamma_i \otimes \Gamma_j$$ ...
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107 views

Is it possible to calculate electronegativity of surface atoms?

As the title asks, is it possible to calculate the electronegativity (EN) of specific atoms on extended surfaces (slabs), more specifically using computational methods? There are a few issues here I ...
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233 views

How are the angle bending parameters defined in the MM2 force field?

I am currently looking through the openbabel implementation of the mm2 forcefield. While I understand most of the implementation, I don't get the definition of the angle bending parameters (see https:/...
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200 views

Gaussian09 and Path Integral Monte Carlo which one predicts the total internal energy more accurately?

I'm learning PIMC with primitive action and currently just testing the code with single methane molecule, I did run a Gaussian ccsd(t) calculation, I notice that at 298.15K & 1atm, the energy ...
6
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117 views

Where to find experimental spin-orbit coupling constants?

I am searching for experimental spin-orbit coupling constants, particularly for main group elements and Cr(0) to calculate correlation consistent Composite Approach (ccCA) energetics. This method ...
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61 views

Additional example determining Marcus parameters searched

Background / theory: The electron transfer in organic materials was formalized by the Marcus theory, introducing $|H_{ab}|$ to describe the how molecules (or more generally: sites) are coupled with ...
6
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122 views

Vibrational Self-Consistent Field

There are a few things about VSCF that I don't understand: Which coordinates do you work in? If you work in normal mode coordinates, how do you evaluate the effect of the average of one normal mode ...
6
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357 views

Two-electron integral algorithm

I am writing a molecular integral code from scratch. Right now my code have the following structure: ...
6
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0answers
234 views

Canonical vs localized orbitals - stationary towards changes?

So regarding Koopman's theorem I found the the explanation that you should not use it to find the ionization potential of localized orbitals because, much unlike canonical orbitals they will not be ...
6
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302 views

Workflow for many-molecule/many-conformer calculations in Spartan, GAMESS, AND Gaussian

I wish to investigate the antioxidant properties of several hydrocarbon compounds, which are each mono- or polyhydroxylated, specifically at the phenyl ring. I wish to gain insight into my workflow ...
6
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168 views

What factors contribute most to solubility of ionic substances in highly polar solvents, esp. ionic liquids and DES?

I am trying to determine a method to dissolve a mineral salt with a lattice energy of ≈18000 kJ/mol. I know that lattice energy is the most significant factor affecting solubility of an ionic ...
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77 views

How to extract force constants for normal modes from ORCA?

I am following the computational method described in Scientific Reports.[1] Where the authors analyze the contribution of each excited state normal-modes to the shift of the transition energy. For ...
5
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89 views

Why the use of MD simulations is less popular for the study of carbohydrates?

In classical all-atom MD simulations, the force fields for proteins, nucleic acids and lipids seem to be more well developed than carbohydrates. It seems to me that the use of MD simulations is not so ...
5
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115 views

Ab initio MD simulations in VASP

I'm not sure if this is an appropriate question for Chemistry.SE, but I'm taking a stab. I'm running ab initio MD calculations in VASP and I'm trying to optimize different input tags. On the VASP ...
5
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129 views

Inverse problems in Computational Chemistry: The case of Inverse eigenvalue Problems for molecule structures

Mathematics Background An inverse eigenvalue problem (IEP) is the problem of reconstructing a matrix with a special structure from prescribed spectral data. By structure we mean the pattern of ...
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60 views

Identifying principal quantum numbers in natural population analysis

Following a Hartree-Fock calculation, I would like my program to perform some kind of Natural Bond Orbital (NBO) analysis. Preceding this I would like to output a list of atomic orbitals, along with ...
5
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147 views

Why is spin-contamination undesirable?

Why is spin-contamination, introduced by e.g. Unrestricted Hartree Fock, undesirable, and to which problems further on can it lead? The only problem I currently see myself is that spin-contamined ...
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70 views

Reactivity of carbon-centered radical

I've read this site for a long time but I had never asked a question, so this is my first time :). So, i'm currently working on a computational chemistry project on radical cyclization reactions and ...
5
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115 views

When is it necessary to consider size consistency?

For what kinds of reactions is it essential to account for size consistency? To my understanding for dissociation reactions $(\ce{AB -> A + B})$ it is important to consider. However, is it also ...
5
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67 views

Methodology and basis set for study in UV-Vis

I am currently working with a system of 30 atoms of a organic molecule. I need to make a study related to determine the UV-Vis graphic as precisely as possible. I am using DFT method. However, I am ...
5
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55 views

Computational modeling of steric repulsion between two polymer mediated magnetic Nanoparticle?

Can you recommend any modern article or research papers on steric interactions and forces between two or multiple magnetic nanoparticles with polymer brushes in a nonpolar solvents? something with ...
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76 views

Program to compute multipoles of water at CCSD(T)-F12 accuracy

I want to compute traceless cartesian electrostatic multipole moment tensors up to fourth order (hexadecapole), at CCSD(T)-F12 accuracy using a large basis set. I'd like to be able to choose the ...
5
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318 views

Calculation of Bond/Angle/Dihedral force constant

I am a big fan of Mopac (Though I have a very little knowledge about the tool). I have some queries regarding some calculations in Mopac2016: Problem: How to calculate Bond or Angle or Dihedral ...
5
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160 views

I found transition states (TS), but calculations aren't supported by experiment. Do I look for more TSs or somewhere else?

I'm using Gaussian to investigate a catalyst system. Experimental evidence showed that one of three analogues (R = phenyl, Ph), yielded a benzosultam when treated with 2,4,6-...
5
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164 views

Why isn't CASPT2 used in surface hopping simulations?

I will write what I think the answer is. I'd like someone to confirm and maybe explain in detail. I think that since surface hopping dynamics simulates movements on PES, it has to calculate gradients ...
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52 views

Paper Data Replication

I read a paper recently - Here. I found the concept of Electride materials very interesting and wanted to mess around with them myself. I tried to replicate the partial electron density plots shown in ...
5
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1answer
88 views

What are energies in computational methods relative to?

As per my understanding, in molecular mechanics (MM) the computed strain energy is based off the strain inherent in the molecule under study relative to an idealized form. For example, cyclobutane to ...
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130 views

What is the dataset with the largest number of molecules?

In computational chemistry we often apply techniques to all molecules of a "dataset". Recently it was asked which dataset contains the largest molecules, and a user accidentally misinterpreted this ...
4
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1answer
73 views

Are primitive GTOs normalised before contraction, or is the resultant basis function normalised afterwards?

I'm quite curious about this: In a basis set (I'll just use minimal-basis STO-nG basis sets for convenience), the basis functions are written as a linear combination of primitive GTOs. Are the GTOs ...
4
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80 views

Variational method: Hydrogen atom ground state in STO-3G basis expansion

I computed numerically the ground state energy of hydrogen by variational procedure, firstly expanding the wave function over the s-wave basis set STO-3G $$\psi(r)=\sum_{i=0}^3 C_{i} e^{-\alpha_ir^2}$$...
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57 views

How can I save and read the CI vector during CASSCF calculations in Gaussian?

I have searched through the GAUSSIAN 16 manual and have not been able to solve these two related issues: (1) I want to be able to save the CI vector and load it as an initial guess for a different ...