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.

205 questions with no upvoted or accepted answers
Filter by
Sorted by
Tagged with
42
votes
0answers
886 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 ...
25
votes
2answers
747 views

Is hybridization used in ab initio valence bond calculation?

Many general chemistry textbooks introduced the concept "hybridization" to construct a symmetry-adapted VB-type wavefunction. In the textbooks, usually the minimal basis is used and without optimizing ...
17
votes
0answers
641 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 ...
15
votes
0answers
2k views

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
votes
1answer
367 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
votes
1answer
166 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 - \...
11
votes
0answers
277 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 ...
10
votes
0answers
387 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
votes
0answers
229 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
votes
0answers
119 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
votes
0answers
87 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.
9
votes
0answers
484 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
votes
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?
8
votes
0answers
162 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
votes
0answers
187 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 ...
8
votes
0answers
160 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 ...
8
votes
0answers
154 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
votes
0answers
283 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 ...
8
votes
0answers
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
votes
0answers
308 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 ...
7
votes
0answers
196 views

Vanishing integral rule for two-electron integrals

I understand the vanishing integral rule for a one-electron integral to be: $$\langle i | \hat{O} | j \rangle = 0 \hspace{1cm} \mathrm{if} \hspace{0.2cm} \Gamma_O \neq \Gamma_i \otimes \Gamma_j$$ ...
7
votes
0answers
111 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 ...
7
votes
0answers
289 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:/...
7
votes
0answers
204 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
votes
0answers
129 views

Have IH₃ and IH₅ already been synthesized?

I've seen a paper by Sikalov [1] that says that $\ce{IH3}$ and $\ce{IH5}$ should be observable. Has anyone actually tried to synthesize such molecules? References Sikalov, A. A. Hypervalent Halogen ...
6
votes
0answers
47 views

Is there a rule of thumb to predict when coupled cluster might dip below the variational limit?

Coupled cluster is a non-variational method, meaning that it can give energies that are below the true FCI energy (the "variational limit" for variational methods). Often coupled cluster still gives ...
6
votes
0answers
120 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 ...
6
votes
0answers
66 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
votes
0answers
124 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
votes
0answers
382 views

Two-electron integral algorithm

I am writing a molecular integral code from scratch. Right now my code have the following structure: ...
6
votes
0answers
244 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
votes
0answers
311 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
votes
0answers
174 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 ...
5
votes
0answers
167 views

Hartee-Fock vs tight binding and others

I was reviewing many electron computational methods recently and got a bit confused about relation between different approaches. In particular in what is essential elemental difference between Hartree-...
5
votes
0answers
92 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
votes
0answers
92 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
votes
0answers
124 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
votes
0answers
130 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 ...
5
votes
0answers
61 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
votes
0answers
154 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 ...
5
votes
0answers
71 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
votes
0answers
116 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
votes
0answers
68 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
votes
0answers
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 ...
5
votes
0answers
77 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
votes
0answers
323 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
votes
0answers
165 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
votes
0answers
167 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 ...
5
votes
0answers
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
votes
1answer
89 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 ...

1 2 3 4 5