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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Identifying Key Chemical Series, Pharmacophores, and Scaffolds in a Large SDF Dataset
fellow computational chemists!
I have encountered a challenge that I'd like to discuss and seek advice on. Suppose I have a substantial dataset in SDF format containing thousands of molecules. My goal ...
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How to read a correlation diagram?
How can I extract practical information from a correlation diagram?
I mean for example diagrams between limit of infinite crystal field and infinite interelectronic repulsion, or between the same ...
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Reduction of direct product representation
When we do the reduction of the reducible representation generated from the total wavefunction expressed as product of MOs of appropriate symmetry, we can find the direct sum of more than one ...
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Group theory and exact Eigenfunctions of Hamiltonian
I think I've understand why the real Eigenfunctions of Hamiltonian belong to a given irreducible representation and I've read that also MOs have to transform as irreducible representation due to the ...
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What is the meaning and unit of the integral in the local density approximation (LDA)?
According to Parr and Weitao (1995), the Dirac exchange-energy formula (1930) comes from
[I am looking only at the last line of the equation and the rest for completeness]
It's an energy, so I'd ...
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Commutating operators of angular momenta
I've studied the formal procedure to pass from the uncoupled basis set of individual angular momenta to the coupled basis set of total angular momenta for polyelectronic atoms.
I start from an ...
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Why do we call STO-nG a basis set?
Why do we call the Hartree Fock basis-set for an atom a "basis set?" In linear algebra, a basis must be linearly independent. Looking at the STO-3G "basis set", the basis functions ...
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How to find the ligand field splitting of d orbitals in a square planar complex?
I am working with a Iron square planar complex with $\ce{NH2-}$ and $\ce{OH-}$ ligands having cis and trans conformation. My question is how to theoretically/computationally calculate the ligand filed ...
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Help with exchange integral interactions!
A single determinant configuration constructed in a basis with 7 spatial orbitals has the following exchange integral interaction energy terms:
-2K12 -K13 -K23 -K14 -K24
(i) Draw a configuration that ...
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Do we know the asymptotic behavior of density functional in DFT?
I was reading a book on DFT the other day, and the author included asymptotic behavior for $E_{xc}[\rho(r)]$.
Given that, do we know the asymptotic behavior for kinetic energy and/or total energy in ...
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Dipole moments of trans and cis nitrous acid
I have a paper due about the isomers of nitrous acid, using various calculations methods to find molecular properties like their dipole moment. I've found the dipole moment of trans isomer to be 1.987 ...
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Derivation of the conversion of Gaussian type orbitals (in cartesian coordinates) to Gaussian type orbitals (in polar coordinates)
While studying basis sets, I came across Gaussian type orbitals (GTOs), which are used as atomic basis sets. I reviewed the polar form of these orbitals, which are very similar to hydrogen atom ...
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Obtaining transition density matrix
I'm trying to assemble a transition density matrix on quantum computer using one-body excitation $\widehat{E}$ operator on 2 active spatial orbitals, i.e. on 4 spin-orbitals. The problem is, I need to ...
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How to convert SMILES to 3D (with higher accuracy than RDKit)?
I am interested in assigning 3D coordinates to (atoms in) some 10K molecules that I have, currently represented by SMILES. This is because as have been shown by many chemoinformatics papers, 3D and 2D ...
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G09 how to I prevent Na-O bond formation doing DFT on a sodium carboxylate?
I am trying to determine Gibbs free energy of solvation for a sodium salt of an alkylcarboxylate. B3LYP/6-31g. The minimized structure makes covalent bonds between sodium and carboxylate oxygens. How ...
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Need for AINR-based simulations (vs. laboratory experimentation)
The Results section of this paper related to ab initio molecular dynamics states that "16 $\ce{H_2O}$ and 15 $\ce{HCN}$ molecules were taken together, and the system was allowed to evolve for 750 ...
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Gaussian simultenous scan with two variables
I am trying to rigid scan two bond distances simultaneously in Gaussian 09/16. For example, I have taken a water molecule and started a rigid scan. Below is my input.
# b3lyp/6-31+g(d,p) scan
Title ...
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What can visual observations of pi-bonding MOs explain about LCAO expansion coefficients?
For examples of CO and N2, what can their MOs tell us about their expansion coefficients?
I've thought that in N2, its symmetric so the expansion coefficients would be equal from the pi-bonding MO due ...
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What does the χ (chi) symbol represent in a Slater determinant? [closed]
Context: Computational Chemistry
So, I am looking at the molecular orbital approximation, which allows the assumption that the overall wavefunction can be written as individual molecular orbitals
Ψ(r1,...
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The need for accurcy in constrained molecular dynamics simulations
In constrained molecular dynamics a system of differential algebraic equations
$$\begin{align} \dot{q} &= v, \\ M\dot{v} & = f(q) - G(q)^T \lambda, \\ g(q) &= 0 \end{align} $$
is solved. ...
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How to determine the unitary transformation from atomic orbitals to symmetry-adapted atomic orbitals of Ethylene
I am trying to find the unitary transformation matrix U from the atomic orbitals $|\mathbf{\chi}\rangle$ of ethylene to the symmetry-adapted atomic orbitals $|\mathbf{\chi}'\rangle$ of Ethylene, i.e $|...
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Thermochemical parameters at high temperature
I wanted to calculate Thermodynamic parameters such as Gibbs Free energy, Enthalpy change and Entropy change using Curtis et al explained as this link: https://gaussian.com/wp-content/uploads/dl/...
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Dependence of the permittivity on solvent mixing ratio
I am doing DFT calculations on an organometalloid compound to assess whether it dissociates into an ion pair in different solvents. I suppose that the more polar the solvent is the more stable this ...
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Why does a symmetric stretch mode not have an imaginary frequency?
Currently studying potential energy systems and our professor asked a question at the end of a lecture and I can't wrap my head around it.
He said, "Picture a 2D PES for the simple reaction of H+...
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Compound of C+Li+F possible? [closed]
Sorry my chemical knowledge is not very deep so some of what you assume is common knowledge will probably be new to me.
For a game i am trying to make i wrote a simple atom / compound simulator where ...
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Gibbs Free Energy for solvation using Gaussian09
I am trying to compute the $\Delta G$ for the solvation of a molecule using the continuum dielectric model in Gaussian09. Following the recomendation in the manual of the software, I am using the SMD (...
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QM9 atomization energies
I am doing experiments with the QM9 dataset from
http://quantum-machine.org/datasets/
and began with some simple checks on results from the literature. Consistent with what the authors of the paper
...
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Difficult in grasping "the extent/limit of conformational space of a compound until it change its stereochemistry"
I have heard that a conformational landscape encompasses all conformers that a compound has for a specific stereoisomer. I think it makes sense verbally, because if all conformers of a stereoisomer ...
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Derivation of the Hartree-Fock equation
I have to do some tutoring about basic quantum chemistry and the main purpose is to give a deep insight into Hartree-Fock theory. My plan is to start from expressing the many-electron wavefunction as ...
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Integral Prescreening in calculation of Electron Repulsion Integrals?
I am trying to write a basic Hartree-Fock program that can calculate the total energy and molecular orbitals of any molecule at arbitrary basis sets largely as a self-taught effort.
I am able to ...
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Software for running dynamics simulation of polymeric and mixed biomaterial (e.g hydrogels)
I was working on the development of a soft solid hydrogel having polymeric chains and molecules of different compounds dissolved in Phosphate Buffered Saline solution. There is a sub-study regarding ...
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How to convert molecule structure to 3D PyTorch tensors for CNN? [closed]
I want to try convolutional neural networks for drugs classification. I use PyTorch for 3D CNN implementation. Is there a way to obtain 3D tensors from SMILES or SDF/PDB structures?
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Line Entry system like SMILES for metals?
SMILES is not designed for metallic compounds.
Is there a similar ASCII line entry notation for metallic compounds, including repeating structure in space, &c.?
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Computing the molar volume for a 2D-simulation of phase separation
I am a mathematician and I want to simulate phase separation that occurs in a sodium silicate glass ($12.5\,\text{Na}_2\text{O}\cdot 87.5\,\text{SiO}_2$) at $T = 923\ \text{K}$ as it was done, for ...
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Multi compartmental ODE's in chemical engineering
I am alien to the field of chemical engineering. And I am confused about equations, written by chemical engineers, including several variables belonging to different compartments.
Assume that,
$[X]$ ...
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Hund’s Rule - Please help explain below using Hunds rule? [closed]
Why is it easier to excite a 2s electron in a carbon atom to a 2p orbital than it would be to do the same in nitrogen?
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What does it mean and what are the implications of individual electrons being identical? [closed]
In Jeremy Harvey's Computational Chemistry, I found the following statement:
[...] all electrons need to be treated as being very strictly identical to each other, so the wavefunction cannot treat ...
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Improper dihedral angles: how to tell between 0 and 180 degress
How can I tell the difference between a 0 and 180 degree value when looking at an improper dihedral. For example, in the molecule below would the dihedral angle 4-2-3-1 have a value of 0 or 180 ...
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Provide a mathematical explanation of why the non-relativistic Schrödinger equation for a Molecular system, cannot be solved analytically?
The non-relativistic Schrödinger Equation is:
$\widehat{H}|\psi\rangle=E|\psi\rangle$
Where $\widehat{H}$ is the Molecular Hamiltonian in Atomic Units and has the following terms:
$$ \widehat{H}
=...
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Are the (133,885) molecules in the QM9 database drug-like?
Are all the individual 133,845 molecules of QM9 drug-like molecules?
Can other drug-like molecules be made from the these 133,845 molecules by some combination or permutation which are not part of QM9?...
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Are the np orbitals of light group 2 elements considered as valence electrons in basis sets?
An old mail archive says that, in the usually used basis sets, polarisation functions are treated by a single-Gaussian treatment even for valence double-zeta basis sets.
A priori, I've done a few NBO ...
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Are diffuse functions necessary for modeling unbound conjugated anions?
According to this paper, and contrary to popular belief, diffuse functions are far from being necessary for the calculation of the electron affinities of the polycyclic aromatic hydrocarbon(PAH)s, due ...
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How is a Barrierless Reaction Confirmed in Quantum Chemistry?
Background:
Some quantum chemistry papers explore potential energy surfaces by characterizing critical points with an ab initio method. Reactants, products, intermediates, and transition states are ...
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How to increase basis set while running cluster calculations
I am running (opt+freq)DFT calculations using 6-311G(d) basis set on polymers with different number of monomer units. Upto 2 monomer units optimization is converged but for 4 units max displacement ...
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SMARTS: distinguish between alcohol and carboxylic acid
I'm new to SMARTS and have to identify substructures with the Python package rdkit, so far so good. Let's say I have a SMILES with an carboxylic acid and a alcohol ...
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Open shell TDDFT excitaion contribution
If I have a open shell system (10 alpha electrons and 9 beta electrons) and running TDDFT calculations, is it possible to have a 9a→10b transition? Or does it have to be 9b→10b? Because both exciation ...
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How to define a chemical bond computationally?
I'm working with an amorphous system. With oxygen, my system has both covalent and ionic bond forming cations. I utilise the Wannier centre to define a covalent bond, and my theory is that if the ...
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Smarts string for querying two N substitutions at any place along bicyclic ring
I'm a newbie to SMARTs string representation and have been stuck on generating the structure that I want. I have a pattern of chemical scaffold of interest which I'd use as a query to screen a library....
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Are there tools or algorithms to detect organic molecules from 3D crystal structures?
The task I'm thinking of is to detect entire molecules from structures, such as in a crystallographic information file (CIF) or from the XYZ file generated in a molecular dynamics simulation. ...
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How to calculate <ab|ab> integrals to carry out Schwarz pre-screening of molecular integrals
During writing my own two-electron integration library I faced an issue of dealing with integrals that have very small values beyond the C/C++ double data type. ...
