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.

Filter by
Sorted by
Tagged with
0
votes
0answers
15 views

How to calculate molecular emission spectra?

Is there free software which can calculate the fluorescence emission spectra of organic molecules? Let's say for example: rubrene There is a bunch of quantum free quantum chemistry software: https://...
-4
votes
0answers
25 views

United Atoms Model book recommendation [duplicate]

Is there a book or paper that someone can recommend that explains what the United atoms model is and how it works in detail.
6
votes
0answers
49 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 ...
-2
votes
0answers
21 views

No change in energy of Hydrogen when uniform electric field is applied using gaussian software?

I have done SCF calculation for hydrogen atom and in the second job i did the SCF calculation on hydrogen atom with uniform electric field field of 0.05 a.u in a particular direction, but there is no ...
-3
votes
0answers
19 views

Compute UV/Vis absorption spectrum for iodine using Gaussian 09 [on hold]

I am trying to compute UV/Vis absorption spectrum for Iodine using Gaussian 09.I use DFT/b3lyp/dgdzvp basis set for this computation and get an absorption peak at about 178 nm which is far appart from ...
2
votes
0answers
27 views

Geometry optimization with GAMESS. Why won't SCF converge?

I'm using GAMESS to run a geometry optimization on a thiourea molecule, using PM6. However, the output file keeps displaying the error message, "NO FORCE FIELD, SCF DOES NOT CONVERGE." Is there an ...
1
vote
1answer
53 views

How do I view a DSN6 file as text?

I am trying to isolate certain pieces of information within a dsn6 file. Specifically, I want to find the electron density around two atoms within a protein. I want to then run a python code to ...
0
votes
1answer
42 views

Reference on Pople basis set

I need to write reference on 6-311++g(d,p) basis set in my work where I used it on atoms of I-II periods. Does anyone know where it was first published?
8
votes
1answer
196 views

DFT vs. MP2 for stacked dimer

Recently, I looked at these two papers analyzing the excited-state properties of modified DNA bases (2-aminopurine and 8-vinyl-A) and how they are influenced by stacking with natural nucleobases: ...
1
vote
1answer
65 views

The influence of diffuse functions on electron density calculations

I am not a quantum chemist, but I am (starting to be) a user of electronic structure software. In the picture (screenshot) is the electron density of the same molecule. On the left I calculated the ...
-3
votes
0answers
31 views

How can I calculate the equilibrium of a reduction reaction? [closed]

I'd like to calculate the equilibrium in reducing the metal in a salt with a more reactive metal, e.g. $$\ce{HgSO4 + Pb → Hg + PbSO4}$$ Which as a side note, I know can only happen at low ...
3
votes
2answers
136 views

Developing Computational Chemistry Software

I want to learn to develop novel methods in computational chemistry (e.g. Grimme's empirical dispersion, DFTB, new DFT functionals, etc.) What is the ideal way to learn this by oneself? I have read ...
9
votes
1answer
125 views

How to calculate the amount charge transfer from a natural population analysis?

I am trying to reproduce the quantity referred to as the degree of charge transfer reported in this publication by Zhu et al. [Ref. 1] for the F4-TCNQ molecule. I am interested in section 3.2 in the ...
0
votes
0answers
33 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 ...
4
votes
1answer
183 views

Can I compare DFT calculations with different grids?

When doing DFT calculations, some integrations are commonly done numerically on grids. [In fact, more than a single grid may be used at the same time for different integrals, e.g. approximations such ...
4
votes
1answer
107 views

How to calculate S² value of a broken-symmetry wave function?

$S$ represents spin, signifies the number of unpaired electrons in the system. For example, if the number of unpaired electrons is $1$, then $S=1/2$. $S^2$ is calculated as $S(S+1)$. From what I have ...
2
votes
0answers
25 views

What kind of algorithm does computational software use to process molecular symmetry?

Background I'm forced into using GAMESS-UK for an older software package. Using a cs-symmetry molecule, I've noticed that GAMESS will reorient the molecule before running a standard SCF calculation. ...
1
vote
1answer
78 views

Calculating Mixing Enthalpy in GROMACS

What is the most reliable way to calculate mixing enthalpy of binary solvent mixture using GROMACS? [EDIT] I have simulated two-component systems of water and organic solvent with GROMACS. In a ...
4
votes
1answer
80 views

Building an average model from MD snapshots

I am performing a molecular dynamics simulation, and I am taking "snapshots" of the system at regular intervals. The aim is that of finding the preferred geometry of a molecule in solution. Are you ...
0
votes
1answer
28 views

Is there a way to export detailed data about atom connectivity, dihedral angle, etc from GaussView?

As far as I know, opening the .com files as .txt files (with a text editor like simple notepad) yields a nicely formatted table ...
3
votes
0answers
33 views

All possible determinants forms a complete basis [closed]

How do we mathematically prove that the set of all possible excited determinants forms a complete basis for expanding the wavefunction (as in full configuration interaction)?
2
votes
0answers
26 views

Guide to DFT functionals [duplicate]

Having recently begun studying Quantum and computational chemistry in depth... I am looking for a manual, text, or guide of any form that could explain the basic formulations and potential of the ...
3
votes
1answer
69 views

Distribution of polymer lengths

Suppose we have a chemical reaction where a linear chain can form (reversibly) from building blocks (e.g. atoms or molecules): $$\ce{X_$i$ + X_$k$ <=>[$k_\mathrm{fwd}$][$k_\mathrm{rev}$] X_$i$...
1
vote
0answers
43 views

Why does a 4-bonded nitrogen atom appears negatively charged after an optimization?

I have a molecule bearing a quaternary ammonium and I optimized it using M062X (also Hartree-Fock) using basis sets 6-31G(d,p) and 6-31G+(d,p) respectively. After optimization, I expect that the ...
3
votes
0answers
119 views

Calculating bond length in VMD (Visual Molecular Dynamics)

Is there a way to calculate bond length in VMD (Visual Molecular Dynamics)? I have a lot of trajectory files of water molecule, and I need to calculate the bond length of $\ce{O-H}$ bond, and find the ...
1
vote
0answers
28 views

What happens if an orbital has no entry in a point group table?

A while ago I cited a few passages from a book on $f$-orbital contributions in metal complexes. And although usually the $4f$-orbitals are too isolated to really do chemistry and the elctron density ...
0
votes
0answers
45 views

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 ...
2
votes
2answers
185 views

How do you calculate the correct charge on F after F2 dissociates?

When you ionize $\ce{F2}$ to $\ce{F2^5+}$, it quickly dissociates. Experiments show that the products of dissociation are $\ce{F^2+}$ and $\ce{F^3+}$. I have tried to model the dissociation of $\ce{...
2
votes
0answers
31 views

Rotating dihedral and Angles And Generate File For Each Degree

I need to optimize a force field I generated. For this, I should apply Genetic Algorithm (G.A). To apply G.A I should do this for 220 molecules: 1) Find all dihedrals for each molecule ( I did this ...
7
votes
1answer
285 views

Why is a LCAO necessary within Hartree Fock?

As I understand it, the electronic Schrödinger equation cannot be solved for polyelectronic systems. To circumvent this problem in the Hartree-Fock method, it is assumed that the polyelectronic ...
1
vote
0answers
24 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 ...
4
votes
0answers
57 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 $$\psi(r)=\sum_{i=0}^3 C_{i} e^{-\alpha_ir^2}$$...
3
votes
0answers
92 views

DFT Exchange-Correlation Two Electron Integrals

Are there any electronic structure programs that print the exchange-correlation (XC) integrals for a given DFT functional? These integrals are of the form $$\langle pq|w|rs\rangle$$ where $w$ is an XC ...
6
votes
2answers
405 views

When does Hartree-Fock fundamentally fail?

The Hartree-Fock approximation (HFA) works by assuming each electron sees the effective electric field from all the other electrons as some self-consistent field. The HFA is known to give pretty ...
2
votes
0answers
57 views

Antisymmetrized Product of Strongly Orthogonal Geminal (APSG) method

To get a deeper understanding of electronic structure methods, like Hartree-Fock, MP2, and Coupled Cluster method, there are many small programs (codes) available in Python, C++ or Fortran, for ...
1
vote
0answers
59 views

Software for conformational search

I need a free software to perform a conformational search on molecules with 10 to 16 rotational bonds. What software would you recommend me? Where can I download it? Where can I find a manual of this ...
3
votes
2answers
53 views

How fast is the interconversion triplet → singlet in organic molecules?

When computational studies are performed on transition state geometries, the "thermodynamic" (that is, with no kinetic considerations) energy of the analyzed state is obtained. I was wondering: if a (...
1
vote
0answers
91 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 ...
3
votes
0answers
35 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 ...
4
votes
0answers
44 views

What is the theoretical justification for state averaging in SA-CASSCF?

According to the molpro manual, section 7.3: In order to compute excited states it is usually best to optimize the energy average for all states under consideration. This avoids root-flipping ...
1
vote
0answers
28 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 ...
3
votes
2answers
81 views

What's the most complete basis set for calculating chemical shifts with DFT?

I'm trying to benchmark some NMR chemical shifts. The literature suggests that the pcS-4 basis set will be the most accurate. I was wondering if there were any basis sets that are more complete than ...
-1
votes
1answer
50 views

Charge, multiplicity, level of theory and coordination coordinates of gold compleaxes [closed]

Good day, I need to learn a trick in answering the following questions: How to come up with cartesian coordinates of a complex say, [Au(CH2)2(S)PPh2]2, to be ran on Gaussian? The charge and its ...
3
votes
0answers
29 views

Factorizing Slater determinant into product of spin-up and spin-down slater determinant

I am reading the book on MONTE CARLO METHODS IN AB INITIO QUANTUM CHEMISTRY by Hammond and Lester. (Chapter 5-Variational Trial Functions, Section 5.3-Hartree Fock and Beyond, Sub-Section 5.3.3 ...
2
votes
0answers
23 views

Perturbation theory for molecules, chromophore group, dipole approximation,

I am interesting in chromophore group and dipole approximation. For example, i have a molecule (acetone or any other ketone/enol) which is belongs to some symmetry group. Because of the symmetry ...
1
vote
1answer
43 views

Computational Efficiency of Periodic Boundary Conditions

From what I understand, in a molecular dynamics simulation the number of molecules included is limited by the computational power available. In order to simulate macroscopic properties, one needs to ...
0
votes
0answers
49 views

Computational Chemistry- MOs of (calculated) ClO2 molecule

I attempted to do a RHF STO-3G calculation on ClO2, assuming that it would return results that are consistent with its C2v point group (i.e. orbitals of appropriate symmetry). Alas, I was wrong. ...
1
vote
1answer
35 views

What is the correlation between electronegativity and the sharing of electrons?

For example in a C-O bond, the electronegativity difference is 1.2. does this mean that the Oxygen has 1.2 of the shared electrons and Carbon 0.8 (or some other numbers)? Is there a specific equation ...
-1
votes
1answer
38 views

How to give different Basis set to different atoms in molecules using GAMESS-US [closed]

I am new to GAMESS-US, I am trying to do UHF for DyC10H10 while giving different basis set to Dy, C, H to reduce the computational cast. Until I tried with following input using manual. OUTPUT *** ...
2
votes
1answer
103 views

How to prepare a Gaussian input file for a binary solvent?

The UV absorption energy spectrum of a molecule has been recorded experimentally using binary solvent (DMSO:Water=9:1 v/v). I am trying to calculate the absorption energy of the same molecule using ...