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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175 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 ...
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203 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?
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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: ...
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111 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 ...
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2answers
222 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 ...
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277 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 ...
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130 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 ...
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1answer
255 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 ...
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1answer
151 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 ...
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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. ...
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250 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 ...
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97 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 ...
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1answer
38 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 ...
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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)?
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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 ...
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1answer
80 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_$i$...
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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 ...
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249 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 ...
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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 ...
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53 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 ...
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2answers
226 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{...
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36 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 ...
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397 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 ...
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46 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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102 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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130 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 ...
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585 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 ...
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81 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 ...
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178 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 ...
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2answers
86 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 (...
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188 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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67 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 ...
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113 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 ...
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52 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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2answers
114 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 ...
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1answer
88 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 ...
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62 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 ...
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0answers
42 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 ...
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1answer
58 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 ...
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1answer
57 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 ...
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1answer
165 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 *** ...
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1answer
521 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 ...
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354 views

What is the ANO-RCC basis set and how does it work?

On the basis set exchange, the ANO-RCC basis looks huge, even for hydrogen: ...
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83 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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1answer
847 views

Gaussian syntax error on the input line

I ran a Gold complex in Gaussian 09 with the following exact Route Section PBE0/LANL2DZ Opt Freq NoSymm and it gave me this error message: ...
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1answer
116 views

Optimized General Contractions using the EMSL Basis Set Exchange

When using the EMSL BSE Database and selecting a basis set, one can choose the "Optimized General Contractions" or not. When doing so for, e.g., Nitrogen and the cc-pVDZ some basis functions are not ...
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1answer
129 views

Help with missing output from cubegen utility after density calculation in Gaussian16

I am busy trying to do density calculations in Gaussian16 as I need the .cube output for input to the PIXEL software. But my Gaussian output seems to be missing an entire chunk of data and I don't ...
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253 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 ...
5
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1answer
169 views

HCl rota-vibrational lab: ab initio simulation of rotation constants

I'm trying to set up the simulation portion of the classic undergraduate lab studying the rotavibrational spectrum of HCl and DCl. In terms of simulation (using Gaussian 16), the equilibrium ...
6
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1answer
332 views

Perturbation theory in Quantum/Computational Chemistry

As we know, the common methods for computation molecular properties in modern Quantum/Computational Chemistry is the Hartree–Fock method and Density Functional Theory. But from university course of ...

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