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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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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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0answers
19 views

how to optimize the huckel stable structure for [16] annulene? [on hold]

It is well known that the geometry of [16] annulene is not planar. But when I am trying to optimize the structure in ORCA, I am getting the final geometry as planar. I have used the geometry with S4 ...
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0answers
39 views

I have been trying to run the attached job (See the input file ) and receiving an error text in its log file: [closed]

I have been trying to run the attached job (See the input file ) and receiving an error text in its log file: ...
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2answers
176 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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0answers
28 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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1answer
269 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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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 ...
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0answers
48 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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79 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
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2answers
386 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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0answers
47 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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44 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
49 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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0answers
73 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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0answers
25 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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0answers
36 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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0answers
24 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
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2answers
74 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
44 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
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0answers
26 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
20 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
40 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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46 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. ...
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1answer
34 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
33 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
43 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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0answers
37 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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0answers
41 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
93 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: ...
4
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0answers
31 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 ...
5
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1answer
33 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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170 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
85 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 ...
5
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1answer
250 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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2answers
120 views

Molecular orbitals used with CCSD(T) geometries

Suppose I am given some geometry data (say, of a water dimer) from CCSD(T). If I were to do a single-point energy calculation to generate orbitals for the system, wouldn't CCSD give something more ...
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0answers
88 views

relaxed dihedral PES scan: symmetry of the system not reflected

Using G16 and performing a relaxed PES scan on a dihedral angle, I performed 72 steps where one phenyl group of a symmetric terphenyl is rotated about the C(aryl)-C(phenyl) bond by 5° in every step. I'...
4
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2answers
142 views

Ab initio calculations

Why are quantum mechanical calculations so computationally expensive? What exactly is the process that makes it so time taking? What I mean is, one can perform classical dynamics simulations on a ...
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0answers
25 views

Is the 12-6 Lennard Jones potential a good description of van der Waals interaction energy?

It seems to me that the Lennard Jones potential oversimplifies the more complex nature of van der Waals forces. However, in most of the MD simulation package, this is generally accepted.
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0answers
81 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 ...
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1answer
36 views

Calculate pKa for lipids

I would like to calculate $\mathrm{p}K_\mathrm{a}$ of lipid molecules using some software tools. I have tried ChemAxon and compared with ChemDraw professional 16.0 version they are mostly similar. I ...
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0answers
29 views

NMR Prediction for compounds at variable pH values

Like the title says, I'm looking for any software package that may be able to simulate a variety of NMR at a variety of different pHs. The majority of the software programs that I've found do not have ...
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1answer
96 views

How do water models fit into force field methods?

What I Understand: In molecular mechanics, it is recognised that molecules tend to be composed of units that are structurally similar in a vast array of environments so atom types are defined from ...
5
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1answer
46 views

Mixing of molecular orbitals in polyatomic molecules

I am trying to solve the following Hamiltonian,$$H=-\frac{1}{2}\nabla^{2}-\sum_{i=1}^{10}\frac{1}{|\vec{r}-\vec{R_{i}}|}$$ Here $Z=1$ . To get all ther molecular orbitals of this system. I took the ...
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0answers
71 views

How do I calculate the full configuration interaction Hamiltonian of H2

I have been trying to follow the paper titled "Towards Quantum Chemistry on a Quantum Computer" (https://arxiv.org/pdf/0905.0887.pdf) by simulating their results on a quantum computer simulator. ...
5
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3answers
137 views

How to index molecules in computer programs?

Is there a standard way how can the index over a molecular structure be kept in the computer? A molecule is a graph, where nodes have labels (chemical element type), and edges are chemical bonds. ...
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0answers
81 views

Good software/module in python to determine nuclear attraction integral in Slater type orbital basis sets

I am trying to solve a Hamiltonian of one electron and 10 stationary nuclear centers. here, the electron is treated quantum mechanically and nuclear centers are treated classically objects. The ...
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1answer
54 views

Why is the ROHF spin density of the propenyl radical not symmetric?

I was preparing some material for my students and in order to illustrate the concept of spin density and how the ROHF method gives a purer description of this property than the UHF method. I prepared ...
2
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0answers
79 views

Amber Force Field Improper Parameterization Huge Kb Problem

I am trying to parameterize a molecule. I know dihedrals and impropers are the same for Amber Force Field. (Source: http://archive.ambermd.org/201004/0334.html) So, I did PET scan for improper and I ...
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0answers
67 views

Know if a molecule is viable with Python [closed]

I'm working with python and I'd like to know if someone knows a python module which is able to check if a molecule is chemically viable (valence, connectivity constraints ...), or not. I know there is ...
2
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0answers
71 views

Amber paramfit “monomer (or ligand)” problem [closed]

I am trying to parameterize a novel molecule which has atoms not included gaff or parm force field. I finished parameterizing vdw-bond and angle force field. Also I did PES Scan for dihedrals and I ...