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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11
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0answers
255 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 ...
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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 ...
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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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2answers
211 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
157 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'...
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2answers
243 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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38 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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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
74 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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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
126 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 ...
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1answer
64 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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217 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. ...
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3answers
192 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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170 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
92 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 ...
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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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93 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 ...
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0answers
150 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 ...
2
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1answer
418 views

Radial pair distribution function (VMD). How to define it for a water NaCl system with multiple Na and Cl?

I'm struggling to understand a paper in which someone has presented radial distribution functions (RDFs) for a system that contains multiple Na, Cl, and water atoms/molecules. I don't know exactly ...
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143 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 ...
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1answer
2k views

How do the def2-SV, def2-SV(P), and def2-SVP basis sets differ?

I am trying to calculate the energy of complex molecules with DFT and have a question about the Ahlrichs (Karlsruhe) def2 basis sets. What is the difference between the def2-SV, def2-SV(P), and def2-...
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1answer
56 views

Molecular Orbital Mixing to get the Molecular Orbitals of a large molecule

I am trying to get the molecular orbital for arbitrarily placed nuclear centres (identical). In other words , I am trying to solve the following one electron hamiltonian. $$h=-\dfrac{1}{2}\nabla^{2}-\...
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0answers
36 views

tolerable error, CASSCF simulation of UV/Vis spectrum

Please forgive my ignorance of experimental spectroscopy. I am a computational chemist, not an experimental one. My question is: what would be considered a tolerable or reasonable difference between ...
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1answer
164 views

Conformer generation for radicals

Is there an automatic way to generate conformers for radical like systems (spin multiplicity is doublet)? My system for the study is a substituted fullerene with a missing H atom from the functional ...
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0answers
199 views

Natural orbital population analysis in Gaussian

Within (restricted) density functional theory and Hartree-Fock, respectively the Kohn-Sham orbitals and spin orbitals are the natural orbitals, with occupation numbers either 2 or 0. As I understood, ...
6
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1answer
166 views

How to Calculate Lennard-Jones Parameters from TDDFT?

I am trying to develop parameters for AMBER force fields and to calculate Lennard-Jones parameters for the $\ce{Fe^3+}$ ion. I did a deep search and found that the best way to do this with a high ...
3
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1answer
362 views

Overlap matrix (H2 molecule, STO-3G) [closed]

I'd want to implement SCF method using Modern Quantum Chemistry (Szabo). But when I want to calculate overlap matrix for H2 (STO-3G basis) my results aren't equal to true overlap matrix that there's ...
4
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0answers
145 views

What algorithm is GaussView using for the clean function?

A colleague showed me GAUSSIAN 09 which comes with GaussView 5 for drawing structures. What impressed me was the snappiness of the Clean function. What algorithm is used for the Clean function? The ...
2
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2answers
489 views

How To Scan “improper dihedrals” in Gaussian 09?

I am trying to parameterize Amber force field for a novel molecule, but I couldn't obtain improper dihedrals. Because if I scan impropers like dihedrals; later or sooner the molecule is overlapping ...
2
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0answers
74 views

Generating density matrix of a wavefunction from common quantum chemistry software

I am looking for density matrixes for a couple of closed shell and open-shell systems, and I wonder if there is a trivial way to make e.g. Gaussian just generate an output for me. I may be wrong but ...
5
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1answer
92 views

Why do people add H(core)+F in Hartree-Fock?

I'm trying to implement my own HF code, and it seem usual that, after building the Fock matrix $F$, they add that to the pre-existing $H_{core}$, from the two-point interactions, when computing final ...
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133 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 ...
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48 views

Geometry optimisation in Gaussian09

I have looked at various sources regarding this, including the Gaussian official website. However, I have not managed to understand the geometry optimisation method used by Gaussian, a method known as ...
2
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0answers
312 views

Putting high symmetry points labels to a band structure plot

So far I've got this plot using Quantum Espresso. I want to put gamma, X, L, etc labels to the k-path. Quantum Espresso's ouput states the following: ...
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15 views

Lipophilicity computational prediction

Is there a web based (or otherwise) computational chemistry tool which is able to calculate lipophilicity of a given compound?
5
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1answer
580 views

Raman spectra in Gaussian [closed]

I want to simulate Raman spectra of benzene in Gaussian 09. Calculated spectra for a single ring Benzene ($\ce{C6H6}$) in Gaussian differs about $\pu{40 cm^{-1}}$ for each peak, compared with ...
8
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1answer
118 views

Does the hydrohelium dication exist?

It is well-known that there exists the $\ce{He2^2+}$ dication, and also $\ce{HHe+}$ and $\ce{H2+}$ cations. But I could not find any definite information about the existence or inexistence of the $\ce{...
4
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1answer
532 views

Diffuse functions for Ahlrichs/Karlsruhe basis sets in Gaussian?

As the question states, can one use the basis sets of Ahlrichs and coworkers (e.g. def2-SVP, def2-TZVP, ...) with diffuse functions (e.g. def2-TZVPD) in Gaussian? The regular basis sets have been ...
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0answers
285 views

How to understand MO diagrams for cationic octahedral transition metal complexes

I am having problems understanding the construction of MO diagrams in octahedral transition metal complexes within ligand field theory (LFT) when the metal center is asumed as an cation: I am ...
2
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1answer
163 views

How to write a cube file?

This is a technical question. I have a real-space representation of a potential in a grid of points, however I have the grid in the format: x y z w v meaning: the coordinates of each point, the ...
0
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1answer
144 views

Finding the weighted parameters of the vertex adjacency matrix for a derivative of azulene

In my last question ( Numbering in a derivative of azulene ), I asked about the numbered of a molecule in order to find the Vertex Adjacency Matrix (VAM) of the same molecule. To explain my question ...
7
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0answers
232 views

Vanishing integral rule for two-electron integrals

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

Can Hartree-Fock mix more orbitals than there are electrons?

I'm trying to understand Hartree-Fock well enough to write my own implementation. A point that I seem to be coming to that I'm not sure is correct: the method only produces one-electron orbitals that ...
0
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1answer
52 views

Maximum metal-metal distance for antiferromagnetic coupling

Imagine a transition metal complex with multiple open-shell transition metal cations. If the metals are relatively close in distance, it is possible that antiferromagnetic coupling will occur between ...
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0answers
323 views

Link1 and multiple output files in Gaussian: doable?

I have recently started learning Gaussian in my Computational Chemistry class, and I have recently learned how to use the "Link1" option, in order to run multiple calculations from a single input file....
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0answers
115 views

Q-chem equivalent solvent settings for Gaussian NMR ab inito methods

I'm attempting to use Q-Chem 5.0 to replicate CHESHIRE-esque http://cheshirenmr.info/ ab initio calculations of chemical shift values. Unfortunately Gaussian seems to be the predominant tool in this ...
4
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1answer
82 views

Multiplication symbol in SMARTS

There is a SMARTS pattern that was published which looks like the following[1] [#6 × 4] and there are actually spaces around the ...
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0answers
70 views

STO 3G basis expansion of p orbitals

I am expanding $2p_{x},2p_{y},2p_{z}$ (slater type )orbitals in gaussian STO-3G basis as follows, $$|2p_{x}\rangle=C_{1}x\exp(-\alpha_{1}r^{2})+C_{2}x\exp(-\alpha_{2}r^{2})+C_{3}x\exp(-\alpha_{3}r^{2}...
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0answers
129 views

Implementing the projected atomic orbital (PAO) localization in Gaussian

I am currently attempting to learn how to setup the active space for performing CASSCF calculations. The textbook I am using as a reference is: Roos, Björn O. "Multiconfigurational quantum ...

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