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
2
votes
1answer
618 views

Excited states and electron addition/removal energies within Hartree-Fock, CI, etc

Coming from a DFT background, I'm used to the concept that the DFT eigenvalues do not correspond to excitation energies (i.e., the band gap, ionization potentials, etc.). To correct for these it's ...
28
votes
1answer
3k views

Suggest methods and basis sets for a variety of systems

Please help me with any/all of the cases below. In the following cases, the named method and basis set are not suitable for the chemical systems. Why aren't they? Could you suggest a suitable method/...
3
votes
1answer
849 views

Configuration Interaction matrix composition from electronic configurations

The six electronic configurations below could all be found in the matrix elements of the CI matrix at CISD level. How do I construct the 6 x 6 CI matrix composed of these six configurations and which ...
10
votes
3answers
1k views

Why is CCSD(T)/aug-cc-pVTZ not a suitable method for the geometry optimisation of omeprazole?

I know that CCSD(T) with the aug-cc-pVTZ basis set for geometry optimization of omeprazole (5-methoxy-2-[(4-methoxy-3,5-dimethylpyridin-2-yl)methanesulfinyl]-1⁠H-benzimidazole, the active substance in ...
10
votes
3answers
9k views

Program that simulates basic reactions in organic chemistry

To explain - a friend and I have been working on a program that would allow you to draw organic molecules, indicate the conditions, and predict the products. This would be primarily aimed at basic, ...
6
votes
1answer
292 views

An alternative basis set for analytical computation of two electron integrals

It is well known that the usage of the Gaussian basis set, in contrast to Slater basis set, leads relative simple semi-analytical expressions for the two electron repulsion integral $(ab|cd)$. Could ...
26
votes
2answers
826 views

Is hybridization used in ab initio valence bond calculation?

Many general chemistry textbooks introduced the concept "hybridization" to construct a symmetry-adapted VB-type wavefunction. In the textbooks, usually the minimal basis is used and without optimizing ...
25
votes
6answers
54k views

Overlap between computer science and chemistry?

This isn't particularly a question about chemistry itself, but more-so the prospect of chemistry. What kind of opportunities arise when you overlap chemistry and computer science? I'm a computer ...
2
votes
1answer
402 views

Free automatic organic synthesis Linux command line program

I'm trying to find a free automatic organic synthesis Linux command line program which take mol or smile files as input. I have random molecules and I'd like to know how difficult above a baseline ...
1
vote
1answer
93 views

What is an algorithm for making a net neutral molecule from a set of guessed positive charges? [closed]

Given a set of partial charges for the atoms in a molecule, which are educated guesses but do not add up to zero, we would like to zero them in an intelligent way. For example, if the net charge is ...
13
votes
1answer
2k views

Why are the total energies of transition states so commonly corrected for zero-point vibrational energy?

So often I see total energies of transition states corrected for zero-point vibrational energy which always confuses me. Zero point energy is the lowest energy that a ground state minimum energy ...
2
votes
1answer
166 views

Coarse-grained force field for ion–water interactions

I want to simulate, at a very coarse grained level, the interaction of water molecules with metal ions, specifically Calcium and Potassium. Is there a standard force field for this. I was told to use ...
3
votes
1answer
279 views

Gaussian vs ABINIT for solids

I see that Gaussian has feature to set periodic boundary conditions specifying the parameter Tv in the input file. Does it do it via the plane wave basis set? Also, the question is whether it is ...
14
votes
2answers
900 views

How should elements be colored? And how many bonds does an atom have?

I'm working on my own 3D molecule viewer for my AP Chem class. So far everything's going together nicely. There's a couple of things I'm not sure about though... Is there a certain rule of thumb or ...
8
votes
1answer
212 views

How should I modify my molecular dynamics simulation so that known chemical reactions can be modelled?

I have written some molecular dynamics code that I want to use to model known chemical reactions. By known I mean that it has been observed in a lab that $\ce{A +B->C}$. I am not interested in ...
9
votes
1answer
589 views

What are simple applications of Monte Carlo simulations in chemistry, that can be done in Matlab?

I am trying to learn simulation myself and I have installed Matlab on my machine for that purpose. In web I have gone through some of the basics of Monte Carlo simulation, but I am unable to find a ...
6
votes
1answer
730 views

Having problems running DFTB using dftb.org parameter files on Gauss 09 (G09)?

I ran into an issue trying to run dftb.org parameter files on G09 and found questions asked on this but not answers. I thought I would post the solution here to help anyone else who may run into this ...
2
votes
2answers
919 views

What tools are used to predict the products of a chemical reaction? [duplicate]

I was wondering if there is a decent and non-complex way to predict the outcome of mixing two chemicals together. I know that molecular dynamics is used in computational chemistry to understand ...
3
votes
1answer
3k views

What is the accuracy of scf=qc when convergence criteria is lowered?

I am trying to run single point calculations with Gaussian 09 for a Mulliken population analysis on large graphene/graphite (940-1411 atoms) sheets/clusters. I was having difficulty with memory ...
5
votes
3answers
293 views

FCI implementation

Could you suggest, please, a manual/textbook/tutorial for implementing FCI (full configuration interaction) method on computers. I am interesting in algorithms mainly. I would like to write my own ...
3
votes
2answers
286 views

CI without Hartree-Fock SCF

Usually textbooks on CI takes the SCF Hartree-Fock orbitals as a starting point. Can one use the configuration interaction method starting directly from the single-particle Slater determinants ...
15
votes
2answers
18k views

How to find a transition state for an electrophilic addition with Gaussian and map the reaction pathway?

I aim for two things with this post – on the one hand to produce a manual for other people to use, but also to verify what I obtained via searching, asking a more experienced user as well as receiving ...
6
votes
3answers
382 views

Gaussian and Surface Reactions - Doable?

Independent from my general kinetics question here - Estimating Surface Reactions - Liquid, Turbulent Flow - I am only interested in responses regarding Gaussian in this question. I would like to ...
3
votes
2answers
1k views

Approximation of electron density of a small molecule

Starting point for Quantum Theory of Atoms in Molecules (AIM) is the electron density $\rho(r)$. It could be determined experimentally (X-ray diffractions). I want to know how can we estimate them ab ...
1
vote
1answer
53 views

Can I deduct heteronuclear van der waals parameters from homonuclear parameters in a forcefield?

I got a forcefield (OPLS-AA in this case) that lists lennard-jones parameters for all homonuclear van der waals interactions. Is there a way to deduct the heteronuclear vdw-interaction parameters from ...
3
votes
1answer
957 views

Chemical reaction calculator

Is there any kind of program that is able to calculate the end result of a specific chemical reaction? Say I wanted to know what happens when you mix $\ce{HClO + NaOH}$, is there anything that could ...
4
votes
3answers
201 views

Unique calling code for a chemical reaction

I'm writing a script and would like to use a "Gödel numbering" to search for specific reactions. Is there any used procedure to assign an symbol (integer, possibly) to a chemical reaction? E.g. $$...
5
votes
1answer
136 views

Are there computer searches for new theoretical minerals in a similar vein to Folding@Home or SETI@Home?

As a surprise gift to a friend I would like to discover a new theoretical mineral and have it named after them. I have some understanding that not all minerals have been discovered, and some minerals ...
11
votes
1answer
381 views

Database for molecular dipole transition moments?

I'm looking for the dipole transition matrix elements for electronic transitions between the ground and excited states of the carbon dioxide cation, $\text{CO}_2^+$, that is, objects like $$\langle\...
7
votes
2answers
5k views

Tool that generates electrostatic maps of molecules?

Do you know any tools that generate electrostatic potential 2d maps of the molecules as an image?
5
votes
2answers
152 views

Obtain chemical insight from neural network results

I have recently read many papers where neural networks (NNs) are trained to predict chemical properties (starting from the structure of small chemical compounds) for compounds rather close to the ones ...
20
votes
1answer
509 views

Is it possible to compute the colour of *any* molecule?

Above are some spectral emission lines for hydrogen, helium and neon. Using the Schroedinger equation, it's possible to derive the colours that hydrogen will emit when light is fired at it. A little ...
8
votes
1answer
804 views

Intrinsic Reaction Coordinate - What does 'Connectivity' really mean?

I am currently in the process of connecting transition state (TS) structures to other minima in order to determine a reaction pathway. Now I understand the basic concepts of this method. You start ...
2
votes
1answer
354 views

Software for chemical reaction simulation in ICE

I want to study what happens in a internal combustion engine in which fossil fuels are mixed along with other chemical additives. Example: Acetone drastically reduces surface tension. Most fuel ...
7
votes
2answers
1k views

Basis sets that can be used for macrocyclic complexes

What could be the possible basis set that can be used for a metal base macrocyclic complex in gaussian09? I am using transition metals such as $\ce{Ni}$, $\ce{Co}$, etc. Also, I have tried using ...
6
votes
1answer
137 views

What is in silico energy optimization?

While doing computational chemistry for both organic and inorganic compounds, an energy optimization of that compound is done before starting a study. For example, if we do drug docking studies using ...
15
votes
1answer
1k views

Naming of quantum chemistry basis sets

For some DFT calculations I performed with localized (Gaussian) basis sets, I wonder how the basis sets I used are properly named. The names I could gather are: H, C and O: 6-311G(d,p) Al: 8-511G* ...
2
votes
1answer
451 views

How does simulation software work at a fundamental level?

There are lots of software packages like Schr­­­ödinger Maestro or Argus Lab, which are used for simulations of docking. I have always been fascinated as to how such software works. What is the ...
5
votes
1answer
173 views

Simulation of a particle and chemical molecule

I am currently studying the basics of simulation and want to try out some experiments. It is a known fact that gold nanoparticles can bind to chemical groups which contains thiol (R–SH group). I want ...
1
vote
1answer
104 views

Methods: Does failing at intermolecular properties mean the same for intramolecular properties?

Let us consider the following: 1.) Method X fails at describing intermolecular non-covalent interactions. 2.) Method X excels at describing molecules of type Y. 3.) Method X ___?___ at describing ...
5
votes
1answer
201 views

Modeling perturbations of a quantum mechanical system

I'm wondering how to properly perturb a quantum mechanical system. I'm looking for a way to express the return to equilibrium of such a perturbed state, where the perturbation is in the Hamiltonian. ...
16
votes
3answers
4k views

Modern alternatives to Gaussian [closed]

Specifically, I'm curious if there are any programs which come close to Gaussian in breadth but also take advantage of things such as GPU processing. There's a page on wikipedia that goes through ...
2
votes
0answers
291 views

Spectral analysis of periodic table of elements in time domain

I'm trying to get the spectral analysis data of the periodic table of elements in the time domain format or find a site that has the data in the time domain format. All the sites I know have the data ...
16
votes
4answers
412 views

Hierarchy of electronic wavefunctions

The previous question contained too much unnecessary information and was edited. I am wondering about the "hierarchy" of wavefunctions. If one can combine atomic orbitals (AO) into molecular orbitals ...
8
votes
1answer
403 views

Efficiency of various Ewald-type schemes for the summation of electrostatic interactions

I am looking into implementation of Ewald summation techniques for a number of point charges in periodic 3D space (i.e. a molecular simulation box with periodic boundary conditions). The “mainstream” ...
7
votes
1answer
217 views

CHARMM parameter files for NBD (nitrobenzoxadiazole)

I have been looking all over the internet for forcefield parameters for a fluorescent probe called NBD (nitrobenzoxadiazole). Here is an example of an NBD labeled fatty. I have so far only found ...
5
votes
1answer
1k views

Bond energies database

I’m looking for a public database of bond energies of biochemical compounds. Does one exist? Otherwise, which is the standard computational methodology to calculate them? Any references would be very ...
26
votes
2answers
2k views

How should I go about picking a functional for DFT calculations?

I've been looking to use time-dependent density functional theory, but reading the literature I keep getting overwhelmed by how many different functionals there are. How should I go about selecting ...
47
votes
0answers
1k views

How can I update a map/mesh and coordinates in a PyMol session file?

I have a PyMol session file I was using to create my figures. It contains a protein and ligand broken into several groups of atoms with a fair bit of overlap. There are also a few meshes built from ...
7
votes
2answers
402 views

Regenerating the imaginary data of a 2D NMR spectrum with a hilbert transform

2D spectrum take up a large amount of hard disk space. At my last lab it was standard practice to delete the imaginary portions of the spectrum with xfb n (We used ...