The use of computers to model and study chemical systems. This usually consists of trying to approximately solve the Schrodinger equation for a molecule or solid.
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29 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 ...
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0answers
62 views
+50
Software Bond Dissociation Energies, Bond Energy and Hybridization with Polarity
I want to calculate BDE to measure the cost of hybridization of two molecules. There are many examples of protein ligand docking on the internet but there are no examples of hybridization of ligand to ...
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2answers
84 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 ...
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1answer
21 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 ...
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1answer
183 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 $HClO$ + $NaOH$, is there anything that could give ...
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3answers
51 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.
...
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1answer
38 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 ...
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0answers
17 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
...
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1answer
38 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?
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2answers
61 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 ...
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1answer
59 views
Is it possible to work out the colour of *any* molecule?
Above are some spectral emission lines for Hydrogen, Helium and Neon.
Using the Schrodinger equation, it's possible to derive the colours that Hydrogen will emit when light is fired at it. A ...
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1answer
59 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 ...
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1answer
53 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 ...
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1answer
61 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 ...
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1answer
86 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 ...
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1answer
138 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*
...
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1answer
117 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 ...
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1answer
59 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 ...
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1answer
67 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 ...
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2answers
94 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. ...
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2answers
277 views
Modern alternatives to Gaussian
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 ...
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0answers
120 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 ...
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4answers
156 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 ...
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0answers
76 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” ...
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1answer
104 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 ...
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1answer
90 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 ...
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2answers
175 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 ...
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1answer
67 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 ...
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3answers
90 views
How can I perform structure alignment on an inorganic species?
I'm attempting to perform atomistic optimal structure alignment on an inorganic species. Can anyone point me in the right direction to software or a technique for performing this?
There exists a wide ...
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1answer
94 views
Is the Springborg 6D phase space model used in modern molecular orbital modeling?
In a series of papers in the early 1980s, Michael Springborg explored an interpretation of the Wigner phase space function as an electron density in a six-dimensional $(q,p)$ phase space. He applied ...
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1answer
44 views
Has QTPIE ever been applied to 1D metals such as polyacetylene?
QTPIE is a fluctuating charge model that substantially improves modeling of polarization and charge transfer. I was curious whether it has ever been applied to 1D metals such as polyacetylene to ...
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1answer
162 views
When simulating spectral line broadening, which convolution is preferred?
Many computational chemistry packages permit the calculation of vibrational and electronic spectra. These spectra are obtained as a set of discrete eigenvalues however they are often convolved with ...
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1answer
70 views
Is a 2-D periodic structure isomorphic with the surface of a torus, a sphere, neither or both?
When I was reading through the ADF-BAND tutorials, one of the toy systems presented was a 1-D periodic structure involving 3 collinear hydrogen atoms. The tutorial pointed out that, topologically ...
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3answers
242 views
What is natural bond orbital theory used for?
My understanding is that the NBO methodology transforms the molecular orbital picture of a molecule into a collection of pairwise interactions (bond orbitals). This is obviously handy for didactic and ...
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1answer
243 views
Are Pulay forces expensive to compute?
In a thesis I am reading, it is said that one of the reasons for using plane-wave basis sets for first-principles molecular dynamics (aka ab initio MD) is that the Pulay forces[1,2] that arise from an ...
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2answers
454 views
Pros and cons of Cartesian vs. Z-matrix representations of molecules?
Over the course of my studies, I have switched largely from using Z-matrix representations of molecular geometries in calculations to Cartesian representations.
The software that I use now makes it ...
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2answers
318 views
Striking examples where Kohn-Sham orbitals clearly have no physical meaning
In Density Functional Theory courses, one is often reminded that Kohn-Sham orbitals are often said to bear no any physical meaning. They only represent a noninteracting reference system which has the ...
