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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Controlling the shape of metal

Is there a way to control the shape of metal? Suppose I have a fast melting metal, is there a way to make it take a specific shape? Of course I don't mean to like put it in a template to take the ...
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33 views

Are multiple transition states possible? Criteria to choose the correct one?

I am studying a reaction using electronic structure methods using various software packages (ORCA,GAMESS, G09) and have found two possible transition structures between product and reactant. Both have ...
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+50

Reaction Pathways: What to do when IRC geometries are relaxed (optimized) and the energy changes significantly

The Story: Reaction pathways can be difficult things to deal with using electronic structure methods. Intrinsic reaction coordinates (IRCs) can be determined a number of ways (a discussion of these ...
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32 views

How to model iso-surface of molecular orbitals of singlet and triplet excited states

I've modelled the iso-surface of the highest occupied molecular orbital of a molecule with DFT in Gaussian.If I were to model the iso-surface of the molecular orbital of the singlet and triplet ...
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120 views

Is there an energy cost associated with flipping the spin of an electron?

THE STORY: A common example used to illustrate the limitations of restricted Hartree-Fock (RHF) theory is the H$_2$ dissociation energy ($D_e$) curves. RHF enforces electrons to be paired into spin ...
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40 views

Remove empty space from structures with R and S groups

We receive structures from a server within our company. Those structures are transferred as MOL files. Some of these structures contain R and/or S groups. Some of the creators of these structures ...
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133 views

Why are excited Slater determinants used to describe electron correlation?

Usually the first step in describing the electronic wave function of a molecule or atom is to describe it with a single Slater determinant. I get that this is an independent particle approximation, ...
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2answers
73 views

How to properly denote imaginary magnitudes of vibrational frequencies

Vibrational frequency computations provide the magnitudes of vibrational frequencies for each vibrational mode of a molecule ($3N-6$ degrees of freedom for non-linear molecules and $3N-5$ for linear ...
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76 views

Software for predicting chemical reactions

I wondered if it was possible to predict the product(s) of a reaction (or even the equilibrium) based on the reactants and the temperature/pressure. I found an answer to a similar question here: ...
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2answers
64 views

Defining and testing custom made DFT functionals?

What is a good and free software for this endeavor? Any recommended articles on the subject? I want to design dft functionals, trying out different parametrizations and optimizing mixing constants for ...
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72 views

DFT optimization of a molecule in gaussian and find electrophilic sides [closed]

I am not a pro, but I have some experience with gaussian. For example, I can optimize a structure, calculate the frequency and rotational energies. In the lab I made a nucleophilic substitution ...
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41 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 ...
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138 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 ...
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76 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 ...
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2answers
76 views

Quantum chemistry: CCSD(T) with aug-cc-pVTZ on omeprazol

I know that CCSD(T) with aug-cc-pVTZ basis set for geometry optimization of omeprazol, i.e. the active substance in Losec is not suitable using the normal computers. The substance is: omprazol Can ...
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86 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, ...
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91 views

Is hybridization used in ab-initio valance 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 ...
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1k views

Overlap between computer science and chemistry?

This isn't particularly a question about chemistry itself, but moreso the prospect of chemistry. I apologize if these are frowned upon here. What kind of opportunities arise when you overlap ...
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97 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 ...
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50 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 ...
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119 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 molecule can have ...
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1answer
57 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 ...
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1answer
56 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 ...
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217 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 ...
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123 views

Montecarlo simulation in chemistry

I am trying to learn simulation myself and i have installed matlab in my machine for that purpose. In web i have gone through some of the basics of montecarlo simulation but i am unable to find a ...
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162 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 ...
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238 views

How to predict chemical reaction or interaction (superacid and piperidone)

I am not very great at chemistry, and I feel like this may be an elementary problem; Howver, I was wondering if there is a decent and non complex way to predict the outcome of mixing two chemicals ...
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355 views

What is the accuracy of scf=qc when convergence criteria is lowered (Gauss 09)?

I am trying to run single point calculations on Gauss 09 for Mulliken population analysis on large graphene/graphite (940-1411 atoms). I was having difficulty with memory issues (single CPU lic) ...
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3answers
93 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 ...
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2answers
112 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 ...
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1answer
2k views

Finding transition states in Gaussian – focus: Electrophilic Addition Reaction

Finding transition states in Gaussian – focus: Electrophilic Addition Reaction First of all, I aim for two things with this post – on the one hand to produce a manual for other people to use, but ...
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81 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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206 views

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
181 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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35 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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337 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
74 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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52 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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50 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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192 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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91 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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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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188 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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99 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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2answers
179 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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101 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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239 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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201 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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79 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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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 ...