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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molecular connectivity index

I would like to know about (question related to computational chemistry): what is valence molecular connectivity index of 3rd order cluster. Please provide an example? Thanks for your help.
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how are the frequencies at a local maximum of PES like?

On the potential energy surface, if you find a local maximum and calculate its frequencies in Gaussian or something like that, will you get all negative frequencies or all positive frequencies? I know ...
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67 views

How can a chemical structure be stored in a matrix?

How do I represent a chemical structure in a matrix format in Matlab? Can I input a chemical structure into Matlab using the S.M.I.L.E.S notation? I have to specify the connectivity of different ...
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72 views

Structure that breaks InChI

I am currently testing a piece of software that generates the InChI for a given structure. I also want to test error situations as end users will also deliver the mol files that will be used as input ...
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12 views

Simulating enzymatic change rates of Carbonic anhydrase

I'm trying to simulate effects of carbonic anhydrase on cellular pH as caused by changes in bicarbonate. I assume a bicarbonate homeostatic mechanisms which replenishes intracellular conenctrations ...
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22 views

Number of orbitals in full configuration interaction

I am using one quantum chemistry package where I am supposed to assign a number of active orbitals I want to be included in the FCI (full configuration interaction) calculation. For example if I have ...
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2answers
46 views

Theoretical principles of molecular simulations

I am pharmacy student and would like to work in the field of drug design. We learn to work with the programs but thats not enough for me. I want to learn the theoretical principles of computational ...
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28 views

Making a reasonable slab of alpha quartz

I want to perform a molecular dynamics simulation with alpha-quartz as my mineral surface. I want to study adsorption of water on alpha-quartz. The most dominant error that I came up with is the ...
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1answer
63 views

Magical reaction tanks

I would be interested to know people's opinion on the following matter. Background Often, when the far-from equilibrium behaviour of a chemical reaction system is analysed mathematically (in papers ...
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1answer
120 views

What's the difference between PBE and B3LYP methods?

I can't find an answer to that question. I was told that in B3LYP, more variables implemented in the method are empirical, but I can't find anywhere if it's true, and I'm sure it's not the only ...
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99 views

Natural Bond Orbital (NBO) analyses: Physical significance/interpretation of E(2) 'stabilization energy'?

PREFACE: I am no expert on this topic. My questions at the bottom may be off base. I have some experience with symmetry-adapted perturbation theory (SAPT) when it comes to analyzing intermolecular ...
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1answer
27 views

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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2answers
105 views

Animate molecular vibrations as multiple xyz coordinate files

I have a frequency calculation by Gaussian09. Now I would like to extract vibrational modes as a set of xyz coordinate files. I would like to manually recompute numerically the points along a ...
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65 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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153 views

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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48 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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189 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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47 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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1answer
202 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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101 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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198 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
77 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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137 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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1answer
69 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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207 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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117 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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101 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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159 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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63 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 ...
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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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4answers
2k 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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133 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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1answer
51 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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157 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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68 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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64 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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245 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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1answer
135 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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1answer
178 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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1answer
257 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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1answer
497 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
96 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
117 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
3k 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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1answer
95 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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1answer
226 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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214 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
36 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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354 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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78 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. ...