A field which implements computers to model and study chemical systems and chemical behavior, usually by approximating the Schrodinger equation for a given chemical system.

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Merge rigid parts and flexible results after docking (Vina)

If I use flexible residues in the binding pocket, they are cut from the file. The protein is broken and the amino acids are unbound in the room. How can I get my results and the protein together ...
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0answers
10 views

Autodock Vina flexible metals and water molecules

I have some problems with water and metals in binding site when using Autodock Vina. Is it possible to make these flexible? They unfortunately remain where they are what leads to wrong interactions. ...
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21 views

Pairwise summation [on hold]

In Quantum mechanics calculations, the U is often taken as 1/2[Uij] , such as in the Lennard Jones potential. Is this simply the summation of energies for the interaction of directly bonded atoms in ...
3
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0answers
23 views

Charge consistency in fragment qm/mm methods

I'm calculating the multipole moments on several fragments of a molecule. What are some procedures to ensure that the charges etc are representative of the complete molecule? How do I ensure I'm not ...
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0answers
22 views

Basis set in the computational software “Gaussian-03” for studying adsorption of a hydrogen atom on a carbon paste electrode dropcasted with Pt-CNT

What is the basis set in the computational software "Gaussian-03" that can be used to study the interaction of $\ce{H}$-atom with $\ce{Pt-CNT}$ dropcasted electrode? How can we study the energy ...
3
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1answer
36 views

Most efficient level of theory for sulphur-containing proline analogues (one that will work)

I'm modelling a small set of proline analogues - extra functional groups, sulphur in the ring. Using Gaussian / DMACRYS. ...
5
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1answer
46 views

Viewing a protein or bio structure in Chembio3D in its natural conformation

I notice when using SMILES or a IUPAC name for many molecules and generating them in Chembio3D, and then running MM2 > Minimize Energy, the structures produced are most of the time not reflections of ...
8
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3answers
165 views

How to define custom force in quantum chemistry packages?

I dont know if this is really applicable but I want to add a custom force ( say F(x,y,z) ) to some atoms in my geometry optimization. Is there any way to add such forces to the DFT or Molecular ...
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2answers
38 views

Gaussian Convergence Issue for N2+N PES

I am trying to obtain a potential energy surface (PES) for $\ce{N2 + N}$ combination using scan feature of Gaussian. I have tried different combinations of basis ...
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1answer
38 views

How to extract wavefunction from GAMESS output?

Is there a way to extract the molecular wavefunction from GAMESS output? I know there are packages that can extract the eigenvalues or the exponents and show them as a table but that is not of much ...
4
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1answer
138 views

Usefulness of the outdated Bohr model?

Whilst the Bohr model is incomplete and incorrect, it had limited usage in predicting spectral lines. In the same way, could it possibly with limited accuracy, be used to predict the outcome of ...
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1answer
48 views

Computational Chemistry (Ab Initio), what should I study?

I am interested in ab initio computational chemistry.I am trying to figure out what I should study. I know that I should study physical chemistry, mathematics, and programming. However, I am not sure ...
3
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2answers
197 views

How to calculate molecular volume from the wavefunction?

Very short question but maybe not a short answer ! As the probability of presence of electrons in a specific spatial position is defined as square of the wave function, I am wondering if there is a ...
3
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2answers
79 views

How to calculate vibrational spectra of organic molecules?

I watched a ted talk (Luca Turin: The science of scent) and was wondering if anyone had any examples of how to calculate vibrational spectra of molecules (used as fragrances)? Would love to figure ...
0
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1answer
26 views

short/extensive training on computational chemistry [closed]

I want to take a training on computational works in chemistry. It should be of a short duration. Where in Europe I can find it?
1
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1answer
39 views

How to get a protein's dihedral angles ordered by variance?

The setting: I want to simulate protein docking and let some dihedral angles vary, but in order to keep it low-dimensional I have to select those which are most likely to change. What I've thought of ...
0
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1answer
54 views

Is there a way to efficiently estimate the enthalpy of formation for an organic molecule in computational chemistry?

I'm exploring the platonic hydrocarbons and one of the methods I'd like to use is to compare their enthalpies of formation. The issue is that carbon's standard form is a covalent lattice and I can't ...
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1answer
54 views
4
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1answer
59 views

Why are C6 dispersion forces named C6?

I'm reading about water models and their dispersion coefficients, and going back to S. C. Wang's work according to the citation of an equation (Google books here) As you can see one citation's to a ...
2
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1answer
139 views

Which is most reliable excitation energy: LUMO-HOMO energy or TD-DFT excitation energies?

After running a TD-DFT , we can calculate the HOMO-LUMO difference and then calculate the the excitation energy. Another approach is just simply pick the energies calculated in the TD-DFT and use ...
7
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1answer
124 views

GAMESS and Gaussian : what is the maximum efficient number of supported nodes?

I have looked at GAMESS and Gaussian manuals but can not find the maximum number of efficient nodes. As I tried GAMESS on our supercomputer, I can add as many CPUs as I want but it really does not ...
2
votes
2answers
60 views

How to find molecular charge of fragments using quantum calculations?

Assume in a software like Avogadro, I put molecules A and B in a specific distance and I know they will involve in a charge transfer reaction ( as Marcus Theory outer sphere transfer ). Then I run a ...
10
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4answers
300 views

DFT Functional Selection Criteria

I have a very very general question: In DFT functional selection , mostly people speak about the most recent ones. For example my professor always asks: " which DFT Functional did you select ? " ...
2
votes
1answer
38 views

How to run crystal simulation on GAMESS?

I know GAMESS is not best suited for crystal simulation but I am not ready to start learning another package as VASP. As I heard GAMESS is able to do some calculations in a "terminated" crystal (I ...
3
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1answer
83 views

How can you manage SCF convergence problems?

"Failure to locate stationary point, SCF has not coverged" This is the most annoying message after Optimization run ( even with a good primary start geometry like UFF we ay see that) . The only ...
2
votes
2answers
70 views

Molecular Assembly Program

I'm not totally sure which Stack Exchange community this would go in, but Chemistry seemed best. I've been thinking for a long time now, that it would be cool to have a program where you could design ...
2
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1answer
163 views

How to Run GAMESS and Avogadro on Command Line?

I always use GAMESS and Avogadro on my own laptop. Recently I installed them on our university supercomputer and started using them by remote logging-in. On the laptop everything was super easy but ...
4
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1answer
80 views

Post-Hartree Fock Methods

I'm new to computational chemistry, so perhaps this question has an obvious answer. I'm wondering what the intuitive reason for constructing Slater determinants that involve excited states is, when ...
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2answers
311 views

Does chemistry need machine learning?

In many fields of science (e.g. biology, medicine, psychology, statistics, physics), machine learning and artificial intelligence techniques are becoming more and more popular to analyze data. Is it ...
2
votes
1answer
19 views

Oxide surfaces develop a charge in H2O. Do we have any, even vague, handle on how long does an indivdual charge last on avg. before being neutralised?

We often know, from e.g. titration experiments, what the average surface charge density of a surface is. How do these charges vary over both time and space (i.e. dynamics)? I have been unable to find ...
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5answers
4k views

Why is FORTRAN so commonly used in computational chemistry?

I've been using Ruby to write scripts for research, but I want to get into some heavier stuff that Ruby is just too slow for. I noticed there are a few things written in C and C++, but there is an ...
2
votes
1answer
121 views

What tools can be used to estimate binding energies?

I want to estimate the binding energies of various molecules. What are the analytical and numerical tools I can use for this purpose? In particular I'm interested in bonding energies of dyes to ...
5
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3answers
64 views

Intrinsic Reaction Coordinate calculation— both sides of TS lead to same minimum

I am currently trying to find an addition transition state and verify it using an IRC calculation. I have found a good candidate, but the IRC calculation gives the same minimum on each side of the ...
3
votes
2answers
88 views

Any popular experiment in chemistry that digital signal processing played a crucial role in?

Is there any famous experiment in chemistry where digital signal processing played an important part? I don't mean using a machine that relies on such techniques (they all do) but an experiment where ...
2
votes
2answers
47 views

What's the reason for discrepancy between DFT calculated image and NC-AFM-acquired one in this article?

Looking at the images in this article, I've noticed that the molecule electron density images showed as calculated via DFT look very symmetric, while those obtained by NC-AFM appear somewhat ...
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1answer
61 views

How to calculate a reaction's DeltaH using a MM forcefield calculator software?

I want to calculate $\Delta H$ for hydrogenation of Benzene and producing Cyclohexane using MM+ Force Field Energy. I am using Hyperchem for energy calculation and optimization. I calculated the ...
6
votes
2answers
71 views

Quick-and-Dirty Molecular Dynamics by Mass-Weighted Atom Translations?

I'm thinking about a quick-and-dirty approach to molecular dynamics, mostly for teaching purposes. At a given temperature, statistical mechanics tells us molecules have translational and rotational ...
0
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0answers
16 views

Carbonation process - Equation in Mathlab

I need some help with the Carbonation process of how soda/fizz water is produced. I just found the equation, but I do not know how to model the process in Mathlab. Can anybody advise me with some ...
3
votes
1answer
73 views

Unitary Transformation of the HF equations

I am working on a code to preform a HF procedure and I am a bit confused about the unitary transformation of the basis. My instructions are as follows. specify the basis and geometry (done) ...
1
vote
2answers
66 views

Confused about parity of atom and chirality

OK. I'm working in computational chemistry and the problem that bothers me is: Given a molecule, I know that it has a central asymmetric atom with some parity which is either "Anticlockwise" or ...
2
votes
2answers
49 views

What is a good (small) model system for ligand metal charge transfer practises?

I am looking for an easy to calculate model system in which I could see a ligand metal charge transfer. Basically I am looking for a model complex, that might have the metal/ligand in different ...
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0answers
23 views

software modelling of 1-Ethyl-3-methylimidazolium tetrafluroborate

what are the molecular details of 1-Ethyl-3-methylimidazolium tetrafluroborate? how we can model this fluid for software analysis?
5
votes
2answers
99 views

What do short-range and long-range corrections mean in DFT methods?

Currently I am looking for the most accurate calculation method for a simple non-conjugate molecule consist of C, N, O and H. Normally I would try each method for a similar and known molecule then ...
6
votes
1answer
151 views

Born-Oppenheimer Approximation reloaded

I'm an undergraduate Chemistry student and I'm currently writing my Final Dissertation. I've written a form of the Born-Oppenheimer approximation with the only initial assumption of parametric ...
0
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1answer
53 views

Gaussian Calculations - What is the Basis?

What am I actually changing when I click 631G(d) or 631G(d,p), etc. when I choose a "basis" in restricted Hartree Fock calculations? What is the difference between using an alternative basis? Many ...
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vote
1answer
44 views

How can I estimate reaction rates in water with computational chemistry?

I want to estimate rates of substitution reaction of esters with nucleophiles in water. How can I estimate them with a computational chemistry software (preferably GAMESS(US))? Or is it practically ...
0
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2answers
37 views

What is the official file extension for SMILES and SMARTS files

I want to know what is the officially used file extension for files containing SMILES and SMARTS strings. Somewhere I see .SMI/.SMA and somewhere its the full .SMILES/.SMARTS.
5
votes
3answers
281 views

How is the bond length calculated from the total electronic energy?

In the quantum chemistry course that I currently attend, it was said several times that one of the key quantities derived from molecules by means of computation is the total electronic energy ...
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0answers
180 views

How to Locate the Excited State Dipole Moment in Turbomole Output (TD-DFT)

I want to calculate the dipole moment for the first excited state with a Q.C. program (TURBOMOLE: TD-DFT). The calculation lists the following output: ground state total dipole moment: ...
3
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1answer
122 views

Representation of chemical formulas as strings?

Is there a standard manner of representing chemical formulas as linear strings? For example, $H_2O$ can be represented with the string H2O. Isotopes are usually ...