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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4
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53 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
74 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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92 views
+100

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
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32 views

Photo-excitation: LUMO energy or LUMO-HOMO energy?

I ran ground state energy calculation for a singlet molecule ( say A ) and the same calculation on its dimer ( its dimer existence has been approved by experimental data ). We also know that this ...
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1answer
28 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 ...
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263 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
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1answer
30 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 ...
2
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1answer
73 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 ...
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2answers
59 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
149 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
77 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 ...
7
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268 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
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1answer
18 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
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1answer
92 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 ...
3
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2answers
46 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
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2answers
86 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
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2answers
46 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
56 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 ...
5
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2answers
68 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
15 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
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1answer
70 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) ...
0
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0answers
30 views

How is N to C ratio measured in forming austenitic stainless steel?

Nitrogen is the future hope of stainless steel industry; since in the production of austenitic steel it can even completely replace Nickel (which is relatively very expensive) in some cases and for ...
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60 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
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2answers
47 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
20 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?
4
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2answers
91 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
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1answer
146 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
48 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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1answer
41 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 ...
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2answers
34 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
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3answers
250 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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163 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
117 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 ...
2
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1answer
31 views

CMAP layout of data

I would like to use the charmm CMAP correction in another program (PyRosetta). I have looked at parmfile.doc and io.doc and this discussion, but nowhere is it distinctly written how the CMAP is laid ...
5
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2answers
239 views

Methods for Determining Partial Charges

I want to run classical molecular dynamics simulations of a periodically replicated surface (rutile $\ce{TiO2}$ with grooves). In order to do so, I first need to solve for the partial charges residing ...
64
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3answers
9k views

Why is gold golden?

Bulk gold has a very characteristic warm yellow shine to it, whereas almost all other metals have a grey or silvery color. Where does this come from? I have heard that this property arises from ...
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1answer
108 views

GAMESS crash course?

I'm still learning about MO theory – and I thought that I would do some calculations with GAMESS to become more familiar with the concept. Even though I look forward to delving into the realm of ...
11
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2answers
488 views

Dipole moment of cis-2-butene

I need someone to back me up on this before I go confront my teacher: I was doing some analysis of the dipole moment of cis-2-butene. Let's say that the alkyl groups are both on top. Would the dipole ...
1
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1answer
47 views

Book recommendations for protein structure refinement

I’m an undergraduate Chemistry student and I’m currently writing my dissertation about semi-empirical methods, particularly PM7, applied to protein structure refinement from X-ray structure. Could you ...
2
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1answer
70 views

Can you calculate the properties of a substance based soley on its atomic properties?

I'm trying to write some software that I can use to determine, roughly, what the physical properties of a pure substance are. I know I could just use a database of the known properties of each ...
2
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3answers
96 views

Which software is suitable to calculate the root mean square deviation between two protein structures?

I need to compute the root mean square deviation (RMSD) between two protein structures: the X-ray determined protein structure and the MOPAC optimized structure. Which software do you suggest?
3
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1answer
93 views

When it comes to bond energy or molecular binding energy, do people mean enthalpy?

When calculating bond energy or molecular binding energy, which value should I use, enthalpy or total energy? For example, A+B=C Should it be C's enthalpy of formation minus (A's+B's)enthalpies of ...
2
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1answer
302 views

Which one, Mulliken charge distribution and NBO, is more reliable?

Sometimes the Mulliken and NBO turn out to be so different that I can't decide which one I can trust. I've heard that Mulliken is inaccurate, but is NBO always accurate? And should I use Gaussian or ...
3
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1answer
137 views

Coefficients and Parameters for contracted Gaussian basis sets

I'm trying to write a program to calculate fixed-point Hartree-Fock level energies of molecules (for my amusement) and everything makes sense but this. I've been agonizing over this for almost 3 hours ...
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1answer
43 views

Using water model in a computer program

I am writing a small simulator for situations where water is the medium of all reactions. A quick googling confirmed that there are water models available in computer readable formats. Being a ...
2
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0answers
119 views

Structure of fluoroalkylsilane

I want to use FAS (fluoroalkylsilane) in my molecular dynamics study. How can I find it's real structure? So that I can find proper forcefield for simulating the molecule. It would be very nice if you ...
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1answer
115 views

Writing Topology file for Ligand for Gromacs

Is there any tutorial for how to manually write the topology file for any Ligand file(PDB for mol2)? There are so many sites which provides it like ProDrug or ATB but no where the actual process is ...
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1answer
90 views

Two-electron Integrals over Gaussian Plane Waves [closed]

Is there an efficient method to compute the two-electron integrals over the basis set represented by a product of a Gaussian function $g(r)$ and plane wave: $\psi(r)=g(r)e^{ikr}$ where $\lambda=1/k$ ...