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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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 ...
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1answer
21 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 ...
2
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1answer
52 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 ...
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2answers
43 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
45 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 ...
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2answers
61 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 ...
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14 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 ...
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1answer
58 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) ...
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27 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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2answers
57 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 ...
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2answers
43 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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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?
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2answers
73 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 ...
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1answer
112 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 ...
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1answer
42 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
36 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
32 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.
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3answers
194 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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125 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: ...
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1answer
106 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 ...
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1answer
30 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 ...
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2answers
197 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 ...
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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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98 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 ...
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2answers
344 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 ...
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1answer
40 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 ...
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1answer
64 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 ...
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3answers
83 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
71 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 ...
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1answer
209 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
111 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
36 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 ...
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0answers
105 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
58 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
79 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 $\lambda=1/k$ ...
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2answers
211 views

When using Gaussian to calculate NMR, what's the default solvent and frequency?

If I choose GIAO HF/STO-3G, is the default solvent $\ce{CD3Cl}$? Is the default frequency for $\ce{^1H-NMR}$ 500 MHz? What about the frequency for $\ce{^13C-NMR}$?
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1answer
78 views

“Electrwd” group?

The Amber force field parameters describe hydrogen atoms in various states: ...
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2answers
306 views

Are there any full worked examples of DFT calculations?

I just started learning DFT and now I am totally confused. Assuming I want to use B3LYP: \begin{align} v_s\left(\textbf{r}\right) &= v_\text{ext}\left(\textbf{r}\right) + \int d^3r\frac{n\left( ...
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1answer
79 views

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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1answer
50 views

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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1answer
120 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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1answer
103 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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0answers
15 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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1answer
54 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
119 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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42 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 ...
5
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1answer
74 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 ...
5
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1answer
277 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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429 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
54 views

Quotable Literature for the Enthalpy of a Proton

A proton obviously has no electronic energy, no vibrational and no rotational degrees of freedom. Therefore I think it is fair to assume, that $$H(\ce{H+})=\frac32\cdot \mathcal{R}\cdot T$$ holds for ...