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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21 views

What closure relations can we use in molecular modelling?

Following my question here about the BBGKY hierarchy I was wondering does anyone have any experience in using the method outlined. In particular how would I take an equation off the page and for some ...
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18 views

Program to covert WFN-file to Molden

I have tried google but without success so here the question: does anybody know a tool that can covert WFN-file to Molden or to Molpro format (including orbital info not the coordinates only).
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26 views

Glycine nucleation simulations

I am trying to run nucleation simulations of glycine in water. To generate a supersaturated solution, a solution that will crystallize, I need to know the solubility. Luckily for me, this data exists. ...
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18 views

What are the details of being able to predict whether a pi or sigma bond will be lower in energy for diatomics (or any system for that matter)? [closed]

I have heard that one can find out the ordering of pi and sigma orbitals (such as the switch between N2 and O2 in their MO diagrams) using quantum mechanical calculations. I am a research student with ...
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1answer
95 views

Calculated 13C NMR Shifts of brominated Carbons

Since I calculate NMR spectra for a while by simply using one of recommendations by CHEmical SHIft REpository: mPW1PW91/6-311+G(2d,p)-SCRF//B3LYP/6-31+G(d,p) ...
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1answer
73 views

Does the delocalization of p-orbitals ensure conductivity?

For example, polyacetylene is a conjugated system, i.e. with de-localized p-orbitals, but accroding to Chiang et. al. (1977) polyacetylene is semiconducting, and becomes conductive only when doped ...
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1answer
21 views

Can you predict the resistance of conjugated polymers as a function of degree of polymerization (DP)?

Electrical properties of very simple systems can be calculated using NEGF. Is there a way to calculate the resistance (and other electrical properties) of a conjugated polymer, as a function of degree ...
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1answer
121 views

Trying to understand SMILES(?) patterns

In the example calculation from the conformer search package fafoom is a mysterious pattern that I'd like to understand. The SMILES code of the given example structure is: ...
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53 views

Question about theoretical modeling of photocatalysis

As a computational materials chemist studying photocatalysis, how close to realistic systems can your modeling get? I have a sort of high-level question about the theoretical modeling of ...
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1answer
51 views

How to define a new solvent in Gaussian09 to run SCRF?

I want to run computation of my system in sulphuric acid with Gaussian 09; however sulphuric acid is not among the built-in solvents in G09. I know I have to give some parameters for the new solvent I ...
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24 views

Distance weighted interpolation

I got stuck while reviewing the journal article "Accurate reaction paths using a Hessian based predictor–corrector integrator". Why is the distance weighted interpolation done in the predictor steps, ...
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21 views

Potential energy Surfaces

I am trying to calculate PES for Molecular Oxygen and Atomic Nitrogen Exchange reaction. This is also known as Zeldowich reaction. I found that for asingle reactions, there are many PES's which I ...
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148 views

Why is MP2 failing to calculate proper IR frequencies for [Co(CO)4]^- and [Fe(CO)4]^{2-}?

I was doing some IR calculations on different 3d transition metal carbonyl complexes during some practical courses where we were introduced to effective core potentials. While doing this we found that ...
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1answer
74 views

Radical Computational Calculations [closed]

I am trying to calculate the total energies for a particular organic molecule that undergoes radical decomposition. I was able to calculate the neutral molecule with the exact results of a paper I ...
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3answers
202 views

Generating neat orbitals/surfaces from molden/wfn-files

I usually use Gaussian/GaussView and don't have to bother with other programs as I think that GaussView is capable of producing nice orbital/surface pictures like this one of one of uracil's ...
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43 views

calculate diffusion coefficient from MSD vs time [closed]

I have a trajectory file from simulation of 20,000 frames with 5 ps time in between every frame, what I want to do is to calculate diffusion in 2 dimension (x and y axis). but to calculate diffusion ...
3
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1answer
72 views

Carbohydrate configurations

I want to study several carbohydrates that includes but not limited to the following molecules: Glucose Galactose Mannose Fructose Tagatose Sorbose I know that for any carbohydrate, possible list ...
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3answers
202 views

InChIKey generation from InChI

I am trying to find some good resources to understand generation of InChIKeys from the InChI. There seems to be no resource available online. I have gone through the Wikipedia article for InChI, but ...
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44 views

What factors contribute most to solubility of ionic substances in highly polar solvents, esp. ionic liquids and DES?

I am trying to determine a method to dissolve a mineral salt with a lattice energy of ≈18000 kJ/mol. I know that lattice energy is the most significant factor affecting solubility of an ionic ...
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49 views

Free Web-Based Orbital Solver to look into the Walsh orbitals of a perturbed cyclopropane

There exists a free online orbital calculator. When I draw cyclopropane it plots three molecular orbitals, but unfortunately it doesn't use the Walsh orbitals. Are there any free online tools which ...
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50 views

Finding Ice CIF files in crystal database

Could anyone please tell me where I could find the the structure of cubic ice (ice Ic) as a .cif file? I have been searching the cambridge structural database using "H2O", "water", "dihyrogen oxide" ...
7
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2answers
93 views

Reliable automatic addition of hydrogens and charge assignment to small molecules at given pH?

I have some molecular PDB structures with missing hydrogens. Is there a software available that places missing hydrogens and assigns a charge to the molecule that is reliable? I have used Avogadro to ...
7
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1answer
144 views

How to read TINKER's force field parameters

I'm going to parameterize AMBER force field for the simulation of some small molecules. I have found the parameter sets provided by TINKER at here. I'm stuck here because I couldn't find any ...
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1answer
191 views

What happens if a polymer's length is equal to its persistence length?

So, I've been looking into polymer chemistry to model breaking polymers for a biological model, and I've been a bit stumped by the concept of persistence length. I know that if a polymer is ...
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1answer
110 views

What is GMEC (Global Minimum Energy Conformation)?

In a paper I have read the term GMEC, which was not further explained. GMEC stands for Global Minimum Energy Conformation. But what is it? Is it just the conformation with the lowest energy?
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34 views

Method of representing molecules as 3d objects with surfaces [closed]

I need a way of representing molecules in 3d form. I wish to be able to define a 3d surface for simple organic molecules. Can anyone advise me on this? Are there any approaches, or solutions to this ...
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2answers
94 views

Fitting parameters of Lennard-Jones potential to properties of real materials

I'm using the Lennard-Jones potential for some (very simple) protein docking simulation* and couldn't find parameters for different materials (like $\ce{C}$, $\ce{N}$, $\ce{O}$, …). Does it even make ...
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78 views

How to simulate surface tension?

I am trying to create a water drop simulation for measuring hydrophobicity of surface. I don't know how to simulate the contact angle which is related by younges equation to the surface tensions for ...
7
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3answers
108 views

Is it wise to use ECPs on light atoms for electronic structure calculations?

So, I have a big organic molecule consisting of $\ce{H}$, $\ce{C}$, $\ce{O}$, and $\ce{N}$ atoms and the goal is to find its equilibrium geometry and US/Vis spectrum. The molecule is so big that I was ...
6
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1answer
157 views

What is the exact meaning of GAMESS (US) SCF density convergence criteria?

In Gaussian the SCF convergence criteria is set to $10^{-N}$ by SCF=(Conver=N) Note that this criteria applies to the root mean square change in density matrix ...
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2answers
91 views

How would you add saccharide residue information to PDB files?

I have multiple PDB files containing a single molecules of polysaccharides, with a single chain and a long list of all the atoms -they are not divided by residue. The PDB files were created from ...
5
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1answer
242 views

What is GAMESS and Gaussian?

I've been seeing a lot of GAMESS and Gaussian questions around here, and most of them seem very hard to answer. I extrapolated that they might be some sort of Chemistry programs, but what do they do ...
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2answers
156 views

How to interpret orbital transition in TDDFT?

Consider the following TDDFT run with GAMESS: ...
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192 views

Why Acetone does not behave like its computational values?

I am trying to simulate the excitation state of acetone. I ran TDDFT for it both in gas phase and solvated state in water (both implicit and explicit water). The experimental data say that acetone ...
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57 views

Andersen thermostat in MD with rigid bond constraints

I have been writing a custom MD code for some time. I have been using the andersen thermostat, mainly because its ease of use, and the fact that I am not concerned with gathering dynamical data, but ...
3
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1answer
115 views

How to calculate molecular dipole moment from a known wavefunction?

Say I have a molecular wavefunction as a set of molecular orbitals and want to calculate the molecule's dipole moment, but don't know how ! I searched a lot but couldn't find any practical example. ...
3
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1answer
126 views

How to interpret TD-DFT results for finding λmax and amplitude

I am trying to understand how to interpret the TDDFT results ( I know there is another post for this but it does not answer my question ). Here is part of the result from GAMESS: I downloaded ...
5
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1answer
54 views

What program could I use to create a protein model from scratch?

I would like to create protein models such as the ones in the Protein Data Bank. I have got GROMACS but I don't know if it can be used to model macromolecules.
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2answers
87 views

Are molecular optimizations in quantum chemistry really in vacuum?

I know that Gaussian (or other quantum chemical packages) assumes the molecule is alone in vacuum, that is, the molecule doesn't interact with anything, when optimizing the molecule. But I've found ...
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0answers
14 views

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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42 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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1answer
38 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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45 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
88 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
65 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 ...
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206 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 ...
3
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2answers
88 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
75 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 ...
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1answer
164 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
73 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 ...