Questions tagged [software]

For questions pertaining to software used by chemists for professional or academic purposes.

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6answers
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Resources for learning Chemistry

Based on various other Stack exchange site (Mandarin Chinese, Russian and German), we adapt this project here for chemistry, since it's a great idea to have all kinds of resources in one place. This ...
23
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1answer
612 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 ...
7
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1answer
10k 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: ...
36
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5answers
11k 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 Kohn-Sham-...
12
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1answer
1k views

Definition of the B3LYP functional in common QC programs

I wanted to use custom functionals with Gaussian and came up with some interesting definitions of the B3LYP functional within Gaussian, Orca and Turbomole, ... $$\small\begin{array}{lcccccc} \hline ...
5
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2answers
253 views

How to obtain the Raman spectrum along every coordinate of a scan in Gaussian?

I am doing a scan calculation using Gaussian09 and adding the Freq=Raman keyword to my input file. My objective is to obtain the ...
26
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2answers
1k views

Equivalent of Szabo and Ostlund book for DFT

Szabo and Ostlund book Modern quantum chemistry [1] is extremely useful to understand Hartree-Fock and post-Hartree-Fock methods. Not only it explains the theory behind such methods, but it is also ...
26
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4answers
3k views

What software can calculate aqueous solution equilibria?

What software is available out there to calculate the equilibrium in a set of reactions in aqueous solution? In particular, I'm interested in software general enough to simulate things like titration ...
8
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1answer
2k views

How to obtain the radial probability distribution function from a quantum chemical calculation?

In the book "Quantum Chemistry" by Ira Levine I found a plot of the radial probability distribution function of argon: The figure appears in the context of the following section: Electron ...
15
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2answers
2k views

Software for viewing a structure and altering bond angles

Does anyone know of any good software that would allow me to view the structure of a compound while also allowing me to change the bond angles in the structure (and give me numeric values for those ...
9
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5answers
1k views

How can I calculate the charge distribution of a water molecule?

I would like to obtain the 3D charge density of a water molecule for plotting purposes (i.e. not necessarily super-accurate). I know this is a tough problem, but I'd like to give it a try. Since I'm ...
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1answer
2k views

Chemical software for solving reactions [closed]

I'm looking for a software which can solve chemical equations. For example something like this (given with result): \begin{align} \ce{CH4 + 2O2 & → CO2 + 2H2O} \\ \ce{C3H6 + HCl & → ...
-1
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1answer
29k views

Titration curve graph, finding exact point of the equivalence point

I plotted all my data points and made this graph in excel. Now I need to find the volume of titrant required to read the equivalence point, as well as the pH after 18.5 mL of titrant have been added. ...
15
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2answers
18k views

How to find a transition state for an electrophilic addition with Gaussian and map the reaction pathway?

I aim for two things with this post – on the one hand to produce a manual for other people to use, but also to verify what I obtained via searching, asking a more experienced user as well as receiving ...
18
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1answer
9k views

Creating energy profile diagrams for publication

Is there automated software to create energy profile diagrams like the ones below? One could use something like Illustrator or Inkscape, but they aren't automated, are expensive (Illustrator), are ...
16
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4answers
2k views

Easiest way (software) to visualize charge density from an .xyz file with point-charges?

I have an .xyz file which contains partial charges calculated by a Quantum-Chemistry software (NWChem). The system looks like this, here I show the partial charges calculated from the electrostatic ...
22
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3answers
9k views

What open-source software can produce 3D PDF representation of molecules?

Most of the existing software I know (like VMD or Pymol) say that they can be used to create PDF files with 3D representations of molecules: actual 3D models, which you can rotate inside the Adobe ...
6
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1answer
3k views

How to calculate Lennard-Jones potential with quantum mechanical methods

I want to know the procedure to calculate the Lennard-Jones potential for a metal-halogen pair (specifically vanadium-chlorine). Is it possible to calculate using any QM packages like Mopac, NWChem, ...
7
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1answer
630 views

Which rings of this heterocyclic compound are aromatic?

I am wondering which of the inner two rings of this compound are aromatic? I know the rules for aromaticity. But this case is difficult for me. Regarding the smaller ring, I guess the sulfur ...
5
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1answer
175 views

In the absence of a physical model, how can I use free software to visualize stereochemistry?

In a different question, the task was to turn a wedge-and-dash representation into a Fischer projection. This involved rotation of a fairly complex molecule - either as a physical model or a mental ...
9
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3answers
1k views

How to add hydrogens to a crystal structure?

PDB protein crystal structures most of the time lack hydrogen atoms. Usually I use PyMOL (h_add) but it does not always seem to be giving the correct result. What ...
8
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2answers
4k views

Extract all structures of Gaussian 09 molecular dynamics calculation using babel?

Is there a way to easily extract all the structures and energies from an ADMP calculation done in Gaussian 09? GaussView can plot them but not export them in a useful way and babel just gives me the ...
7
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1answer
3k views

Calculating singlet-triplet gap and open-shell singlet character

I am trying to calculate the singlet-triplet energy gap ($S_0-T_1$) of a conjugated system (18 atoms). For the singlet $S_0$ state, assumed to be closed shell, the Gaussian options were ...
7
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1answer
8k views

Definition of Electronic energy

Using Born-Oppenheimer approximation, we separate the nuclear and electronic parts of the wavefunction, and treat them separately. We include the terms that have direct dependence on the electronic ...
7
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1answer
4k views

Converting a PDB file to XYZ file

I am trying to convert a pdb file of gold nanoparticle to the xyz file format to get the atomic coordinates. But when I try to use openbabel to do this, I get the following error. ...
5
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2answers
2k views

Which Chemical Database Software Are Available?

By chemical database software I mean software with similar functionalities to Instant JChem in that they have a large database of different compounds and have the basic capabilities you, or at least I ...
5
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1answer
178 views

Extracting “Crystal Radii” from a CIF file

I'm currently downloading .cif files from various online databases and using openbabel to convert the fractional coordinates that are in the .cif files into .xyz files. The typical output will look ...
5
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1answer
695 views

Software for visualizing molecular force vectors

I would like to visualize molecular normal modes as vectors sitting on each atom, and not as actual vibrations. I am able to do this, in part, with Molden by copying in the vector into a file readable ...
14
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2answers
958 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 ...
10
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2answers
2k 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 ...
7
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1answer
836 views

How do I perform a partial optimisation in GAMESS?

Sometimes it is necessary to perform a partial optimisation of a molecule, i.e. keeping certain variables constant. One example might be to pre-optimise a transition state, taking advantage of not ...
7
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1answer
1k views

Software for visualization of 3D models of chemical structures with atomic orbitals

A number of programs are available that let you build, visualize, and analyze 3D models of chemical structures (I use Chem3D/ChemBio3D). Current versions usually include various possibilities for the ...
4
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1answer
1k views

How do I print property matrices in Avogadro?

I'd like to print the content of property matrices (i.e., the matrices shown after selecting View→Properties→X where X is one of the six options shown, including <...
3
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2answers
357 views

Represent bonds spanning a unit cell boundary plane

Is there a chemical input format that is- Supported by Open Babel (and hence supports visualization in avogadro??) Can represent a bond connecting an atom to its partner in a neighbouring unit cell, ...
2
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3answers
2k views

Software/server for calculation of protonation states of small molecules depending on pH

For docking calculations at different values of pH, I am working with flavonoids and would like to know about any software/server that can prepare ligands depending on the pH. Up to now I read about ...
2
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0answers
56 views

How to obtain spectroscopic constants Omega_e, Alpha_e, B_e, D_e and D_0 from centrifugal constants?

I need to compute a spectroscopic constants of $N_2^+$ states and I would like to do it using LEVEL16 software, due to its high interpolation flexibility. But it seems, that LEVEL16 can only compute ...
9
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3answers
11k views

How to convert SPC files to ASCII without original spectroscopy software?

IR and Raman spectroscopy are typically saved in *.SPC files (chemical/x-galactic-spc), which are binary files. Collected data is save to SPC files by default, but ...
7
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1answer
258 views

How to obtain curve energy and non-bonded interaction parameters (e.g. Lennard Jones parameters) with Gaussian?

I am parameterizing a force field and would need to obtain non-bonded interaction parameters of atoms (e.g., Lennard-Jones parameters). My primary idea is to obtain a potential energy curve using the ...
6
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2answers
1k views

How to make a CP2K input file with Avogadro?

I am trying to learn to work with CP2K and now need to make its input file. CP2K has kind of adaptor for Avogadro2 but not Avogadro ( I don't know what is the relation between them !). I also tried ...
6
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2answers
275 views

Freely available software for generating 3D coordinates of molecules

As part of some research I am doing, I want to do a head-to-head comparison of software for generating 3D atomic coordinates for molecules. Is there a list anywhere of chemical software that does this?...
5
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3answers
979 views

Thermodynamic properties software

I am looking for a software (can be freeware or purchased) to look up water and steam thermodynamic properties (e.g. density, enthalpy, entropy) preferably a macro in excel. What do you use for this ...
5
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2answers
744 views

Counting valency of atoms, in a molecule with python

The documentation for the indigo module can be found here http://ggasoftware.com/opensource/indigo/api#inputoutput So for instance if I have a molecule object for some SMILES string, e.g. ...
5
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1answer
222 views

Azathioprine CIF data file rendering problem in Accelrys

I have been working on a CIF data file based on experimental data [1] (free full text isn't available, but the page 2 with the experiment details can be found in the free preview provided by Springer)....
5
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4answers
3k views

Open Source tools to draw a set of 2d molecular graphs from sdf file

I have a sdf file for around 50 small-molecules for which I am doing structure-activity study. I would like to draw 2d graphs of all the molecules such that the image would fit into a single journal ...
4
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1answer
4k views

How to construct a QST2 input file for Gaussian16 for multiple reactants and products?

I am attempting to determine the transition state structure for the following reaction using the QST2 method on Gaussian 16: $$\ce{CH3 + N -> HCN + H2 }$$ However, I am struggling to put together ...
4
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2answers
4k views

ChemDraw: Automatic Caption with Number for Molecules

When working on some reaction schemes in ChemDraw, I sometimes forget to add text/captions with numbering and align it with my molecules before placing all the molecules in a reaction scheme and ...
3
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2answers
4k views

Gaussian scan function help for constructing input file

I have the cartesian coordinates for two molecules that are in a stacked position and I want to be able to calculate the potential energy at 0.2 angstrom steps from when the top molecule is 3.0 ...
3
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1answer
964 views

Why is predicting products of chemical reactions difficult? [closed]

I was going to ask whether there are software that could be used to predict the products of any given chemical reaction. However, I then noticed these two earlier questions Chemical software for ...
2
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2answers
427 views

A Chemdrawing software? [duplicate]

I would like to know about a Chemdrawing sotware for 2-d molecular structures. it should be mainly linux based (but if it supports other OS's then that would be great)
1
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1answer
141 views

CIF fields that are available for some atoms, but not others

I've been working on another CIF file, this time for (-)-threo-methylphenidate based on Pharma Res, 1995 (sadly the relevant crystallography data isn't supplied in the free preview at Springer). I ...