# Tagged Questions

For questions related to chemical concepts such as solving equations related to reaction kinetics, graphically visualizing molecules, and using the chemistry-related curated data sets.

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### Gillespie Stochastic Simulation Algorithm

The Gillespie SSA is a Monte Carlo stochastic simulation algorithm to find the trajectory a dynamic system described by a reaction (or interaction) network, e.g. chemical reactions or ecological ...
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### Problem with a chemical optimization problem [closed]

First of all, I want to say that I'm quite new to Mathematica. I searched a lot on this site to learn how to solve my problem, which this is the problem of my life! I want to minimize a function. It ...
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### How can I draw ternary plot by these data?

I have these data and want to draw similar fifures in mathematica. any one can help me? ...
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### Parsing/validating CAS registry number identifiers

Mathematica includes a lot of curated information on molecular structure and properties available through ChemicalData and ...
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### Adding text on an .xyz file of an atom

I know it is possible to view .xyz files of coordinates in Mathematica. I tried to write some text on a specific atom using Text, but I was not successful. How can i do that? Thanks for the help in ...
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### How can I get the solubility value of nitrogen in water at 10 degrees Celsius with Mathematica?

How can I get the solubility value of nitrogen in water at 10 Â°C with Mathematica? The site engineering toolbox dot com gives graphs of such values, but I want the numerical value. Related thread ...
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### Calculate the partial vapor pressures of a variable at xB = 0.75 based on the interpolation functions of the data

I'm having troubles in solving an exercise for an assignment in my Chemistry course. Talking about interpolations, I've already have a graph but I need to calculate the partial vapor pressures of ...
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### Change the colors of individual atoms in a .mol or XYZ file

Similar to (Changing the atom color for plotting xyz-files), I want to take a molecule and then simply change the colors of individual atoms. I don't want to change all atoms of a type to a color (say,...
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### Accessing chemical property data for specific conditions?

There is a wealth of data for various chemicals available through Mathematica. For instance: ...
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### Changing the atom color for plotting xyz-files

Mathematica takes the standard color code for atoms when plotting an *.xyz file, but I want to customize the color for the specific atoms. I really become desperate as I did not get it so far. ...
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### Constructing primitive cell using information from ChemicalData

I would like to construct a primitive cell (figure shown) and possibly the two-dimensional layout (figure from here) using the following input. Any clues as to how this can be done? ...
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### Sorting out atom types in an XYZ file

I am trying to rewrite the output of "VertexCoordinates" such that instead of a hybrid list of atoms and coordinates that result from using the following input program, I want all coordinates of the ...
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### Creating a three dimensional fullerene molecule

How do I modify the following program to create a nice coloured molecular plot of C60 or fullerene as shown in the attached figure This figure was retrieved from http://asserttrue.blogspot.com.au/...
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### Attaching a legend to BallAndStick picture

I am looking for a way to add a legend showing the identity of various atoms (with different colours) to this picture. Any Clues? ...
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### Combining separate CHColorStructureDiagrams to form one molecular structure

I am trying to attach a fructose molecule to a sucrose molecule by using information obtained from the following ...
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### Retrieving coordinate positions using ChemicalData for input to quanutm modelling software

I am trying to set up an input file for a quantum chemical modelling software. How do I obtain the (XYZ) coordinate positions in Angstroms using information obtained using ChemicalData. Have some ...