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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19
votes
4answers
662 views

Accessing list elements by name

First, a bit of a long introduction to my problem: I only have a few weeks of Mathematica experience. I am creating a mathematica application that calculates some material properties of steel based ...
14
votes
3answers
700 views

How to get rid of the perspective effect in a 3D graphics

I have plotted a figure of MoS2 crytal structure. But the actual output looks like the spheres are not in the correct position due to the perspective effect. I obtained the correct position figure ...
24
votes
1answer
331 views

How to save ChemicalData queries so that they are available immediately on notebook load?

If I put some viscosity (or density, ...) lookups in my notebook, such as: ...
14
votes
4answers
1k views

How to change element color in Periodic Table?

The command ColorData["Atoms", "Panel"] generates a periodic table. As I don't want to reinvent the wheel, I asked myself how to change the color of each cell ...
2
votes
0answers
332 views

Generating a function which outputs possible chemical reactions

I want to make a list of chemical reactions and I write them down in a $\require{mhchem}\LaTeX$ format. They are of the following form $$NA_n^i+MB_m^j \rightarrow \hat NA_{\hat n}^{\hat i}+\hat ...
15
votes
1answer
394 views

Find elements in a decay chain using IsotopeData

I am trying to write a program using the Mathematica function IsotopeData, but am finding the code troublesome. Due to my (relative) familiarity with Python, I am ...
6
votes
1answer
429 views

Building a molecule viewer: aesthetic rotations

I am working on building a molecule viewer in Mathematica and am running in to problems with controlling rotation of the molecule (which is rendered as a ...
10
votes
2answers
381 views

How can I access the internal function that plots a molecule from a formatted XYZ file?

Mathematica has the ability to plot a molecule using the data contained in an XYZ file. This is a simple text file, of which this is an example. The molecule is plotted using the Import command. ...
4
votes
3answers
191 views

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. ...
2
votes
1answer
176 views

How to enter chemical equations?

When I want to take chemistry notes and write down a formula such as H_2O or C_2H_5OH it enters "Math mode" which changes the font size and italicizes the letters. Is there an easy way to properly ...
4
votes
2answers
119 views

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 ...
2
votes
2answers
713 views

Using ChemicalData to make molecule graphics

I would like to take the acetone $((CH_3)_2CO)$ and chloroform $(HCl_3)$ molecules that Mathematica's chemical data provides, and plot them together. I want to show how chloroform can hydrogen bond ...