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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24
votes
1answer
332 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: ...
19
votes
4answers
667 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 ...
15
votes
1answer
395 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 ...
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 ...
14
votes
3answers
707 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 ...
13
votes
1answer
531 views

How to identify chemical substance from tattoo?

A friend of mine made a tattoo on his chest of some chemical substance formula. He challenged us to identify which substance is that. I thought that perhaps a combination of: Mathematica image ...
10
votes
1answer
601 views

Creating a Mathieu stability diagram

I am attempting to re-create a Mathieu stability diagram like the one shown here: I expected that I could use MathieuC to generate this graph by assuming that ...
10
votes
2answers
384 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. ...
8
votes
2answers
251 views

Problem importing a JCAMP-DX mass spectral file

I have some problems importing a JCAMP-DX EI-mass spectral file using Mathematica 9. For example, if I download the mass spectrum of nonacosane in JCAMP format from NIST, ...
8
votes
2answers
347 views

Look up info associated with a given CAS chemical identifier from the NIST webbook & NCI CADD Chemical Identifier Resolver

I would like to retrieve information associated with a given CAS registry number (Chemical Abstracts Service nr) from the NIST webbook web site in Mathematica, using the provided API (e.g. for ...
6
votes
1answer
89 views

Duplicated output from chemical curated data

I just discovered something rather odd while using chemical curated data in Mathematica. I tried to extract EdgeRules for some molecules and some molecules gave me ...
6
votes
1answer
433 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 ...
6
votes
1answer
129 views

Moles/Liters doesn't get simplified to Molar even though Molar*Liters gets simplified to Moles

Why can't Mathematica 9 simplify mol/L to M, when it can simplify M*L to mol? ...
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. ...
4
votes
2answers
121 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 ...
4
votes
1answer
178 views

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 ...
4
votes
2answers
161 views
4
votes
2answers
206 views

How to set up and minimize a large system of equations to resolve the individual components

I am trying to set up a system of 400*N equations to deconvolute spectral data for four different compounds. I monitored 400 different wavelengths in N solvents (3 solvents in this case). In order ...
4
votes
0answers
44 views

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 ...
3
votes
3answers
243 views

How to deal with units in logarithms?

I'm trying to take a formula, take it's integral which yields a formula with logarithms, and then directly plug in values with units and get an answer. However if the units go into any of the ...
3
votes
2answers
112 views

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 ...
3
votes
1answer
107 views

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 http://en.wikipedia.org/wiki/Transition_metal_dichalcogenide_monolayers) using the ...
3
votes
1answer
57 views

SpaceFillingMolecularPlot using CAS number of a compound

When I tried to get 3D graphics for molecule CAS52364-73-5 using Mathematica 10 it produced following result ...
3
votes
0answers
102 views

random Poisson process over multiple variables (state vector) for chemical kinetics

Has anyone figured out how to coerce ContinuousMarkovProcess to work with a state vector, transition matrix, and rate (propensity) vector, and RandomFunction to return pairs of state vector and time, ...
2
votes
2answers
716 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 ...
2
votes
1answer
99 views

How to program a clickPanel for chemical elements (like a periodic table)?

The command ColorData["Atoms", "Panel"] indicates RGBColors of "Atoms" by clicking a panel. As I don't want to reinvent the wheel, I asked myself: How to ...
2
votes
1answer
166 views

How to combine multiple Graphics3D scenes into a single Graphics3D scene?

ProteinData["A2M", "MoleculePlot"] gives you a Graphics3D object below. I'd like to display multiple of these proteins in a ...
2
votes
1answer
177 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 ...
2
votes
0answers
334 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 ...
1
vote
1answer
262 views

Finding 111 plane of Carbon Diamond

All, I looked at the example on the Mathematica Website with the Carbon Diamond Lattice. Example I am referring to I am wondering is there a way to highlight an individual plane such as the 111 or ...
1
vote
2answers
144 views

How to fit exponential function which is not converging

I performed an experiment where I measured diffusion in a lipid bilayer. I performed the measurement by fluorescently labeling some molecules in the bilayer, and the irradiating them with light ...
1
vote
2answers
79 views

How to construct a new list made from a function that operates on two lists

I need to take two lists (each list contains the number of moles of a chemical). I have a function calledFraction that takes the each entry of the list and then calculates the mole fraction of ...
1
vote
1answer
210 views

Exporting as .PDB extension

I am working with the 3-D coordinates of proteins. The file format I import and modify coordinates of is in the .PDB format, and the string to import is also in this same format. Currently, when I try ...
1
vote
1answer
130 views

Partitioning a numerical integral: need to integrate spectra

I am trying to integrate a spectrum I obtained from a fourier transform infrared spectroscopy experiment, in order to determine the global warming potential of green house gases. In order to do this, ...
1
vote
1answer
89 views

Problem with importing a JCAMP-DX IR spectrum file

I wrote a little function to import JCAMP-DX electron ionization or mass spectral files from the NIST webbook web site (e.g. mass spectrum of hydrogen chloride at ...
0
votes
1answer
87 views

How can I speed up this multi-equation Solve problem?

I'm trying to solve a set of equations (chemical kinetics for a complex system, but don't worry about that). I ran it for 24 hours and I got no output. Here is the relatively simple code (I want to ...
0
votes
1answer
81 views

Bar Chart: How to adjust the font size for the bar labels as the chart size is manipulated

I have data that represents the binding energy of oxygen on different surfaces. Each bar is a different transition metal, and the length of the bar is the binding energy of oxygen. How do I make the ...
0
votes
0answers
79 views

Improving a function that filters each table from a list of tables

I have written the following function which can take in a list of tables as an arguement, and then filters each one. The function I wrote is below, and the commands I combined are listed below the ...