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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1answer
165 views

Modeling a stellar atmosphere

I'm trying to model a stellar atmosphere using Mathematica. Basically I'm working in a physical and chemical model which combined should give me a profile of the chemical abundance in the atmosphere. ...
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1answer
63 views

Van der Waals Isotherms [closed]

I have the following code: ...
4
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1answer
145 views

Solving a chemical system using NDSolve

I have to solve a set of coupled differential equations and am not sure how to proceed. It is a model of a chemical process where I'm interested to find the species concentration as $r$ varies. For a ...
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3answers
125 views

Using NDSolve within Manipulate

I'm trying to use NDSolve inside manipulate. Specifically, I have a series of differential equations with coefficients, k1, k2, ...
5
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2answers
111 views

Generating and Imaging of the water molecules with Graphics3D [duplicate]

my problem is I don't know how to generate e.g. 20 water molecules: Graphics3D[ Rotate[First@ChemicalData["Water", "MoleculePlot"], 45 Degree, {8, .5, 0}]] ...
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2answers
111 views

How can export into an .XYZ file using decimals without scientific notation?

I have seen the other posts relating to this however there seems to be more restrictions when exporting to .XYZ. I am pretty new to this but I have been searching for hours. Basically, I have a ...
2
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1answer
189 views

How can I get the solubility value of nitrogen in water at 10 degree Celsius with Mathematica?

How can I get the solubility value of nitrogen in water at 10 degree Celsius with Mathematica? The site engineering toolbox dot com gives graphs of such values but I want the numerical value. ...
2
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1answer
69 views

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 ...
2
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1answer
96 views

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 ...
1
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1answer
147 views

Input of ions and compounds in Wolfram's Mathematica [closed]

I want to use Wolfram's Mathematica to see some data about certain ions. I don't know how to write the chemical's compounds or ions full names, so that at this time I need to write its "formula". ...
6
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3answers
314 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. ...
6
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1answer
375 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 here) using the following input. Any clues as to how this can be done? ...
5
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2answers
153 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 ...
5
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1answer
277 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 ...
9
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2answers
267 views

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? ...
4
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0answers
58 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
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2answers
134 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
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1answer
72 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 ...
14
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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
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1answer
314 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 ...
3
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1answer
124 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 ...
1
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1answer
100 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 ...
6
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1answer
92 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 ...
0
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0answers
92 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 ...
12
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1answer
961 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 ...
1
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2answers
170 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 ...
0
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1answer
146 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 ...
4
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2answers
220 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 ...
3
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0answers
134 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, ...
1
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1answer
157 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
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1answer
103 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 ...
8
votes
2answers
479 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 ...
1
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1answer
293 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 ...
8
votes
2answers
300 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, ...
2
votes
1answer
215 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 ...
28
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4answers
2k views

Is there something like DensityPlot3D to visualize atomic orbitals?

I'm visualizing some hydrogen like atomic orbitals. For looking at plane slices of the probability density, the DensityPlot function works well, and with something ...
16
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1answer
616 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 ...
6
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1answer
155 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? ...
5
votes
2answers
174 views
15
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3answers
1k 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 ...
6
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1answer
501 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
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2answers
565 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. ...
5
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2answers
929 views

Using ChemicalData to make molecule graphics

$\require{mhchem}$I would like to take the acetone $\cf{((CH3)2CO)}$ and chloroform $\cf{(HCCl_3)}$ molecules that Mathematica's chemical data provides, and plot them together. I want to show how ...
1
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2answers
83 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 ...
19
votes
4answers
815 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 ...
3
votes
3answers
265 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 ...
1
vote
1answer
252 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 ...
2
votes
0answers
411 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
423 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 ...
28
votes
1answer
394 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: ...