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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29 views

Calculate protein-protein RMSD from PDB files using Mathematica?

I have the PDB files of the same protein in two different conformations. I know that Mathematica allows me to Import PDB files. Does Mathematica come with ...
6
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3answers
129 views

How to find the standard names of chemicals in ChemicalData?

When I try to get info on acetic acid with the ChemicalData function there are only "aceticAcid$l^{1}oxidanylEster" and ...
1
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0answers
51 views

Random protein in 3D [closed]

I would like to ask for help how to encode the following: I make a random sequence of aminoacids to make a protein, but how to make this visible like this: ...
2
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1answer
50 views

Setting an upper limit in the NDSOLVE calculations

I have built a code to solve a system of differential equations in the form: $\displaystyle \frac{d(AB)}{dt}=kn(A)n(B)$ Here I present a small version of it: ...
3
votes
3answers
169 views

Trying to model a chemical reaction - NDSolve::litarg error

I am trying to model a chemical reaction with NDSolve. I have specified the known differential equations and parameters, ...
1
vote
1answer
189 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. ...
1
vote
1answer
166 views

Van der Waals Isotherms [closed]

I have the following code: ...
4
votes
1answer
164 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 ...
4
votes
3answers
241 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
134 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}]] ...
4
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2answers
154 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
votes
1answer
206 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
votes
1answer
70 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
137 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
vote
1answer
186 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
votes
3answers
375 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
votes
1answer
614 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
votes
2answers
164 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
votes
1answer
358 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
300 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
66 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
138 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
78 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
votes
4answers
2k 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
1answer
411 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
votes
1answer
143 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
vote
1answer
109 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 ...
7
votes
1answer
94 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 ...
12
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1answer
1k 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
vote
2answers
187 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
votes
1answer
197 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
votes
2answers
235 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
votes
0answers
150 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
172 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
108 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
545 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
vote
1answer
333 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
330 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
265 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 ...
34
votes
4answers
3k 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
659 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
votes
1answer
183 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
180 views
20
votes
4answers
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
votes
1answer
536 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
669 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
votes
2answers
1k 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
vote
2answers
86 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 ...
20
votes
4answers
914 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
282 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 ...