Questions tagged [chemistry]

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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2
votes
1answer
248 views

Solving ODES in order to find unknown constants

I am trying to solve a set of ODES which represent a second order consecutive chemical reaction. ...
2
votes
1answer
95 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 ...
3
votes
1answer
350 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 (say,...
2
votes
2answers
212 views

Accessing chemical property data for specific conditions?

There is a wealth of data for various chemicals available through Mathematica. For instance: ...
9
votes
3answers
789 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. ...
8
votes
1answer
2k 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
307 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 ...
7
votes
1answer
948 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 http://asserttrue.blogspot.com.au/...
10
votes
3answers
582 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
votes
0answers
95 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
2answers
174 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 ...
8
votes
2answers
219 views

SpaceFillingMolecularPlot using CAS number of a compound

When I tried to get 3D graphics for the molecule with CAS number 52364-73-5 using Mathematica 10, it produced the following result: ...
15
votes
4answers
4k 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 ...
3
votes
1answer
975 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 ...
6
votes
2answers
361 views

How to program a click panel 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 ...
2
votes
1answer
230 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
110 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 ...
17
votes
1answer
3k 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
456 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
1answer
1k 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
307 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
209 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
vote
1answer
233 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, ...
2
votes
1answer
163 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 http://webbook.nist.gov/cgi/cbook.cgi?...
11
votes
2answers
1k 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 ...
2
votes
1answer
752 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 ...
9
votes
2answers
481 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, http://webbook.nist.gov/cgi/...
2
votes
1answer
2k views

Newton-Raphson Method and the Van der Waal Equation Coding question

So I need to find Specific Volumes using the Newton Method from the Van der Waal equation over a change of constant Temperature but variant Pressure. I have been able to make a list of however many ...
2
votes
1answer
888 views

Avoiding zero (empty set) solution with NDSolve

I'm trying to use NDSolve for a chemical kinetics equation where the rate of conversion is given by this relationship as typed in Mathematica: ...
6
votes
1answer
1k views

How to transform and combine multiple Graphics3D into one?

ProteinData["A2M", "MoleculePlot"] gives you a Graphics3D object below. I'd like to display multiple of these proteins in a ...
44
votes
4answers
13k 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 ...
17
votes
1answer
932 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 ...
8
votes
1answer
440 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
236 views

How to fit a one-dimensional dataset with respect to several bounded parameters?

I have this set of data ...
30
votes
5answers
4k 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 ...
4
votes
2answers
373 views

Modifying imported 3D file

Since I am visualizing my work using Mathematica, I import some 3D models of molecules to my notebook. So, the question is, is there any way to modify somehow that imported models inside Mathematica ...
6
votes
1answer
807 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 Graphics3D...
10
votes
2answers
1k 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 ...
5
votes
5answers
1k views

Problems with NDSolve and stiffness

I am trying to solve an ODE in chemical kinetics: $$\begin{align*} \frac{\mathrm d[x]}{\mathrm dt} &= -k_1 [x][y]\\ \frac{\mathrm d[y]}{\mathrm dt} &= k_1 [x][y] - k_3[y] \end{align*}$$ My ...
7
votes
1answer
1k views

How can I efficiently write formatted data to a Gaussian Cube file?

I am working with data files that contain information about electronic wave functions. The data format is specified by the quantum chemistry program Gaussian. I need to import the data, manipulate ...
5
votes
2answers
2k 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
93 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
2k 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 ...
4
votes
2answers
676 views

RefProp in Mathematica

RefProp by NIST is a program that calculates the thermodynamic properties of fluids. I need to call certain RefProp functions ...
3
votes
3answers
322 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
460 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
626 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 MA_{\...
15
votes
1answer
665 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 ...
7
votes
1answer
2k views

Efficient implementation of cubic equation of state

...In this case the Peng Robinson Equation of State. Equations of state are empirical equations with parameters derived from experimental data. They are used to predict pure component and mixture ...
3
votes
1answer
459 views

Efficiently importing XPM matrix data into Mathematica

The XPM file format is an image file format. Although it is primarily intended for icon pixmaps, it can also be used to store matrix data. For example, the GROMACS chemical simulation package uses ...