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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45
votes
4answers
16k 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 ...
31
votes
1answer
687 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: ...
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 ...
26
votes
1answer
3k views

Gillespie Stochastic Simulation Algorithm

The Gillespie SSA is a Monte Carlo stochastic simulation algorithm to find the trajectory of a dynamic system described by a reaction (or interaction) network, e.g. chemical reactions or ecological ...
25
votes
3answers
3k views

Plot 3D model of DNA in Mathematica

My friend asked me if we can plot a 3D model of DNA (deoxyribonucleic acid) in Mathematica. However, I am not really familiar with this and I don't know if Mathematica can do this. Could you answer ...
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 ...
19
votes
4answers
978 views

How to apply different equations to different parts of a geometry in PDE?

I want to solve two coupled partial differential equations on two dimension. There are two variables v and m. The geometry is a ...
19
votes
1answer
4k views

Creating a Mathieu stability diagram

I am attempting to re-create a Mathieu stability diagram like the one shown in a paper by Leary and Schmidt [1]: I expected that I could use MathieuC to generate ...
17
votes
1answer
1k 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 ...
16
votes
3answers
579 views

Computing the surface area and volume of molecules

Here is a somewhat difficult problem I've had for a long while. Space-filling models of molecules can be easily generated by ChemicalData[], ...
15
votes
4answers
5k 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 ...
15
votes
3answers
783 views

Proteins, ProteinData, WolframAlpha

Apologies in advance, this is the first I've messed with ProteinData and access through WolframAlpha, so clearly I may not know ...
15
votes
1answer
627 views

Automatic formatting of isotope symbols in a text cell

InputAutoReplacements is an obvious choice for formatting isotope names in text cells. I'd like to be able to type "1H", for ...
15
votes
1answer
690 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
2answers
1k views

Pulsed NMR animation

I'm new here and have never interacted with the community so excuse me if this has been asked before or if I format incorrectly or anything like that. Anyway, I'm trying to make an animation for a ...
13
votes
1answer
1k views

visualizing a normal mode vibration of a molecule in mathematica

How can I visualize the normal mode vibrations of a molecule in Mathematica? Something like the following GIF: (from here) I have the XYZ file of the benzene molecule and the normal mode ...
12
votes
3answers
3k views

Radial distribution function

I have tried to rewrite my old IDL code to calculate the radial correlation function for a regular 2D crystal structure. The theory behind this function is given here: https://en.wikipedia.org/wiki/...
11
votes
3answers
875 views

Minimum energy path of a potential energy surface

I have calculated the energies of a molecule by varying two parameters (Data points are here data). I want to find the minimum energy path from the point (180.0, 179.99, 21.132) to (124.5, 124.49, 0) ...
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 ...
10
votes
6answers
1k views

Faking MoleculePlot for compounds where it isn't available

Mathematica's ChemicalData has a lot of useful information, but many compounds only have flat 2D structure diagrams rather than the cool 3D ...
10
votes
3answers
596 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? ...
10
votes
3answers
659 views

DFT for Helium atom

I'm trying to solve this problem I'm not a Mathematica expert, but my program works perfect when vhartree={0,0,..,0} This is the program I wrote: ...
10
votes
2answers
349 views

What's the principle behind the new MoleculeRecognize function?

I played a bit with the new MoleculeRecognize function implemented in the newly released WM 12.1: which simply recognizes a molecule in image and returns it as a Molecule object. ...
10
votes
4answers
482 views

MoleculePlot3D - how to replace spheres?

How to replace the spheres in the plot with other 3d figures, say "N" with a Cylinder, "O" with a Cuboid, and "H" with a sphere. ...
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 ...
9
votes
3answers
850 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. ...
9
votes
3answers
397 views

Mass Transport Model

I've asked similar questions before about Mathematica's Mass Transport model. My aim is to model these systems and show how they change by manipulating various parameters. This time it's the following ...
9
votes
3answers
416 views

Chemical data of Lactic acid [duplicate]

I'm using the next Mathematica command in order to plot molecules: ChemicalData["name", "MoleculePlot"] But I'm not sure if the Mathematica database of molecules ...
9
votes
2answers
378 views

Plot polygonal surface

I have a list of 120 elements of the form $\{q,x,y,z\}$. In fact, each element of the represents the nuclear charge and 3 coordinates of an atom of some large molecule. ...
9
votes
2answers
520 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/...
9
votes
1answer
169 views

MoleculePlot draws sucrose benzoate with overlapping bonds

Recently I learned that in Mathematica it is possible to create chemical structures here: Chemical formulas with Mathematica I am having a problem with a structure called "Sucrose benzoate" (...
9
votes
1answer
3k 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 ...
8
votes
2answers
415 views

ChemistryData — where is specific gravity?

I cannot seem to find the basic chemical property specific gravity with ChemicalData or other comparable functions.
8
votes
2answers
248 views

When looking at a chemical's bond lengths, which bonds do they represent?

Looking at, for example, the bond lengths of styrene: ...
8
votes
2answers
246 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: ...
8
votes
1answer
336 views

Why does `Molecule` return a molecule for an incorrect SMILES string?

When I type an incorrect SMILES into the Molecule function, the output a large, unrelated molecule. What is Molecule doing here, and is it possible for the command ...
8
votes
3answers
4k views

Why are Dalton and Grams / Moles not equivalent units?

The following code throws an error: UnitConvert[Quantity["Daltons"], "Grams"/"Moles"] Why?
8
votes
1answer
306 views

Constructing Icosahedral Fullerene Graphs

I am interested in constructing graphs of icosahedral fullerenes, following the construction explained in the first few pages of this article (alternate link). Mathematica has built-in information ...
8
votes
1answer
3k 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? ...
8
votes
1answer
94 views

Are the lists from “BondList” and EdgeList for a molecule guaranteed to be aligned?

Consider the following: ...
8
votes
1answer
457 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? ...
8
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 ...
7
votes
3answers
568 views

ChemicalData returns the correct result for “Sulfuric” but an empty list for “Sulfuric Acid”. Why?

I am new to this site so I hope my question is valid. My code is: ...
7
votes
2answers
660 views

How to I extract the element name of a chemical compound in a string?

Say I have a compound Fe3O4, and I want to separate the name of elements and number. The code I write for separate number is ...
7
votes
2answers
210 views

Visualizing only the chain of a protein and color each residue in Mathematica

Is there a way to visualize in cartoon a single chain of a protein using ProteinData and color the residues by its chemical properties e.g. hydrophobicity, acidic ...
7
votes
3answers
251 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 ...
7
votes
2answers
142 views

How can I prevent Molecule from adding hydrogens automatically?

Consider the following: cacl = Molecule[{Atom["Ca"], Atom["Cl"]}, {Bond[{1, 2}, "Single"]}]; MoleculeValue[cacl, "CanonicalSMILES"] (* Cl[CaH] *) Notice the ...
7
votes
1answer
1k 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/...
7
votes
1answer
167 views

Suggestions to increase the speed of a fugacity calculation

I'm writing code to simulate a chemical reaction. This requires the calculation of the fugacity of a mixture of gases. The underlying model is the SRK equation of state. First the physical ...
7
votes
1answer
119 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 ...

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