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.
278
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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 ...
- 6,458
32
votes
1
answer
4k
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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 ...
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31
votes
1
answer
763
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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:
...
- 6,458
30
votes
5
answers
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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 ...
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27
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3
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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 ...
- 2,111
20
votes
4
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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 ...
- 305
20
votes
1
answer
5k
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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 ...
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19
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4
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1k
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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 ...
- 3,876
18
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3
answers
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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[], ...
17
votes
1
answer
1k
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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 ...
- 3,074
16
votes
4
answers
5k
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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 ...
- 407
16
votes
3
answers
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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 ...
- 1,800
16
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1
answer
750
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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 ...
- 263
15
votes
1
answer
784
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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 ...
- 5,141
14
votes
2
answers
2k
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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 ...
- 141
14
votes
2
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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.
...
- 265
13
votes
1
answer
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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
3
answers
4k
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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/...
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11
votes
3
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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
3
answers
614
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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 ...
- 351
11
votes
2
answers
1k
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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 ...
11
votes
1
answer
252
views
protein visualization: display a residue in balls and sticks over the structure
I am trying to visualize a cytochrome c protein and display one of the residues in ball and sticks over it.
I am using the PDB file 1AKK for it (https://www.rcsb.org/structure/1akk). The Import ...
- 133
11
votes
0
answers
267
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Produce the same color scheme as IboView
I can use the following command to produce the HOMO (highest occupied molecular orbital) in chemistry:
...
- 1,582
10
votes
6
answers
1k
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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 ...
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10
votes
3
answers
607
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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?
...
- 3,268
10
votes
3
answers
945
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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.
...
- 101
10
votes
3
answers
994
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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:
...
- 141
10
votes
4
answers
561
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.
...
- 551
10
votes
2
answers
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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 ...
- 69.7k
9
votes
3
answers
442
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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 ...
- 377
9
votes
2
answers
432
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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.
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9
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2
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568
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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/...
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9
votes
2
answers
476
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How can I rotate and reflect a molecule plot?
Consider:
MoleculePlot[Molecule[Entity["Chemical", "Theobromine"]]]
How can I rotate and reflect it? This is my current method:
...
- 27k
9
votes
1
answer
199
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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" (...
- 1,651
9
votes
1
answer
434
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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 ...
- 6,311
9
votes
1
answer
3k
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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 ...
- 11k
8
votes
2
answers
438
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ChemistryData — where is specific gravity?
I cannot seem to find the basic chemical property specific gravity with ChemicalData or other comparable functions.
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votes
2
answers
300
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When looking at a chemical's bond lengths, which bonds do they represent?
Looking at, for example, the bond lengths of styrene:
...
- 277
8
votes
2
answers
300
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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:
...
- 349
8
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1
answer
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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 ...
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8
votes
3
answers
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Why are Dalton and Grams / Moles not equivalent units?
The following code throws an error:
UnitConvert[Quantity["Daltons"], "Grams"/"Moles"]
Why?
- 11.5k
8
votes
1
answer
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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?
...
- 3,268
8
votes
1
answer
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Are the lists from "BondList" and EdgeList for a molecule guaranteed to be aligned?
Consider the following:
...
- 5,331
8
votes
1
answer
469
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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?
...
- 1,555
8
votes
1
answer
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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 ...
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7
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3
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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:
...
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7
votes
2
answers
768
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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
...
- 81
7
votes
2
answers
457
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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 ...
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7
votes
3
answers
292
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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 ...
- 1,897
7
votes
1
answer
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Molecule fingerprint functions v13
I am looking for calculation of molecular fingerprints (FingerprintFunction) in v13 of Mathematica. There was a WTC talk around v12.2 showing this functionality, however, I can't seem to find this in ...
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