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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6
votes
2answers
239 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 ...
16
votes
2answers
776 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 ...
1
vote
2answers
106 views

Specify the color of each residue in a protein (PDB)?

I'm importing a *.pdb file containing a single protein. Mathematica automatically produces a plot of the protein. I want to specify the color of each residue independently, in this plot. Is this ...
4
votes
2answers
98 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
2answers
620 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 ...
14
votes
1answer
412 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 ...
0
votes
0answers
31 views

ChemicalData, only index downloaded

I do not have access to internet on my PC , so as in Wolfram's KB, I preloaded ChemicalData from an online PC, and then transferred it to my PC. The problem is only the index got downloaded, so how ...
8
votes
5answers
531 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 ...
4
votes
4answers
256 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, ...
5
votes
1answer
68 views

ElementData possible oxidation states

Is there any way to find out the possible oxidation states for a given element? Something like this: ElementData[1, "OxidationStates"] -> {-1, 1} Here is a ...
3
votes
1answer
126 views

Modeling chemical reactions: can Mathematica tell the end result of a reaction?

I am curious about using Mathematica for modelling chemical reactions but don't really know much about the Mathematica software yet. So I was reading this page at wolfram.com which explains some of ...
6
votes
1answer
131 views

Calculate the ESP Grid based on Density Grid

I want to build a fast way to convert a density grid file into a grid file of the respective electrostatic potential (ESP; also known as MEP, the molecular electrostatic potential). This ...
1
vote
2answers
101 views

How Do i Extract Only The Coordinates xyz (Number) From This Log file

this Log contains the information of all coordinates of many atoms in a molecular dynamics simulation for a long sequence of time steps, along with some extra information other than the coordinates. ...
-4
votes
2answers
132 views

How do I write a function that returns the atomic mass given an element's symbol?

I want to write a function atomMass that, given an element's symbol, say "He", returns the atomic mass for the element (in this case ~ 4.0026). I do not even know where to start with this question. ...
3
votes
2answers
118 views

How to Import This XYZ format file

Here is the .XYZ format file NP3D.XYZ Somehow i cannot import this file.It return an error box :- "Cannot Import Data As XYZ Format." it contains 1000 snapshot of 10 Carbon particles coordinate ...
5
votes
2answers
142 views

How to refer to amino acids by their single-letter abbreviations in ChemicalData[]?

ChemicalData["AminoAcids"] returns the 20 amino acids. There are some properties available, like the molar mass: ...
4
votes
2answers
261 views

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

How can I get the solubility value of nitrogen in water at 10 °C with Mathematica? The site engineering toolbox dot com gives graphs of such values, but I want the numerical value. Related thread ...
9
votes
3answers
456 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. ...
10
votes
2answers
793 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
2answers
70 views

ChemicalData[] error: “L-Cysteine” is not a known entity, class,

If I execute: ChemicalData["L-Cysteine", "MolarMass"] I get the following error: ChemicalData::notent: "L-Cysteine" is not a known entity, class, or tag for ...
-1
votes
1answer
93 views

Double integrals in quantum chemistry [closed]

In quantum chemistry we often encounter integrals like this: I can't understand what is the problem. Can anybody help me?
10
votes
3answers
408 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: ...
2
votes
1answer
80 views

Change bond cutoff distance when plotting .xyz files

When plotting a molecule from a xyz data file, Mathematica automatically adds the bonds between the atoms. But in my case it adds too many bonds, not only between nearest neighbours but also between ...
1
vote
1answer
187 views

Raman spectra collected at over 200 spatial points and in separate text files, how can I collate and visualize the data?

I need to do density plot and contour plot of Raman spectra with a specific peak, Raman mode, as a way to study the intensity distribution of such peak throughout the sample used. As such ...
17
votes
1answer
710 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
2answers
245 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 ...
2
votes
1answer
78 views

Can't obtain Real results using NSolve

I am trying to find the critical properties of the Carnahan-Starling equation of state, $$p=\rho R T\frac{1+b\rho /4+(b\rho/4)^2-(b\rho/4)^3}{(1-b\rho /4)^3}-a\rho^2$$ using this system of equations, ...
3
votes
1answer
119 views

Adding text on an .xyz file of an atom

I know it is possible to view .xyz files of coordinates in Mathematica. I tried to write some text on a specific atom using Text, but I was not successful. How can i do that? Thanks for the help in ...
6
votes
3answers
135 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 ...
6
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 ...
1
vote
0answers
57 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: ...
20
votes
4answers
2k 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 ...
2
votes
1answer
54 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: ...
37
votes
4answers
4k 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 ...
5
votes
2answers
144 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}]] ...
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
1answer
204 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. ...
2
votes
1answer
72 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 ...
1
vote
1answer
277 views
8
votes
1answer
833 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? ...
4
votes
1answer
171 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
343 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, ...
4
votes
2answers
194 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 ...
9
votes
2answers
314 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? ...
15
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
162 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 ...
12
votes
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 ...
6
votes
1answer
208 views
5
votes
2answers
174 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 ...
6
votes
1answer
437 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 ...