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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3
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1answer
106 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 ...
5
votes
1answer
126 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
95 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
110 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
137 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
251 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 ...
8
votes
3answers
443 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
775 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
66 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 ...
3
votes
0answers
31 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 ...
-1
votes
1answer
89 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
374 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
70 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
166 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
704 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
238 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
76 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
118 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
134 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
54 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
53 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
191 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, ...
36
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
142 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
199 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
250 views
8
votes
1answer
779 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
168 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
311 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
182 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
307 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 ...
1
vote
1answer
201 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". ...
2
votes
1answer
154 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
205 views
3
votes
1answer
152 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 ...
5
votes
2answers
173 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
420 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 ...
4
votes
0answers
70 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
140 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
81 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 ...
20
votes
4answers
968 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 ...
2
votes
1answer
474 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 ...
2
votes
1answer
124 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 ...