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
2answers
106 views

Accessing chemical property data for specific conditions?

There is a wealth of data for various chemicals available through Mathematica. For instance: ...
4
votes
1answer
205 views

PDB Graphics Options: Opacity and Scale to superimpose on 3D point plot

I am trying to superimpose a pdb file into a 3D plot of points extracted from the pdb model, while making the pdb somewhat transparent for easy viewing of plotted points. My problems are as follows. ...
14
votes
1answer
503 views

Gillespie Stochastic Simulation Algorithm

The Gillespie SSA is a Monte Carlo stochastic simulation algorithm to find the trajectory a dynamic system described by a reaction (or interaction) network, e.g. chemical reactions or ecological ...
7
votes
3answers
132 views

How can I draw ternary plot by these data?

I have these data and want to draw similar fifures in mathematica. any one can help me? ...
-1
votes
1answer
89 views

Problem with a chemical optimization problem [closed]

First of all, I want to say that I'm quite new to Mathematica. I searched a lot on this site to learn how to solve my problem, which this is the problem of my life! I want to minimize a function. It ...
2
votes
3answers
79 views

Parsing/validating CAS registry number identifiers

Mathematica includes a lot of curated information on molecular structure and properties available through ChemicalData and ...
14
votes
2answers
675 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 ...
0
votes
0answers
67 views

Nonlinear coupled equation (heat equation with source term)

I modeled simple chemical reaction-diffusion equation in spherical region $0\le r\le L$ $${\partial T\over\partial t}={{1\over r^2}{\partial\over \partial r}(r^2{\partial T\over \partial r})+qACexp(-...
4
votes
1answer
70 views

Atom weight in SI units

In chemistry is very common to use the units grams/mol for the atomic weigth, so the mass of one atom (of Tin, for example) is calculated as : massOfOneAtom = (0.11871 (Kg/mol))/(AvogadroConstant (1/...
6
votes
2answers
261 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
853 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
114 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
102 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
1answer
417 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
552 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
262 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
69 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
145 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
137 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
107 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
137 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
137 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
156 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
268 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
479 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
815 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 ...
6
votes
2answers
73 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
104 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
468 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/...
2
votes
1answer
87 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
192 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
715 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
255 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
85 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
121 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
136 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
64 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
148 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
208 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
73 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
298 views
8
votes
1answer
907 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
177 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
419 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, <...