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.

learn more… | top users | synonyms

-1
votes
1answer
72 views

Problem with a chemical optimization problem [on hold]

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
74 views

Parsing/validating CAS registry number identifiers

Mathematica includes a lot of curated information on molecular structure and properties available through ChemicalData and ...
0
votes
0answers
64 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
67 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/...
14
votes
2answers
670 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 ...
16
votes
2answers
836 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 ...
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
545 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 ...
3
votes
1answer
138 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 ...
1
vote
2answers
111 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 ...
1
vote
2answers
103 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. ...
3
votes
2answers
128 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
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 ...
5
votes
2answers
150 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: ...
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 ...
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 ...
-1
votes
1answer
96 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
457 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
83 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
188 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 ...
6
votes
2answers
249 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 ...
-4
votes
2answers
136 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. ...
2
votes
1answer
83 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
120 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 ...
1
vote
0answers
61 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: ...
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: ...
4
votes
4answers
259 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, ...
1
vote
1answer
205 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. ...
1
vote
1answer
287 views

Van der Waals Isotherms [closed]

I have the following code: ...
4
votes
1answer
176 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
399 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, <...
5
votes
2answers
145 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
202 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 $n\...
4
votes
2answers
263 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 ...
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 ...
2
votes
1answer
164 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 (say,...
9
votes
3answers
467 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. ...
8
votes
1answer
873 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? ...
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 ...
7
votes
1answer
457 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/...
9
votes
2answers
317 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? ...
4
votes
0answers
74 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
145 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 ...
4
votes
2answers
101 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 ...
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
502 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 ...
6
votes
2answers
249 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 ...
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 ...
7
votes
1answer
97 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 ...