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.

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44
votes
4answers
12k 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 ...
29
votes
5answers
4k 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 ...
6
votes
1answer
951 views

How to transform and combine multiple Graphics3D into one?

ProteinData["A2M", "MoleculePlot"] gives you a Graphics3D object below. I'd like to display multiple of these proteins in a ...
5
votes
5answers
1k views

Problems with NDSolve and stiffness

I am trying to solve an ODE in chemical kinetics: $$\begin{align*} \frac{\mathrm d[x]}{\mathrm dt} &= -k_1 [x][y]\\ \frac{\mathrm d[y]}{\mathrm dt} &= k_1 [x][y] - k_3[y] \end{align*}$$ My ...
23
votes
1answer
2k views

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 ...
17
votes
4answers
740 views

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 ...
20
votes
4answers
2k 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 ...
31
votes
1answer
639 views

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: ...
24
votes
3answers
2k 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 ...
15
votes
4answers
4k 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 ...
15
votes
1answer
563 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 ...
10
votes
2answers
1k 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 ...
8
votes
1answer
2k 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
2k 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 ...
17
votes
1answer
3k 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 ...
9
votes
3answers
776 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. ...
5
votes
3answers
970 views

How to fit parameters in a system of coupled differential equations

Problem description: I'm studying a chemical reaction that can be modeled by a system of coupled differential equations, and I want to use measured data to determine the parameters that appear in the ...
4
votes
3answers
2k 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, <...
2
votes
0answers
624 views

Generating a function which outputs possible chemical reactions

I want to make a list of chemical reactions and I write them down in a $\require{mhchem}\LaTeX$ format. They are of the following form $$NA_n^i+MB_m^j \rightarrow \hat NA_{\hat n}^{\hat i}+\hat MA_{\...
2
votes
1answer
340 views

Connectivity in a molecule and permutations

What am I trying to do is to make a script that calculates all chemically reasonable torsion angles in any molecule. For one torsional angle I need 4 CONNECTED atoms, 1-2-3-4, 1-2-3 defining one ...
8
votes
1answer
250 views

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 ...
15
votes
1answer
654 views

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 ...
6
votes
1answer
797 views

Building a molecule viewer: aesthetic rotations

I am working on building a molecule viewer in Mathematica and am running in to problems with controlling rotation of the molecule (which is rendered as a Graphics3D...
6
votes
3answers
640 views

When using NDsolve, how to determine the positions of steady states?

I am currently trying to numerically solve a set of ordinary differential equations of chemical kinetics. However, I want to implement perturbations only when system reach steady states. For example ...
7
votes
3answers
486 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? ...
12
votes
3answers
2k 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/...
6
votes
2answers
354 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 ...
6
votes
1answer
634 views

Radial distribution function (pair correlation function) for particles in rectangular image

Some time ago I asked the following question on how to calculate the radial distribution function. I have here an add-on question, but before asking it I try to summarize and visualize my problem. ...
7
votes
3answers
225 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 ...
7
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 ...
5
votes
2answers
399 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: ...
3
votes
1answer
956 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
1answer
424 views

Chemical Kinetics: fitting multiple sets of time series data using multiple differential reaction equations

Let me start by saying that this is my first post, so if there are suggestions on proper formatting that is annoying you, please let fly and I will do my best to modify. I was doing well solving the ...
5
votes
2answers
300 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 ...
3
votes
1answer
227 views

Fails to apply NonlinearModelFit on a numerically evaluated model defined as a system of ODEs

I call for your help with because I'm getting troubles to fit a model defined through a system of ODEs. The system of ODEs is as follows: ...
2
votes
1answer
728 views

Finding 111 plane of Carbon Diamond

All, I looked at the example on the Mathematica Website with the Carbon Diamond Lattice. Example I am referring to I am wondering is there a way to highlight an individual plane such as the 111 or ...
2
votes
1answer
234 views

Solving ODES in order to find unknown constants

I am trying to solve a set of ODES which represent a second order consecutive chemical reaction. ...
1
vote
2answers
294 views

Visualizing .xyz file in Mathematica

If i import a .xyz file in Mathematica that will show me the moelcule in the default way. But i want to visualise the .xyz file in the following manner.
1
vote
2answers
310 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 ...
0
votes
2answers
348 views

Michaelis–Menten kinetics using Gillespie Algorithm

I am trying to implement Michaelis–Menten kinetics using Gillespie Algorithm. $$\text{Reaction 1:}\quad E+S\rightarrow C$$ $$\text{Reaction 2:}\quad C\rightarrow E+S$$ $$\text{Reaction 1:}\quad C\...