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.
146
questions
6
votes
1answer
71 views
Are the lists from “BondList” and EdgeList for a molecule guaranteed to be aligned?
Consider the following:
...
14
votes
3answers
224 views
Computing the surface area and volume of molecules
Here is a somewhat difficult problem I've had for a long while.
Space-filling models of molecules can be easily generated by ChemicalData[], ...
0
votes
0answers
73 views
How to plot and simulate reaction networks in Mathematica?
I am trying to simulate reaction networks like it's done in the Simulation methods
in this paper. They used Xcellerator, so I after installing on Mathmatica 11.2 and trying to run their Belousov-...
17
votes
4answers
733 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 ...
3
votes
1answer
88 views
Producing MoleculePlots of pigments
Of course no chemical database is complete, but I would like to create as large a list of MoleculePlots of pigments (organic or inorganic) as is available through ...
0
votes
1answer
59 views
How do I obtain the characteristics and properties of an alloy? [closed]
I would like to obtain the characteristics and properties of the Alloy Chromel. How do I download that information from the database of Wolfram Alpha and then print it in a Mathematica Notebook?
...
6
votes
1answer
197 views
Maxwell construction problem with FindRoot
A Maxwell construction is just an integral of area and then solving for a root to find vapor pressure.
This must be exactly the same value as where the Gibbs energy plot crosses at a point. I found ...
11
votes
3answers
470 views
Minimum energy path of a potential energy surface
I have calculated the energies of a molecule by varying two parameters (Data points are here data). I want to find the minimum energy path from the point (180.0, 179.99, 21.132) to (124.5, 124.49, 0) ...
4
votes
2answers
126 views
Is it possible to use chemical data in polymers?
I would like to plot the ABS polymer.
It is made of Styrene, Acrylonitrile and 1,3 Butadine.
I can plot those components separately
But the command
...
9
votes
3answers
377 views
Chemical data of Lactic acid [duplicate]
I'm using the next Mathematica command in order to plot molecules:
ChemicalData["name", "MoleculePlot"]
But I'm not sure if the Mathematica database of molecules ...
1
vote
0answers
59 views
ProteinData Error: “Cannot import data as PDB format” [closed]
I'm trying to use the Mathematica examples for plotting proteins:
But when I type the command I get the next error:
How can I import data as PDB format?
13
votes
1answer
747 views
visualizing a normal mode vibration of a molecule in mathematica
How can I visualize the normal mode vibrations of a molecule in Mathematica?
Something like the following GIF:
(from here)
I have the XYZ file of the benzene molecule and the normal mode ...
4
votes
2answers
271 views
Periodic table with color code
Is it possible to do this table (from here) in Mathematica?
In this table, the color code indicates the element’s dipolar character $(~ m\mu_m^2)$ in atomic units.
2
votes
1answer
59 views
Visualizing a imported XYZ-file and graphic object at same time
I want visualize a imported xyz-file and a graphic object at same time.
g = Import["H2O.xyz", "XYZ"];
Show[g, Graphics3D[{Opacity[0.5], Sphere[]}]]
But this ...
2
votes
1answer
67 views
Convert a Java object to interface via J/Link
I'm trying to use a Java library called CDK with Mathematica's J/Link.
...
10
votes
3answers
465 views
DFT for Helium atom
I'm trying to solve this problem
I'm not a Mathematica expert, but my program works perfect when
vhartree={0,0,..,0}
This is the program I wrote:
...
7
votes
1answer
145 views
Suggestions to increase the speed of a fugacity calculation
I'm writing code to simulate a chemical reaction. This requires the calculation of the fugacity of a mixture of gases. The underlying model is the SRK equation of state.
First the physical ...
1
vote
0answers
78 views
How can i set up an If or Do loop to follow this calculation procedure?
The following picture depicts the calculation procedure I wish to set up.
The inputs are $T_r$, the chemical composition of the feedstock and constraints defined by the equivalence ratio.
This ...
5
votes
1answer
92 views
WolframAlpha function does not return structure diagram for chemicals
Neither one of
WolframAlpha["Caffeine"]
WolframAlpha["Caffeine","FullOutput"]
returns a structure diagram for the molecule. It's consistent since ...
0
votes
0answers
68 views
Encountering error messages with both DSolve and NDSolve
Reposting my question in a more legible and understandable way. The earlier one was flouting a few too many posting guidelines.
I am trying to solve the heat conduction partial differential equation, ...
8
votes
2answers
404 views
ChemistryData — where is specific gravity?
I cannot seem to find the basic chemical property specific gravity with ChemicalData or other comparable functions.
1
vote
2answers
179 views
Assign a unit to a variable in a function
I have the following input:
PVW[V_, T_] := (R*T/(V - b)) - (a/(V^2))
Where I have already defined R as the molecular gas constant with its corresponding units ...
1
vote
0answers
65 views
Dealing with Vector Outputs from ItoProcess, RandomProcess (Stochastic Differential Equations)
I'm modeling stochastic chemical kinetics and the ItoProcess[] function has served me well. I am trying to write an efficient code to analyze many (Paths) trajectories of several different reagents (...
6
votes
1answer
621 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
553 views
ChemicalData returns the correct result for “Sulfuric” but an empty list for “Sulfuric Acid”. Why?
I am new to this site so I hope my question is valid.
My code is:
...
4
votes
1answer
402 views
Map volumetric data onto an isosurface
this question originates from an attempt to visualize molecular electrostatic potentials, but hopefully should be of general interest.
Suppose that you have two sets of data, S1 and S2. Each set ...
5
votes
2answers
126 views
Delete duplicates of isomerism
I written some code to generate all partens of $\ \mathrm{C_2H_5O}$, but theres some isomerisms need to be deleted.
Here's the raw output after DeleteDuplicates.
<...
7
votes
1answer
133 views
1
vote
2answers
288 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.
5
votes
1answer
166 views
Michaelis–Menten kinetics using Tau-Leaping
I am trying to implement Michaelis–Menten kinetics using Tau-Leaping. It works fine as expected. Only issue here is when substrate reaches zero the algorithm stop since PoissonDistribution[0] gives ...
8
votes
1answer
248 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 ...
2
votes
2answers
391 views
Solve for several constants using a set of initial conditions
I have a set of differential equations that I am trying to solve for chemical reaction rate constants. So far I can get DSolve to solve the ODEs with initial conditions which provides the chemical ...
0
votes
2answers
340 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\...
0
votes
2answers
108 views
Solving Catalyst/Enzyme Diffusion Equation
Evening all,
I am attempting to solve a second order differential equation to get an equation of the substrate concentration as a function of r (i.e. S(r)). I have developed this equation, $\frac{d^...
8
votes
3answers
878 views
Why are Dalton and Grams / Moles not equivalent units?
The following code throws an error:
UnitConvert[Quantity["Daltons"], "Grams"/"Moles"]
Why?
2
votes
1answer
131 views
How to use FindFit to do kinetic simulation?
I'd like to simulate the chemical kinetic model by fitting the experimental data. Here are my codes for simulation.
...
5
votes
0answers
75 views
Helping Mandy become a better speller [duplicate]
tl;dr Can you improve upon this code, which checks to see if a word can be spelled using the element symbols from the periodic table?
I recently created a periodic table that lights up. The design ...
2
votes
2answers
111 views
Question about getting the table behind ElementData
I am interested in retrieving the entire table (preferably in text or csv format) that is behind the ElementData function for ALL the elements. The table (or perhaps multiple tables) record(s) many ...
1
vote
2answers
100 views
How can I add new columns to a Table after each evaluation?
I'm interested in simulating chemical reactions with perturbations. I can simulate a given reaction using NDSolve ("rxn"} with a given added noise component ("noise1"). Due to the noise, each ...
9
votes
2answers
316 views
Plot polygonal surface
I have a list of 120 elements of the form $\{q,x,y,z\}$. In fact, each element of the represents the nuclear charge and 3 coordinates of an atom of some large molecule.
...
15
votes
3answers
717 views
Proteins, ProteinData, WolframAlpha
Apologies in advance, this is the first I've messed with ProteinData and access through WolframAlpha, so clearly I may not know ...
1
vote
2answers
3k views
How to plot Compressibility factor Z vs Pressure P using ParametricPlot?
I am trying to get my plot to look like this:
but I cannot seem to get it right when I try to plot each curve as a parametric equation. Here is what I have been trying:
...
1
vote
0answers
126 views
DNA Modeling In Three Dimensions? [closed]
I can find any number of base pair nucleotide sequences for any number of genes in the fasta format. (Check out the COSMIC Tumor Database, for example). I'm having trouble finding base pair nucleotide ...
2
votes
1answer
337 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 ...
6
votes
1answer
416 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 ...
3
votes
1answer
129 views
How do I get the MeanPredictionBands from the fitting of the numerical solution of coupled differential equations to data?
This is my first post, and I will preface my question by stating that I am relatively new to Mathematica.
In any case, I would like to fit the solution of chemical kinetics equations to data and get ...
2
votes
0answers
57 views
Another question on Mma data sources/syntax
Let's say I want to have the vapor pressure of mercury, as a function of temperature. I know that this information is available, for any specific temperature, from Wolfram Alpha, and I can also get ...
2
votes
1answer
169 views
How can I plot all solutions for a system of equations across a given domain for a selected variable?
I have a coupled chemical equilibria system consisting of 12 equations in 12 unknowns. I have managed use the Solve function to write a command that will find a particular solution at any fixed value ...
1
vote
0answers
78 views
Representing vertices as spheres in Graphics 3D [closed]
I'm representing a portion of molecule, P3HT, in Mathematica as a pentagon that I build using Polygon and Graphics3D.
I would like to represent the vertices of the pentagon as spheres(corresponding ...
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 ...
