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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.

4
votes
2answers
103 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 ...
8
votes
2answers
316 views

Chemical data of Lactic acid

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 ...
12
votes
1answer
530 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 gif shown in the following link.benzene b_2u vibrational mode. I have the XYZ fileben-xyz-file of the ...
4
votes
2answers
199 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
53 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
51 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
346 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
136 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
70 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
79 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
54 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
400 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
122 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
43 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 (...
5
votes
1answer
400 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. ...
4
votes
1answer
283 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
120 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
119 views

Identify chemical expressions

Background I written a chemical equation balancing program. ...
1
vote
2answers
197 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
144 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
214 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
268 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
281 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
99 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
662 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
113 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
73 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
92 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
93 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
301 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
684 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
2k 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
114 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
300 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
328 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
111 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
52 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
141 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
71 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 ...
-1
votes
1answer
137 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 ...
7
votes
3answers
401 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? ...
2
votes
3answers
123 views

Parsing/validating CAS registry number identifiers

Mathematica includes a lot of curated information on molecular structure and properties available through ChemicalData and ...
6
votes
2answers
198 views

Atom weight in SI units

In chemistry is very common to use the units grams/mol for the atomic weight, so the mass of one atom (of Tin, for example) is calculated as : massOfOneAtom = (0.11871 (Kg/mol))/(AvogadroConstant (1/...
14
votes
2answers
1k 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 ...
23
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 ...
8
votes
5answers
900 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
630 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
254 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
217 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. ...