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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5
votes
1answer
54 views

FindMoleculeSubstructure fails on SMARTS MoleculePattern, but MoleculePlot is OK?

Background Info: SMARTS is a convention for specifying molecular patterns. It is supported by Mathematica 12's MoleculePattern function. Problem Setup: Consider ...
2
votes
0answers
50 views

PubChem Service doesn't support isomeric SMILES specifications?

Consider the molecule defined by the following SMILES string: example = "C(/C=C/Cl)Cl" (the slashes indicate cis/trans isomerism). Molecule[] has no problem ...
2
votes
1answer
27 views

SDF Metadata Import fails when structure information is missing

Background Information: In Mathematica 12, SDF Import automatically triggers the generation of Molecule[] representations. SDF files contain both structural information as well as metadata, and a ...
1
vote
0answers
34 views

PubChem service doesn't support looking up compounds given an assay ID?

Mathematica's PubChem Service Connection has many requests that return the properties of a compound (or substance). It also provides requests that return all the assays for which a given compound (or ...
2
votes
1answer
84 views

How do I use Solve with conditional equations?

Short version: How do I have Solve handle a system of equations where some of the equations may be conditional? Simplified Problem: I am solving the following system of equations: a * b = 10^-14 b^...
7
votes
2answers
103 views

How can I prevent Molecule from adding hydrogens automatically?

Consider the following: cacl = Molecule[{Atom["Ca"], Atom["Cl"]}, {Bond[{1, 2}, "Single"]}]; MoleculeValue[cacl, "CanonicalSMILES"] (* Cl[CaH] *) Notice the ...
4
votes
2answers
85 views

Possible error in IsotopeData

I found 2 isotopes in Wolfram database which are marked as unstable, but their lifetime is indicated as infinite (germanium-76 and selenium-82). The following chunck of code illustrates the issue: <...
11
votes
3answers
555 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
1answer
53 views

Inconsistent sign changes in Molecule[] AtomDiagramCoordinates property and MoleculePlot[]

I'm trying to resolve a problem with the new Molecule[] functionality in Mathematica 12. The "AtomDiagramCoordinates" property returns 2D coordinates of the molecular graph. These coordinates can be ...
15
votes
3answers
291 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[], ...
7
votes
3answers
557 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: ...
6
votes
1answer
76 views
15
votes
1answer
665 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 ...
10
votes
3answers
582 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? ...
0
votes
0answers
79 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-...
5
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, <...
4
votes
2answers
677 views

RefProp in Mathematica

RefProp by NIST is a program that calculates the thermodynamic properties of fluids. I need to call certain RefProp functions ...
17
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4answers
775 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 ...
13
votes
1answer
840 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 ...
3
votes
1answer
94 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 ...
6
votes
1answer
246 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 ...
9
votes
3answers
390 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 ...
0
votes
1answer
65 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
729 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. ...
1
vote
0answers
65 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?
4
votes
2answers
148 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 ...
5
votes
1answer
156 views

Get Isotope Data and Electron Mass in Same Units - kg and Kilograms

I'm trying to find the nuclear mass of $^{238}\text{U}$. To do this, I subtract the electron mass from the atomic mass. I'd like to find the final answer in kilograms. I'd also like to use Mathematica'...
4
votes
2answers
316 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.
5
votes
1answer
458 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. ...
2
votes
1answer
60 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
75 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
504 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: ...
1
vote
1answer
339 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
0answers
83 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 ...
7
votes
1answer
149 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 ...
5
votes
1answer
95 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 ...
1
vote
2answers
224 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 ...
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 ...
0
votes
0answers
76 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
408 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
0answers
81 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 (...
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/...
4
votes
1answer
459 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
131 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. <...
30
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 ...
0
votes
2answers
378 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\...
7
votes
1answer
142 views

Identify chemical expressions

Background I written a chemical equation balancing program. ...
1
vote
2answers
323 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
172 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 ...
6
votes
2answers
259 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/...