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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1answer
54 views

How to plot a thermodynamic cycle?

I try to plot a thermodynamic cycle with the data displayed using the tool, "Piecewise", but in the case of isochoric and isobaric processes, Mathematica shows nothing. Could someone please tell me ...
3
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1answer
86 views

Solve a system of three stiff ODEs and plot graphs of it - Oregonator

I want to plot a system of three stiff ODEs (Oregonator model). That model describes a chemical oscillator. I do not have much experience with plotting ODEs, but I have obtained a Mathematica file ...
3
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0answers
67 views

Right or wrong answer obtained when using two ways to represent the same number [closed]

Using Mathematica 10.1 Depending on whether I write a numerical constant as 0.6 * 10^-15, or 6 * 10^-16, I get very different ...
2
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1answer
45 views

What algorithm(s) are used by MoleculeModify's GenerateConformers?

Starting with Mathematica 12, the MoleculeModify function has a "GenerateConformers" option. What is the algorithm used to ...
2
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0answers
32 views

OscillatorStrength[Helium] and OscillatorStrength[Rubidium] do not return results

I am new to working with the Resonance Absorption Lines Pacgage << ResonanceAbsorptionLines` and trying to write code using the OscillatorStrength command. ...
1
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1answer
57 views

Can Mathematica interpret Condensed formula?

Im trying to Create a molecule using a condensed formula as input.I tried some other condensed formulas but it always get an unevaluated Result: ...
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1answer
48 views

LibraryFunctionLoad with Cool Prop documentation

I use the following command ...
2
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1answer
36 views

Plot colored spectral lines using spectral line data?

Suppose I've retrieved spectral line data for an element, as so: hydrogenSpectralLines =SpectralLineData[EntityClass["AtomicLine", {"Hydrogen", 1}]]; From that, ...
1
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0answers
19 views

Fitting Experimental Data To SRK-Type Equation of State. Minimization

I'm trying to find parameters to fit an EoS to saturation pressures to different temperatures. My experimental data are like this ...
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0answers
25 views

is it possible to calculate the HOMO, LUMO and charge distribution of a molecule after minimising it in Mathematica?

I want to calculate HOMO (highest occupied molecular orbitals), LUMO (lowest unoccupied molecular orbitals) charge distribution of a molecule, How ca I do it in Mathematica? Thank you in advance..
10
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1answer
254 views

What's the principle behind the new MoleculeRecognize function?

I played a bit with the new MoleculeRecognize function implemented in the newly released WM 12.1: which simply recognizes a molecule in image and returns it as a Molecule object. ...
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0answers
36 views

Translating standard form of EOS to its polynomial form

Is there a standard form for an equation like the others such as PR/SRK/... . Z = (v - a b) / (v - b) - a / ((RT^1.5) (v + 2.6382 b)) for predicting pure ...
3
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1answer
78 views

Which argument of MoleculeValue returns the SAS?

UPDATE The question was asked when version 12.0 was the current version. But version 12.1 of Mathematica includes the synthetic accessibility score! ...
3
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2answers
79 views

How can I highlight a single atom in MoleculePlot?

Consider the following molecule: mol1 = Molecule["O=C(N(CC(NCC(F)(F)F)=O)CN1C2=CC=CC=C2)C31CCN(C(C4=CC(C=NN5)=C5C=C4)=O)CC3"]; In ...
5
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1answer
57 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
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0answers
65 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
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1answer
35 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 ...
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0answers
37 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 ...
5
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1answer
64 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 ...
7
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2answers
116 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 ...
8
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1answer
91 views

Are the lists from “BondList” and EdgeList for a molecule guaranteed to be aligned?

Consider the following: ...
15
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3answers
336 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[], ...
4
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2answers
89 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: <...
2
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1answer
96 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
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2answers
160 views

Visualizing only the chain of a protein and color each residue in Mathematica

Is there a way to visualize in cartoon a single chain of a protein using ProteinData and color the residues by its chemical properties e.g. hydrophobicity, acidic ...
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0answers
94 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-...
19
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4answers
834 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 ...
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1answer
98 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 ...
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1answer
68 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
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1answer
286 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
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3answers
646 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
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2answers
167 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
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3answers
405 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
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0answers
76 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
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1answer
896 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
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2answers
343 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
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1answer
62 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
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1answer
77 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
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3answers
539 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
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1answer
156 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 ...
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0answers
89 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
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1answer
100 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 ...
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0answers
90 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
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2answers
410 views

ChemistryData — where is specific gravity?

I cannot seem to find the basic chemical property specific gravity with ChemicalData or other comparable functions.
1
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2answers
275 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
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0answers
107 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
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1answer
811 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
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3answers
561 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
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1answer
509 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
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2answers
137 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. <...