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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2
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1answer
44 views

Substituting Atoms in .XYZ File

I have a crystal structure in which I'd like to randomize the placement of cations from an initial structure. I have a .xyz file (given here https://pastebin.com/d5UcNr2h) which gives atomic ...
0
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0answers
39 views

2d list contour plot

I have plotted a ListContour plot with a large set of data i have and most of the points do not seem to have a distinguised colour, i.e, the color function needs to be re-scaled for my data. How can i ...
0
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2answers
54 views

Contour plot a 2d array

I have the calculated data for an interaction potential. My variables are distances (48 values) and angles(15 values) and my energy data is a 2d matrix of 48 x 15 values. How do i plot the energy as a ...
2
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1answer
72 views

How to determine the frequency of oscillations in system of three ODEs?

I want to determine the frequency of oscillations in a system of three stiff ODEs (Oregonator model). That model describes a chemical oscillator. I have a slightly more advanced model of the default ...
1
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1answer
25 views

Exporting to PDB seems to lose aromaticity

I have a molecule with the following SMILES: ClearAll[sml]; sml = "O=C(NCC1=CC(NC(C2=CN=C3C=CC=CN23)=O)=C(C)C=C1)NC4=CC=CC(F)=C4"; The plot looks as ...
4
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2answers
127 views

Symmetry unique atom coordinates

One thing I love about Mathematica is how easily I can go from the name of a molecule to estimated coordinates of its atoms, with a command like ...
6
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3answers
314 views

How can I get material property data past what's provided via ElementData[], ChemicalData[], etc.?

Background Let's say I want information (e.g. bulk modulus or space group) on an element or chemical compound that isn't available via e.g. ElementData[], ...
2
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1answer
68 views

How do I make a general solver for a system of equations (e.g. thermodynamic processes) with different inputs and outputs?

Background Let's say I have a system of equations (e.g. thermodynamics equations), where the "knowns" and "unknowns" are subject to change, and the system of equations can also ...
18
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1answer
4k 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 ...
5
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1answer
211 views

Building large chemical models such as VANTAblack

I would like to build a (large) molecular model of the nanotubes that make up VANTAblack, which consists of a sheet of hexagonally connected carbon atoms all rolled into a (teeny) tube. I can easily ...
1
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0answers
54 views

Are atom coordinates in Molecules the real equilibrium positions or simple heuristic guesses? [duplicate]

If I do, for example, Export["~/Downloads/tnt.xyz", Molecule["TNT"]] I get a nice set of coordinates for atoms within a molecule of the ...
0
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0answers
40 views

Can I get atomization energy of a chemical?

A pretty basic property of a chemical is the atomization energy. Another similar property is the heat of formation. I'm looking at ...
8
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2answers
233 views

When looking at a chemical's bond lengths, which bonds do they represent?

Looking at, for example, the bond lengths of styrene: ...
2
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1answer
101 views

PubChem Service doesn't support isomeric SMILES specifications?

Update 04 Sept 2020: The problem described below occurs in Mathematica 12.0. It has been fixed in Mathematica 12.1, so that ServiceExecute returns the correct ...
2
votes
1answer
49 views

SDF Metadata Import fails when structure information is missing

UPDATE 04 Sept 2020: This behavior been fixed in Mathematica 12.1. Background Information: In Mathematica 12.0, SDF Import automatically triggers the generation of Molecule[] representations. SDF ...
3
votes
1answer
93 views

Graph3D - replace vertices with MoleculePlot3D

How can we replace the vertices in a 3-dim graph with individual Graphics3D objects? In my concrete case I want to visualize a chemical network and replace vertices ...
0
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0answers
82 views

Error in Monte Carlo simulation. Now Random walk (dotted curve) doesn't fit to the analytical curve (dashed curve)

I've been trying to code a kinetic monte carlo simulation for a system of consecutive chemical reactions using a fixed (repaired) code that the user flinty gives me in the last questions I post: ...
-1
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1answer
55 views

solving an equation by suggested method [closed]

I have an equation I want to do this issue: T(dV/dT)-V=0 and obtain T that satisfy this relation. How can I do it? we should at first obtain V and then Drivate it. How can?
1
vote
1answer
81 views

Strange error not found in a monte carlo code, Infinite expression 1/0 encountered

I've been trying to code a kinetic monte carlo simulation for a dimerization reaction, 2M ---> D. However I have a kinetic Monte Carlo code for a first order decomposition reaction of AIBN (that's ...
3
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1answer
128 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 ...
7
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1answer
1k views

How can I efficiently write formatted data to a Gaussian Cube file?

I am working with data files that contain information about electronic wave functions. The data format is specified by the quantum chemistry program Gaussian. I need to import the data, manipulate ...
1
vote
1answer
65 views

How to plot a thermodynamic cycle? [duplicate]

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 ...
8
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1answer
92 views
9
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6answers
1k 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 ...
7
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2answers
176 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 ...
3
votes
0answers
68 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 ...
4
votes
1answer
74 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
37 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
64 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: ...
8
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2answers
239 views

SpaceFillingMolecularPlot using CAS number of a compound

When I tried to get 3D graphics for the molecule with CAS number 52364-73-5 using Mathematica 10, it produced the following result: ...
3
votes
1answer
46 views

Plot colored spectral lines using spectral line data? [duplicate]

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
20 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 ...
0
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0answers
32 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
votes
1answer
282 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. ...
3
votes
1answer
86 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! ...
9
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1answer
3k 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 ...
1
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0answers
38 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 ...
7
votes
1answer
195 views

Identify chemical expressions

Background I written a chemical equation balancing program. ...
3
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2answers
86 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
votes
1answer
67 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 ...
1
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0answers
57 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
103 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
128 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
91 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
721 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) ...
5
votes
1answer
69 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
384 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
565 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: ...
15
votes
1answer
677 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 ...