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.

Mathematica is a useful tool for analyzing chemical data, understanding chemical processes and visualizing chemical species.

The curated datasets ChemicalData, ElementData and IsotopeData have lots of useful information that some users want to access while not online and others want to display in graphical format. Graphical visualization of chemical systems such as finding lattice planes of solid state structures or merely viewing them appropriately are appropriate for this tag.

Mathematica can read a variety of molecular formats, although some require a bit of spelunking to use properly.

Also, although this particular question is not tagged with Chemistry, it demonstrates how one can explore the kinetics of fairly complex reactions using Mathematica.

273 questions
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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 artificial insertion of the hydrogen atom to fill the valency of the calcium atom. I…
Shredderroy
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Orientation of the molecules in MoleculePlot

Why the plot of the molecules with similar structures is not in the same orientation? Row@{MoleculePlot@Molecule@"N1(c2c(Sc3c1cccc3)cccc2)CCCN(C)C",MoleculePlot@Molecule@"C\\1(/c2c(Sc3c1cccc3)ccc(c2)Cl)=C\\CCN(C)C"} Is it possible to force…
6
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Chemistry context in Mathematica 13

Version: 13.0.1 on Linux Hello, I am curious about the Chemistry` context in Mathematica. I noticed some new things; however, there doesn't seem to be documentation on them. I wonder if anyone here has tried some of these things, or if there is a…
bhopshang
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How can I get the solubility value of nitrogen in water at 10 degrees Celsius with Mathematica?

How can I get the solubility value of nitrogen in water at 10 °C with Mathematica? The site engineering toolbox dot com gives graphs of such values, but I want the numerical value. Related thread on chemistry.SE
Mats Granvik
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4
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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! MoleculeValue[mol, "SyntheticAccessibilityScore"] A big thank you to @Jason B. for such prompt…
Shredderroy
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4
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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 AtomList[mol1], the first atom is an oxygen. According to the documentation of MoleculePattern, one of the formats of…
Shredderroy
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4
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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 the capabilities of Mathematica. The page explains…
user100487
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Does MoleculeValue use a non-standard definition of bridgehead atoms?

According to many sources (e.g., this), there should be four bridgehead atoms in phenanthrene. But MoleculeValue returns an empty list. "phenanthrene" // (Molecule /* {MoleculeValue[#, "BridgeheadAtoms"] &, MoleculePlot} /* Through /* Row) How does…
Shredderroy
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3
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Question about the addition of hydrogen to a molecule undergoing MoleculeModify

I would like to identify the atom that used to participate in a bond before the molecule was modified by MoleculeModify[mol, {"DeleteBond", {idx1, idx2}}]. According to the official documentation of MoleculeModify: When removing or replacing an…
Shredderroy
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2
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1 answer

Zoom MolecularPlot on protein region

When I import protein and ligand from two PDB files and display them together using Show I cannot see the ligand since it is tiny in comparison with protein. How can I zoom the MoleculePlot on ligand automatically?
2
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NDSolve: InterpolatingFunction of Chemical Kinetics System Differs From Expected (AKA - Why Are My Plots Squiggly?)

I'm trying to use Mathematica (12.0.0) to model radiation chemical kinetics using a known reaction set, in this case it's water radiolysis. It solves the set of equations I throw at it without any errors, however the InterpolatingFunction it's…
CMcBride
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MoleculeValue option IncludeHydrogens does not work everywhere?

The coordination number property of a molecule seems to ignore the IncludeHydrogens flag. Adjacency matrix, on the other hand, seems to respect it. mol = Molecule["CCCCC", IncludeHydrogens -> False] dV = MoleculeValue[mol, "CoordinationNumber",…
bhopshang
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Are atom coordinates in Molecules the real equilibrium positions or simple heuristic guesses?

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 explosive TNT. I don't know where these coordinates actually come from. They could just be simple guesses based…
user54038
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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: Molecule["(CH3)2CHOH"] Where did i go wrong?
Arman
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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..
P Pyne
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