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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GraphDiameter for molecule graphs error [closed]

I was looking into GraphDiameter for molecules and ended up on this [page][1], which gives examples in various modalities to calculate the graph diameter for this molecule.'CC(C)C(C(=O)NC(=O)C1CCCN1C(=...
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Identifying and tracking cluster elements in ClusterClassify for multiple time-steps of data

I have multiple time-steps of {x,y,z}coordinates data for some atoms. I would like to cluster the data for each frame and later identify how cluster compositions change and how each atom changes from ...
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3 votes
1 answer
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Extremely slow import of mx files with Molecule objects [closed]

Version: 13.0.1 on Linux Hello, I recently found a collection of 39,361 SMILES strings that I converted to Molecule format with Mathematica. I then exported the resulting list of Molecule objects into ...
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5 votes
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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 ...
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How to convert PQR Entity to Mathematica Molecule format

I am using the Pitt Quantum Repository and am trying to convert the format from Entity to Molecule, so that I can get the MoleculeValue Properties of the PQR chemicals in addition to the EntityValue ...
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How to compute the electronic energy reported by Gaussian from the AlphaOrbitalEnergies

I followed the instructions on https://reference.wolfram.com/language/ref/format/FCHK.html to analyze the fchk file. Ran an energy calculation on Gaussian , converted the results to .fchk files. The ....
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3 votes
1 answer
53 views

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. ...
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1 vote
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Gaussian 16 fchk and log file import in mathematica

I am working with Gaussian log files and fchk files imported into Mathematica and I noticed a few things. The ExampleData in documentation for these files use Gaussian 03 output files, while the ...
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Molecule fingerprint MorganConnectivity

I am looking for a way to calculate the MorganConnectivity finger print for molecule object in Mathematica. v12.1 seemed to have an undocumented function MoleculeFingerprint ...
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0 answers
82 views

How to plot Energy line diagram

how to plot like this picture,In chemistry the ''Energy line diagram'' is important. I can use "chemdraw",but I have to manually adjust the data and everything, which is a hassle, right.
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1 vote
2 answers
99 views

How to get x and y values and function of xy pairs (H[x,y]) from Histogramlist?

So I have generated a set of random data points as shown below sample1 = RandomVariate[BinormalDistribution[{0, 0.4}, {1.2, 1.2}, 0], 250]; From the sample, I ...
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1 vote
1 answer
28 views

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. ...
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3 votes
0 answers
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MoleculeModify[{"DeleteAtom", a}] behaving strangely

I am encountering a strange error with the following molecule: ...
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0 answers
66 views

Gay-Berne potential in Mathematica

Cross-posting from Physics SE. I am trying to make a plot of the Gay-Berne potential using Mathematica. I am following this paper and I am trying to recreate Fig. 2. This is figure 2: To save time, ...
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4 votes
0 answers
184 views

How do I generate SMILES using machine learning in Mathematica

I am wondering if anyone has experience with generating molecules using machine learning in Mathematica. There are a bunch of papers these days with such applications/developments. For example, https:/...
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3 votes
2 answers
126 views

Animating Particle Motion Using Parametric Plot and Animate

I am attempting to animate my parametric plot and add a particle to move on the line but I am having difficulties. Here is my graph for the trajectory: ...
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2 votes
1 answer
65 views

Does anyone know how to fix the issue not having the hydrogen atoms accounted for when converting to a .mol file?

Hi I am using moleculeRecognize function to upload structures from images and I am attempting to convert the structures in .mol files. However every time I convert to .mol files the hydrogen atoms in ...
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5 votes
1 answer
126 views

Molecule fingerprint functions v13

I am looking for calculation of molecular fingerprints (FingerprintFunction) in v13 of Mathematica. There was a WTC talk around v12.2 showing this functionality, however, I can't seem to find this in ...
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1 vote
1 answer
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ServiceExecute for PubChem error when CID not found

I am trying to download properties of compounds from PubChem using ServiceExecute. However, I only possess names of compounds as strings. It appears that ServiceExecute exits completely even if the ...
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0 answers
67 views

How to calculate torsion angles (phi and psi) from ResidueCoordinates of protein?

I am trying to compute the torsion angles (phi, psi) from coordinates of protein (using pdb file in Mathematica). I am following the approach explained here. The output values are in the range of -180 ...
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5 votes
2 answers
167 views

Select behaving differently with Dataset and List

I have just encountered what I would term an unexpected disagreement in behaviour between Dataset and List. Consider the ...
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4 votes
1 answer
86 views

Included hydrogens not always included in Molecule adjacency matrix?

Bug fixed in 13.0.0 Consider the following molecule, specified by a SMILES string: ...
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5 votes
0 answers
89 views

MoleculePlot is completely unfunctional when DefaultStyleDefinitions sets to ReverseColor.nb [duplicate]

If you set the DefaultStyleDefinitions sets to ReverseColor.nb then when you try to execute the example from the MoleculePlot document, your MoleculePlot will have blank result like even if you ...
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1 vote
0 answers
77 views

Show distances, angles, and torsions with MoleculePlot3D

I would like to display some bond lengths, bond angles, and torsion angles of a molecule with MoleculePlot3D. For the example ...
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  • 169
3 votes
1 answer
63 views

Label the atoms of a molecule imported from an XYZ file

I would like to label the atoms of a molecule imported from an XYZ file. The only example that I found is the following (How to label with numbers atoms when MoleculePlot3D): ...
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  • 169
5 votes
2 answers
201 views

MoleculePlot always returns an empty plot

MoleculePlot@Molecule["O=C(C1CCC1)S[C@@H]1CCC1(C)C"] This is a documented example usage of MoleculePlot, but it ...
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1 vote
1 answer
141 views

Density of water at a given temperature and pressure

In Wolfram|Alpha if I write: density water at 500°C and 100 atm instantly I read: 30.92 kg/m^3 (kilograms per cubic meter) ...
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1 vote
1 answer
45 views

Enter an object into a FormPage

I am currently trying to make a FormPage that plots a Molecule and I try to add a possibility to input a custom Molecule. Entering the data for a Molecule makes Mathematica crash. Code: FormPage["...
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1 vote
0 answers
140 views

NDSolve Error test failure at t == 5082.429032772312`; unable to continue

I am quite new to Mathematica, please help me struggling out of this question. I want to know how the HNO3 and HNO2 change in the system. first, I put the kinetics of some reactions: ...
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1 vote
0 answers
101 views

obabel_mod.exe not found [closed]

I don't know if this question has any connection to this question about TCP sockets. I encountered the problem after I was able to run my code base again following the resolution to that question. My ...
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4 votes
1 answer
109 views

Looking for the documentation of "AtomicLevel" specifications

New to version 12, one can retrieve a really extensive data base entities about chemical elements. It is initiated via Entity["Element",name] For example,...
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0 answers
39 views

Simplify function to find rate constants

I have a function to calculate rate constants using nonlinear least square modeling from a 2011 paper by Jia et al. https://www.cell.com/cell/fulltext/S0092-8674(11)00536-8?_returnURL=https%3A%2F%...
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11 votes
3 answers
511 views

Mass Transport Model

I've asked similar questions before about Mathematica's Mass Transport model. My aim is to model these systems and show how they change by manipulating various parameters. This time it's the following ...
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4 votes
1 answer
162 views

How to label with numbers atoms when MoleculePlot3D

I want to place a number on each atom (on a sphere) upon 3D plotting a molecule. For example, from: ...
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6 votes
1 answer
280 views

Animating a random walk of 3D water molecules?

Inspired by David G. Stork’s post https://mathematica.stackexchange.com/a/84097/10361, I tried to have the molecules perform a random walk ...
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2 votes
2 answers
247 views

Finding Temperature as function of pressure and entropy in Mathematica

While Mathematica's ThermodynamicData[] is very useful, is there a method in Mathematica to find Temperature as a function of Pressure and Entropy? ...
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1 vote
1 answer
118 views

Interactive Machine Learning App to make Predictions using Descriptors

I have developed a Machine Learning algorithm that uses 4 chemical descriptors to calculate a chosen chemical property. I would like to create an interactive app on Mathematica (using the manipulate ...
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0 votes
1 answer
46 views

SphericalPlot3D generates flat surfaces [duplicate]

I'm trying to plot a function r(theta, phi) but having some difficulty. It's also possible that I've misinterpreted the paper I'm pulling these formula from, but I think I'm most likely making some ...
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0 votes
2 answers
143 views

Unknown plotting issue

I'm trying to model a surface based on the parameters listed here, it's a 2p orbital isosurface using the equations S10, S11, and S12 My model is of a 2p surface, and should look like this: But no ...
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0 votes
1 answer
73 views

Parametric plotting of molecular orbitals [closed]

I'm trying to plot a parametric curve, but I only get a blank plot. I don't usually use mathematica, but my end user needs to be able to do this using that software, so I'm really struggling on syntax ...
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1 vote
0 answers
95 views

Molecule export to PDB fails in WL but succeeds in rdkit

The following is one of a whole list of molecules which Mathematica fails to export to PDB: ...
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9 votes
1 answer
180 views

MoleculePlot draws sucrose benzoate with overlapping bonds

Recently I learned that in Mathematica it is possible to create chemical structures here: Chemical formulas with Mathematica I am having a problem with a structure called "Sucrose benzoate" (...
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4 votes
1 answer
147 views

Chemical formulas with Mathematica

I am aware that there are many many things that we can do in Mathematica, but I am wondering if it is also possible to construct chemical compunds such as for example the one below?: EDIT: Using @...
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3 votes
1 answer
128 views

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}}]....
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6 votes
1 answer
181 views

Workaround for a breaking change in ConnectedMoleculeComponents from 12.1.1 to 12.2.0

The following code used to work in Mathematica Version 12.1.1: ...
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6 votes
1 answer
158 views

How to properly use the function ThermodynamicData

I've been trying to use the function ThermodynamicData, and it is going fine when I try to calculate properties such as Enthalpy or Entropy or even phase as a ...
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1 vote
2 answers
132 views

How to use Import to extract data from website?

I would like to extract data of surface properties and grain boundary properties for Cu polymorph #0 from the website: http://crystalium.materialsvirtuallab.org using Mathematica. So far I tried with <...
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8 votes
1 answer
356 views

Why does `Molecule` return a molecule for an incorrect SMILES string?

When I type an incorrect SMILES into the Molecule function, the output a large, unrelated molecule. What is Molecule doing here, and is it possible for the command ...
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  • 303
10 votes
4 answers
501 views

MoleculePlot3D - how to replace spheres?

How to replace the spheres in the plot with other 3d figures, say "N" with a Cylinder, "O" with a Cuboid, and "H" with a sphere. ...
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  • 541
2 votes
1 answer
51 views

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 ...
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