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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3 votes
0 answers
47 views

How can I find the Solution properties in water like "Solubility"?

The official documentation of function ChemicalData says it can find solution properties in water below: But I have made several attempts, none of them have ...
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6 votes
1 answer
117 views

Graph Convolution Network, molecule activity

I am trying to translate an example code for graph convolution network from Deep Learning for Physical Scientists: Accelerating Research with Machine Learning. Edward O. Pyzer-Knapp et. al. They have ...
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5 votes
0 answers
50 views

Can the Wolfram Language perform conversions between organic compounds?

My question is straightforward - if I have a starting organic compound, say chlorobenzene and an ending organic compound, say aniline, can Wolfram give me a set of equations to go from chlorobenzene ...
3 votes
2 answers
230 views

Aligning two molecules in XYZ format, before v12.3

I have two molecules in "XYZ" format and I want to align them. As I am using Mathematica version 12.0, which does not have this ...
11 votes
0 answers
167 views

Produce the same color scheme as IboView

I can use the following command to produce the HOMO (highest occupied molecular orbital) in chemistry: ...
9 votes
2 answers
390 views

How can I rotate and reflect a molecule plot?

Consider: MoleculePlot[Molecule[Entity["Chemical", "Theobromine"]]] How can I rotate and reflect it? This is my current method: ...
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7 votes
0 answers
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MoleculeModify not working in Mathematica 13.1

This question is related to an older question, which was acknowledged to have uncovered a bug. Unlike in the previous question, this time I am not trying to delete a hydrogen atom. But in ...
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11 votes
1 answer
142 views

protein visualization: display a residue in balls and sticks over the structure

I am trying to visualize a cytochrome c protein and display one of the residues in ball and sticks over it. I am using the PDB file 1AKK for it (https://www.rcsb.org/structure/1akk). The Import ...
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0 votes
0 answers
45 views

3D Cylinder with uniform distribution in volume

I would like to draw a figure in 3D where I have a cylinder (or ellipsoid) and some spheres in volume with fixed distenced between. I understand how to build a cylinder or Random spheres in cube, but ...
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4 votes
1 answer
53 views

"MoleculeFeatures" in FeatureExtractor

"MoleculeFeatures" is one possible Feature Extractor method. What molecule properties does "MoleculeFeatures" entail?
3 votes
1 answer
56 views

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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0 votes
0 answers
35 views

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 ...
  • 569
3 votes
1 answer
95 views

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
0 answers
91 views

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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3 votes
1 answer
45 views

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 ...
1 vote
0 answers
32 views

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 ....
3 votes
1 answer
56 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
0 answers
53 views

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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2 votes
1 answer
67 views

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 votes
0 answers
104 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.
1 vote
2 answers
125 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 ...
1 vote
1 answer
31 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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4 votes
0 answers
75 views

MoleculeModify[{"DeleteAtom", a}] behaving strangely

I am encountering a strange error with the following molecule: ...
  • 4,871
0 votes
0 answers
73 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
197 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
149 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: ...
2 votes
1 answer
73 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 ...
7 votes
1 answer
174 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
37 views

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 votes
0 answers
95 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
171 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
87 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: ...
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
79 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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3 votes
1 answer
76 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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5 votes
2 answers
208 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
158 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["...
1 vote
0 answers
178 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
115 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 votes
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
525 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
176 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
291 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
267 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 ...
0 votes
2 answers
161 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 ...
0 votes
1 answer
83 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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