# 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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### How Can I Relax a Molecule in Mathematica?

I have a molecule in Mathematica. It consists of around 70 atoms, but let us for simplicity assume that we only have four atoms: ...
• 11
193 views

### Using ReactionBalance on chemical entities with missing formula

I am currently working on a project (turns out: a bigger project, than originally thought...) with all hypothetically "thinkable" products for a reaction with two given educts. These educts ...
136 views

### Is it possible to obtain the atomic indices of a bond by clicking on a MoleculePlot?

Consider the following MoleculePlot: MoleculePlot["ammonia", Bond[{1, 2}]] Its output is the following: I have ...
• 5,251
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### Drawing the Graph of a complex chemical reaction network

I'm interested in how Mathematica or IGraph/M package can help with the visualization of complex chemical reaction mechanisms applied in fields like combustion, biochemistry, water radiolysis, or ...
125 views

### Method of lines - Dirichlet and mixed BC

I have a dissolution problem to solve with two equations (everything is in dimensionless form - concentration, time and distance - EDIT: that came from the second Fick's law, where the distance was ...
1 vote
71 views

### Newton Raphson apply to Van der Waal Equation

I need assistance with this problem. I have two functions, where f1 corresponds to the dimensionless van der Waals equation of state, and function 2 corresponds to the dimensionless chemical potential ...
126 views

### Newton-Raphson Method Errors

I need assistance with this problem. I have two functions, where f1 corresponds to the dimensionless van der Waals equation of state, and function 2 corresponds to the dimensionless chemical potential ...
95 views

### Chemdraw (CDX) import fails to yield complete molecules for implicit alkyl chains

Mathematica has supported Chemdraw file (CDX) import since 12.1. However, there appear to be an error when side chains are defined in an abbreviated fashion (as is common in organic chemistry): ...
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128 views

### Import fails for Gaussian calculation output file

Mathematica seems to import Gaussian16 calculation output files usually without any troubles. However, with the recent 13.3.0 version, I noticed that some calculation output files are not imported, ...
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1 vote
125 views

### Trace animation of spherical and $\pi$ atomic orbital

I want to get trace animation, which forms 3D object at last. Though I saw ring shape structural animation in the website: https://community.wolfram.com/groups/-/m/t/1991109 also Creating a movie of ...
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### Is there a way to make Mathematica support Chemmacros of LaTeX?

On Mathematica 13 or later version, the ChemicalFormula and ChemicalReaction functions helpe a lot to deal with chemical formula ...
• 567
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### How can the units of the "AtomCoordinates" in a Molecule be changed while keeping the resulting MoleculePlot3D consistent?

Mathematica provides the Molecule function that can be visualized with MoleculePlot3D since version 12.0. Before, importing "XYZ" files would produce a ...
83 views

### How to export SD file with metadata?

Despite the fact that Mathematica (V13.2) is able to import an SD file with corresponding metadata for each structure, e.g. ...
151 views

### Are there plans to support multiple molecules in the Molecule function?

I am playing around with Molecule to run simple optimization on several water molecules in a single frame. The Molecule function only seems to create coordinates for a single molecule to use in ...
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1 vote
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### Create a hollow polymer structure and simulate its mechanical strength under compression [closed]

I want to create a hollow cylinder structure surrounded by 13 cross-sections (structure details refer to https://elifesciences.org/articles/34695#s1). Each cross-section is connected by same spherical ...
455 views

### Plotting the molecular isosurface electrostatic potential map

After performing Gaussian calculation, cube files can be obtained. The distributions are the potential cube and esp cube, both of which contain volume data. What I want to do now is to project the ...
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### Drawing of a cube file [closed]

The following is a description of a typical cube file Based on the above instructions, I wrote the following mathematica code： ...
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1 vote
155 views

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1 vote
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### Generating molecules using a GAN in Mathematica

I have been unable to find any tutorials or examples of creating molecules using a Generative Adversarial Network (GAN) in the Wolfram language. It appears that the Selfies paclet was created to ...
• 739
106 views

### How to change atom sizes and colors in MoleculePlot3D? [duplicate]

I would like to use an individual size and color for each atom in a molecule (independently of the atom types). Could you please help me how to achive this? My MWE is the following: ...
• 254
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### Problems with plotting spherical harmonics

I have tried to graph the real angular functions of the px and py atomic orbitals, using the Mathematica command SphericalHarmonicY, but for some reason, in both ...
123 views

### 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 ...
• 3,491
103 views

### Orientation of the molecules in MoleculePlot

Why the plot of the molecules with similar structures is not in the same orientation? ...
• 3,491
1 vote
61 views

### VEHICLe dataset - aromatic ring counts problem

I was recently exploring the VEHICLe data set and seem to have run into an inconsistency. The dataset is described as, The VEHICLe database, short for Virtual Exploratory heterocyclic library, ...
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### Using different colors for the same type of atoms in MoleculePlot3D

I would like to plot a molecule in 3D and use different colors for the same atom type in the molecule. For example, by using: ...
• 367
111 views

### Getting Molecular Weight for Stoichiometry Calculations

I love the units system in Mathematica, it's an extremely useful addition to the language. Unfortunately there are still some sharp corners that I run into on a daily basis. For example, if I want to ...
• 490
189 views

### How to chain/compose multiple ChemicalReaction?

v13 added some interesting-sounding chemical species functions like ChemicalReaction. But they don't seem to have any operations. For example the most common operation would be adding / composing ...
• 155
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### FindIsomers produces disconnected fragments

I was playing around with FindIsomers and got this strange result, FindIsomers[Molecule["butane"]] output This seems unexpected in the sense that you ...
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### 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 ...
• 483
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### 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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61 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 ...
336 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 ...
249 views

### Produce the same color scheme as IboView

I can use the following command to produce the HOMO (highest occupied molecular orbital) in chemistry: ...
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465 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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147 views

### 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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237 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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### 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 ...
60 views

### "MoleculeFeatures" in FeatureExtractor

"MoleculeFeatures" is one possible Feature Extractor method. What molecule properties does "MoleculeFeatures" entail?
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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 ...
• 739
142 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 ...
• 739
156 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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65 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
68 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 ....
64 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
126 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 ...
• 739
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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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202 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