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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: ...
flg's user avatar
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5 votes
2 answers
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 ...
Armin Vollmer's user avatar
4 votes
1 answer
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 ...
Shredderroy's user avatar
  • 5,251
3 votes
0 answers
90 views

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 ...
Javier J Navarro's user avatar
2 votes
1 answer
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 ...
Larissa Santos's user avatar
1 vote
1 answer
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 ...
Larissa Santos's user avatar
0 votes
1 answer
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 ...
Larissa Santos's user avatar
4 votes
1 answer
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): ...
Joshua Schrier's user avatar
2 votes
1 answer
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, ...
bhopshang's user avatar
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1 vote
1 answer
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 ...
rani's user avatar
  • 343
2 votes
1 answer
88 views

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 ...
Y. zeng's user avatar
  • 567
4 votes
1 answer
109 views

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 ...
ZehDeckel's user avatar
5 votes
1 answer
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. ...
Armin Vollmer's user avatar
3 votes
1 answer
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 ...
bhopshang's user avatar
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1 vote
0 answers
46 views

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 ...
Yucheng Ye's user avatar
2 votes
1 answer
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 ...
我心永恒's user avatar
  • 1,572
3 votes
1 answer
283 views

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: ...
我心永恒's user avatar
  • 1,572
1 vote
2 answers
155 views

Extract coordinates from the Gaussian09 calculation file

...
我心永恒's user avatar
  • 1,572
1 vote
1 answer
136 views

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 ...
bhopshang's user avatar
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3 votes
1 answer
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: ...
TobiR's user avatar
  • 254
3 votes
1 answer
273 views

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 ...
Arturo García Flores's user avatar
2 votes
1 answer
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 ...
Филипп Цветков's user avatar
6 votes
1 answer
103 views

Orientation of the molecules in MoleculePlot

Why the plot of the molecules with similar structures is not in the same orientation? ...
Филипп Цветков's user avatar
1 vote
1 answer
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, ...
bhopshang's user avatar
  • 739
3 votes
2 answers
180 views

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: ...
ogledala's user avatar
  • 367
4 votes
1 answer
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 ...
BesselFunct's user avatar
4 votes
2 answers
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 ...
alexchandel's user avatar
5 votes
1 answer
92 views

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 ...
bhopshang's user avatar
  • 739
3 votes
0 answers
52 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 ...
AlbertLew's user avatar
  • 483
6 votes
1 answer
151 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 ...
bhopshang's user avatar
  • 739
5 votes
0 answers
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 ...
arujbansal's user avatar
3 votes
2 answers
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 ...
sravankumar perumalla's user avatar
11 votes
0 answers
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: ...
我心永恒's user avatar
  • 1,572
9 votes
2 answers
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: ...
yode's user avatar
  • 26.8k
7 votes
0 answers
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 ...
Shredderroy's user avatar
  • 5,251
11 votes
1 answer
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 ...
J. Rouxel's user avatar
  • 133
0 votes
0 answers
69 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 ...
Maria's user avatar
  • 1
4 votes
1 answer
60 views

"MoleculeFeatures" in FeatureExtractor

"MoleculeFeatures" is one possible Feature Extractor method. What molecule properties does "MoleculeFeatures" entail?
Tahiryfr's user avatar
3 votes
1 answer
60 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(=...
bhopshang's user avatar
  • 739
0 votes
0 answers
60 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 ...
bhopshang's user avatar
  • 739
3 votes
1 answer
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 ...
bhopshang's user avatar
  • 739
6 votes
1 answer
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 ...
bhopshang's user avatar
  • 739
3 votes
1 answer
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 ...
mostafa100000's user avatar
1 vote
0 answers
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 ....
mostafa100000's user avatar
3 votes
1 answer
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. ...
Shredderroy's user avatar
  • 5,251
1 vote
0 answers
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 ...
bhopshang's user avatar
  • 739
2 votes
1 answer
82 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 ...
bhopshang's user avatar
  • 739
0 votes
0 answers
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.
我心永恒's user avatar
  • 1,572
1 vote
2 answers
182 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 ...
Yona Romes's user avatar
1 vote
1 answer
33 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. ...
bhopshang's user avatar
  • 739

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