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.
196
questions
9
votes
1answer
142 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" (...
4
votes
1answer
114 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 @...
3
votes
1answer
113 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}}]....
6
votes
1answer
147 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:
...
6
votes
1answer
92 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 ...
1
vote
2answers
90 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 <...
7
votes
1answer
315 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 ...
10
votes
4answers
468 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.
...
2
votes
1answer
38 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 ...
1
vote
0answers
57 views
How can I try to debug this discrepancy between Map and ParallelMap?
It is hard for me to present the actual set of functions that is prompting this question, because it is part of a very large code base. But to summarise, I have a setup like the following:
...
1
vote
1answer
54 views
List Contour plot
My data for List Contour plot ranges from -30 to 2500. The contour plot i am getting fails to distinguish the highest or the lowest ranges. How can i make it plot all the values with a colour?
This is ...
2
votes
1answer
60 views
Substituting Atoms in .XYZ File
I have a crystal structure in which I'd like to randomize the placement of cations from an initial structure. I have a .xyz file (given here https://pastebin.com/d5UcNr2h) which gives atomic ...
0
votes
0answers
53 views
2d list contour plot
I have plotted a ListContour plot with a large set of data i have and most of the points do not seem to have a distinguised colour, i.e, the color function needs to be re-scaled for my data. How can i ...
0
votes
2answers
74 views
Contour plot a 2d array
I have the calculated data for an interaction potential. My variables are distances (48 values) and angles(15 values) and my energy data is a 2d matrix of 48 x 15 values. How do i plot the energy as a ...
2
votes
1answer
79 views
How to determine the frequency of oscillations in system of three ODEs?
I want to determine the frequency of oscillations in a system of three stiff ODEs (Oregonator model). That model describes a chemical oscillator.
I have a slightly more advanced model of the default ...
1
vote
1answer
26 views
Exporting to PDB seems to lose aromaticity
I have a molecule with the following SMILES:
ClearAll[sml];
sml = "O=C(NCC1=CC(NC(C2=CN=C3C=CC=CN23)=O)=C(C)C=C1)NC4=CC=CC(F)=C4";
The plot looks as ...
6
votes
3answers
320 views
How can I get material property data past what's provided via ElementData[], ChemicalData[], etc.?
Background
Let's say I want information (e.g. bulk modulus or space group) on an element or chemical compound that isn't available via e.g. ElementData[], ...
2
votes
1answer
76 views
How do I make a general solver for a system of equations (e.g. thermodynamic processes) with different inputs and outputs?
Background
Let's say I have a system of equations (e.g. thermodynamics equations), where the "knowns" and "unknowns" are subject to change, and the system of equations can also ...
5
votes
2answers
143 views
Symmetry unique atom coordinates
One thing I love about Mathematica is how easily I can go from the name of a molecule to estimated coordinates of its atoms, with a command like
...
5
votes
1answer
218 views
Building large chemical models such as VANTAblack
I would like to build a (large) molecular model of the nanotubes that make up VANTAblack, which consists of a sheet of hexagonally connected carbon atoms all rolled into a (teeny) tube.
I can easily ...
1
vote
0answers
55 views
Are atom coordinates in Molecules the real equilibrium positions or simple heuristic guesses? [duplicate]
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 ...
0
votes
0answers
46 views
Can I get atomization energy of a chemical?
A pretty basic property of a chemical is the atomization energy. Another similar property is the heat of formation.
I'm looking at
...
8
votes
2answers
239 views
When looking at a chemical's bond lengths, which bonds do they represent?
Looking at, for example, the bond lengths of styrene:
...
3
votes
1answer
96 views
Graph3D - replace vertices with MoleculePlot3D
How can we replace the vertices in a 3-dim graph with individual Graphics3D objects?
In my concrete case I want to visualize a chemical network and replace vertices ...
0
votes
0answers
86 views
Error in Monte Carlo simulation. Now Random walk (dotted curve) doesn't fit to the analytical curve (dashed curve)
I've been trying to code a kinetic monte carlo simulation for a system of consecutive chemical reactions using a fixed (repaired) code that the user flinty gives me in the last questions I post:
...
-1
votes
1answer
55 views
solving an equation by suggested method [closed]
I have an equation
I want to do this issue: T(dV/dT)-V=0 and obtain T that satisfy this relation. How can I do it? we should at first obtain V and then Drivate it. How can?
1
vote
1answer
81 views
Strange error not found in a monte carlo code, Infinite expression 1/0 encountered
I've been trying to code a kinetic monte carlo simulation for a dimerization reaction, 2M ---> D. However I have a kinetic Monte Carlo code for a first order decomposition reaction of AIBN (that's ...
1
vote
1answer
73 views
How to plot a thermodynamic cycle? [duplicate]
I try to plot a thermodynamic cycle with the data displayed using the tool, "Piecewise", but in the case of isochoric and isobaric processes, Mathematica shows nothing. Could someone please tell me ...
3
votes
1answer
131 views
Solve a system of three stiff ODEs and plot graphs of it - Oregonator
I want to plot a system of three stiff ODEs (Oregonator model). That model describes a chemical oscillator. I do not have much experience with plotting ODEs, but I have obtained a Mathematica file ...
3
votes
0answers
69 views
Right or wrong answer obtained when using two ways to represent the same number [closed]
Using Mathematica 10.1
Depending on whether I write a numerical constant as 0.6 * 10^-15, or 6 * 10^-16, I get very different ...
4
votes
1answer
80 views
What algorithm(s) are used by MoleculeModify's GenerateConformers?
Starting with Mathematica 12, the MoleculeModify function has a "GenerateConformers" option.
What is the algorithm used to ...
2
votes
0answers
39 views
OscillatorStrength[Helium] and OscillatorStrength[Rubidium] do not return results
I am new to working with the Resonance Absorption Lines Pacgage
<< ResonanceAbsorptionLines`
and trying to write code using the OscillatorStrength command. ...
1
vote
1answer
68 views
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:
...
1
vote
1answer
65 views
3
votes
1answer
46 views
Plot colored spectral lines using spectral line data? [duplicate]
Suppose I've retrieved spectral line data for an element, as so:
hydrogenSpectralLines =SpectralLineData[EntityClass["AtomicLine", {"Hydrogen", 1}]];
From that, ...
1
vote
0answers
20 views
Fitting Experimental Data To SRK-Type Equation of State. Minimization
I'm trying to find parameters to fit an EoS to saturation pressures to different temperatures.
My experimental data are like this
...
0
votes
0answers
38 views
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..
10
votes
2answers
324 views
What's the principle behind the new MoleculeRecognize function?
I played a bit with the new MoleculeRecognize function implemented in the newly released WM 12.1:
which simply recognizes a molecule in image and returns it as a Molecule object.
...
1
vote
0answers
44 views
Translating standard form of EOS to its polynomial form
Is there a standard form for an equation like the others such as PR/SRK/... .
Z = (v - a b) / (v - b) - a / ((RT^1.5) (v + 2.6382 b))
for predicting pure ...
3
votes
1answer
91 views
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!
...
4
votes
2answers
93 views
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 ...
6
votes
1answer
72 views
FindMoleculeSubstructure fails on SMARTS MoleculePattern, but MoleculePlot is OK?
Background Info: SMARTS is a convention for specifying molecular patterns. It is supported by Mathematica 12's MoleculePattern function.
Problem Setup: Consider
...
2
votes
1answer
105 views
PubChem Service doesn't support isomeric SMILES specifications?
Update 04 Sept 2020: The problem described below occurs in Mathematica 12.0. It has been fixed in Mathematica 12.1, so that ServiceExecute returns the correct ...
2
votes
1answer
52 views
SDF Metadata Import fails when structure information is missing
UPDATE 04 Sept 2020: This behavior been fixed in Mathematica 12.1.
Background Information: In Mathematica 12.0, SDF Import automatically triggers the generation of Molecule[] representations. SDF ...
1
vote
0answers
57 views
PubChem service doesn't support looking up compounds given an assay ID?
Mathematica's PubChem Service Connection has many requests that return the properties of a compound (or substance). It also provides requests that return all the assays for which a given compound (or ...
5
votes
1answer
70 views
Inconsistent sign changes in Molecule[] AtomDiagramCoordinates property and MoleculePlot[]
I'm trying to resolve a problem with the new Molecule[] functionality in Mathematica 12.
The "AtomDiagramCoordinates" property returns 2D coordinates of the molecular graph. These coordinates can be ...
7
votes
2answers
134 views
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 ...
8
votes
1answer
92 views
Are the lists from “BondList” and EdgeList for a molecule guaranteed to be aligned?
Consider the following:
...
16
votes
3answers
436 views
Computing the surface area and volume of molecules
Here is a somewhat difficult problem I've had for a long while.
Space-filling models of molecules can be easily generated by ChemicalData[], ...
4
votes
2answers
93 views
Possible error in IsotopeData
I found 2 isotopes in Wolfram database which are marked as unstable, but their lifetime is indicated as infinite (germanium-76 and selenium-82). The following chunck of code illustrates the issue:
<...
