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.
208
questions
1
vote
0answers
98 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 ...
3
votes
1answer
93 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,...
0
votes
0answers
34 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%...
9
votes
3answers
391 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 ...
4
votes
1answer
96 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:
...
6
votes
1answer
242 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
...
2
votes
2answers
166 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? ...
0
votes
1answer
104 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 ...
0
votes
1answer
44 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
2answers
96 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
1answer
56 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
...
1
vote
0answers
29 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:
...
9
votes
1answer
168 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
130 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
119 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
163 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
108 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
100 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
335 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
482 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
44 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
61 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
76 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
60 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
98 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 ...
4
votes
2answers
181 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
31 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
328 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
103 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
164 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
223 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
48 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
248 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
102 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
93 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
109 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
136 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
81 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
41 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
73 views
3
votes
1answer
52 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
22 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
59 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
349 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.
...
