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.
156
questions
2
votes
1answer
60 views
Which argument of MoleculeValue returns the SAS?
I have been trying to calculate the synthetic accessibility score of a molecule. But I don't know which property from the extensive list returned by ...
3
votes
2answers
69 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 ...
5
votes
1answer
55 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
0answers
53 views
PubChem Service doesn't support isomeric SMILES specifications?
Consider the molecule defined by the following SMILES string:
example = "C(/C=C/Cl)Cl"
(the slashes indicate cis/trans isomerism). Molecule[] has no problem ...
2
votes
1answer
32 views
SDF Metadata Import fails when structure information is missing
Background Information: In Mathematica 12, SDF Import automatically triggers the generation of Molecule[] representations. SDF files contain both structural information as well as metadata, and a ...
1
vote
0answers
35 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 ...
4
votes
1answer
58 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
107 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 ...
6
votes
1answer
77 views
Are the lists from “BondList” and EdgeList for a molecule guaranteed to be aligned?
Consider the following:
...
15
votes
3answers
302 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
87 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:
<...
2
votes
1answer
86 views
How do I use Solve with conditional equations?
Short version: How do I have Solve handle a system of equations where some of the equations may be conditional?
Simplified Problem:
I am solving the following system of equations:
a * b = 10^-14
b^...
0
votes
0answers
84 views
How to plot and simulate reaction networks in Mathematica?
I am trying to simulate reaction networks like it's done in the Simulation methods
in this paper. They used Xcellerator, so I after installing on Mathmatica 11.2 and trying to run their Belousov-...
17
votes
4answers
786 views
How to apply different equations to different parts of a geometry in PDE?
I want to solve two coupled partial differential equations on two dimension.
There are two variables v and m. The geometry is a ...
3
votes
1answer
97 views
Producing MoleculePlots of pigments
Of course no chemical database is complete, but I would like to create as large a list of MoleculePlots of pigments (organic or inorganic) as is available through ...
0
votes
1answer
66 views
How do I obtain the characteristics and properties of an alloy? [closed]
I would like to obtain the characteristics and properties of the Alloy Chromel. How do I download that information from the database of Wolfram Alpha and then print it in a Mathematica Notebook?
...
6
votes
1answer
250 views
Maxwell construction problem with FindRoot
A Maxwell construction is just an integral of area and then solving for a root to find vapor pressure.
This must be exactly the same value as where the Gibbs energy plot crosses at a point. I found ...
11
votes
3answers
589 views
Minimum energy path of a potential energy surface
I have calculated the energies of a molecule by varying two parameters (Data points are here data). I want to find the minimum energy path from the point (180.0, 179.99, 21.132) to (124.5, 124.49, 0) ...
4
votes
2answers
151 views
Is it possible to use chemical data in polymers?
I would like to plot the ABS polymer.
It is made of Styrene, Acrylonitrile and 1,3 Butadine.
I can plot those components separately
But the command
...
9
votes
3answers
394 views
Chemical data of Lactic acid [duplicate]
I'm using the next Mathematica command in order to plot molecules:
ChemicalData["name", "MoleculePlot"]
But I'm not sure if the Mathematica database of molecules ...
1
vote
0answers
71 views
ProteinData Error: “Cannot import data as PDB format” [closed]
I'm trying to use the Mathematica examples for plotting proteins:
But when I type the command I get the next error:
How can I import data as PDB format?
13
votes
1answer
854 views
visualizing a normal mode vibration of a molecule in mathematica
How can I visualize the normal mode vibrations of a molecule in Mathematica?
Something like the following GIF:
(from here)
I have the XYZ file of the benzene molecule and the normal mode ...
4
votes
2answers
323 views
Periodic table with color code
Is it possible to do this table (from here) in Mathematica?
In this table, the color code indicates the element’s dipolar character $(~ m\mu_m^2)$ in atomic units.
2
votes
1answer
60 views
Visualizing a imported XYZ-file and graphic object at same time
I want visualize a imported xyz-file and a graphic object at same time.
g = Import["H2O.xyz", "XYZ"];
Show[g, Graphics3D[{Opacity[0.5], Sphere[]}]]
But this ...
2
votes
1answer
76 views
Convert a Java object to interface via J/Link
I'm trying to use a Java library called CDK with Mathematica's J/Link.
...
10
votes
3answers
512 views
DFT for Helium atom
I'm trying to solve this problem
I'm not a Mathematica expert, but my program works perfect when
vhartree={0,0,..,0}
This is the program I wrote:
...
7
votes
1answer
149 views
Suggestions to increase the speed of a fugacity calculation
I'm writing code to simulate a chemical reaction. This requires the calculation of the fugacity of a mixture of gases. The underlying model is the SRK equation of state.
First the physical ...
1
vote
0answers
84 views
How can i set up an If or Do loop to follow this calculation procedure?
The following picture depicts the calculation procedure I wish to set up.
The inputs are $T_r$, the chemical composition of the feedstock and constraints defined by the equivalence ratio.
This ...
5
votes
1answer
98 views
WolframAlpha function does not return structure diagram for chemicals
Neither one of
WolframAlpha["Caffeine"]
WolframAlpha["Caffeine","FullOutput"]
returns a structure diagram for the molecule. It's consistent since ...
0
votes
0answers
79 views
Encountering error messages with both DSolve and NDSolve
Reposting my question in a more legible and understandable way. The earlier one was flouting a few too many posting guidelines.
I am trying to solve the heat conduction partial differential equation, ...
8
votes
2answers
408 views
ChemistryData — where is specific gravity?
I cannot seem to find the basic chemical property specific gravity with ChemicalData or other comparable functions.
1
vote
2answers
242 views
Assign a unit to a variable in a function
I have the following input:
PVW[V_, T_] := (R*T/(V - b)) - (a/(V^2))
Where I have already defined R as the molecular gas constant with its corresponding units ...
1
vote
0answers
84 views
Dealing with Vector Outputs from ItoProcess, RandomProcess (Stochastic Differential Equations)
I'm modeling stochastic chemical kinetics and the ItoProcess[] function has served me well. I am trying to write an efficient code to analyze many (Paths) trajectories of several different reagents (...
6
votes
1answer
747 views
Radial distribution function (pair correlation function) for particles in rectangular image
Some time ago I asked the following question on how to calculate the radial distribution function.
I have here an add-on question, but before asking it I try to summarize and visualize my problem.
...
7
votes
3answers
559 views
ChemicalData returns the correct result for “Sulfuric” but an empty list for “Sulfuric Acid”. Why?
I am new to this site so I hope my question is valid.
My code is:
...
4
votes
1answer
472 views
Map volumetric data onto an isosurface
this question originates from an attempt to visualize molecular electrostatic potentials, but hopefully should be of general interest.
Suppose that you have two sets of data, S1 and S2. Each set ...
5
votes
2answers
134 views
Delete duplicates of isomerism
I written some code to generate all partens of $\ \mathrm{C_2H_5O}$, but theres some isomerisms need to be deleted.
Here's the raw output after DeleteDuplicates.
<...
7
votes
1answer
178 views
1
vote
2answers
330 views
Visualizing .xyz file in Mathematica
If i import a .xyz file in Mathematica that will show me the moelcule in the default way. But i want to visualise the .xyz file in the following manner.
5
votes
1answer
173 views
Michaelis–Menten kinetics using Tau-Leaping
I am trying to implement Michaelis–Menten kinetics using Tau-Leaping. It works fine as expected. Only issue here is when substrate reaches zero the algorithm stop since PoissonDistribution[0] gives ...
8
votes
1answer
259 views
Constructing Icosahedral Fullerene Graphs
I am interested in constructing graphs of icosahedral fullerenes, following the construction explained in the first few pages of this article (alternate link). Mathematica has built-in information ...
2
votes
2answers
442 views
Solve for several constants using a set of initial conditions
I have a set of differential equations that I am trying to solve for chemical reaction rate constants. So far I can get DSolve to solve the ODEs with initial conditions which provides the chemical ...
0
votes
2answers
391 views
Michaelis–Menten kinetics using Gillespie Algorithm
I am trying to implement Michaelis–Menten kinetics using Gillespie Algorithm.
$$\text{Reaction 1:}\quad E+S\rightarrow C$$
$$\text{Reaction 2:}\quad C\rightarrow E+S$$
$$\text{Reaction 1:}\quad C\...
0
votes
2answers
115 views
Solving Catalyst/Enzyme Diffusion Equation
Evening all,
I am attempting to solve a second order differential equation to get an equation of the substrate concentration as a function of r (i.e. S(r)). I have developed this equation, $\frac{d^...
8
votes
3answers
2k views
Why are Dalton and Grams / Moles not equivalent units?
The following code throws an error:
UnitConvert[Quantity["Daltons"], "Grams"/"Moles"]
Why?
2
votes
1answer
139 views
How to use FindFit to do kinetic simulation?
I'd like to simulate the chemical kinetic model by fitting the experimental data. Here are my codes for simulation.
...
5
votes
0answers
76 views
Helping Mandy become a better speller [duplicate]
tl;dr Can you improve upon this code, which checks to see if a word can be spelled using the element symbols from the periodic table?
I recently created a periodic table that lights up. The design ...
2
votes
2answers
119 views
Question about getting the table behind ElementData
I am interested in retrieving the entire table (preferably in text or csv format) that is behind the ElementData function for ALL the elements. The table (or perhaps multiple tables) record(s) many ...
1
vote
2answers
106 views
How can I add new columns to a Table after each evaluation?
I'm interested in simulating chemical reactions with perturbations. I can simulate a given reaction using NDSolve ("rxn"} with a given added noise component ("noise1"). Due to the noise, each ...
9
votes
2answers
323 views
Plot polygonal surface
I have a list of 120 elements of the form $\{q,x,y,z\}$. In fact, each element of the represents the nuclear charge and 3 coordinates of an atom of some large molecule.
...
