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.

22 questions with no upvoted or accepted answers
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96 views

Combining separate CHColorStructureDiagrams to form one molecular structure

I am trying to attach a fructose molecule to a sucrose molecule by using information obtained from the following ...
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212 views

random Poisson process over multiple variables (state vector) for chemical kinetics

Has anyone figured out how to coerce ContinuousMarkovProcess to work with a state vector, transition matrix, and rate (propensity) vector, and RandomFunction to return pairs of state vector and time, ...
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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. ...
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64 views

Another question on Mma data sources/syntax

Let's say I want to have the vapor pressure of mercury, as a function of temperature. I know that this information is available, for any specific temperature, from Wolfram Alpha, and I can also get ...
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218 views

integration of a list of gaussian type orbitals (GTO)

I am currently trying to integrate various components of a current density (j={jx,jy,jz}) over space. The problem is that the current j is extracted from a quantum chemical computation and is a sum of ...
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647 views

Generating a function which outputs possible chemical reactions

I want to make a list of chemical reactions and I write them down in a $\require{mhchem}\LaTeX$ format. They are of the following form $$NA_n^i+MB_m^j \rightarrow \hat NA_{\hat n}^{\hat i}+\hat MA_{\...
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71 views

NDSolve Error test failure at t == 5082.429032772312`; unable to continue

I am quite new to Mathematica, please help me struggling out of this question. I want to know how the HNO3 and HNO2 change in the system. first, I put the kinetics of some reactions: ...
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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: ...
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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: ...
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23 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 ...
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0answers
46 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 ...
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60 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 ...
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97 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 ...
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152 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 (...
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35 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%...
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2answers
111 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 ...
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61 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 ...
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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 ...
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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: ...
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62 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..
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106 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-...
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108 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, ...