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.

11 questions with no upvoted or accepted answers
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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 ...
4
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0answers
209 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, ...
2
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0answers
50 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
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0answers
59 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 ...
2
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0answers
177 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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0answers
626 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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0answers
34 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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0answers
83 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 ...
1
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0answers
81 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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79 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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76 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, ...