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.

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4
votes
2answers
377 views

Modifying imported 3D file

Since I am visualizing my work using Mathematica, I import some 3D models of molecules to my notebook. So, the question is, is there any way to modify somehow that imported models inside Mathematica ...
6
votes
1answer
845 views

Building a molecule viewer: aesthetic rotations

I am working on building a molecule viewer in Mathematica and am running in to problems with controlling rotation of the molecule (which is rendered as a Graphics3D...
10
votes
2answers
1k views

How can I access the internal function that plots a molecule from a formatted XYZ file?

Mathematica has the ability to plot a molecule using the data contained in an XYZ file. This is a simple text file, of which this is an example. The molecule is plotted using the ...
5
votes
5answers
1k views

Problems with NDSolve and stiffness

I am trying to solve an ODE in chemical kinetics: $$\begin{align*} \frac{\mathrm d[x]}{\mathrm dt} &= -k_1 [x][y]\\ \frac{\mathrm d[y]}{\mathrm dt} &= k_1 [x][y] - k_3[y] \end{align*}$$ My ...
7
votes
1answer
1k views

How can I efficiently write formatted data to a Gaussian Cube file?

I am working with data files that contain information about electronic wave functions. The data format is specified by the quantum chemistry program Gaussian. I need to import the data, manipulate ...
5
votes
2answers
2k views

Using ChemicalData to make molecule graphics

$\require{mhchem}$I would like to take the acetone $\cf{((CH3)2CO)}$ and chloroform $\cf{(HCCl_3)}$ molecules that Mathematica's chemical data provides, and plot them together. I want to show how ...
1
vote
2answers
93 views

How to construct a new list made from a function that operates on two lists

I need to take two lists (each list contains the number of moles of a chemical). I have a function calledFraction that takes the each entry of the list and then calculates the mole fraction of ...
20
votes
4answers
2k views

Accessing list elements by name

First, a bit of a long introduction to my problem: I only have a few weeks of Mathematica experience. I am creating a mathematica application that calculates some material properties of steel based ...
4
votes
2answers
710 views

RefProp in Mathematica

RefProp by NIST is a program that calculates the thermodynamic properties of fluids. I need to call certain RefProp functions ...
3
votes
3answers
330 views

How to deal with units in logarithms?

I'm trying to take a formula, take it's integral which yields a formula with logarithms, and then directly plug in values with units and get an answer. However if the units go into any of the ...
1
vote
1answer
483 views

Exporting as .PDB extension

I am working with the 3-D coordinates of proteins. The file format I import and modify coordinates of is in the .PDB format, and the string to import is also in this same format. Currently, when I try ...
2
votes
0answers
634 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_{\...
15
votes
1answer
674 views

Find elements in a decay chain using IsotopeData

I am trying to write a program using the Mathematica function IsotopeData, but am finding the code troublesome. Due to my (relative) familiarity with Python, I am ...
9
votes
1answer
3k views

Efficient implementation of cubic equation of state

...In this case the Peng Robinson Equation of State. Equations of state are empirical equations with parameters derived from experimental data. They are used to predict pure component and mixture ...
3
votes
1answer
468 views

Efficiently importing XPM matrix data into Mathematica

The XPM file format is an image file format. Although it is primarily intended for icon pixmaps, it can also be used to store matrix data. For example, the GROMACS chemical simulation package uses ...
5
votes
1answer
372 views

Noticeable slowdown in graphical performance when using manipulate

I have been making these mathematica 3D objects that involve a molecule with some sort of surface displayed above them. This is done fairly easily by: ...
15
votes
1answer
591 views

Automatic formatting of isotope symbols in a text cell

InputAutoReplacements is an obvious choice for formatting isotope names in text cells. I'd like to be able to type "1H", for ...
31
votes
1answer
674 views

How to save ChemicalData queries so that they are available immediately on notebook load?

If I put some viscosity (or density, ...) lookups in my notebook, such as: ...
4
votes
1answer
842 views

NDSolve Problem

I am trying to solve a chemical equilibrium ODE with NDSolve where one function is the argument to another. I.E. My equations look like: ...

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