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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1
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0answers
78 views

Representing vertices as spheres in Graphics 3D [closed]

I'm representing a portion of molecule, P3HT, in Mathematica as a pentagon that I build using Polygon and Graphics3D. I would like to represent the vertices of the pentagon as spheres(corresponding ...
23
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1answer
2k views

Gillespie Stochastic Simulation Algorithm

The Gillespie SSA is a Monte Carlo stochastic simulation algorithm to find the trajectory of a dynamic system described by a reaction (or interaction) network, e.g. chemical reactions or ecological ...
-1
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1answer
147 views

Problem with a chemical optimization problem [closed]

First of all, I want to say that I'm quite new to Mathematica. I searched a lot on this site to learn how to solve my problem, which this is the problem of my life! I want to minimize a function. It ...
7
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3answers
487 views

How can I draw ternary plot by these data?

I have these data and want to draw similar fifures in mathematica. any one can help me? ...
2
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3answers
132 views

Parsing/validating CAS registry number identifiers

Mathematica includes a lot of curated information on molecular structure and properties available through ChemicalData and ...
6
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2answers
239 views

Atom weight in SI units

In chemistry is very common to use the units grams/mol for the atomic weight, so the mass of one atom (of Tin, for example) is calculated as : massOfOneAtom = (0.11871 (Kg/mol))/(AvogadroConstant (1/...
14
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2answers
1k views

Pulsed NMR animation

I'm new here and have never interacted with the community so excuse me if this has been asked before or if I format incorrectly or anything like that. Anyway, I'm trying to make an animation for a ...
24
votes
3answers
2k views

Plot 3D model of DNA in Mathematica

My friend asked me if we can plot a 3D model of DNA (deoxyribonucleic acid) in Mathematica. However, I am not really familiar with this and I don't know if Mathematica can do this. Could you answer ...
8
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5answers
989 views

Faking MoleculePlot for compounds where it isn't available

Mathematica's ChemicalData has a lot of useful information, but many compounds only have flat 2D structure diagrams rather than the cool 3D ...
4
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1answer
727 views

Modeling chemical reactions: can Mathematica tell the end result of a reaction?

I am curious about using Mathematica for modelling chemical reactions but don't really know much about the Mathematica software yet. So I was reading this page at wolfram.com which explains some of ...
1
vote
2answers
310 views

Specify the color of each residue in a protein (PDB)?

I'm importing a *.pdb file containing a single protein. Mathematica automatically produces a plot of the protein. I want to specify the color of each residue independently, in this plot. Is this ...
1
vote
2answers
243 views

How Do i Extract Only The Coordinates xyz (Number) From This Log file

this Log contains the information of all coordinates of many atoms in a molecular dynamics simulation for a long sequence of time steps, along with some extra information other than the coordinates. ...
3
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2answers
665 views

How to Import This XYZ format file

Here is the .XYZ format file NP3D.XYZ Somehow i cannot import this file.It return an error box :- "Cannot Import Data As XYZ Format." it contains 1000 snapshot of 10 Carbon particles coordinate ...
6
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2answers
128 views

ChemicalData[] error: “L-Cysteine” is not a known entity, class,

If I execute: ChemicalData["L-Cysteine", "MolarMass"] I get the following error: ChemicalData::notent: "L-Cysteine" is not a known entity, class, or tag for ...
5
votes
2answers
399 views

How to refer to amino acids by their single-letter abbreviations in ChemicalData[]?

ChemicalData["AminoAcids"] returns the 20 amino acids. There are some properties available, like the molar mass: ...
6
votes
1answer
269 views

Calculate the ESP Grid based on Density Grid

I want to build a fast way to convert a density grid file into a grid file of the respective electrostatic potential (ESP; also known as MEP, the molecular electrostatic potential). This calculation ...
5
votes
1answer
111 views

ElementData possible oxidation states

Is there any way to find out the possible oxidation states for a given element? Something like this: ElementData[1, "OxidationStates"] -> {-1, 1} Here is a ...
-1
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1answer
341 views

Double integrals in quantum chemistry [closed]

In quantum chemistry we often encounter integrals like this: I can't understand what is the problem. Can anybody help me?
12
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3answers
2k views

Radial distribution function

I have tried to rewrite my old IDL code to calculate the radial correlation function for a regular 2D crystal structure. The theory behind this function is given here: https://en.wikipedia.org/wiki/...
0
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1answer
208 views

Conditional function plot in Manipulate

I'm looking into the stability of solution of a set of chemical rate equations. There is a set of rate constants {$k_i$} I which to manipulate, and I want to find the stable solutions where $\frac{\...
2
votes
2answers
404 views

Change bond cutoff distance when plotting .xyz files

When plotting a molecule from a xyz data file, Mathematica automatically adds the bonds between the atoms. But in my case it adds too many bonds, not only between nearest neighbours but also between ...
4
votes
2answers
138 views

How to format inline chemical formulas?

So I like using Mathematica for quickly typing up notes and progress reports. However, I've never liked the way in which it autoformats inline cells. I've been able to modify style sheets to some ...
2
votes
1answer
485 views

Raman spectra collected at over 200 spatial points and in separate text files, how can I collate and visualize the data?

I need to do density plot and contour plot of Raman spectra with a specific peak, Raman mode, as a way to study the intensity distribution of such peak throughout the sample used. As such ...
5
votes
1answer
138 views

Get Isotope Data and Electron Mass in Same Units - kg and Kilograms

I'm trying to find the nuclear mass of $^{238}\text{U}$. To do this, I subtract the electron mass from the atomic mass. I'd like to find the final answer in kilograms. I'd also like to use Mathematica'...
7
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2answers
591 views

How to I extract the element name of a chemical compound in a string?

Say I have a compound Fe3O4, and I want to separate the name of elements and number. The code I write for separate number is ...
-4
votes
2answers
402 views

How do I write a function that returns the atomic mass given an element's symbol?

I want to write a function atomMass that, given an element's symbol, say "He", returns the atomic mass for the element (in this case ~ 4.0026). I do not even know where to start with this question. ...
2
votes
1answer
132 views

Can't obtain Real results using NSolve

I am trying to find the critical properties of the Carnahan-Starling equation of state, $$p=\rho R T\frac{1+b\rho /4+(b\rho/4)^2-(b\rho/4)^3}{(1-b\rho /4)^3}-a\rho^2$$ using this system of equations, ...
3
votes
1answer
189 views

Adding text on an .xyz file of an atom

I know it is possible to view .xyz files of coordinates in Mathematica. I tried to write some text on a specific atom using Text, but I was not successful. How can i do that? Thanks for the help in ...
7
votes
3answers
225 views

How to find the standard names of chemicals in ChemicalData?

When I try to get info on acetic acid with the ChemicalData function there are only "aceticAcid$l^{1}oxidanylEster" and ...
1
vote
0answers
85 views

Random protein in 3D [closed]

I would like to ask for help how to encode the following: I make a random sequence of aminoacids to make a protein, but how to make this visible like this: ...
2
votes
0answers
508 views

Fitting data using ParametricNDSolveValue and NonlinearModelFit [closed]

I'm trying to evaluate the kinetics of the chemical reaction. For that I need to fit my experimental data to the kinetic equation. These are my steps in Mathematica. ...
2
votes
1answer
112 views

Setting an upper limit in the NDSOLVE calculations

I have built a code to solve a system of differential equations in the form: $\displaystyle \frac{d(AB)}{dt}=kn(A)n(B)$ Here I present a small version of it: ...
2
votes
0answers
168 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 ...
4
votes
4answers
860 views

Trying to model a chemical reaction - NDSolve::litarg error

I am trying to model a chemical reaction with NDSolve. I have specified the known differential equations and parameters, ...
3
votes
1answer
227 views

Fails to apply NonlinearModelFit on a numerically evaluated model defined as a system of ODEs

I call for your help with because I'm getting troubles to fit a model defined through a system of ODEs. The system of ODEs is as follows: ...
5
votes
1answer
441 views

PDB Graphics Options: Opacity and Scale to superimpose on 3D point plot

I am trying to superimpose a PDB file into a 3D plot of points extracted from the PDB model, while making the PDB somewhat transparent for easy viewing of plotted points. My problems are as follows. ...
1
vote
1answer
333 views

Modeling a stellar atmosphere

I'm trying to model a stellar atmosphere using Mathematica. Basically I'm working in a physical and chemical model which combined should give me a profile of the chemical abundance in the atmosphere. ...
6
votes
3answers
643 views

When using NDsolve, how to determine the positions of steady states?

I am currently trying to numerically solve a set of ordinary differential equations of chemical kinetics. However, I want to implement perturbations only when system reach steady states. For example ...
4
votes
1answer
281 views

Solving a chemical system using NDSolve

I have to solve a set of coupled differential equations and am not sure how to proceed. It is a model of a chemical process where I'm interested to find the species concentration as $r$ varies. For a ...
4
votes
3answers
2k views

Using NDSolve within Manipulate

I'm trying to use NDSolve inside manipulate. Specifically, I have a series of differential equations with coefficients, k1, k2, <...
5
votes
2answers
250 views

Generating and Imaging of the water molecules with Graphics3D [duplicate]

my problem is I don't know how to generate e.g. 20 water molecules: Graphics3D[ Rotate[First@ChemicalData["Water", "MoleculePlot"], 45 Degree, {8, .5, 0}]] ...
7
votes
2answers
478 views

How can export into an .XYZ file using decimals without scientific notation?

I have seen the other posts relating to this however there seems to be more restrictions when exporting to .XYZ. I am pretty new to this but I have been searching for hours. Basically, I have a $n\...
5
votes
3answers
970 views

How to fit parameters in a system of coupled differential equations

Problem description: I'm studying a chemical reaction that can be modeled by a system of coupled differential equations, and I want to use measured data to determine the parameters that appear in the ...
4
votes
2answers
406 views

How can I get the solubility value of nitrogen in water at 10 degrees Celsius with Mathematica?

How can I get the solubility value of nitrogen in water at 10 °C with Mathematica? The site engineering toolbox dot com gives graphs of such values, but I want the numerical value. Related thread on ...
2
votes
1answer
234 views

Solving ODES in order to find unknown constants

I am trying to solve a set of ODES which represent a second order consecutive chemical reaction. ...
2
votes
1answer
94 views

Calculate the partial vapor pressures of a variable at xB = 0.75 based on the interpolation functions of the data

I'm having troubles in solving an exercise for an assignment in my Chemistry course. Talking about interpolations, I've already have a graph but I need to calculate the partial vapor pressures of ...
3
votes
1answer
345 views

Change the colors of individual atoms in a .mol or XYZ file

Similar to (Changing the atom color for plotting xyz-files), I want to take a molecule and then simply change the colors of individual atoms. I don't want to change all atoms of a type to a color (say,...
2
votes
2answers
203 views

Accessing chemical property data for specific conditions?

There is a wealth of data for various chemicals available through Mathematica. For instance: ...
9
votes
3answers
776 views

Changing the atom color for plotting xyz-files

Mathematica takes the standard color code for atoms when plotting an *.xyz file, but I want to customize the color for the specific atoms. I really become desperate as I did not get it so far. ...
8
votes
1answer
2k views

Constructing primitive cell using information from ChemicalData

I would like to construct a primitive cell (figure shown) and possibly the two-dimensional layout (figure from here) using the following input. Any clues as to how this can be done? ...