LaTeX/Chemical Graphics

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LaTeX

Getting Started
  1. Introduction
  2. Installation
  3. Installing Extra Packages
  4. Basics

Common Elements

  1. Document Structure
  2. Text Formatting
  3. Paragraph Formatting
  4. Colors
  5. Fonts
  6. List Structures
  7. Special Characters
  8. Internationalization
  9. Rotations
  10. Tables
  11. Title creation
  12. Page Layout
  13. Importing Graphics
  14. Floats, Figures and Captions
  15. Footnotes and Margin Notes
  16. Hyperlinks
  17. Labels and Cross-referencing

Mechanics

  1. Errors and Warnings
  2. Lengths
  3. Counters
  4. Boxes
  5. Rules and Struts

Technical Texts

  1. Mathematics
  2. Advanced Mathematics
  3. Theorems
  4. Chemical Graphics
  5. Algorithms
  6. Source Code Listings
  7. Linguistics

Special Pages

  1. Indexing
  2. Glossary
  3. Bibliography Management
  4. More Bibliographies

Special Documents

  1. Letters
  2. Presentations
  3. Teacher's Corner
  4. Curriculum Vitae

Creating Graphics

  1. Introducing Procedural Graphics
  2. MetaPost
  3. Picture
  4. PGF/TikZ
  5. PSTricks
  6. Xy-pic
  7. Creating 3D graphics

Programming

  1. Macros
  2. Plain TeX
  3. Creating Packages
  4. Themes

Miscellaneous

  1. Modular Documents
  2. Collaborative Writing of LaTeX Documents
  3. Export To Other Formats

Help and Recommendations

  1. FAQ
  2. Tips and Tricks

Appendices

  1. Authors
  2. Links
  3. Package Reference
  4. Sample LaTeX documents
  5. Index
  6. Command Glossary

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chemfig is a package used to draw 2D chemical structures. It is an alternative to ochem. Whereas ochem requires Perl to draw chemical structures, chemfig uses the tikz package to produce its graphics. chemfig is used by adding the following to the preamble:

\usepackage{chemfig}

Basic Usage[edit]

The primary command used in this package is \chemfig{}:

\chemfig{<atom1><bond type>[<angle>,<coeff>,<tikz code>]<atom2>}

<angle> is the bond angle between two atoms (or nodes). There are three types of angles: absolute, relative, and predefined. Absolute angles give a precise angle (generally, 0 to 360, though they can also be negative), and are represented with the syntax [:<absolute angle>]. Relative angles require the syntax [::<relative angle>] and produce an angle relative to the angle of the preceding bond. Finally, predefined angles are whole numbers from 0 to 7 indicating intervals of 45 degrees. These are produced with the syntax [< predefined angle>]. The predefined angles and their corresponding absolute angles are represented in the diagram below.



\chemfig{(-[:0,1.5,,,draw=none]\scriptstyle\color{red}0)
(-[1]1)(-[:45,1.5,,,draw=none]\scriptstyle\color{red}45)
(-[2]2)(-[:90,1.5,,,draw=none]\scriptstyle\color{red}90)
(-[3]3)(-[:135,1.5,,,draw=none]\scriptstyle\color{red}135)
(-[4]4)(-[:180,1.5,,,draw=none]\scriptstyle\color{red}180)
(-[5]5)(-[:225,1.5,,,draw=none]\scriptstyle\color{red}225)
(-[6]6)(-[:270,1.5,,,draw=none]\scriptstyle\color{red}270)
(-[7]7)(-[:315,1.5,,,draw=none]\scriptstyle\color{red}315)
-0
}

Chemfig angles.png


<bond type> describes the bond attaching <atom1> and <atom2>. There are 9 different bond types:


\chemfig{A-B}\\
\chemfig{A=B}\\
\chemfig{A~B}\\
\chemfig{A>B}\\
\chemfig{A<B}\\
\chemfig{A>:B}\\
\chemfig{A<:B}\\
\chemfig{A>|B}\\
\chemfig{A<|B
}\\

Chemfig bonds.png


<coeff> represents the factor by which the bond's length will be multiplied.

<tikz code> includes additional options regarding the color or style of the bond.


A methane molecule, for instance, can be produced with the following code:


\chemfig{C(-[:0]H)(-[:90]H)(-[:180]H)(-[:270]H)}

Methane chemfig.png


Linear molecules (such as methane) are a weak example of this, but molecules are formed in chemfig by nesting.

Skeletal Diagrams[edit]

Skeleton diagrams can be produced as follows:


\chemfig{-[:30]-[:-30]-[:30]}

Butane-skeletal.png


\chemfig{-[:30]=[:-30]-[:30]}

Skeletondiagram2.png

Rings[edit]

Rings follow the syntax <atom>*<n>(code), where "n" indicates the number of sides in the ring and "code" represents the specific content of each ring (bonds and atoms).

\chemfig{A*6(-B-C-D-E-F-)}

Ring chemfig.png

\chemfig{A*5(-B-C-D-E-)}

Ring2 chemfig.png

\chemfig{*6(=-=-=-)}

Ring3 chemfig.png

\chemfig{**5(------)}

Ring4 chemfig.png

Lewis Structures[edit]

Lewis structures can be created by using the command

\lewis{<electron angle><electron>,<atom>}

within \chemfig{}.


Ions[edit]

For example, consider an acetate ion:

\chemfig{-(-[1]O^{-})=[7]O}

Acetate-ion2.png

Because the chemfig commands enters the math mode, ion charges can be added as superscripts (one caveat: a negative ion requires that the minus sign be enclosed in brackets, as in the example).

The charge of an ion can be circled by using \oplus and \ominus:

\chemfig{-(-[1]O^{\ominus})=[7]O}

Acetate-ion.png

Alternatively, charges can be placed above ions using \chemabove{}{}:

\chemfig{-\chemabove{N}{\scriptstyle\oplus}(=[1]O)-[7]O^{\ominus}}

Ion-example.png

Resonance Structures and Formal Charges[edit]

Resonance structures require a few math commands:

% see "Advanced Mathematics" for use of \left and \right
% add to preamble:
%	\usepackage{mathtools}	% \Longleftrightarrow
$\left\{\chemfig{O-N(=[:60]O)-[:300]O}\right\}
\Longleftrightarrow 
\left\{\chemfig{O=N(-[:60]O)-[:300]O}\right\} 
\Longleftrightarrow 
\left\{\chemfig{O-N(-[:60]O)=[:300]O}\right\}$


Chemical Reactions[edit]

Chemical reactions can be created with the following commands:

\chemrel[<arg1>][<arg2>]{<arrow code>}
\chemsign+	% produces a +

In \chemrel{}, <arg1> and <arg2> represent text placed above and below the arrow, respectively.

There are four types of arrows that can be produced with \chemrel{}:

A\chemrel{->}B\par 
A\chemrel{<-}B\par 
A\chemrel{<->}B\par 
A\chemrel{<>}B

Naming Chemical Graphics[edit]

Molecules can be named with the command

\chemname[<dim>]{\chemfig{<code of the molecule>}}{<name>}

<dim> is inserted between the bottom of the molecule and the top of the name defined by <name>. It is 1.5ex by default.

<name> will be centered relative to the molecule it describes.

\chemname{\chemfig{R-C(-[:-30]OH)=[:30]O}}{Carboxylic acid} 
\chemsign{+} 
\chemname{\chemfig{R’OH}}{Alcohol} 
\chemrel{->} 
\chemname{\chemfig{R-C(-[:-30]OR’)=[:30]O}}{Ester} 
\chemsign{+} 
\chemname{\chemfig{H_2O}}{Water}

In the reaction above, \chemname{} inserts 1.5ex plus the depth of the carboxylic acid molecule in between each molecule and their respective names. This is because the graphic for the first molecule in the reaction (carboxylic acid) extends deeper than the rest of the molecules. A different result is produced by putting the alcohol first:

\chemname{\chemfig{R’OH}}{Alcohol} 
\chemsign{+} 
\chemname{\chemfig{R-C(-[:-30]OH)=[:30]O}}{Carboxylic acid} 
\chemrel{->} 
\chemname{\chemfig{R-C(-[:-30]OR’)=[:30]O}}{Ester} 
\chemsign{+} 
\chemname{\chemfig{H_2O}}{Water}

This is fixed by adding \chemnameinit{<deepest molecule>} before the first instance of \chemname{} in a reaction and by adding \chemnameinit{} after the reaction:

\chemnameinit{\chemfig{R-C(-[:-30]OH)=[:30]O}} 
\chemname{\chemfig{R’OH}}{Alcohol} 
\chemsign{+} 
\chemname{\chemfig{R-C(-[:-30]OH)=[:30]O}}{Carboxylic acid} 
\chemrel{->} 
\chemname{\chemfig{R-C(-[:-30]OR’)=[:30]O}}{Ester} 
\chemsign{+} 
\chemname{\chemfig{H_2O}}{Water} 
\chemnameinit{}

Lastly, adding \\ in <name> will produce a line-break, allowing the name to span multiple lines.

Advanced Graphics[edit]

For advanced commands and examples, refer to the chemfig manual, where a more thorough and complete introduction to the package can be found.


Previous: Theorems Index Next: Algorithms


mhchem Package[edit]

mhchem is a package used to typeset chemical formulae and equations. As well as typeset basic 2D chemical structures. To use this package, add the following to your preamble:

\usepackage[version=3]{mhchem}

Chemical species are included using the \ce command. For example


\ce{3H2O} \\
\ce{1/2H2O} \\
\ce{AgCl2-} \\
\ce{H2_{(aq)}} \\

A few things here are automatically typeset; The 2 in \ce{H2O} is automatically subscripted without requiring additional commands. The amount of the species precedes the formula. 1/2 and other fractional amounts are automatically typeset as in \ce{1/2H2O}. The charge in \ce{AgCl2-} is automatically superscripted. If the charge is neither 1 or -1, a ^ will superscript it, as in \ce{AgCl2-}. The phase is not automatically subscripted and needs to be enclosed in parenthesis preceded with a _ as in \ce{H2_{(aq)}.

XyMTeX package[edit]

The following code produces the image for corticosterone below.

\documentclass{letter}
\usepackage{epic,carom}
\pagestyle{empty}
\begin{document}
\begin{picture}(1000,500)
   \put(0,0){\steroid[d]{3D==O;{{10}}==\lmoiety{H$_{3}$C};{{13}}==\lmoiety{H$_{3}$C};{{11}}==HO}}
   \put(684,606){\sixunitv{}{2D==O;1==OH}{cdef}}
\end{picture}
\end{document}
Corticosterone as rendered by XyMTeX