Cfrgtkky

Can you create diagrams of chemical structures in LaTeX?

Example(s) of "chemical structure diagrams":

The answer is: yes. There is actually more than one package to do that:

• chemfig


• ochem


• streeTeX


• XyMTeX


• ConTeXt's PPCHTeX
  

I have used all but XyMTeX and PPCHTeX myself but nowadays only use chemfig any more.

XyMTeX is in my opinion far from being intuitive so I never bothered learning it. It also is not regularly updated to CTAN and not part of TeX Live. CTAN has v4.06 but the newest version is v5.00.

ochem nearly offers all one needs but 1) is not available from either major free distribution and 2) the work is done by a Perl script that translates formulae and reaction schemes into PostScript, which means it doesn't work with pdflatex.

streeTeX is just too limited in its capabilities besides the fact that it is rather old, is not available from either major free distribution and also doesn't work with pdflatex.

chemfig is a rather new and actively maintained package that not only allows to draw skeletal formulae but also has commands for creating whole reaction schemes. It uses TikZ for the drawing.

PPCHTeX is ConTeXt's chemistry module but it can actually be used with LaTeX, too. I have never used it before and trying to typeset the examples below with it has proven to be more complicated than I thought. That's why I simply copied an example from the conTeXtgarden.

So if you want to draw your formulas and schemes with LaTeX rather than an external program like ChemDraw I can only recommend chemfig.

A chemfig example:

documentclass{article}

usepackage{chemfig}

renewcommand*printatom[1]{ensuremath{mathsf{#1}}}

begin{document}



setcrambond{2pt}{}{}

chemfig{

  HO-[2,.5,2]?<[7,.7](-[2,.5]OH)-[,,,,line width=2.4pt](-[6,.5]OH)>[1,.7]

    (-[:-65,.7]O-[:65,.7]?[b](-[2,.7]CH_2OH)<[:-60,.707](-[6,.5]OH)

      -[,,,,line width=2.4pt](-[2,.5,,2]HO)>[:60,.707](-[6,.5]CH_2OH)-[:162,.9]O?[b])

  -[3,.7]O-[4]?(-[2,.3]-[3,.5]HO)}



setatomsep{2em}

chemfig{

  H_3C-[:72]{color{blue}N}

    *5(-

      *6(-(={color{red}O})-{color{blue}N}(-CH_3)-(={color{red}O})-{color{blue}N}(-CH_3)-=)

    --{color{blue}N}=-)}



end{document}

An ochem example:

documentclass{article}

usepackage{ochem}

begin{document}



begin{chemistry}

  set("rLenN",20)

  formula(L,R)

    {

      ring(,,H1=)

        {

          0: bond(r,=C) atom("O") ;

          3: atom("N") bond(r) atom("C",C,R) atom("H$_3$",L) ;

          4: bond(r,=C) atom("O") ;

          5: atom("N") bond(r) atom("CH$_3$",L) ;

          vertex(,1,4,H2=,5)

            {

              1: atom("N") bond(r) atom("C",C,L) atom("H$_3$",R) ;

              3: atom("N") ;

            } ;

        }

    }

end{chemistry}



end{document}

A streetex example:

documentclass{article}

usepackage{stree}

begin{document}



sffamily

stree{0[2N[0{CH$_3$}]4[=2O]6N[4{CH$_3$}]8[=6O]10]/10N=75N[/7{H$_3$C}]/2}



end{document}

A XyMTeX example:

documentclass{article}

usepackage{xymtex}

letsubstfontsffamily

begin{document}



sixheterovi[{ffivefusev[d]{1==N;4==N}{1S==CH$_3$}{b}}e]

  {2==N;4==N}

  {1D==O;3D==O;4S==CH$_3$}



end{document}

A PPCHTeX example

documentclass{article}

usepackage{m-pictex}

usepackage{m-ch-en}% or `m-ch-de' if you like a German interface



begin{document}



startchemical

  chemical[FIVE,FRONT,BB125,+SB3,-SB4,Z4][O]

  chemical[FIVE,FRONT,+R1235,+RZ1235][H,H,SR{HOH_2C},OH]

  chemical[FIVE,FRONT,-R1235,-RZ1235][H,OH,H,H]

stopchemical



end{document}

For the purpose of rational comparison,
more and updated information on XyMTeX would be desirable,
because the example shown in the preceding answer has been
drawn by the plain mode of XyMTeX (providing slightly poor
printing quality within the picture enviroment of LaTeX) and
because the comment on the availability of XyMTeX would
provide readers with a misleading impression.

The latest version (Version 5.00a) of XyMTeX is available
from the XyMTeX homepage (http://xymtex.com/):

http://xymtex.com/fujitas3/xymtex/indexe.html

The two structural formulas shown in the question can be
drawn by using the PostScript-compatible mode (as well
as the PDF-compatible mode) of XyMTeX.

(1) Disaccharide

documentclass{article}

usepackage{xymtexps}%PostScript Mode

%usepackage{xymtexpdf}%PDF Mode

begin{document}



changeunitlength{0.08pt}

utrigonal{0==O;2==%

furanose{4==(yl);1Sa==CH$_{2}$OH;2Sb==lmoiety{HO};%

2Sa==H;3Sb==H;3Sa==OH;4Sb==HOCrlap{H$_{2}$}};%

3==pyranose{1==(yl);2Sa==OH;3Sb==OH;4Sa==HO;5Sb==CH$_{2}$OH}}

hskip4cm

utrigonal{0==O;2==%

fivesugarh{5==O;%

1s==WedgeAsSubst(0,0)(-3,-5){120};%

4s==WedgeAsSubst(0,0)(3,-5){120};%

3s==PutBondLine(-15,0)(305,0){3.2pt}%

}{4==(yl);1Sa==CH$_{2}$OH;2Sb==lmoiety{HO};2Sa==H;%

3Sb==H;3Sa==OH;4Sb==HOCrlap{H$_{2}$}}[abc];%

3==sixsugarh{6==O;1s==WedgeAsSubst(0,0)(-3,-5){120};%

4s==WedgeAsSubst(0,0)(3,-5){120};%

3s==PutBondLine(-15,0)(305,0){3.2pt}%

}{1==(yl);2Sa==OH;3Sb==OH;4Sa==HO;5Sb==CH$_{2}$OH}[abc]}



end{document}

(2) Caffeine

documentclass{article}

usepackage{xymtexps}%PostScript Mode

%usepackage{xymtexpdf}%PDF Mode

usepackage{graphicx}

%pagestyle{empty}

begin{document}



changeunitlength{0.08pt}

sixheterov[e{efivefusev[d]{1==bluex{N};4==bluex{N}}{1==CH$_{3}$}{b}}]

{1==bluex{N};3==bluex{N}}

{1==CH$_{3}$;3==CH$_{3}$;2D==redx{O};4D==redx{O}}

\ vskip0.5cm

{%

letsubstfont=sffamily

purinev[aj]{3==CH$_{3}$;%

4D==addbscolor{green}{redx{O}};5==CH$_{3}$;%

6D==addbscolor{green}{redx{O}};7==CH$_{3}$}

quad

defgrayx#1{xymcolor{gray}{#1}}

nonaheterov[aj]{1==bluex{N};3==bluex{N};5==bluex{N};7==bluex{N}}%

{3==addbscolor{red}{grayx{CH$_{3}$}};%

4D==addbscolor{green}{redx{O}};5==addbscolor{red}{grayx{CH$_{3}$}};%

6D==addbscolor{green}{redx{O}};7==addbscolor{red}{grayx{CH$_{3}$}}}

}



end{document}

For further information, please see XyMTeX-tips in the XyMTeX homepage
(http://xymtex.com/):

http://xymtex.com/fujitas3/xymtex-tips/indexe.html

The present topic has been deposited as 130208a-ps.pdf, 130208b-ps.pdf etc.

As for a tool for publishing a book on organic chemistry, the combination of
XyMTeX-LaTeX has been used to publish the following book:

S. Fujita, "Organic Chemistry of Photography", Springer-Verlag (2004),

in which all of the structural formulas (among 480 illustrations) have been
drawn by using XyMTeX.