% !arara: pdflatex % !arara: biber % arara: pdflatex % arara: pdflatex % -------------------------------------------------------------------------- % the CHEMMACROS bundle % chemmacros_en.tex % macros and commands for chemists % -------------------------------------------------------------------------- % Clemens Niederberger % -------------------------------------------------------------------------- % https://bitbucket.org/cgnieder/chemmacros/ % contact@mychemistry.eu % -------------------------------------------------------------------------- % If you have any ideas, questions, suggestions or bugs to report, please % feel free to contact me. % -------------------------------------------------------------------------- % Copyright 2011-2013 Clemens Niederberger % % This work may be distributed and/or modified under the % conditions of the LaTeX Project Public License, either version 1.3 % of this license or (at your option) any later version. % The latest version of this license is in % http://www.latex-project.org/lppl.txt % and version 1.3 or later is part of all distributions of LaTeX % version 2005/12/01 or later. % % This work has the LPPL maintenance status `maintained'. % % The Current Maintainer of this work is Clemens Niederberger. % -------------------------------------------------------------------------- \documentclass[load-preamble+]{cnltx-doc} \usepackage[utf8]{inputenc} \usepackage[greek=newtx]{chemmacros} \setcnltx{ package = {chemmacros}, title = \huge the \chemmacros\ bundle, url = https://bitbucket.org/cgnieder/chemmacros/ , authors = Clemens Niederberger , email = contact@mychemistry.eu , info = { packages \chemmacros\ (v\csname chemmacros@version\endcsname), \chemformula\ (v\csname chemformula@version\endcsname), \ghsystem\ (v\csname ghsystem@version\endcsname) and \chemgreek\ (v\csname chemgreek@version\endcsname)\\[2ex] {\Large documentation for the \chemmacros\ package}} , abstract = {% \centering \includegraphics{chemmacros-logo.pdf} \par } , add-cmds = { abinitio, activatechemgreekmapping, AddRxnDesc, anti, aq, aqi, ba, bond, bridge, cd, ch, changechemgreeksymbol, charrow, chcpd, chemabove, chemalpha, chembeta, chemgamma, chemdelta, chemDelta, chemformula@bondlength, chemomega, chemphi, chemPhi, chemsetup, chlewis, chname , cip, cis, ch, CNMR, data, DeclareChemArrow, DeclareChemBond, DeclareChemBondAlias, declarechemgreekmapping, DeclareChemIUPAC, DeclareChemLatin, DeclareChemNMR, DeclareChemParticle, DeclareChemPhase, DeclareChemReaction, DeclareChemState, delm, delp, Delta, Dfi, el, ElPot, endo, Enthalpy, enthalpy, Entropy, fmch, fpch, fscrm, fscrp, gas, ghs, ghslistall, ghspic, Gibbs, gram, hapto, HNMR, Helmholtz, hydrogen, insitu, invacuo, iupac, Ka, Kb, Kw, Lfi, listofreactions, lqd, mch, mega, meta, mhName, NewChemArrow, NewChemBond, NewChemBondAlias, newchemgreekmapping, NewChemIUPAC, NewChemLatin, NewChemNMR, NewChemParticle, NewChemPhase, NewChemReaction, NewChemState, newman, nitrogen, NMR, Nu, Nuc, orbital, ortho, ox, OX, oxygen, para, pch, per, pH, phase, phosphorus, photon, pKa, pKb, pOH, pos, positron, Pot, prt, Rad, redox, RenewChemArrow, RenewChemBond, renewchemgreekmapping, RenewChemIUPAC, RenewChemLatin, RenewChemNMR, RenewChemParticle, RenewChemPhase, RenewChemState, Sf, scrm, scrp, second, selectchemgreekmapping, setchemformula, ShowChemArrow, ShowChemBond, sld, Sod, State, sulfur, trans, val } , add-silent-cmds = { addplot, bottomrule, cancel, cdot, ce, cee, celsius, centering, chemfig, chemname, clap, cnsetup, color, cstack, cstsetup, DeclareInstance, DeclareSIUnit, definecolor, draw, electronvolt, footnotesize, glqq, grqq, hertz, hspace, includegraphics, intertext, IUPAC, joule, kilo, latin, lewis, Lewis, liquid, ltn, metre, midrule, milli, mmHg, mole, nano, nicefrac, num, numrange, ominus, oplus, percent, pgfarrowsdeclarealias, pgfarrowsrenewalias, renewtagform, rightarrow, sample, scriptscriptstyle, setatomsep, setbondoffset, sfrac, shorthandoff, si, SI, sisetup, square, subsection, textcolor, textendash, textsuperscript, tiny, toprule, upbeta, upeta, upgamma, usetikzlibrary, volt, vphantom, vspave, xspace, z@, z@skip } } \usepackage{chemfig,booktabs,cancel,varioref,csquotes} \expandafter\def\csname libertine@figurestyle\endcsname{LF} \usepackage[libertine]{newtxmath} \expandafter\def\csname libertine@figurestyle\endcsname{OsF} \usepackage[biblatex]{embrac} \ChangeEmph{[}[,.02em]{]}[.055em,-.08em] \ChangeEmph{(}[-.01em,.04em]{)}[.04em,-.05em] \usepackage[accsupp]{acro} \acsetup{ long-format = \scshape , short-format = \scshape } \DeclareAcronym{ghs}{ short = ghs , long = Globally Harmonized System of Classification and Labelling of Chemicals , pdfstring = GHS , accsupp = GHS } \DeclareAcronym{eu}{ short = EU , long = European Union , pdfstring = EU , accsupp = EU } \DeclareAcronym{iupac}{ short = iupac , long = International Union of Pure and Applied Chemistry , pdfstring = IUPAC , accsupp = IUPAC } \DeclareAcronym{UN}{ short = un , long = United Nations , pdfstring = UN , accsupp = UN } \DeclareAcronym{dvi}{ short = dvi , long = device independent file format , pdfstring = DVI , accsupp = DVO } \DeclareAcronym{pdf}{ short = pdf , long = portable document file , pdfstring = PDF , accsupp = PDF } \DeclareAcronym{id}{ short = id , long = identification string , pdfstring = ID , accsupp = ID } \chemsetup{ option/synchronize , chemformula/format = \libertineLF } % \colorlet{chemformula}{black!90} \sisetup{ detect-mode=false, mode=text, text-rm=\libertineLF } \usepackage{filecontents} \defbibheading{bibliography}{\addsec{References}} \addbibresource{\jobname.bib} \begin{filecontents*}{\jobname.bib} @book{iupac:greenbook, author = {E. Richard Cohan and Tomislav Cvita\v{s} and Jeremy G. Frey and Bertil Holmstr\"om and Kozo Kuchitsu and Roberto Marquardt and Ian Mills and Franco Pavese and Martin Quack and J\"urgen Stohner and Herbert L. Strauss and Michio Takami and Anders J Thor} , title = {``Quantities, Symbols and Units in Physical Chemistry'', \acs{iupac} Green Book} , sorttitle = {Quantities, Symbols and Units in Physical Chemistry} , indexsorttitle = {Quantities, Symbols and Units in Physical Chemistry} , edition = {3rd Edition. 2nd Printing} , year = {2008} , publisher = {\acs{iupac} \&\ RSC Publishing, Cambridge} } @book{iupac:redbook, author = {Neil G. Connelly and Ture Damhus and Richard M. Hartshorn and Alan T. Hutton} , title = {``Nomenclature of Inorganic Chemistry'', \acs{iupac} Red Book} , sorttitle = {Nomenclature of Inorganic Chemistry} , indexsorttitle = {Nomenclature of Inorganic Chemistry} , year = {2005} , publisher = { \acs{iupac} \&\ RSC Publishing, Cambridge} , isbn = {0-85404-438-8} } @book{iupac:bluebook, author = {R. Panico and W. H. Powell and J-C. Richer}, title = {``Nomenclature of Organic Chemistry, Sections A, B, C, D, E, F, and H'', \acs{iupac} Blue Book}, edition = {\mkbibacro{draft}}, date = {2004-10-07}, url = {http://old.iupac.org/reports/provisional/abstract04/BB-prs310305/CompleteDraft.pdf}, urldate = {2013-07-07} } @misc{eu:ghsystem_regulation, author = {{The European Parliament and The Council of the European Union}}, title = {Regulation (EC) No 1272/2008 of the European Parliament and of the Council} , subtitle = {on classification, labelling and packaging of substances and mixtures, amending and repealing Directives 67/548/EEC and 1999/45/EC, and amending Regulation (EC) No 1907/2006} , journal = {Official Journal of the European Union} , date = {2008-12-16} } @online{unece:ghsystem_implementation, author = {{United Nations Economic Commission for Europe}} , title = {GHS Implementation} , url = {http://www.unece.org/trans/danger/publi/ghs/implementation_e.html} , urldate = {2012-03-20} , date = {2012-03-20} } \end{filecontents*} \DeclareInstance{xfrac}{chemformula-text-frac}{text} { scale-factor = 1 , denominator-bot-sep = -.2ex , denominator-format = \scriptsize #1 , numerator-top-sep = -.2ex , numerator-format = \scriptsize #1 , slash-right-kern = .05em , slash-left-kern = .05em } \usetikzlibrary{calc,positioning,decorations.pathmorphing,patterns} % \newpackagename\chemmacros{chemmacros} \newpackagename\chemformula{chemformula} \newpackagename\ghsystem{ghsystem} \newpackagename\chemgreek{chemgreek} \newidxcmd\manual{\textsf{#1}}[\ (manual)] \newenvironment{codedesc} {% \def\Code##1{\item\code{##1}\hfill\newline}% \cnltxlist } {\endcnltxlist} \renewcommand*\AmS{\hologo{AmS}} \newcommand*\TikZ{Ti\textit{k}Z} \newcommand*\tablehead[1]{\textrm{\bfseries#1}} \NewChemPhase{\aqi}{aq,$\infty$}% aqueous solution at infinite dilution \NewChemPhase{\cd}{cd}% condensed phase \NewChemPhase{\lc}{lc}% liquid crystal \newname\hensel{Martin}{Hensel} \newname\pedersen{Bjørn}{Pedersen} \begin{document} \part{Preliminaries} \section{Licence, Requirements and \textsc{README}} \license The \chemmacros\ bundle needs the bundles \bnd{l3kernel}~\cite{bnd:l3kernel} and \bnd{l3packages}~\cite{bnd:l3packages}. It also needs the packages \needpackage{siunitx}~\cite{pkg:siunitx}, \needpackage{mathtools}~\cite{pkg:mathtools}, \needpackage{bm}~\cite{pkg:bm}, \needpackage{nicefrac}~\cite{pkg:nicefrac} and \needpackage{environ}~\cite{pkg:environ} as well as \pkg{tikz}\footnote{\CTANurl[graphics]{pgf}}~\cite{pkg:pgf} and the \TikZ\ libraries \code{calc} and \code{arrows}. Language support is done with the help of the \needpackage{translations}~\cite{pkg:translations}. The \chemmacros\ package also loads the other packages of this bundle. The package option \option{xspace} also loads the package \pkg{xspace}~\cite{pkg:xspace}. The \chemmacros\ bundle bundles four packages: \chemmacros, \chemformula, \ghsystem\ and \chemgreek. The package dependencies of the other packages are described in the respective manuals. \section{Motivation and Background} \chemmacros\ started some years ago as a growing list of custom macros that I frequently used. I cannot completely recall when and why I decided to release them as a package. Well -- here we go and you might find it useful, too, I hope. Both the macros and their functionality have changed over time and quite a lot have been added. Many things have been unified and what's probably most important: many possibilities to customize have been added, too. Probably every chemist using \LaTeXe\ is aware of the great \pkg{mhchem} package by \hensel. There have always been some difficulties intertwining it with \chemmacros, though. Also, some other minor points in \pkg{mhchem} always bothered me, but they hardly seemed enough for a new package. They weren't even enough for a feature request to the \pkg{mhchem} author. The challenge and the fun of creating a new package and the wish for a highly customizable alternative led to \chemformula\ after all. \chemformula\ works very similar to \pkg{mhchem} but is more strict as to how compounds, stoichiometric factors and arrows are input. In the same time \chemformula\ offers possibilities to customize the output that \pkg{mhchem} does not. Although \chemformula\ is meant as an \emph{alternative} to \pkg{mhchem} \chemmacros\ only loads \chemformula\ and uses it at various places internally, too. As a chemist you are probably aware of the fact that the \acl{UN} have developed the \ac{ghs} as a global replacement for the various different systems in different countries. While it has not been implemented by all countries yet~\cite{unece:ghsystem_implementation}, it is only a matter of time. The package \ghsystem\ enables you to typeset all the hazard and precautionary statements and pictograms in a very easy way. The statements are taken from \acs{eu} regulation 1272/2008~\cite{eu:ghsystem_regulation}. There are four points I hope I have achieved with this bundle: \begin{itemize} \item intuitive usage as far as the syntax of the commands is concerned \item the commands shall not only make typesetting easier and faster but also the document source more readable with respect to semantics (\code{\cs{ortho}-dichlorobenzene} is easier to read and understand than \code{\cs*{textit}\Marg{o}-dichlorobenzene}) \item as much customizability as I could think of so every user can adapt the commands to his or her own wishes \item default settings compliant with the recommendations of the \acf{iupac}. \end{itemize} Especially the last point needed some pushing from users to get things right in many places. If you find anything not compliant with \ac{iupac} recommendations\footnote{This does not concern the \cs{ox} command. The \ac{iupac} version is \cs{ox}\sarg.} I would welcome an email very much! \section{News} \subsection{Version~4.0} With version~4.0 some changes have been made: \begin{itemize} \item first of all the packages \chemformula\ and \ghsystem\ do not load \chemmacros\ any more which means they can be used independently. \item the option \option{bpchem} has been dropped. \item the commands \cs{mch} and \cs{pch} now match \chemformula's charges. \item the option \option{method} has been dropped. \item the option \option{append} has deprecated. \item the option \option{greek} has been extended to support other uppercase greek letters, for example those provided by \pkg{kpfonts}. This is handled internally by the new package in the family: \chemgreek. This package is not really a package for usage at a user-level but could in principle be used to extend the \option{greek} option. \item language support is now done with the help of the \pkg{translations}. This means that with version~4.0 the document language is recognized automatically. \item the status of the commands \cs{Lfi} and \cs{Dfi} has been changed from \emph{deprecated} to \emph{dropped}. \item various other changes like bug fixes and improvements on the typographical appearance of \chemformula's inline formulae with \cs{ch}. \end{itemize} \subsection{Version~4.2} \begin{itemize} \item Changed particles with electron pairs such as \cs{ba} to use \chemformula's new macro \cs{chlewis} for the Lewis electrons. \item Changed the implicit \cs*{Delta} in the thermodynamic state variables into \cs*{ChemDelta} to ensure that an upright symbol is used. \item Change in the syntax of \cs{DeclareChemState} and \cs{RenewChemState}. The old syntax is still supported but discouraged. \end{itemize} \subsection{Version 4.3} \begin{itemize} \item All one-letter \acs{iupac} macros have been exchanged in favour of more meaningful macro names. The one-letter commands still exist for backward compatibility (and to some users no doubt also for convenience). They are no longer recommended though. One-letter commands seldomly have meaningful names and often they've also been defined by other packages. This means they make collaboration more difficult than it needs to be and are a source for package conflicts. \chemmacros\ used to solved the latter problem by only providing them inside the argument of \cs{iupac}\label{desc:one-letter-commands}. The one exception \chemmacros\ makes is the command \cs{p} (for things like \pH) which is and will remain an official command. \item The environment \env{experimental} has got a number of new options, see section~\ref{sec:experimental-customization}. \item The commands \cs*{DeclareChem\meta{...}} now don't give an error any more if the command already exists. This is more consistent with \LaTeX's \cs*{DeclareRobustCommand}. For all those commands a version \cs*{NewChem\meta{...}} is introduced that \emph{does} give an error if the new command is already defined. \item The package option \option{strict} has been deprecated. \item The package option \option{cmversion} has been deprecated. \item The command \cs{mhName} has been dropped. \end{itemize} \section{Package Options}\label{sec:options} \chemmacros\ has several package options. They all are used as key/value pairs like \begin{sourcecode} \usepackage[option1 = , option2 = ]{chemmacros} \end{sourcecode} Some also can be used without value (\verbcode+\usepackage[option1]{chemmacros}+), which means that the \default{underlined} value is used. Both \chemformula\ and \ghsystem\ don't have package options of their own. If you load them explicitly any given option will silently fail. Options can then only be set using the setup command. \begin{options} % circled \keychoice{circled}{\default{formal},all,none}\Module{option}\Default{formal} \chemmacros\ uses two different kinds of charges which indicate the usage of real ($+/-$) and formal (\fplus/\fminus) charges. The option \code{formal} distinguishes between them, option \code{none} displays them all without circle, option \code{all} circles all. % circletype \keychoice{circletype}{\default{chem},math}\Module{option}\Default{chem} This option switches between two kinds of circled charge symbols: \cs{fplus} \fplus\ and \verbcode+$\oplus$+ $\oplus$. % ghsystem \keybool{ghsystem}\Module{option}\Default{true} \keyis{ghsystem}{false} disables the automatic loading of the \ghsystem\ package. % greek \keychoice{greek}{\default{auto},upgreek,textgreek,mathdesign,kpfonts,newtx,% fourier,textalpha}\Module{option}{}% empty group pushes default value to % next line \Default{auto} This option determines how the letters \cs{chemalpha} and friends are typeset. See pages~\pageref{desc:greek} and~\pageref{par:greek_letters} for more information. Please note that this option \emph{does not load either \pkg{upgreek}, \pkg{kpfonts} or any other package!} It only determines which one to choose if available. The option \code{auto} will detect if any of the packages needed for one of the options has been loaded and use it if available. If more than one of the packages has been loaded the option will choose the one listed first in the above choice list. If you explicitly choose an option other than \code{auto} or \code{math} you also have to load the corresponding package. \emph{This option can only be chosen in the preamble}. % iupac \keychoice{iupac}{auto,restricted,strict}\Module{option}\Default{auto} Take care of how \ac{iupac} naming commands are defined, see page~\pageref{desc:iupac}. % language \keychoice{language}{american,british,english,french,german,italian,ngerman}% \Module{option}\Default Load the language used by \chemmacros. \emph{This option can only be chosen in the preamble}. % Nu \keychoice{Nu}{\default{chemmacros},mathspec}\Module{option}\Default{chemmacros} The package \pkg{mathspec} also defines a macro \cs{Nu}. This option chooses which definition holds, see page~\pageref{Nu}. \emph{This option can only be chosen in the preamble}. % synchronize \keybool{synchronize}\Module{option}\Default{false} The setting \code{true} will tell \chemmacros\ to adapt the font settings of \chemformula. % xspace \keybool{xspace}\Module{option}\Default{true} With this option most commands are defined with a \cs*{xspace}. \end{options} \section{Setup}\label{sec:setup} Various of \chemmacros', \chemformula's and \ghsystem's commands have key/value pairs with which they can be customized. Most times they can be used as (optional) argument of the commands themselves. They also can most times be used with the \cs{chemsetup} command. \begin{commands} \command{chemsetup}[\oarg{module}\Marg{\meta{key} = \meta{value}}] Set up the options for module \meta{module} only or \command{chemsetup}[\Marg{\meta{module}/\meta{key} = \meta{value}}] in combination with options from other modules. \end{commands} The keys each belong to a module, which defines for which commands they are intended for. If a key is presented, you'll see the module to which it belongs in the left margin. You have two ways to use keys with the \cs{chemsetup}, as you can see above. The package options can also be seen as keys belonging to the module \module{option}. This means they can also be used with the \cs{chemsetup} command (except for the option \choicekey{version}{1,2,3}). \begin{example} \chemsetup[option]{circled=none} \leavevmode\mch\ \pch\ \fmch\ \fpch\ \el\ \prt \par \chemsetup[option]{circled=formal} \leavevmode\mch\ \pch\ \fmch\ \fpch\ \el\ \prt \par \chemsetup[option]{circletype=math} \leavevmode\mch\ \pch\ \fmch\ \fpch\ \el\ \prt \par \chemsetup{option/circletype=chem,option/circled=all}% \leavevmode\mch\ \pch\ \fmch\ \fpch\ \el\ \prt \par \chemsetup{option/circletype=math} \leavevmode\mch\ \pch\ \fmch\ \fpch\ \el\ \prt \end{example} Keys \emph{not} belonging to a module \emph{cannot} be used with \cs{chemsetup}! All options of \chemformula\ belong to the module \module{chemformula} and all of \ghsystem's options belong to the module \module{ghsystem}. \section{Language Settings}\label{sec:languages} \subsection{How it Works} \chemmacros\ uses the \pkg{translations} package for a number of language dependent strings. That means that if a suitable translation to those strings is given the \pkg{babel}~\cite{pkg:babel} or \pkg{polyglossia}~\cite{pkg:polyglossia} language will be picked up automatically. You can, however, overwrite this mechanism by explicitly chosing the language you want. This is done with the package option \option{language}. Section~\ref{sec:supported-languages} lists all language dependent strings and the provided translations. \subsection{Supported Languages}\label{sec:supported-languages} By choosing the option \begin{commands} \command{chemsetup}[\oarg{option}\Marg{language=\meta{language}}] Selection of the language \meta{language}. \end{commands} you can set the language that is used by \chemmacros\ if you want it to be a \emph{different language than your main document language}. There are some language definitions made by \chemmacros. They include \begin{itemize} \item the header of the list of reactions, \item the beginning of the entries in the list of reactions, and \item the H- and P-statements of the \ac{ghs} statements. \end{itemize} \chemmacros\ uses the \pkg{translations} to get translated strings sensitive to \pkg{babel} or \pkg{polyglossia} settings. All pre-defined \pkg{translations} keys are listed in table~\ref{tab:language-dependent-strings}. To some of those a few non-English translations are provided. \begin{table} \centering \caption{Language dependent strings.} \label{tab:language-dependent-strings} \begin{tabular}{>{\ttfamily}ll} \toprule \normalfont\bfseries \pkg{translations} key & \bfseries English default \\ \midrule K-acid & \GetTranslation{K-acid} \\ K-base & \GetTranslation{K-base} \\ K-water & \GetTranslation{K-water} \\ \midrule phase-sld & \GetTranslation{phase-lqd} \\ phase-lqd & \GetTranslation{phase-sld} \\ phase-gas & \GetTranslation{phase-gas} \\ phase-aq & \GetTranslation{phase-aq} \\ \midrule list-of-reactions & \GetTranslation{list-of-reactions} \\ reaction & \GetTranslation{lor-reaction} \\ \bottomrule \end{tabular} \end{table} Currently this includes the following translations: \begin{sourcecode} % subscript used in \Ka: \DeclareTranslation{German}{K-acid}{S} % the phases \sld and \lqd: \DeclareTranslation{German}{phase-sld}{f} \DeclareTranslation{German}{phase-lqd}{f{}l} % heading of the list of reactions: \DeclareTranslation{English}{list-of-reactions}{List of reactions} \DeclareTranslation{German} {list-of-reactions}{Reaktionsverzeichnis} \DeclareTranslation{Italian}{list-of-reactions}{Elenco delle reazioni} \DeclareTranslation{French} {list-of-reactions}{Table des r\'eactions} % name at the beginning of each entry in the list of reactions: \DeclareTranslation{English}{reaction}{Reaction} \DeclareTranslation{German} {reaction}{Reaktion} \DeclareTranslation{Italian}{reaction}{Reazione} \DeclareTranslation{French} {reaction}{R\'eaction} \end{sourcecode} All other languages will fall back to English. However, you can always add the translation you want. If you send me an email with translations you'd like to have added to \chemmacros\ I'll gladly add them. \subsection{Specialties} \subsubsection{German} If you choose \code{german/ngerman} the phase commands \cs{sld} and \cs{lqd} and the command \cs{pKa} are translated. \subsubsection{Italian} \NewChemIUPAC{\ter}{\textit{ter}}\NewChemIUPAC{\sin}{\textit{sin}}% Choosing the language \code{italian} defines two additional \ac{iupac} commands: \begin{commands} \command{ter} \iupac{\ter} \command{sin} \iupac{\sin} \end{commands} \part{\chemmacros}\label{part:chemmacros} \section{Particles, Ions and Symbols}\label{sec:particles} \subsection{Predefined} \chemmacros\ defines some simple macros for displaying often needed particles and symbols. Please note, that they're displayed differently depending on the package options used, see section~\ref{sec:options}. These commands can be used in text as well as in math mode. Note that they are not meant to be used in \chemformula's \cs{ch}. \begin{commands} \command{Hpl} \Hpl\ (proton) \command{Hyd} \Hyd\ (hydroxide) \command{HtO} \HtO\ (oxonium ion) (\textbf{H} \textbf{t}hree \textbf{O}) \command{water} \water \command{el} \el\ (electron) \command{prt} \prt\ (proton) \command{ntr} \ntr\ (neutron) \command{Nu} \Nu\ (nucleophile)\par The package \pkg{mathspec} also defines a macro \cs{Nu}. If you chose package option \keyis{Nu}{mathspec} \chemmacros\ defines \cs{Nuc} instead\label{Nu}. \command{El} \El\ (electrophile) \command{ba} \ba\ (base) \command{fplus} \fplus \command{fminus} \fminus \command{transitionstatesymbol} \transitionstatesymbol \command{standardstate} \standardstate\par This symbol is only provided by \chemmacros, if the package \pkg{chemstyle} is not loaded; the idea is borrowed from there\footnote{many thanks to the package author \href{http://www.texdev.net/}{Joseph Wright}.}. \command{changestate} $\changestate$\par A math operator symbol for denoting the change in an extensive thermodynamic quantity for a process such as \State{H}. This symbol is used in the definitions presented in section~\ref{sec:stand-state-therm}. \command{chemalpha}[ \chemalpha, \cs{chemAlpha} \chemAlpha] For each of the 24 greek letters a lowercase and uppercase \cs*{Chem...} command is defined that maps to the upright greek letter as set with the option \option{greek}. More details on this can be found in the manual of the \chemgreek\ package. \end{commands} The two particles \cs{Nu} and \cs{ba} can be modified. To do that you use the option \begin{options} \keychoice{elpair}{false,\default{dots},dash}\Module{particle}\Default{false} Set how the electron pair of the particles \cs{Nu} and \cs{ba} are set. \end{options} \begin{example}[side-by-side] \ba[elpair] \Nu[elpair=dash] \chemsetup[particle]{elpair} \ba\ \Nu \end{example} \label{desc:greek}The greek letters aren't newly defined symbols but are defined differently depending on the packages you've loaded. The default definition is the corresponding math letter. If you have loaded the \pkg{textgreek} package the letters are taken from there, and if you have loaded the package \pkg{upgreek} the macros of that package are used. This is also described in the description of the package option \option{greek}, other details can be found in the documentation of the \chemgreek\ package. Which package you have to load for a specific choice for the package option \option{greek} is listed in table~\ref{tab:option:greek}. This documentation uses \pkg{newtxmath} and the setting \keyis{greek}{newtx} for instance. \begin{table} \centering \caption{Packages needed for the \option*{greek} package option..} \label{tab:option:greek} \begin{tabular}{>{\ttfamily}ll} \toprule \tablehead{option} & \tablehead{needed package} \\ \midrule auto & --- \\ math & --- \\ textgreek & \pkg{textgreek} \cite{pkg:textgreek} \\ upgreek & \pkg{upgreek} \cite{pkg:upgreek} \\ newtx & \pkg{newtxmath} \cite{pkg:newtx} \\ kpfonts & \pkg{kpfonts} \cite{pkg:kpfonts} \\ mathdesign & \pkg{mathdesign} \cite{pkg:mathdesign} \\ fourier & \pkg{fourier} \cite{pkg:fourier} \\ textalpha & \pkg{textalpha} \cite{bnd:greek-fontenc} \\ \bottomrule \end{tabular} \end{table} The reason why \chemmacros\ uses these macros in the first place is \ac{iupac} compliance. \ac{iupac} recommends to use upright greek letters in nomenclature. \begin{cnltxquote}[{\ac{iupac} Green Book {\cite[][p.\,9]{iupac:greenbook}}}] Greek letters are used in systematic organic, inorganic, macromolecular and biochemical nomenclature. These should be roman (upright), since they are not symbols for physical quantities. \end{cnltxquote} \chemmacros\ uses these commands now to define nomenclature commands, see page~\pageref{par:greek_letters}. \subsection{Own Particles} Surely sometimes it can be handy to have other particle macros defined such as \cs*{positron} or \cs*{photon}. This can easily be done with this command: \begin{commands} \command{NewChemParticle}[\marg{cs}\marg{definition}] \sinceversion{4.3}Define a new particle command. Gives an error if \meta{cs} already exists. \command{DeclareChemParticle}[\marg{cs}\marg{definition}] \changedversion{4.3}Define a new particle command. \command{RenewChemParticle}[\marg{cs}\marg{definition}] Renew the definition of a particle command. \end{commands} The particle defined this way behaves uses \chemformula's \cs{ch} to typeset the particle which means that the \meta{definition} should be a vaild \chemformula\ compound. Please have a look at the \chemformula\ manual for details. The particle will obey the \option{circled} option. \begin{example} \NewChemParticle\positron{\chembeta+} \NewChemParticle\photon{\chemgamma} \RenewChemParticle\el{\chembeta-} \positron\ \photon\ \el \end{example} \section{Nomenclature, Stereo Descriptors, Latin Phrases}\label{sec:stereo} \subsection{\acs{iupac} Names} Similar to the \pkg{bpchem} package \chemmacros\ provides a command\footnote{The idea and the implementation is shamelessly borrowed from \pkg{bpchem} by \pedersen.} to typeset \ac{iupac} names. Why is that useful? \ac{iupac} names can get very long. So long indeed that they span over more than two lines, especially in two-column documents. This means they must be allowed to be broken more than one time. This is what the following command does. \begin{commands} \command{iupac}[\marg{IUPAC name}] Inside this command use \cs{\textbar} and \cs{-} to indicate a breaking point or a breaking dash. Use \cs{\textasciicircum} as a shortcut for \cs*{textsuperscript}. \end{commands} \begin{example} \begin{minipage}{.4\linewidth} \iupac{% Tetra\|cyclo[2.2.2.1\^{1,4}]\-un\|decane-2\-dodecyl\-% 5\-(hepta\|decyl\|iso\|dodecyl\|thio\|ester)% } \end{minipage} \end{example} The \cs{iupac} command is more of a semantic command. Most times you can achieve (nearly) the same thing by using \cs{-} instead of \cs{\textbar}, \code{-} instead of \cs{-} and \cs*{textsuperscript} instead of \cs{\textasciicircum}. There are some subtleties: \cs{-} inserts a small space before the hyphen and removes a small space after it. The command \cs{\textbar} not only prevents ligatures but also inserts a small space. \begin{example}[side-by-side] \huge\iupac{2,4\-Di\|chlor\|pentan} \par 2,4-Dichlorpentan \end{example} The spaces inserted by these commands can be customized. \begin{options} \keyval{hyphen-pre-space}{dim}\Module{iupac}\Default{.01em} Set the space that is inserted before the hyphen set with \cs{-}. \keyval{hyphen-post-space}{dim}\Module{iupac}\Default{-.03em} Set the space that is inserted after the hyphen set with \cs{-}. \keyval{break-space}{dim}\Module{iupac}\Default{.01em} Set the space inserted by \cs{\textbar}. \end{options} The command \cs{iupac} serves another purpose, too, however. Regardless of the setting of the \option{iupac} option all the commands presented in this section are always defined \emph{inside} \cs{iupac}. Quite a number of the naming commands have very general names: \cs{meta}, \cs{D}, \cs{E}, \cs{L}, \cs{R}, \cs{S}, \cs{trans} and so forth\footnote{Please read page~\pageref{desc:one-letter-commands} before you consider using the one-letter commands}. This means they either are predefined already (\cs{L} \L) or are easily defined by another package or class (the \pkg{cool} package defines both \cs{D} and \cs{E}, for example). In order to give you control which commands are defined in which way, there is the package option \option{iupac}\label{desc:iupac}. It has three modes: \begin{itemize} \item \keyis{iupac}{auto}: if the commands are \emph{not} defined by any package or class you're using they are available generally, otherwise only \emph{inside} \cs{iupac}. \item \keyis{iupac}{restricted}: all naming commands are \emph{only} defined inside \cs{iupac}. If the commands are defined by another package they of course have that meaning outside. They're not defined outside otherwise. \item \keyis{iupac}{strict}: \chemmacros\ overwrites any other definition and makes the commands available throughout the document. Of course the commands can be redefined (but only in the document body). They will still be available inside \cs{iupac} then. \end{itemize} Table~\ref{tab:iupac_modes} demonstrates the different modes. \begin{table} \centering \caption{Demonstration of \option*{iupac}'s modes.}\label{tab:iupac_modes} \begin{tabular}{lccc} \toprule & auto & restricted & strict \\ \midrule \cs{L} & \L & \L & \iupac{\L} \\ \cs{iupac}\Marg{\cs{L}} & \iupac{\L} & \iupac{\L} & \iupac{\L} \\ \cs{D} & \D & -- & \D \\ \cs{iupac}\Marg{\cs{D}} & \iupac{\D} & \iupac{\D} & \iupac{\D} \\ \bottomrule \end{tabular} \end{table} \subsubsection{Predefined Commands} The macros in this section are intended to make the writing of \ac{iupac} names more convenient. \paragraph{Greek Letters}\label{par:greek_letters} Greek\changedversion{4.3} letters in compound names are typeset upright. For this there are for example the packages \pkg{upgreek} and \pkg{textgreek}. If you have loaded one of them\footnote{There are other options, see the description of the \option{greek} option.} the following commands typeset upright Greek letters: \begin{commands} \command{chemalpha}[\quad\chemalpha] Upright lowercase alpha \command{chembeta}[\quad\chembeta] Upright lowercase alpha \command{chemgamma}[\quad\chemgamma] Upright lowercase alpha \command{chemdelta}[\quad\chemdelta] Upright lowercase alpha \end{commands} The exist two commands for each of the twenty-four Greek letters: a lowercase and an uppercase version (\cs{chemalpha} and \cs{chemAlpha}). Those commands are actually provided by the \chemgreek\ package. For more details refer to its documentation. There are a number of one-letter commands that some people may find convenient to use which use above mentioned commands to pint Greek letters inside \cs{iupac}. They're listed in table~\ref{tab:iupac-greek-shortcuts}. But please read page~\pageref{desc:one-letter-commands} first before you use them. \begin{table} \centering \caption{\acs*{iupac} shortcuts for Greek letters.} \label{tab:iupac-greek-shortcuts} \begin{tabular}{*9l} \toprule macro & \cs{a} & \cs{b} & \cs{g} & \cs{d} & \cs{k} & \cs{m} & \cs{n} & \cs{w} \\ \midrule letter & \iupac{\a} & \iupac{\b} & \iupac{\g} & \iupac{\d} & \iupac{\k} & \iupac{\m} & \iupac{\n} & \iupac{\w} \\ \bottomrule \end{tabular} \end{table} \begin{example} \iupac{5\chemalpha\-androstan\-3\chembeta\-ol} \par \iupac{\chemalpha\-(tri\|chloro\|methyl)\-\chemomega \-chloro\|poly(1,4\-phenylene\|methylene)} \end{example} \paragraph{Hetero Atoms and added Hydrogen} Attachments to hetero atoms\changedversion{4.3} and added hydrogen atoms are indicated by italic letters~\cite{iupac:greenbook}. \chemmacros\ defines a few macros for the most common ones. \begin{commands} \command{hydrogen}[\quad\iupac{\hydrogen}] The italic H for hydrogen. (An alias for this command is \cs{H}. But please read page~\pageref{desc:one-letter-commands} first before you use it.) \command{oxygen}[\quad\iupac{\oxygen}] The italic O for oxygen. (An alias for this command is \cs{O}. But please read page~\pageref{desc:one-letter-commands} first before you use it.) \command{nitrogen}[\quad\iupac{\nitrogen}] The italic N for nitrogen. (An alias for this command is \cs{N}. But please read page~\pageref{desc:one-letter-commands} first before you use it.) \command{sulfur}[\quad\iupac{\sulfur}] The italic S for sulfur. (An alias for this command is \cs{Sf}. But please read page~\pageref{desc:one-letter-commands} first before you use it.) \command{phosphorus}[\quad\iupac{\phosphorus}] The italic P for phosphorus. (An alias for this command is \cs{P}. But please read page~\pageref{desc:one-letter-commands} first before you use it.) \end{commands} \begin{example}[side-by-side] \iupac{\nitrogen\-methyl\|benz\|amide} \iupac{3\hydrogen\-pyrrole} \iupac{\oxygen\-ethyl hexanethioate} \end{example} \paragraph{Cahn-Ingold-Prelog}\label{par:cip} \begin{commands} \command{cip}[\marg{conf}] Typeset Cahn-Ingol-Prelog descriptors, \eg: \cs{cip}\Marg{R,S} \cip{R,S} \command{rectus}[\quad\iupac{\rectus}] Typeset rectus descriptor. (An alias for this command is \cs{R}. But please read page~\pageref{desc:one-letter-commands} first before you use it.) \command{sinister}[\quad\iupac{\sinister}] Typeset sinister descriptor. (An alias for this command is \cs{S}. But please read page~\pageref{desc:one-letter-commands} first before you use it.) \end{commands} Both these commands and the entgegen/zusammen descriptors get a small additional amount of kerning after the closing parenthesis. This amount can be changed through the following option: \begin{options} \keyval{cip-kern}{dim}\Module{iupac}\Default{.075em} Set the amount of kerning after the closing parenthesis. \end{options} \paragraph{Fischer} \begin{commands} \command{dexter}[\quad\iupac{\dexter}] Typeset dexter descriptor. (An alias for this command is \cs{D}. But please read page~\pageref{desc:one-letter-commands} first before you use it.) \command{laevus}[\quad\iupac{\laevus}] Typeset laevus descriptor. (An alias for this command is \cs{L}. But please read page~\pageref{desc:one-letter-commands} first before you use it.) \end{commands} \paragraph{cis/trans, zusammen/entgegen, syn/anti \& tert} \begin{itemize} \item[] \cs{cis} \iupac{\cis} \quad \cs{trans} \iupac{\trans} \quad \cs{fac} \iupac{\fac} \quad \cs{mer} \iupac{\mer} \quad \cs{zusammen} \iupac{\zusammen} \quad \cs{entgegen} \iupac{\entgegen} \quad \cs{syn} \iupac{\syn} \quad \cs{anti} \iupac{\anti} \quad \cs{tert} \iupac{\tert} \end{itemize} An alias for \cs{entgegen} is \cs{E} and an alias for \cs{zusammen} is \cs{Z}. But please read page~\pageref{desc:one-letter-commands} first before you use them. \paragraph{ortho/meta/para} \begin{itemize} \item[] \cs{ortho} \iupac{\ortho} \quad \cs{meta} \iupac{\meta} \quad \cs{para} \iupac{\para} \end{itemize} Although these commands are provided I like to cite~\cite{iupac:bluebook}: \begin{cnltxquote}[{\acs{iupac} Blue Book {\cite[][p.\,90]{iupac:bluebook}}}] The letters \iupac{\ortho}, \iupac{\meta}, and \iupac{\para} have been used in place of \textit{ortho}, \textit{meta}, and \textit{para}, respectively, to designate the 1,2-, 1,3-, and 1,4- isomers of disubstituted benzene. This usage is strongly discouraged and is not used in preferred \acs{iupac} names. \end{cnltxquote} \paragraph{Absolute Configuration} (uses \TikZ) \begin{commands} \command{Rconf}[\oarg{letter}] \cs{Rconf}: \Rconf \quad \cs{Rconf}\oarg{}: \Rconf[] \command{Sconf}[\oarg{letter}] \cs{Sconf}: \Sconf \quad \cs{Sconf}\oarg{}: \Sconf[] \end{commands} Examples:\nopagebreak \begin{example} \iupac{\dexter\-Wein\|s\"aure} = \iupac{\cip{2S,3S}\-Wein\|s\"aure} \par \iupac{\dexter\-($-$)\-Threose} = \iupac{\cip{2S,3R}\-($-$)\-2,3,4\-Tri\|hydroxy\|butanal} \par \iupac{\cis\-2\-Butene} = \iupac{\zusammen\-2\-Butene}, \par \iupac{\cip{2E,4Z}\-Hexa\|diene} \par \iupac{\meta\-Xylol} = \iupac{1,3\-Di\|methyl\|benzene} \end{example} \paragraph{Coordination Chemistry} \chemmacros\ provides a few commands useful with coordination chemistry: \begin{commands} \command{bridge}[\marg{num}\quad\bridge{3}] Denote bridging ligand connection. \command{hapto}[\marg{num}\quad\hapto{5}] Denote hapticity. \command{dento}[\marg{num}\quad\dento{2}] \sinceversion{4.3}Denote denticity. \end{commands} \begin{example} Ferrocene = \iupac{bis(\hapto{5}cyclo\|penta\|dienyl)iron} \par \iupac{tetra\-\bridge{3}iodido\-tetrakis[tri\|methyl\|platinum(IV)]} \end{example} Two options allow customization: \begin{options} \keychoice{bridge-number}{sub,super}\Module{iupac}\Default{sub} Appends the number as a subscript or superscript. \ac{iupac} recommendation is the subscript~\cite{iupac:redbook}. \keybool{coord-use-hyphen}\Module{iupac}\Default{true} Append a hyphen to \cs{hapto}, \cs{dent} and \cs{bridge} or don't. \end{options} \subsubsection{Own Naming Commands} If you find any commands missing you can define them using \begin{commands} \command{NewChemIUPAC}[\marg{cs}\marg{declaration}] \sinceversion{4.3}Define a new \ac{iupac} command that is in any case defined inside of \cs{iupac} regardless if \meta{cs} is defined elsewhere already. \command{RenewChemIUPAC}[\marg{cs}\marg{declaration}] Redefine an existing \ac{iupac} command that is in any case defined inside of \cs{iupac} regardless if \meta{cs} is defined elsewhere already. \command{DeclareChemIUPAC}[\marg{cs}\marg{declaration}] \changedversion{4.3}Define a new \ac{iupac} command that is in any case defined inside of \cs{iupac} regardless if \meta{cs} is defined elsewhere already. This silently overwrites an existing \ac{iupac} definition. \end{commands} A command defined in this way will obey the setting of the option \option{iupac}. This means any existing command is only overwritten with \keyis{iupac}{strict}. However, \cs{NewChemIUPAC} will \emph{not} change the definition of an existing \ac{iupac} naming command but issue an error if the \ac{iupac} naming command already exists. \cs{DeclareChemIUPAC} \emph{will} overwrite an existing \ac{iupac} command. \begin{example} \NewChemIUPAC\endo{\textit{endo}} \RenewChemIUPAC\anti{\textit{anti}} \iupac{(2\-\endo,7\-\anti)\-2\-bromo\-7\-fluoro\|bicyclo[2.2.1]heptane} \end{example} \cs{RenewChemIUPAC} allows you to redefine the existing \ac{iupac} naming commands. \begin{example}[side-by-side] \iupac{\meta\-Xylol} \par \RenewChemIUPAC\meta{\textup{m}} \iupac{\meta\-Xylol} \end{example} \subsection{Latin Phrases} The package \pkg{chemstyle} provides the command \cs{latin} to typeset common latin phrases in a consistent way. \chemmacros\ defines a similar \cs{latin} only if \pkg{chemstyle} has \emph{not} been loaded and additionally provides these commands: \begin{itemize} \item[] \cs{insitu} \insitu \quad \cs{abinitio} \abinitio \quad \cs{invacuo} \invacuo \end{itemize} If the package \pkg{chemstyle} has been loaded they are defined using \pkg{chemstyle}'s \cs{latin} command. This means that then the appearance depends on \pkg{chemstyle}'s option \code{abbremph}. The commands are defined through \begin{commands} \command{NewChemLatin}[\marg{cs}\marg{phrase}] \sinceversion{4.3}Define a new latin phrase. Gives an error if \meta{cs} already exists. \command{DeclareChemLatin}[\marg{cs}\marg{phrase}] \changedversion{4.3}Define a new latin phrase. \command{RenewChemLatin}[\marg{cs}\marg{phrase}] Redefine an existing latin phrase. \end{commands} \begin{example}[side-by-side] \NewChemLatin\ltn{latin text}\ltn \end{example} If you have \emph{not} loaded \pkg{chemstyle} you can change the appearance with this option: \begin{options} \keyval{format}{definition}\Module{latin}\Default{\cs*{itshape}} Set the format of the latin phrases. \end{options} \section{Units for the Usage With \pkg*{siunitx}}\label{sec:einheiten} In chemistry some non-SI units are very common. \pkg{siunitx} provides the command \cs*{DeclareSIUnit}\marg{command}\marg{unit} to add arbitrary units. \chemmacros\ uses that command to provide some units. Like all \pkg{siunitx} units they're only valid inside \cs*{SI}\marg{num}\marg{unit} and \cs*{si}\marg{unit}. \begin{commands} \command{atmosphere} \si{\atmosphere} \command{atm} \si{\atm} \command{calory} \si{\calory} \command{cal} \si{\cal} \command{cmc} \si{\cmc} \par The units \cs{cmc}, \cs{molar}, and \cs{Molar} are defined by the package \pkg{chemstyle} as well. \chemmacros\ only defines them, if \pkg{chemstyle} is not loaded. \command{molar} \si{\molar} \command{moLar} \si{\moLar} \command{Molar} \si{\Molar} \command{MolMass} \si{\MolMass} \command{normal} \si{\normal} \command{torr} \si{\torr} \end{commands} By the way: \cs*{mmHg} \si{\mmHg} already is defined by \pkg{siunitx} and \pkg{chemstyle}. \section{Acid/Base}\label{sec:saeure_base} Easy representation of \pH, \pKa \ldots\ (the command \cs{pKa} depends on the package option \option{language}). The translations may be adapted, though, see section~\ref{sec:languages}. \begin{commands} \command{pH} \pH \command{pOH} \pOH \command{Ka} \Ka \command{Kb} \Kb \command{Kw} \Kw \command{pKa}[\oarg{num}] \cs{pKa}: \pKa, \cs{pKa}\Oarg{1}: \pKa[1] \command{pKb}[\oarg{num}] \cs{pKb}: \pKb, \cs{pKb}\Oarg{1}: \pKb[1] \command{p}[\marg{anything}] \eg\ \cs{p}\Marg{\cs{Kw}} \p{\Kw} \end{commands} \begin{example}[side-by-side] \Ka \Kb \pKa \pKa[1] \pKb \pKb[1] \end{example} \begin{cnltxquote}[{\acs{iupac} Green Book {\cite[][p.\,103]{iupac:greenbook}}}] The operator \p{} \textelp{} shall be printed in Roman type. \end{cnltxquote} There is one option which changes the style the \p{} is typeset: \begin{options} \keychoice{p-style}{italics,slanted,upright}\Module{acid-base}\Default{upright} Set the style of the \p{} operator. \keyval{K-acid}{text}\Module{acid-base}\Default{A} The subscript to \cs{Ka} and \cs{pKa}. \keyval{K-base}{text}\Module{acid-base}\Default{B} The subscript to \cs{Kb} and \cs{pKb}. \keyval{K-water}{text}\Module{acid-base}\Default{W} The subscript to \cs{Kw}. \end{options} \begin{example} \pH, \pKa \par \chemsetup[acid-base]{p-style=slanted} \pH, \pKa \par \chemsetup[acid-base]{p-style=italics} \pH, \pKa \end{example} As\sinceversion{4.2d} you can see the default subscripts of \cs{Kw}, \cs{Ka} and \cs{Kb} are uppercase letters. The literature is inconclusive about if this is the right way or if lowercase letters should be preferred. In textbooks the uppercase variant usually seems to be used while journals seem to prefer the lowercase variant. Since I like the uppercase version better this is the default. If you want to change this you have two possibilities: \begin{example} % this works only in the preamble: % \DeclareTranslation{English}{K-acid}{a}% use your language here % alternative: \chemsetup{acid-base/K-acid=a}% overwrites language dependent settings \pKa \end{example} \section{Oxidation Numbers, Real and Formal Charges}\label{sec:ladungen} \chemmacros\ distinguishes between real ($+$/$-$) and formal (\fplus/\fminus) charge symbols, also see section~\ref{sec:options}. All commands using formal charge symbols start with a \code{f}. \subsection{Ion Charges}\label{ssec:ionen} Simple displaying of (real) charges. It is worth noting that these commands really are relicts from a time when \chemmacros\ tried hard to be compliant with \pkg{mhchem} and \chemformula\ didn't exist, yet. They are still provided for backwards compatibility but \emph{my recommendation is to use} \cs{ch} (see the documentation of the \chemformula\ package) \emph{and forget about these commands:} \begin{commands} \command{pch}[\oarg{number}] positive charge (\textbf{p}lus + \textbf{ch}arge) \command{mch}[\oarg{number}] negative charge (\textbf{m}inus + \textbf{ch}arge) \end{commands} \begin{example}[side-by-side] \leavevmode \pch, Na\pch, Ca\pch[2]\par \leavevmode \mch, F\mch, S\mch[2] \end{example} The same for formal charges: \begin{commands} \command{fpch}[\oarg{number}] positive charge \command{fmch}[\oarg{number}] negative charge \end{commands} \begin{example}[side-by-side] \leavevmode \fpch\ \fmch\ \fpch[3] \fmch[3] \end{example} \subsection{Oxidation Numbers}\label{ssec:oxidationszahlen} Typesetting oxidation numbers: \begin{commands} \command{ox}[\oarg{options}\Marg{\meta{number},\meta{atom}}] Places \meta{number} above \meta{atom}; \meta{number} has to be a (rational) number! \end{commands} \begin{example} \ox{+1,Na}, \ox{2,Ca}, \ox{-2,S}, \ox{-1,F} \end{example} There are a number of keys, that can be used to modify the \cs{ox} command. \begin{options} \keybool{parse}\Module{ox}\Default{true} When \code{false} an arbitrary entry can be used for \code{}. \keybool{roman}\Module{ox}\Default{false} Switches from roman to arabic numbers. \keychoice{pos}{top,super,side}\Module{ox}\Default{top} \code{top} places \meta{number} above \meta{atom}, \code{super} to the upper right as superscript and \code{side} to the right and inside brackets. \keybool{explicit-sign}\Module{ox}\Default{false} Shows the $+$ for positiv numbers and the $\pm$ for $0$. \keychoice{decimal-marker}{comma,point}\Module{ox}\Default{point} Choice for the decimal marker for formal oxidation numbers like \ox{1.2,X}. \keychoice{align}{center,right}\Module{ox}\Default{center} Center the oxidation number relative to the atom or right-align it. \end{options} \begin{example}[side-by-side] \ox[roman=false]{2,Ca} \ox{2,Ca} \\ \ox[pos=super]{3,Fe}-Oxide \\ \ox[pos=side]{3,Fe}-Oxide \\ \ox[parse=false]{?,Mn} \\ \ox[align=right]{2,Ca} \end{example} The \keyis{pos}{super} variant also can be set with the shortcut \cs{ox}\sarg: \begin{example}[side-by-side] \ox{3,Fe} \ox*{3,Fe} \end{example} Using the \option{explicit-sign} key will always show the sign of the oxidation number: \begin{example} \chemsetup[ox]{explicit-sign = true} \ox{+1,Na}, \ox{2,Ca}, \ox{-2,S}, \ch{"\ox{0,F}" {}2} \end{example} \begin{example} Compare \ox{-1,\ch{O2^2-}} to \ch{"\ox{-1,O}" {}2^2-} \end{example} Sometimes one might want to use formal oxidation numbers like \num{.5} or $\frac{1}{3}$: \begin{example}[side-by-side] \ox{.5,\ch{Br2}} \ch{"\ox{1/3,I}" {}3+} \end{example} The fraction uses the \cs*{sfrac} command of the \pkg{xfrac} package. For this purpose the instance \code{chemmacros-ox-frac} is defined. \begin{sourcecode} \DeclareInstance{xfrac}{chemmacros-ox-frac}{text}{ scale-factor = 1.2 , denominator-bot-sep = -.5ex , numerator-top-sep = -.3ex , slash-left-kern = -.2em , slash-right-kern = -.2em , slash-symbol-font = lmr } \end{sourcecode} Of course you can redefine it so that it suits your needs as the output often strongly depends on the used font. \subsection{Partial Charges and Similar Stuff}\label{ssec:partialladungen} The next ones probably are seldomly needed but nevertheless useful: \begin{commands} \command{delp} \delp\ (\textbf{del}ta + \textbf{p}lus) \command{delm} \delm\ (\textbf{del}ta + \textbf{m}inus) \command{fdelp} \fdelp \command{fdelm} \fdelm \end{commands} These macros for example can be used with the \cs{ox} command or with the \pkg{chemfig} package: \begin{example} \chemsetup{ option/circled = all, ox/parse = false } \ch{"\ox{\delp,H}" -{} "\ox{\delm,Cl}"} \hspace*{1cm} \chemfig{\chemabove[3pt]{\lewis{246,Br}}{\delm}-\chemabove[3pt]{H}{\delp}} \end{example} The following macros are useful together with \pkg{chemfig}, too. \begin{commands} \command{scrp} \scrp\ (\textbf{scr}iptstyle + \textbf{p}lus) \command{scrm} \scrm\ (\textbf{scr}iptstyle + \textbf{m}inus) \command{fscrp} \fscrp \command{fscrm} \fscrm \command{fsscrp} \fsscrp\ (using \cs*{scriptscriptstyle}) \command{fsscrm} \fsscrm \end{commands} \begin{example} \setatomsep{1.8em}\chemfig{CH_3-\chemabove{C}{\scrp}(-[6]C|H_3)-\vphantom{H_3}CH_3} \chemfig{\fmch{}|O-\chemabove{N}{\fscrp}(-[1]O|\fmch)-[7]O|\fmch} \end{example} \section{Reaction Mechanisms}\label{sec:mechanismen} \begin{commands} \command{mech}[\oarg{type}] Allows to specify the most common reaction mechanisms. \end{commands} \meta{type} can have one of the following values: \begin{commands} \command{mech} (empty, no opt. argument) nucleophilic substitution \mech \command{mech}[\Oarg{1}] unimolecular nucleophilic substitution \mech[1] \command{mech}[\Oarg{2}] bimolecular nucleophilic substitution \mech[2] \command{mech}[\Oarg{se}] electrophilic substitution \mech[se] \command{mech}[\Oarg{1e}] unimolecular electrophilic substitution \mech[1e] \command{mech}[\Oarg{2e}] bimolecular electrophilic substitution \mech[2e] \command{mech}[\Oarg{ar}] electrophilic aromatic substitution \mech[ar] \command{mech}[\Oarg{e}] elimination \mech[e] \command{mech}[\Oarg{e1}] unimolecular elimination \mech[e1] \command{mech}[\Oarg{e2}] bimolecular elimination \mech[e2] \command{mech}[\Oarg{cb}] unimolecular elimination \enquote{conjugated base}, \ie, via carbanion \mech[cb] \end{commands} \section{Redox Reactions}\label{sec:redoxreaktionen}% TODO: watch pagebreaks! \chemmacros\ provides two commands to visualize the transfer of electrons in redox reactions. Both commands are using \TikZ. \begin{commands} \command{OX}[\Marg{\meta{name},\meta{atom}}] Label \meta{atom} with the label \meta{name}. \command{redox}[\Darg{\meta{name1},\meta{name2}}\oarg{tikz}\oarg{num}\marg{text}] Connect two \meta{atom}s previously labelled with \cs{OX}. Only the first argument \Darg{\meta{name1},\meta{name2}} is required, the others are all optional. \end{commands} \cs{OX} places \meta{atom} into a node, which is named with \meta{name}. If you have set two \cs{OX}, they can be connected with a line using \cs{redox}. To do so the names of the two nodes that are to be connected are written in the round braces. Since \cs{redox} draws a \code{tikzpicture} with options \code{remember picture,overlay}, the document needs to be \emph{compiled at least two times}. \begin{example} \vspace{7mm} \OX{a,Na} $\rightarrow$ \OX{b,Na}\pch\redox(a,b){oxidation} \end{example} This line can be customized using \TikZ\ keys in \oarg{tikz}: \begin{example} \vspace{7mm} \OX{a,Na} $\rightarrow$ \OX{b,Na}\pch\redox(a,b)[->,red]{ox} \end{example} With the argument \oarg{num} the length of the vertical parts of the line can be adjusted. The default length is \code{.6em}. This length is multiplied with \meta{num}. If you use a negative value the line is placed \emph{below} the text. \begin{example} \vspace{7mm} \OX{a,Na} $\rightarrow$ \OX{b,Na}\pch \redox(a,b)[->,red]{ox} \redox(a,b)[<-,blue][-1]{red} \vspace{7mm} \end{example} The default length of the vertical lines can be customized with the option \begin{options} \keyval{dist}{dim}\Module{redox}\Default{.6em} A \TeX\ dimension. \end{options} \begin{example} \vspace{7mm} \chemsetup{redox/dist=1em} \OX{a,Na} $\rightarrow$ \OX{b,Na}\pch\redox(a,b)[->,red]{ox} \end{example} \begin{options} \keyval{sep}{dim}\Module{redox}\Default{.2em} The option can be used to change the distance between the atom and the beginning of the line. \end{options} \begin{example} \vspace{7mm} \chemsetup{redox/sep=.5em} \OX{a,Na} $\rightarrow$ \OX{b,Na}\pch\redox(a,b)[->,red]{ox} \end{example} Examples:\nopagebreak% TODO: watch pagebreaks! \begin{example} \vspace{7mm} \ch{ 2 "\OX{o1,Na}" + "\OX{r1,Cl}" {}2 -> 2 "\OX{o2,Na}" {}+ + 2 "\OX{r2,Cl}" {}- } \redox(o1,o2){\small OX: $- 2\el$} \redox(r1,r2)[][-1]{\small RED: $+ 2\el$} \vspace{7mm} \end{example} \begin{example} \vspace{7mm} \ch{ 2 "\OX{o1,\ox{0,Na}}" + "\OX{r1,\ox{0,Cl}}" {}2 -> 2 "\OX{o2,\ox{+1,Na}}" {}+ + 2 "\OX{r2,\ox{-1,Cl}}" {}- } \redox(o1,o2){\small OX: $- 2\el$} \redox(r1,r2)[][-1]{\small RED: $+ 2\el$} \vspace{7mm} \end{example} \begin{example} \vspace{14mm} \ch{ 2 "\OX{o1,\ox{0,Na}}" + "\OX{r1,\ox{0,Cl}}" {}2 -> 2 "\OX{o2,\ox{+1,Na}}" {}+ + 2 "\OX{r2,\ox{-1,Cl}}" {}- } \redox(o1,o2)[draw=red,->][3.33]{\small OX: $- 2\el$} \redox(r1,r2)[draw=blue,->]{\small RED: $+ 2\el$} \end{example} \begin{example} \vspace{7mm} \ch{ 2 "\OX{o1,\ox{0,Na}}" + "\OX{r1,\ox{0,Cl}}" {}2 -> 2 "\OX{o2,\ox{+1,Na}}" {}+ + 2 "\OX{r2,\ox{-1,Cl}}" {}- } \redox(o1,o2)[green,-stealth]{\small OX} \redox(r1,r2)[purple,-stealth][-1]{\small RED} \vspace{7mm} \end{example} \section{(Standard) State, Thermodynamics}\label{sec:stand-state-therm} \subsection{Thermodynamic Variables}\label{sec:therm-vari} The following commands use \pkg{siunitx}: \begin{commands} \command{Enthalpy}[\oarg{options}\darg{subscript}\marg{value}] Typeset the amount of enthalpy. \command{Entropy}[\oarg{options}\darg{subscript}\marg{value}] Typeset the amount of entropy. \command{Gibbs}[\oarg{options}\darg{subscript}\marg{value}] Typeset the amount of Gibbs enthalpy. \end{commands} Their usage is pretty much self-explaining: \begin{example}[side-by-side] \Enthalpy{123} \par \Entropy{123} \par \Gibbs{123} \end{example} The argument \darg{subscript} adds a subscript for specification: \cs{Enthalpy}\Darg{r}\Marg{123} \Enthalpy(r){123}. There are several keys to customize the commands. They do not belong to a module and can only be used in the optional arguments of the commands. \begin{options} \keyval{exponent}{anything} Choose \meta{anything} as exponent. \keychoice{delta}{\meta{anything},false} Disable or choose a symbol in front of the main symbol. \meta{anything} will be placed in math mode! \keychoice{subscript}{left,right} Choose if the subscript is placed to the left or the right of the main symbol. \keyval{unit}{unit} Set the unit of the variable. \end{options} The default values depend on the command. \begin{example}[side-by-side] \Enthalpy[unit=\kilo\joule]{-285} \par \Gibbs[delta=false]{0} \par \Entropy[delta=\Delta,exponent=]{56.7} \end{example} The unit is set corresponding to the rules of \pkg{siunitx} and depends on its settings: \begin{example}[side-by-side] \Enthalpy{-1234.56e3} \par \sisetup{ per-mode=symbol, exponent-product=\cdot, output-decimal-marker={,}, group-four-digits=true } \Enthalpy{-1234.56e3} \end{example} \subsubsection{Create New Variables or Redefine Existing Ones}\label{sec:create-new-variables} \begin{commands} \command{NewChemState}[\marg{name}\oarg{options}\marg{symbol}\marg{unit}] \sinceversion{4.3}Define new corresponding commands. \meta{name} may either be a control sequence token or a control sequence name without leading backslash. This means that \cs{DeclareChemState}\Marg{name} and \cs{DeclareChemState}\Marg{\cs*{name}} are equivalent. The reason for this rather strange definition is a syntax change in \cs{DeclareChemState} while retaining backwards compaitibility. The latter version is recommended though and the former version may deprecate in the future. Gives an error if \meta{name} already exists \command{RenewChemState}[\marg{name}\oarg{options}\marg{symbol}\marg{unit}] Redefine existing state commands. \meta{name} may either be a control sequence token or a control sequence name without leading backslash. \changedversion{4.2}This means that \cs{RenewChemState}\Marg{name} and \cs{RenewChemState}\Marg{\cs*{name}} are equivalent. The reason for this rather strange definition is a syntax change in \cs{RenewChemState} while retaining backwards compaitibility. The latter version is recommended though and the former version may deprecate in the future. \command{DeclareChemState}[\marg{name}\oarg{options}\marg{symbol}\marg{unit}] \changedversion{4.3}Like \cs{NewChemState} but gives now error if \meta{name} already exists. \end{commands} \begin{example} \NewChemState\Helmholtz{A}{\kilo\joule\per\mole} \NewChemState\ElPot[subscript-left=false,exponent=]{E}{\volt} \Helmholtz{123.4} \par \ElPot{-1.1} \par \ElPot[exponent=0]($\ch{Sn}|\ch{Sn^2+}||\ch{Pb^2+}|\ch{Pb}$){0.01} \end{example} The command has some keys with which the default behaviour of the new command can be set. \begin{options} \keyval{exponent}{anything}\Default{\cs{standardstate}} Set the default exponent. \keychoice{delta}{\meta{anything},false}\Default{\cs{changestate}} Choose the default ``delta'' symbol that is placed in front of the main symbol. \meta{anything} will be placed in math mode! \keybool{subscript-left}\Default{true} Choose the default position of the sybscript. \keyval{subscript}{anything}\Default Choose the default subscript symbol. \end{options} \begin{example}[side-by-side] \RenewChemState\Enthalpy{h}{\joule} \Enthalpy(f){12.5} \end{example} The existing commands have been defined like this: \begin{sourcecode} \NewChemState\Enthalpy{H}{\kilo\joule\per\mole} \NewChemState\Entropy[delta=false,subscript-left=false]{S} {\joule\per\kelvin\per\mole} \NewChemState\Gibbs{G}{\kilo\joule\per\mole} \end{sourcecode} So -- for following thermodynamic conventions -- one could define a molar and an absolute variable: \begin{example} \NewChemState\enthalpy[exponent=]{h}{\kilo\joule\per\mole}% molar \RenewChemState\Enthalpy[exponent=]{H}{\kilo\joule}% absolute \enthalpy{-12.3} \Enthalpy{-12.3} \end{example} \subsection{State}\label{ssec:state} The commands presented in section~\ref{sec:therm-vari} internally all use the command\footnote{Please note that \marg{subscript} is an \emph{optional} argument.} \begin{commands} \command{State}[\oarg{options}\marg{symbol}\marg{subscript}] Typeset a state variable. \end{commands} It can be used to write the thermodynamic state variables without value and unit. \begin{example} \State{A}, \State{G}{f}, \State[subscript-left=false]{E}{\ch{Na}}, \State[exponent=\SI{1000}{\celsius}]{H} \end{example} Again there are some keys to customize the command: \begin{options} \keyval{exponent}{anything}\Module{state} Set the default exponent symbol. \keybool{subscript-left}\Module{state} Set the default subscript position. \keychoice{delta}{\meta{anything},false}\Module{state} Set the default ``delta'' symbol. \meta{anything} will be placed in math mode! \end{options} \section{Spectroscopy and Experimental Data}\label{sec:spektroskopie} \subsection{The \cs*{NMR} Command} When you're trying to find out if a compound is the one you think it is often NMR spectroscopy is used. The experimental data are typeset similar to this: \begin{center} \NMR(400)[CDCl3] = \num{1.59} \end{center} \chemmacros\ provides a command which simplifies the input (uses \pkg{siunitx}). \begin{commands} \command{NMR}[\sarg\Marg{\meta{num},\meta{element}}% \Darg{\meta{num},\meta{unit}}\oarg{solvent}] Typeset nuclear magnetic resonance data. \end{commands} \emph{All} Argument are optional! Without arguments we get: \begin{example}[side-by-side] \NMR \par \NMR* \end{example} The first argument specifies the kind of NMR: \begin{example}[side-by-side] \NMR{13,C} \end{example} The second argument sets the frequency (in \si{\mega\hertz}): \begin{example}[side-by-side] \NMR(400) \end{example} You can choose another unit: \begin{example}[side-by-side] \NMR(4e8,\hertz) \end{example} Please note that the setup of \pkg{siunitx} also affects this command: \begin{example}[side-by-side] \sisetup{exponent-product=\cdot} \NMR(4e8,\hertz) \end{example} The third argument specifies the solvent: \begin{example}[side-by-side] \NMR[CDCl3] \end{example} \subsection{Short Cuts} It is possible to define short cut commands for specific nuclei. \begin{commands} \command{NewChemNMR}[\marg{cs}\Marg{\meta{num},\meta{atom}}] \sinceversion{4.3}Define a new shortcut macro for typesetting a certain type of magnetic resonence data. Gives an error if \meta{cs} already exists. \command{DeclareChemNMR}[\marg{cs}\Marg{\meta{num},\meta{atom}}] \changedversion{4.3}Define a new shortcut macro for typesetting a certain type of magnetic resonence data. \command{RenewChemNMR}[\marg{cs}\Marg{\meta{num},\meta{atom}}] Redefine an existing shortcut macro for typesetting a certain type of magnetic resonence data. \end{commands} This defines a command with the same arguments as \cs{NMR} \emph{except} for \Marg{\meta{num},\meta{atom}}: \begin{example}[side-by-side] \NewChemNMR\HNMR{1,H}% \NewChemNMR\CNMR{13,C}% \CNMR*(100) \par \HNMR*(400) \end{example} \subsection{An Environment to Typeset Experimental Data} \chemmacros\ provides an environment to ease the input of experimental data. \begin{environments} \environment{experimental} Environment for the output of experimental data. Inside the environment the following commands are defined. \end{environments} \begin{commands} \command{data}[\marg{type}\oarg{specification}] Type of data, \eg\ IR, MS\ldots\ The optional argument takes further specifications which are output in parentheses. \command{data}[\sarg\marg{type}\oarg{specification}] Like \cs{data} but changes the \code{=} into a \code{:}, given that \keyis{use-equal}{true} is used. \command{NMR}[\Marg{\meta{num},\meta{elem}\oarg{coupling core}}\Darg{\meta{num},\meta{unit}}\oarg{solvent}] This command gets an additional argument: \cs{NMR}\Marg{13,C[\textasciicircum 1H]} \NMR{13,C[^1H]} \command{J}[\Darg{\meta{bonds};\meta{nuclei}}\oarg{unit}\marg{list of nums}] Coupling constant, values are input separated by \code{;} (NMR). The argument \Darg{\meta{bonds};\meta{nuclei}} and \oarg{unit} are optional and enable further specifications of the coupling. \command{\#}[\marg{num}] Number of nuclei (NMR). \command{pos}[\marg{num}] Position of nuclues (NMR). \command{val}[\marg{num}] A number, an alias of \pkg{siunitx}' \cs*{num}\marg{num}. \command{val}[\Marg{\meta{num1}--\meta{num2}}] An alias of \pkg{siunitx}' \cs*{numrange}\marg{num1}\marg{num2}. \end{commands} \begin{example} \begin{experimental} \data{type1} Data. \data{type2}[specifications] More data. \data*{type3} Even more data. \end{experimental} \end{example} \subsection{Customization}\label{sec:experimental-customization} The output of the environment and of the NMR commands can be customized be a number of options. For historical reasons they all belong to the module \module{nmr}. \begin{options} \keyval{unit}{unit}\Module{nmr}\Default{\cs*{mega}\cs*{hertz}} The used default unit. \keychoice{nucleus}{\Marg{\meta{num},\meta{atom}}}\Module{nmr}\Default{\Marg{1,H}} The used default nucleus. \keyval{format}{commands}\Module{nmr}\Default For example \cs*{bfseries}. \keychoice{pos-number}{side,sub,super}\Module{nmr}\Default{side} \changedversion{4.3}Position of the number next to the atom. \keyval{coupling-symbol}{code}\Module{nmr}\Default{J} \sinceversion{4.3}The symbol used for the coupling constant. \keyval{coupling-unit}{unit}\Module{nmr}\Default{\cs*{hertz}} A \pkg{siunitx} unit. \keychoice{coupling-pos}{side,sub}\Module{nmr}\Default{side} \sinceversion{4.3}Placement of the coupling nuclei next to the symbol $J$ (or rather the symbol specified with option \option{coupling-symbol}). \keyval{coupling-nuclei-pre}{code}\Module{nmr}\Default{(} \sinceversion{4.3}Code inserted before the coupling nuclei when \keyis{coupling-pos}{side}. \keyval{coupling-nuclei-post}{code}\Module{nmr}\Default{)} \sinceversion{4.3}Code inserted after the coupling nuclei when \keyis{coupling-pos}{side}. \keyval{coupling-bonds-pre}{code}\Module{nmr}\Default \sinceversion{4.3}Code inserted before the coupling bonds. \keyval{coupling-bonds-post}{code}\Module{nmr}\Default{\cs*{!}} \sinceversion{4.3}Code inserted after the coupling bonds. \keybool{parse}\Module{nmr}\Default{true} Treat the solvent as \chemformula\ formula or not. \keyval{delta}{tokens}\Module{nmr}\Default The \meta{tokens} are added after $\delta$. \keybool{list}\Module{nmr}\Default{false} The environment \env{nmr}[]{} is formatted as a list \keyval{list-setup}{setup}\Module{nmr} Setup of the list. See below for the default settings. \keybool{use-equal}\Module{nmr}\Default{false} Add egual sign after \cs{NMR} and \cs{data}. \end{options} The default setup of the list: \begin{sourcecode} \topsep\z@skip \partopsep\z@skip \itemsep\z@ \parsep\z@ \itemindent\z@ \leftmargin\z@ \end{sourcecode} \begin{example} \begin{experimental}[format=\bfseries] \data{type1} Data. \data{type2}[specifications] More data. \data*{type3} Even more data. \end{experimental} \end{example} The command \cs{NMR} and all commands defined through \cs{NewChemNMR} can be used like \cs{data} for the NMR data. \begin{example} \begin{experimental}[format=\bfseries,use-equal] \data{type1} Data. \data{type2}[specifications] More data. \NMR Even more data. \end{experimental} \end{example} \subsection{An Example} The code below is shown with different specifications for \meta{options}. Of course options can also be chosen with \cs{chemsetup}. \begin{sourcecode} \sisetup{separate-uncertainty,per-mode=symbol,detect-all,range-phrase=--} \begin{experimental}[] \data*{yield} \SI{17}{\milli\gram} yellow needles (\SI{0.04}{\milli\mole}, \SI{13}{\percent}). % \data{mp.} \SI{277}{\celsius} (DSC). % \NMR(600)[CDCl3] \val{2.01} (s, \#{24}, \pos{5}), \val{2.31} (s, \#{12}, \pos{1}), \val{6.72--6.74} (m, \#{2}, \pos{11}), \val{6.82} (s, \#{8}, \pos{3}), \val{7.05--7.07} (m, \#{2}, \pos{12}), \val{7.39--7.41} (m, \#{4}, \pos{9}), \val{7.48--7.49} (m, \#{4}, \pos{8}). % \NMR{13,C}(150)[CDCl3] \val{21.2} ($+$, \#{4}, \pos{1}), \val{23.4} ($+$, \#{8}, \pos{5}), \val{126.0} ($+$, \#{4}, \pos{9}), \val{128.2} ($+$, \#{8}, \pos{3}), \val{130.8} ($+$, \#{2}, \pos{12}), \val{133.6} ($+$, \#{2}, \pos{11}), \val{137.0} ($+$, \#{4}, \pos{8}), \val{138.6} (q, \#{4}, \pos{2}), \val{140.6} (q, \#{2}, \pos{10}), \val{140.8} (q, \#{8}, \pos{4}), \val{141.8} (q, \#{4}, \pos{6}), \val{145.6} (q, \#{2}, \pos{7}). % \data{MS}[DCP, EI, \SI{60}{\electronvolt}] \val{703} (2, \ch{M+}), \val{582} (1), \val{462} (1), \val{249} (13), \val{120} (41), \val{105} (100). % \data{MS}[\ch{MeOH + H2O + KI}, ESI, \SI{10}{\electronvolt}] \val{720} (100, \ch{M+ + OH-}), \val{368} (\ch{M+ + 2 OH-}). % \data{IR}[KBr] \val{3443} (w), \val{3061} (w), \val{2957} (m), \val{2918} (m), \val{2856} (w), \val{2729} (w), \val{1725} (w), \val{1606} (s), \val{1592} (s), \val{1545} (w), \val{1446} (m), \val{1421} (m), \val{1402} (m), \val{1357} (w), \val{1278} (w), \val{1238} (s), \val{1214} (s), \val{1172} (s), \val{1154} (m), \val{1101} (w), \val{1030} (w), \val{979} (m), \val{874} (m), \val{846} (s), \val{818} (w), \val{798} (m), \val{744} (w), \val{724} (m), \val{663} (w), \val{586} (w), \val{562} (w), \val{515} (w). % \data*{UV-Vis} \SI{386}{\nano\metre} ($\varepsilon = \val{65984}$), \SI{406}{\nano\metre} ($\varepsilon = \val{65378}$). % \data*{quantum yield} $\Phi = \val{0.74+-0.1}$\,. \end{experimental} \end{sourcecode} \subsubsection{Nearly Standard} Output with these options: \begin{sourcecode} delta=(ppm),pos-number=sub,use-equal \end{sourcecode} \begin{experimental}[delta=(ppm),pos-number=sub,use-equal] \sisetup{separate-uncertainty,per-mode=symbol,detect-all,range-phrase=--} \data*{yield} \SI{17}{\milli\gram} yellow needles (\SI{0.04}{\milli\mole}, \SI{13}{\percent}). % \data{mp.} \SI{277}{\celsius} (DSC). % \NMR(600)[CDCl3] \val{2.01} (s, \#{24}, \pos{5}), \val{2.31} (s, \#{12}, \pos{1}), \val{6.72--6.74} (m, \#{2}, \pos{11}), \val{6.82} (s, \#{8}, \pos{3}), \val{7.05--7.07} (m, \#{2}, \pos{12}), \val{7.39--7.41} (m, \#{4}, \pos{9}), \val{7.48--7.49} (m, \#{4}, \pos{8}). % \NMR{13,C}(150)[CDCl3] \val{21.2} ($+$, \#{4}, \pos{1}), \val{23.4} ($+$, \#{8}, \pos{5}), \val{126.0} ($+$, \#{4}, \pos{9}), \val{128.2} ($+$, \#{8}, \pos{3}), \val{130.8} ($+$, \#{2}, \pos{12}), \val{133.6} ($+$, \#{2}, \pos{11}), \val{137.0} ($+$, \#{4}, \pos{8}), \val{138.6} (q, \#{4}, \pos{2}), \val{140.6} (q, \#{2}, \pos{10}), \val{140.8} (q, \#{8}, \pos{4}), \val{141.8} (q, \#{4}, \pos{6}), \val{145.6} (q, \#{2}, \pos{7}). % \data{MS}[DCP, EI, \SI{60}{\electronvolt}] \val{703} (2, \ch{M+}), \val{582} (1), \val{462} (1), \val{249} (13), \val{120} (41), \val{105} (100). % \data{MS}[\ch{MeOH + H2O + KI}, ESI, \SI{10}{\electronvolt}] \val{720} (100, \ch{M+ + OH-}), \val{368} (\ch{M+ + 2 OH-}). % \data{IR}[KBr] \val{3443} (w), \val{3061} (w), \val{2957} (m), \val{2918} (m), \val{2856} (w), \val{2729} (w), \val{1725} (w), \val{1606} (s), \val{1592} (s), \val{1545} (w), \val{1446} (m), \val{1421} (m), \val{1402} (m), \val{1357} (w), \val{1278} (w), \val{1238} (s), \val{1214} (s), \val{1172} (s), \val{1154} (m), \val{1101} (w), \val{1030} (w), \val{979} (m), \val{874} (m), \val{846} (s), \val{818} (w), \val{798} (m), \val{744} (w), \val{724} (m), \val{663} (w), \val{586} (w), \val{562} (w), \val{515} (w). % \data*{UV-Vis} \SI{386}{\nano\metre} ($\varepsilon = \val{65984}$), \SI{406}{\nano\metre} ($\varepsilon = \val{65378}$). % \data*{quantum yield} $\Phi = \val{0.74+-0.1}$\,. \end{experimental} \subsubsection{Formatted List} Output with these options: \begin{sourcecode} format=\bfseries,delta=(ppm),list=true,use-equal \end{sourcecode} \begin{experimental}[format=\bfseries,delta=(ppm),list=true,use-equal] \sisetup{separate-uncertainty,per-mode=symbol,detect-all,range-phrase=--} \data*{yield} \SI{17}{\milli\gram} yellow needles (\SI{0.04}{\milli\mole}, \SI{13}{\percent}). % \data{mp.} \SI{277}{\celsius} (DSC). % \NMR(600)[CDCl3] \val{2.01} (s, \#{24}, \pos{5}), \val{2.31} (s, \#{12}, \pos{1}), \val{6.72--6.74} (m, \#{2}, \pos{11}), \val{6.82} (s, \#{8}, \pos{3}), \val{7.05--7.07} (m, \#{2}, \pos{12}), \val{7.39--7.41} (m, \#{4}, \pos{9}), \val{7.48--7.49} (m, \#{4}, \pos{8}). % \NMR{13,C}(150)[CDCl3] \val{21.2} ($+$, \#{4}, \pos{1}), \val{23.4} ($+$, \#{8}, \pos{5}), \val{126.0} ($+$, \#{4}, \pos{9}), \val{128.2} ($+$, \#{8}, \pos{3}), \val{130.8} ($+$, \#{2}, \pos{12}), \val{133.6} ($+$, \#{2}, \pos{11}), \val{137.0} ($+$, \#{4}, \pos{8}), \val{138.6} (q, \#{4}, \pos{2}), \val{140.6} (q, \#{2}, \pos{10}), \val{140.8} (q, \#{8}, \pos{4}), \val{141.8} (q, \#{4}, \pos{6}), \val{145.6} (q, \#{2}, \pos{7}). % \data{MS}[DCP, EI, \SI{60}{\electronvolt}] \val{703} (2, \ch{M+}), \val{582} (1), \val{462} (1), \val{249} (13), \val{120} (41), \val{105} (100). % \data{MS}[\ch{MeOH + H2O + KI}, ESI, \SI{10}{\electronvolt}] \val{720} (100, \ch{M+ + OH-}), \val{368} (\ch{M+ + 2 OH-}). % \data{IR}[KBr] \val{3443} (w), \val{3061} (w), \val{2957} (m), \val{2918} (m), \val{2856} (w), \val{2729} (w), \val{1725} (w), \val{1606} (s), \val{1592} (s), \val{1545} (w), \val{1446} (m), \val{1421} (m), \val{1402} (m), \val{1357} (w), \val{1278} (w), \val{1238} (s), \val{1214} (s), \val{1172} (s), \val{1154} (m), \val{1101} (w), \val{1030} (w), \val{979} (m), \val{874} (m), \val{846} (s), \val{818} (w), \val{798} (m), \val{744} (w), \val{724} (m), \val{663} (w), \val{586} (w), \val{562} (w), \val{515} (w). % \data*{UV-Vis} \SI{386}{\nano\metre} ($\varepsilon = \val{65984}$), \SI{406}{\nano\metre} ($\varepsilon = \val{65378}$). % \data*{quantum yield} $\Phi = \val{0.74+-0.1}$\,. \end{experimental} \subsubsection{Crazy} Output for these options: \begin{sourcecode} format=\color{red}\itshape, list=true, delta=\textcolor{green}{\ch{M+ + H2O}}, pos-number=side, coupling-unit=\mega\gram\per\square\second, list-setup=, use-equal \end{sourcecode} \begin{experimental}[ format=\color{red}\itshape, list=true, delta=\textcolor{green}{\ch{M+ + H2O}}, pos-number=side, coupling-unit=\mega\gram\per\square\second, list-setup=,use-equal] \sisetup{separate-uncertainty,per-mode=symbol,detect-all,range-phrase=--} \data*{yield} \SI{17}{\milli\gram} yellow needles (\SI{0.04}{\milli\mole}, \SI{13}{\percent}). % \data{mp.} \SI{277}{\celsius} (DSC). % \NMR(600)[CDCl3] \val{2.01} (s, \#{24}, \pos{5}), \val{2.31} (s, \#{12}, \pos{1}), \val{6.72--6.74} (m, \#{2}, \pos{11}), \val{6.82} (s, \#{8}, \pos{3}), \val{7.05--7.07} (m, \#{2}, \pos{12}), \val{7.39--7.41} (m, \#{4}, \pos{9}), \val{7.48--7.49} (m, \#{4}, \pos{8}). % \NMR{13,C}(150)[CDCl3] \val{21.2} ($+$, \#{4}, \pos{1}), \val{23.4} ($+$, \#{8}, \pos{5}), \val{126.0} ($+$, \#{4}, \pos{9}), \val{128.2} ($+$, \#{8}, \pos{3}), \val{130.8} ($+$, \#{2}, \pos{12}), \val{133.6} ($+$, \#{2}, \pos{11}), \val{137.0} ($+$, \#{4}, \pos{8}), \val{138.6} (q, \#{4}, \pos{2}), \val{140.6} (q, \#{2}, \pos{10}), \val{140.8} (q, \#{8}, \pos{4}), \val{141.8} (q, \#{4}, \pos{6}), \val{145.6} (q, \#{2}, \pos{7}). % \data{MS}[DCP, EI, \SI{60}{\electronvolt}] \val{703} (2, \ch{M+}), \val{582} (1), \val{462} (1), \val{249} (13), \val{120} (41), \val{105} (100). % \data{MS}[\ch{MeOH + H2O + KI}, ESI, \SI{10}{\electronvolt}] \val{720} (100, \ch{M+ + OH-}), \val{368} (\ch{M+ + 2 OH-}). % \data{IR}[KBr] \val{3443} (w), \val{3061} (w), \val{2957} (m), \val{2918} (m), \val{2856} (w), \val{2729} (w), \val{1725} (w), \val{1606} (s), \val{1592} (s), \val{1545} (w), \val{1446} (m), \val{1421} (m), \val{1402} (m), \val{1357} (w), \val{1278} (w), \val{1238} (s), \val{1214} (s), \val{1172} (s), \val{1154} (m), \val{1101} (w), \val{1030} (w), \val{979} (m), \val{874} (m), \val{846} (s), \val{818} (w), \val{798} (m), \val{744} (w), \val{724} (m), \val{663} (w), \val{586} (w), \val{562} (w), \val{515} (w). % \data*{UV-Vis} \SI{386}{\nano\metre} ($\varepsilon = \val{65984}$), \SI{406}{\nano\metre} ($\varepsilon = \val{65378}$). % \data*{quantum yield} $\Phi = \val{0.74+-0.1}$\,. \end{experimental} \section{Reaction Environments}\label{sec:reactions} \subsection{Defined by \chemmacros} You can use these environments for numbered\ldots \begin{environments} \environment{reaction} A single reaction where \chemformula\ code is placed directly in the environment body. A wrapper around the \env*{equation} environment. \environment{reactions} Several aligned reactions. A wrapper around \pkg{amsmath}'s \env*{align} environment. \end{environments} \ldots and their starred versions for unnumbered reactions. \begin{environments} \environment{reaction*} A wrapper around the \env*{equation*} environment. \environment{reactions*} A wrapper around \pkg{amsmath}'s \env*{align*} environment. \end{environments} With them you can create (un)numbered reaction equations similar to mathematical equations. Theses environments use the \env*{equation}/\env*{equation*} environments or the \env*{align}/\env*{align*} environments, respectively, to display the reactions. \begin{example} Reaction with counter: \begin{reaction} A -> B \end{reaction} \end{example} \begin{example} Reaction without counter: \begin{reaction*} C -> D \end{reaction*} \end{example} \begin{example} Several aligned reactions with counter: \begin{reactions} A &-> B + C \\ D + E &-> F \end{reactions} \end{example} \begin{example} Several aligned reactions without counter: \begin{reactions*} G &-> H + I \\ J + K &-> L \end{reactions*} \end{example} If you want to change the layout of the counter tags, you can use \cs{renewtagform}\marg{tagname}\oarg{format}\marg{right delimiter}\marg{left delimiter}\footnote{Provided by the \pkg{mathtools} package}. \begin{example} \renewtagform{reaction}[R \textbf]{[}{]} \begin{reaction} H2O + CO2 <<=> H2CO3 \end{reaction} \end{example} With version~3.3 referencing and the use of \AmS math's \cs{intertext} also function properly: \begin{example} \begin{reactions} A + 2 B &-> 3 C + D \label{rxn:test} \intertext{Some text in between aligned reactions} 3 E + F &<=> G + 1/2 H \end{reactions} See reaction~\ref{rxn:test}. \end{example} \emph{You should not use \cs{mch} and its relatives inside the \env{reaction} environments.} \subsection{Own Reactions} You can create new types of reactions with the command: \begin{commands} \command{NewChemReaction}[\oarg{options}\marg{name}\marg{math name}] \sinceversion{4.3}\meta{name} will be the name of the new environment. \meta{math name} is the underlying math environment. Gives an error if \meta{name} already exists. \command{DeclareChemReaction}[\oarg{options}\marg{name}\marg{math name}] \changedversion{4.3}\meta{name} will be the name of the new environment. \meta{math name} is the underlying math environment. \command{RenewChemReaction}[\oarg{options}\marg{name}\marg{math name}] \sinceversion{4.3}Renew an existing definition. \end{commands} The command has two options. \begin{options} \keybool{star} Also create a starred variant. \keybool{arg} Add a mandatory argument to the defined environment. \end{options} There is \option{star}, which will also define a starred version of the new environment, if the starred math environment exists. If it doesn't exist, this will cause an error. Then there is \option{arg}, which is used to define an environment with a mandatory argument. Of course this only works, if the used math environment has a mandatory argument. The predefined environments are defined via \begin{sourcecode} \NewChemReaction[star]{reaction}{equation} \NewChemReaction[star]{reactions}{align}. \end{sourcecode} Let's suppose, you'd like to have the alignment behaviour of the \env{alignat} environment for \chemformula\ reactions. You could do the following: \begin{sourcecode} \NewChemReaction[star,arg]{reactionsat}{alignat} \end{sourcecode} With this the \env{reactionsat} environment is defined. \begin{example} \NewChemReaction[star,arg]{reactionsat}{alignat} \begin{reactionsat}{3} A &-> B &&-> C &&-> D \\ aaaaa &-> bbbbb &&-> ccccc &&-> ddddd \end{reactionsat} \begin{reactionsat*}{2} A &-> B & C &-> D \\ aaaaa &-> bbbbb &\quad{} ccccc &-> ddddd \end{reactionsat*} \end{example} \subsection{List of Reactions} \chemmacros\ also provides a command to display a list of the reactions created with the \env{reaction} environment. \begin{commands} \command{listofreactions} Print a list of reactions. \end{commands} \begin{example} \listofreactions \end{example} The output of this list can be modified by two options: \begin{options} \keyval{list-name}{name of the list}\Module{reaction}\Default{List of reactions} Let's you set the name of the list manually. The default name is language dependent, see section~\ref{sec:languages}. \keyval{list-entry}{prefix to each entry}\Module{reaction}\Default{Reaction} Let's you set a prefix to each list entry. The default name is language dependent, see section~\ref{sec:languages}. \end{options} Instead of using the option \option{list-name} you also could redefine \cs{reactionlistname}. The list lists all reactions with a number and disregards reactions without number. All reaction environments without star have an optional argument which let's you add a description (or caption) for the entry in the list. \begin{example} \begin{reaction}[Autoprotolyse] 2 H2O <<=> H3O+ + OH- \end{reaction} \end{example} If you use the \env{reactions} environment this will not work, though. In this case you can use \begin{commands} \command{AddRxnDesc}[\marg{description}] Add a description to a reaction. \end{commands} \begin{example} \begin{reactions} Cl "\Lewis{0.,\vphantom{Cl}}" + CH4 & -> HCl + "\Lewis{4.,\vphantom{CH}}" CH3 \AddRxnDesc{first~step~of~chain} \\ "\Lewis{4.,\vphantom{CH}}" CH3 + Cl2 & -> CH3Cl + Cl "\Lewis{0.,\vphantom{Cl}}" \AddRxnDesc{second~step~of~chain} \end{reactions} \end{example} Note: you don't have to use the phantom commands if you haven't changed the format of the atoms (see the documentation of the \chemformula\ package for information on how to do this). \section{Phases}\label{sec:phasen} \subsection{Basics} These commands are intended to indicate the phase of a compound. \begin{itemize} \item[] \cs{sld} \sld \quad \cs{lqd} \lqd \quad \cs{gas} \gas \quad \cs{aq} \aq \end{itemize} \begin{example} \ch{C\sld{} + 2 H2O\lqd{} -> CO2\gas{} + 2 H2\gas}\par To make it complete: NaCl\aq. \end{example} The \ac{iupac} recommendation to indicate the state of aggregation is to put it in parentheses after the compound \cite{iupac:greenbook}. However, you might want to put it as a subscript which is also very common. \begin{cnltxquote}[{\acs{iupac} Green Book {\cite[][p.\,54]{iupac:greenbook}}}] The \textelp{} symbols are used to represent the states of aggregation of chemical species. The letters are appended to the formula in parentheses and should be printed in Roman (upright) type without a full stop (period). \end{cnltxquote} There are two options to customize the output: \begin{options} \keychoice{pos}{side,sub}\Module{phases}\Default{side} Switch the position of the phase indicator. \keyval{space}{dim}\Module{phases}\Default{.1333em} Change the default spacing between compound a phase indicator if \keyis{pos}{side}. A \TeX\ dimension. \end{options} \begin{example} \chemsetup[phases]{pos=sub} \ch{C\sld{} + 2 H2O\lqd{} -> CO2\gas{} + 2 H2\gas}\par To make it complete: NaCl\aq. \end{example} \subsection{Define Own Phases} Depending on the subject of your document you might need to indicate other states of aggregation. You can easily define them. \begin{commands} \command{NewChemPhase}[\marg{cs}\oarg{german}\marg{english}] \sinceversion{4.3}Define a new phase command. Actually the optional argument is an artefact of an earlier implementation of the command. It has no effect at all. See section~\ref{sec:lang-depend} for a way to define language dependent settings. Gives an error if \meta{cs} already exists. \command{DeclareChemPhase}[\marg{cs}\oarg{german}\marg{english}] Define a new phase command. Actually the optional argument is an artefact of an earlier implementation of the command. It has no effect at all. See section~\ref{sec:lang-depend} for a way to define language dependent settings. \command{RenewChemPhase}[\marg{cs}\oarg{german}\marg{english}] Redefine an existing pahse command. Actually the optional argument is an artefact of an earlier implementation of the command. It has no effect at all. See section~\ref{sec:lang-depend} for a way to define language dependent settings. \command{phase}[\marg{phase}] If you need a phase indicator just once or twice. \end{commands} \cs{NewChemPhase} only defines a phase if \meta{cs} is not already used by any other command. If it \emph{is} already used \chemmacros\ will either give an error \cs{RenewChemPhase} \emph{only} defines a phase if \meta{cs} \emph{is} already used and issues an error otherwise. \cs{DeclareChemPhase} does not check if the phase command already exists but simply defines it with the new meaning. Unlike the other declaration commands of \chemmacros\ \cs{NewChemPhase}, \cs{RenewChemPhase} and \cs{DeclareChemPhase} \emph{can only be used in the preamble.} \begin{example} % preamble: % \NewChemPhase{\aqi}{aq,$\infty$}% aqueous solution at infinite dilution % \NewChemPhase{\cd}{cd}% condensed phase % \NewChemPhase{\lc}{lc}% liquid crystal NaOH\aqi\ \ch{H2O\cd} U\phase{cr} A\lc \par \chemsetup[phases]{pos=sub} NaOH\aqi\ \ch{H2O\cd} U\phase{cr} A\lc \end{example} \subsection{Language Dependencies}\label{sec:lang-depend} For each pahse command a translation into the custom language can be defined. If a phase is declared with \cs{NewChemPhase} no translation exists and for every \pkg{babel} languuage the literal string is used that was provided as a definition. Let's say you define the phase \begin{sourcecode} \NewChemPhase\liquid{l} \end{sourcecode} and want to add the German translation ``f{}l''. Then you could do \begin{sourcecode} \DeclareTranslation{German}{phase-liquid}{f{}l} \end{sourcecode} This way, when you use it in a German document using the appropriate \pkg{babel} option using \cs*{liquid} would correctly translate. For this the package \pkg{translations} is used. The \acs{id} always is \code{phase-\meta{csname}} where \meta{csname} is the name of the phase command you defined without leading backslash. See section~\ref{sec:languages} for predefined translations. \section{Newman Projections}\label{sec:newman} \chemmacros\ provides a command to draw Newman projections. \begin{commands} \command{newman}[\oarg{options}\darg{angle}% \Marg{\meta{1},\meta{2},\meta{3},\meta{4},\meta{5},\meta{6}}] Create Newman projections. This command uses \TikZ\ internally. \meta{angle} rotates the back atoms counter clockwise with respect to the front atoms and is an optional argument. \meta{1} to \meta{6} are the positions, the first three are the front atoms, the last three the back atoms. \end{commands} \begin{example} \newman{} \newman(170){} \newman{1,2,3,4,5,6} \newman{1,2,3} \newman{,,,4,5,6} \end{example} Several options allow customization: \begin{options} \keyval{angle}{angle}\Module{newman}\Default{0} Default angle. \keyval{scale}{factor}\Module{newman}\Default{1} Scale the whole projection by factor \meta{factor}. \keyval{ring}{tikz}\Module{newman}\Default Customize the ring with \TikZ\ keys. \keyval{atoms}{tikz}\Module{newman}\Default Customize the nodes within which the atoms are set with \TikZ\ keys. \keyval{back-atoms}{tikz}\Module{newman}\Default Explicitly customize the nodes of the back atoms with \TikZ\ keys. \end{options} \begin{example} \chemsetup[newman]{angle=45} \newman{} \newman[scale=.75,ring={draw=blue,fill=blue!20}]{} \end{example} \begin{example} \chemsetup[newman]{atoms={draw=red,fill=red!20,inner sep=2pt,rounded corners}} \newman{1,2,3,4,5,6} \end{example} \begin{example} \chemsetup[newman]{ atoms = {draw=red,fill=red!20,inner sep=2pt,rounded corners}, back-atoms = {draw=blue,fill=blue!20,inner sep=2pt,rounded corners} } \newman{1,2,3,4,5,6} \newman(170){1,2,3,4,5,6} \end{example} \section{s, p, and Hybrid Orbitals}\label{sec:orbitale} \chemmacros\ provides the following command to create orbitals: \begin{commands} \command{orbital}[\oarg{options}\marg{type}] Draw an orbital shape of type \meta{type}. This command uses \TikZ\ internally. \end{commands} There are the following types available for \meta{type}: \begin{itemize} \item[] \code{s} \quad \code{p} \quad \code{sp} \quad \code{sp2} \quad \code{sp3} \end{itemize} \begin{example} \orbital{s} \orbital{p} \orbital{sp} \orbital{sp2} \orbital{sp3} \end{example} Depending on the type you have different options to modify the orbitals: \begin{options} \keychoice{phase}{\default{+},-}\Module{orbital}\Default{+} changes the phase of the orbital (all types) \keyval{scale}{factor}\Module{orbital}\Default{1} changes the size of the orbital (all types) \keyval{color}{color}\Module{orbital}\Default{black} changes the color of the orbital (all types) \keyval{angle}{angle}\Module{orbital}\Default{0} rotates the orbitals with a p contribution counter clockwise (all types except \code{s}) \keybool{half}\Module{orbital}\Default{false} displays only half an orbital (only \code{p}) \end{options} \begin{example} \orbital{s} \orbital[phase=-]{s} \orbital{p} \orbital[phase=-]{p} \orbital{sp3} \orbital[phase=-]{sp3} \orbital[angle=0]{p} \orbital[color=red!50]{p} \orbital[angle=135,scale=1.5]{p} \orbital[half]{p} \end{example} Additionally there are two options, with which the \TikZ\ behaviour can be changed. \begin{options} \keybool{overlay}\Module{orbital} The orbital \enquote{doesn't need space}; it is displayed with the \TikZ\ option \code{overlay}. \keyval{opacity}{num}\Module{orbital} The orbital becomes transparent; \meta{value} can have values between \code{1} (fully opaque) to \code{0} (invisible). \end{options} \begin{example} \vspace{7mm} \chemsetup[orbital]{ overlay, p/color = black!70 } \setbondoffset{0pt} \chemfig{ ?\orbital{p} -[,1.3]{\orbital[phase=-]{p}} -[:30,1.1]\orbital{p} -[:150,.9]{\orbital[phase=-]{p}} -[4,1.3]\orbital{p} -[:-150,1.1]{\orbital[phase=-]{p}}? } \vspace{7mm} \end{example} \begin{example} \vspace{7mm} \setbondoffset{0pt} \chemsetup[orbital]{ overlay , opacity = .75 , p/scale = 1.6 , s/color = blue!50 , s/scale = 1.6 } \chemfig{ \orbital{s} -[:-20]{\orbital[scale=2]{p}} {\orbital[half,angle=0]{p}} {\orbital[angle=170,half]{p}} {\orbital[angle=-150,half]{p}} (-[:-150]\orbital{s})-\orbital{s} } \vspace{1cm} \end{example} \part{Other Packages of the Bundle} The other three packages, \chemformula, \ghsystem\ and \chemgreek, all have their own documentation (if you click on the name the corresponding file will open): \begin{itemize} \item \url{chemformula_en.pdf} \item \url{ghsystem_en.pdf} \item \url{chemgreek_en.pdf} \end{itemize} This change has been made \sinceversion{4.0}with version~4.0 since with this version every of those packages can be used independently from the \chemmacros\ package. It made sense to give each of them an own documentation file. You should be able to find them in the same folder as this document as well as via the \code{texdoc} program. You can also try and click on the names in the list above. They are links and \emph{should} open the respective file. \appendix \part{Appendix} \addsec{Suggestions and Bug Reports} Feedback on \chemmacros, \chemformula, \chemgreek, and \ghsystem\ is highly appreciated and welcome! If you have suggestions for macros, missing features \etc, please don't hesitate to contact me. If you recognize any errors, be it chemical ones, wrong documentation and the like, I'd be grateful about a short email\footnote{\href{mailto:contact@mychemistry.eu}{contact@mychemistry.eu}}. If you find any bugs, it would be best, if you'd send me a minimal example, with which I can reproduce the bug. You can also submit an issue on \url{https://bitbucket.org/cgnieder/chemmacros/} instead. Many thanks to all the people who already provided me with feedback, especially (in alphabetical order): \begin{itemize} \item Peter Cao \item Christina Lüdigk \item Dr.~Paul King \item Jonas Rivetti (Special thanks for his translation of the hazard and precautionary statements into Italian!) \item Christoph Schäfer \item Timo Stein \end{itemize} \end{document}