%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % ----------------------------------------------------------------------------- % - the CHEMMACROS bundle % - chemmacros_en.tex % - macros and commands for chemists % ----------------------------------------------------------------------------- % - Clemens Niederberger % - 2012/05/18 % ----------------------------------------------------------------------------- % - 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 2011-2012 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. % ----------------------------------------------------------------------------- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % if you want to compile this documentation % a) you'll need the document class `cnpkgdoc' which you can get here: % https://bitbucket.org/cgnieder/cnpkgdoc/ % the class is licensed LPPL 1.3 or later % b) you need the following compilation order: % > xelatex chemmacros_en (2 or probably 3 times) % > biber chemmacros_en % > makeindex -sl index_en.ist chemmacros_en.idx % > xelatex chemmacros_en % \documentclass[DIV11,toc=index,toc=bib]{cnpkgdoc} \docsetup{ pkg = chemmacros, title = the \Chemmacros\ bundle, subtitle = {packages \Chemmacros, \Chemformula\ and \Ghsystem}, modules = true, code-box = {skipabove=1ex,skipbelow=1ex} } \usepackage{polyglossia} \setmainlanguage{english} \usepackage{chemfig,chemstyle,upgreek,textgreek,booktabs,cancel} \usepackage[version=3]{mhchem} \usepackage{hologo} \chemsetup[option]{synchronize} \colorlet{chemformula}{darkgray} \begin{filecontents}{index_en.ist} preamble "\\begin{theindex}\n Section titles are indicated \\textbf{bold}, packages \\textsf{sans serif}, commands \\code{\\textbackslash\\textcolor{code}{brown}}, options \\textcolor{key}{\\code{green}} and modules (only \\chemmacros) \\textcolor{module}{\\code{red}}.\\newline\n\n" heading_prefix "{\\bfseries " heading_suffix "\\hfil}\\nopagebreak\n" headings_flag 1 delim_0 "\\dotfill " delim_1 "\\dotfill " delim_2 "\\dotfill " delim_r "\\textendash" suffix_2p "\\nohyperpage{\\,f.}" suffix_3p "\\nohyperpage{\\,ff.}" \end{filecontents} \usepackage[backend=biber,style=alphabetic,maxbibnames=20]{biblatex} \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 Holmström and Kozo Kuchitsu and Roberto Marquardt and Ian Mills and Franco Pavese and Martin Quack and Jürgen Stohner and Herbert L. Strauss and Michio Takami and Anders J Thor}, title = {“Quantities, Symbols and Units in Physical Chemistry”, \IUPAC Green Book}, edition = {3rd Edition. 2nd Printing}, year = {2008}, publisher = {\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”, \IUPAC Red Book}, year = {2005}, publisher = { \IUPAC \&\ RSC Publishing, Cambridge}, isbn = {0-85404-438-8} } @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 } \newcommand*\chemformula{{\scshape\textcolor{cnpkgblue}{chemformula}}\xspace} \newcommand*\ghsystem{{\scshape\textcolor{cnpkgblue}{ghsystem}}\xspace} \newcommand*\Chemmacros{{\fontspec[Color=cnpkgblue,Scale=1.2]{Linux Biolinum Shadow O}chemmacros}} \newcommand*\Chemformula{{\fontspec[Color=cnpkgblue,Scale=1.2]{Linux Biolinum Shadow O}chemformula}} \newcommand*\Ghsystem{{\fontspec[Color=cnpkgblue,Scale=1.2]{Linux Biolinum Shadow O}ghsystem}} \newcommand*\IUPAC{\mbox{IUPAC}\xspace} \renewcommand*\AmS{\hologo{AmS}} \newcommand*\pdfTeX{\hologo{pdfTeX}} \newcommand*\LuaTeX{\hologo{LuaTeX}} \TitlePicture{% \ch[font-spec={[Color=chemformula]Augie}]{ 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)[red,-cf]{\small\ch[font-spec={[Color=red]Augie},math-space=.3em]{$-$ 2 e-}} \redox(r1,r2)[blue,-cf][-1]{\small\ch[font-spec={[Color=blue]Augie},math-space=.3em]{$+$ 2 e-}}} \addcmds{ a,abinitio,AddRxnDesc,anti,aq,aqi,b,ba,bottomrule,bridge,cancel,cd,cdot,ce,cee,celsius, centering,chemabove,Chemalpha,Chembeta,Chemgamma,Chemdelta,ChemDelta,chemfig, chemname,Chemomega,chemsetup,cip,cis,ch,cnsetup,CNMR,color,cstsetup,d,D,data, DeclareChemArrow,DeclareChemIUPAC,DeclareChemLatin,DeclareChemNMR, DeclareChemParticle,DeclareChemPhase,DeclareChemReaction,DeclareChemState, DeclareInstance,DeclareSIUnit,definecolor,delm,delp,Delta,Dfi,draw,E,el, electronvolt,ElPot,endo,Enthalpy,enthalpy,Entropy,footnotesize,fmch,fpch,fscrm, fscrp,g,gas,ghs,ghslistall,ghspic,Gibbs,glqq,gram,grqq,H,hapto,HNMR,Helmholtz, hertz,hspace,includegraphics,insitu,intertext,invacuo,iupac,IUPAC,J,joule,Ka, Kb,kilo,Kw,L,latin,lewis,Lewis,Lfi,listofreactions,lqd,ltn,mch,mega,meta,metre, mhName,midrule,milli,mmHg,mole,N,nano,nicefrac,newman,NMR,Nu,Nuc,num,numrange,O,ominus, orbital,ortho,oplus,ox,OX,p,P,para,pch,per,percent,pgfarrowsdeclarealias, pgfarrowsrenewalias,pH,phase,photon,pKa,pKb,pOH,pos,positron,Pot,prt,R,Rad, redox,RenewChemArrow,RenewChemIUPAC,RenewChemLatin,RenewChemNMR, RenewChemParticle,RenewChemPhase,RenewChemState,renewtagform,rightarrow,S,Sf, sample,scriptscriptstyle,scrm,scrp,setatomsep,setbondoffset,sfrac, shorthandoff,ShowChemArrow,si,SI,sisetup,sld,Sod,State,subsection,textcolor, textendash,textsuperscript,tiny,toprule,trans,upbeta,upeta,upgamma,val,volt, vphantom,vspave,w,xspace,Z} \makeindex \begin{document} \chemsetup[chemformula]{font-spec={[Color=chemformula]Latin Modern Sans}} \renewcommand*\glqq{„} \renewcommand*\grqq{“} \part{Preliminaries}\secidx{PRELIMINARIES} \section{Licence, Requirements and README} The \chemmacros bundle underlies the \LaTeX\ project public license (lppl) version 1.3 or later (\url{http://www.latex-project.org/lppl.txt}) and has the status “maintained”. The \chemmacros bundle needs the bundles \paket{l3kernel} and \paket{l3packages}. It also needs the packages \paket{siunitx}, \paket{mathtools}, \paket{bm}, \paket{nicefrac} and \paket{environ} as well as \paket*{tikz}\footnote{CTAN: \href{http://www.ctan.org/pkg/pgf/}{pgf}} and the \TikZ libraries \code{calc} and \code{arrows}. Package option \key{bpchem} (section \ref{sec:optionen}) needs the package \paket{bpchem}, package option \key{xspace} needs the package \paket{xspace} and package option \key{method}{mhchem} needs the package \paket{mhchem}. With v3.0 the \chemmacros package has been bundled with the new packages \chemformula and \ghsystem. \chemformula provides an alternative to \paket{mhchem}. This leads to some internal changes in \chemmacros. On the same time the documentation has been redesigned. You might remember that \chemmacros' options all belong to different modules, see section \ref{sec:setup} for further information. These are typeset in the left margin when the option is first mentioned. In section \ref{sec:overview} all options and the module the belong to are listed. Throughout the document options are typeset \textcolor{key}{\code{green}} and modules \textcolor{module}{\code{red}}. The package \ghsystem needs the packages \chemmacros, \paket{tabu}, \paket{longtable}, \paket{ifpdf} and \paket{graphicx}. \ghsystem has no own package options but passes all options on to \chemmacros. \achtung{There are some deprecated commands and options which are not explained in the manual any more but still exist to ensure backwards compatibility. These commands issue a warning. They may be dropped some time in the future.} \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 \textendash\ 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 \paket{mhchem} package by Martin Hensel. There have always been some difficulties intertwining it with \chemmacros, though. Also, some other minor points in \paket{mhchem} always bothered me, but they hardly seemed enough for a new package. They weren't even enough for a feature request to the \paket{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 \paket{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 \paket{mhchem} does not. Since \chemformula is meant as an \emph{alternative} to \paket{mhchem} \chemmacros offers a package option allowing you to choose which one of the two is used. The default however is \chemmacros own way: \chemformula. As a chemist you are probably aware of the fact that the \textsc{United Nations} have developed the \enquote{\textbf{G}lobally \textbf{H}armonized \textbf{S}ystem of Classification and Labelling of Chemicals} (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 as only a matter of time. The package \ghsystem now enables you to typeset all the hazard and precautionary statements and pictograms in a very easy way. The statements are taken from 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 (\lstinline=\ortho-dichlorobenzene= is easier to read and understand than \lstinline=\textsl{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 \IUPAC compliant default settings \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 \IUPAC recommendations\footnote{This does not convern the \cmd{ox} command. The \IUPAC version is \cmd[oxa]{ox*}.} I would welcome an email very much! In a package this large with older parts and rather new parts (which have to be considered being in beta state) it is unavoidable that there are flaws and bugs. I am very keen on correcting and improving this package so please: if you find anything that bothers you and may it be just so small please send me a short email and I'll see what I can do. I would especially like feedback on \chemformula (see part \ref{part:chemformula}) and \ghsystem (see part \ref{part:ghsystem}) but also welcome feedback on every other part of this bundle. \section{Installation, Loading the Bundle}\secidx{Loading the Bundle}\secidx{Installation} The bundle comes with three style files\footnote{Those ending \code{sty}.}, a directory called \code{language/} containing the language-definition files for GHS (ending \code{def}), and a directory \code{pictures/} containing \code{eps}, \code{jpg} and \code{png} files (the GHS pictogramms). If you install the bundle manually \emph{please make sure to place the directories \code{language/} and \code{pictures/} in the \emph{same} directory as the style files}. Loading \chemmacros with \begin{beispiel}[code only] \usepackage{chemmacros} % `chemmacros', `chemformula' and `ghsystem' are loaded \end{beispiel} will also load \chemformula and \ghsystem. However, you can prevent \chemmacros from loading \ghsystem: \begin{beispiel}[code only] \usepackage[ghsystem=false]{chemmacros} % `chemmacros' and `chemformula' are loaded \end{beispiel} Loading \chemformula or \ghsystem explicitly is possible and will also load \chemmacros if it hasn't been loaded yet, and will therefore implicitly load the other package, too. \begin{beispiel}[code only] \usepackage{chemformula} % `chemmacros', `chemformula' and `ghsystem' are loaded or \usepackage[ghsystem=false]{chemformula} % `chemmacros' and `chemformula' are loaded \end{beispiel} However, it is recommended to simply use \lstinline=\usepackage{chemmacros}= and setup the required options with \lstinline=\chemsetup= (also see section \ref{sec:setup}). \secidx*{Installation}\secidx*{Loading the Bundle} \section{Package Options}\label{sec:optionen}\secidx{Package Options} \chemmacros has several package options. They all are used as key/value pairs like \begin{beispiel}[code only] \usepackage[option1 = , option2 = ]{chemmacros} \end{beispiel} Some also can be used without value (\lstinline+\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 you can give them \chemmacros' options instead and they will pass them on to \chemmacros. \begin{beschreibung} % bpchem \option[option]{bpchem}{\default{true}/false} This option loads the package \paket{bpchem} and adjusts the layout of the \cmd{NMR} command to the \paket{bpchem} commands \lstinline+\HNMR+ and \lstinline+\CNMR+. (default = \code{false}) % circled \option[option]{circled}{\default{formal}/all/none} \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 (default = \code{formal}) % circletype \option[option]{circletype}{\default{chem}/math} This option switches between two kinds of circled charge symbols: \cmd{fplus} \fplus\ and \lstinline+$\oplus$+ $\oplus$. (default = \code{chem}) % cmversion \option[option]{cmversion}{1/2/bundle} This option restores the old definitions of some commands, so documents set with v1.* will still compile correctly. (default = \code{bundle}). Actually \code{2} and \code{bundle} are only aliases. \emph{This option can only be chosen in the preamble}. % ghsystem \option[option]{ghsystem}{\default{true}/false} Disable the use of the \ghsystem package. Setting \key{ghs}{false} will prevent \chemmacros from loading \ghsystem. (default = \code{true}) % greek \option[option]{greek}{math/textgreek/\default{upgreek}} This Options determines how the letters \cmd{Chemalpha} and friends are typeset. See page \pageref{desc:upgreek} for more information. \emph{This option can only be chosen in the preamble}. (default = \code{upgreek}) % iupac \option[option]{iupac}{auto/restricted/strict} Take care of how iupac naming commands are defined, see page \pageref{desc:iupac} (default = \code{auto}) % language \option[option]{language}{american/british/english/french/german/italian/ngerman} Load language specific options. \code{english}, \code{american} and \code{british} are aliases, as are \code{german} and \code{ngerman}. \emph{This option can only be chosen in the preamble}. (default = \code{english}). % method \option[option]{method}{\default{chemformula}/mhchem} You can choose the method which \chemmacros will use for the reaction environments (see section \ref{sec:reactions}) and the typesetting of the particles (see section \ref{sec:teilchen}). (default = \code{chemformula}). \emph{This option can only be chosen in the preamble}. % Nu \option[option]{Nu}{\default{chemmacros}/mathspec} The package \paket{mathspec} also defines a macro \cmd{Nu}. This option chooses which definition holds, see page \pageref{Nu}. (default = \code{chemmacros}). \emph{This option can only be chosen in the preamble}. % strict \option[option]{strict}{\default{true}/false} Setting \key{strict}{true} will turn all warning messages into erros messages. (default = \code{false}) % synchronize \option[option]{synchronize}{\default{true}/false} The setting \code{true} will tell \chemmacros the adapt the font settings of \chemformula if that method has been chosen (default = \code{false}). In order to demonstrate this feature this document is set with \key{synchronize}{true} and the \chemformula setting \lstinline+\chemsetup[chemformula]{font-spec={[Color=darkgray]Latin Modern Sans}}+. % xspace \option[option]{xspace}{\default{true}/false} With this option most commands are defined with a \lstinline+\xspace+. (default = \code{true}) \end{beschreibung} \secidx*{Package Options} \section{Setup}\label{sec:setup}\secidx{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 \cmd{chemsetup} command. \begin{beschreibung} \Befehl{chemsetup}[]{ = } or \Befehl{chemsetup}{/ = } \end{beschreibung} 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 \cmd{chemsetup}, as you can see above. The package options can also be seen as keys belonging to the module \textcolor{module}{\code{option}}. This means they can also be used with the \cmd{chemsetup} command (except for the option \key[option]{version}{1/2/3}). \begin{beispiel} \chemsetup[option]{circled=none}\mch\ \pch\ \fmch\ \fpch\ \el\ \prt \\ \chemsetup[option]{circled=formal}\mch\ \pch\ \fmch\ \fpch\ \el\ \prt \\ \chemsetup[option]{circletype=math}\mch\ \pch\ \fmch\ \fpch\ \el\ \prt \\ \chemsetup{option/circletype=chem,option/circled=all}\mch\ \pch\ \fmch\ \fpch\ \el\ \prt \\ \chemsetup{option/circletype=math}\mch\ \pch\ \fmch\ \fpch\ \el\ \prt \end{beispiel} Keys \emph{not} belonging to a module \emph{cannot} be used with \cmd{chemsetup}! All options of \chemformula belong to the module \textcolor{module}{\code{chemformula}} and all of \ghsystem's options belong to the module \textcolor{module}{\code{ghs}}. \secidx*{Setup} \section{Language Settings}\label{sec:languages}\secidx{Language Settings} \subsection{Supported Languages} By choosing the option \begin{beispiel}[code only] \chemsetup[option]{language=} \end{beispiel} you can set one of these languages: \code{american/british/english/french/german/italian/ngerman}. The languages \code{american/british/english} are aliases, as are \code{german/ngerman}. These translate \begin{itemize} \item The header of the list of reactions. \item The beginning of the entries in the list of reactions. \item The H- and P-statements of the GHS. \end{itemize} \achtung{Please note, that the GHS statements are not provided in all languages, see also section \ref{sec:ghsystem_language}.} \subsection{Specialties} \subsubsection{German} If you choose \code{german/ngerman} the phase commands \cmd{sld} and \cmd{lqd} and the command \cmd{pKa} are translated. \subsubsection{Italian} \DeclareChemIUPAC{\ter}{\textit{ter}}\DeclareChemIUPAC{\sin}{\textit{sin}}% Choosing the language \code{italian} defines two additional IUPAC commands: \begin{beschreibung} \befehl{ter} \iupac{\ter} \befehl{sin} \iupac{\sin} \end{beschreibung} \secidx*{Language Settings} \section{News}\secidx{News} \subsection{Version 3.3} \begin{itemize} \item With v3.3 there is the environment \env{experimental}{}, see section \ref{sec:spektroskopie}. It can be used together with some new options and commands for the consistent typesetting of experimental data. \item The environment \env{reaction}{} and its kin can now cope with \lstinline+\label+, \lstinline+\ref+ and \lstinline+\intertext+, see section \ref{sec:reactions}. \item The package options \key{german} and \key{ngerman} are deprecated, the replacement is \key{language}, see page \pageref{key:option_language} and section \ref{sec:languages} from page \pageref{sec:languages}. \item The package option \key{upgreek} got renamed into \key{greek}. \item Some additional \code{\textbackslash\textcolor{code}{Chem}}-commands are provided, see section \ref{sec:teilchen}. \end{itemize} \subsection{Version 3.3a} \begin{itemize} \item The IUPAC commands \cmd{hapto} and \cmd{bridge} are new. \item The H and P statements now are available in Italian. \end{itemize} \secidx*{News}\secidx*{PRELIMINARIES} \part{\texorpdfstring{\Chemmacros}{chemmacros}}\secidx{CHEMMACROS}\label{part:chemmacros} \section{Particles, Ions and Symbols}\label{sec:teilchen}\secidx{Particles, Ions and Symbols} \subsection{Predefined}\secidx[predefined]{Particles, Ions and Symbols} \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:optionen}. These commands can be used in text as well as in math mode. \begin{beschreibung} \befehl{Hpl} \Hpl (proton) \befehl{Hyd} \Hyd (hydroxide) \befehl{HtO} \HtO (oxonium ion) (\textbf{H} \textbf{t}hree \textbf{O}) \befehl{water} \water \befehl{el} \el (electron) \befehl{prt} \prt (proton) \befehl{ntr} \ntr (neutron) \befehl{Nu} \Nu (nucleophile). The package \paket{mathspec} also defines a macro \cmd{Nu}. If you chose package option \key[option]{Nu}{mathspec} \chemmacros defines \cmd{Nuc} instead\label{Nu}. \befehl{El} \El (electrophile) \befehl{ba} \ba (base) \befehl{fplus} \fplus \befehl{fminus} \fminus \befehl{transitionstatesymbol} \transitionstatesymbol \befehl{standardstate} \standardstate. This symbol is only provided by \chemmacros, if the package \paket{chemstyle} is not loaded; the idea is borrowed from there\footnote{many thanks to the package author \href{http://www.texdev.net/}{Joseph Wright}.}. \befehl{Chemalpha} \Chemalpha \befehl{Chembeta} \Chembeta \befehl{Chemgamma} \Chemgamma \befehl{Chemdelta} \Chemdelta \befehl{Chemepsilon} \Chemepsilon \befehl{Chemeta} \Chemeta \befehl{Chemkappa} \Chemkappa \befehl{Chemmu} \Chemmu \befehl{Chemnu} \Chemnu \befehl{Chemrho} \Chemrho \befehl{Chempi} \Chempi \befehl{Chemsigma} \Chemsigma \befehl{Chemomega} \Chemomega \befehl{ChemDelta} \ChemDelta \end{beschreibung} \achtung{The command \cmd{Rad} has been dropped!} The two particles \cmd{Nu} and \cmd{ba} can be modified. To do that you use the option \begin{beschreibung} \Option[particle]{elpair}{false/\default{dots}/dash}. \end{beschreibung} It only has any effect, if the package \paket{chemfig} is loaded, since it uses it's command \lstinline+\Lewis+. \begin{beispiel} % needs package `chemfig' \ba[elpair] \Nu[elpair=dash] \chemsetup[particle]{elpair} \ba \Nu \end{beispiel} \label{desc:upgreek}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 \paket{textgreek} package the letters are taken from there, and if you have loaded the package \paket{upgreek} the macros of that package are used. This documentation uses \paket{upgreek} for instance. If you load both \paket{upgreek} and \paket{textgreek} the letters from \paket{upgreek} are used. If you don't want \chemmacros to use a package automatically but want to decide for yourself, there is the option \key[option]{greek}. \ref{tab:upgreek_mode} shows the different styles for some of the letters. \begin{table}[h] \centering \begin{tabular}{lccc}\toprule & math & upgreek & textgreek \\\midrule \cmd{Chemalpha} & $\alpha$ & $\upalpha$ & \textalpha \\ \cmd{Chembeta} & $\beta$ & $\upbeta$ & \textbeta \\ \cmd{ChemDelta} & $\Delta$ & $\Updelta$ & \textDelta \\ \bottomrule \end{tabular} \caption{The greek letters}\label{tab:upgreek_mode} \end{table} The reason why \chemmacros defines these macros in the first place is \IUPAC compliance. \IUPAC recommends to use upright greek letters in nomenclature. \begin{zitat}[\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{zitat} \chemmacros uses these commands now to defined nomenclature commands, see page \pageref{par:greek_letters}. \subsection{Own Particles}\secidx[own]{Particles, Ions and Symbols} Surely sometimes it can be handy to have other particle macros defined such as \lstinline+\positron+ or \lstinline+\photon+. This can easily be done with this command: \begin{beschreibung} \Befehl{DeclareChemParticle}{}\ma{} \Befehl{RenewChemParticle}{}\ma{} \end{beschreibung} Depending on the \key{method} you chose as option the \code{} will either be a formula defined with \paket{mhchem} or with \chemformula. The particle defined this way behaves like the predefined ones with one exception: if you chose \key{method}{mhchem} the particle \emph{will not} obey the option \key{circled}. If you want formal charges with this method you need to use \chemmacros' commands (see section \ref{sec:ladungen}) explicitly. If you chose \key{method}{chemformula} the partictle \emph{will} obey the \key{circled} option. \begin{beispiel} % uses the `upgreek' package \DeclareChemParticle{\positron}{$\upbeta$+} \DeclareChemParticle{\photon}{$\upgamma$} \RenewChemParticle{\el}{$\upbeta$-} \positron\ \photon\ \el \end{beispiel} \cmd{DeclareChemParticle} only defines a particle if \code{} is not already used by any other command. If it \emph{is} already used \chemmacros will either give a warning or an error, depending on the option \key{strict}. \cmd{RenewChemParticle} \emph{only} defines a particle if \code{} \emph{is} already used and issues a warning/error otherwise. \secidx*{Particles, Ions and Symbols} \section{Nomenclature, Stereo Descriptors, Latin Phrases}\label{sec:stereo} \subsection{\IUPAC Names}\secidx{IUPAC Names} Similar to the \paket{bpchem} package \chemmacros provides a command\footnote{The idea and the implementation is shamelessly borrowed from \paket*{bpchem} by Bjørn Pedersen.} to typeset \IUPAC names. Why is that useful? \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{beschreibung} \item\cmd{iupac}{} Inside this command use \cmd{|} and \cmd{-} to indicate a breaking point or a breaking dash. Use {\catcode`\^=11\relax\cmd{^}} as a shortcut for \lstinline=\textsuperscript=\footnote{Actually another mechanism is used, but the effect is essentially the same.}. \end{beschreibung} \begin{beispiel} \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{beispiel} The \cmd{iupac} command is more of a semantic command. Most times you can achieve (nearly) the same thing by using \cmd{-} instead of \cmd{|}, \code{-} instead of \cmd{-} and \lstinline=\textsuperscript= instead of {\catcode`\^=11\relax\cmd{^}}. There are some subtleties: \cmd{-} inserts a small space before the hyphen a removes a small space after it. The command \cmd{|} not only prevents ligatures but also inserts a small space. \begin{beispiel} \huge\iupac{2,4\-Di\|chlor\|pentan} \\ 2,4-Dichlorpentan \end{beispiel} The spaces inserted by these commands can be customized. \begin{beschreibung} \option[iupac]{hyphen-pre-space}{} Default = \code{.01em} \option[iupac]{hyphen-post-space}{} Default = \code{-.03em} \option[iupac]{break-space}{} Default = \code{.01em} \end{beschreibung} The command \cmd{iupac} serves another purpose, too, however. Regardless of the setting of the \key[option]{iupac} option all the commands presented in this section are always defined \emph{inside} \cmd{iupac}. Quite a number of the naming commands have very general names: \cmd{meta}, \cmd{D}, \cmd{E}, \cmd{L}, \cmd{R}, \cmd{S}, \cmd{trans} and so forth. This means they either are predefined already (\cmd{L} \L) or are easily defined by another package or class (the \paket{cool} package defines both \cmd{D} and \cmd{E}, for example). In order to give you control which commands are defined in which way, there is the package option \key[option]{iupac}\label{desc:iupac}. It has three modes: \begin{itemize} \item \key{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} \cmd{iupac}. \item \key{iupac}{restricted}: all naming commands are \emph{only} defined inside \cmd{iupac}. If the commands are defined by another package they of course have that meaning outside. They're not defined outside otherwise. \item \key{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 \cmd{iupac} then. \end{itemize} \ref{tab:iupac_modes} demonstrates the different modes. \begin{table}[h] \centering \begin{tabular}{lccc}\toprule & auto & restricted & strict \\\midrule \lstinline=\L= & \L & \L & \iupac{\L} \\ \lstinline=\iupac{\L}= & \iupac{\L} & \iupac{\L} & \iupac{\L} \\ \lstinline=\D= & \D & -- & \D \\ \lstinline=\iupac{\D}= & \iupac{\D} & \iupac{\D} & \iupac{\D} \\\bottomrule \end{tabular} \caption{Demonstration of \protect\key{iupac}'s modes.}\label{tab:iupac_modes} \end{table} \subsubsection{Predefined Commands}\secidx[predefined]{IUPAC Names}\secidx{Stereo Descriptors and Nomenclature} The macros in this section are intended to make the writing of \IUPAC names more convenient. \paragraph{Greek Letters}\label{par:greek_letters}\secidx[greek letters]{IUPAC Names} Greek letters in compound names are typeset upright. For this there are the packages \paket{upgreek} and \paket{textgreek}. If you have loaded one of them \chemmacros typesets the following commands upright: \begin{beschreibung} \befehl{a} \iupac{\a} \befehl{b} \iupac{\b} \befehl{g} \iupac{\g} \befehl{d} \iupac{\d} \befehl{k} \iupac{\k} \befehl{m} \iupac{\m} \befehl{n} \iupac{\n} \befehl{w} \iupac{\w} \end{beschreibung} \begin{beispiel} \iupac{5\a\-androstan\-3\b\-ol} \\ \iupac{\a\-(tri\|chloro\|methyl)\-\w\-chloro\|poly(1,4\-phenylene\|methylene)} \end{beispiel} \paragraph{Hetero Atoms and added Hydrogen}\secidx[hetero atoms]{IUPAC Names} Attachments to hetero atoms and added hydrogen atoms are indicated by italic letters \cite{iupac:greenbook}. \chemmacros defines a few shortcuts for the most common ones. \begin{beschreibung} \befehl{H} \iupac{\H} \befehl{O} \iupac{\O} \befehl{N} \iupac{\N} \befehl{Sf} \iupac{\Sf} \befehl{P} \iupac{\P} \end{beschreibung} \begin{beispiel} \iupac{\N\-methyl\|benz\|amide} \\ \iupac{3\H\-pyrrole} \\ \iupac{\O\-ethyl hexanethioate} \end{beispiel} \paragraph{Cahn-Ingold-Prelog}\index{Cahn-Ingold-Prelog}\secidx[Cahn-Ingold-Prelog]{IUPAC Names} \begin{beschreibung} \befehl{cip}{} \eg: \cmd{cip}{R,S} \cip{R,S} \befehl{R} \iupac{\R} \befehl{S} \iupac{\S} \end{beschreibung} Since the command \cmd{S} has another meaning already (\S) it is only available inside \cmd{iupac} in the default setting. \paragraph{Fischer}\index{Fischer}\secidx[Fischer]{IUPAC Names} \begin{beschreibung} \befehl{D} \iupac{\D} \befehl{L} \iupac{\L} \end{beschreibung} Since the command \cmd{L} has another meaning already (\L) it is only available inside \cmd{iupac} in the default setting. \paragraph{cis/trans, zusammen/entgegen, syn/anti \& tert}\index{tert}\secidx[tert]{IUPAC Names}\index{cis/trans}\secidx[cis/trans]{IUPAC Names}\index{zusammen/entgegen}\secidx[zusammen/entgegen]{IUPAC Names}\secidx[syn/anti]{IUPAC Names} \begin{beschreibung} \befehl{cis} \cis \befehl{trans} \trans \befehl{Z} \Z \befehl{E} \E \befehl{syn} \syn \befehl{anti} \anti \befehl{tert} \tert \end{beschreibung} The package \paket{cool} defines the commands \cmd{E} and \cmd{D}, too. If you load it, the \chemmacros version will only be available inside \cmd{iupac} in the default setting. \paragraph{ortho/meta/para}\index{ortho/meta/para}\secidx[ortho/meta/para]{IUPAC Names} \begin{beschreibung} \befehl{ortho} \ortho \befehl{meta} \meta \befehl{para} \para \end{beschreibung} \paragraph{Absolute Configuration}\index{absolute configuration} (uses \TikZ) \begin{beschreibung} \befehl{Rconf}[] \cmd{Rconf}: \Rconf \quad\cmd{Rconf}[]: \Rconf[] \befehl{Sconf}[] \cmd{Sconf}: \Sconf \quad\cmd{Sconf}[]: \Sconf[] \end{beschreibung} Examples: \begin{beispiel} \iupac{\D\-Wein\|s\"aure} = \\ \iupac{\cip{2S,3S}\-Wein\|s\"aure} \\ \iupac{\D\-($-$)\-Threose} = \\ \iupac{\cip{2S,3R}\-($-$)\-2,3,4\-Tri\|hydroxy\|butanal} \\ \iupac{\cis\-2\-Butene} = \\ \iupac{\Z\-2\-Butene}, \\ \iupac{\cip{2E,4Z}\-Hexa\|diene} \\ \iupac{\meta\-Xylol} = \\ \iupac{1,3\-Di\|methyl\|benzene} \end{beispiel} \secidx*{Stereo Descriptors and Nomenclature} \paragraph{Coordination Chemistry} \chemmacros provides two commands useful with coordination chemistry: \begin{beschreibung} \befehl{bridge}{} \bridge{3} \befehl{hapto}{} \hapto{5} \end{beschreibung} \begin{beispiel} Ferrocene = \iupac{bis(\hapto{5}cyclo\|penta\|dienyl)iron} \\ \iupac{tetra\-\bridge{3}iodido\-tetrakis[tri\|methyl\|platinum(IV)]} \end{beispiel} Two options allow customization: \begin{beschreibung} \option[iupac]{bridge-number}{sub/super} appends the number as a supscript or superscript. IUPAC recommendation is the subscript \cite{iupac:redbook}. Default = \code{sub} \option[iupac]{coord-use-hyphen}{\default{true}/false} append a hyphen to \cmd{hapto} and \cmd{bridge} or don't. Default = \code{true} \end{beschreibung} \subsubsection{Own Naming Commands}\secidx[own]{IUPAC Names} If you find any commands missing you can define them using \begin{beschreibung} \befehl{DeclareChemIUPAC}{}\ma{} \befehl{RenewChemIUPAC}{}\ma{} \end{beschreibung} A command defined in this way will obey the setting of the option \key[option]{iupac}. This means any existing command is only overwritten with \key{iupac}{strict}. However, \cmd{DeclareChemIUPAC} will \emph{not} change the definition of an existing \IUPAC naming command but issue a warning/an error (depending on the package option \key{strict}) if the \IUPAC naming command already exists. \begin{beispiel} \DeclareChemIUPAC\endo{\textit{endo}} \DeclareChemIUPAC\anti{\textit{anti}} \iupac{(2\-\endo,7\-\anti)\-2\-bromo\-7\-fluoro\|bicyclo[2.2.1]heptane} \end{beispiel} \cmd{RenewChemIUPAC} allows you to redefine the existing iupac naming commands. \begin{beispiel} \iupac{\meta\-Xylol} \\ \RenewChemIUPAC\meta{\textit{m}} \iupac{\meta\-Xylol} \end{beispiel} \secidx*{IUPAC Names} \subsection{Latin Phrases}\secidx{Latin Phrases} The package \paket{chemstyle} provides the command \cmd{latin} to typeset common latin phrases in a consistent way. \chemmacros defines a similar \cmd{latin} only if \paket{chemstyle} has \emph{not} been loaded and additionally provides these commands: \begin{beschreibung} \befehl{insitu} \insitu \befehl{abinitio} \abinitio \befehl{invacuo} \invacuo \end{beschreibung} If the package \paket{chemstyle} has been loaded they are defined using \paket{chemstyle}'s \cmd{latin} command. This means that then the appearance depends on \paket{chemstyle}'s option \code{abbremph}: \begin{beispiel} \insitu, \abinitio\\ \cstsetup{abbremph=false} \insitu, \abinitio \end{beispiel} The commands are defined through \begin{beschreibung} \befehl{DeclareChemLatin}{}\ma{} \befehl{RenewChemLatin}{}\ma{} \end{beschreibung} \begin{beispiel} \DeclareChemLatin\ltn{latin text} \ltn \cstsetup{abbremph=false} \ltn \end{beispiel} If you have \emph{not} loaded \paket{chemstyle} you can change the appearance with this option: \begin{beschreibung} \option[latin]{format}{} Default = \lstinline+\itshape+ \end{beschreibung} \secidx*{Latin Phrases} \section{Units for the Usage With \textsf{siunitx}}\label{sec:einheiten}\secidx{Units} In chemistry some non-SI units are very common. \paket{siunitx} provides the command \lstinline+\DeclareSIUnit{}{}+ to add arbitrary units. \chemmacros uses that command to provide some units. Like all \paket{siunitx} units they're only valid inside \lstinline+\SI{}{}+ and \lstinline+\si{}+. \begin{beschreibung} \befehl{atmosphere} \si{\atmosphere} \befehl{atm} \si{\atm} \befehl{calory} \si{\calory} \befehl{cal} \si{\cal} \befehl{cmc} \si{\cmc} The units \cmd{cmc}, \cmd{molar}, and \cmd{Molar} are defined by the package \paket{chemstyle} as well. \chemmacros only defines them, if \paket{chemstyle} is not loaded. \befehl{molar} \si{\molar} \befehl{moLar} \si{\moLar} \befehl{Molar} \si{\Molar} \befehl{MolMass} \si{\MolMass} \befehl{normal} \si{\normal} \befehl{torr} \si{\torr} \end{beschreibung} By the way: \lstinline+\mmHg+ \si{\mmHg} already is defined by \paket{siunitx} and \paket{chemstyle} \secidx*{Units} \section{Acid/Base}\label{sec:saeure_base}\secidx{Acid/Base} Easy representation of \pH, \pKa \ldots\ (the command \cmd{pKa} depends on the package option \key[option]{language}). \begin{beschreibung} \befehl{pH} \pH \befehl{pOH} \pOH \befehl{Ka} \Ka \befehl{Kb} \Kb \befehl{Kw} \Kw \befehl{pKa}[] \cmd{pKa}: \pKa, \cmd{pKa}[1]: \pKa[1] \befehl{pKb}[] \cmd{pKb}: \pKb, \cmd{pKb}[1]: \pKb[1] \befehl{p}{} \eg \cmd{p}{\cmd{Kw}} \p{\Kw} \end{beschreibung} \begin{beispiel} \Ka \Kb \pKa \pKa[1] \pKb \pKb[1] \end{beispiel} \achtung{The default appearance of the \p{}-commands has changed to follow \IUPAC recommendations.} \begin{zitat}[\IUPAC Green Book \cite[][p.\,103]{iupac:greenbook}] The operator \p{} […] shall be printed in Roman type. \end{zitat} There is one option which changes the style the \p{} is typeset: \begin{beschreibung} \option[acid-base]{p-style}{italics/slanted/upright} Default = \code{upright} \end{beschreibung} \begin{beispiel} \pH, \pKa \chemsetup[acid-base]{p-style=slanted} \pH, \pKa \chemsetup[acid-base]{p-style=italics} \pH, \pKa \end{beispiel} \secidx*{Acid/Base} \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:optionen}. All commands using formal charge symbols start with a \code{f}. \subsection{Ion Charges}\label{ssec:ionen}\secidx{Ion Charges} Simple displaying of (real) charges: \begin{beschreibung} \befehl{pch}[] positive charge (\textbf{p}lus + \textbf{ch}arge) \befehl{mch}[] negative charge (\textbf{m}inus + \textbf{ch}arge) \end{beschreibung} \begin{beispiel} \pch, Na\pch, Ca\pch[2]\\ \mch, F\mch, S\mch[2] \end{beispiel} The same for formal charges: \begin{beschreibung} \befehl{fpch}[] positive charge \befehl{fmch}[] negative charge \end{beschreibung} \begin{beispiel} \fpch\ \fmch\ \fpch[3] \fmch[3] \end{beispiel} There is a key which influences the behaviour of the charges. \begin{beschreibung} \option[charges]{append}{\default{true}/false} if set \code{true}, the charge is appended together with an empty group. \end{beschreibung} This is how the key influences the behaviour: \begin{beispiel} % uses package `mhchem' \chemsetup{charges/append=false,phases/pos=sub} \ce{H\pch\aq} \ce{H\aq\pch} \chemsetup[charges]{append=true} \ce{H\pch\aq} \ce{H\aq\pch} \end{beispiel} In most cases this behaviour will be unwanted. However, in some cases it might be useful, for example together with the \cmd{ox} command (see next section): \begin{beispiel} \chemsetup{charges/append=false,phases/pos=sub} \ce{\ox{1,H}\pch\aq} \chemsetup[charges]{append=true} \ce{\ox{1,H}\pch\aq} \end{beispiel} \secidx*{Ion Charges} \subsection{Oxidation Numbers}\label{ssec:oxidationszahlen}\secidx{Oxidation Numbers} Typesetting oxidation numbers: \begin{beschreibung} \befehl{ox}[]{,} places \code{} above \code{}; \code{} has to be a (rational) number! \end{beschreibung} \begin{beispiel} \ox{+1,Na}, \ox{2,Ca}, \ox{-2,S}, \ox{-1,F} \end{beispiel} There are a number of keys, that can be used to modify the \cmd{ox} command. \begin{beschreibung} \option[ox]{parse}{\default{true}/false} when \code{false} an arbitrary entry can be used for \code{}. Default = \code{true} \option[ox]{roman}{\default{true}/false} switches from roman to arabic numbers. Default = \code{true} \option[ox]{pos}{top/super/side}; \code{top} places \code{} above \code{}, \code{super} to the upper right as superscript and \code{side} to the right and inside brackets. Default = \code{top} \option[ox]{explicit-sign}{\default{true}/false} shows the $+$ for positiv numbers and the $\pm$ for $0$. Default = \code{false} \option[ox]{decimal-marker}{comma/point} choice for the decimal marker for formal oxidation numbers like \ox{1.2,X}. Default = \code{point} \end{beschreibung} \begin{beispiel} \ox[roman=false]{2,Ca} \ox{2,Ca} \\ \ox[pos=super]{3,Fe}-Oxide \\ \ox[pos=side]{3,Fe}-Oxide \\ \ox[parse=false]{?,Mn} \end{beispiel} The \key[ox]{pos}{super} variant also can be set with the shortcut \cmd[oxa]{ox*}: \begin{beispiel} \ox{3,Fe} \ox*{3,Fe} \end{beispiel} Using the \key[ox]{explicit-sign} key will always show the sign of the oxidation number: \begin{beispiel} \chemsetup[ox]{explicit-sign = true} \ox{+1,Na}, \ox{2,Ca}, \ox{-2,S}, \ch{"\ox{0,F}" {}2} \end{beispiel} \begin{beispiel} Compare \ox{-1,\ch{O2^2-}} to \ch{"\ox{-1,O}" {}2^2-} \end{beispiel} Sometimes one might want to use formal oxidation numbers like \num{.5} or $\frac{1}{3}$: \begin{beispiel} \ox{.5,\ch{Br2}} \ch{"\ox{1/3,I}" {}3+} \end{beispiel} The fraction uses the \lstinline+\sfrac+ command of the \paket{xfrac} package. For this purpose the instance \lstinline+chemmacros-ox-frac+ is defined. \begin{beispiel}[code only] \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{beispiel} Of course you can redefine it so that it suits your needs as the output often strongly depends on the used font. \secidx*{Oxidation Numbers} \subsection{Partial Charges and Similar Stuff}\label{ssec:partialladungen}\secidx{Partial Charges} The next ones probably are seldomly needed but nevertheless useful: \begin{beschreibung} \befehl{delp} \delp\ (\textbf{del}ta + \textbf{p}lus) \befehl{delm} \delm\ (\textbf{del}ta + \textbf{m}inus) \befehl{fdelp} \fdelp \befehl{fdelm} \fdelm \end{beschreibung} These macros for example can be used with the \cmd{ox} command or with the \paket{chemfig} package: \begin{beispiel} \chemsetup{ option/circled = all, ox/parse = false } \ce{\ox{\delp,H}-\ox{\delm,Cl}} \hspace*{1cm} \chemfig{\chemabove[3pt]{\lewis{246,Br}}{\delm}-\chemabove[3pt]{H}{\delp}} \end{beispiel} The following macros are useful together with \paket{chemfig}, too. \begin{beschreibung} \befehl{scrp} \scrp\ (\textbf{scr}iptstyle + \textbf{p}lus) \befehl{scrm} \scrm\ (\textbf{scr}iptstyle + \textbf{m}inus) \befehl{fscrp} \fscrp \befehl{fscrm} \fscrm \befehl{fsscrp} \fsscrp\ (using \lstinline+\scriptscriptstyle+) \befehl{fsscrm} \fsscrm \end{beschreibung} \begin{beispiel} \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{beispiel} \secidx*{Partial Charges} \section{Reaction Mechanisms}\label{sec:mechanismen}\secidx{Reaction Mechanisms} With the command \begin{beschreibung} \Befehl{mech}[] \end{beschreibung} one can specify the most common reaction mechanisms. \code{} can have one of the following values: \begin{beschreibung} \befehl{mech} (empty, no opt. argument) nucleophilic substitution \mech \befehl{mech}[1] unimolecular nucleophilic substitution \mech[1] \befehl{mech}[2] bimolecular nucleophilic substitution \mech[2] \befehl{mech}[se] electrophilic substitution \mech[se] \befehl{mech}[1e] unimolecular electrophilic substitution \mech[1e] \befehl{mech}[2e] bimolecular electrophilic substitution \mech[2e] \befehl{mech}[ar] electrophilic aromatic substitution \mech[ar] \befehl{mech}[e] elimination \mech[e] \befehl{mech}[e1] unimolecular elimination \mech[e1] \befehl{mech}[e2] bimolecular elimination \mech[e2] \befehl{mech}[cb] unimolecular elimination \enquote{conjugated base}, \ie via carbanion \mech[cb] \end{beschreibung} \secidx*{Reaction Mechanisms} \section{Redox Reactions}\label{sec:redoxreaktionen}\secidx{Redox Reactions}% TODO: watch pagebreaks! \chemmacros provides two commands to visualize the transfer of electrons in redox reactions. Both commands are using \TikZ. \begin{beschreibung} \Befehl{OX}{,} \Befehl{redox}(,)[]\oa{}{} \cnpkgdocarrow\ Only the first argument \da{,} is required, the others are all optional. \end{beschreibung} \cmd{OX} places \code{} into a node, which is named with \code{}. If you have set two \cmd{OX}, they can be connected with a line using \cmd{redox}. To do so the names of the two nodes that are to be connected are written in the round braces. Since \cmd{redox} draws a tikzpicture with options \code{remember picture,overlay}, the document needs to be \emph{compiled at least two times}. \begin{beispiel}[dist] \OX{a,Na} $\rightarrow$ \OX{b,Na}\pch\redox(a,b){oxidation} \end{beispiel} This line can be customized using \TikZ keys in \oa{}: \begin{beispiel}[ox] \OX{a,Na} $\rightarrow$ \OX{b,Na}\pch\redox(a,b)[->,red]{ox} \end{beispiel} With the argument \oa{} the length of the vertical parts of the line can be adjusted. The default length is \code{.6em}. This length is multiplied with \code{}. If you use a negative value the line is placed \emph{below} the text. \begin{beispiel}[dist] \OX{a,Na} $\rightarrow$ \OX{b,Na}\pch \redox(a,b)[->,red]{ox} \redox(a,b)[<-,blue][-1]{red} \vspace{7mm} \end{beispiel} The default length of the vertical lines can be customized with the option \begin{beschreibung} \option[redox]{dist}{} A \TeX\ dimension. Default = \code{.6em} \end{beschreibung} \begin{beispiel}[dist] \chemsetup{redox/dist=1em} \OX{a,Na} $\rightarrow$ \OX{b,Na}\pch\redox(a,b)[->,red]{ox} \end{beispiel} Additionally the option \begin{beschreibung} \option[redox]{sep}{} Default = \code{.2em} \end{beschreibung} can be used to change the distance between the atom and the beginning of the line. \begin{beispiel}[dist] \chemsetup{redox/sep=.5em} \OX{a,Na} $\rightarrow$ \OX{b,Na}\pch\redox(a,b)[->,red]{ox} \end{beispiel} Examples:% TODO: watch pagebreaks! \begin{beispiel}[dist] \ch{ 2 "\OX{o1,Na}" + "\OX{r1,Cl}" {}2 -> 2 "\OX{o2,Na}" \pch{} + 2 "\OX{r2,Cl}" \mch } \redox(o1,o2){\small OX: $- 2\el$} \redox(r1,r2)[][-1]{\small RED: $+ 2\el$} \vspace{7mm} \end{beispiel} \begin{beispiel}[dist] \ch{ 2 "\OX{o1,\ox{0,Na}}" + "\OX{r1,\ox{0,Cl}}" {}2 -> 2 "\OX{o2,\ox{+1,Na}}" \pch{} + 2 "\OX{r2,\ox{-1,Cl}}" \mch } \redox(o1,o2){\small OX: $- 2\el$} \redox(r1,r2)[][-1]{\small RED: $+ 2\el$} \vspace{7mm} \end{beispiel} \bspmidlength{dist}{15mm} \begin{beispiel}[dist] \ch{ 2 "\OX{o1,\ox{0,Na}}" + "\OX{r1,\ox{0,Cl}}" {}2 -> 2 "\OX{o2,\ox{+1,Na}}" \pch{} + 2 "\OX{r2,\ox{-1,Cl}}" \mch } \redox(o1,o2)[draw=red,->][3.33]{\small OX: $- 2\el$} \redox(r1,r2)[draw=blue,->]{\small RED: $+ 2\el$} \end{beispiel} \bspmidlength{dist}{7mm} \begin{beispiel}[dist] \ch{ 2 "\OX{o1,\ox{0,Na}}" + "\OX{r1,\ox{0,Cl}}" {}2 -> 2 "\OX{o2,\ox{+1,Na}}" \pch{} + 2 "\OX{r2,\ox{-1,Cl}}" \mch } \redox(o1,o2)[green,-stealth]{\small OX} \redox(r1,r2)[purple,-stealth][-1]{\small RED} \vspace{7mm} \end{beispiel} \secidx*{Redox Reactions} \section{(Standard) State, Thermodynamics}\label{sec:standardstate}\secidx{Thermodynamics} \subsection{Thermodynamic Variables}\label{ssec:siunitx} The following commands use \paket{siunitx}: \begin{beschreibung} \Befehl{Enthalpy}[]\da{}\ma{} \Befehl{Entropy}[]\da{}\ma{} \Befehl{Gibbs}[]\da{}\ma{} \end{beschreibung} Their usage is pretty much self-explaining: \begin{beispiel} \Enthalpy{123} \\ \Entropy{123} \\ \Gibbs{123} \end{beispiel} The argument \da{} adds a subscript for specification: \cmd{Enthalpy}(r){123} \Enthalpy(r){123}. There are several keys to customize the commands. \begin{beschreibung} \Option*{exponent}{} \Option*{delta}{/false} \Option*{subscript}{left/right} \Option*{unit}{} \end{beschreibung} The default values depend on the command. \begin{beispiel} \Enthalpy[unit=\kilo\joule]{-285} \\ \Gibbs[delta=false]{0} \\ \Entropy[delta=\Delta,exponent=]{56.7} \end{beispiel} The unit is set corresponding to the rules of \paket{siunitx} and depends on its settings: \begin{beispiel} \Enthalpy{-1234.56e3} \\ \sisetup{per-mode=symbol,exponent-product=\cdot,output-decimal-marker={,},group-four-digits=true} \Enthalpy{-1234.56e3} \end{beispiel} \subsubsection{Create New Variables} You can use the command \begin{beschreibung} \Befehl{DeclareChemState}[]{}\ma{}\ma{} \end{beschreibung} to create new corresponding commands: \begin{beispiel} \DeclareChemState{Helmholtz}{A}{\kilo\joule\per\mole} \DeclareChemState[subscript-left=false,exponent=]{ElPot}{E}{\volt} \Helmholtz{123.4} \\ \ElPot{-1.1} \\ \ElPot[exponent=0]($\ch{Sn}|\ch{Sn^2+}||\ch{Pb^2+}|\ch{Pb}$){0.01} \end{beispiel} The command has some keys with which the default behaviour of the new command can be set. \begin{beschreibung} \Option*{exponent}{} \Option*{delta}{/false} \Option*{subscript-left}{true/false} \Option*{subscript}{} \end{beschreibung} \subsubsection{Redefine Variables} With \begin{beschreibung} \Befehl{RenewChemState}[]{}\ma{}\ma{} \end{beschreibung} you can redefine the already existing commands: \begin{beispiel} \RenewChemState{Enthalpy}{h}{\joule} \Enthalpy(f){12.5} \end{beispiel} The command is analogous to \cmd{DeclareChemState}, \ie it has the same keys. So \textendash\ for following thermodynamic conventions \textendash\ one could define a molar and an absolute variable: \begin{beispiel} \DeclareChemState[exponent=]{enthalpy}{h}{\kilo\joule\per\mole}% molar \RenewChemState[exponent=]{Enthalpy}{H}{\kilo\joule}% absolute \enthalpy{-12.3} \Enthalpy{-12.3} \end{beispiel} \subsection{State}\label{ssec:state} The commands presented in section \ref{ssec:siunitx} internally all use the command\footnote{Please note that \ma{} is an \emph{optional} argument.} \begin{beschreibung} \Befehl{State}[]{}\ma{} \end{beschreibung} It can be used to write the thermodynamic variables without value and unit. Examples: \begin{beispiel} \State{A}, \State{G}{f}, \State[subscript-left=false]{E}{\ch{Na}}, \State[exponent=\SI{1000}{\celsius}]{H} \end{beispiel} Again there are some keys to customize the command: \begin{beschreibung} \Option[state]{exponent}{} \Option[state]{subscript-left}{true/false} \Option[state]{delta}{/false} \end{beschreibung} \secidx*{Thermodynamics} \section{Spectroscopy and Experimental Data}\label{sec:spektroskopie}\secidx{Spectroscopy} \subsection{The \code{\textbackslash\textcolor{code}{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 \paket{siunitx}). \begin{beschreibung} \Befehl{NMR}{,}\da{,}\oa{} \Befehl{NMR*}{,}\da{,}\oa{} \end{beschreibung} \emph{All} Argument are optional! Without arguments we get: \begin{beispiel} \NMR \\ \NMR* \end{beispiel} The first argument specifies the kind of NMR: \begin{beispiel} \NMR{13,C} \end{beispiel} The second argument sets the frequency (in \si{\mega\hertz}): \begin{beispiel} \NMR(400) \end{beispiel} You can choose another unit: \begin{beispiel} \NMR(4e8,\hertz) \end{beispiel} Please note that the setup of \paket{siunitx} also affects this command: \begin{beispiel} \sisetup{exponent-product=\cdot}\NMR(4e8,\hertz) \end{beispiel} The third argument specifies the solvent: \begin{beispiel} \NMR[CDCl3] \end{beispiel} \subsection{Short Cuts} It is possible to define short cut commands for specific nuclei. \begin{beschreibung} \Befehl{DeclareChemNMR}{}\ma{,} \Befehl{RenewChemNMR}{}\ma{,} \end{beschreibung} This defines a command with the same arguments as \cmd{NMR} \emph{except} for \ma{,}. \begin{beispiel} \DeclareChemNMR\HNMR{1,H}% \DeclareChemNMR\CNMR{13,C}% \CNMR*(100) \\ \HNMR*(400) \end{beispiel} \subsection{An Environment to Typeset Experimental Data} \chemmacros provides an environment to ease the input of experimental data. \begin{beschreibung}\catcode`\#=11 \umg{experimental}{data} Environment for the output of experimental data. Inside theis environment the following commands are defined. \Befehl{data}{}\oa{} \cnpkgdocarrow\ Type of data, \eg\ IR, MS\ldots\ The optional argument takes further specifications which are output in parentheses. \Befehl{data*}{}\oa{} \cnpkgdocarrow\ Like \cmd{data} but changes the \code{=} into a \code{:}, given that \key{use-equal}{true} is used. \befehl{J}[]{} Coupling constant, values are input separated by \code{;} (NMR). \befehl{#}{} Number of nuclei (NMR). \befehl{pos}{} Position of nuclues (NMR). \befehl{val}{} A number, an alias of \paket*{siunitx}' \lstinline+\num{}+ \befehl{val}{-{}-} An alias of \paket*{siunitx}' \lstinline+\numrange{}{}+ \end{beschreibung} \begin{beispiel} \begin{experimental} \data{type1} Data. \data{type2}[specifications] More data. \data*{type3} Even more data. \end{experimental} \end{beispiel} \subsection{Customization} The output of the environment and of the NMR commands can be customized be y number of options. For historical reasons they all belong to the module \textcolor{module}{\code{nmr}}. \begin{beschreibung} \option[nmr]{unit}{} Default = \lstinline=\mega\hertz= \option[nmr]{nucleus}{\{,\}} Default = \ma{1,H} \option[nmr]{format}{} for example \lstinline=\bfseries= \option[nmr]{pos-number}{side/sub} Position of the number next to the atom. Default = \code{side} \option[nmr]{coupling-unit}{} A \paket{siunitx} unit. Default = \lstinline=\hertz= \option[nmr]{parse}{true/false} Treat the solvent as \paket{mhchem}/\chemformula formula or not. Default = \code{true} \option[nmr]{delta}{} The \code{} are added after $\delta$. \option[nmr]{list}{true/false} The environment \env{nmr}[]{} is formatted as a list. Default = \code{false} \option[nmr]{list-setup}{} Setup of the list. Default = see below. \option[nmr]{use-equal}{\default{true}/false} Add egual sign after \cmd{NMR} and \cmd{data}. Default = \code{false} \end{beschreibung} The default setup of the list: \begin{beispiel}[code only] \topsep\z@skip \partopsep\z@skip \itemsep\z@ \parsep\z@ \itemindent\z@ \leftmargin\z@ \end{beispiel} \begin{beispiel} \begin{experimental}[format=\bfseries] \data{type1} Data. \data{type2}[specifications] More data. \data*{type3} Even more data. \end{experimental} \end{beispiel} The command \cmd{NMR} and all commands defined through \cmd{DeclareChemNMR} can be used like \cmd{data} for the NMR data. \begin{beispiel} \begin{experimental}[format=\bfseries,use-equal] \data{type1} Data. \data{type2}[specifications] More data. \NMR Even more data. \end{experimental} \end{beispiel} \subsection{An Example} The code below is shown with different specifications for \code{}. Of course options can also be chosen with \cmd{chemsetup}. \begin{lstlisting} \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{lstlisting} \subsubsection{Nearly Standard} Output with these options: \lstinline+: delta=(ppm),pos-number=sub,use-equal+ \bigskip \begin{experimental}[delta=(ppm),pos-number=sub,use-equal]\sisetup{separate-uncertainty,per-mode=symbol,detect-all,range-phrase=--}\chemsetup[chemformula]{format=} \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: \lstinline+: format=\bfseries,delta=(ppm),list=true,use-equal+ \bigskip \begin{experimental}[format=\bfseries,delta=(ppm),list=true,use-equal]\sisetup{separate-uncertainty,per-mode=symbol,detect-all,range-phrase=--}\chemsetup[chemformula]{format=} \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: \code{}: \begin{lstlisting} 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{lstlisting} \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=--}\chemsetup[chemformula]{format=} \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} \secidx*{Spectroscopy} \section{Commands for \textsf{mhchem}}\label{sec:mhchem}\secidx{Commands for mhchem} \paket{mhchem} isn't loaded automatically any more but only if you've specified \key[option]{method}{mhchem} in the preamble. In the default settings \chemmacros uses \chemformula instead. \chemmacros provides only one command specifically for \paket{mhchem}\footnote{\chemformula provides its own possibility.}. It is meant to place text below of compounds. \begin{beschreibung} \Befehl{mhName}[]{}\ma{} \end{beschreibung} For example: \begin{beispiel} \ce{4 C2H5Cl + Pb / Na -> \mhName{Pb(C2H5)4}{former antiknock additive} + NaCl} \end{beispiel} There are several keys to customize \cmd{mhName}. \begin{beschreibung} \option[mhName]{align}{} the alignment of the text in the box it is placed in, default = \lstinline+\centering+ \option[mhName]{format}{} the format of the text \option[mhName]{fontsize}{} the fontsize of the text, default = \lstinline+\tiny+ \option[mhName]{width}{/auto} the width of the box the text is placed in, default = \code{auto} \end{beschreibung} \begin{beispiel} \ce{4 C2H5Cl + Pb / Na -> \mhName[fontsize=\footnotesize]{Pb(C2H5)4}{former antiknock additive} + NaCl}\\ \chemsetup[mhName]{align=\raggedright,fontsize=\small,format=\bfseries\color{red},width=3cm} \ce{4 C2H5Cl + Pb / Na -> \mhName{Pb(C2H5)4}{former antiknock additive} + NaCl} \end{beispiel} \secidx*{Commands for mhchem} \section{Reaction Environments}\label{sec:reactions}\secidx{Reaction Environments} \subsection{Defined by \chemmacros} You can use these environments for numbered\ldots \begin{beschreibung} \Umg{reaction}{} \Umg{reactions}{} \end{beschreibung} \ldots and their starred versions for unnumbered reactions. \begin{beschreibung} \Umg{reaction*}{} \Umg{reactions*}{} \end{beschreibung} With them you can create (un)numbered reaction equations similar to mathematical equations. Theses environments use the \code{equation}/\code{equation*} environments or the \code{align}/\code{align*} environments, respectively, to display the reactions. \begin{beispiel} Reaction with counter: \begin{reaction} A -> B \end{reaction} \end{beispiel} \begin{beispiel} Reaction without counter: \begin{reaction*} C -> D \end{reaction*} \end{beispiel} \begin{beispiel} Several aligned reactions with counter: \begin{reactions} A &-> B + C \\ D + E &-> F \end{reactions} \end{beispiel} \begin{beispiel} Several aligned reactions without counter: \begin{reactions*} G &-> H + I \\ J + K &-> L \end{reactions*} \end{beispiel} If you want to change the layout of the counter tags, you can use \cmd{renewtagform}{}\oa{}\ma{}\ma{}\footnote{Provided by the \paket*{mathtools} package}. \begin{beispiel} \renewtagform{reaction}[R \textbf]{[}{]} \begin{reaction} H2O + CO2 <<=> H2CO3 \end{reaction} \end{beispiel} With version 3.3 referencing and the use of \AmS math's \cmd{intertext} also function properly: \begin{beispiel} \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{beispiel} \achtung{In the standard setting, \ie using \key{method}{chemformula} you should not use \cmd{mch} and its relatives inside the \code{reaction} environments. They will very likely mess with spacing. In the standard setting charges inside the environments automatically recognize the setting of the option \key{circled} so there's also no need for the charge commands.} \subsection{Own Reactions} You can create new types of reactions with the command: \begin{beschreibung} \Befehl{DeclareChemReaction}[]{}\ma{} \end{beschreibung} \code{} will be the name of the new environment. \code{} is the used math environment. The command has two options. \begin{beschreibung} \Option*{star}{\default{true}/false} \Option*{arg}{\default{true}/false} \end{beschreibung} There is \key*{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 \key*{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{beschreibung} \Befehl{DeclareChemReaction}[star]{reaction}\ma{equation} and \Befehl{DeclareChemReaction}[star]{reactions}\ma{align}. \end{beschreibung} Let's suppose, you'd like to have the alignment behaviour of the \code{alignat} environment for \chemformula/\paket{mhchem} reactions. You could do the following: \cmd{DeclareChemReaction}[star,arg]{reactionsat}\ma{alignat} With this the \code{reactionsat} environment is defined. \begin{beispiel} \DeclareChemReaction[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{beispiel} \subsection{List of Reactions} \chemmacros also provides a command to display a list of the reactions created with the \lstinline+reaction+ environment. \begin{beschreibung} \Befehl{listofreactions} \end{beschreibung} \begin{beispiel}[below] \listofreactions \end{beispiel} The Output of this list can be modified by two options: \begin{beschreibung} \option[reaction]{list-name}{} Let's you set the name of the list manually. Default = \code{List of reactions} \option[reaction]{list-entry}{} Let's you set a prefix to each list entry. Default = \code{Reaction} \end{beschreibung} Both default option values recognize the package option \key[option]{german}. Instead of using the option \key{list-name} you also could redefine \cmd{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{beispiel} \begin{reaction}[Autoprotolyse] 2 H2O <<=> H3O+ + OH- \end{reaction} \end{beispiel} If you use the \code{reactions} environment this will not work, though. In this case you can use \begin{beschreibung} \Befehl{AddRxnDesc}{} \end{beschreibung} \begin{beispiel} \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{beispiel} Note: you don't have to use the phantom commands if you haven't changed the format of the atoms, see section \ref{sec:format} on page \pageref{sec:format}. \secidx*{Reaction Environments} \section{Phases}\label{sec:phasen}\secidx{Phases} \subsection{Basics}\secidx[basics]{Phases} These commands are intended to indicate the phase of a compound. \begin{beschreibung} \befehl{sld} \sld \befehl{lqd} \lqd \befehl{gas} \gas \befehl{aq} \aq \end{beschreibung} \achtung{The default behaviour of the phases commands has changed to be consistent with \IUPAC recommendations. Both \cmd{sld} and \cmd{lqd} have lost their optional argument.} \begin{beispiel} \ch{C\sld{} + 2 H2O\lqd{} -> CO2\gas{} + 2 H2\gas}\\ To make it complete: NaCl\aq. \end{beispiel} With the package option \key{language}{german} (see section \ref{sec:optionen}) you get the german versions. The \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{zitat}[{\IUPAC Green Book \cite[][p.\,54]{iupac:greenbook}}] The [\ldots] 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{zitat} There are two options to customize the output: \begin{beschreibung} \option[phases]{pos}{side/sub} Switch the position of the phase indicator. Default = \code{side} \option[phases]{space}{} Change the default spacing between compound a phase indicator if \key{pos}{side}. A \TeX\ dimension. Default = \code{.1333em} \end{beschreibung} \begin{beispiel} \chemsetup[phases]{pos=sub} \ch{C\sld{} + 2 H2O\lqd{} -> CO2\gas{} + 2 H2\gas}\\ To make it complete: NaCl\aq. \end{beispiel} \subsection{Define Own Phases}\secidx[own]{Phases} Depending on the subject of your document you might need to indicate other states of aggregation. You can easily define them. \begin{beschreibung} \Befehl{DeclareChemPhase}{}\oa{}\ma{} \Befehl{RenewChemPhase}{}\oa{}\ma{} \befehl{phase}{} If you need a phase indicator just once or twice. \end{beschreibung} \cmd{DeclareChemPhase} only defines a phase if \code{} is not already used by any other command. If it \emph{is} already used \chemmacros will either give a warning or an error, depending on the option \key{strict}. \cmd{RenewChemPhase} \emph{only} defines a phase if \code{} \emph{is} already used and issues a warning/error otherwise. \begin{beispiel} \DeclareChemPhase{\aqi}{aq,$\infty$}% aqueous solution at infinite dilution \DeclareChemPhase{\cd}{cd}% condensed phase \RenewChemPhase{\lqd}{lc}% liquid crystal NaOH\aqi\ \ch{H2O\cd} U\phase{cr} A\lqd \\ \chemsetup[phases]{pos=sub} NaOH\aqi\ \ch{H2O\cd} U\phase{cr} A\lqd \end{beispiel} \secidx*{Phases} \section{Newman Projections}\label{sec:newman}\secidx{Newman Projections} \chemmacros provides the command \begin{beschreibung} \Befehl{newman}[]\da{}\ma{<1>,<2>,<3>,<4>,<5>,<6>} \end{beschreibung} which allows you to create newman projections (uses \TikZ). With \code{} the back atoms are rotated counter clockwise with respect to the front atoms. \begin{beispiel} \newman{} \newman(170){} \newman{1,2,3,4,5,6} \newman{1,2,3} \newman{,,,4,5,6} \end{beispiel} Several options allow customization: \begin{beschreibung} \option[newman]{angle}{} default angle \option[newman]{scale}{} scale the whole projection \option[newman]{ring}{} customize the ring with \TikZ keys \option[newman]{atoms}{} customize the nodes within which the atoms are set \option[newman]{back-atoms}{} explicitly customize the back atoms \end{beschreibung} \begin{beispiel} \chemsetup[newman]{angle=45} \newman{} \newman[scale=.75,ring={draw=blue,fill=blue!20}]{} \end{beispiel} \begin{beispiel} \chemsetup[newman]{atoms={draw=red,fill=red!20,inner sep=2pt,rounded corners}} \newman{1,2,3,4,5,6} \end{beispiel} \begin{beispiel} \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{beispiel} \secidx*{Newman Projections} \section{s, p, and Hybrid Orbitals}\label{sec:orbitale}\secidx{Orbitals} \chemmacros provides the following command to create orbitals: \begin{beschreibung} \Befehl{orbital}[]{}: \begin{description} \item \code{s} \item \code{p} \item \code{sp} \item \code{sp2} \item \code{sp3} \end{description} \begin{beispiel} \orbital{s} \orbital{p} \orbital{sp} \orbital{sp2} \orbital{sp3} \end{beispiel} Depending on the type you have different options to modify the orbitals: \begin{beschreibung} \option[orbital]{phase}{\default{+}/-} changes the phase of the orbital (all types) \option[orbital]{scale}{} changes the size of the orbital (all types) \option[orbital]{color}{} changes the color of the orbital (all types) \option[orbital]{angle}{} rotates the orbitals with a p contribution counter clockwise (all types except \code{s}) \option[orbital]{half}{\default{true}/false} displays only half an orbital (only \code{p}) \end{beschreibung} \begin{beispiel} \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{beispiel} Additionally there are two options, with which the \TikZ behaviour can be changed. \begin{beschreibung} \option[orbital]{overlay}{\default{true}/false} the orbital \enquote{doesn't need space}; it is displayed with the \TikZ option \code{overlay}. \option[orbital]{opacity}{} the orbital becomes transparent; \code{} can have values between \code{1} (fully opaque) to \code{0} (invisible). \end{beschreibung} \begin{beispiel}[dist] \hspace{1cm} \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{beispiel} \bspmidlength{dist}{10mm} \begin{beispiel}[dist] \hspace{2cm} \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{beispiel} \bspmidlength{dist}{7mm} \secidx*{Orbitals}\secidx*{CHEMMACROS} \part{\texorpdfstring{\Chemformula}{chemformula}}\chemsetup[chemformula]{format=}\secidx{CHEMFORMULA}\label{part:chemformula} \section{Setup} All of \chemformula's options belong to the module \textcolor{module}{\code{chemformula}}. This means they can be setup with \begin{beispiel}[code only] \chemsetup[chemformula]{} or \chemsetup{chemformula/,chemformula/} \end{beispiel} \section{The Basic Principle} \chemformula offers one main command. \begin{beschreibung} \Befehl{ch}[]{