%xymaliph.tex %Copyright (C) 1993, Shinsaku Fujita, All rights reserved. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %This file is a part of xymtex.tex that is the manual of the macro %package `XyMTeX' for drawing chemical structural formulas. %This file is not permitted to be translated into Japanese and any other %languages. \typeout{``xymaliph.tex''--- This file is a part of xymtex.tex that is the manual of the macro % package `XyMTeX'. 1993/12/1 S. Fujita} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \chapter{Aliphatic Compounds} \section{Drawing Tetrahedral Units} The macro \verb/\tetrahedral/ is used to draw a tetrahedral unit (aliphat.sty). The format of this command is as follows: \begin{verbatim} \tetrahedral[AUXLIST]{SUBSLIST} \end{verbatim} % ******************** % * tetrahedral unit * % ******************** % % The following numbering is adopted in this macro. % % 1 % % | % 2 -- 0 -- 4 0 <== the original point % | % % 3 % % The following diagram shows the numbering for designating substitution positions: \begin{xymspec} \begin{picture}(800,880)(0,0) \put(0,0){\tetrahedral{1==1;2==2;3==3;4==4;0==0}} \end{picture} \qquad\fbox{\parbox{2cm}{$\circ$: (300,300) \\ $\bullet$: (\the\noshift,\the\noshift)}} \end{xymspec} in which the same macro is used to typeset both saturated and unsaturated derivatives. The optional argument AUXLIST is used to specify a charge on the central atom: {\em i.e.}, \{0+\} represents a + charge (or another one chararacter) on the center. The argument SUBSLIST is used to specify each substituent with a locant number and a bond modifier shown in Table \ref{tt:ali1}, in which $n$ is an arabic numeral between 1 and 4. \begin{table}[hptb] \caption{SUBSLIST for {\tt $\backslash$tetrahedral}} \label{tt:ali1} \begin{center} \begin{tabular}{ll} \hline Character & \multicolumn{1}{c}{Structures printed} \\ \hline $n$T & triple bond at $n$-atom \\ $n$D & double bond at $n$-atom \\ $n$ or $n$S & single bond at $n$-atom\\ $n$A & alpha single bond at $n$-atom\\ $n$B & beta single bond at $n$-atom\\ \hline \end{tabular} \end{center} \end{table} The central carbon atom is asigned by writing 0==C. The structural formula of an ammonium ion can also be obtained with this command. \medskip \noindent Example: \begin{verbatim} \tetrahedral{0==C;1==H;2==Cl;3==F;4==Br}\qquad \tetrahedral{0==C;1D==O;2==Cl;4==Cl}\qquad \tetrahedral[{}{0+}]{0==N;1==H;2==CH$_{3}$;3==H;4==H} \end{verbatim} produce the following structures: \begin{center} \tetrahedral{0==C;1==H;2==Cl;3==F;4==Br}\qquad \tetrahedral{0==C;1D==O;2==Cl;4==Cl}\qquad \tetrahedral[{}{0+}]{0==N;1==H;2==CH$_{3}$;3==H;4==H} \end{center} The macro \verb/\square/ is used to draw a tetrahedral unit of another type (aliphat.sty). The format of this command is as follows: \begin{verbatim} \square[AUXLIST]{SUBSLIST} \end{verbatim} % *************** % * square unit * % *************** % % The following numbering is adopted in this macro. % % 4 1 % ` / % ` / % (0) <== the original point % / ` % / ` % 3 2 % The following diagram shows the numbering for designating substitution positions: \begin{xymspec} \begin{picture}(800,880)(0,0) \put(0,0){\square{1==1;2==2;3==3;4==4;0==0}} \end{picture} \qquad\fbox{\parbox{2cm}{$\circ$: (300,300) \\ $\bullet$: (\the\noshift,\the\noshift)}} \end{xymspec} \medskip \noindent Example: \begin{verbatim} \square{0==C;1==H;2==Cl;3==F;4==Br}\qquad \square{0==C;1D==O;2==Cl;4==Cl} \end{verbatim} produce the following structures: \begin{center} \square{0==C;1==H;2==Cl;3==F;4==Br}\qquad \square{0==C;1D==O;2==Cl;4==Cl} \end{center} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \section{Drawing Trigonal Units} The macro \verb/\rtrigonal/ and \verb/\ltrigonal/ are used to draw right-handed and left-handed trigonal units (aliphat.sty). The formats of these commands are as follows: \begin{verbatim} \rtrigonal[AUXLIST]{SUBSLIST} \ltrigonal[AUXLIST]{SUBSLIST} \end{verbatim} % ************************* % * trigonal unit (right) * % ************************* % % The following numbering is adopted in this macro. % % 3 % / % / % 1 --- 0 90 0 <== the original point % ` % ` % 2 % % % ************************ % * trigonal unit (left) * % ************************ % % The following numbering is adopted in this macro. % % 2 % ` % ` % 90 0 --- 1 0 <== the original point % / % / % 3 % The bond angles of 2--0--3 are 90$^{\circ}$ in the trigonal units printed with these commands. The arguments AUXLIST and SUBSLIST are the same as those of \verb/\tetrahedral/. \medskip \noindent Example: \begin{verbatim} \rtrigonal{0==C;1D==O;2==Cl;3==F}\qquad \ltrigonal{0==C;1D==O;2==Cl;3==F} \end{verbatim} produce the following structures: \begin{center} \rtrigonal{0==C;1D==O;2==Cl;3==F}\qquad \ltrigonal{0==C;1D==O;2==Cl;3==F} \end{center} The macros \verb/\utrigonal/ and \verb/\Utrigonal/ are used to draw upward trigonal units with angles 90$^{\circ}$ and 120$^{\circ}$ (aliphat.sty). The formats of these commands are as follows: \begin{verbatim} \utrigonal[AUXLIST]{SUBSLIST} \Utrigonal[AUXLIST]{SUBSLIST} \end{verbatim} % ********************** % * trigonal unit (up) * % ********************** % % The following numbering is adopted in this macro. % % 3 . 2 % ` 90 / % ` / % 0 0 <== the original point % | % | % 1 % % % ********************** % * trigonal unit (up) * % ********************** % % The following numbering is adopted in this macro. % % 3 2 % ` 120 / % ` / % 0 0 <== the original point % | % | % 1 % % The arguments AUXLIST and SUBSLIST are the same as those of \verb/\tetrahedral/. \medskip \noindent Example: \begin{verbatim} \utrigonal{0==C;1D==O;2==Cl;3==F}\qquad \Utrigonal{0==C;1D==O;2==Cl;3==F} \end{verbatim} produce the following structures: \begin{center} \utrigonal{0==C;1D==O;2==Cl;3==F}\qquad \Utrigonal{0==C;1D==O;2==Cl;3==F} \end{center} On the other hand, the macros \verb/\dtrigonal/ and \verb/\Dtrigonal/ are used to draw downward trigonal units with angles 90$^{\circ}$ and 120$^{\circ}$ (aliphat.sty). The formats of these commands are as follows: \begin{verbatim} \dtrigonal[AUXLIST]{SUBSLIST} \Dtrigonal[AUXLIST]{SUBSLIST} \end{verbatim} % ************************ % * trigonal unit (down) * % ************************ % % The following numbering is adopted in this macro. % % 1 % | % | % 0 0 <== the original point % / ` % / 90 ` % 2 3 % % ************************ % * trigonal unit (down) * % ************************ % % The following numbering is adopted in this macro. % % 1 % | % | % 0 0 <== the original point % / ` % / 120 ` % 2 3 % % The arguments AUXLIST and SUBSLIST are the same as those of \verb/\tetrahedral/. \medskip \noindent Example: \begin{verbatim} \dtrigonal{0==C;1D==O;2==Cl;3==F}\qquad \Dtrigonal{0==C;1D==O;2==Cl;3==F} \end{verbatim} produce the following structures: \begin{center} \dtrigonal{0==C;1D==O;2==Cl;3==F}\qquad \Dtrigonal{0==C;1D==O;2==Cl;3==F} \end{center} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \section{Drawing Ethylene Derivatives} The macro \verb/\ethylene/ is used to draw ethylene derivatives with angles 90$^{\circ}$ (aliphat.sty). The format of this command is as follows: \begin{verbatim} \ethylene[BONDLIST]{ATOMLIST}{SUBSLIST} \end{verbatim} % ***************** % * ethylene unit * % ***************** % % The following numbering is adopted in this macro. % % 1 4 % ` / % ` / % 90 (1)===(2) 90 (1) <== the original point % / ` % / ` % 2 3 % % The following diagram shows the numbering for designating substitution positions: \begin{xymspec} \begin{picture}(800,880)(0,0) \put(0,0){\ethylene{1==1;2==2}{1==1;2==2;3==3;4==4;0==0}} \end{picture} \qquad\fbox{\parbox{2cm}{$\circ$: (300,300) \\ $\bullet$: (\the\noshift,\the\noshift)}} \end{xymspec} \begin{table}[hptb] \caption{BONDLIST for {\tt $\backslash$ethylene}} \label{tt:ali2} \begin{center} \begin{tabular}{ll} \hline Character & \multicolumn{1}{c}{Structures printed} \\ \hline $\{n+\}$ & + charge (or another one chararacter) on $n$-atom \\ d & inner double bond (between centers 1 and 2) \\ t & inner triple bond (between centers 1 and 2) \\ \hline \end{tabular} \end{center} \end{table} The argument ATOMLIST is used for giving central atoms. The argument SUBSLIST is the same as that of \verb/\tetrahedral/. \medskip \noindent Example: \begin{verbatim} \ethylene{1==C;2==C}{1==F;2==Cl;3==H;4==Br}\qquad \ethylene{1==C;2==C}{1==CH$_{3}$;2==H;3==CH$_{2}$OH;4==H}\par \ethylene{1==C;2==N}{1==Ph;2==Ph;3==OH}\qquad \ethylene[t{2+}]{1==C;2==N}{1==CH$_{3}$;2==CH$_{3}$;3==H} \end{verbatim} produce the following structures: \begin{center} \ethylene{1==C;2==C}{1==F;2==Cl;3==H;4==Br}\qquad \ethylene{1==C;2==C}{1==CH$_{3}$;2==H;3==CH$_{2}$OH;4==H}\par \ethylene{1==C;2==N}{1==Ph;2==Ph;3==OH}\qquad \ethylene[t{2+}]{1==C;2==N}{1==CH$_{3}$;2==CH$_{3}$;3==H} \end{center} The macro \verb/\ethylenev/, which is the vertical counterpart of \verb/\ethylene/, is used to draw ethylene derivatives with angles 90$^{\circ}$ (aliphat.sty). The format of this command is as follows: \begin{verbatim} \ethylenev[BONDLIST]{ATOMLIST}{SUBSLIST} \end{verbatim} % **************************** % * ethylene unit (vertical) * % **************************** % % The following numbering is adopted in this macro. % % 4 3 % ` 90 / % ` / % (2) % || % || % (1) <== the original point % / ` % / 90 ` % 1 2 % The following diagram shows the numbering for designating substitution positions: \begin{xymspec} \begin{picture}(800,880)(0,0) \put(0,0){\ethylenev{1==1;2==2}{1==1;2==2;3==3;4==4;0==0}} \end{picture} \qquad\fbox{\parbox{2cm}{$\circ$: (300,300) \\ $\bullet$: (\the\noshift,\the\noshift)}} \end{xymspec} \medskip \noindent Example: \begin{verbatim} \ethylenev{1==C;2==C}{1==F;2==Cl;3==H;4==Br}\qquad \ethylenev{1==C;2==N}{1==Ph;2==Ph;3==OH}\qquad \ethylenev[t{2+}]{1==C;2==N}{1==H$_{3}$C;2==CH$_{3}$;3==H} \end{verbatim} produce the following structures: \begin{center} \ethylenev{1==C;2==C}{1==F;2==Cl;3==H;4==Br}\qquad \ethylenev{1==C;2==N}{1==Ph;2==Ph;3==OH}\qquad \ethylenev[t{2+}]{1==C;2==N}{1==H$_{3}$C;2==CH$_{3}$;3==H} \end{center} The macro \verb/\Ethylenev/ is used to draw ethylene derivatives with angles 120$^{\circ}$ (aliphat.sty). It is the vertical counterpart of \verb/\ethylene/. The format of the command is as follows: \begin{verbatim} \Ethylenev[BONDLIST]{ATOMLIST}{SUBSLIST} \end{verbatim} % **************************** % * ethylene unit (vertical) * % **************************** % % The following numbering is adopted in this macro. % % 4 3 % ` 120 / % ` / % (2) % || % || % (1) <== the original point % / ` % / 120 ` % 1 2 % The following diagram shows the numbering for designating substitution positions: \begin{xymspec} \begin{picture}(800,880)(0,0) \put(0,0){\Ethylenev{1==1;2==2}{1==1;2==2;3==3;4==4;0==0}} \end{picture} \qquad\fbox{\parbox{2cm}{$\circ$: (300,300) \\ $\bullet$: (\the\noshift,\the\noshift)}} \end{xymspec} \medskip \noindent Example: \begin{verbatim} \Ethylenev{1==C;2==C}{1==F;2==Cl;3==H;4==Br}\qquad \Ethylenev{1==C;2==N}{1==Ph;2==Ph;3==OH}\qquad \Ethylenev[t{2+}]{1==C;2==N}{1==H$_{3}$C;2==CH$_{3}$;3==H} \end{verbatim} produce the following structures: \begin{center} \Ethylenev{1==C;2==C}{1==F;2==Cl;3==H;4==Br}\qquad \Ethylenev{1==C;2==N}{1==Ph;2==Ph;3==OH}\qquad \Ethylenev[t{2+}]{1==C;2==N}{1==H$_{3}$C;2==CH$_{3}$;3==H} \end{center} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \section{Drawing Configurations} The macros \verb/tetrastereo/ and \verb/dtetrastereo/ typset fragments which show actural configuration of a tetrahedral carbon in different modes of projections. The formats of these commands are as follows: \begin{verbatim} \tetrastereo[AUXLIST]{SUBSLIST} \dtetrastereo[AUXLIST]{SUBSLIST} \end{verbatim} The arguments AUXLIST and SUBSLIST are the same as those of \verb/\tetrahedral/. The following diagram shows the numbering for designating substitution positions: \begin{xymspec} \begin{picture}(1600,880)(0,0) \put(0,0){\tetrastereo{1==1;2==2;3==3;4==4}} \put(800,0){\dtetrastereo{1==1;2==2;3==3;4==4}} \put(1400,0){\fbox{\parbox{2cm}{$\circ$: (300,300) \\ $\bullet$: (\the\noshift,\the\noshift)}}} \end{picture} \end{xymspec} \medskip \noindent Example: \begin{verbatim} \tetrastereo{1==F;2==Cl;3==H;4==Br}\qquad \dtetrastereo{1==F;2==Cl;3==H;4==Br} \end{verbatim} produce the following structures: \begin{center} \tetrastereo{1==F;2==Cl;3==H;4==Br}\qquad \dtetrastereo{1==F;2==Cl;3==H;4==Br} \end{center} The configuration of ethane is typeset by the macro \verb/\ethanestereo/. The format of the command is as follows: \begin{verbatim} \ethanestereo[AUXLIST]{ATOMLIST}{SUBSLIST} \end{verbatim} The argument ATOMLIST is used for giving central atoms. The arguments AUXLIST and SUBSLIST are the same as those of \verb/\tetrahedral/. % **************************** % * ethylene unit (vertical) * % **************************** % % The following numbering is adopted in this macro. % % 5 % | % 6 -- (2) -- 4 % | % | % 1 -- (1) -- 3 <== the original point % | % 2 % \begin{xymspec} \begin{picture}(800,880)(0,0) \put(0,0){\ethanestereo{1==1;2==2}{1==1;2==2;3==3;4==4;5==5;6==6}} \put(800,0){\fbox{\parbox{2cm}{$\circ$: (300,300) \\ $\bullet$: (\the\noshift,\the\noshift)}}} \end{picture} \end{xymspec} \medskip \noindent Example: \begin{verbatim} \ethanestereo{1==C;2==C}{1==F;2==Cl;3==H;4==Br;6==H;5==Ph}\qquad \ethanestereo{}{1==OH;2==H;3==Ph;4==H;5==COR;6==H} \end{verbatim} produce the following structures: \begin{center} \ethanestereo{1==C;2==C}{1==F;2==Cl;3==H;4==Br;6==H;5==Ph}\qquad \ethanestereo{}{1==OH;2==H;3==Ph;4==H;5==COR;6==H} \end{center} Further examples of typesetting the configurations of ethane derivatives have been described in an article concerning sterochemistry \cite{fujita4}. \endinput