%xymcycl.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{``xymcycl''--- This file is a part of xymtex.tex that is the manual of the macro % package `XyMTeX'. 1993/12/1 S. Fujita} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \chapter{Further Cyclic Compounds} \section{Drawing Chair Form of Cylohexane} The macro \verb/\chair/ is used to draw cyclohexane derivatives of chair-form (ccycle.sty). The format of this command is as follows: \begin{verbatim} \chair[BONDLIST]{SUBSLIST} \end{verbatim} % *************************** % * cyclohexane derivatives * % * (chair type) * % *************************** % The following numbering is adopted in this macro. % % 6 4 % * ` 5 * % 1 * 2 * % ` 3 % % Locant numbers for designating substitution positions are represented by the following diagram: \begin{xymspec} \begin{picture}(1500,800)(0,-200) \put(0,0){\chair{1Se==1Se(l);1Sa==1Sa(l);% 2Se=={\lower1ex\hbox{2Se(l)}};2Sa==2Sa(r);% 3Se==3Se(l);3Sa==\lmoiety{3Sa(lr)};% 4Se=={\lower1ex\hbox{4Se(l)}};4Sa==4Sa(l);% 5Se=={\raise1ex\hbox{5Se(l)}};5Sa==5Sa(l);% 6Se==6Se(l);6Sa==6Sa(r)}} %\put(0,0){\sxlocant} %\put(0,0){\bdlocant} \end{picture} \qquad\fbox{\parbox{2cm}{$\circ$: (\the\shiftii,\the\shifti) \\ $\bullet$: (\the\noshift,\the\noshift)}} \end{xymspec} Each character set in parentheses represents the handedness of the corresponding postion, which is fixed in this type of macros. The option argument BONDLIST is an character string in a pair of brackets, where each character indicates the presence of a double bond at the edge corresponding to the character. The bond-correspondence is rather arbitrary in some cases but conforms to chemical conventions as faithfully as possible if such conventions are presence (Table \ref{tt:ano1}). \begin{table}[hpbt] \caption{Argument BONDLIST for commands {\tt$\backslash$chair}} \label{tt:ano1} \begin{center} \begin{tabular}{ll} \hline Character & \multicolumn{1}{c}{Printed structure} \\ \hline none & cyclohexane \\ a & 1,2-double bond \\ b & 2,3-double bond \\ c & 4,3-double bond \\ d & 4,5-double bond \\ e & 5,6-double bond \\ f & 6,1-double bond \\ \hline \end{tabular} \end{center} \end{table} The argument SUBSLIST for this macro takes a general format, except that modifiers are selected from `Sa' for an axial substitutent, `Se' for an equatorial substitutent, and `D' for a substitutent through an double bond. \medskip \noindent Example: \begin{verbatim} \chair{1D==O;2Se==H$_{3}$C;2Sa==CH$_{3}$;% 6Se==CH$_{3}$;6Sa==CH$_{3}$} \qquad\qquad \chair[b]{1D==O;4Se==CH$_{3}$;4Sa==CH$_{3}$} \end{verbatim} produce the following diagrams: \\ %\begin{center} \begin{picture}(2000,800)(0,-200) \chair{1D==O;2Se==H$_{3}$C;2Sa==CH$_{3}$;% 6Se==CH$_{3}$;6Sa==CH$_{3}$} \qquad\qquad \chair[b]{1D==O;4Se==CH$_{3}$;4Sa==CH$_{3}$} \end{picture} %\end{center} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \section{Drawing Bicyclo[2.2.1]heptane} The macro \verb/\bicychepv/ is used to draw bicyclo[2.2.1]heptane derivatives of vertical type in a flat fashion. The format of this command is as follows: \begin{verbatim} \bicychepv[BONDLIST]{SUBSLIST} \end{verbatim} % ************************************** % * bicycloe[2.2.1]heptane derivatives * % * (flat, vertical type) * % ************************************** % The following numbering is adopted in this macro. % % 1 % * % 6 * * 2 % | 7 | % | | % 5 * * 3 % * % 4 <===== the original point % Locant numbers for designating substitution positions and bond descriptors for assigning double bonds are shown in the following diagram: \begin{xymspec} \begin{picture}(800,880)(0,0) \put(0,0){\bicychepv{1Sb==1Sb(l);1Sa==1Sb(r);% 2Sb==2Sb(r);2Sa==2Sa(r);3Sb==3Sb(r);3Sa==3Sa(r);% 4Sb==4Sb(l);4Sa==4Sa(r);5Sb==5Sb(l);5Sa==5Sa(l);% 6Sb==6Sb(l);6Sa==6Sa(l)}} \put(0,0){\sxlocant} \put(0,0){\bdlocant} \end{picture} \qquad\fbox{\parbox{2cm}{$\circ$: (\the\shiftii,\the\shifti) \\ $\bullet$: (\the\noshift,\the\noshift)}} \end{xymspec} Each character set in parentheses represents the handedness of the corresponding postion, which is fixed in this type of macros. The option argument BONDLIST is an character string in a pair of brackets, where each character indicates the presence of a double bond at the edge corresponding to the character (Table \ref{tt:ano2}). \begin{table}[hpbt] \caption{Argument BONDLIST for commands {\tt$\backslash$bicychepv} and {\tt$\backslash$bicycheph}} \label{tt:ano2} \begin{center} \begin{tabular}{ll} \hline Character & \multicolumn{1}{c}{Printed structure} \\ \hline none & cyclohexane \\ a & 1,2-double bond \\ b & 2,3-double bond \\ c & 4,3-double bond \\ d & 4,5-double bond \\ e & 5,6-double bond \\ f & 6,1-double bond \\ A & aromatic circle \\ 7 & 7,7-dimethyl \\ \hline \end{tabular} \end{center} \end{table} The argument SUBSLIST for this macro takes a general format, in which the modifiers listed in Table \ref{tt:a2} are used. \medskip \noindent Example: \begin{verbatim} \bicychepv{2D==O} \bicychepv[b]{2==OMe;3==OMe} \bicychepv{3B==OH;2A==OH} \bicychepv[7]{1==CH$_{3}$;2==OH} \end{verbatim} produce the following diagrams: \begin{center} \bicychepv{2D==O} \bicychepv[b]{2==OMe;3==OMe} \bicychepv{3B==OH;2A==OH} \bicychepv[7]{1==CH$_{3}$;2==OH} \end{center} The macro \verb/\bicycheph/ is used to draw bicyclo[2.2.1]heptane derivatives of vertical type in a flat fashion. The format of this command is as follows: \begin{verbatim} \bicycheph[BONDLIST]{SUBSLIST} \end{verbatim} % ************************************** % * bicycloe[2.2.1]heptane derivatives * % * (flat, horizontal type) * % ************************************** % The following numbering is adopted in this macro. % % 2 3 % ----- % * * % the original point ===> 1 * 7 * 4 % (0,0) * * % ----- % 6 5 Locant numbers for designating substitution positions along with bond desciptors are found in the following diagram: \begin{xymspec} \begin{picture}(800,880)(0,0) \put(0,0){\bicycheph{1Sb==1Sb(l);1Sa==1Sb(l);% 2Sb==2Sb(l);2Sa==\lmoiety{2Sa(lr)};3Sb==3Sb(r);3Sa==3Sa(lr);% 4Sb==4Sb(r);4Sa==4Sa(r);5Sb==5Sb(r);5Sa==5Sa(lr);% 6Sb==6Sb(l);6Sa==\lmoiety{6Sa(lr)}}} \put(0,0){\sxlocnth} \put(0,0){\bdlocnth} \end{picture} \qquad\fbox{\parbox{2cm}{$\circ$: (\the\shifti,\the\shiftii) \\ $\bullet$: (\the\noshift,\the\noshift)}} \end{xymspec} Each character set in parentheses represents the handedness of the corresponding postion, which is fixed in this type of macros. For the SUBSLIST and the BONDLIST, see Table \ref{tt:a2} and \ref{tt:ano2}. . \medskip \noindent Example: \begin{verbatim} \bicycheph{2D==O} \bicycheph[b]{2==OMe;3==OMe} \bicycheph{3B==OH;2A==OH} \bicycheph[7]{1==CH$_{3}$;2==OH} \end{verbatim} produce the following diagrams: \begin{center} \bicycheph{2D==O} \bicycheph[b]{2==OMe;3==OMe} \bicycheph{3B==OH;2A==OH} \bicycheph[7]{1==CH$_{3}$;2==OH} \end{center} For the purpose of depicting the stereochemisty of bicyclo[2.2.1]heptane derivatives, you can use the command \verb/\bornane/ instead of the commands \verb/\bicychepv/ and \verb/\bicycheph/. The format of this command is as follows: \begin{verbatim} \bornane[BONDLIST]{SUBSLIST} \end{verbatim} % *********************************************** % * bornane derivatives * % * (bicycloe[2.2.1]heptane derivatives) * % *********************************************** % The following numbering is adopted in this macro. % % 7 g % f / ` % _ / - 1_ a % e 6 / h - 2 % * / * % 5 - 4 * b % d c` 3 % % Locant numbers for designating substitution positions are represented by the following diagram: \begin{xymspec} \begin{picture}(1500,1200)(0,-200) \put(0,0){\bornane{1==1;% 7Sb==7Sb(r);7Sa==7Sa(l);2Sb==2Sb(r);2Sa==2Sa(r);% 3Sb==3Sb(r);3Sa==3Sa(r);4==4;% 5Sb==5Sb(l);5Sa==5Sa(l);6Sb==6Sb(l);6Sa==6Sa(l)}} %\put(0,0){\sxlocant} %\put(0,0){\bdlocant} \end{picture} \qquad\fbox{\parbox{2cm}{$\circ$: (200,\the\shifti) \\ $\bullet$: (\the\noshift,\the\noshift)}} \end{xymspec} Each character set in parentheses represents the handedness of the corresponding postion, which is fixed in this type of macros. The option argument BONDLIST is an character string in a pair of brackets, where each character indicates the presence of a double bond at the edge corresponding to the character (Table \ref{tt:ano3}). The SUBSLIST format is shown in Table \ref{tt:a2}. \begin{table}[hpbt] \caption{Argument BONDLIST for commands {\tt$\backslash$bornane}} \label{tt:ano3} \begin{center} \begin{tabular}{ll} \hline Character & \multicolumn{1}{c}{Printed structure} \\ \hline none & cyclohexane \\ a & 1,2-double bond \\ b & 2,3-double bond \\ c & 4,3-double bond \\ d & 4,5-double bond \\ e & 5,6-double bond \\ f & 6,1-double bond \\ g & 1,7-double bond \\ h & 4,7-double bond \\ \hline \end{tabular} \end{center} \end{table} \medskip \noindent Example: \begin{verbatim} \bornane{2D==O} \bornane[b]{2==OMe;3==OMe}\par \bornane{3B==OH;2A==OH} \bornane{7Sa==CH$_{3}$;7Sb==CH$_{3}$;1==CH$_{3}$;2==OH} \end{verbatim} produce the following diagrams: \begin{center} \bornane{2D==O} \bornane[b]{2==OMe;3==OMe}\par \bornane{3B==OH;2A==OH} \bornane{7Sa==CH$_{3}$;7Sb==CH$_{3}$;1==CH$_{3}$;2==OH} \end{center} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \section{Drawing Adamantane Derivatives} The macro \verb/\adamantane/ prints adamantane derivatives by means of the following format: \begin{verbatim} \adamantane[BONDLIST]{SUBSLIST} \end{verbatim} where BONDLIST is not effective in the present specification. \begin{xymspec} \begin{picture}(1000,1500)(0,0) \put(0,0){\adamantane{1==1;3==3;5==5;7==7;% 2b==2b;2a==2a;4b==4b;4a==4a;% 6b==6b;6a==6a;8b==8b;8a==8a;9b==9b;9a==9a;% {{10}b}==10b;{{10}a}==10a}} %\put(0,0){\sxlocnth} %\put(0,0){\bdlocnth} \end{picture} \qquad\fbox{\parbox{2cm}{$\circ$: (550,300) \\ $\bullet$: (\the\noshift,\the\noshift)}} \end{xymspec} % ************************************************* % * For preparing adamantane derivatives * % * with 4 substituents on bridgehead positions * % * (1, 3, 5 and 7) * % * with 12 substituents on bridge positions * % * (2, 4, 6, 8, 9, 10) * % ************************************************* The argument SUBSLIST is slightly different from general conventions, as shown in Table \ref{tt:ano4}. \begin{table}[hpbt] \caption{Argument SUBSLIST for command {\tt$\backslash$adamantane}} \label{tt:ano4} \begin{center} \begin{tabular}{ll} \hline Character & \multicolumn{1}{c}{Printed structure} \\ \hline \multicolumn{2}{l}{for $n = 1, 3, 5,$ and $7$ (bridgeheads)} \\ $n$ or $n$a & exocyclic single bond at $n$-atom \\ \hline \multicolumn{2}{l}{for $n = 2, 4, 6, 8, 9,$ and $10$ (bridges)} \\ $n$a & exocyclic single bond at n-atom (axial) \\ $n$b & exocyclic single bond at n-atom (equatorial) \\ $n$D & exocyclic double bond at n-atom (2 and 6) \\ \hline \end{tabular} \end{center} \end{table} \medskip \noindent Example: \begin{verbatim} \adamantane{2D==O;6D==O} \adamantane{2D==O;6D==O;1==F;3==Cl} \end{verbatim} produce the following diagrams: \begin{center} \adamantane{2D==O;6D==O} \adamantane{2D==O;6D==O;1==F;3==Cl} \end{center} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \section{Drawing Furanoses and Pyranoses} For drawing furanoses, the command \verb/furanose/ is used. The format of this command is as follows: \begin{verbatim} \furanose[BONDLIST]{SUBSLIST} \end{verbatim} % *********************** % * furanose derivative * % *********************** % % The following numbering is adopted in this macro. % % 5 % O % d * * e % the original point ===> 4 * * 1 % (0,0) * * a % c ----- % 3 b 2 % Locant numbers for designating substitution positions and bond descriptors are represented by the following diagram: \begin{xymspec} \begin{picture}(800,880)(0,0) \put(0,0){\furanose{1Sb==1Sb(r);1Sa==1Sb(r);% 2Sb==\lmoiety{2Sb};2Sa==2Sa(r);3Sb==3Sb;3Sa==\lmoiety{3Sa(lr)};% 4Sb==4Sb(l);4Sa==4Sa(l);5Sb==5Sb(l);5Sa==5Sa(r)}} \end{picture} \qquad\fbox{\parbox{2cm}{$\circ$: (\the\shifti,\the\shiftii) \\ $\bullet$: (\the\noshift,\the\noshift)}} \end{xymspec} Each character set in parentheses represents the handedness of the corresponding postion, which is fixed in this type of macros. The option argument BONDLIST is an character string in a pair of brackets, where each character indicates the presence of a double bond at the edge corresponding to the character (Table \ref{tt:ano5}). \begin{table}[hpbt] \caption{Argument BONDLIST for commands {\tt$\backslash$bicychepv} and {\tt$\backslash$bicycheph}} \label{tt:ano5} \begin{center} \begin{tabular}{ll} \hline Character & \multicolumn{1}{c}{Printed structure} \\ \hline none & mother skeleton \\ a & 1,2-double bond \\ b & 2,3-double bond \\ c & 4,3-double bond \\ d & 4,5-double bond \\ e & 5,1-double bond \\ \hline \end{tabular} \end{center} \end{table} The argument SUBSLIST for this macro takes a general format, in which the modifiers listed in Table \ref{tt:a2} are used. \medskip \noindent Example: \begin{verbatim} \furanose{1Sa==H;1Sb==CH$_{2}$OPO(OH)$_{2}$;2Sb==\lmoiety{HO};3Sa==OH;% 4Sb==(HO)$_{2}$OPOH$_{2}$C;4Sa==HO}\hskip5cm \furanose[b]{1D==O;2Sa==OH;3Sa==\lmoiety{HO};4Sb==HOH$_{2}$C(HO)HC} \end{verbatim} produce the following diagrams: \begin{center} \furanose{1Sa==H;1Sb==CH$_{2}$OPO(OH)$_{2}$;2Sb==\lmoiety{HO};3Sa==OH;% 4Sb==(HO)$_{2}$OPOH$_{2}$C;4Sa==HO}\hskip5cm \furanose[b]{1D==O;2Sa==OH;3Sa==\lmoiety{HO};4Sb==HOH$_{2}$C(HO)HC} \end{center} For drawing furanoses, the command \verb/pyranose/ is used. The format of this command is as follows: \begin{verbatim} \pyranose[BONDLIST]{SUBSLIST} \end{verbatim} % *********************** % * pyranose derivative * % *********************** % % The following numbering is adopted in this macro. % % 5 e 6 % ----O % d * * f % the original point ===> 4 * * 1 % (0,0) * * a % c ----- % 3 b 2 % % Locant numbers for designating substitution positions are represented by the following diagram: \begin{xymspec} \begin{picture}(800,880)(0,0) \put(0,0){\pyranose{1Sb==1Sb(r);1Sa==1Sb(r);% 2Sb==\lmoiety{2Sb};2Sa==2Sa(r);3Sb==3Sb;3Sa==\lmoiety{3Sa(lr)};% 4Sb==4Sb(l);4Sa==4Sa(l);5Sb==5Sb(l);5Sa==5Sa(l)}} \end{picture} \qquad\fbox{\parbox{2cm}{$\circ$: (\the\shifti,\the\shiftii) \\ $\bullet$: (\the\noshift,\the\noshift)}} \end{xymspec} Each character set in parentheses represents the handedness of the corresponding postion, which is fixed in this type of macros. The option argument BONDLIST is an character string in a pair of brackets, where each character indicates the presence of a double bond at the corresponding edge (Table \ref{tt:ano6}). \begin{table}[hpbt] \caption{Argument BONDLIST for commands {\tt$\backslash$bicychepv} and {\tt$\backslash$bicycheph}} \label{tt:ano6} \begin{center} \begin{tabular}{ll} \hline Character & \multicolumn{1}{c}{Printed structure} \\ \hline none & mother skeleton \\ a & 1,2-double bond \\ b & 2,3-double bond \\ c & 4,3-double bond \\ d & 4,5-double bond \\ e & 5,6-double bond \\ f & 6,1-double bond \\ \hline \end{tabular} \end{center} \end{table} The argument SUBSLIST for this macro takes a general format, in which the modifiers listed in Table \ref{tt:a2} are used. \medskip \noindent Example: \begin{verbatim} \pyranose[a]{3Sb==OAc;4Sa==AcO;5Sb==CH$_{2}$OTs} \pyranose[b]{2D==O;5Sb==CH$_{2}$OTs} \end{verbatim} produce the following diagrams: \begin{center} \pyranose[a]{3Sb==OAc;4Sa==AcO;5Sb==CH$_{2}$OTs} \pyranose[b]{1D==O;4Sa==AcO;5Sb==CH$_{2}$OTs} \end{center} \endinput