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diff --git a/Master/texmf-dist/doc/latex/xymtex/xymyl.tex b/Master/texmf-dist/doc/latex/xymtex/xymyl.tex deleted file mode 100644 index daae2314c7d..00000000000 --- a/Master/texmf-dist/doc/latex/xymtex/xymyl.tex +++ /dev/null @@ -1,2900 +0,0 @@ -%xymyl.tex -%Copyright (C) 1998, Shinsaku Fujita, All rights reserved. -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -%This file is a part of xymtx200.tex that is the manual of the macro -%package `XyMTeX' (version 2.00) for drawing chemical structural formulas. -%This file is not permitted to be translated into Japanese and any other -%languages. -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\chapter{Introduction} - -\section{History} -\subsection{Version 1.00 (1993)} - -The first version of the \XyMTeX{} system (version 1.00, 1993) -with a detailed on-line manual -has been depositted to NIFTY-Serve archives (FPRINT library No.\ 7) -by the author\cite{fujita2a} and to the CTAN by volunteers\cite{fujita2b}. -The articles on the construction and usage of \XyMTeX{} have appeared in -Ref. \cite{fujita1,fujita1a}. -Although the packages (style files) of the \XyMTeX{} system have -originally aimed at using under -the \LaTeX{}2.09 system, they also work effectively -under the \LaTeXe{} system \cite{lamport2,goossens} without any changes. Thus, -what you have to do is to rewrite a top statement for \LaTeX{}2.09 such as -\begin{verbatim} -\documentstyle[epic,carom,hetarom]{article} -\end{verbatim} -into the counterpart for \LaTeXe{}, {\em e.g.}, -\begin{verbatim} -\documentclass{article} -\usepackage{epic,carom,hetarom} -\end{verbatim} - -\subsection{Version 1.01 (1996)} - -The Version 1.01 of the \XyMTeX{} system has been released in 1996, -when the system with a detailed on-line manual -was depositted to NIFTY-Serve archives (FPRINT library No.\ 7) -by the author \cite{fujita2c}. The system is now available -from Fujita's homepage \cite{fujita2d} via internet -or from a CD-ROM that is attached to the referece manual published -in 1997 \cite{XyMTeXbook}.\footnote{% -The basic items described in the \XyMTeX book are -common and applied also in Version 2.00. -Please refer to the \XyMTeX book, when -they are used without explanations in this manual.} - -The purpose of version 1.01 is -the updating of \XyMTeX{} to meet the \LaTeXe{} way of -preparing packages (option style files). -The following items have -been revised or added for encouraging the \XyMTeX{} users -to write articles of chemical fields. - -\begin{enumerate} -\item Each of the old sty files of \XyMTeX{} has been rewritten -into a dtx file, from which we have prepared a new sty file by using -the {\sf docstrip} utility of \LaTeXe. -If you want to obtain the document of each source -file, you may apply \LaTeXe{} to the corresponding drv file, which -has also been prepared from the dtx file by using the {\sf docstrip} -utility. -\item Macros for drawing chair-form cyclohexanes and -for drawing adamantanes of an alternative type have been added. -\item Macros for drawing polymers have been added. -\item The package {\sf chemist.sty}, which was originally -prepared for \cite{fujita2}, has been rewritten into a dtx file and -added to \XyMTeX{} as a new component. This package enables us -to use various functions such as - \begin{enumerate} - \item the numbering and cross-reference - of chemical compounds and derivatives, - \item various arrows of fixed and flexible length for chemical equations, - \item `chem' version and chemical environments for describing - chemical equations, and - \item various box-preparing macros for chemical or general use. - \end{enumerate} -\end{enumerate} - -\subsection{Version 1.02 (1998, not released)} - -The Version 1.02 of \XyMTeX{} has been devoted to the -development of the nested-substitution method, -which simplifies the coding of \XyMTeX{} commands. -In \XyMTeX{} version 1.01, each subsitituent is assumed to be rather small -so that it can be specified by means of a substitution list ``SUBSLIST''. -For example, 1-fluorobenzene, -\begin{center} -\bzdrh{4==F} -\end{center} -is drawn by the following code: -\begin{verbatim} -\bzdrh{4==F} -\end{verbatim} -To draw a substituent with a complicated structure, -a designation of the same line produces an insufficient result. -Thus, if we simply write the code -\begin{verbatim} -\bzdrh{4==\bzdrh{}} -\end{verbatim} -to draw a biphenyl structure, -we have a separate structure as follows: - -\vskip1.5\baselineskip -\begin{center} -\bzdrh{4==\bzdrh{}} -\end{center} - -Within the scope of \XyMTeX version 1.01, -such a substituent with a complicated structure -can be treated by three distinct methods -(see Chapters 14 and 15 of \XyMTeX book). - -\begin{enumerate} -\item(Method I) -When we write a code \verb/\bzdrh{4==}\bzdrh{}/ -to draw a biphenyl structure, -we obtain an insufficient result such as -\begin{center} -\bzdrh{4==}\bzdrh{} -\end{center} -since each command has an area to draw its target sturucture. -To remedy this situation, we can write -\begin{verbatim} -\bzdrh{4==}\kern-33pt\bzdrh{} -\end{verbatim} -Then, we obtain the following structure: -\begin{center} -\bzdrh{4==}\kern-33pt\bzdrh{} -\end{center} -However, a more complicated adjustment is -necessary to apply this method to a case in which -the components of a structual formula are not linearly aligned. -\item (Method II) -We can carry out the same task by using -the \LaTeX{} picture einvironment. -The code -\begin{verbatim} -\begin{picture}(1400,700)(0,0) -\put(0,0){\bzdrh{4==}} -\put(546,0){\bzdrh{}} -\end{picture} -\end{verbatim} -produces the following structure: -\begin{center} -\begin{picture}(1400,700)(0,0) -\put(0,0){\bzdrh{4==}} -\put(546,0){\bzdrh{}} -\end{picture} -\end{center} -This method realizes such a complicated adustment as mentioned above, -since the \verb/\put/ is capable of putting components at arbitrary positions. -\item (Method III) -In a further method of drawing the biphenyl structure, -one phenyl group is regarded as a substituent of the other phenyl. -These two parts can be combined by writing a code, -\begin{verbatim} -\bzdrh{4==\kern-25pt\lower37pt\hbox to0pt{\bzdrh{}}} -\end{verbatim} -in which the commands \verb/\kern/ (for horizontal adjustment) and -\verb/\lower/ (for vertical adjustment) are used to adjust the -substitution site. Thereby, we have -\begin{center} -\bzdrh{4==\kern-25pt\lower37pt\hbox to0pt{\bzdrh{}}} -\end{center} -This method has a disadvantage of calculating -adjustment values manually for every formula to be drawn. -\end{enumerate} - -These three methods are useful for drawing complicated structure. -However, they have an essential disadvantage: their codes give -no, or at most partial, connectivity data between parts to be combined, though -such parts appear to be combined as a picture. -For example, the code -\begin{verbatim} -\bzdrh{4==\kern-25pt\lower37pt\hbox to0pt{\bzdrh{3==Cl}}} -\end{verbatim} -producing -\begin{center} -\bzdrh{4==\kern-25pt\lower37pt\hbox to0pt{\bzdrh{3==Cl}}} -\end{center} -has no connectivity data at the meta position to the chlorine -atom of the scecond benzene ring. - -As clarified by the discussion in the preceding paragraphs, -the \XyMTeX{} system should have a function to place -substituents at appropriate sites without complex designation, -where connectivity data are maintained during the process -of drawing. -The target of \XyMTeX{} Version 1.02 is to treat nested -substitution with the automatic adjustment of subsitution sites -(named as the nested-substitution method). -Concretely speaking, for example, -such a code as -\begin{verbatim} -\bzdrh{1==F;4==\bzdrh{1==(yl);3==Cl}} -\end{verbatim} -directly produces -\begin{center} -\bzdrh{1==F;4==\bzdrh{1==(yl);3==Cl}} -\end{center} -where the code shows that the second benzene ring is -linked to the para position of the first benzene ring -at the meta position to the chlorine atom. -Thus the target accomplished by the ``yl''-function, -as shown in this code. - -\section{Version 2.00 (1998)} - -The ``yl''-function developed in \XyMTeX{} Version 1.02 -is regarded as a modification of SUSBLISTs. -As an extention of this mothodology, -BONDLISTs can be modified to treat ring fusion, -since each ring fusion is considered to be a kind of -substitution on a bond. In addition, -ATOMLIST can also be used to -treat spiro rings, since each spiro ring -is a kind of atom replacement at an appropriate vertex. - -To expand the scope of the \XyMTeX{} system, -we introduce several new functions as follows. -\begin{enumerate} -\item Several bond modifiers are added to draw -alternative up- and down-bonds as well as -to treat ring fusion. -\item The ``yl''-function for SUBSLISTs is further improved. -The commands \verb/\ryl/ and \verb/\lyl/ are -prepared to typeset intervening moieties. -\item Ring fusion is treated by adding a fusing unit to -the BONDLIST of each command. -\item Several fusing units (three- to six-membered units) -are developed (fusering.sty). -\item A new function for typesetting a spiro ring is -introduced in each command for general use. -A spiro ring is treated by ring-replacement technique, -where the corresponding code is -written in the ATOMLIST of each command. -\item Commands for typeseting zigzag polymethylenes are -developed (methylen.sty). -\item Commands for drawing six-six fused carbocycles -and heterocycles are added. -\item An optional argument SKBONDLIST is added to -each command of general use for drawing -boldfaced and dotted skeletal bonds. -\item An optional argument OMIT is added to -each command of general use for drawing related -skeletons by bond deletion. -\end{enumerate} - -The \XyMTeX{} system (version 2.00) consists of package files -listed in Table \ref{tt:200a1}. -The package file `\textsf{chemstr.sty}' is the basic file -that is automatically read within any other package file of \XyMTeX{}. -It contains macros for internal use, {\em e.g.}, -common commands for bond-setting and atom-setting. -The other package files contain macros for users. -These files are designed to work not only as packages for \LaTeXe -but also as option style files for \LaTeX{}2.09 (native mode). -\begin{table}[hpbt] -\caption{Package Files of \protect\XyMTeX{}} -\label{tt:200a1} -\begin{center} -\begin{tabular}{lp{10cm}} -\hline -package name & \multicolumn{1}{c}{included functions} \\ -\hline -\textsf{aliphat.sty} - & macros for drawing aliphatic compounds \\ -\textsf{carom.sty} - & macros for drawing vertical and horizontal types - of carbocyclic compounds \\ -\textsf{lowcycle.sty} - & macros for drawing five-or-less-membered carbocyles. \\ -\textsf{ccycle.sty} - & macros for drawing bicyclic compounds etc. \\ -\textsf{hetarom.sty} - & macros for drawing vertical types of heterocyclic compounds \\ -\textsf{hetaromh.sty} - & macros for drawing horizontal types of heterocyclic compounds \\ -\textsf{hcycle.sty} - & macros for drawing pyranose and furanose derivatives \\ -\textsf{chemstr.sty} - & basic commands for atom- and bond-typesetting \\ -\textsf{locant.sty} - & commands for printing locant numeres \\ -\textsf{polymers.sty} - & commands for drawing polymers \\ -\textsf{fusering.sty} - & commands for drawing units for ring fusion \\ -\textsf{methylen.sty} - & commands for drawing zigzag polymethylene chains \\ -\textsf{xymtex.sty} - & a package for calling all package files \\ -\textsf{chemist.sty} - & commands for using `chem' version and chemical environments \\ -\hline -\end{tabular} -\end{center} -\end{table} - -The use of \textsf{xymtex.sty} calling all package files -may sometimes cause the ``\TeX{} capacity exceeded'' error. -In this case, you should call necessary packages distinctly -by using the \verb/\usepackage/ command. - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\chapter{Bond Modifiers Added} - -\section{Alternative Bond Modifiers for Up and Down Bonds} - -In addition to the original bond modifiers (see the \XyMTeX book), -the present version of \XyMTeX{} -provides us with several bond modifiers that can be used -in the argument SUBSLIST of each \XyMTeX{} command. -These modifiers are listed in Table \ref{tt:200a} -along with the original bond modifiers. - -\begin{table} -\caption{Locant numbering and bond modifiers for SUBSLIST} -\label{tt:200a} -\begin{center} -\begin{tabular}{lp{12cm}} -\hline -Bond Modifiers & \multicolumn{1}{c}{Printed structures} \\ -\hline -\multicolumn{2}{l}{\bfseries Original Bond Modifiers} \\ - $n$ or $n$S & exocyclic single bond at $n$-atom \\ - $n$D & exocyclic double bond at $n$-atom \\ - $n$A & alpha single bond at $n$-atom \\ - $n$B & beta single bond at $n$-atom \\ - $n$Sa & alpha (not specified) single bond at $n$-atom \\ - $n$Sb & beta (not specified) single bond at $n$-atom \\ - $n$SA & alpha single bond at $n$-atom (dotted line) \\ - $n$SB & beta single bond at $n$-atom (boldface) \\ -\hline -\multicolumn{2}{l}{\bfseries Bond Modifiers Added} \\ - $n$Sd & alpha single bond at $n$-atom (dotted line) - with an alternative direction to $n$SA \\ - $n$Su & beta single bond at $n$-atom (boldface) - with an alternative direction to $n$SB \\ - $n$FA & alpha single bond at $n$-atom (dotted line) - for ring fusion \\ - $n$FB & beta single bond at $n$-atom (boldface) - for ring fusion \\ - $n$GA & alpha single bond at $n$-atom (dotted line) - for the other ring fusion \\ - $n$GB & beta single bond at $n$-atom (boldface) - for the other ring fusion \\ -\hline -\end{tabular} -\end{center} -\end{table} - -The added bond modifiers, `Sd' (d for down) and `Su' (u for up), designate -$\alpha$- and $\beta$-bonds in such an exchanged -manner as the original bond modifiers, `SA' and `SB' designate. -Figure \ref{ff:200a} shows the comparison between -the added bond modifiers and the original ones -by using a cyclohexane skeleton (\verb/\cyclohexanev/). - -\begin{figure}[h] -\begin{center} -\cyclohexanev{1Sd==1Sd;1Su==1Su;% -2Sd==2Sd;2Su==2Su;3Sd==3Sd;3Su==3Su;% -4Sd==4Sd;4Su==4Su;5Sd==5Sd;5Su==5Su;% -6Sd==6Sd;6Su==6Su} \qquad\qquad -\cyclohexanev{1SA==1SA;1SB==1SB;% -2SA==2SA;2SB==2SB;3SA==3SA;3SB==3SB;% -4SA==4SA;4SB==4SB;5SA==5SA;5SB==5SB;% -6SA==6SA;6SB==6SB} -\caption{Bond Modifiers for $\alpha$- and $\beta$-Bonds} -\label{ff:200a} -\end{center} -\end{figure} - -\section{Bond Modifiers for Ring Fusion} - -In the present verstion (2.00), we have added a new function for ring fusion. -Since the function requires bond modifiers -for desiginating substitution at such fused positions, -we have added the modifiers, `FA', `FB', `GA', and `GB'. -These modifiers are illustrated in Figure \ref{ff:200b} - - -\begin{figure} -\begin{center} -\cyclohexanev{1FA==1FA;1GB==1GB;3FA==3FA;3GB==3GB;5FA==5FA;5GB==5GB} -\qquad\qquad -\cyclohexanev{1FB==1FB;1GA==1GA;3FB==3FB;3GA==3GS;5FB==5FB;5GA==5GA} - - -\cyclohexanev{2FA==2FA;2GB==2GB;4FA==4FA;4GB==4GB;6FA==6FA;6GB==6GB} -\qquad\qquad -\cyclohexanev{2FB==2FB;2GA==2GA;4FB==4FB;4GA==4GA;6FB==6FB;6GA==6GA} -\caption{Bond Modifiers for Ring Fusion} -\label{ff:200b} -\end{center} -\end{figure} - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\chapter{Nested-Substituent Method} - -\section{Introduction} - -Chapter 14 (Combining Structures) -and Chapter 15 (Large Substituents) of the \XyMTeX book -have described several techniques to draw complicated formulas. -Among them, the nested-substituent method is most promising. -For example, the code -\begin{verbatim} -\bzdrh{1==Cl;4==\kern-25pt\lower37pt\hbox to0pt{\bzdrh{3==F}}} -\end{verbatim} -gives a combined structure, -\begin{center} -\bzdrh{1==Cl;4==\kern-25pt\lower37pt\hbox to0pt{\bzdrh{3==F}}} -\end{center} -Although the code shows the connectivity between the two phenyl -groups, the following disadvantages remain: -\begin{enumerate} -\item The code contains no data indicating that the connection site -is the meta-position concerning the fluorine atom. -\item The commands \verb/\kern/ (for horizontal adjustment) and -\verb/\lower/ (for vertical adjustment) are necessary to adjust the -subsitutution site. -\end{enumerate} - -As clarified by the above examples, the main target of \XyMTeX{} -Version 2.00 is to extend the nested-substituent method -so that it provides a function of indicating full connectivity data -as well as a function of -automatical adjustment without using such commands -as \verb/\kern/ and \verb/\lower/. - -\section{``yl''-Functions} - -In \XyMTeX{} Version 2.00, the ``yl''-function is -added so as to improve the nested-subsituent method. -Thereby, any structure drawn by a \XyMTeX{} -command (except a few special commands) -can be converted into the corresponding substituent -by adding the code \verb/(yl)/ with a locant number. -The resulting code for the substituent can be added -to the SUBSLIST of any other command for -drawing a mother skeleton, where the final code -contains the full connectivity data of the combined structure. -For example, the code -\begin{verbatim} -\bzdrh{1==Cl;4==\bzdrh{1==(yl);3==F}} -\end{verbatim} -typesets the following structure, -\begin{center} -\bzdrh{1==Cl;4==\bzdrh{1==(yl);3==F}} -\end{center} -Thus, fluorobenzene produced by the command \verb/\bzdrh{3==F}/ -is converted into a subsituent, i.e. 3-fluorophenyl, -by adding the code \verb/(yl)/, as shown in the -code, \verb/\bzdrh{1==(yl);3==F}/. Then, the resulting code -is added to the SUBSLIST of another command \verb/\bzdrh/. - -The connectivity at the meta-position is -represented by the statement \verb/1==(yl)/ of -the innner code \verb/\bzdrh{1==(yl);3==F}/. -Note that the inner code \verb/\bzdrh{1==(yl);3==F}/ produces -a substituent with no height and no width and that -the reference point of the substituent is shifted to -the point no.~1 by the (yl)-statement in order to -link to the mother structure (the phenyl group -produced by the code \verb/\bzdrh{1==Cl;4=={...}}/). - -The shift of a reference point becomes clear when -we examine a formula, -\begin{center} -\vspace*{2cm} -\bzdrh{1==Cl;3==\bzdrh{6==(yl);3==F}} -\end{center} -generated by the code, -\begin{verbatim} -\bzdrh{1==Cl;3==\bzdrh{6==(yl);3==F}} -\end{verbatim} -The original structure of the substituent with no ``yl'' function -is found to be -\begin{center} -\begin{picture}(700,800)(0,0) -\put(0,0){\bzdrh{3==F}} -\put(0,0){\circle*{50}} -\end{picture} -\end{center} -as generated by the code -\begin{verbatim} -\begin{picture}(700,800)(0,0) -\put(0,0){\bzdrh{3==F}} -\put(0,0){\circle*{50}} -\end{picture} -\end{verbatim} -where the solid circle is the reference point. -The picture shown above -indicates that the reference point -is different from any vertices of the benzene ring. -On the other hand, the code with a ``yl''-function, -\begin{verbatim} -\begin{picture}(700,800)(0,-200) -\put(0,0){\bzdrh{6==(yl);3==F}} -\put(0,0){\circle*{50}} -\end{picture} -\end{verbatim} -typesets the following structure, -\begin{center} -\begin{picture}(700,800)(0,-200) -\put(0,0){\bzdrh{6==(yl);3==F}} -\put(0,0){\circle*{50}} -\end{picture} -\end{center} -The picture shown above -indicates that the reference point is shifted to the position -no.~6 of the benzene ring. - -The code \verb/\bzdrh{1==(yl);3==F}/ producing the substituent -can be used in the argument of any structure-drawing command -of \XyMTeX{}. The following example is the one -in which it is placed in the argument of a command \verb/\bzdrv/. -Thus, the code -\begin{verbatim} -\bzdrv{1==Cl;3==\bzdrh{1==(yl);3==F}} -\end{verbatim} -typesets the following structure, -\begin{center} -\bzdrv{1==Cl;3==\bzdrh{1==(yl);3==F}} -\end{center} - -The structural formula of 1-chloro-4-morphorinobenzene -can be drawn in two different ways. The codes, -\begin{verbatim} -\bzdrh{1==Cl;4==\sixheteroh[]{1==N;4==O}{1==(yl)}} -\hskip 6cm -\sixheteroh[]{1==N;4==O}{1==\bzdrh{1==Cl;4==(yl)}} -\end{verbatim} -produce the following formulas: -\begin{center} -\bzdrh{1==Cl;4==\sixheteroh[]{1==N;4==O}{1==(yl)}} -\hskip 6cm -\sixheteroh[]{1==N;4==O}{1==\bzdrh{1==Cl;4==(yl)}} -\end{center} -In the former code, -the morphorino group is regareded as a substituent, -as the name ``1-chloro-4-morphori\-nobenzene'' indicates. -On the other hand, the chlorophenyl group -is considered to be a substituent in the latter code -so as to correspond to the name ``N-(4-chlorophenyl)morphorine''. - -The ``yl''-function is quite versatile, as indicated by the code, -\begin{verbatim} -\decaheterov[]{4a==N}{4D==O;7B==HO;{{10}A}==H;% -5==\bzdrv{3==OMe;4==OMe;6==Br;1==(yl)}} -\end{verbatim} -producing the following structure: -\begin{center} -\decaheterov[]{4a==N}{4D==O;7B==HO;{{10}A}==H;% -5==\bzdrv{3==OMe;4==OMe;6==Br;1==(yl)}} -\end{center} -\par\vskip2cm -\noindent -where the substituted phenyl group is regarded as a substituent. -An opposite view can be realized by the code -\begin{verbatim} -\bzdrv{3==OMe;4==OMe;6==Br;% -1==\decaheterov[]{4a==N}{4D==O;7B==HO;{{10}A}==H;5==(yl)}} -\end{verbatim} -which typesets the same structure: -\vskip2cm -\begin{center} -\bzdrv{3==OMe;4==OMe;6==Br;% -1==\decaheterov[]{4a==N}{4D==O;7B==HO;{{10}A}==H;5==(yl)}} -\end{center} -where the moiety drawn by the command \verb/\decaheterov/ is -regarded as a substituent. - -Two or more substituents generated by the ``yl''-function -can be introduced into an ATOMLIST. For example, -\begin{verbatim} -\bzdrh{1==\bzdrh{4==(yl)};4==\bzdrh{1==(yl);3==F}} -\end{verbatim} -typesets the following structure, -\begin{center} -\bzdrh{1==\bzdrh{4==(yl)};4==\bzdrh{1==(yl);3==F}} -\end{center} - -The structural formula of hexaphenylbenzene can be -drawn by this technique. Thus the code, -\begin{verbatim} -\bzdrv{1==\bzdrv{4==(yl)};% -2==\bzdrv{5==(yl)};3==\bzdrv{6==(yl)};% -4==\bzdrv{1==(yl)};5==\bzdrv{2==(yl)};% -6==\bzdrv{3==(yl)}} -\end{verbatim} -generates the following formula: -\begin{center} -\vspace*{1cm} -\bzdrv{1==\bzdrv{4==(yl)};% -2==\bzdrv{5==(yl)};3==\bzdrv{6==(yl)};% -4==\bzdrv{1==(yl)};5==\bzdrv{2==(yl)};% -6==\bzdrv{3==(yl)}} - -\vspace*{1cm} -\end{center} - -\section{Nested ``yl''-functions} - -Two or more ``yl''-functions can be nested. -For example, a structure -\begin{center} -\tetrahedral{0==C;1D==O;4==\bzdrh{1==(yl)}} -\end{center} -depicted by the code, -\begin{verbatim} -\tetrahedral{0==C;1D==O;4==\bzdrh{1==(yl)}} -\end{verbatim} -can be converted into a substituent by adding -``yl''-function, as shown in the following code: -\begin{verbatim} -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}} -\end{verbatim} -Then this substituent is nested in the SUBSLIST of -the command \verb/\cyclohexaneh/ to give a code, -\begin{verbatim} -\cyclohexaneh[]{4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}} -\end{verbatim} -Thereby we have the structural formula of -benzoylcyclohexane: -\begin{center} -\cyclohexaneh[]{4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}} -\end{center} - -The resulting structure can be further converted into -a substituent by adding ``yl''-function. The -following example shows that the substituent is -linked to the 4-position of a naphthol ring: -\begin{center} -\naphdrh{1==HO;4==% -\cyclohexaneh[]{1==(yl);4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}}} -\end{center} -which is typeset by the triply nested code: -\begin{verbatim} -\naphdrh{1==HO;4==% -\cyclohexaneh[]{1==(yl);4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}}} -\end{verbatim} -The same structural formula can be drawn by regarding -the 1-naphthol-4-yl group and the benzoyl group as -substituents, as shown in the following code: -\begin{verbatim} -\cyclohexaneh[]{% -1==\naphdrh{1==HO;4==(yl)};% -4==\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}} -\end{verbatim} -Accordingly, we have -\begin{center} -\cyclohexaneh[]{% -1==\naphdrh{1==HO;4==(yl)};% -4==\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}} -\end{center} - -\bigskip -The structure of benzoylcyclohexane can also be drawn by considering -the \verb/\tetrahedral/ moiety as a mother skeleton, -as shown in the code: -\begin{verbatim} -\tetrahedral{0==C;1D==O;4==\bzdrh{1==(yl)};2==\cyclohexaneh[]{4==(yl)}} -\end{verbatim} -Thereby, we have the formula, -\begin{center} -\tetrahedral{0==C;1D==O;4==\bzdrh{1==(yl)};2==\cyclohexaneh[]{4==(yl)}} -\end{center} -which shows that -two or more substituents produced by the ``yl''-function -can be written in a SUBSLIST. -This treatment corresponds to the alternative name of -benzoylcyclohexane, i.e., cyclohexyl phenyl ketone, -since the codes \verb/\cyclohexaneh{4==(yl)}/ and -\verb/\bzdrh{1==(yl)}/ represent -a cyclohexyl and a phenyl group, respectively. - -Although -the resulting structure cannot be used as a substituent concerning -the cyclohexane ring, the SUBSLIST of the command \verb/\cyclohexaneh/ -is capable of accomodating the substituent \verb/\naphdrh{1==HO;4==(yl)}/ -to give -\begin{verbatim} -\tetrahedral{0==C;1D==O;4==\bzdrh{1==(yl)};% -2==\cyclohexaneh[]{4==(yl);1==\naphdrh{1==HO;4==(yl)}}} -\end{verbatim} -which typesets the same structural formula: -\begin{center} -\tetrahedral{0==C;1D==O;4==\bzdrh{1==(yl)};% -2==\cyclohexaneh[]{4==(yl);1==\naphdrh{1==HO;4==(yl)}}} - -\vspace*{1cm} -\end{center} - - -The formula, -\begin{center} -\vspace*{2cm} -\bzdrv{% -1==\bzdrv{4==(yl);2==\bzdrv{5==(yl)}};% -2==\bzdrv{5==(yl);3==\bzdrv{6==(yl)}};% -3==\bzdrv{6==(yl);4==\bzdrv{1==(yl)}};% -4==\bzdrv{1==(yl);5==\bzdrv{2==(yl)}};% -5==\bzdrv{2==(yl);6==\bzdrv{3==(yl)}};% -6==\bzdrv{3==(yl);1==\bzdrv{4==(yl)}}} - -\vspace*{2cm} -\end{center} -illustrates the more complicated structure of a code -with nested ``yl''-functions: -\begin{verbatim} -\bzdrv{% -1==\bzdrv{4==(yl);2==\bzdrv{5==(yl)}};% -2==\bzdrv{5==(yl);3==\bzdrv{6==(yl)}};% -3==\bzdrv{6==(yl);4==\bzdrv{1==(yl)}};% -4==\bzdrv{1==(yl);5==\bzdrv{2==(yl)}};% -5==\bzdrv{2==(yl);6==\bzdrv{3==(yl)}};% -6==\bzdrv{3==(yl);1==\bzdrv{4==(yl)}}} -\end{verbatim} - -To simplify the coding, we define a macro -drawing a biphenyl unit as follows: -\begin{verbatim} -\def\biph#1#2#3{\bzdrv{#1==(yl);#2==\bzdrv{#3==(yl)}}} -\end{verbatim} -Then, this macro is used in the SUBSLIST of \verb/\bzdrv/ -to give the code, -\begin{verbatim} -\bzdrv{% -1==\biph{4}{2}{5};% -2==\biph{5}{3}{6};% -3==\biph{6}{4}{1};% -4==\biph{1}{5}{2};% -5==\biph{2}{6}{3};% -6==\biph{3}{1}{4}} -\end{verbatim} -Thereby, we have -\begin{center} -\vspace*{2cm} -\def\biph#1#2#3{\bzdrv{#1==(yl);#2==\bzdrv{#3==(yl)}}} -\bzdrv{% -1==\biph{4}{2}{5};% -2==\biph{5}{3}{6};% -3==\biph{6}{4}{1};% -4==\biph{1}{5}{2};% -5==\biph{2}{6}{3};% -6==\biph{3}{1}{4}} - -\vspace*{2cm} -\end{center} - -A more complex nested code, - -\begin{verbatim} -\vspace*{8cm} -\bzdrv{% -1==\bzdrv{4==(yl);2==\bzdrv{5==(yl);3==\bzdrv{6==(yl);% -3==\bzdrv{6==(yl);4==\bzdrv{1==(yl);4==\bzdrv{1==(yl);% -4==\bzdrv{1==(yl);5==\bzdrv{2==(yl);5==\bzdrv{2==(yl);% -5==\bzdrv{2==(yl)}}}}}}}}}};% -2==\bzdrv{5==(yl);3==\bzdrv{6==(yl);4==\bzdrv{1==(yl);% -4==\bzdrv{1==(yl);5==\bzdrv{2==(yl);5==\bzdrv{2==(yl);% -5==\bzdrv{2==(yl);6==\bzdrv{3==(yl);6==\bzdrv{3==(yl);% -6==\bzdrv{3==(yl)}}}}}}}}}};% -3==\bzdrv{6==(yl);4==\bzdrv{1==(yl);5==\bzdrv{2==(yl);% -5==\bzdrv{2==(yl);6==\bzdrv{3==(yl);6==\bzdrv{3==(yl);% -6==\bzdrv{3==(yl);1==\bzdrv{4==(yl);1==\bzdrv{4==(yl);% -1==\bzdrv{4==(yl)}}}}}}}}}};% -4==\bzdrv{1==(yl);5==\bzdrv{2==(yl);6==\bzdrv{3==(yl);% -6==\bzdrv{3==(yl);1==\bzdrv{4==(yl);1==\bzdrv{4==(yl);% -1==\bzdrv{4==(yl);2==\bzdrv{5==(yl);2==\bzdrv{5==(yl);% -2==\bzdrv{5==(yl)}}}}}}}}}};% -5==\bzdrv{2==(yl);6==\bzdrv{3==(yl);1==\bzdrv{4==(yl);% -1==\bzdrv{4==(yl);2==\bzdrv{5==(yl);2==\bzdrv{5==(yl);% -2==\bzdrv{5==(yl);3==\bzdrv{6==(yl);3==\bzdrv{6==(yl);% -3==\bzdrv{6==(yl)}}}}}}}}}};% -6==\bzdrv{3==(yl);1==\bzdrv{4==(yl);2==\bzdrv{5==(yl);% -2==\bzdrv{5==(yl);3==\bzdrv{6==(yl);3==\bzdrv{6==(yl);% -3==\bzdrv{6==(yl);4==\bzdrv{1==(yl);4==\bzdrv{1==(yl);% -4==\bzdrv{1==(yl)}}}}}}}}}}} -\end{verbatim} -produces the following formula: - -\clearpage%to avoid ! TeX capacity exceeded - -\begin{center} -\vspace*{8cm} -\bzdrv{% -1==\bzdrv{4==(yl);2==\bzdrv{5==(yl);3==\bzdrv{6==(yl);% -3==\bzdrv{6==(yl);4==\bzdrv{1==(yl);4==\bzdrv{1==(yl);% -4==\bzdrv{1==(yl);5==\bzdrv{2==(yl);5==\bzdrv{2==(yl);% -5==\bzdrv{2==(yl)}% -}}}% -}}}% -}}};% -2==\bzdrv{5==(yl);3==\bzdrv{6==(yl);4==\bzdrv{1==(yl);% -4==\bzdrv{1==(yl);5==\bzdrv{2==(yl);5==\bzdrv{2==(yl);% -5==\bzdrv{2==(yl);6==\bzdrv{3==(yl);6==\bzdrv{3==(yl);% -6==\bzdrv{3==(yl)}% -}}}% -}}}% -}}};% -3==\bzdrv{6==(yl);4==\bzdrv{1==(yl);5==\bzdrv{2==(yl);% -5==\bzdrv{2==(yl);6==\bzdrv{3==(yl);6==\bzdrv{3==(yl);% -6==\bzdrv{3==(yl);1==\bzdrv{4==(yl);1==\bzdrv{4==(yl);% -1==\bzdrv{4==(yl)}% -}}}% -}}}% -}}};% -4==\bzdrv{1==(yl);5==\bzdrv{2==(yl);6==\bzdrv{3==(yl);% -6==\bzdrv{3==(yl);1==\bzdrv{4==(yl);1==\bzdrv{4==(yl);% -1==\bzdrv{4==(yl);2==\bzdrv{5==(yl);2==\bzdrv{5==(yl);% -2==\bzdrv{5==(yl)}% -}}}% -}}}% -}}};% -5==\bzdrv{2==(yl);6==\bzdrv{3==(yl);1==\bzdrv{4==(yl);% -1==\bzdrv{4==(yl);2==\bzdrv{5==(yl);2==\bzdrv{5==(yl);% -2==\bzdrv{5==(yl);3==\bzdrv{6==(yl);3==\bzdrv{6==(yl);% -3==\bzdrv{6==(yl)}% -}}}% -}}}% -}}};% -6==\bzdrv{3==(yl);1==\bzdrv{4==(yl);2==\bzdrv{5==(yl);% -2==\bzdrv{5==(yl);3==\bzdrv{6==(yl);3==\bzdrv{6==(yl);% -3==\bzdrv{6==(yl);4==\bzdrv{1==(yl);4==\bzdrv{1==(yl);% -4==\bzdrv{1==(yl)}% -}}}% -}}}% -}}}} -\end{center} - -\clearpage - -The code to draw this structural formula is -too complicated to cause the ``\TeX{} capacity exceeded'' error. -To avoid the error, we use \verb/\clearpage/ commands before -and after the output of the formula. -In addition, we call only necessary packages -to treat this cocument without the use of \textsf{xymtex.sty} -calling all package files. - -\section{Remarks} -\subsection{Drawing Domains} -Substituents produced by the ``yl''-function have no dimensions. -For example, benzoylcyclohexane -\begin{center} -\fbox{% -\cyclohexaneh[]{4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}}% -} -\end{center} -produced by the code -\begin{verbatim} -\cyclohexaneh[]{4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}} -\end{verbatim} -has a drawing domain around the cyclohexane mother skeleton, -as encircled by a frame. Since the bezoyl moiety occupies no area, -it may be superimposed on other contexts -so as to require some space adjustments. -For example, the above code duplicated without -any space adjustment, -\begin{verbatim} -\cyclohexaneh[]{4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}} -\cyclohexaneh[]{4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}}% -\end{verbatim} -gives an insufficient result: -\begin{center} -\cyclohexaneh[]{4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}} -\cyclohexaneh[]{4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}}% -\end{center} -This superposition can be avoided by a horizontal spacing. Thus -the code -\begin{verbatim} -\cyclohexaneh[]{4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}} -\hskip2cm -\cyclohexaneh[]{4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}}% -\end{verbatim} -typesets improved formulas: -\begin{center} -\cyclohexaneh[]{4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}} -\hskip2cm -\cyclohexaneh[]{4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}}% -\end{center} - -If a more thorough adjustment is required, -a formula should be placed in a \LaTeX{} picture environment -as follows. -\begin{verbatim} -\begin{picture}(1600,900)(0,0) -\cyclohexaneh[]{4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}} -\end{picture} -\end{verbatim} -This code produces -\begin{center} -\fbox{% -\begin{picture}(1600,900)(0,0) -\cyclohexaneh[]{4==% -\tetrahedral{2==(yl);0==C;1D==O;4==\bzdrh{1==(yl)}}} -\end{picture} -} -\end{center} -where a frame is added by means of a \verb/\fbox/ command. - -A drawing domain around a formula depends upon a mother skeleton -selected. For example, the formula of benzoylcyclohexane at the top -of this section has a drawing domain shown by the frame, since -a \verb/\cyclohexaneh/ is selected as a mother skeleton. -On the other hand, the alternative formula -of benzoylcyclohexane depicted by the code, -\begin{verbatim} -\tetrahedral{0==C;1D==O;4==\bzdrh{1==(yl)};2==\cyclohexaneh[]{4==(yl)}} -\end{verbatim} -has a drawing domain due to the \verb/\tetrahedral/ skeleton. -Thus, the code gives the following output: -\begin{center} -\fbox{% -\tetrahedral{0==C;1D==O;4==\bzdrh{1==(yl)};2==\cyclohexaneh[]{4==(yl)}} -} -\end{center} -where the frame indicates such a drawing domain, -when an \verb/\fbox/ command is used around -the \verb/\tetrahedral/ command. -The domain shown by the frame (due to \verb/\fbox/) is equal to -any domain based on the simple use of the \verb/\tetrahedral/ command -(without using the ``yl''-function). -For example, compare the above frame with the one -appearing in the formula, -\begin{center} -\fbox{\tetrahedral{0==C;1D==O;4==Cl;2==Cl}} -\end{center} -depicted by the code, -\begin{verbatim} -\fbox{\tetrahedral{0==C;1D==O;4==Cl;2==Cl}} -\end{verbatim} - -\subsection{Reference Points} - -Each \XyMTeX{} command for drawing a mother skeleton -has its reference point and its inner reference point. -These points can be printed out by switching -\verb/\origpt/ on. For example, the code -\begin{verbatim} -{ -\origpttrue -\cyclohexanev{} -} -\end{verbatim} -generates the diagram: -\begin{center} -{ -\origpttrue -\cyclohexanev{} -} -\end{center} -where the solid circle indicates the reference point (0,0) and -the open circle indicates the inner reference point (400,240). -The values of cooridates are output on a display and in a log file: -\begin{verbatim} -command `sixheterov' origin: (0,0) ---> (400,240) -\end{verbatim} -since \verb/\cyclohexanev/ is based on \verb/\sixheterov/. - - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\chapter{Linking Units} - -The commands \verb/\ryl/ and \verb/\lyl/ described -in this chapter are added to -the {\sf chemstr} package (file name: chemstr.sty). -The \verb/\divalenth/ command is added to -the {\sf aliphat} package (file name: aliphat.sty). - -\section{$\backslash$ryl command}. - -The ``yl''-function provides us with -a tool to generate a substituent that -is linked {\itshape directly} to a substitution site -of a mother skeleton. There are, however, -many cases in which a substituent -is linked to a substitution site by an intervening unit -(e.g., O, SO$_{2}$ and NH). -The command \verb/\ryl/ is used to -generate a right-hand substituent with a linking unit. -For example, the code -\begin{verbatim} -\ryl(5==NH--SO$_{2}$){4==\bzdrh{1==(yl)}} -\end{verbatim} -produces a benzenesulfonamido substituent, -\bigskip -\begin{center} -\ryl(5==NH--SO$_{2}$){4==\bzdrh{1==(yl)}} - -\vspace*{1cm} -\end{center} -The resulting unit is added to the SUBSLIST of -a command for drawing a skeletal command. -For example, the code -\begin{verbatim} -\bzdrh{3==\ryl(5==NH--SO$_{2}$){4==\bzdrh{1==(yl)}}} -\end{verbatim} -generates the following formula: -\begin{center} -\vspace*{1cm} -\bzdrh{3==\ryl(5==NH--SO$_{2}$){4==\bzdrh{1==(yl)}}} -\end{center} - -The \verb/\ryl/ command takes two arguments. -\begin{verbatim} -\ryl(LINK){GROUP} -\end{verbatim} -The first argument LINK in the parentheses indicates -an intervening unit with an integer showing -the slope of a left incidental bond. -For example, the number 5 of the code \verb/5==NH--SO$_{2}$/ -shown above represents that the left terminal is to be linked -through $(-5,-3)$ bond, though the linking bond -is not typeset by the \verb/\ryl/ command only. -The slopes of the linking bonds are designated by -integers between 0 and 8: -\begin{center} -\begin{tabular}{cc|cc|cc} -0 & $(0,1)$ & 1 & $(-3,5)$ & 2 & $(-1,1)$ \\ -3 & $(-5,3)$ & 4 & $(-1,0)$ & 5 & $(-5,-3)$ \\ -6 & $(-1,-1)$ & 7 & $(-3,-5)$ & 8 & $(0,-1)$ \\ -\end{tabular} -\end{center} - -The second argument GROUP of \verb/\ryl/ is -a substituent produced by a ``yl''-function, -where a number before a delimiter (==) indicates -the slope of a right incidental bond. -For example, the number 4 of the code -\verb/4==\bzdrh{1==(yl)}/ shown above -represents that the right terminal is to be linked -through $(1,0)$ bond to the benzene ring generated by -the \verb/\bzdrh/ command. -The slopes of the linking bonds are designated by -integers between 0 and 8: -\begin{center} -\begin{tabular}{cc|cc|cc} -0 & $(0,1)$ & 1 & $(3,5)$ & 2 & $(1,1)$ \\ -3 & $(5,3)$ & 4 & $(1,0)$ & 5 & $(5,-3)$ \\ -6 & $(1,-1)$ & 7 & $(3,-5)$ & 8 & $(0,-1)$ \\ -\end{tabular} -\end{center} - -To illustrate linking bonds with various slopes, -the code -\begin{verbatim} -\cyclohexanev[]{% -1==\ryl(8==NH--SO$_{2}$){1==\bzdrh{6==(yl)}}; -2==\ryl(5==NH--SO$_{2}$){4==\bzdrh{1==(yl)}}; -3==\ryl(3==NH--SO$_{2}$){4==\bzdrh{1==(yl)}};% -4==\ryl(0==NH--SO$_{2}$){7==\bzdrh{2==(yl)}}} -\end{verbatim} -is written to give - -\vspace*{2cm} -\begin{center} -\cyclohexanev[]{% -1==\ryl(8==NH--SO$_{2}$){1==\bzdrh{6==(yl)}}; -2==\ryl(5==NH--SO$_{2}$){4==\bzdrh{1==(yl)}}; -3==\ryl(3==NH--SO$_{2}$){4==\bzdrh{1==(yl)}};% -4==\ryl(0==NH--SO$_{2}$){7==\bzdrh{2==(yl)}}} -\end{center} -\vspace*{2cm} - -Other examples are drawn by the code -\begin{verbatim} -\cyclohexaneh[]{% -3==\ryl(7==NH--SO$_{2}$){4==\bzdrh{1==(yl)}}; -5==\ryl(1==NH--SO$_{2}$){4==\bzdrh{1==(yl)}};% -4==\ryl(4==NH--SO$_{2}$--NH){4==\bzdrh{1==(yl)}}} -\end{verbatim} -giving -\vspace*{1cm} -\begin{center} -\cyclohexaneh[]{% -3==\ryl(7==NH--SO$_{2}$){4==\bzdrh{1==(yl)}}; -5==\ryl(1==NH--SO$_{2}$){4==\bzdrh{1==(yl)}};% -4==\ryl(4==NH--SO$_{2}$--NH){4==\bzdrh{1==(yl)}}} -\end{center} -\vspace*{1cm} - -The first argument in the parentheses of the -command \verb/\ryl/ contains a string of letters -after an intermediate delimiter ==, where -a left linking site is shifted according to the -length of the letter string. -The above formula shows such an example -as having NH--SO$_{2}$--NH. - - -The following examples compare the -``yl''-function with the \verb/\ryl/ command. -\begin{verbatim} -\cyclohexaneh{4==\bzdrh{1==(yl)}} -\hskip2cm -\cyclohexaneh{4==\ryl(4==O){4==\bzdrh{1==(yl)}}} -\end{verbatim} - -\begin{center} -\cyclohexaneh{4==\bzdrh{1==(yl)}} -\hskip2cm -\cyclohexaneh{4==\ryl(4==O){4==\bzdrh{1==(yl)}}} -\end{center} - -The compound {\bfseries 21} -on page 299 of the \XyMTeX book -%``\XyMTeX{}---Typesetting Chemical -%Structural Formulas'' (Addison-Wesley Publishers Japan, 1997) -can be alternatively drawn by using -the \verb/\ryl/ command, as shown in the code: -\begin{verbatim} -\fiveheterov[d]{1==N;5==N}{4==NC;1==\bzdrv{1==(yl)};2D==O;% -3D==\ryl(5==N-NH){4==\bzdrh{1==(yl);2==\lmoiety{MeO};5==SO$_{2}$Cl}}} -\end{verbatim} -which typeset the following formula: -\begin{center} -\vspace*{1cm} -\fiveheterov[d]{1==N;5==N}{4==NC;1==\bzdrv{1==(yl)};2D==O;% -3D==\ryl(5==N-NH){4==\bzdrh{1==(yl);2==\lmoiety{MeO};5==SO$_{2}$Cl}}} - -\vspace*{2cm} -\end{center} - -The first argument of the \verb/\ryl/ is optional; i.e., it can be -omitted. Such an omitted case is useful to draw a methylene as -a vertex. For example, a methylene is represented as -a character string ``CH$_{2}$'', as shown in the formula, -\begin{center} -\sixheterov[d]{2==S}{5==\null;% -3==\ryl(3==CH$_{2}$){3==\sixheterov[d]{2==S}{5==(yl)}}} -\end{center} -This formula is generated by the code, -\begin{verbatim} -\sixheterov[d]{2==S}{5==\null;% -3==\ryl(3==CH$_{2}$){3==\sixheterov[d]{2==S}{5==(yl)}}} -\end{verbatim} -where the \verb/\ryl/ command takes an optional argument -in parentheses to draw CH$_{2}$ exciplicitly. -Such a methylene can alternatively be represented as a simple vertex, -as shown in the formula, -\begin{center} -\sixheterov[d]{2==S}{5==\null;% -3==\ryl{3==\sixheterov[d]{2==S}{5==(yl)}}} -\end{center} -This formula is generated by the code, -\begin{verbatim} -\sixheterov[d]{2==S}{5==\null;% -3==\ryl{3==\sixheterov[d]{2==S}{5==(yl)}}} -\end{verbatim} -where the \verb/\ryl/ command takes no optional argument. - -The second argument of the \verb/\ryl/ command can -accomodate substituents other than a substituent -generated by the ``yl'' function. For example, -the inner code \verb/\ryl{0A==Me;...}/ in the code, -\begin{verbatim} -\sixheterov({bB}{eA}){3==O;5==O}{1A==Me;4Sa==\null;4Sb==\null;% -6==\pentamethylenei[a]{}{4B==OH;5B==Me;5==(yl)};% -2==\ryl{0A==Me;5==\sixheterov({eA}){3==O;5==O}{6==(yl);1B==Me;% -4Sa==\null;4Sb==\null}}} -\end{verbatim} -represents a methyl group on a vertex due to the command \verb/\ryl/. -Thereby, we have -\begin{center} -\vspace*{1cm} -\sixheterov({bB}{eA}){3==O;5==O}{1A==Me;4Sa==\null;4Sb==\null;% -6==\pentamethylenei[a]{}{4B==OH;5B==Me;5==(yl)};% -2==\ryl{0A==Me;5==\sixheterov({eA}){3==O;5==O}{6==(yl);1B==Me;% -4Sa==\null;4Sb==\null}}} - -\vspace*{1cm} -\end{center} - - - -\section{$\backslash$lyl command} - -The command \verb/\lyl/ is the left-hand -counterpart of the command \verb/\ryl/. -\begin{verbatim} -\lyl(LINK){GROUP} -\end{verbatim} -The slopes of the linking bonds -concerning the right terminal are designated by -integers between 0 and 8: -\begin{center} -\begin{tabular}{cc|cc|cc} -0 & $(0,1)$ & 1 & $(3,5)$ & 2 & $(1,1)$ \\ -3 & $(5,3)$ & 4 & $(1,0)$ & 5 & $(5,-3)$ \\ -6 & $(1,-1)$ & 7 & $(3,-5)$ & 8 & $(0,-1)$ \\ -\end{tabular} -\end{center} -The slopes of the linking bonds concerning -the left terminal are designated by -integers between 0 and 8: -\begin{center} -\begin{tabular}{cc|cc|cc} -0 & $(0,1)$ & 1 & $(-3,5)$ & 2 & $(-1,1)$ \\ -3 & $(-5,3)$ & 4 & $(-1,0)$ & 5 & $(-5,-3)$ \\ -6 & $(-1,-1)$ & 7 & $(-3,-5)$ & 8 & $(0,-1)$ \\ -\end{tabular} -\end{center} - -To illustrate linking bonds with various slopes, -the code -\begin{verbatim} -\cyclohexanev[]{% -1==\lyl(8==SO$_{2}$--HN){1==\bzdrh{5==(yl)}};% -6==\lyl(5==SO$_{2}$--NH){4==\bzdrh{4==(yl)}};% -5==\lyl(3==SO$_{2}$--NH){4==\bzdrh{4==(yl)}};% -4==\lyl(0==SO$_{2}$--HN){7==\bzdrh{3==(yl)}}} -\end{verbatim} -is written to give - - -\vspace*{2cm} -\begin{center} -\cyclohexanev[]{% -1==\lyl(8==SO$_{2}$--HN){1==\bzdrh{5==(yl)}};% -6==\lyl(5==SO$_{2}$--NH){4==\bzdrh{4==(yl)}};% -5==\lyl(3==SO$_{2}$--NH){4==\bzdrh{4==(yl)}};% -4==\lyl(0==SO$_{2}$--HN){7==\bzdrh{3==(yl)}}} -\end{center} -\vspace*{2cm} - -Other examples are drawn by the code -\begin{verbatim} -\cyclohexaneh[]{% -2==\lyl(7==SO$_{2}$--NH){4==\bzdrh{4==(yl)}}; -6==\lyl(1==SO$_{2}$--NH){4==\bzdrh{4==(yl)}};% -1==\lyl(4==NH--SO$_{2}$--HN){4==\bzdrh{4==(yl)}}} -\end{verbatim} -giving -\vspace*{1cm} -\begin{center} -\cyclohexaneh[]{% -2==\lyl(7==SO$_{2}$--NH){4==\bzdrh{4==(yl)}}; -6==\lyl(1==SO$_{2}$--NH){4==\bzdrh{4==(yl)}};% -1==\lyl(4==NH--SO$_{2}$--NH){4==\bzdrh{4==(yl)}}} -\end{center} -\vspace*{1cm} - -The first argument in the parentheses of the -command \verb/\lyl/ contains a string of letters -after an intermediate delimiter ==, where -a left linking site is shifted according to the -length of the letter string. -The above formula shows such an example -as having NH--SO$_{2}$--NH. - -The structural formula of adonitoxin, -which has once been depicted in a different way -in Chapter 15 of the \XyMTeX book -%``\XyMTeX{}---Typesetting Chemical -%Structural Formulas'' (Addison-Wesley Publishers Japan, 1997) -can be obtained by the code, -\begin{verbatim} -\steroid{{{10}}==\lmoiety{OHC};{{14}}==OH;% -{{13}}==\lmoiety{H$_{3}$C};{{16}}==OH;% -{{17}}==\fiveheterov[e]{3==O}{4D==O;1==(yl)};% -3==\lyl(3==O){8==% -\pyranose{1Sb==(yl);1Sa==H;2Sb==H;2Sa==OH;3Sb==H;3Sa==OH;4Sb==HO;% -4Sa==H;5Sb==H;5Sa==CH$_{3}$}}} -\end{verbatim} - -\begin{quotation} -\vspace*{1cm} -\hspace*{4cm} -\steroid{{{10}}==\lmoiety{OHC};{{14}}==OH;% -{{13}}==\lmoiety{H$_{3}$C};{{16}}==OH;% -{{17}}==\fiveheterov[e]{3==O}{4D==O;1==(yl)};% -3==\lyl(3==O){8==% -\pyranose{1Sb==(yl);1Sa==H;2Sb==H;2Sa==OH;3Sb==H;3Sa==OH;4Sb==HO;% -4Sa==H;5Sb==H;5Sa==CH$_{3}$}}} -\end{quotation} - -\vskip1cm - - -\section{Nested $\backslash$ryl and $\backslash$lyl commands} - -Two or more \verb/\ryl/ and \verb/\lyl/ commands can be nested. -Let us illustrate nesting processes by drawing a cyan -dye releaser, which has once been depicted in different ways -(see Chapters 14 and 15 of the \XyMTeX book). -%in ``\XyMTeX{}---Typesetting Chemical -%Structural Formulas'' (Addison-Wesley Publishers Japan, 1997)). - -\vspace*{1cm} -\bzdrv{1==OH;5==CH$_{3}$;4==OC$_{16}$H$_{33}$;% -2==\ryl(4==NH--SO$_{2}$){4==\bzdrh{1==(yl);2==OCH$_{2}$CH$_{2}$OCH$_{3}$;% -5==\ryl(2==NH--SO$_{2}$){4==\bzdrh{1==(yl);% -5==\ryl(2==SO$_{2}$--NH){4==\naphdrh{1==(yl);5==OH;% -8==\lyl(4==N=N){4==\bzdrh{4==(yl);1==NO$_{2}$;5==SO$_{2}$CH$_{3}$}}}}}}}}} - -\vskip3cm -First, the code -\begin{verbatim} -\ryl(4==NH--SO$_{2}$){4==\bzdrh{1==(yl);2==OCH$_{2}$CH$_{2}$OCH$_{3}$;% -5==\null}} -\end{verbatim} -generates a substituent: -\begin{quotation} -\vspace*{1cm} -\ryl(4==NH--SO$_{2}$){4==\bzdrh{1==(yl);2==OCH$_{2}$CH$_{2}$OCH$_{3}$;% -5==\null}} - -\vspace*{1cm} -\end{quotation} -in which the command \verb/\null/ is used to show a further -substitution site. The resulting substituent is -nested in the SUBSLIT of another \verb/\bzdrv/ command -as shown in the code: -\begin{verbatim} -\bzdrv{1==OH;5==CH$_{3}$;4==OC$_{16}$H$_{33}$;% -2==\ryl(4==NH--SO$_{2}$){4==\bzdrh{1==(yl);2==OCH$_{2}$CH$_{2}$OCH$_{3}$;% -5==\null}}} -\end{verbatim} -Thereby we have -\begin{quotation} -\vskip1cm -\bzdrv{1==OH;5==CH$_{3}$;4==OC$_{16}$H$_{33}$;% -2==\ryl(4==NH--SO$_{2}$){4==\bzdrh{1==(yl);2==OCH$_{2}$CH$_{2}$OCH$_{3}$;% -5==\null}}} -\end{quotation} - -\vskip1cm \noindent -The inner code \verb/5==\null/ is replaced by a further -code of substitution: -\begin{verbatim} -5==\ryl(2==NH--SO$_{2}$){4==\bzdrh{1==(yl);5==\null}}% -\end{verbatim} -to give a code, -\begin{verbatim} -\bzdrv{1==OH;5==CH$_{3}$;4==OC$_{16}$H$_{33}$;% -2==\ryl(4==NH--SO$_{2}$){4==\bzdrh{1==(yl);2==OCH$_{2}$CH$_{2}$OCH$_{3}$;% -5==\ryl(2==NH--SO$_{2}$){4==\bzdrh{1==(yl);5==\null}}% -}}} -\end{verbatim} -This code generates the following structure (Formula A): -\begin{quotation} -\vskip1cm -\bzdrv{1==OH;5==CH$_{3}$;4==OC$_{16}$H$_{33}$;% -2==\ryl(4==NH--SO$_{2}$){4==\bzdrh{1==(yl);2==OCH$_{2}$CH$_{2}$OCH$_{3}$;% -5==\ryl(2==NH--SO$_{2}$){4==\bzdrh{1==(yl);% -5==\null}}}}} -\end{quotation} - -\vskip1cm -Another substituent is typeset by the code, -\begin{verbatim} -\ryl(2==SO$_{2}$--NH){4==\naphdrh{1==(yl);5==OH;% -8==\lyl(4==N=N){4==\bzdrh{4==(yl);1==NO$_{2}$;5==SO$_{2}$CH$_{3}$}}}} -\end{verbatim} -Then, we have a substituent (Formula B): -\begin{quotation} -\vskip1cm -\hspace*{4cm}\ryl(2==SO$_{2}$--NH){4==\naphdrh{1==(yl);5==OH;% -8==\lyl(4==N=N){4==\bzdrh{4==(yl);1==NO$_{2}$;5==SO$_{2}$CH$_{3}$}}}} -\end{quotation} - -\vspace{3cm} -Finally, the inner code \verb/5==\null/ for Formula A is replaced -by the code for Formula B -in order to combine Formula A with Formula B. -Then we obtain a code represented by -\begin{verbatim} -\bzdrv{1==OH;5==CH$_{3}$;4==OC$_{16}$H$_{33}$;% -2==\ryl(4==NH--SO$_{2}$){4==\bzdrh{1==(yl);2==OCH$_{2}$CH$_{2}$OCH$_{3}$;% -5==\ryl(2==NH--SO$_{2}$){4==\bzdrh{1==(yl);% -5==\ryl(2==SO$_{2}$--NH){4==\naphdrh{1==(yl);5==OH;% -8==\lyl(4==N=N){4==\bzdrh{4==(yl);1==NO$_{2}$;5==SO$_{2}$CH$_{3}$}}}}}}}}} -\end{verbatim} -Thereby, we have a target formula: - -\vspace*{1cm} -\bzdrv{1==OH;5==CH$_{3}$;4==OC$_{16}$H$_{33}$;% -2==\ryl(4==NH--SO$_{2}$){4==\bzdrh{1==(yl);2==OCH$_{2}$CH$_{2}$OCH$_{3}$;% -5==\ryl(2==NH--SO$_{2}$){4==\bzdrh{1==(yl);% -5==\ryl(2==SO$_{2}$--NH){4==\naphdrh{1==(yl);5==OH;% -8==\lyl(4==N=N){4==\bzdrh{4==(yl);1==NO$_{2}$;5==SO$_{2}$CH$_{3}$}}}}}}}}} - -\vskip3cm - -The structural formula of adonitoxin, -which has benn drawn by considering the steroid nucleus to be -a mother skeleton in the preceding subsection, -can be alternatively drawn by nesting -a ``yl''-function and a \verb/\ryl/ command. -In this case, the pyranose ring is regarded as a mother skeleton. -Thus, the code -\begin{verbatim} -\pyranose{1Sa==H;2Sb==H;2Sa==OH;3Sb==H;3Sa==OH;4Sb==HO;% -4Sa==H;5Sb==H;5Sa==CH$_{3}$;% -1Sb==\ryl(8==O){3==% -\steroid{3==(yl);{{10}}==\lmoiety{OHC};{{14}}==OH;% -{{13}}==\lmoiety{H$_{3}$C};{{16}}==OH;% -{{17}}==\fiveheterov[e]{3==O}{4D==O;1==(yl)}}}} -\end{verbatim} -typesets the following formula: -\begin{quotation} -\vspace*{4cm} -\pyranose{1Sa==H;2Sb==H;2Sa==OH;3Sb==H;3Sa==OH;4Sb==HO;% -4Sa==H;5Sb==H;5Sa==CH$_{3}$;% -1Sb==\ryl(8==O){3==% -\steroid{3==(yl);{{10}}==\lmoiety{OHC};{{14}}==OH;% -{{13}}==\lmoiety{H$_{3}$C};{{16}}==OH;% -{{17}}==\fiveheterov[e]{3==O}{4D==O;1==(yl)}}}} -\end{quotation} - -\section{$\backslash$divalenth command} - -The command \verb/\divalenth/ generates a divalent skeleton -with variable length. -\begin{verbatim} -\divalenth{GROUP}{SUBSLIST} -\end{verbatim} -The divalent skeleton is given by -a string of alphabets in the GROUP argument. -The locant number in the GROUP argument is fixed to be zero. -For example, the code -\begin{verbatim} -\divalenth{0==NHCONH}{1==CH$_{3}$;2==CH$_{3}$} -\end{verbatim} -generates a linear formula: -\begin{center} -\divalenth{0==NHCONH}{1==CH$_{3}$;2==CH$_{3}$} -\end{center} - -4,4$^{\prime}$-Methylenedibenzoic acid can be drawn in the same line. -The code -\begin{verbatim} -\divalenth{0==CH$_{2}$}{1==\bzdrh{4==(yl);1==HOOC};2==\bzdrh{1==(yl);4==COOH}} -\end{verbatim} -generates -\begin{center} -\divalenth{0==CH$_{2}$}{1==\bzdrh{4==(yl);1==HOOC};2==\bzdrh{1==(yl);4==COOH}} -\end{center} - -In place of the CH$_{2}$ unit described in the preceding example, -we introduce the O--CH$_{2}$--O unit so as to give -4,4$^{\prime}$-methylenedioxydibenzoic acid. The structurel formula -can be drawn to be -\begin{center} -\divalenth{0==O--CH$_{2}$--O}% -{1==\bzdrh{4==(yl);1==HOOC};2==\bzdrh{1==(yl);4==COOH}} -\end{center} -by means of the code: -\begin{verbatim} -\divalenth{0==O--CH$_{2}$--O}% -{1==\bzdrh{4==(yl);1==HOOC};2==\bzdrh{1==(yl);4==COOH}} -\end{verbatim} -Note that the starting point of the moiety -generated by the code \verb/2==\bzdrh{1==(yl);4==COOH}/ is -automatically shifted so as to accomodate the O--CH$_{2}$--O unit. - - -An additional example of the use of the \verb/\divalenth/ command -is the drawing of -1,6$^{\prime}$-ureylenedi-2-naphthalenesulfonic acid -\begin{quotation} -\vspace*{2cm}\hspace*{4cm} -\divalenth{0==NH--CO--NH}% -{1==\naphdrh{4==(yl);3==SO$_{3}$H};2==\naphdrv{6==(yl);2==SO$_{3}$H}} - -\vspace*{2cm} -\end{quotation} -by means of the code -\begin{verbatim} -\divalenth{0==NH--CO--NH}% -{1==\naphdrh{4==(yl);3==SO$_{3}$H};2==\naphdrv{6==(yl);2==SO$_{3}$H}} -\end{verbatim} - - -$p$-[2-($m$-Carboxyphenoxy)ethyl]benzoic acid is -drawn by the code -\begin{verbatim} -\divalenth{0==O--CH$_{2}$--CH$_{2}$}% -{1==\bzdrh{4==(yl);6==COOH};2==\bzdrh{1==(yl);4==COOH}} -\end{verbatim} -which generates a formula: -\begin{center} -\divalenth{0==O--CH$_{2}$--CH$_{2}$}% -{1==\bzdrh{4==(yl);6==COOH};2==\bzdrh{1==(yl);4==COOH}} - -\vspace*{1cm} -\end{center} -The same structure can be depicted by applying -the ``yl''-function to the \verb/\divalenth/ command. -The code -\begin{verbatim} -\bzdrh{6==COOH;4==% -\divalenth{0==O--CH$_{2}$--CH$_{2}$}{1==(yl);2==\bzdrh{1==(yl);4==COOH}}} -\end{verbatim} -generates the same formula: -\begin{center} -\bzdrh{6==COOH;4==% -\divalenth{0==O--CH$_{2}$--CH$_{2}$}{1==(yl);2==\bzdrh{1==(yl);4==COOH}}} - -\vspace*{1cm} -\end{center} -This type of usage gives an equivalent function of -the command \verb/\ryl/ or \verb/\lyl/. Compare this with -an example using the \verb/\ryl/ command: -\begin{verbatim} -\bzdrh{6==COOH;4==% -\ryl(4==O--CH$_{2}$--CH$_{2}$){4==\bzdrh{1==(yl);4==COOH}}} -\end{verbatim} -This code gives the same formula: -\begin{center} -\bzdrh{6==COOH;4==% -\ryl(4==O--CH$_{2}$--CH$_{2}$){4==\bzdrh{1==(yl);4==COOH}}} -\end{center} - -\section{Remarks} - -The use of \verb/\divalenth/ with a ``yl''-function has -no means of adjusting the left-hand point of linking. -For example, the code, -\begin{verbatim} -\bzdrv{2==COOH;4==% -\divalenth{0==O--CH$_{2}$--CH$_{2}$}{1==(yl);2==\bzdrh{1==(yl);4==COOH}}} -\end{verbatim} -give an insufficient formula: -\begin{center} -\bzdrv{2==COOH;4==% -\divalenth{0==O--CH$_{2}$--CH$_{2}$}{1==(yl);2==\bzdrh{1==(yl);4==COOH}}} - -\vspace*{1cm} -\end{center} -where the left-hand point of linking should be shifted to -a more appropiate direction. On the other hand, -the \verb/\ryl/ (or \verb/\lyl/) command can correctly -specify the left-hand point of linking. Thus the code, -\begin{verbatim} -\bzdrv{2==COOH;4==% -\ryl(0==O--CH$_{2}$--CH$_{2}$){4==\bzdrh{1==(yl);4==COOH}}} -\end{verbatim} -typesets a formula: -\begin{center} -\bzdrv{2==COOH;4==% -\ryl(0==O--CH$_{2}$--CH$_{2}$){4==\bzdrh{1==(yl);4==COOH}}} - -\vspace*{1cm} -\end{center} -where the code \verb/0==O--CH$_{2}$--CH$_{2}$/ specifies -the left-hand terminal of the unit O--CH$_{2}$--CH$_{2}$ -is linked at the upper point of the oxygen atom. - - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\chapter{Ring Fusion} - -\section{Ring Fusion on Carbocyclic Compounds} -\subsection{Designation of Fused Bonds} - -A unit to be fused is written in the BONDLIST of a command with -a bond specifier (a lowercase or uppercase alphabet). -For example, the code -\begin{verbatim} -\hanthracenev[{A\sixfusev{}{}{d}}]{} -\end{verbatim} -gives a perhydroanthracene with a fused six-membered ring -at the bond `a' of the perhydroanthracene nucleus: -\begin{quotation} -\vskip1cm -\hanthracenev[{A\sixfusev{}{}{d}}]{} -\end{quotation} -The letter `A' of the code -\verb/{A\sixfusev{}{}{d}}/ is a bond specifier that represents -the older terminal of the bond `a' of the -perhydroanthracene nucleus -(For the designation of the bonds of perhydroanthracene, -see Chapter 5 of the \XyMTeX book.% -%``\XyMTeX{}---Typesetting Chemical -%Structural Formulas'' (Addison-Wesley Publishers Japan, 1997).% -\footnote{% -The word `older' or `younger' is concerned with the order of numbering -of vertices. For a six-membered ring, the numbering -1---2---3---4---5---6---1 shows that -the terminal 1 of the -bond `a' (1---2) is youger, while the terminal 2 of the bond -`a' is older. It should be noted that the terminal 6 of the -bond `f' (6---1) is youger, while the terminal 1 of the bond -`f' is older.} -Note that the younger -terminal of the bond `a' is designated by the letter `a'. -On the other hand, -the code \verb/\sixfusev{}{}{d}/ of \verb/{A\sixfusev{}{}{d}}/ -in the BONDLIST represents the fused six-membered ring -with the bond `d' omitted. The letter `d' indicates -that the fusing point of the unit is the youger terminal -of the omitted bond `d'. If the the fusing point of the unit -is the other (older) terminal, the -corresponding uppercase letter `D' should be used. - -Accordingly, the same formula can be drawn by the -code exchanging uppercase and lowercase letters, -\begin{verbatim} -\hanthracenev[{a\sixfusev{}{}{D}}]{} -\end{verbatim} -Thereby, we have -\begin{quotation} -\vskip1cm -\hanthracenev[{a\sixfusev{}{}{D}}]{} -\end{quotation} - -Two or more rings can be fused. For example, -the code -\begin{verbatim} -\hanthracenev[{A\sixfusev{}{}{d}}{C\sixfusev{}{}{f}}]{} -\end{verbatim} -generates a formula with two fused rings at the -bonds `a' and `c' of a perhydroanthracene nucleus. -\begin{quotation} -\vskip1cm -\hanthracenev[{A\sixfusev{}{}{d}}{C\sixfusev{}{}{f}}]{} - -\vskip1cm -\end{quotation} - -The BONDLIST can accomodates usual bond specifiers without -a fusing unit in order to designate inner double bonds. -For example, the code -\begin{verbatim} -\hanthracenev[aco{A\sixfusev[a]{}{}{d}}]{} -\end{verbatim} -gives a hydroanthracene that have inner double bonds -as well as a fused six-membered ring: -\begin{quotation} -\vskip1cm -\hanthracenev[aco{A\sixfusev[a]{}{}{d}}]{} -\end{quotation} -Note that the command \verb/\sixfusev/ can take -an optional argument to designate inner double bonds, -as shown by the code \verb/\sixfusev[a]{}{}{d}/. - -In order to specify substituents in addition, -we can use the SUBSLIST of the command \verb/\hanthracenev/ as well -as the one of the command \verb/\sixfusev/. For example, the code -\begin{verbatim} -\hanthracenev[aco{A\sixfusev[a]{}{1==F;2==Cl}{d}}]{5==OH;6==HO} -\end{verbatim} -gives a hydroanthracene having additional substituents: -\begin{quotation} -\vspace*{1cm} -\hanthracenev[aco{A\sixfusev[a]{}{1==F;2==Cl}{d}}]{5==OH;6==HO} -\end{quotation} - -The compound {\bfseries 13} on page 294 -(Chapter IV-4) of the \XyMTeX book -%``\XyMTeX{}---Typesetting Chemical -%Structural Formulas'' (Addison-Wesley Publishers Japan, 1997) -can alternatively be drawn by applying the -present technique. Thus, the code -\begin{verbatim} -\hanthracenev[achjop{b\sixfusev{}{2==R}{E}}]{% -1==OCH$_{3}$;4==OH;{10}D==O;% -9==\lyl(8==C\rlap{O}){4==CH$_{3}$O}} -\end{verbatim} -gives the following formula: -\begin{quotation} -\hanthracenev[achjop{b\sixfusev{}{2==R}{E}}]{% -1==OCH$_{3}$;4==OH;{10}D==O;% -9==\lyl(8==C\rlap{O}){4==CH$_{3}$O}} -\end{quotation} - - -\section{Ring Fusion on Heterocyclic Compounds} - -The methodology of ring fusion for heterocyclic compounds -is the same as described for carbocyclic compounds. -Thus, a unit to be fused is written in the BONDLIST of -a command with a bond specifier (a lowercase or uppercase alphabet). -For example, the code -\begin{verbatim} -\nonaheterov[begj{b\sixfusev[ac]{}{}{e}}]{1==N}{1==H} -\end{verbatim} -gives the structural formula of carbazole: -\begin{quotation} -\nonaheterov[begj{b\sixfusev[ac]{}{}{e}}]{1==N}{1==H} -\end{quotation} -which is depicted by attaching a six-membered ring -(\verb/\sixfusev[ac]{}{}{e}}/) -to the bond `b' of an indole nucleus. - -Let us consider the substitution of a carbon atom -with a nitrogen atom at one of the fused positions -in the above compound, as shown by the following formula: -\begin{quotation} -\nonaheterov[begj{b\sixfusev[ac]{6==\null}{}{e}}]{1==N;3==N}{1==H} -\end{quotation} -This formula is obtained by writing the code: -\begin{verbatim} -\nonaheterov[begj{b\sixfusev[ac]{6==\null}{}{e}}]{1==N;3==N}{1==H} -\end{verbatim} -where the code \verb/6==\null/ in the ATOMLIST of -\verb/\sixfusev/ (for the fused six-membered ring) -and the code \verb/3==N/ in the ATOMLIST of -\verb/\nonaheterov/ produces the nitrogen -atom at the fused position. -The specification of the nitrogen atom -is also available by exchanging \verb/\null/ and \verb/N/. -Thus the code -\begin{verbatim} -\nonaheterov[begj{b\sixfusev[ac]{6==N}{}{e}}]{1==N;3==\null}{1==H} -\end{verbatim} -gives the same structural formula: -\begin{quotation} -\nonaheterov[begj{b\sixfusev[ac]{6==N}{}{e}}]{1==N;3==\null}{1==H} -\end{quotation} - -The ring fusion at the bond `a' of perhydroindole -is represented by the code -\begin{verbatim} -\nonaheterov[{a\sixfusev{6==\null}{}{f}}]{1==N}{} -\end{verbatim} -which gives a heterocycle: -\begin{quotation} -\nonaheterov[{a\sixfusev{6==\null}{}{f}}]{1==N}{} -\end{quotation} - - - -Benz[{\itshape h}]isoquinoline, -\begin{quotation} -\vspace*{1cm} -\decaheterovt[acfhk{h\sixfusev[df]{}{}{B}}]{2==N}{} -\end{quotation} -can be typset by the code, -\begin{verbatim} -\decaheterovt[acfhk{h\sixfusev[df]{}{}{B}}]{2==N}{} -\end{verbatim} -in which the bond specifier `h' corresponds to -the {\itshape h} of the IUPAC name. -Note that the IUPAC name regards the structure as -an isoquinoline (drawn by \verb/\decaheterovt/) fused by a benzo moiety. -The same structure -can be drawn by the alternative code: -\begin{verbatim} -\decaheterov[acfhk{a\sixfusev[bf]{1==N}{}{D}}]{}{} -\end{verbatim} -which regards the structure as a naphthalene (drawn by -\verb/\decaheterov/) with -a fused heterocycle. Thereby, we have - \begin{quotation} -\vspace*{1cm} -\decaheterov[acfhk{a\sixfusev[bf]{1==N}{}{D}}]{}{} -\end{quotation} - -\section{Neted Ring Fusion} - -The \verb/\sixfusev/ command is capable of -accomodating another \verb/\sixfusev/ command in -a nested fashion. By this technique, -the carbazole structure can take a further -fused ring so as to produce the structural formula -of 7{\itshape H}-pyrazino[2,3-{\itshape c}]carbaozole. -Thus, the code, -\begin{verbatim} -\nonaheterov[begj{b\sixfusev[% -ac{a\sixfusev[bf]{6==N;3==N}{}{D}}]{}{}{e}}]{1==N}{1==H} -\end{verbatim} -gives the structural formula of the fused heterocycle: -\begin{quotation} -\vspace*{1cm} -\nonaheterov[begj{b\sixfusev[% -ac{a\sixfusev[bf]{6==N;3==N}{}{D}}]{}{}{e}}]{1==N}{1==H} -\end{quotation} -which is depicted by attaching a six-membered ring -(\verb/\sixfusev[ac]{}{}{e}}/) -to the bond `b' of an indole nucleus. - -The structural formula of -pyrido[1$^{\prime}$,2$^{\prime}$:1,2]imidazo[4,5-{\itshape b}]quinoxaline, -\begin{center} -\nonaheterov[adh% -{b\sixfusev[ac]{6==\null}{}{e}}% -{f\sixfusev[ace]{}{}{b}}]{1==N;3==N;4==N;7==N}{} -\end{center} -is generated by the code, -\begin{verbatim} -\nonaheterov[adh% -{b\sixfusev[ac]{6==\null}{}{e}}% -{f\sixfusev[ace]{}{}{b}}]{1==N;3==N;4==N;7==N}{} -\end{verbatim} -Since this code is intended to contain no nested ring fusion, -the order of structure construction is different -from that of the IUPAC name. - -The IUPAC name, -pyrido[1$^{\prime}$,2$^{\prime}$:1,2]imidazo[4,5-{\itshape b}]quinoxaline, -corresponds to a quinaxaline with a fused five-membered ring (an imidazo -moiety) which is in turn fused by a six-membered ring (a pyrido moiety). -The order of constructing the IUPAC name is realized in the code -with nested ring fusion, -\begin{verbatim} -\decaheterov[acegi% -{b\fivefusev[a{b\sixfusev[ac]{6==\null}{}{e}}]{1==N;3==N}{}{d}}] -{1==N;4==N}{} -\end{verbatim} -which produces the same structure, -\begin{center} -\decaheterov[acegi% -{b\fivefusev[a{b\sixfusev[ac]{6==\null}{}{e}}]{1==N;3==N}{}{d}}] -{1==N;4==N}{} -\end{center} - -Note that the indicators `1$^{\prime}$,2$^{\prime}$' and `1,2'of -the locant [1$^{\prime}$,2$^{\prime}$:1,2] in the IUPAC name -correspond respectively to the -bond specifiers , `E' and `b', appeared in the code, -\verb/{b\sixfusev[ac]{6==\null}{}{E}}/. -On the other hand, the indicators, -`4,5' and `{\itshape b}' of of the locant [4,5-{\itshape b}] -are respectively associated with -the specifiers, `d' and `b', appeared in the code, -\verb/{b\fivefusev[...]{1==N;3==N}{}{d}}/. - -An alkaloid with a coryanthe skeleton -(R. T. Brown and C. L. Chapple, {\itshape Chem. Commun.}, -1973, 887) can be typeset by the code with nested fusion, -\begin{verbatim} -\nonaheterov[begj{b\sixfusev[% -{c\sixfusev{1==\null}{3SB==H;3SA==Et;% -4GA==H;% -4B==\dimethylenei[a]{}{1==(yl);2W==OMe;1W==MeOCO}}{F}}]% -{3==N}{4GB==H;2B==COOMe}{e}}]{1==N}{1==H} -\end{verbatim} -where a six-five ring drawn by the command \verb/\nonaheterov/ -is regarded as a mother skeleton. Thus, we have -\begin{quotation} -\nonaheterov[begj{b\sixfusev[% -{c\sixfusev{1==\null}{3SB==H;3SA==Et;% -4GA==H;% -4B==\dimethylenei[a]{}{1==(yl);2W==OMe;1W==MeOCO}}{F}}]% -{3==N}{4GB==H;2B==COOMe}{e}}]{1==N}{1==H} -\vspace*{2cm} -\end{quotation} -For the command \verb/\dimethylenei/, see the chapter at issue. - -When a six-six ring drawn by the command \verb/\decaheterovb/ -is regarded as a mother skeleton, as shown in the code with -another nested ring fusion, -\begin{verbatim} -\decaheterovb[f{f\fivefusev[d{d\sixfusev[df]{}{}{b}}]% -{1==N}{1==H}{b}}]{8a==N}{9B==H;2SA==Et;2SB==H;8B==COOMe;% -3GA==H;% -3B==\dimethylenei[a]{}{1==(yl);2W==OMe;1W==MeOCO}} -\end{verbatim} -we find another way of drawing the same structural formula, -\begin{center} -\decaheterovb[f{f\fivefusev[d{d\sixfusev[df]{}{}{b}}]% -{1==N}{1==H}{b}}]{8a==N}{9B==H;2SA==Et;2SB==H;8B==COOMe;% -3GA==H;% -3B==\dimethylenei[a]{}{1==(yl);2W==OMe;1W==MeOCO}} - -\vspace*{1cm} -\end{center} - -The following example shows a code with complicated -nested structure: -\begin{verbatim} -\cyclohexanev[% -{a\sixfusev[{b\sixfusev[{c\sixfusev[{c\sixfusev[% -{d\sixfusev[{d\sixfusev[{d\sixfusev[% -{e\sixfusev[{e\sixfusev[{e\sixfusev[{e\sixfusev[% -{f\sixfusev[{f\sixfusev[]{}{}{C}}]{}{}{C}}% -]{}{}{B}}]{}{}{B}}]{}{}{B}}]{}{}{B}}% -]{}{}{A}}]{}{}{A}}]{}{}{A}}]{}{}{F}}% -]{}{}{F}}]{}{}{E}}]{}{}{D}}% -{c\sixfusev[{d\sixfusev[{e\sixfusev[{e\sixfusev[% -{f\sixfusev[{f\sixfusev[{f\sixfusev[% -{a\sixfusev[{a\sixfusev[{a\sixfusev[{a\sixfusev[% -{b\sixfusev[{b\sixfusev[]{}{}{E}}]{}{}{E}}% -]{}{}{D}}]{}{}{D}}]{}{}{D}}]{}{}{D}}% -]{}{}{C}}]{}{}{C}}]{}{}{C}}]{}{}{B}}% -]{}{}{B}}]{}{}{A}}]{}{}{F}}% -{e\sixfusev[{f\sixfusev[{a\sixfusev[{a\sixfusev[% -{b\sixfusev[{b\sixfusev[{b\sixfusev[% -{c\sixfusev[{c\sixfusev[{c\sixfusev[{c\sixfusev[% -{d\sixfusev[{d\sixfusev[]{}{}{A}}]{}{}{A}}% -]{}{}{F}}]{}{}{F}}]{}{}{F}}]{}{}{F}}% -]{}{}{E}}]{}{}{E}}]{}{}{E}}]{}{}{D}}% -]{}{}{D}}]{}{}{C}}]{}{}{B}}% -]{} -\end{verbatim} -This code generates a multiply fused formula: - -\clearpage - -\begin{center} -\vspace*{8cm} -\cyclohexanev[% -{a\sixfusev[{b\sixfusev[{c\sixfusev[{c\sixfusev[% -{d\sixfusev[{d\sixfusev[{d\sixfusev[% -{e\sixfusev[{e\sixfusev[{e\sixfusev[{e\sixfusev[% -{f\sixfusev[{f\sixfusev[]{}{}{C}}]{}{}{C}}% -]{}{}{B}}]{}{}{B}}]{}{}{B}}]{}{}{B}}% -]{}{}{A}}]{}{}{A}}]{}{}{A}}% -]{}{}{F}}% -]{}{}{F}}]{}{}{E}}]{}{}{D}}% -{c\sixfusev[{d\sixfusev[{e\sixfusev[{e\sixfusev[% -{f\sixfusev[{f\sixfusev[{f\sixfusev[% -{a\sixfusev[{a\sixfusev[{a\sixfusev[{a\sixfusev[% -{b\sixfusev[{b\sixfusev[]{}{}{E}}]{}{}{E}}% -]{}{}{D}}]{}{}{D}}]{}{}{D}}]{}{}{D}}% -]{}{}{C}}]{}{}{C}}]{}{}{C}}% -]{}{}{B}}% -]{}{}{B}}]{}{}{A}}]{}{}{F}}% -{e\sixfusev[{f\sixfusev[{a\sixfusev[{a\sixfusev[% -{b\sixfusev[{b\sixfusev[{b\sixfusev[% -{c\sixfusev[{c\sixfusev[{c\sixfusev[{c\sixfusev[% -{d\sixfusev[{d\sixfusev[]{}{}{A}}]{}{}{A}}% -]{}{}{F}}]{}{}{F}}]{}{}{F}}]{}{}{F}}% -]{}{}{E}}]{}{}{E}}]{}{}{E}}% -]{}{}{D}}% -]{}{}{D}}]{}{}{C}}]{}{}{B}}% -]{} -\end{center} - - - -\clearpage - - - -\section{Remarks} - -\subsection{OPT Arguments} - -It should be noted that the OPT arguments of -such commands as \verb/\bzdrv/, \verb/\naphdrv/, -and \verb/\anthracenev/ cannot be used -for the ring-fusion technique. In place of the OPT argument, -the BONDLIST argument of the corresponding general -command, e.g. \verb/\cyclohexanev/ or \verb/\sixheterov/ -correspoding to \verb/\bzdrv/, -should be used for the purpose of ring fusion. . -For example, a bezene ring of the formula, -\begin{center} -\vspace*{1cm} -\cyclohexanev[ace{a\sixfusev{}{}{D}}]{} -\end{center} -should be drawn by using the \verb/\cyclohexanev/ command, -as shown in the code: -\begin{verbatim} -\cyclohexanev[ace{a\sixfusev{}{}{D}}]{} -\end{verbatim} - -\subsection{\protect\XyMTeX{} Warning} - -An incorrect result due to -a wrong specification of a fused bond is -notified by a \XyMTeX{} warning. -For example, the code, -\begin{verbatim} -\hanthracenev[{a\sixfusev{}{}{d}}]{} -\end{verbatim} -gives a formula of wrong fusion: -\begin{center} -\vspace*{2cm} -\hanthracenev[{a\sixfusev{}{}{d}}]{} -\end{center} -According to this wrong situation, -a \XyMTeX{} warning appears in a display or in a log file, e.g., -\begin{verbatim} - XyMTeX Warning: Mismatched fusion at bond `a, i, or other' - on input line 1904 -\end{verbatim} -There are two ways to correct the wrong fusion and, -as a result, to avoid such a \XyMTeX{} warning. -First, the code -\begin{verbatim} -\hanthracenev[{A\sixfusev{}{}{d}}]{} -\end{verbatim} -in which the acceptor bond specifier `a' is changed into `A', -gives a correct result, as found in the top example of -this chapter. Alternatively, -the donor bond specifier `d' can be changed into `D'. -Thus, the code, -\begin{verbatim} -\hanthracenev[{a\sixfusev{}{}{D}}]{} -\end{verbatim} -also typesets the second formula with correct fusion. - - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\chapter{Fusing Units} - -The commands described in this chapter are stored in -the {\sf fusering} package (file name: fusering.sty). - -\section{Six-membered Fusing Units} -\subsection{Vertical Units of Normal and Inverse Types} -In \XyMTeX{} version 1.01, we can use \verb/\sixunitv/ -and \verb/\fiveunitv/ as building blocks, where -one or more bonds can be omitted. -In the present version, we prepare -such commands as \verb/\sixfusev/ an \verb/\sixfusevi/, -producing building blocks with only one deleted bond. -These commands can be used in the BONDLIST of another -command so as to give a fused structural formula, -as described in the preceding chapter. -The commands \verb/\sixfusev/ and \verb/\sixfusevi/ have formats -represented by -\begin{verbatim} -\sixfusev[BONDLIST]{ATOMLIST}{SUBSLIST}{FUSE} -\sixfusevi[BONDLIST]{ATOMLIST}{SUBSLIST}{FUSE} -\end{verbatim} -where the argument FUSE is an alphabetical character (a--f) -or the uppercase counterpart (A--F), -each of which is a bond specifier representing one bond to be omitted. -A lowercase character (a--f) represents the younger terminal of -the omitted bond. -The corresponding uppercase character (A--F) designates -the other terminal of the bond to be omitted. -The other arguments have the same formats as described -in the general conventions (see \XyMTeX book). -The locant numbers and the bond specifiers of -the command \verb/\sixfusev/ correspond to -those of the command \verb/\sixheterov/ (see \XyMTeX book). -The command \verb/\sixfusevi/ is the inverse counterpart -of \verb/\sixfusev/ and corresponds to the command \verb/\sixheterovi/. -Moreover, the BONDLIST is capbable of -accormodating the ring-fusion function described -in the preseding chapter, -the ATOMLIST can accomodate the spiro-ring function -described afterward, and -the SUBSLIST serves a method producing subsituents (``yl''-function) -describe previously. - -For example, the last argument `F' of the \verb/\sixfusev/ -appearing in the code, -\begin{verbatim} -\sixfusev[]{1==\null}% -{3==C$_2$H$_5$;4==CH$_2$COOC$_2$H$_5$}{F} -\end{verbatim} -results in the deletion of the bond `f' between atom no.~6 (youger -teminal) and atom no.~1 (older terminal) from a hexagon, -typesetting the following building block: -\begin{center} -\sixfusev[]{1==\null}{3==C$_2$H$_5$;4==CH$_2$COOC$_2$H$_5$}{F} - -\vspace*{3cm} -\end{center} -where the reference point for superposition is -the older terminal (i.e. atom no.~1) of the bond `f'. -The code \verb/1==\null/ gives a vacancy at the position of atom no.~1. -When the building block is used in the BONDLIST of -the \verb/\decaheterov/, as shown in the code, -\begin{verbatim} -\decaheterov[fhk% -{c\sixfusev[]{1==\null}% -{3==C$_2$H$_5$;4==CH$_2$COOC$_2$H$_5$}{F}}]{3==N}{6==CH$_3$O;7==CH$_3$O} -\end{verbatim} -we have the following structure, -\begin{center} -\decaheterov[fhk% -{c\sixfusev[]{1==\null}% -{3==C$_2$H$_5$;4==CH$_2$COOC$_2$H$_5$}{F}}]{3==N}{6==CH$_3$O;7==CH$_3$O} -\vspace*{2cm} -\end{center} - -The last argument `F' of the \verb/\sixfusev/ -can be changed into `f', as found in the code, -\begin{verbatim} -\decaheterovi[fhk% -{a\sixfusev[]{1==\null}% -{3==C$_2$H$_5$;4==CH$_2$COOC$_2$H$_5$}{f}}]{2==N}{6==CH$_3$O;7==CH$_3$O} -\end{verbatim} -where we use \verb/\decaheterovi/ in place of -\verb/\decaheterov/ for drawing the bicyclic mother skeleton. -Thereby, we have the following structure, -\begin{center} -\decaheterovi[fhk% -{a\sixfusev[]{1==\null}% -{3==C$_2$H$_5$;4==CH$_2$COOC$_2$H$_5$}{f}}]{2==N}{6==CH$_3$O;7==CH$_3$O} -\vspace*{2cm} -\end{center} - -The vertically opposite formula can be drawn by the combination of -\verb/\sixfusevi/ and \verb/\decaheterovi/ with no other changes -of designation (in comparison with the first code of this -section), i.e. -\begin{verbatim} -\decaheterovi[fhk% -{c\sixfusevi[]{1==\null}% -{3==C$_2$H$_5$;4==CH$_2$COOC$_2$H$_5$}{F}}]{3==N}{6==CH$_3$O;7==CH$_3$O} -\end{verbatim} -Thereby we have -\begin{center} -\vspace*{2cm} -\decaheterovi[fhk% -{c\sixfusevi[]{1==\null}% -{3==C$_2$H$_5$;4==CH$_2$COOC$_2$H$_5$}{F}}]{3==N}{6==CH$_3$O;7==CH$_3$O} -\end{center} - -\subsection{Horizontal Units of Normal and Inverse Types} - -For drawing horizontal fusing units, -we can use the commands \verb/\sixfuseh/ and \verb/\sixfusehi/, -which are represented by -\begin{verbatim} -\sixfuseh[BONDLIST]{ATOMLIST}{SUBSLIST}{FUSE} -\sixfusehi[BONDLIST]{ATOMLIST}{SUBSLIST}{FUSE} -\end{verbatim} - -The horizontal formula of normal type related to the tricyclic -formulas described in the preceding subsection -can be drawn by the combination of -\verb/\sixfuseh/ and \verb/\decaheteroh/ with few changes -of designation (CH$_{3}$O to OCH$_{3}$), i.e. -\begin{verbatim} -\decaheteroh[fhk% -{c\sixfuseh[]{1==\null}% -{3==C$_2$H$_5$;4==CH$_2$COOC$_2$H$_5$}{F}}]{3==N}{6==OCH$_3$;7==OCH$_3$} -\end{verbatim} -which typsets the following structure, -\begin{center} -\vspace*{1cm} -\decaheteroh[fhk% -{c\sixfuseh[]{1==\null}% -{3==C$_2$H$_5$;4==CH$_2$COOC$_2$H$_5$}{F}}]{3==N}{6==OCH$_3$;7==OCH$_3$} -\end{center} - -The horizontally opposite formula can be drawn by the combination of -\verb/\sixfusehi/ and \verb/\decaheterohi/ with -slight changes concerning the handedness of subsitutents, i.e. -\begin{verbatim} -\decaheterohi[fhk% -{c\sixfusehi[]{1==\null}% -{3==C$_2$H$_5$;4==C$_2$H$_5$OCOCH$_2$}{F}}]{3==N}{6==OCH$_3$;7==OCH$_3$} -\end{verbatim} -Thereby we have -\begin{center} -\vspace*{1cm} -\decaheterohi[fhk% -{c\sixfusehi[]{1==\null}% -{3==C$_2$H$_5$;4==C$_2$H$_5$OCOCH$_2$}{F}}]{3==N}{6==OCH$_3$;7==OCH$_3$} -\end{center} - -\section{Five-membered Fusing Units} -\subsection{Vertical Units of Normal and Inverse Types} -To obtain a vertical five-membered building block, -we can use \verb/\fivefusev/ and \verb/\fivefusevi/: -\begin{verbatim} -\fivefusev[BONDLIST]{ATOMLIST}{SUBSLIST}{FUSE} -\fivefusevi[BONDLIST]{ATOMLIST}{SUBSLIST}{FUSE} -\end{verbatim} -where the argument FUSE is an alphabetical character (a--e) -or the uppercase counterpart (A--E), -each of which is a bond specifier representing one bond to be omitted. -The other specifications have the same formats -as found in the preceding section. - -The following example (left) gives the use of the \verb/\fivefusevi/ -command by itself, where its SUBSLIST contains some substituents: -\begin{verbatim} -\fivefusevi{4==O}{2D==;3D==O}{E} \hskip 3cm -\fivefusevi{4==O}{1GA==H;5GB==H;2D==;3D==O}{E} -\end{verbatim} -\begin{center} -%\vspace*{1cm} -\fivefusevi{4==O}{2D==;3D==O}{E} \hskip 3cm -\fivefusevi{4==O}{1GA==H;5GB==H;2D==;3D==O}{E} - -\vspace*{2cm} -\end{center} -To show hydrogen substitution at the fused positions, we -add the designation of \verb/1GA==H;5GB==H/ to the -SUBSLIST of the \verb/\fivefusevi/ command (right above). -Then, the latter code is written in the BONDLIST of -a command \verb/\decalinev/, as found in the code: -\begin{verbatim} -\decalinev[h{c\fivefusevi{4==O}{1GA==H;5GB==H;2D==;3D==O}{E}}]% -{6D==O;5A==;0FB==;0GA==H} -\end{verbatim} -Thereby, we obtain -\begin{center} -\decalinev[h{c\fivefusevi{4==O}{1GA==H;5GB==H;2D==;3D==O}{E}}]% -{6D==O;5A==;0FB==;0GA==H} - -\vspace*{1cm} -\end{center} - -Fusing units such as \verb/\fivefusev/ -can be multiply nested in itself and in other types of fusing units. -The following example shows such a trebly-nested case. -\begin{verbatim} -\decaheterovi[AB% -{b\fivefusev[{a\sixfusev[ce% -{c\sixfusev{3==O}{4D==O;5SB==HO;5SA==Et}{F}}]{1==\null}{2D==O}{f}}]% -{2==N}{}{D}}]{1==N}{} -\end{verbatim} -\begin{quotation} -\decaheterovi[AB% -{b\fivefusev[{a\sixfusev[ce% -{c\sixfusev{3==O}{4D==O;5SB==HO;5SA==Et}{F}}]{1==\null}{2D==O}{f}}]% -{2==N}{}{D}}]{1==N}{} - -\vspace*{2cm} -\end{quotation} - -When all of the commands in the above code are -changed into the inverse counterparts -(\verb/\decaheterovi/ to \verb/\decaheterov/; -\verb/\fivefusev/ and \verb/\fivefusevi/; and -\verb/\sixfusev/ to \verb/\sixfusevi/), -the code is transformed into another code, -\begin{verbatim} -\decaheterov[AB% -{b\fivefusevi[{a\sixfusevi[ce% -{c\sixfusevi{3==O}{4D==O;5SB==HO;5SA==Et}{F}}]{1==\null}{2D==O}{f}}]% -{2==N}{}{D}}]{1==N}{} -\end{verbatim} -Thereby, we can obtain the formula of vertically inverse type. -\begin{quotation} -\vspace*{2cm} -\decaheterov[AB% -{b\fivefusevi[{a\sixfusevi[ce% -{c\sixfusevi{3==O}{4D==O;5SB==HO;5SA==Et}{F}}]{1==\null}{2D==O}{f}}]% -{2==N}{}{D}}]{1==N}{} -\end{quotation} - -\subsection{Horizontal Units of Normal and Inverse Types} -Horizontal five-membered building block are -obtained by using \verb/\fivefuseh/ and \verb/\fivefusehi/: -\begin{verbatim} -\fivefuseh[BONDLIST]{ATOMLIST}{SUBSLIST}{FUSE} -\fivefusehi[BONDLIST]{ATOMLIST}{SUBSLIST}{FUSE} -\end{verbatim} -where the argument FUSE is an alphabetical character (a--e) -or the uppercase counterpart (A--E), -each of which is a bond specifier representing one bond to be omitted. -The other specifications have the same formats -as found in the preceding section. - -The example given for \verb/\fivefusevi/ is -changed into the one using the horizontal counterpart \verb/\fivefusehi/: -\begin{verbatim} -\decalineh[h{c\fivefusehi{4==O}{1GA==H;5GB==H;2D==;3D==O}{E}}]{5A==;6D==O} -\end{verbatim} -\begin{center} -\vspace*{1cm} -\decalineh[h{c\fivefusehi{4==O}{1GA==H;5GB==H;2D==;3D==O}{E}}]{5A==;6D==O} -\end{center} -Note that no changes of other designation are necessary except that -\verb/\decalineh/ and \verb/\fivefusehi/ are used -in place of the vertical counterpart described above. - -The multiply nested example described above for drawing -a structure of vertical type can be changed into -the corresponding one of horizontal type, -if all of the commmands are changed into horizontal types -(\verb/\decaheterovi/ to \verb/\decaheterohi/; -\verb/\fivefusev/ to \verb/\fivefuseh/; and -\verb/\sixfusev/ to \verb/\sixfuseh/). - -\begin{verbatim} -\decaheterohi[AB% -{b\fivefuseh[{a\sixfuseh[ce% -{c\sixfuseh{3==O}{4D==O;5SB==OH;5SA==Et}{F}}]{1==\null}{2D==O}{f}}]% -{2==N}{}{D}}]{1==N}{} -\end{verbatim} -\begin{quotation} -\vspace*{2cm}\hspace*{4cm} -\decaheterohi[AB% -{b\fivefuseh[{a\sixfuseh[ce% -{c\sixfuseh{3==O}{4D==O;5SB==OH;5SA==Et}{F}}]{1==\null}{2D==O}{f}}]% -{2==N}{}{D}}]{1==N}{} -\end{quotation} - -When all the commands in the above code are -changed into the inverse counterparts -(\verb/\decaheterohi/ to \verb/\decaheteroh/; -\verb/\fivefuseh/ and \verb/\fivefusehi/; and -\verb/\sixfuseh/ to \verb/\sixfusehi/), -the code is transformed into another code, -\begin{verbatim} -\decaheteroh[AB% -{b\fivefusehi[{a\sixfusehi[ce% -{c\sixfusehi{3==O}{4D==O;5SB==HO;5SA==Et}{F}}]{1==\null}{2D==O}{f}}]% -{2==N}{}{D}}]{1==N}{} -\end{verbatim} -Thereby, we can obtain the formula of horizontally inverse type. -\begin{quotation} -\vspace*{2cm}\hspace*{4cm} -\decaheteroh[AB% -{b\fivefusehi[{a\sixfusehi[ce% -{c\sixfusehi{3==O}{4D==O;5SB==HO;5SA==Et}{F}}]{1==\null}{2D==O}{f}}]% -{2==N}{}{D}}]{1==N}{} -\end{quotation} - -\section{Four-membered Fusing Units} - -To obtain a four-membered building block, -we can use \verb/\fourfuse/: -\begin{verbatim} -\fourfuse[BONDLIST]{ATOMLIST}{SUBSLIST}{FUSE} -\end{verbatim} -where the argument FUSE is an alphabetical character (a--d) -or the uppercase counterpart (A--D), -each of which is a bond specifier representing one bond to be omitted. -The assignment of characters (a to d) and locants (1 to 4) -for the command \verb/\fourhetero/ is applied -in the same way to this case. -The other specifications have the same formats -as those of the command \verb/\fourhetero/. - -For example, the code, -\begin{verbatim} -\sixheterov[{e\fourfuse{}{}{b}}]{}{} -\sixheterov[{b\fourfuse{}{}{d}}]{}{} -\sixheteroh[{b\fourfuse{}{}{a}}]{}{} -\sixheteroh[{e\fourfuse{}{}{c}}]{}{} -\end{verbatim} -produces the following structural formulas. -\begin{center} -\sixheterov[{e\fourfuse{}{}{b}}]{}{} -\sixheterov[{b\fourfuse{}{}{d}}]{}{} -\sixheteroh[{b\fourfuse{}{}{a}}]{}{} -\sixheteroh[{e\fourfuse{}{}{c}}]{}{} -\end{center} - -A hetero atom at a fused position is designated in the ATOMLIST -of \verb/\fourfuse/, which is associated the code \verb/\null/ -in the ATOMLIST of a command for drawing a mother skeleton. -For example, the code -\begin{verbatim} -\sixheterov[{e\fourfuse{3==N}{}{b}}]{6==\null}{} -\sixheterov[{b\fourfuse{4==N}{}{d}}]{2==\null}{} -\sixheteroh[{b\fourfuse{2==N}{}{a}}]{3==\null}{} -\sixheteroh[{e\fourfuse{3==N}{}{c}}]{5==\null}{} -\end{verbatim} -produces the following structural formulas. -\begin{center} -\sixheterov[{e\fourfuse{3==N}{}{b}}]{6==\null}{} -\sixheterov[{b\fourfuse{4==N}{}{d}}]{2==\null}{} -\sixheteroh[{b\fourfuse{2==N}{}{a}}]{3==\null}{} -\sixheteroh[{e\fourfuse{3==N}{}{c}}]{5==\null}{} -\end{center} - -Penicillin G can be drawn by using the \verb/\fourfuse/ command -in the code, -\begin{verbatim} -\fiveheterovi[{d\fourfuse{2==\null}{1D==O;4Su==PhCH$_{2}$CONH;4Sd==H}{b}}]% -{1==S;4==N}{2Sa==CH$_{3}$;2Sb==CH$_{3}$;3SA==COOH;3SB==H;5GA==H} -\end{verbatim} -which typeset the following formula: -\begin{center} -\fiveheterovi[{d\fourfuse{2==\null}{1D==O;4Su==PhCH$_{2}$CONH;4Sd==H}{b}}]% -{1==S;4==N}{2Sa==CH$_{3}$;2Sb==CH$_{3}$;3SA==COOH;3SB==H;5GA==H} -\end{center} - -\section{Three-membered Fusing Units} -\subsection{Vertical Units of Normal and Inverse Types} -To obtain three-membered building blocks of -vertical type, we can use \verb/\threefusev/ and \verb/\threefusevi/: -\begin{verbatim} -\threefusev[BONDLIST]{ATOMLIST}{SUBSLIST}{FUSE} -\threefusevi[BONDLIST]{ATOMLIST}{SUBSLIST}{FUSE} -\end{verbatim} -where the argument FUSE is an alphabetical character (a--c) -or the uppercase counterpart (A--C), -each of which is a bond specifier representing one bond to be omitted. -The assignment of characters (a to c) and locants (1 to 3) -for the command \verb/\threeheterov/ or \verb/\threeheterovi/ is applied -in the same way to this case. -The other specifications have the same formats -as those of the command \verb/\threeheterov/ or \verb/\threeheterovi/. - -For example, the code using \verb/\threefusev/, -\begin{verbatim} -\sixheteroh[{a\threefusev{}{}{a}}]{}{} -\sixheteroh[{e\threefusev{}{}{b}}]{}{} -\sixheteroh[{c\threefusev{}{}{c}}]{}{} -\end{verbatim} -produces the following structural formulas. -\begin{center} -\sixheteroh[{a\threefusev{}{}{a}}]{}{} -\sixheteroh[{e\threefusev{}{}{b}}]{}{} -\sixheteroh[{c\threefusev{}{}{c}}]{}{} -\end{center} -The use of the inverse type is shown in the code, -\begin{verbatim} -\sixheteroh[{F\threefusevi{}{}{a}}]{}{} -\sixheteroh[{B\threefusevi{}{}{b}}]{}{} -\sixheteroh[{D\threefusevi{}{}{c}}]{}{} -\end{verbatim} -which produces the following structural formulas. -\begin{center} -\sixheteroh[{F\threefusevi{}{}{a}}]{}{} -\sixheteroh[{B\threefusevi{}{}{b}}]{}{} -\sixheteroh[{D\threefusevi{}{}{c}}]{}{} -\end{center} - -Hetero-atoms at fused positions can be typeset by designating -ATOMLISTs. For example, the code, -\begin{verbatim} -\sixheteroh[{a\threefusev{1==N}{}{a}}]{1==\null}{} -\sixheteroh[{e\threefusev{2==N}{}{b}}]{5==\null}{} -\sixheteroh[{c\threefusev{3==N}{}{c}}]{3==\null}{} -\end{verbatim} -produces the following structural formulas. -\begin{center} -\sixheteroh[{a\threefusev{1==N}{}{a}}]{1==\null}{} -\sixheteroh[{e\threefusev{2==N}{}{b}}]{5==\null}{} -\sixheteroh[{c\threefusev{3==N}{}{c}}]{3==\null}{} -\end{center} - -\subsection{Horizontal Units of Normal and Inverse Types} -Three-membered building blocks of -horizontal type can be obtained by using -\verb/\threefuseh/ and \verb/\threefusehi/: -\begin{verbatim} -\threefuseh[BONDLIST]{ATOMLIST}{SUBSLIST}{FUSE} -\threefusehi[BONDLIST]{ATOMLIST}{SUBSLIST}{FUSE} -\end{verbatim} -where the argument FUSE is an alphabetical character (a--c) -or the uppercase counterpart (A--C), -each of which is a bond specifier representing one bond to be omitted. -The assignment of characters (a to c) and locants (1 to 3) -for the command \verb/\threeheteroh/ or \verb/\threeheterohi/ is applied -in the same way to this case. -The other specifications have the same formats -as those of the command \verb/\threeheteroh/ or \verb/\threeheterohi/. - -For example, the code using \verb/\threefuseh/, -\begin{verbatim} -\sixheterov[{F\threefuseh{}{}{a}}]{}{} -\sixheterov[{B\threefuseh{}{}{b}}]{}{} -\sixheterov[{D\threefuseh{}{}{c}}]{}{} -\end{verbatim} -produces the following structural formulas. -\begin{center} -\sixheterov[{F\threefuseh{}{}{a}}]{}{} -\sixheterov[{B\threefuseh{}{}{b}}]{}{} -\sixheterov[{D\threefuseh{}{}{c}}]{}{} -\end{center} -The use of the inverse type is shown in the code, -\begin{verbatim} -\sixheterov[{a\threefusehi{}{}{a}}]{}{} -\sixheterov[{e\threefusehi{}{}{b}}]{}{} -\sixheterov[{c\threefusehi{}{}{c}}]{}{} -\end{verbatim} -which produces the following structural formulas. -\begin{center} -\sixheterov[{a\threefusehi{}{}{a}}]{}{} -\sixheterov[{e\threefusehi{}{}{b}}]{}{} -\sixheterov[{c\threefusehi{}{}{c}}]{}{} -\end{center} - -Hetero-atoms at fused positions can be typeset by designating -ATOMLISTs. For example, the code, -\begin{verbatim} -\sixheterov[{F\threefuseh{1==N}{}{a}}]{1==\null}{} -\sixheterov[{B\threefuseh{2==N}{}{b}}]{3==\null}{} -\sixheterov[{D\threefuseh{3==N}{}{c}}]{5==\null}{} -\end{verbatim} -produces the following structural formulas. -\begin{center} -\sixheterov[{F\threefuseh{1==N}{}{a}}]{1==\null}{} -\sixheterov[{B\threefuseh{2==N}{}{b}}]{3==\null}{} -\sixheterov[{D\threefuseh{3==N}{}{c}}]{5==\null}{} -\end{center} - -An aziridine derivative, -\begin{center} -\sixheterov[{B\threefuseh{1==N}{1==COOC$_{2}$H$_{5}$}{b}}]{}{} -\end{center} -can be drawn by the code, -\begin{verbatim} -\sixheterov[{B\threefuseh{1==N}{1==COOC$_{2}$H$_{5}$}{b}}]{}{} -\end{verbatim} - - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\chapter{Spiro Rings} -\section{General Conventions for Spiro-Ring Attachment} - -There are several ways for naming spiro compounds -in the light of the IUPAC nomenclature. -Rule A-41.4 allows us to use such a name as -spiro[cyclopentane-1,1$^{\prime}$-indene] -for representing the following structure: -\begin{center} -\vspace*{1cm} -\nonaheterovi[begj]{1s==\fiveheterov{}{1==(yl)}}{} -\end{center} -The same structure is named indene-1-spiro-1$^{\prime}$-cyclohexane -in terms of Rule A-42.1. -Spiro[5.5]undecane, the name due to Rule A-41.1 and A-41.2, -is alternatively referred to as -cyclohexanespirocyclohexane in terms of Rule A-42.1: -\begin{center} -\vspace*{1cm} -\sixheterov[]{1s==\sixheterov[]{}{4==(yl)}}{} -\end{center} -where the `cyclohexanespiro' shows the replacement of a -carbon atom in a cyclohexne by another cyclohexane ring. -These rules essentially have the same methodology as the -IUPAC replacement nomenclature, e.g., -oxacyclohexane (more formally, oxane or tetrahydropyran) -for the formula -\begin{center} -\sixheterov[]{1==O}{} -\end{center} -generated by the code, -\begin{verbatim} -\sixheterov[]{1==O}{} -\end{verbatim} -where the prefix `oxa' shows the replacement of a -carbon atom with an oxygen atom. -Obviously, the prefix `cyclohexanespiro' of the name -`cyclohexanespirocyclohexane' is akin to -the prefix `oxa' of the name `oxacyclohexane' or `oxane' -from the viewpoint of the construction of names. -Since the unit due to the latter prefix is designated by -the \verb/1==O/ involved in the ATOMLIST, -the former prefix can be treated in the same way. -Hence, spiro compounds are drawn as follows: -\begin{enumerate} -\item -\XyMTeX{} regards a spiro ring -as a unit for the IUPAC replacement nomenclature, -which is generated from an appropriate structure by ``yl''-function. -\item the code of the unit due to the ``yl''-function is added to -the ATOMLIST of a mother skeleton. -\end{enumerate} - -Spiro[5.5]undecane is regarded as `cyclohexana'-cyclohexane -(more formally, `cyclohexanespiro'-cyclo\-hexane), -as found in the code, -\begin{verbatim} -\sixheterov[]{1s==\sixheterov[]{}{4==(yl)}}{} -\end{verbatim} -where the code -\verb/\sixheterov[]{}{4==(yl)}/ produced by the ``yl''-function -corresponds to the suffix `cyclohexana' and -is written in the ATOMLIST of the outer \verb/sixheterov/ command. -Thereby, we can obtain -\begin{center} -\vspace*{1cm} -\sixheterov[]{1s==\sixheterov[]{}{4==(yl)}}{} -\end{center} - -Note that the atom modifier `s' in the code -\verb/1s==\sixheterov[]{}{4==(yl)}/ represents no -hetero-atom at the spiro position. -When a hetero-atom is present at the spiro position, -an atom modifier `h' is used in place of `s'. -For example, the code -\begin{verbatim} -\sixheterov[]{1h==\sixheterov[]{4==N}{4==(yl)}}{} -\end{verbatim} -typeset the following formula: -\begin{center} -\vspace*{1cm} -\sixheterov[]{1h==\sixheterov[]{4==N}{4==(yl)}}{} -\end{center} - -It should be noted that the absence of such atom -modifiers represents a usual replacement by -a hetero atom, as found in the formula of -oxane shown above or in the one of -thiacyclohexane (tetrahydrothiane): -\begin{center} -\sixheterov[]{1==S}{} -\end{center} -generated by the code, -\begin{verbatim} -\sixheterov[]{1==S}{} -\end{verbatim} - -\section{Several Examples} - -Spiro[cyclopentane-1,1$^{\prime}$-indene] described above -can be drawn in two ways: -\begin{center} -\vspace*{1cm} -\nonaheterovi[begj]{1s==\fiveheterov{}{1==(yl)}}{} -\fiveheterov{1s==\nonaheterovi[begj]{}{1==(yl)}}{} - -\vspace*{1cm} -\end{center} -where we use two different codes: -\begin{verbatim} -\nonaheterovi[begj]{1s==\fiveheterov{}{1==(yl)}}{} -\fiveheterov{1s==\nonaheterovi[begj]{}{1==(yl)}}{} -\end{verbatim} -which correspond to -`cyclohexane-1-spiro-1$^{\prime}$-indene' and -`indene-1-spiro-1$^{\prime}$-cyclohexane' (formal), -respectively. - -A spiro dienone -\begin{center} -\vspace*{1cm} -\sixheterov[be]{% -1s==\fiveheterov{4==N}{1==(yl);3SB==H;3SA==COOCH$_{2}$Ph;% -4==PhCH$_{2}$OCO;5D==O}}{4D==O} -\end{center} -can be drawn by writing a code, -\begin{verbatim} -\sixheterov[be]{% -1s==\fiveheterov{4==N}{1==(yl);3SB==H;3SA==COOCH$_{2}$Ph;% -4==PhCH$_{2}$OCO;5D==O}}{4D==O} -\end{verbatim} - -1-Azaspiro[5.5]undecene -which is the skeleton present in histrionicotoxin -(Tetrahedron Lett., 1981, {\bf 22}, 2247) -\begin{center} -\sixheterov[]{1==N;6s==\cyclohexanev[a]{3==(yl)}}{1==CH$_{2}$Ph} -\end{center} -can be drawn by the code, -\begin{verbatim} -\sixheterov[]{1==N;6s==\cyclohexanev[a]{3==(yl)}}{1==CH$_{2}$Ph} -\end{verbatim} - -The following example shows a case -to which both ring fusion and spiro attachment are applied. -The code, -\begin{verbatim} -\decaheterov[fhk% -{g\fivefusev{1==O;4==O}{}{b}}% -]{1s==\cyclohexanev[be]{1D==O;4==(yl)}}{} -\end{verbatim} -gives the following formula: -\begin{center} -\vspace*{2cm} -\decaheterov[fhk% -{g\fivefusev{1==O;4==O}{}{b}}% -]{1s==\cyclohexanev[be]{1D==O;4==(yl)}}{} -\end{center} - -A 1,3-dioxolane derivative -\begin{center} -\fiveheterov{2==O;5==O;% -1s==\trimethylenei{}{3==(yl);1W==PhSO$_{2}$;3W==R}}{}% -\end{center} -can be drawn by the code, -\begin{verbatim} -\fiveheterov{2==O;5==O;1s==\trimethylenei{}{3==(yl);1W==PhSO$_{2}$;3W==R}}{}% -\end{verbatim} -The same compound is also drawn by usual techniques -as follows: -\begin{verbatim} -\fiveheterov{2==O;5==O}{1Sb==\dimethylenei{}{2==(yl);1W==PhSO$_{2}$};1Sa==R} -\end{verbatim} -\begin{center} -\fiveheterov{2==O;5==O}{1Sb==\dimethylenei{}{2==(yl);1W==PhSO$_{2}$};1Sa==R} -\end{center} - -\begin{verbatim} -\fiveheterov{2==O;5==O}{1G==\dimethylenei{}{2==(yl);1W==PhSO$_{2}$};1F==R} -\end{verbatim} -\begin{center} -\fiveheterov{2==O;5==O}{1G==\dimethylenei{}{2==(yl);1W==PhSO$_{2}$};1F==R} -\end{center} - -1,2,3,4-Tetrahydroquinoline-4-spiro-4$^{\prime}$-piperidine, -\begin{quotation} -\vspace*{2cm} -\decaheterovi[fhk]{1==N;4s==\sixheterov[]{1==N}{4==(yl);1==H}}{1==H} -\end{quotation} -can be drawn by writing a code, -\begin{verbatim} -\decaheterovi[fhk]{1==N;4s==\sixheterov[]{1==N}{4==(yl);1==H}}{1==H} -\end{verbatim} - -3,3$^{\prime}$-Spirobi[3{\it H}-indole], -\begin{quotation} -\vspace*{1cm} -\nonaheterovi[begj]{3==N;% -1s==\fiveheterov[bd{b\sixfusev[ac]{}{}{e}}]{4==N}{1==(yl)}}{} -\end{quotation} -is typeset by the code, -\begin{verbatim} -\nonaheterovi[begj]{3==N;% -1s==\fiveheterov[bd{b\sixfusev[ac]{}{}{e}}]{4==N}{1==(yl)}}{} -\end{verbatim} - -The code, -\begin{verbatim} -\sixheterov[]{1s==\fiveheterov{2==O;5==O}{1==(yl)}}{% -5==\threeheteroh{1==O}{3Sb==Me$_{3}$Si;3==(yl)}} -\end{verbatim} -typesets the following structure: -\begin{center} -\vspace*{1cm} -\sixheterov[]{1s==\fiveheterov{2==O;5==O}{1==(yl)}}{% -5==\threeheteroh{1==O}{3Sb==Me$_{3}$Si;3==(yl)}} -\end{center} - -A spiro intermediate during spiro annelation -(T.\ S.\ T.\ Wang, {\em Tetrahedron Lett.}, 1975, 1637), -\begin{quotation} -\vspace*{1cm} -\nonaheterov[aA]{1==N;% -3s==\decaheterovb[B]{8==N}{5==(yl);8==\dimethylenei{}{1D==O;1==(yl)}}}{} -\end{quotation} -can be drawn by the code, -\begin{verbatim} -\nonaheterov[aA]{1==N;% -3s==\decaheterovb[B]{8==N}{5==(yl);8==\dimethylenei{}{1D==O;1==(yl)}}}{} -\end{verbatim} - -A lactone intermediate containing a protected ketone -(A. Grieco and M. Nishizawa, {\em Chem. Commun.}, 1976, 582), -\begin{center} -\decaheterov[h{c\fivefusevi{4==O}{1GA==H;5GB==H;2B==;3D==O}{E}}]{% -6s==\fiveheterovi{1==O;3==O}{2==(yl)}}{5A==;{10}B==;9A==H} - -\vspace*{1cm} -\end{center} -is drawn by the code, -\begin{verbatim} -\decaheterov[h{c\fivefusevi{4==O}{1GA==H;5GB==H;2B==;3D==O}{E}}]{% -6s==\fiveheterovi{1==O;3==O}{2==(yl)}}{5A==;{10}B==;9A==H} -\end{verbatim} - -\section{Multi-Spiro Derivatives} - -Multi-sipro derivatives are drawn by nesting spiro function. -For example, cyclohexanespirocyclopentane-3$^{\prime}$-% -spirocyclohexane (Rule A-42.4), -\begin{center} -\sixheteroh[]{4s==\fiveheterov{% -2s==\sixheteroh[]{}{1==(yl)}}{5==(yl)}}{} -\end{center} -is typeset by the code, -\begin{verbatim} -\sixheteroh[]{4s==\fiveheterov{% -2s==\sixheteroh[]{}{1==(yl)}}{5==(yl)}}{} -\end{verbatim} -When \verb/\fiveheterov/ is a mother skeleton, -such a nested command is unnecessary: -\begin{verbatim} -\fiveheterov{2s==\sixheteroh[]{}{1==(yl)};% -5s==\sixheteroh[]{}{4==(yl)}}{} -\end{verbatim} -\begin{center} -\fiveheterov{2s==\sixheteroh[]{}{1==(yl)};% -5s==\sixheteroh[]{}{4==(yl)}}{} -\end{center} - -The name (Rule A-42.4), -fluorene-9-spiro-1$^{\prime}$-cyclohexane-4$^{\prime}$-% -spiro-1$^{\prime}$-indene, corresponds to the code, -\begin{verbatim} -\nonaheterovi[begj{b\sixfusev[ac]{}{}{E}}]{% -1s==\sixheterov[]{1s==\nonaheterov[begj]{}{1==(yl)}}{4==(yl)}}{} -\end{verbatim} -which gives -\begin{quotation} -\vspace*{2cm} -\nonaheterovi[begj{b\sixfusev[ac]{}{}{E}}]{% -1s==\sixheterov[]{1s==\nonaheterov[begj]{}{1==(yl)}}{4==(yl)}}{} -\end{quotation} - - -\section{Atom Replacement} - -The ATOMLIST of each command is capable of -accommodating a group if a sufficient space is available. -For example, compare two codes, -\begin{verbatim} -\sixheteroh{4==NCOOEt}{} -\hskip 2cm -\sixheteroh{4==N}{4==COOEt} -\end{verbatim} -generating formulas equivalent chemically to each other: -\begin{center} -\sixheteroh{4==NCOOEt}{} -\hskip 2cm -\sixheteroh{4==N}{4==COOEt} -\end{center} -Note that the former example uses an ATOMLIST and -the latter uses an SUBSLIST for describing substituents. - -Even when no such space is available, the use of -a command, \verb/\upnobond/ or \verb/\downnobond/, -give a solution (see \XyMTeX book pages 259--260). -Compare the following formulas, -\begin{center} -\sixheterov{4==\downnobond{N}{COOEt}}{} -\sixheterov{4==N}{4==COOEt} -\sixheterov{1==\upnobond{N}{COOEt}}{} -\sixheterov{1==N}{1==COOEt} -\end{center} -generated by the code, -\begin{verbatim} -\sixheterov{4==\downnobond{N}{COOEt}}{} -\sixheterov{4==N}{4==COOEt} -\sixheterov{1==\upnobond{N}{COOEt}}{} -\sixheterov{1==N}{1==COOEt} -\end{verbatim} - -These examples show that a substituent (e.g. NCOOEt) can -be regarded as a component for atom replacement using a ATOMLIST. -This methodology can be applied to a case in which -such a substituent is generated by the ``yl''-function or -by such a linking command as \verb/\ryl/ or \verb/\lyl/. -The following example shows the use the \verb/\ryl/ command -in the ATOMLIST of \verb/\sixheteroh/. -\begin{verbatim} -\sixheteroh{4h==\ryl(4==NCOO){4==\bzdrh{1==(yl)}}}{} -\hskip2cm -\sixheterov{3h==\ryl(4==NCOO){4==\bzdrh{1==(yl)}}}{} -\hskip2cm -\sixheterov{4h==\ryl(0==N){8==\bzdrv{1==(yl)}}}{} -\end{verbatim} -\begin{center} -\sixheteroh{4h==\ryl(4==NCOO){4==\bzdrh{1==(yl)}}}{} -\hskip2cm -\sixheterov{3h==\ryl(4==NCOO){4==\bzdrh{1==(yl)}}}{} -\hskip2cm -\sixheterov{4h==\ryl(0==N){8==\bzdrv{1==(yl)}}}{} - -\vspace*{1cm} -\end{center} - -A bond bewtween a COO unit and a phenyl group is frequently -omitted. For this purpose, we use command \verb/\ayl/ -defined as -\begin{verbatim} -\makeatletter -\def\ayl{\@ifnextchar({\@ayl@}{\@ayl@(10,40)}} -\def\@ayl@(#1,#2)#3{% -\begingroup\yl@xdiff=0 \yl@ydiff=0% -\kern#1\unitlength\raise#2\unitlength\hbox to0pt{#3\hss}% -\endgroup} -\makeatother -\end{verbatim} -Thereby, we have the following examples. -\begin{verbatim} -\sixheteroh{4==NCOO\ayl{\bzdrh{1==(yl)}}}{} -\hskip2cm -\sixheterov{3==NCOO\ayl{\bzdrh{1==(yl)}}}{} -\hskip2cm -\sixheterov{4==\downnobond{N}{COO\ayl{\bzdrh{1==(yl)}}}}{} -\end{verbatim} -\begin{center} -\sixheteroh{4==NCOO\ayl{\bzdrh{1==(yl)}}}{} -\hskip2cm -\sixheterov{3==NCOO\ayl{\bzdrh{1==(yl)}}}{} -\hskip2cm -\sixheterov{4==\downnobond{N}{COO\ayl{\bzdrh{1==(yl)}}}}{} -\end{center} - -\begin{verbatim} -\tetramethylene[a]{3==\downnobond{N}{COO\ayl{\bzdrh{1==(yl)}}}}{} -\hskip2cm -\tetramethylene[a]{3==N}{3==COO\ayl{\bzdrh{1==(yl)}}} -\end{verbatim} -\begin{center} -\tetramethylene[a]{3==\downnobond{N}{COO\ayl{\bzdrh{1==(yl)}}}}{} -\hskip2cm -\tetramethylene[a]{3==N}{3==COO\ayl{\bzdrh{1==(yl)}}} -\end{center} - - -\endinput - - -\begin{verbatim} -\end{verbatim} -\begin{center} -\end{center} - - -\begin{verbatim} -\end{verbatim} -\begin{quotation} -\end{quotation} - -
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