From 0a17be9af1c1cd8e5452befa92ff920a401c47fb Mon Sep 17 00:00:00 2001 From: Karl Berry Date: Tue, 2 Jan 2007 22:42:25 +0000 Subject: remove xymtex (again), it is nonfree git-svn-id: svn://tug.org/texlive/trunk@3102 c570f23f-e606-0410-a88d-b1316a301751 --- Master/texmf-dist/doc/latex/xymtex/readme2.doc | 22 - Master/texmf-dist/doc/latex/xymtex/readme2.jpn | 66 - Master/texmf-dist/doc/latex/xymtex/xymadd.tex | 2792 ---------------------- Master/texmf-dist/doc/latex/xymtex/xymman.sty | 63 - Master/texmf-dist/doc/latex/xymtex/xymtex2.doc | 94 - Master/texmf-dist/doc/latex/xymtex/xymtx200.dvi | Bin 412660 -> 0 bytes Master/texmf-dist/doc/latex/xymtex/xymtx200.tex | 56 - Master/texmf-dist/doc/latex/xymtex/xymyl.tex | 2900 ----------------------- 8 files changed, 5993 deletions(-) delete mode 100644 Master/texmf-dist/doc/latex/xymtex/readme2.doc delete mode 100644 Master/texmf-dist/doc/latex/xymtex/readme2.jpn delete mode 100644 Master/texmf-dist/doc/latex/xymtex/xymadd.tex delete mode 100644 Master/texmf-dist/doc/latex/xymtex/xymman.sty delete mode 100644 Master/texmf-dist/doc/latex/xymtex/xymtex2.doc delete mode 100644 Master/texmf-dist/doc/latex/xymtex/xymtx200.dvi delete mode 100644 Master/texmf-dist/doc/latex/xymtex/xymtx200.tex delete mode 100644 Master/texmf-dist/doc/latex/xymtex/xymyl.tex (limited to 'Master/texmf-dist/doc/latex') diff --git a/Master/texmf-dist/doc/latex/xymtex/readme2.doc b/Master/texmf-dist/doc/latex/xymtex/readme2.doc deleted file mode 100644 index 90355a56c29..00000000000 --- a/Master/texmf-dist/doc/latex/xymtex/readme2.doc +++ /dev/null @@ -1,22 +0,0 @@ -readme2.doc -Notes for XyMTeX -Copyright (C) 1993, 1996, 1998 by Shinsaku Fujita, All rights reserved. -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -(old) readme1.doc -Notes for XyMTeX -Copyright (C) 1993, 1996 by Shinsaku Fujita, All rights reserved. -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% - -Name: XyMTeX -Description: Macro Package including LaTeX document-style options for - typesetting chemical structural formulas -Keywords: LaTeX, chemistry, structural formula -Author: Shinsaku Fujita -Supported: http://www.chem.kit.ac.jp/fujita/fujitas/fujita.html -Latest Version: 2.00 -Archives: http://www.chem.kit.ac.jp/fujita/fujitas/fujita.html -Note: Documentation in xymtx200.tex (xymtx200.dvi) - -For Installment, see xymtex2.doc (xymtex2.jpn) - - \ No newline at end of file diff --git a/Master/texmf-dist/doc/latex/xymtex/readme2.jpn b/Master/texmf-dist/doc/latex/xymtex/readme2.jpn deleted file mode 100644 index 4144fe7a1b4..00000000000 --- a/Master/texmf-dist/doc/latex/xymtex/readme2.jpn +++ /dev/null @@ -1,66 +0,0 @@ -readme2.jpn -Notes for XyMTeX (in Japanese) -Copyright (C) 1993, 1996, 1998 by Shinsaku Fujita. All rights reserved. -=========================================================================== -(旧)readme1.jpn -Notes for XyMTeX (in Japanese) -Copyright (C) 1993, 1996 by Shinsaku Fujita. All rights reserved. -=========================================================================== -名 称: XyMTeX -登録名: xymtex2.lzh for drawing chem. structures -概 要: 化学構造式を描くためのマクロパッケージ -    (LaTeX用のオプションファイル類を含む) -鍵 語: LaTeX, 化学, 構造式 -作 者: Shinsaku Fujita (藤田 眞作) -登録者: 藤田 眞作 -最新版: 2.00 -本 籍: http://www.chem.kit.ac.jp/fujita/fujitas/fujita.html -覚 書: ドキュメントは、xymtx200.tex (xymtx200.dvi) -=========================================================================== -Name: XyMTeX -Description: Macro Package including LaTeX document-style options for - typesetting chemical structural formulas -Keywords: LaTeX, chemistry, structural formula -Author: Shinsaku Fujita -Supported: http://www.chem.kit.ac.jp/fujita/fujitas/fujita.html -Latest Version: 2.00 -Archives: http://www.chem.kit.ac.jp/fujita/fujitas/fujita.html -Note: Documentation in xymtx200.tex (xymtx200.dvi) -=========================================================================== - -<説明> - XyMTeXは、化学構造式を描くためののマクロパッケージです。 これは、 -LaTeX2e用のパッケージファイル群から成り立っています。各ファイルには -化学構造式を描くためのコマンドのマクロコードが含まれています。各コマンドは、 -広範囲の化合物の構造が描けるように、新しい構想のもとに作成したものです。 -LaTeXのpicture環境を前提にして、その範囲内 (図形組版)で構造式が描けるように -なっています。したがって、構造式出力のプリンターは (プリンタードライバーさえ -あれば) 種類を選ばず、たとえば写植機でも出力が可能です。 - - 約100ページのマニュアル (xymtx200.dvi) が付属しています。この中に、Version -2.00で追加した機能とコマンドの書式 (仕様) と描画例を多数記載しましたので、 -解凍後、まずどのようなことができるのかをご覧ください。 - - chemist.styやmathchem.sty (下記拙著に付録として付いているフロッピーディスク -に収録)に含まれるコマンドを併用すれば、さらにいろいろな反応スキームなどを -描くことができるようになります。XyMTeX(version1.01)から、chemist.styも同梱 -してあります。 - -  「化学者・生化学者のためのLaTeX---パソコンによる論文作成の手引」 -   藤田 眞作 著、東京化学同人 (1993) FD付 - -基本的な使用法は、XyMTeX verion 2.00でも以前のバージョンでも同じです。 -このため、付属のマニュアル (xymtx200.dvi)では、基本的な使用法を記載 -してありません。これらは、次のレファレンスマニュアルを参照してください。 - - 「XyMTeX--Typesetting Chemical Structural Formulas」 - 藤田眞作著、アジソン・ウェスレイ・ジャパン (1997) CD-DOM付 - -<ダウンロード・解凍> -(1) ファイル名xymtex2.lzhでダウンロードしてください -(2) TeXのメインディレクトリー内でlhaで解凍してください。 -   a:\tex>lha x b:\xymtex2 - -詳しいインストールの方法は、xymtex2.docをご覧下さい。 - - \ No newline at end of file diff --git a/Master/texmf-dist/doc/latex/xymtex/xymadd.tex b/Master/texmf-dist/doc/latex/xymtex/xymadd.tex deleted file mode 100644 index 10cfa37c649..00000000000 --- a/Master/texmf-dist/doc/latex/xymtex/xymadd.tex +++ /dev/null @@ -1,2792 +0,0 @@ -%xymadd.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{Added Commands} - -\section{Six-six Fused Carbocycles} -\subsection{Vertical-Bottom Forms of Decaline Derivatives} - -The macro \verb/\decalinevb/ is used to draw -decaline derivatives of vertical-bottom -type (added to \textsf{carom.sty}), -where the numbering of atoms is given from the bottom -to the left-upper part. -The word ``vertical'' means that each benzene ring is a vertical type. -The word ``bottom'' means that the benzene ring with young -locant numbers is located at the bottom. -The format of this command is as follows: -\begin{verbatim} - \decalinevb[BONDLIST]{SUBSLIST} -\end{verbatim} -% -% *************************** -% * decaline derivatives * -% * (vertical bottom type) * -% *************************** -% The following numbering is adopted in this macro. -% -% 7 -% * -% 6 * * 8 -% | | -% | | 0G (4a) -% 5 * * * -% 0F(4a) * * 1 -% | | -% | | -% 4 * * 2 -% * -% 3 -% ^ -% | -% the original point -% - -Locant numbers for designating substitution positions -and characters for showing bonds to be doubled -are represented by the following diagram: -{\origpttrue -\begin{center} -\begin{picture}(1000,1200)(0,0) -\put(0,0){\decalinevb{% -1Sb==1Sb(r);1Sa==1Sa(r);2Sb==2Sb(r);2Sa==2Sa(r);% -3Sb==3Sb(l);3Sa==3Sa(r);4Sb==4Sb(l);4Sa==4Sa(l);% -5Sb==5Sb(l);5Sa==5Sa(l);6Sb==6Sb(l);6Sa==6Sa(l);% -7Sb==7Sb(l);7Sa==7Sa(r);8Sb==8Sb(r);8Sa==8Sb(r);% -0F==0F;0G==0G}} -{\footnotesize -\put(171,0){\bdloocant{j}{a}{b}{c}{d}{k}} -\put(0,303){\bdloocant{h}{i}{}{e}{f}{g}}} -\end{picture} -\qquad\qquad\fbox{\parbox{2cm}{$\circ$: (550,\the\shifti) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{center} -} -The handedness for each oriented or double-sided position -is shown with a character set in parentheses. -The option argument BONDLIST is based on the -assignment of characters (a--k) to respective bonds -as shown in the above diagram. -A bond modifier in the argument SUBSLIST for $n=1\mbox{--}8$ can be -one of bond modifiers shown in Table \ref{tt:200a}. -The substitution at the bridgehead positions is -designated as shown in Table 4.3 of \XyMTeX book. - -\medskip -\noindent -Example: -\begin{verbatim} -\decalinevb{1D==O;0FB==H;0GA==H} \qquad -\decalinevb{1B==CH$_{2}$OSiR$_{3}$;3D==O;4A==CH$_{3}$OCO;% -0FB==CH$_{3}$;0GA==H} -\end{verbatim} -These commands produce: -\begin{center} -\decalinevb{1D==O;0FB==H;0GA==H} \qquad -\decalinevb{1B==CH$_{2}$OSiR$_{3}$;3D==O;4A==CH$_{3}$OCO;% -0FB==CH$_{3}$;0GA==H} -\end{center} - -The related commands, \verb/\naphdrvb/ and \verb/\tetralinevb/, -have been defined on the basis of the command \verb/\decalinevb/. - -\subsection{Vertical-Top Forms of Decaline Derivatives} - -The macro \verb/\decalinevt/ (added to \textsf{carom.sty}) -is used for drawing decaline derivatives -of vertical-bottom type (numbering from the top to the left-down part). -The word ``vertical'' means that each benzene ring is a vertical type. -The word ``top'' means that the benzene ring with young locant -numbers is located at the top. -% ************************ -% * decaline derivatives * -% * (vertical-top type) * -% ************************ -% The following numbering is adopted in this macro. -% -% 2 -% * -% 1 * * 3 -% | | -% | | -% 0G (8a) * * 4 -% 8 * * 0F(4a) -% | | -% | | -% 7 * * 5 -% * -% 6 -% ^ -% | -% the original point -% -The format of this command is as follows: -\begin{verbatim} - \decalinevt[BONDLIST]{SUBSLIST} -\end{verbatim} - -Locant numbers for designating substitution positions -and characters for showing bonds to be doubled -are represented by the following diagram: -{\origpttrue -\begin{center} -\begin{picture}(1000,1200)(0,0) -\put(0,0){\decalinevt{% -1Sb==1Sb(l);1Sa==1Sa(l);2Sb==2Sb(l);2Sa==2Sa(r);% -3Sb==3Sb(r);3Sa==3Sa(r);4Sb==4Sb(r);4Sa==4Sa(r);% -5Sb==5Sb(r);5Sa==5Sa(r);6Sb==6Sb(l);6Sa==6Sa(r);% -7Sb==7Sb(l);7Sa==7Sa(l);8Sb==8Sb(l);8Sa==8Sb(l);% -0F==0F;0G==0G}} -{\footnotesize -\put(171,303){\bdloocant{b}{c}{d}{k}{j}{a}} -\put(0,0){\bdloocant{}{e}{f}{g}{h}{i}}} -\end{picture} -\qquad\qquad\fbox{\parbox{2cm}{$\circ$: (400,\the\shifti) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{center} -} - -The handedness for each oriented or double-sided position -is shown with a character set in parentheses. -The option argument BONDLIST is based on the -assignment of characters (a--k) to respective bonds -as shown in the above diagram. -A bond modifier in the argument SUBSLIST for $n=1\mbox{--}8$ can be -one of bond modifiers shown in Table \ref{tt:200a}. -The substitution at the bridgehead positions is -designated as shown in Table 4.3 of \XyMTeX book. - -\medskip -\noindent -Example: -\begin{verbatim} -\decalinevt{1D==O;0FB==H;0GA==H} \qquad -\decalinevt{1B==R$_{3}$SiOCH$_{2}$;3D==O;4A==COOHCH$_{3}$;% -0FB==CH$_{3}$;0GA==H} -\end{verbatim} -These commands produce: -\begin{center} -\decalinevt{1D==O;0FB==H;0GA==H} \qquad -\decalinevt{1B==R$_{3}$SiOCH$_{2}$;3D==O;4A==COOHCH$_{3}$;% -0FB==CH$_{3}$;0GA==H} -\end{center} - -The related commands, \verb/\naphdrvt/ and \verb/\tetralinevt/, -have been defined on the basis of the command \verb/\decalinevt/. - - -\section{Six-six Fused Heterocycles} -\subsection{Vertical-Bottom Forms} - -The macro \verb/\decaheterovb/ is generally used to draw -six-six-fused heterocycles of vertical-bottom type (\textsf{hetarom.sty}). -\begin{verbatim} - \decaheterovb[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -% *************************** -% * decahetro derivatives * -% * (vertical bottom type) * -% *************************** -% The following numbering is adopted in this macro. -% -% 7 -% * -% 6 * * 8 -% | | -% | | 0G (4a) -% 5 * * * -% 0F(4a) * * 1 -% | | -% | | -% 4 * * 2 -% * -% 3 -% ^ -% | -% the original point - - -Locant numbers for designating substitution positions -as well as characters for setting double bonds -are shown in the following diagram: -{ -\begin{xymspec} -\begin{picture}(1000,1200)(0,0) -\put(0,0){\decaheterovb[]{1==1;2==2;3==3;4==4;5==5;% -6==6;7==7;8==8;9==9;{{10}}==10}{% -1Sb==1Sb(r);1Sa==1Sa(r);2Sb==2Sb(r);2Sa==2Sa(r);% -3Sb==3Sb(l);3Sa==3Sa(r);4Sb==4Sb(l);4Sa==4Sa(l);% -5Sb==5Sb(l);5Sa==5Sa(l);6Sb==6Sb(l);6Sa==6Sa(l);% -7Sb==7Sb(l);7Sa==7Sa(r);8Sb==8Sb(r);8Sa==8Sa(r);% -9==9;{{10}}==10}} -{\footnotesize -\put(171,0){\bdloocant{j}{a}{b}{c}{d}{k}} -\put(0,303){\bdloocant{h}{i}{}{e}{f}{g}}} -%\put(0,0){\bdloocant{i}{k}{e}{f}{g}{h}} -%\put(342,0){\bdloocant{a}{b}{c}{d}{}{j}}} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (550,\the\shifti) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{xymspec} -} -The handedness for each oriented or double-sided position -is shown with a character set in parentheses. -The optional argument BONDLIST is used to specify a bond pattern. - -The argument ATOMLIST has a similar format concerning the positions of -$n$ = 1 to 8. A hetero-atom on the 4a-position is -designated to be 4a==N or 9==N; -and a hetero-atom on the 8a-position is given as to be -8a==N or \{\{10\}\}==N. - -The argument SUBSLIST for this macro takes a general format, -in which the modifiers listed in Table \ref{tt:200a} are used. -Note that 9 and 10 should be used for designating -4a and 8a positions. - -\medskip -\noindent -Example: -\begin{verbatim} -\decaheterovb[]{7==O}{6D==O;9A==H;{{10}A}==CH=CH$_{2}$} -\decaheterovb[]{5==O}{9==HO;{{10}}==OH} -\decaheterovb[ch]{1==O}{9A==HOCH$_{2}$;{{10}A}==H;% -4==CH$_{3}$;7==CH$_{3}$} -\end{verbatim} -produce the following structures: -\begin{center} -\decaheterovb[]{7==O}{6D==O;9A==H;{{10}A}==CH=CH$_{2}$} -\decaheterovb[]{5==O}{9==HO;{{10}}==OH} -\decaheterovb[ch]{1==O}{9A==HOCH$_{2}$;{{10}A}==H;% -4==CH$_{3}$;7==CH$_{3}$} -\end{center} - -Macros for drawing related fused heterocycles are also defined. -The formats of these commands are as follows: -\begin{verbatim} - \quinolinevb[BONDLIST]{SUBSLIST} - \isoquinolinevb[BONDLIST]{SUBSLIST} - \quinoxalinevb[BONDLIST]{SUBSLIST} - \quinazolinevb[BONDLIST]{SUBSLIST} - \cinnolinevb[BONDLIST]{SUBSLIST} - \pteridinevb[BONDLIST]{SUBSLIST} -\end{verbatim} - -\subsection{Vertical-Top Forms} -The macro \verb/\decaheterovt/ is generally used to draw -six-six-fused heterocycles of vertical-top type (\textsf{hetarom.sty}). -\begin{verbatim} - \decaheterovt[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -% **************************** -% * decaheterovt derivatives * -% * (vertical-top type) * -% **************************** -% The following numbering is adopted in this macro. -% -% 2 -% * -% 1 * * 3 -% | | -% | | -% 0G (8a) * * 4 -% 8 * * 0F(4a) -% | | -% | | -% 7 * * 5 -% * -% 6 -% ^ -% | -% the original point -% \end{verbatim} - -Locant numbers for designating substitution positions -as well as characters for setting double bonds -are shown in the following diagram: -{ -\begin{xymspec} -\begin{picture}(1000,1200)(0,0) -\put(0,0){\decaheterovt[]{1==1;2==2;3==3;4==4;5==5;% -6==6;7==7;8==8;9==9;{{10}}==10}{% -1Sb==1Sb(l);1Sa==1Sa(l);2Sb==2Sb(l);2Sa==2Sa(r);% -3Sb==3Sb(r);3Sa==3Sa(r);4Sb==4Sb(r);4Sa==4Sa(r);% -5Sb==5Sb(r);5Sa==5Sa(r);6Sb==6Sb(l);6Sa==6Sa(r);% -7Sb==7Sb(l);7Sa==7Sa(l);8Sb==8Sb(l);8Sa==8Sa(l);% -9==9;{{10}}==10}} -{\footnotesize -\put(171,303){\bdloocant{b}{c}{d}{k}{j}{a}} -\put(0,0){\bdloocant{}{e}{f}{g}{h}{i}}} -%\put(171,0){\bdloocant{j}{a}{b}{c}{d}{k}} -%\put(0,303){\bdloocant{h}{i}{}{e}{f}{g}}} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (400,\the\shifti) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{xymspec} -} -The handedness for each oriented or double-sided position -is shown with a character set in parentheses. -The optional argument BONDLIST is used to specify a bond pattern. - -The argument ATOMLIST has a similar format concerning the positions of -$n$ = 1 to 8. A hetero-atom on the 4a-position is -designated to be 4a==N or 9==N; -and a hetero-atom on the 8a-position is given as to be -8a==N or \{\{10\}\}==N. - -The argument SUBSLIST for this macro takes a general format, -in which the modifiers listed in Table \ref{tt:200a} are used. -Note that 9 and 10 should be used for designating -4a and 8a positions. - -\medskip -\noindent -Example: -\begin{verbatim} -\decaheterovt[]{7==O}{6D==O;9A==H;{{10}A}==CH$_{2}$=CH} -\decaheterovt[]{5==O}{9==OH;{{10}}==HO} -\decaheterovt[ch]{1==O}{9A==CH$_{2}$OH;{{10}A}==H;% -4==CH$_{3}$;7==CH$_{3}$} -\end{verbatim} -produce the following structures: -\begin{center} -\vspace*{1cm} -\decaheterovt[]{7==O}{6D==O;9A==H;{{10}A}==CH$_{2}$=CH} -\decaheterovt[]{5==O}{9==OH;{{10}}==HO} -\decaheterovt[ch]{1==O}{9A==CH$_{2}$OH;{{10}A}==H;% -4==CH$_{3}$;7==CH$_{3}$} -\end{center} - -Macros for drawing related fused heterocycles are also defined. -The formats of these commands are as follows: -\begin{verbatim} - \quinolinevt[BONDLIST]{SUBSLIST} - \isoquinolinevt[BONDLIST]{SUBSLIST} - \quinoxalinevt[BONDLIST]{SUBSLIST} - \quinazolinevt[BONDLIST]{SUBSLIST} - \cinnolinevt[BONDLIST]{SUBSLIST} - \pteridinevt[BONDLIST]{SUBSLIST} -\end{verbatim} - -\section{Three-Membered Carbocycles} - -The macro \verb/\cyclopropanev/ (the same command -as \verb/\cyclopropane/) -for drawing three-membered carbocycles -has the following format (\textsf{lowcycle.sty}) -\begin{verbatim} - \cyclopropanev[BONDLIST]{SUBSLIST} -\end{verbatim} -% **************************** -% * cyclopropane derivatives * -% * (vertical type) * -% **************************** -% The following numbering is adopted in this macro. -% -% b -% 3--------2 -% c ` / a -% `1/ <===== the original point -% -% -% -The locant numbering (1--3) -and the bond description (a--c) are common as -shown in the following diagram: -\begin{xymspec} -\begin{picture}(1000,600)(0,0) -\put(0,0){\cyclopropanev[]{% -1Sb==1Sb(l);1Sa==1Sa(r);2Sb==2Sb(r);2Sa==2Sa(r);% -3Sb==3Sb(l);3Sa==3Sa(l)}} -\put(0,0){\circle{80}} -\put(400,240){\circle{80}} -\put(500,250){a} -\put(300,250){c} -\put(380,460){b} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (\the\shiftii,\the\shifti) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{xymspec} - -For the arguments, BONDLIST and SUBSLIST, see \XyMTeX book. - -\medskip -\noindent -Example: -\begin{verbatim} - \cyclopropanev{2Sa==COOCH$_{3}$;2Sb==COOCH$_{3}$}\qquad - \cyclopropanev{2Sa==COOH;2Sb==COOH}\qquad\qquad - \cyclopropanev{3Sa==H$_{3}$C;3Sb==H$_{3}$C} -\end{verbatim} -produce the following structures: -\begin{center} - \cyclopropanev{2Sa==COOCH$_{3}$;2Sb==COOCH$_{3}$}\qquad - \cyclopropanev{2Sa==COOH;2Sb==COOH}\qquad\qquad - \cyclopropanev{3Sa==H$_{3}$C;3Sb==H$_{3}$C} -\end{center} - -The macro \verb/\cyclopropanevi/ -(the same command as \verb/\cyclopropanei/) -for drawing three-membered carbocycles of inverse type -has the following format (\textsf{lowcycle.sty}) -\begin{verbatim} - \cyclopropanevi[BONDLIST]{SUBSLIST} -\end{verbatim} -% **************************** -% * cyclopropane derivatives * -% * (inverse vertical type) * -% **************************** -% The following numbering is adopted in this macro. -% -% /1` <===== the original point -% c / ` a -% 3--------2 -% b -% -% \cyclopropanei[BONDLIST]{SUBSLIST} -% \cyclopropanevi[BONDLIST]{SUBSLIST} - -The following diagram shows -The locant numbering (1--3) -and the bond description (a--c): -\begin{xymspec} -\begin{picture}(1000,600)(0,0) -\put(0,0){\cyclopropanevi[]{% -1Sb==1Sb(l);1Sa==1Sa(r);2Sb==2Sb(r);2Sa==2Sa(r);% -3Sb==3Sb(l);3Sa==3Sa(l)}} -\put(0,0){\circle{80}} -\put(400,340){\circle{80}} -\put(500,250){a} -\put(250,250){c} -\put(380,50){b} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (\the\shiftii,340) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{xymspec} - -For the arguments, BONDLIST and SUBSLIST, see the counterparts -of \verb/\cyclopropane/ described in \XyMTeX book. - -\medskip -\noindent -Example: -\begin{verbatim} - \cyclopropanevi{2Sa==COOCH$_{3}$;2Sb==COOCH$_{3}$}\qquad - \cyclopropanevi{2Sa==COOH;2Sb==COOH}\qquad\qquad - \cyclopropanevi{3Sa==H$_{3}$C;3Sb==H$_{3}$C} -\end{verbatim} -produce the following structures: -\begin{center} - \cyclopropanevi{2Sa==COOCH$_{3}$;2Sb==COOCH$_{3}$}\qquad - \cyclopropanevi{2Sa==COOH;2Sb==COOH}\qquad\qquad - \cyclopropanevi{3Sa==H$_{3}$C;3Sb==H$_{3}$C} -\end{center} - -The macro \verb/\cyclopropaneh/ -for drawing three-membered carbocycles of horizontal type -has the following format (\textsf{lowcycle.sty}) -\begin{verbatim} - \cyclopropaneh[BONDLIST]{SUBSLIST} -\end{verbatim} -% **************************** -% * cyclopropane derivatives * -% * (horizontal type) * -% **************************** -% -% aaa fff -% 3 -% | ` c -% b | 1 bbb ccc -% | / a -% 2/ -% ddd eee -% - -The locant numbering (1--3) -and the bond description (a--c) are common as -shown in the following diagram: -\begin{xymspec} -\begin{picture}(600,1000)(0,0) -\put(0,0){\cyclopropaneh[]{% -1Sb==1Sb(r);1Sa==1Sa(r);2Sb==2Sb(l);2Sa==2Sa(r);% -3Sb==3Sb(l);3Sa==3Sa(r)}} -\put(0,0){\circle{80}} -\put(200,240){\circle{80}} -\put(300,150){a} -\put(100,320){b} -\put(300,450){c} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (200,240) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{xymspec} - -For the arguments, BONDLIST and SUBSLIST, see \XyMTeX book. - -\medskip -\noindent -Example: -\begin{verbatim} - \cyclopropaneh{2Sa==COOCH$_{3}$;2Sb==CH$_{3}$OCO}\qquad - \cyclopropaneh{2Sa==COOH;2Sb==HOCO}\qquad\qquad - \cyclopropaneh{3Sa==CH$_{3}$;3Sb==CH$_{3}$} -\end{verbatim} -produce the following structures: -\begin{center} - \cyclopropaneh{2Sa==COOCH$_{3}$;2Sb==CH$_{3}$OCO}\qquad - \cyclopropaneh{2Sa==COOH;2Sb==HOCO}\qquad\qquad - \cyclopropaneh{3Sa==CH$_{3}$;3Sb==CH$_{3}$} -\end{center} - -The macro \verb/\cyclopropanehi/ -for drawing three-membered carbocycles of inverse horizontal type -has the following format (\textsf{lowcycle.sty}) -\begin{verbatim} - \cyclopropanehi[BONDLIST]{SUBSLIST} -\end{verbatim} -% **************************** -% * cyclopropane derivatives * -% * (inverse horizontal type)* -% **************************** -% -% aaa bbb -% c 3 -% / | -% eee 1 | b -% fff a` | -% 2 <---original point -% ccc ddd - -The locant numbering (1--3) -and the bond description (a--c) are common as -shown in the following diagram: -\begin{xymspec} -\begin{picture}(600,1000)(0,0) -\put(0,0){\cyclopropanehi[]{% -1Sb==1Sb(l);1Sa==1Sa(l);2Sb==2Sb(r);2Sa==2Sa(r);% -3Sb==3Sb(r);3Sa==3Sa(r)}} -\put(0,0){\circle{80}} -\put(400,240){\circle{80}} -\put(300,150){a} -\put(450,320){b} -\put(300,450){c} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (400,240) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{xymspec} - -For the arguments, BONDLIST and SUBSLIST, see \XyMTeX book. - -\medskip -\noindent -Example: -\begin{verbatim} - \cyclopropanehi{2Sa==COOCH$_{3}$;2Sb==COOCH$_{3}$}\qquad - \cyclopropanehi{2Sa==COOH;2Sb==COOH}\qquad\qquad - \cyclopropanehi{3Sa==CH$_{3}$;3Sb==CH$_{3}$} -\end{verbatim} -produce the following structures: -\begin{center} - \cyclopropanehi{2Sa==COOCH$_{3}$;2Sb==COOCH$_{3}$}\qquad - \cyclopropanehi{2Sa==COOH;2Sb==COOH}\qquad\qquad - \cyclopropanehi{3Sa==CH$_{3}$;3Sb==CH$_{3}$} -\end{center} - -\section{Three-Membered Heterocycles} - -The macro \verb/\threeheterov/ -(the same command as \verb/\threehetero/) -for drawing three-membered heterocycles -has the following format (\textsf{hetarom.sty}) -\begin{verbatim} - \threeheterov[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -% **************************** -% * threeheterov derivatives * -% * (vertical type) * -% **************************** -% The following numbering is adopted in this macro. -% -% b -% 3--------2 -% c ` / a -% `1/ <===== the original point -% -% -% -The locant numbering (1--3) -and the bond description (a--c) are common as -shown in the following diagram: -\begin{xymspec} -\begin{picture}(1000,600)(0,0) -\put(0,0){\threeheterov[]{1==1;2==2;3==3}{% -1Sb==1Sb(l);1Sa==1Sa(r);2Sb==2Sb(r);2Sa==2Sa(r);% -3Sb==3Sb(l);3Sa==3Sa(l)}} -\put(0,0){\circle{80}} -\put(400,240){\circle{80}} -\put(500,250){a} -\put(300,250){c} -\put(380,460){b} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (\the\shiftii,\the\shifti) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{xymspec} - -For the arguments, BONDLIST and SUBSLIST, see \XyMTeX book. - -\medskip -\noindent -Example: -\begin{verbatim} - \threeheterov{1==O}{2Sa==COOCH$_{3}$;2Sb==COOCH$_{3}$}\qquad - \threeheterov{1==O}{2Sa==COOH;2Sb==COOH}\qquad\qquad - \threeheterov{2==O}{3Sa==H$_{3}$C;3Sb==H$_{3}$C} -\end{verbatim} -produce the following structures: -\begin{center} - \threeheterov{1==O}{2Sa==COOCH$_{3}$;2Sb==COOCH$_{3}$}\qquad - \threeheterov{1==O}{2Sa==COOH;2Sb==COOH}\qquad\qquad - \threeheterov{2==O}{3Sa==H$_{3}$C;3Sb==H$_{3}$C} -\end{center} - -The macro \verb/\threeheterovi/ -(the same command as \verb/\threeheteroi/) -for drawing three-membered heterocycles of inverse type -has the following format (\textsf{hetarom.sty}) -\begin{verbatim} - \threeheterovi[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -% **************************** -% * threehetero derivatives * -% * (inverse vertical type) * -% **************************** -% The following numbering is adopted in this macro. -% -% /1` <===== the original point -% c / ` a -% 3--------2 -% b -% -% \threeheteroi[BONDLIST]{ATOMLIST}{SUBSLIST} -% \threeheterovi[BONDLIST]{ATOMLIST}{SUBSLIST} - -The following diagram shows -The locant numbering (1--3) -and the bond description (a--c): -\begin{xymspec} -\begin{picture}(1000,600)(0,0) -\put(0,0){\threeheterovi[]{1==1;2==2;3==3}{% -1Sb==1Sb(l);1Sa==1Sa(r);2Sb==2Sb(r);2Sa==2Sa(r);% -3Sb==3Sb(l);3Sa==3Sa(l)}} -\put(0,0){\circle{80}} -\put(400,340){\circle{80}} -\put(500,250){a} -\put(250,250){c} -\put(380,50){b} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (\the\shiftii,340) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{xymspec} - -For the arguments, BONDLIST and SUBSLIST, see the counterparts -of \verb/\threehetero/ described in \XyMTeX book. - -\medskip -\noindent -Example: -\begin{verbatim} - \threeheterovi{1==O}{2Sa==COOCH$_{3}$;2Sb==COOCH$_{3}$}\qquad - \threeheterovi{1==O}{2Sa==COOH;2Sb==COOH}\qquad\qquad - \threeheterovi{1==O}{3Sa==H$_{3}$C;3Sb==H$_{3}$C} -\end{verbatim} -produce the following structures: -\begin{center} - \threeheterovi{1==O}{2Sa==COOCH$_{3}$;2Sb==COOCH$_{3}$}\qquad - \threeheterovi{1==O}{2Sa==COOH;2Sb==COOH}\qquad\qquad - \threeheterovi{1==O}{3Sa==H$_{3}$C;3Sb==H$_{3}$C} -\end{center} - -The macro \verb/\threeheteroh/ -for drawing three-membered heterocycles of horizontal type -has the following format (\textsf{hetaromh.sty}) -\begin{verbatim} - \threeheteroh[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -% **************************** -% * threehetero derivatives * -% * (horizontal type) * -% **************************** -% -% aaa fff -% 3 -% | ` c -% b | 1 bbb ccc -% | / a -% 2/ -% ddd eee -% - -The locant numbering (1--3) -and the bond description (a--c) are common as -shown in the following diagram: -\begin{xymspec} -\begin{picture}(600,1000)(0,0) -\put(0,0){\threeheteroh[]{1==1;2==2;3==3}{% -1Sb==1Sb(r);1Sa==1Sa(r);2Sb==2Sb(l);2Sa==2Sa(r);% -3Sb==3Sb(l);3Sa==3Sa(r)}} -\put(0,0){\circle{80}} -\put(200,240){\circle{80}} -\put(300,150){a} -\put(100,320){b} -\put(300,450){c} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (200,240) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{xymspec} - -For the arguments, BONDLIST and SUBSLIST, see \XyMTeX book. - -\medskip -\noindent -Example: -\begin{verbatim} - \threeheteroh{1==O}{2Sa==COOCH$_{3}$;2Sb==CH$_{3}$OCO}\qquad - \threeheteroh{1==O}{2Sa==COOH;2Sb==HOCO}\qquad\qquad - \threeheteroh{1==O}{3Sa==CH$_{3}$;3Sb==CH$_{3}$} -\end{verbatim} -produce the following structures: -\begin{center} - \threeheteroh{1==O}{2Sa==COOCH$_{3}$;2Sb==CH$_{3}$OCO}\qquad - \threeheteroh{1==O}{2Sa==COOH;2Sb==HOCO}\qquad\qquad - \threeheteroh{1==O}{3Sa==CH$_{3}$;3Sb==CH$_{3}$} -\end{center} - -The macro \verb/\threeheterohi/ -for drawing three-membered heterocycles of inverse horizontal type -has the following format (\textsf{hetatomh.sty}) -\begin{verbatim} - \threeheterohi[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -% **************************** -% * threehetero derivatives * -% * (inverse horizontal type)* -% **************************** -% -% aaa bbb -% c 3 -% / | -% eee 1 | b -% fff a` | -% 2 <---original point -% ccc ddd - -The locant numbering (1--3) -and the bond description (a--c) are common as -shown in the following diagram: -\begin{xymspec} -\begin{picture}(600,1000)(0,0) -\put(0,0){\threeheterohi[]{1==1;2==2;3==3}{% -1Sb==1Sb(l);1Sa==1Sa(l);2Sb==2Sb(r);2Sa==2Sa(r);% -3Sb==3Sb(r);3Sa==3Sa(r)}} -\put(0,0){\circle{80}} -\put(400,240){\circle{80}} -\put(300,150){a} -\put(450,320){b} -\put(300,450){c} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (400,240) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{xymspec} - -For the arguments, BONDLIST and SUBSLIST, see \XyMTeX book. - -\medskip -\noindent -Example: -\begin{verbatim} - \threeheterohi{1==O}{2Sa==COOCH$_{3}$;2Sb==COOCH$_{3}$}\qquad - \threeheterohi{1==O}{2Sa==COOH;2Sb==COOH}\qquad\qquad - \threeheterohi{1==O}{3Sa==CH$_{3}$;3Sb==CH$_{3}$} -\end{verbatim} -produce the following structures: -\begin{center} - \threeheterohi{1==O}{2Sa==COOCH$_{3}$;2Sb==COOCH$_{3}$}\qquad - \threeheterohi{1==O}{2Sa==COOH;2Sb==COOH}\qquad\qquad - \threeheterohi{1==O}{3Sa==CH$_{3}$;3Sb==CH$_{3}$} -\end{center} - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\section{Aliphatic Moieties} -\subsection{Trigonal Units} - -In addition to the macros \verb/\rtrigonal/ and \verb/\ltrigonal/ -(see \XyMTeX book), macros for broader bond angles, -\verb/\Rtrigonal/ and \verb/\Ltrigonal/, are -added to the \textsf{aliphat} package (\textsf{aliphat.sty}). -The formats of these commands are as follows: -\begin{verbatim} - \Rtrigonal[AUXLIST]{SUBSLIST} - \Ltrigonal[AUXLIST]{SUBSLIST} -\end{verbatim} -% ************************* -% * trigonal unit (right) * -% ************************* -% -% 3 -% / -% / -% 1 --- 0 120 0 <== the original point -% ` -% ` -% 2 -% ************************ -% * trigonal unit (left) * -% ************************ -% -% 2 -% ` -% ` -% 120 0 --- 1 0 <== the original point -% / -% / -% 3 - -The bond angles of 2--0--3 are 120$^{\circ}$ in the trigonal units -printed with these commands. The arguments AUXLIST and SUBSLIST are -the same as those of \verb/\tetrahedral/. - -\medskip -\noindent -Example: -\begin{verbatim} -\Rtrigonal{0==C;1D==O;2==Cl;3==F}\qquad -\Ltrigonal{0==C;1D==O;2==Cl;3==F} -\end{verbatim} -produce the following structures: -\begin{center} -\Rtrigonal{0==C;1D==O;2==Cl;3==F}\qquad -\Ltrigonal{0==C;1D==O;2==Cl;3==F} -\end{center} - -\subsection{Ethylenes} - -The macro \verb/\Ethyleneh/ or \verb/\Ethylene/ is -a braoder-angled counterpart of -the macro \verb/\ethyleneh/ or \verb/\ethylene/ (see \XyMTeX book), -which is used to draw ethylene derivatives with angles 120$^{\circ}$ -(\textsf{aliphat.sty}). -The format of this command is as follows: -\begin{verbatim} - \Ethyleneh[BONDLIST]{ATOMLIST}{SUBSLIST} - \Ethylene[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -% ***************** -% * ethylene unit * -% ***************** -% -% The following numbering is adopted in this macro. -% -% 1 4 -% ` / -% ` / -% 120 (1)===(2) 120 (1) <== the original point -% / ` -% / ` -% 2 3 -% -% -The following diagram shows the numbering -for designating substitution positions: -\begin{xymspec} -\begin{picture}(800,880)(0,0) -\put(0,0){\Ethyleneh{1==1;2==2}{1==1;2==2;3==3;4==4;0==0}} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (300,300) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{xymspec} -The argument BONSLIST is used for giving the C--C bond. -The argument ATOMLIST is used for giving central atoms. -The argument SUBSLIST is -the same as that of \verb/\tetrahedral/. - -\medskip -\noindent -Example: -\begin{verbatim} -\Ethyleneh{1==C;2==C}{1==F;2==Cl;3==H;4==Br}\qquad -\Ethyleneh{1==C;2==C}{1==CH$_{3}$;2==H;3==CH$_{2}$OH;4==H}\par -\Ethyleneh{1==C;2==N}{1==Ph;2==Ph;3==OH}\qquad -\Ethyleneh[t{2+}]{1==C;2==N}{1==CH$_{3}$;2==CH$_{3}$;3==H} -\end{verbatim} -produce the following structures: -\begin{center} -\Ethyleneh{1==C;2==C}{1==F;2==Cl;3==H;4==Br}\qquad -\Ethyleneh{1==C;2==C}{1==CH$_{3}$;2==H;3==CH$_{2}$OH;4==H}\par -\Ethyleneh{1==C;2==N}{1==Ph;2==Ph;3==OH}\qquad -\Ethyleneh[t{2+}]{1==C;2==N}{1==CH$_{3}$;2==CH$_{3}$;3==H} -\end{center} - -A butadiene derivative, -\begin{center} -\Ethyleneh{1==C;2==C}{1==F;2==Cl;4==Br;% -3==\Ethyleneh{1==C;2==C}{1==(yl);2==H;3==H;4==H}} -\vspace*{1cm} -\end{center} -can be drawn by the code, -\begin{verbatim} -\Ethyleneh{1==C;2==C}{1==F;2==Cl;4==Br;% -3==\Ethyleneh{1==C;2==C}{1==(yl);2==H;3==H;4==H}} -\end{verbatim} - - -\chapter{Zigzag Polymethylene Skeletons} - -\section{Dimethylenes} - -The macro \verb/\dimethylene/ has two arguments ATOMLIST and SUBSLIST -as well as an optional argument BONDLIST (\textsf{methylen.sty}): -% -% \begin{verbatim} -% -% bbb -% 2 -% a / (or uppercase letters) -% / -% 1 -% aaa -% \end{verbatim} -% -\begin{verbatim} - \dimethylene[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -The BONDLIST argument contains one character a or A, -each of which indicates the presence of an inner (endo-chain) double -bond on the corresponding position. A lowercase letter is used -to typeset a double bond at a lower-side of an outer skeletal bond, -while an uppercase letter typesets a double bond at a upper-side of -an outer skeletal bond -(Note that the option `A' represents an aromatic circle in - commands \verb/\sixheterov/ etc. ). -The ATOMLIST and SUBSLIST arguments follow -the conventions of the \XyMTeX{} system. - -The following diagram shows the numbering -for designating substitution positions: -\begin{xymspec} -\begin{picture}(500,500)(0,0) -\put(0,0){\dimethylene{1==1;2==2}{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb}} -\put(100,250){a} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (50,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{xymspec} - -Lowercase vs. uppercase letters (`a' vs. `A') in the BONDLIST of -the \verb/\dimethylene/ command designate the position of -an bond added to the bond `a', as shown in the code, -\begin{verbatim} -\dimethylene[a]{}{1W==\bzdrv{3==(yl)};1==Cl;2W==H;2==F} -\hskip2cm -\bzdrv{3==\dimethylene[A]{}{1W==(yl);1==Cl;2W==H;2==F}} -\end{verbatim} -which typesets the following formulas: -\begin{center} -\dimethylene[a]{}{1W==\bzdrv{3==(yl)};1==Cl;2W==H;2==F} -\hskip2cm -\bzdrv{3==\dimethylene[A]{}{1W==(yl);1==Cl;2W==H;2==F}} -\end{center} - -In addition to the standard bond modifiers -listed in Table \ref{tt:200a}, -the terminal positions of the \verb/\dimethylene/ command -can take a bond modifier `W'. -For example, the code, -\begin{verbatim} -\dimethylene{1==S;2==S}{1W==H;2W==H} -\hskip4cm -\dimethylene{1==S;2==S}{1W==\bzdrv{3==(yl)};2W==H} -\hskip1cm -\bzdrv{3==\dimethylene{1==S;2==S}{1W==(yl);2W==H}} -\end{verbatim} -generates the following formulas: -\begin{center} -\dimethylene{1==S;2==S}{1W==H;2W==H} -\hskip4cm -\dimethylene{1==S;2==S}{1W==\bzdrv{3==(yl)};2W==H} -\hskip1cm -\bzdrv{3==\dimethylene{1==S;2==S}{1W==(yl);2W==H}} -\end{center} -where the ATOMLIST is used to set two sulfur atoms in -the dimethylene chain. - -The macro \verb/\dimethylenei/ is the inverse counterpart of -\verb/\dimethylene/, where arguments ATOMLIST, SUBSLIST, and -BONDLIST take such common formats as found in the -definition of the latter (\textsf{methylen.sty}): -\begin{verbatim} - \dimethylenei[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -The following diagram shows the numbering -for designating substitution positions: -\begin{xymspec} -\begin{picture}(500,500)(0,0) -\put(0,0){\dimethylenei{1==1;2==2}{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb}} -\put(150,280){a} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (50,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{xymspec} -Note that the coodinate of position no.~1 is (50, 283), -where 180 + 103 = 283. -The following example shows a specification of the SUBSLIST. -\begin{verbatim} -\dimethylenei{}{1W==R$^{\prime}$;2W==R$^{\prime}$;1D==O;2==OH} -\hskip3cm -\dimethylenei{}{1W==R$^{\prime}$;% -2Sa==R$^{\prime}$;2Sb==R$^{\prime\prime}$;1D==O;2W==OH} -\end{verbatim} - -\begin{center} -\dimethylenei{}{1W==R$^{\prime}$;2W==R$^{\prime}$;1D==O;2==OH} -\hskip3cm -\dimethylenei{}{1W==R$^{\prime}$;% -2Sa==R$^{\prime}$;2Sb==R$^{\prime\prime}$;1D==O;2W==OH} -\end{center} - -\section{Trimethylenes} - -The macros \verb/\trimethylene/ and \verb/\trimethylenei/ -and have two arguments ATOMLIST and SUBSLIST -as well as an optional argument BONDLIST (\textsf{methylen.sty}). -% -% \begin{verbatim} -% -% bbb -% 2 -% a / ` b (or uppercase letters) -% / ` -% 1 3 -% aaa ccc -% \end{verbatim} -% -% -\begin{verbatim} - \trimethylene[BONDLIST]{ATOMLIST}{SUBSLIST} - \trimethylenei[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} - -The following diagram shows the numbering -for designating substitution positions: -\begin{xymspec} -\begin{picture}(600,500)(0,0) -\put(0,0){\trimethylene{1==1;2==2;3==3}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\lower10pt\hbox{3Sb};3Sa==3Sa}} -\put(100,250){a} -\put(300,250){b} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (50,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\hskip2cm -\begin{picture}(600,500)(0,0) -\put(0,0){\trimethylenei{1==1;2==2;3==3}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\raise10pt\hbox{3Sb};3Sa==3Sa}} -\put(150,250){a} -\put(250,250){b} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (50,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\end{xymspec} - -\vskip1cm -\noindent -Examples: -\begin{verbatim} -\trimethylene[b]{}{1W==R$^{1}$;1==OH;2==R$^{2}$} -\hskip2cm -\trimethylene[a]{}{1W==R$^{1}$;2==R$^{2}$;3W==CHO} -\hskip2cm -\trimethylene[B]{}{2==\null;3W==COOEt;3==Br} -\end{verbatim} -\begin{center} -\trimethylene[b]{}{1W==R$^{1}$;1==OH;2==R$^{2}$} -\hskip2cm -\trimethylene[a]{}{1W==R$^{1}$;2==R$^{2}$;3W==CHO} -\hskip2cm -\trimethylene[B]{}{2==\null;3W==COOEt;3==Br} -\end{center} - -\vskip1cm -\begin{verbatim} -\trimethylenei{}{1W==\bzdrv{2==(yl);1==COOH;5==HO;6==HO};% -3W==CHO;3SA==H;3SB==Me} -\end{verbatim} -\begin{center} -\trimethylenei{}{1W==\bzdrv{2==(yl);1==COOH;5==HO;6==HO};% -3W==CHO;3SA==H;3SB==Me} - -\vspace*{1cm} -\end{center} - -\section{Tetramethylenes} - -The macros \verb/\tetramethylene/ and \verb/\tetramethylenei/ -have two arguments ATOMLIST and SUBSLIST -as well as an optional argument BONDLIST (\textsf{methylen.sty}). -\begin{verbatim} - \tetramethylene[BONDLIST]{ATOMLIST}{SUBSLIST} - \tetramethylenei[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -The following diagram shows the numbering -for designating substitution positions: -\begin{xymspec} -\vspace*{.5cm} -\begin{picture}(600,500)(0,0) -\put(0,0){\tetramethylene{1==1;2==2;3==3;4==4}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\lower10pt\hbox{3Sb};3Sa==3Sa;4Sa==4Sa;% -4Sb==\raise10pt\hbox{4Sb}}} -\put(250,250){a} -\put(450,250){b} -\put(600,250){c} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\hskip3cm -\begin{picture}(600,500)(0,0) -\put(0,0){\tetramethylenei{1==1;2==2;3==3;4==4}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\raise10pt\hbox{3Sb};3Sa==3Sa;4Sa==4Sa;% -4Sb==\lower10pt\hbox{4Sb}}} -\put(280,250){a} -\put(400,250){b} -\put(650,250){c} -\end{picture} -\qquad\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} - -\vspace*{.5cm} -\end{xymspec} - -\vskip1cm -\noindent -Examples: -\begin{verbatim} -\tetramethylenei{}{1W==Cl;1D==O;2B==Br;4W==Cl} -\end{verbatim} -\begin{center} -\tetramethylenei{}{1W==Cl;1D==O;2B==Br;4W==Cl} - -\vspace*{.5cm} -\end{center} - - -\begin{verbatim} -\tetramethylene{}{1W==TBDMS-O;2D==\null;3B==OH;% -4W==\cyclohexanev[e]{6==(yl);3B==\null}} -\end{verbatim} -\begin{center} -\tetramethylene{}{1W==TBDMS-O;2D==\null;3B==OH;% -4W==\cyclohexanev[e]{6==(yl);3B==\null}} - -\vspace*{1cm} -\end{center} - -\begin{verbatim} -\tetramethylene[b]{}{1W==\bzdrv{5==\null;3==(yl)};4W==OH} -\end{verbatim} -\begin{center} -\vspace*{.5cm} -\tetramethylene[b]{}{1W==\bzdrv{5==\null;3==(yl)};4W==OH} -\vspace*{1cm} -\end{center} - -\section{Pentamethylenes} - -The macros \verb/\pentamethylene/ and \verb/\pentamethylenei/ -have two arguments ATOMLIST and SUBSLIST -as well as an optional argument BONDLIST (\textsf{methylen.sty}). -\begin{verbatim} - \pentamethylene[BONDLIST]{ATOMLIST}{SUBSLIST} - \pentamethylenei[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -The following diagram shows the numbering -for designating substitution positions: -\begin{xymspec} -\vspace*{.5cm} -\begin{picture}(600,500)(0,0) -\put(0,0){\pentamethylene{1==1;2==2;3==3;4==4;5==5}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\lower10pt\hbox{3Sb};3Sa==3Sa;% -4Sa==4Sa;4Sb==\raise10pt\hbox{4Sb};% -5Sa==5Sa;5Sb==\lower10pt\hbox{5Sb}% -}} -\put(250,250){a} -\put(450,250){b} -\put(600,250){c} -\put(800,250){d} -\end{picture} -\qquad\qquad\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\hskip2cm -\begin{picture}(600,500)(0,0) -\put(0,0){\pentamethylenei{1==1;2==2;3==3;4==4;5==5}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\raise10pt\hbox{3Sb};3Sa==3Sa;% -4Sa==4Sa;4Sb==\lower10pt\hbox{4Sb};% -5Sa==5Sa;5Sb==\raise10pt\hbox{5Sb}% -}} -\put(280,250){a} -\put(400,250){b} -\put(650,250){c} -\put(750,250){d} -\end{picture} -\qquad\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} - -\vspace*{.5cm} -\end{xymspec} - -\vskip1cm -\noindent -Examples:\nobreak -\begin{verbatim} -\pentamethylene{}{1W==AcO;2B==\null;4B==\null;5W==OH} -\end{verbatim} -\begin{center} -\pentamethylene{}{1W==AcO;2B==\null;4B==\null;5W==OH} -\end{center} - -\begin{verbatim} -\pentamethylenei{}{1W==\fiveheterovi{2==N;5==O}{1D==O;2==(yl);3B==Bn};% -1D==O;2A==OMe;3A==OH;5W==OTBDMS} -\end{verbatim} -\begin{center} -\vspace*{.5cm} -\pentamethylenei{}{1W==\fiveheterovi{2==N;5==O}{1D==O;2==(yl);3B==Bn};% -1D==O;2A==OMe;3A==OH;5W==OTBDMS} - -\vspace*{.5cm} -\end{center} - - -\begin{verbatim} -\pentamethylenei{1==S}{1W==\bzdrv{2==(yl);5==O$_{2}$N};% -1D==O;3==Cl;5==COO$^{-}$;5W==NH$_{3}^{+}$} -\end{verbatim} -\begin{center} -\vspace*{.5cm} -\pentamethylenei{1==S}{1W==\bzdrv{2==(yl);5==O$_{2}$N};% -1D==O;3==Cl;5==COO$^{-}$;5W==NH$_{3}^{+}$} - -\vspace*{.5cm} -\end{center} - -\section{Hexamethylenes} - -The macros \verb/\hexamethylene/ and \verb/\hexamethylenei/ -have two arguments ATOMLIST and SUBSLIST -as well as an optional argument BONDLIST (\textsf{methylen.sty}). -\begin{verbatim} - \hexamethylene[BONDLIST]{ATOMLIST}{SUBSLIST} - \hexamethylenei[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -The following diagram shows the numbering -for designating substitution positions: -\begin{xymspec} -\vspace*{.5cm} -\begin{picture}(800,500)(0,0) -\put(0,0){\hexamethylene{1==1;2==2;3==3;4==4;5==5;6==6}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\lower10pt\hbox{3Sb};3Sa==3Sa;% -4Sa==4Sa;4Sb==\raise10pt\hbox{4Sb};% -5Sa==5Sa;5Sb==\lower10pt\hbox{5Sb};% -6Sa==6Sa;6Sb==\raise10pt\hbox{6Sb}% -}} -\put(250,250){a} -\put(450,250){b} -\put(600,250){c} -\put(800,250){d} -\put(950,250){e} -\end{picture} -\qquad\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\hskip1cm -\begin{picture}(850,500)(0,0) -\put(0,0){\hexamethylenei{1==1;2==2;3==3;4==4;5==5;6==6}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\raise10pt\hbox{3Sb};3Sa==3Sa;% -4Sa==4Sa;4Sb==\lower10pt\hbox{4Sb};% -5Sa==5Sa;5Sb==\raise10pt\hbox{5Sb};% -6Sa==6Sa;6Sb==\lower10pt\hbox{6Sb}% -}} -\put(280,250){a} -\put(400,250){b} -\put(650,250){c} -\put(750,250){d} -\put(1000,250){e} -\end{picture} -\qquad\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} - -\vspace*{.5cm} -\end{xymspec} - -\vskip1cm -\noindent -Examples:\nobreak -\begin{verbatim} -\hexamethylene{}{2==\null;4D==O;6D==O;6W==OEt} -\end{verbatim} -\begin{center} -\hexamethylene{}{2==\null;4D==O;6D==O;6W==OEt} -\end{center} - -\begin{verbatim} -\hexamethylene[a]{}{4B==OH;5B==NHBoc;6W==OTBDPS} -\end{verbatim} -\begin{center} -\hexamethylene[a]{}{4B==OH;5B==NHBoc;6W==OTBDPS} -\end{center} - -\begin{verbatim} -\hexamethylene{}{1W==PhSO$_{2}$;1B==OMe;2A==OH;5D==\null;6W==SiMe$_{3}$} -\end{verbatim} -\begin{center} -\hexamethylene{}{1W==PhSO$_{2}$;1B==OMe;2A==OH;5D==\null;6W==SiMe$_{3}$} -\end{center} - -\begin{verbatim} -\hexamethylenei[a]{}{1W==Ph;3B==\null;4A==OTBS;6D==O;6W==H} -\end{verbatim} -\begin{center} -\hexamethylenei[a]{}{1W==Ph;3B==\null;4A==OTBS;6D==O;6W==H} -\end{center} - -\section{Heptamethylenes} - -The macros \verb/\heptamethylene/ and \verb/\heptamethylenei/ -have two arguments ATOMLIST and SUBSLIST -as well as an optional argument BONDLIST (\textsf{methylen.sty}). -\begin{verbatim} - \heptamethylene[BONDLIST]{ATOMLIST}{SUBSLIST} - \heptamethylenei[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -The following diagram shows the numbering -for designating substitution positions: -\begin{xymspec} -\vspace*{.5cm} -\begin{picture}(1000,500)(0,0) -\put(0,0){\heptamethylene{1==1;2==2;3==3;4==4;5==5;6==6;7==7}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\lower10pt\hbox{3Sb};3Sa==3Sa;% -4Sa==4Sa;4Sb==\raise10pt\hbox{4Sb};% -5Sa==5Sa;5Sb==\lower10pt\hbox{5Sb};% -6Sa==6Sa;6Sb==\raise10pt\hbox{6Sb};% -7Sa==7Sa;7Sb==\lower10pt\hbox{7Sb}% -}} -\put(250,250){a} -\put(450,250){b} -\put(600,250){c} -\put(800,250){d} -\put(950,250){e} -\put(1150,250){f} -\end{picture} -\qquad\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\hskip1cm -\begin{picture}(1050,500)(0,0) -\put(0,0){\heptamethylenei{1==1;2==2;3==3;4==4;5==5;6==6;7==7}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\raise10pt\hbox{3Sb};3Sa==3Sa;% -4Sa==4Sa;4Sb==\lower10pt\hbox{4Sb};% -5Sa==5Sa;5Sb==\raise10pt\hbox{5Sb};% -6Sa==6Sa;6Sb==\lower10pt\hbox{6Sb};% -7Sa==7Sa;7Sb==\raise10pt\hbox{7Sb}% -}} -\put(280,250){a} -\put(400,250){b} -\put(650,250){c} -\put(750,250){d} -\put(1000,250){e} -\put(1100,250){f} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} - -\vspace*{.5cm} -\end{xymspec} - - -\vskip1cm -\noindent -Examples:\nobreak -\begin{verbatim} -\heptamethylene[a]{}{1W==\cyclopentanevi[b]{3==(yl);5Sa==\null;5Sb==\null};% -5D==O;6D==N$_{2}$} -\end{verbatim} -\begin{center} -\vspace*{1cm} -\heptamethylene[a]{}{1W==\cyclopentanevi[b]{3==(yl);5Sa==\null;5Sb==\null};% -5D==O;6D==N$_{2}$} - -\vspace*{1cm} -\end{center} - - -\begin{verbatim} -\heptamethylenei{}{1W==\bzdrv{1==COOH;2==(yl);5==HO;6==HO};% -3B==Me;4B==OH;5A==Me;6D==O;7A==Et;% -7W==\fiveheterov{1==O}{5==(yl);5SB==H;4GB==Me;2GA==Et;% -2Su==\sixheterovi{1==O}{6==(yl);6FA==H;3SB==OH;3SA==Et;2A==Me}}} -\end{verbatim} -\begin{center} -\vspace*{1cm} -\heptamethylenei{}{1W==\bzdrv{1==COOH;2==(yl);5==HO;6==HO};% -3B==Me;4B==OH;5A==Me;6D==O;7A==Et;% -7W==\fiveheterov{1==O}{5==(yl);5SB==H;4GB==Me;2GA==Et;% -2Su==\sixheterovi{1==O}{6==(yl);6FA==H;3SB==OH;3SA==Et;2A==Me}}} - -\vspace*{1cm} -\end{center} - - -\section{Octamethylenes} - -The macros \verb/\octamethylene/ and \verb/\octamethylenei/ -have two arguments ATOMLIST and SUBSLIST -as well as an optional argument BONDLIST (\textsf{methylen.sty}). -\begin{verbatim} - \octamethylene[BONDLIST]{ATOMLIST}{SUBSLIST} - \octamethylenei[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -The following diagram shows the numbering -for designating substitution positions: -\begin{xymspec} -\vspace*{.5cm} -\begin{picture}(1300,700)(0,0) -\put(0,0){\octamethylene{1==1;2==2;3==3;4==4;5==5;6==6;7==7;8==8}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\lower10pt\hbox{3Sb};3Sa==3Sa;% -4Sa==4Sa;4Sb==\raise10pt\hbox{4Sb};% -5Sa==5Sa;5Sb==\lower10pt\hbox{5Sb};% -6Sa==6Sa;6Sb==\raise10pt\hbox{6Sb};% -7Sa==7Sa;7Sb==\lower10pt\hbox{7Sb};% -8Sa==8Sa;8Sb==\raise10pt\hbox{8Sb}% -}} -\put(250,250){a} -\put(450,250){b} -\put(600,250){c} -\put(800,250){d} -\put(950,250){e} -\put(1150,250){f} -\put(1250,250){g} -\end{picture} -\qquad\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\par -\begin{picture}(1300,700)(0,0) -\put(0,0){\octamethylenei{1==1;2==2;3==3;4==4;5==5;6==6;7==7;8==8}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\raise10pt\hbox{3Sb};3Sa==3Sa;% -4Sa==4Sa;4Sb==\lower10pt\hbox{4Sb};% -5Sa==5Sa;5Sb==\raise10pt\hbox{5Sb};% -6Sa==6Sa;6Sb==\lower10pt\hbox{6Sb};% -7Sa==7Sa;7Sb==\raise10pt\hbox{7Sb};% -8Sa==8Sa;8Sb==\lower10pt\hbox{8Sb}% -}} -\put(280,250){a} -\put(400,250){b} -\put(650,250){c} -\put(750,250){d} -\put(1000,250){e} -\put(1100,250){f} -\put(1300,250){g} -\end{picture} -\qquad\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} - -\vspace*{.5cm} -\end{xymspec} - -\vskip1cm -\noindent -Examples:\nobreak -\begin{verbatim} -\octamethylene[eg]{}{1W==HOHN;1D==O;4B==OBn} -\end{verbatim} -\begin{center} -\octamethylene[eg]{}{1W==HOHN;1D==O;4B==OBn} -\end{center} - - -\begin{verbatim} -\octamethylenei[af]{}{1W==Ph;3B==\null;4A==OH;8D==O;% -8W==\ryl(4==NH){% -5==\tetramethylene{3==O}{1==(yl);2D==O;4W==CCl$_{3}$;% -1SA==\ryl{8==\bzdrv{1==(yl);3==Cl;4==OMe}}}}} -\end{verbatim} -\begin{center} -\vspace*{1cm} -\octamethylenei[af]{}{1W==Ph;3B==\null;4A==OH;8D==O;% -8W==\ryl(4==NH){% -5==\tetramethylene{3==O}{1==(yl);2D==O;4W==CCl$_{3}$;% -1SA==\ryl{8==\bzdrv{1==(yl);3==Cl;4==OMe}}}}} - -\vspace*{2cm} -\end{center} - - -\section{Nonamethylenes} - -The macros \verb/\nonamethylene/ and \verb/\nonamethylenei/ -have two arguments ATOMLIST and SUBSLIST -as well as an optional argument BONDLIST (\textsf{methylen.sty}). -\begin{verbatim} - \nonamethylene[BONDLIST]{ATOMLIST}{SUBSLIST} - \nonamethylenei[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -The following diagram shows the numbering -for designating substitution positions: -\begin{xymspec} -\vspace*{.5cm} -\begin{picture}(1500,700)(0,0) -\put(0,0){\nonamethylene{1==1;2==2;3==3;4==4;5==5;6==6;7==7;8==8;9==9}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\lower10pt\hbox{3Sb};3Sa==3Sa;% -4Sa==4Sa;4Sb==\raise10pt\hbox{4Sb};% -5Sa==5Sa;5Sb==\lower10pt\hbox{5Sb};% -6Sa==6Sa;6Sb==\raise10pt\hbox{6Sb};% -7Sa==7Sa;7Sb==\lower10pt\hbox{7Sb};% -8Sa==8Sa;8Sb==\raise10pt\hbox{8Sb};% -9Sa==9Sa;9Sb==\lower10pt\hbox{9Sb}% -}} -\put(250,250){a} -\put(450,250){b} -\put(600,250){c} -\put(800,250){d} -\put(950,250){e} -\put(1150,250){f} -\put(1250,250){g} -\put(1450,250){h} -\end{picture} -\qquad\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\par -\begin{picture}(1500,700)(0,0) -\put(0,0){\nonamethylenei{1==1;2==2;3==3;4==4;5==5;6==6;7==7;8==8;9==9}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\raise10pt\hbox{3Sb};3Sa==3Sa;% -4Sa==4Sa;4Sb==\lower10pt\hbox{4Sb};% -5Sa==5Sa;5Sb==\raise10pt\hbox{5Sb};% -6Sa==6Sa;6Sb==\lower10pt\hbox{6Sb};% -7Sa==7Sa;7Sb==\raise10pt\hbox{7Sb};% -8Sa==8Sa;8Sb==\lower10pt\hbox{8Sb};% -9Sa==9Sa;9Sb==\raise10pt\hbox{9Sb}% -}} -\put(280,250){a} -\put(400,250){b} -\put(650,250){c} -\put(750,250){d} -\put(1000,250){e} -\put(1100,250){f} -\put(1300,250){g} -\put(1450,250){h} -\end{picture} -\qquad\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} - -\vspace*{.5cm} -\end{xymspec} - -\vskip1cm -\noindent -Examples:\nobreak -\begin{verbatim} -\nonamethylene[a]{}{6D==O;9W==COOEt;9==COOEt} -\end{verbatim} -\begin{center} -\nonamethylene[a]{}{6D==O;9W==COOEt;9==COOEt} -\end{center} - -\begin{verbatim} -\nonamethylenei[a]{}{1W==Ph;4SB==\null;4SA==H;8==\null} -\end{verbatim} -\begin{center} -\nonamethylenei[a]{}{1W==Ph;4SB==\null;4SA==H;8==\null} -\end{center} - - -\section{Decamethylenes} - -The macros \verb/\decamethylene/ and \verb/\decamethylenei/ -have two arguments ATOMLIST and SUBSLIST -as well as an optional argument BONDLIST (\textsf{methylen.sty}). -\begin{verbatim} - \decamethylene[BONDLIST]{ATOMLIST}{SUBSLIST} - \decamethylenei[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -The following diagram shows the numbering -for designating substitution positions: -\begin{xymspec} -\vspace*{.5cm} -\begin{picture}(1700,700)(0,0) -\put(0,0){\decamethylene{1==1;2==2;3==3;4==4;5==5;6==6;7==7;% -8==8;9==9;{{10}}==10}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\lower10pt\hbox{3Sb};3Sa==3Sa;% -4Sa==4Sa;4Sb==\raise10pt\hbox{4Sb};% -5Sa==5Sa;5Sb==\lower10pt\hbox{5Sb};% -6Sa==6Sa;6Sb==\raise10pt\hbox{6Sb};% -7Sa==7Sa;7Sb==\lower10pt\hbox{7Sb};% -8Sa==8Sa;8Sb==\raise10pt\hbox{8Sb};% -9Sa==9Sa;9Sb==\lower10pt\hbox{9Sb};% -{10}Sa==10Sa;{10}Sb==\raise10pt\hbox{10Sb}% -}} -\put(250,250){a} -\put(450,250){b} -\put(600,250){c} -\put(800,250){d} -\put(950,250){e} -\put(1150,250){f} -\put(1250,250){g} -\put(1450,250){h} -\put(1650,250){i} -\end{picture} -\qquad\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\par -\begin{picture}(1700,700)(0,0) -\put(0,0){\decamethylenei{1==1;2==2;3==3;4==4;5==5;6==6;7==7;% -8==8;9==9;{{10}}==10}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\raise10pt\hbox{3Sb};3Sa==3Sa;% -4Sa==4Sa;4Sb==\lower10pt\hbox{4Sb};% -5Sa==5Sa;5Sb==\raise10pt\hbox{5Sb};% -6Sa==6Sa;6Sb==\lower10pt\hbox{6Sb};% -7Sa==7Sa;7Sb==\raise10pt\hbox{7Sb};% -8Sa==8Sa;8Sb==\lower10pt\hbox{8Sb};% -9Sa==9Sa;9Sb==\raise10pt\hbox{9Sb};% -{10}Sa==10Sa;{10}Sb==\lower10pt\hbox{10Sb}% -}} -\put(280,250){a} -\put(400,250){b} -\put(650,250){c} -\put(750,250){d} -\put(1000,250){e} -\put(1100,250){f} -\put(1300,250){g} -\put(1450,250){h} -\put(1650,250){i} -\end{picture} -\qquad\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} - -\vspace*{.5cm} -\end{xymspec} - -\vskip1cm -\noindent -Examples:\nobreak -\begin{verbatim} -\decamethylene[acf]{}{9==OH} -\end{verbatim} -\begin{center} -\decamethylene[acf]{}{9==OH} -\end{center} - -\begin{verbatim} -\decamethylenei[b]{}{1==\lmoiety{TBMSO};3==\null;4A==MeO;6A==OTBDMS;% -9B==\null;{10}D==O;% -{10}W==\ryl(4==O){5==\dimethylene{}{1==(yl);2D==O;2W==OMe}}} -\end{verbatim} -\begin{center} -\decamethylenei[b]{}{1==\lmoiety{TBMSO};3==\null;4A==MeO;6A==OTBDMS;% -9B==\null;{10}D==O;% -{10}W==\ryl(4==O){5==\dimethylene{}{1==(yl);2D==O;2W==OMe}}} -\end{center} - -\begin{verbatim} -\decamethylenei[b]{}{1==\lmoiety{TBMSO};3==\null;4A==MeO;6A==OTBDMS;% -9B==\null;{10}D==O;% -{10}W==\trimethylenei{1==O}{1==(yl);3D==O;3W==OMe}} -\end{verbatim} -\begin{center} -\decamethylenei[b]{}{1==\lmoiety{TBMSO};3==\null;4A==MeO;6A==OTBDMS;% -9B==\null;{10}D==O;% -{10}W==\trimethylenei{1==O}{1==(yl);3D==O;3W==OMe}} -\end{center} - -\section{Longer Polymethylene Chains} - -A polymethylene chain longer than ten carbons -should be written by combining two or more units -selected from the above-mentioned di- to deca-methylenes. - -To do this task, we regard one unit -as a substituent of another unit. In this method, -the code for the former unit is written in the -SUBSLIST of the code for the latter. For example, the code, -\begin{verbatim} -\decamethylene{}{9D==\null;% -{10}W==\pentamethylene{}{1==(yl);3==\null;4==OBz}} -\end{verbatim} -generates the following formula: -\begin{center} -\decamethylene{}{9D==\null;% -{10}W==\pentamethylene{}{1==(yl);3==\null;4==OBz}} -\end{center} -Alternatively, we regard one unit as a -replacement part of another unit, where -the code for the former unit is written in the -BONDLIST of the code for the latter (see spiro compounds). -The same formula with slightly different appearance -can be typeset by the code, -\begin{verbatim} -\decamethylene{{10}s==\hexamethylenei{}{1==(yl);4==\null;5==OBz}% -}{9D==\null} -\end{verbatim} -which gives -\begin{center} -\decamethylene{{10}s==\hexamethylenei{}{1==(yl);4==\null;5==OBz}% -}{9D==\null} -\end{center} - -\section{Cisoid Tetramethylenes} - -The macros \verb/\tetramethylenecup/ and \verb/\tetramethylenecap/ -have two arguments ATOMLIST and SUBSLIST -as well as an optional argument BONDLIST (\textsf{methylen.sty}). -\begin{verbatim} - \tetramethylenecup[BONDLIST]{ATOMLIST}{SUBSLIST} - \tetramethylenecap[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -The following diagram shows the numbering -for designating substitution positions: -\begin{xymspec} -\vspace*{.5cm} -\begin{picture}(600,500)(0,0) -\put(0,0){\tetramethylenecup{1==1;2==2;3==3;4==4}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\lower10pt\hbox{3Sb};3Sa==3Sa;4Sa==4Sa;4Sb==4Sb}} -\put(300,250){a} -\put(450,200){b} -\put(600,250){c} -\end{picture} -\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} -\hskip3cm -\begin{picture}(600,500)(0,0) -\put(0,0){\tetramethylenecap{1==1;2==2;3==3;4==4}% -{1Sa==1Sa;1Sb==1Sb;2Sa==2Sa;2Sb==2Sb;% -3Sb==\raise10pt\hbox{3Sb};3Sa==3Sa;4Sa==4Sa;4Sb==4Sb}} -\put(200,250){a} -\put(500,150){b} -\put(650,250){c} -\end{picture} -\qquad\qquad\fbox{\parbox{2cm}{$\circ$: (200,180) \\ - $\bullet$: (\the\noshift,\the\noshift)}} - -\vspace*{.5cm} -\end{xymspec} - -\vskip1cm -\noindent -Examples:\nobreak -\begin{verbatim} -\tetramethylenecap[b]{1s==\dimethylenei{}{1W==HO;2==(yl)};% -4s==\trimethylene{}{3W==CN;1==(yl)}}{} -\end{verbatim} -\begin{center} -\tetramethylenecap[b]{1s==\dimethylenei{}{1W==HO;2==(yl)};% -4s==\trimethylene{}{3W==CN;1==(yl)}}{} -\end{center} - -\begin{verbatim} -\cyclopentanevi{1D==O;4A==HO;% -2A==\tetramethylenecup[b]{% -4s==\trimethylenei{}{1==(yl);3W==COOMe}}{1==(yl)};% -3B==\trimethylene[a]{}{1==(yl);3A==OH;3W==C$_{5}$H$_{11}$}} -\end{verbatim} -\begin{center} -\cyclopentanevi{1D==O;4A==HO;% -2A==\tetramethylenecup[b]{% -4s==\trimethylenei{}{1==(yl);3W==COOMe}}{1==(yl)};% -3B==\trimethylene[a]{}{1==(yl);3A==OH;3W==C$_{5}$H$_{11}$}} -\end{center} - -\section{Ring Fusion to Polymethylenes} - -The BONDLIST of each ``methylene'' command can accept bond fusion. - -\vskip1cm -\noindent -Examples:\nobreak -\begin{verbatim} -\nonamethylene[{h\threefusehi({cA}){3==O}{}{a}}]{}{1W==Me;1A==OH} -\end{verbatim} -\begin{center} -\vspace*{1cm} -\nonamethylene[{h\threefusehi({cA}){3==O}{}{a}}]{}{1W==Me;1A==OH} - -\vspace*{1cm} -\end{center} - -\begin{verbatim} -\tetramethylenecup[{b\threefusev({aB}{cB}){1==O}{}{B}}]% -{}{1D==O;1W==H$_{2}$N;4D==O;4W==nC$_{8}$H$_{17}$} -\end{verbatim} -\begin{center} -\vspace*{1cm} -\tetramethylenecup[{b\threefusev({aB}{cB}){1==O}{}{B}}]% -{}{1D==O;1W==H$_{2}$N;4D==O;4W==nC$_{8}$H$_{17}$} - -\vspace*{1cm} -\end{center} - - -\begin{verbatim} -\pentamethylenei[{c\threefusehi({bA}{cA}){3==O}{}{a}}]{}{1W==Ph;5W==OH} -\end{verbatim} -\begin{center} -\vspace*{1cm} -\pentamethylenei[{c\threefusehi({bA}{cA}){3==O}{}{a}}]{}{1W==Ph;5W==OH} - -\vspace*{1cm} -\end{center} - - -\section{Ring Replacement to Polymethylenes} - - -The ATOMLIST of each ``methylene'' command can accept atom or -ring replacement. - -\vskip1cm -\noindent -Examples:\nobreak -\begin{verbatim} -\trimethylenei{3s==\fiveheterov{2==O;5==O}{1==(yl)}}{1W==PhSO$_{2}$;3W==R} -\end{verbatim} -\begin{center} -\vspace*{1cm} -\trimethylenei{3s==\fiveheterov{2==O;5==O}{1==(yl)}}{1W==PhSO$_{2}$;3W==R} - -\vspace*{1cm} -\end{center} - - -\begin{verbatim} -\tetramethylenecup[b]{% -1s==\nonamethylenei{3s==\fiveheterov{2==O;5==O}{1==(yl)}}{9==(yl)};% -4s==\ryl{5A==\sixheterovi{1==N}{1==Bn;% -2B==\ryl{8==OBn};3A==OBn;6==(yl)}}}{} -\end{verbatim} -\begin{center} -\vspace*{1cm} -\tetramethylenecup[b]{% -1s==\nonamethylenei{3s==\fiveheterov{2==O;5==O}{1==(yl)}}{9==(yl)};% -4s==\ryl{5A==\sixheterovi{1==N}{1==Bn;% -2B==\ryl{8==OBn};3A==OBn;6==(yl)}}}{} - -\vspace*{1cm} -\end{center} - -\begin{verbatim} -\tetramethylene{% -2s==\sixheterovi{2==O;6==O}{4Sa==\null;4Sb==\null;1==(yl)};% -4s==\ryl{5B==\cyclohexanev[d]{6==(yl);1A==\null;% -5==\Utrigonal{0==C;1D==O;2==(yl);3==H}}}}{} -\end{verbatim} -\begin{center} -\vspace*{1cm} -\tetramethylene{% -2s==\sixheterovi{2==O;6==O}{4Sa==\null;4Sb==\null;1==(yl)};% -4s==\ryl{5B==\cyclohexanev[d]{6==(yl);1A==\null;% -5==\Utrigonal{0==C;1D==O;2==(yl);3==H}}}}{} - -\vspace*{1cm} -\end{center} - -\section{Branched Chains} - -Branched chains can be drawn by using a ``methylene'' command -with the ``yl''-function. - -\vskip1cm -\noindent -Examples:\nobreak -\begin{verbatim} -\decamethylene[bf]{}{% -2==\dimethylene{}{1==(yl)};6==\dimethylene{}{1==(yl)};% -{10}W==OH;{{10}}==\null} -\end{verbatim} -\begin{center} -\vspace*{1cm} -\decamethylene[bf]{}{% -2==\dimethylene{}{1==(yl)};6==\dimethylene{}{1==(yl)};% -{10}W==OH;{{10}}==\null} - -\vspace*{1cm} -\end{center} - -\begin{verbatim} -\tetramethylene{}{1W==BuO;1D==O;4W==OTBDPS;% -2==\dimethylene{}{1==(yl);2D==O;2W==H}} -\end{verbatim} -\begin{center} -\vspace*{1cm} -\tetramethylene{}{1W==BuO;1D==O;4W==OTBDPS;% -2==\dimethylene{}{1==(yl);2D==O;2W==H}} - -\vspace*{1cm} -\end{center} - - -\begin{verbatim} -\octamethylene[bd]{}{1W==MEMO;% -6==\tetramethylenei[a]{}{4==(yl);1W==EtOCO}} -\end{verbatim} -\begin{center} -\vspace*{1cm} -\octamethylene[bd]{}{1W==MEMO;% -6==\tetramethylenei[a]{}{4==(yl);1W==EtOCO}} - -\vspace*{1cm} -\end{center} - - -\chapter{Enhanced Functions of Commands for General Use} - -\section{Expanded Format} - -Commands for general use, e.g. \verb/\sixheterov/, have originally -taken a comman format: -\begin{verbatim} -\genCOM[BONDLIST]{ATOMLIST}{SUBSLIST} -\end{verbatim} -where \verb/\genCOM/ represents a command name such as -\verb/\sixheterov/. In \XyMTeX{} version 2.00, -we add a top optional argument SKBONDLIST -to treat stereochemical information as well as -an end optional argument OMIT to treat a bond-deleted skeleton. -Thus, the expanded format of each command for general use -is represented by -\begin{verbatim} -\genCOM(SKBONDLIST)[BONDLIST]{ATOMLIST}{SUBSLIST}[OMIT] -\end{verbatim} -The argument SKBONDLIST contains pairs of two alphabets in braces, -where each pair consists of a bond specifier (a lowercase letter) -and an uppercase letter (A or B). -The letter A represents an $\alpha$ (downward) bond, -while B represents a $\beta$ (upward) bond. For example, -an SKBONDLIST, \verb/({aA}{cB})/, represents that -bond `a' is an $\alpha$ bond in a dotted form and -that bond `c' is a $\beta$ bond in a boldfaced form. -The argument OMIT is a list of bond specifiers, each of -which designates a bond to be deleted. As a matter of course, -SKBONDLIST and OMIT take no common bond specifiers. - -\section{Boldfaced and Dotted Bonds} - -The following example shows that -the \verb/\sixheterov/ command takes an optional SKBONDLIST, -\verb/({eB})/, which typesets a boldfaced bond at `e' in -the resulting tetrahydropyran ring. -\begin{verbatim} -\sixheterov({eB}){6==O}{1D==O;2A==\null;4A==\null;% -5==\tetramethylenei{}{1W==HO;1D==O;2B==\null;3B==OH;4B==\null;4==(yl)}} -\end{verbatim} -\begin{center} -\sixheterov({eB}){6==O}{1D==O;2A==\null;4A==\null;% -5==\tetramethylenei{}{1W==HO;1D==O;2B==\null;3B==OH;4B==\null;4==(yl)}} -\end{center} -This is an example of the substitution technique in which -the side-chain is based on \verb/\tetramethylenei/ written in the -SUBSLIST of the outer \verb/\sixheterov/ command. - -The same structural formula can alternatively drawn by -means of the replacement technique, in which -the BONDLIST of the \verb/\sixheterov/ command is used -for specifying the side-chain. Thus, the code, -\begin{verbatim} -\sixheterov({eB}){6==O;% -5s==\pentamethylenei{}{1W==HO;1D==O;2B==\null;3B==OH;4B==\null;5==(yl)}% -}{1D==O;2A==\null;4A==\null} -\end{verbatim} -generates the following formula: -\begin{center} -\sixheterov({eB}){6==O;% -5s==\pentamethylenei{}{1W==HO;1D==O;2B==\null;3B==OH;4B==\null;5==(yl)}% -}{1D==O;2A==\null;4A==\null} -\end{center} - -We have further examples in which the \verb/\sixheterov/ command -takes an optional SKBONDLIST. -The following two examples show the comparison between -the substitution and the replacement technique, -giving formulas of chemically equivalence with -slightly different bond lengthes. -\begin{verbatim} -\sixheterov({bA}{eB}){3==O;5==O}{1A==Me;4Sa==\null;4Sb==\null;% -6==\hexamethylene{}{1W==MeS;1==Cl;3B==OMe;4B==Me;5A==OAc;6A==Me;6==(yl)}; -2==\hexamethylenei[bd]{}{1==(yl);1B==Me;5==COOMe}} -\end{verbatim} -\begin{center} -\sixheterov({bA}{eB}){3==O;5==O}{1A==Me;4Sa==\null;4Sb==\null;% -6==\hexamethylene{}{1W==MeS;1==Cl;3B==OMe;4B==Me;5A==OAc;6A==Me;6==(yl)}; -2==\hexamethylenei[bd]{}{1==(yl);1B==Me;5==COOMe}} -\end{center} - - -\begin{verbatim} -\sixheterov({bA}{eB}){3==O;5==O;% -6s==\heptamethylene{}{1W==MeS;1==Cl;3B==OMe;4B==Me;5A==OAc;6A==Me;7==(yl)}; -2s==\heptamethylene[ce]{}{1==(yl);2B==Me;6==COOMe}% -}{1A==Me;4Sa==\null;4Sb==\null} -\end{verbatim} -\begin{center} -\sixheterov({bA}{eB}){3==O;5==O;% -6s==\heptamethylene{}{1W==MeS;1==Cl;3B==OMe;4B==Me;5A==OAc;6A==Me;7==(yl)}; -2s==\heptamethylene[ce]{}{1==(yl);2B==Me;6==COOMe}% -}{1A==Me;4Sa==\null;4Sb==\null} -\end{center} - -The following structure shows the use of SKBONDLIST in -drawing a spiro ring. - -\begin{verbatim} -\sixheterov[be]{% -1s==\fiveheterov({aA}{eB}){4==N}% -{4==PhCH$_{2}$OCO;3SB==H;3SA==COOCH$_{2}$Ph;5D==O;1==(yl)}% -}{4D==O} -\end{verbatim} -\begin{center} -\vspace*{1cm} -\sixheterov[be]{% -1s==\fiveheterov({aA}{eB}){4==N}% -{4==PhCH$_{2}$OCO;3SB==H;3SA==COOCH$_{2}$Ph;5D==O;1==(yl)}% -}{4D==O} -\end{center} - -\section{Bond Deletion} - -The OMIT argument of each command for general use is used -to draw a large ring. The following example is -a simple case in which one bond is deleted: -\begin{verbatim} -\decaheterov{9==O}{4==O;8D==O;5==CH$_{3}$}[k] -\end{verbatim} -\begin{center} -\decaheterov{9==O}{4==O;8D==O;5==CH$_{3}$}[k] -\end{center} - -The absence and presence of the OMIT argument -give different formulas as follows. -\begin{verbatim} -\decaheterov[{k\threefuseh{}{}{b}}]{}{} -\decaheterov[{k\threefuseh{}{}{b}}]{}{}[k] -\end{verbatim} -\begin{center} -\decaheterov[{k\threefuseh{}{}{b}}]{}{} -\decaheterov[{k\threefuseh{}{}{b}}]{}{}[k] -\end{center} - -A complicated case contains a ring fusion as follows. -First, the code -\begin{verbatim} -\decaheterov[cegi]{2==\null}{6==MeO;8==OMe;1D==O}[b] -\end{verbatim} -generates the follwing formula: -\begin{center} -\decaheterov[cegi]{2==\null}{6==MeO;8==OMe;1D==O}[b] -\end{center} -where \verb/[b]/ indicates the deletion of bond `b'. -A similar mechanism is also available in a fusing unit, -\verb/\sixunitv/. The code, -\begin{verbatim} -\sixfusev{6==O}{}{E}[b] -\end{verbatim} -generates a formula: -\begin{center} -\sixfusev{6==O}{}{E}[b] - -\vspace*{2cm} -\end{center} -where bond `e' is deleted by means of the FUSE argument (E) -and bond `b' is deleted by means of the OMIT argument (b). -Finally, we have the structural formula of zearalenone: -\begin{verbatim} -\decaheterov[cegi% -{b\sixfusev[% -{b\sixfusev{}{3D==O}{E}}% -]{6==O}{}{E}[b]}% -]{2==\null% -}{6==MeO;8==OMe;1D==O}[b] -\end{verbatim} -\begin{center} -\decaheterov[cegi% -{b\sixfusev[% -{b\sixfusev{}{3D==O}{E}}% -]{6==O}{}{E}[b]}% -]{2==\null% -}{6==MeO;8==OMe;1D==O}[b] -\end{center} - -Intermediates for steroid synthesis via intermolecular -cycloadditions of $o$-quinodimethane derivatives -(Kametani, et al. {\em J. Org. Chem.}, 1980, {\bf 45}, 2204; -Grieco, et al. {\em J. Org. Chem.}, 1980, {\bf 45}, 2247) -can be drawn by the bond deletion of \verb/\decaheterov/ and -\verb/\nonaheterov/. -\begin{verbatim} -\decaheterov({jA}{dB}){% -2s==\fourhetero[{b\sixfusev[ace]{}{2==OMe}{e}}]% -{}{1==(yl)}% -}{6B==HO;9A==H;{10}B==\null;1D==\null}[a] -\end{verbatim} -\begin{center} -\vspace*{1cm} -\decaheterov({jA}{dB}){% -2s==\fourhetero[{b\sixfusev[ace]{}{2==OMe}{e}}]% -{}{1==(yl)}% -}{6B==HO;9A==H;{10}B==\null;1D==\null}[a] -\end{center} - - -\begin{verbatim} -\nonaheterov({dA}{hB}){% -6s==\fourhetero[% -{d\sixfusev[bdf]{}{5==MeO}{b}}]% -{}{3==(yl)}% -}{3B==OH;8B==\null;7D==\null;9A==H}[g] -\end{verbatim} -\begin{center} -\nonaheterov({dA}{hB}){% -6s==\fourhetero[% -{d\sixfusev[bdf]{}{5==MeO}{b}}]% -{}{3==(yl)}% -}{3B==OH;8B==\null;7D==\null;9A==H}[g] - -\vspace*{1cm} -\end{center} - -A remarkable merit of using a skeleton with deleted bonds -appears in drawing a starting compound with an acyclic part -along with the resulting product via cyclization, -since their codes are akin to each other. -\begin{verbatim} -\decaheterov[{4+}% -{c\fivefusevi[e]{5==\null}{4D==O}{E}}% -]{4==N}{1D==\null;9B==H;{10}B==H}[ab] -\hskip2cm -\decaheterov[% -{c\fivefusevi{5==\null}{4D==O}{E}}% -]{4==N}{1B==OCHO;9B==H;{10}B==H;3FA==H} -\end{verbatim} -\begin{center} -\decaheterov[{4+}% -{c\fivefusevi[e]{5==\null}{4D==O}{E}}% -]{4==N}{1D==\null;9B==H;{10}B==H}[ab] -\hskip2cm -\decaheterov[% -{c\fivefusevi{5==\null}{4D==O}{E}}% -]{4==N}{1B==OCHO;9B==H;{10}B==H;3FA==H} - -\vspace*{1cm} -\end{center} -The latter compound was obtained by -the cyclization of the former -(D. J. Hart, et al., {\em J. Am. Chem. Soc.}, 1980, {\bf 102}, -397). - -Some polymethylene chains are drawn in a folded form. -The bond-deletion technique can be applied to -drawing such folded formulas. - -\begin{verbatim} -\sixheterov{% -3s==\fiveheterovi{1==O;4==O}{5==(yl)};% -6s==\dimethylenei{}{1D==\null;2==(yl)};% -5s==\trimethylenei{}{1W==EtO;1D==O;3==(yl)}% -}{}[e] -\end{verbatim} -\begin{center} -\sixheterov{% -3s==\fiveheterovi{1==O;4==O}{5==(yl)};% -6s==\dimethylenei{}{1D==\null;2==(yl)};% -5s==\trimethylenei{}{1W==EtO;1D==O;3==(yl)}% -}{}[e] -\end{center} - -The following formula, which is an intermediate for -synthesizing steroid skeletons, can also been -drawn by this technique. - -\begin{verbatim} -\decaheterov[k% -{f\fivefusevi{2==\null;5==O}{}{A}}% -{a\sixfusev[d% -{b\fivefusevi[d% -{a\sixfusev{% -3s==\trimethylenei[a]{}{1==(yl);2==\null}% -}{6==\null}{D}[c]}% -]{}{}{D}}% -]{}{3G==\null}{D}[c]}% -]{5==O}{{10}Sb==\null;2G==\null}[ej] -\end{verbatim} -\begin{center} -\vspace*{2cm} -\decaheterov[k% -{f\fivefusevi{2==\null;5==O}{}{A}}% -{a\sixfusev[d% -{b\fivefusevi[d% -{a\sixfusev{% -3s==\trimethylenei[a]{}{1==(yl);2==\null}% -}{6==\null}{D}[c]}% -]{}{}{D}}% -]{}{3G==\null}{D}[c]}% -]{5==O}{{10}Sb==\null;2G==\null}[ej] -\end{center} - - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\chapter{Enhanced Functions of Commands for Ring Fusion} - -\section{Expanded Format} - -Commands for ring fusion, e.g. \verb/\sixfusev/, have originally -taken a comman format (version 1.02 not released): -\begin{verbatim} -\fuseCOM[BONDLIST]{ATOMLIST}{SUBSLIST}{FUSE} -\end{verbatim} -where \verb/\fuseCOM/ represents a command name such as -\verb/\sixfusev/. In \XyMTeX{} version 2.00, -we add a top optional argument SKBONDLIST -to treat stereochemical information as well as -an end optional argument OMIT to treat a bond-deleted skeleton. -Thus, the expanded format of each command for general use -is represented by -\begin{verbatim} -\fuseCOM(SKBONDLIST)[BONDLIST]{ATOMLIST}{SUBSLIST}{FUSE}[OMIT] -\end{verbatim} -The argument SKBONDLIST contains pairs of two alphabets in braces, -where (1) each pair consists of a bond specifier (a lowercase letter) -and an uppercase letter (A or B); and (2) the letter A represents -an $\alpha$ (downward) bond, -while B represents a $\beta$ (upward) bond. -The argument OMIT is a list of bond specifiers, each of -which designates a bond to be deleted. As a matter of course, -SKBONDLIST takes no common bond specifiers with FUSE and OMIT. - -\section{Boldfaced and Dotted Bonds} - -The first example shows that the command -\verb/\fivefusev/ with a SKBONDLIST -generates a formula with dotted bonds at fused positions. -\begin{verbatim} -\nonaheterov[% -{e\fivefusev({bA}{eA}){5==O}{3B==\null;4D==O}{A}}% -]{1==N}{1==COOMe;8A==H;9B==H;% -6B==\trimethylene[a]{}{3==(yl)};% -7A==\dimethylene{}{2==(yl);1==OH}} -\end{verbatim} -\begin{center} -\vspace*{1cm} -\nonaheterov[% -{e\fivefusev({bA}{eA}){5==O}{3B==\null;4D==O}{A}}% -]{1==N}{1==COOMe;8A==H;9B==H;% -6B==\trimethylene[a]{}{3==(yl)};% -7A==\dimethylene{}{2==(yl);1==OH}} - -\vspace*{1cm} -\end{center} - -The next example shows the use of the SKBONDLISTS of -\verb/\threefuseh/ and \verb/\fivefusevi/ -to indicate stereochemical information. -\begin{verbatim} -\sixheterov[% -{b\threefuseh({aA}{cA}){1==O}{}{B}}% -{d\fivefusevi({bB}{eB}){3==N;5==O}{3==BOM;4D==O}{A}}% -]{1==O}{6A==PMPO-CH$_{2}$} -\end{verbatim} -\begin{center} -\sixheterov[% -{b\threefuseh({aA}{cA}){1==O}{}{B}}% -{d\fivefusevi({bB}{eB}){3==N;5==O}{3==BOM;4D==O}{A}}% -]{1==O}{6A==PMPO-CH$_{2}$} -\end{center} - -\section{Bond Deletion} -\subsection{Larger Rings from Two or More Three-Membered Rings} -To draw a fused four-membered ring, we can -use two \verb/\threefuseh(i)/ commands in a nested fashion. -Four example, the code -\begin{verbatim} -\threefusehi[{b\threefuseh{1==O}{}{b}}]{}{}{c}[b]% -\end{verbatim} -generates a four-membered unit: -\begin{center} -\threefusehi[{b\threefuseh{1==O}{}{b}}]{}{}{c}[b]% - -\vspace*{1cm} -\end{center} -The resulting unit is used to draw a four-membered -fused ring, as shown below: -\begin{verbatim} -\sixheterov[% -{c\threefusehi[{b\threefuseh{1==O}{}{b}}% -]{}{}{c}[b]}% -]{}{} -\end{verbatim} -\begin{center} -\sixheterov[% -{c\threefusehi[{b\threefuseh{1==O}{}{b}}% -]{}{}{c}[b]}% -]{}{} -\end{center} - -In a similar way, -a five-membered fusing usit can be drawn -by combining three \verb/\threefuseh(i)/ commands, -as shown in the following example: -\begin{verbatim} -\decaheterov[% -{d\threefuseh[% -{a\threefusehi[% -{a\threefuseh{1==\null;3==\null}{2D==O}{c}}% -]{2==O;1==\null}{}{c}[a]}% -]{2==O}{}{C}[a]}% -]{}{} -\end{verbatim} -\begin{center} -\decaheterov[% -{d\threefuseh[% -{a\threefusehi[% -{a\threefuseh{1==\null;3==\null}{2D==O}{c}}% -]{2==O;1==\null}{}{c}[a]}% -]{2==O}{}{C}[a]}% -]{}{} - -\vspace*{1cm} -\end{center} - -\subsection{Further Rings} - -A six-membered ring fused by a four-membered unit -gives an eight-membered ring as follows: -\begin{verbatim} -\sixheterov[{b\fourfuse{}{}{d}}]{}{}[b] -\end{verbatim} -\begin{center} -\sixheterov[{b\fourfuse{}{}{d}}]{}{}[b] -\end{center} -The bond `b' of the four-membered unit in -the resulting ring is deleted and used -as an acceptor ring of a six-membered fusing -unit. Then, we have a twelve-membered ring: -\begin{verbatim} -\sixheterov[{b\fourfuse[{b\sixfusev{}{}{e}}]{}{}{d}[b]}]{}{}[b] -\end{verbatim} -\begin{center} -\sixheterov[{b\fourfuse[{b\sixfusev{}{}{e}}]{}{}{d}[b]}]{}{}[b] -\end{center} -After applying the bond-deletion technique to the -twelve-membered ring, this is used as an acceptor of -a five-membered fusing unit. Then we have a -fifteen-membered ring: -\begin{verbatim} -\sixheterov[{b\fourfuse[{b\sixfusev[% -{b\fivefusev{}{}{d}}% -]{}{}{e}[b]}]{}{}{d}[b]}]{}{}[b] -\end{verbatim} -\begin{center} -\sixheterov[{b\fourfuse[{b\sixfusev[% -{b\fivefusev{}{}{d}}% -]{}{}{e}[b]}]{}{}{d}[b]}]{}{}[b] -\end{center} -A further fusion of a six-membered unit gives -a ninteen-membered ring: -\begin{verbatim} -\sixheterov[{b\fourfuse[{b\sixfusev[% -{b\fivefusev[% -{a\sixfusev{}{}{f}}% -]{}{}{d}[a]}% -]{}{}{e}[b]}]{}{}{d}[b]}]{}{}[b] -\end{verbatim} -\begin{center} -\sixheterov[{b\fourfuse[{b\sixfusev[% -{b\fivefusev[% -{a\sixfusev{}{}{f}}% -]{}{}{d}[a]}% -]{}{}{e}[b]}]{}{}{d}[b]}]{}{}[b] -\end{center} - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% - -\chapter{Reaction Schemes} -\section{Compound Numbers} - -\begingroup -%%%%%%%%%%%%%%% -\makeatletter -\def\DeclareMathVersion#1{} -\def\SetSymbolFont#1#2#3#4#5#6{} -\@@input chemist.sty -\makeatother -%%%%%%%%%%%%%%% - -The XyMcompd environment has two functions: -\begin{enumerate} -\itemsep=0pt \parskip=0pt -\item for giving a compound number and specifying a reference key and -\item for specifyin the size of a domain to draw a structural formula. -\end{enumerate} -For example, the code: -\begin{verbatim} -\begin{XyMcompd}(400,750)(220,200){cPhCL}{} -\bzdrv{1==Cl} -\end{XyMcompd} -\end{verbatim} -produces the following formula, -\begin{center} -\begin{XyMcompd}(400,750)(220,200){cPhCL}{} -\bzdrv{1==Cl} -\end{XyMcompd} -\end{center} -The compound number (\cref{cPhCL}) can be referred to -by designating \verb/\cref{cPhCL}/. -The code \verb/(400,750)/ specifies the size of -the drawing domain and the code \verb/(220,200)/ represents -x- and y-shift values. -When the XyMcompd environment is -surrounded by a frame generated by the \verb/\fbox/ command, -we obtain the following diagram: -\begin{center} -\fbox{% -\begin{XyMcompd}(400,750)(220,200){c1PhCL}{} -\bzdrv{1==Cl} -\end{XyMcompd}} -\end{center} -The original \verb/\bzdrv/ command -has a domain to accomodate substituents as follows: -\begin{center} -\fbox{\bzdrv{1==Cl}} -\end{center} -If such adjustment and cross-reference are unnecessary, -we write the code: -\begin{verbatim} -\begin{XyMcompd}(,)(,){}{} -\sixheterov{1==S;4==S}{} -\end{XyMcompd} -\end{verbatim} -Thereby, we obtain the formula of the original -specification: -\begin{center} -\begin{XyMcompd}(,)(,){}{} -\sixheterov{1==S;4==S}{} -\end{XyMcompd} -\end{center} -which is the same formula generated by the code: -\begin{verbatim} -\sixheterov{1==S;4==S}{} -\end{verbatim} -The last argument of the XyMcompd environment is -to specify the subnumber of a compound number. -For example, the code: -\begin{verbatim} -\begin{XyMcompd}(400,750)(220,200){PhF}{a} -\bzdrv{1==F} -\end{XyMcompd} -\end{verbatim} -produces the following formula, -\begin{center} -\begin{XyMcompd}(400,750)(220,200){PhF}{a} -\bzdrv{1==F} -\end{XyMcompd} -\end{center} - -Derivatives of a compound -numbered in the XyMderiv environment -are designated by -subnumbering using a \verb/\derivlist/ command -in the XyMderiv environment. -For example, the code: -\begin{verbatim} -\begin{XyMderiv} -\begin{XyMcompd}(400,750)(220,200){PhX}{} -\bzdrv{1==X} -\end{XyMcompd} -\derivlist{X = Cl;X = NO$_{2}$;X = F} -\end{XyMderiv} -\end{verbatim} -produces the following formula: -\begin{center} -\begin{XyMderiv} -\begin{XyMcompd}(400,750)(220,200){PhX}{} -\bzdrv{1==X} -\end{XyMcompd} -\derivlist{X = Cl;X = NO$_{2}$;X = F} -\end{XyMderiv} -\end{center} - -\section{Reaction Arrows} - -In addition of the reaction arrows described in -Ref.\ \cite{fujita2}, we have added -further reaction arrows shown in Fig.\ \ref{FFA1KKKR}. -They are defined in the package {\sf chemist.sty}. -Each arrow command is the following format: -\begin{verbatim} -\ARROWNAME[xshift]{yshift}{length}{itemover}{itemunder} -\end{verbatim} -where \verb/\ARROWNAME/ represents a command name; -\verb/xshift/ is an optional argument to show a -horizontal adjustment value; -\verb/yshift/ is an argument to show a vertical adjustment value; -\verb/length/ is an argument to desiginate the length of the arrow; -and the arguments -\verb/itemover/ and \verb/itemunder/ -represent items placed over and under the arrow. -The name (\verb/\ARROWNAME/) of each reaction arrow take the format of -\verb/\react/$\ldots$\verb/arrow/ in which $\ldots$ -is selected from the following list: -r = right arrow, l = left arrow, lr = leftright arrow, -d = down arrow, u = up arrow, du = down up arrow, -eq = equilibium arrow, veq = vertical equiliblium arrow, -deq = down equiliblium arrow, leq = up equilibium arrow, -dlr = down leftright arrow, ulr = up leftright arrow, -sw = southwest arrow, se = southeast arrow, -nw = northwest arrow, and ne = northeast arrow. - -\begin{figure} -\begin{center} -\begin{center}\begin{tabular}{ccccccccc} -(r) & -\hskip0\unitlength -\reactrarrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&(l) & -\hskip0\unitlength -\reactlarrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&(d) & -\hskip0\unitlength -\reactdarrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&(u) & -\hskip0\unitlength -\reactuarrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&\\(sw) & -\hskip0\unitlength -\reactswarrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&(se)& -\hskip0\unitlength -\reactsearrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&(nw) & -\hskip0\unitlength -\reactnwarrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&(ne) & -\hskip0\unitlength -\reactnearrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&\\(du)& -\hskip0\unitlength -\reactduarrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&(lr) & -\hskip0\unitlength -\reactlrarrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&(ulr)& -\hskip0\unitlength -\reactulrarrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&(dlr)& -\hskip0\unitlength -\reactdlrarrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&\\(eq) & -\hskip0\unitlength -\reacteqarrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&(ueq) & -\hskip0\unitlength -\reactueqarrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&(deq)& -\hskip0\unitlength -\reactdeqarrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&(veq) & -\hskip0\unitlength -\reactveqarrow{0\unitlength}{400\unitlength} -{\strut{}HCl\\}{\strut{}H\mbox{$_{2}$}O\\}&\\\end{tabular}\end{center}\end{center} -\def\tblref{FFA1KKKR} -\caption{Reaction arrows of various types} -\label{\expandafter\tblref} -\end{figure} - -\section{Display Formulas and Tabular Schemes} - -Display formulas containing structural formulas and -reaction arrows are -drawn by using the equation environment of \LaTeX{} or -the chemeqn environment of the {\sf chemist} package. -For example, the code, -\begin{verbatim} -\begin{equation}\label{EQ1} -\begin{XyMcompd}(400,750)(220,200){BPHOH}{} -\bzdrv{1==OH} -\end{XyMcompd} -\reactrarrow[10\unitlength]{60\unitlength}{500\unitlength} -{CH\mbox{$_{3}$}OH\\}{HCl\\} -\begin{XyMcompd}(400,750)(220,200){PHOME}{} -\bzdrv{1==OCH\mbox{$_{3}$}} -\end{XyMcompd} -\end{equation} -\end{verbatim} -produces the following display formula: -\begin{equation}\label{EQ1} -\begin{XyMcompd}(400,750)(220,200){AAPHOH}{} -\bzdrv{1==OH} -\end{XyMcompd} -\reactrarrow[10\unitlength]{60\unitlength}{500\unitlength} -{CH\mbox{$_{3}$}OH\\}{HCl\\} -\begin{XyMcompd}(400,750)(220,200){PHOME}{} -\bzdrv{1==OCH\mbox{$_{3}$}} -\end{XyMcompd} -\end{equation} - -Tabular schemes containing structural formulas and -reaction arrows are drawn by using -the XyMtab environment of the {\sf chemist} package. -For example, the code, -\begin{verbatim} -\begin{XyMtab}{cccccc} -\begin{XyMcompd}(400,750)(220,200){AAPHCL}{} -\bzdrv{{1}==Cl;} -\end{XyMcompd} -& -\reactrarrow[10\unitlength]{60\unitlength}{600\unitlength} -{\strut{}H\mbox{$_{2}$}O\\}{\strut{}High press.\\}& -% -\begin{XyMcompd}(400,750)(220,200){AAPHOH}{} -\bzdrv{{1}==OH;} -\end{XyMcompd} -& -\reactrarrow[10\unitlength]{60\unitlength}{500\unitlength} -{\strut{}CH\mbox{$_{3}$}I\\}{\strut{}NaOH\\}& -% -\begin{XyMcompd}(400,750)(220,200){AAPHOME}{} -\bzdrv{{1}==OCH\mbox{$_{3}$};} -\end{XyMcompd} -% -&\\&&& -\reactswarrow[0\unitlength]{300\unitlength}{400\unitlength} -{\strut{}HNO\mbox{$_{3}$}\\}{\strut{}}& -% -\begin{XyMcompd}(400,850)(220,0){APHNO2}{} -\bzdrv{{1}==OH;{4}==NO\mbox{$_{2}$};} -\end{XyMcompd} -&\\ -\end{XyMtab} -\end{verbatim} -generates a tabular scheme as follows: -\begin{XyMtab}{cccccc} -\begin{XyMcompd}(400,750)(220,200){AAPHCL}{} -\bzdrv{{1}==Cl;} -\end{XyMcompd} -& -\reactrarrow[10\unitlength]{60\unitlength}{600\unitlength} -{\strut{}H\mbox{$_{2}$}O\\}{\strut{}High press.\\}& -% -\begin{XyMcompd}(400,750)(220,200){AAPHOH}{} -\bzdrv{{1}==OH;} -\end{XyMcompd} -& -\reactrarrow[10\unitlength]{60\unitlength}{500\unitlength} -{\strut{}CH\mbox{$_{3}$}I\\}{\strut{}NaOH\\}& -% -\begin{XyMcompd}(400,750)(220,200){AAPHOME}{} -\bzdrv{{1}==OCH\mbox{$_{3}$};} -\end{XyMcompd} -% -&\\&&& -\reactswarrow[0\unitlength]{300\unitlength}{400\unitlength} -{\strut{}HNO\mbox{$_{3}$}\\}{\strut{}}& -% -\begin{XyMcompd}(400,850)(220,0){APHNO2}{} -\bzdrv{{1}==OH;{4}==NO\mbox{$_{2}$};} -\end{XyMcompd} -&\\ -\end{XyMtab} - - -\endgroup - - - - -\begin{thebibliography}{99} - -\bibitem{fujita2a} NIFTY-Serve achives, -FPRINT library No. 7, Item Nos. 201, 202, 204. -\bibitem{fujita2b} CTAN, -tex-archive/macros/latex209/contrib/xymtex/. -\bibitem{fujita1} Fujita S., ``Typesetting structural formulas with -the text formatter \TeX{}/\LaTeX{}'', -{\em Comput. Chem.}, {\bf 18}, 109 (1994). -\bibitem{fujita1a} Fujita S., ``\XyMTeX{} for Drawing Chemical -Structural Formulas'', -{\em TUGboat}, {\bf 16} (1), 80 (1995). -\bibitem{lamport2} -Lamport L., {\em \LaTeX{}. A document Preparation System}, -2nd ed. for \LaTeXe{}, Addison-Wesley, Reading (1994). -See also -Lamport L., {\em \LaTeX{}. A document Preparation System}, -Addison-Wesley, Reading (1986). -\bibitem{goossens} -Goossens, M., Mittelbach, F., \& Samarin, A., -{\em The \LaTeX{} Companion}, -Addison-Wesley, Reading (1994). -\bibitem{fujita2c} NIFTY-Serve achives, -FPRINT library No. 7, Item Nos. 385, 386. -\bibitem{fujita2d} -http://www.chem.kit.ac.jp/fujita/fujitas/fujita.html -\bibitem{XyMTeXbook} -Fujita, S., {\em \XyMTeX{}---Typesetting Chemical Structural -Formulas}, Addison-Wesley, Tokyo (1997). -The book title is abbreviated as ``\XyMTeX book'' in -the present manual. -\bibitem{knuth} -For the \TeX{} system, see - Knuth D. E., {\em The \TeX{}book}, -Addison-Wesley, Reading (1984). -\bibitem{haas} -For the Chem\TeX{} macros, see - Haas R. T. \& O'Kane K. C., {\em Comput. Chem.}, {\bf 11}, 251 (1987). -\bibitem{ramek} -For drawing chemical formulas by \TeX{}, see -Ramek, M., in Clark, M. (ed), \TeX: Applications, Uses, Methods, -Ellis Horwood, London (1990), p. 277. -\bibitem{fujita2} -For chemical application of the \LaTeX{} system, see -Fujita S., {\em Kagakusha-Seikagakusha no tame no -\LaTeX{} (\LaTeX{} for Chemists and Biochemists)}, -Tokyo Kagaku Dozin, Tokyo (1993). -\bibitem{podar} -For epic macros, see -Podar S., ``Enhancements to the picture environment -of \LaTeX{}'', Manual for Version 1.2 dated July 14, 1986. -\bibitem{graphic} -For graphic applications of \TeX{}, \LaTeX{} and relevant systems, -see Goossens, M., Rahtz, S., \& Mittelbach, F., -{\em \LaTeX{} Graphics Companion}, -Addison Wesley Longman, Reading (1997). -\end{thebibliography} - -\endinput - -\begin{verbatim} -\end{verbatim} -\begin{center} -\end{center} - - \ No newline at end of file diff --git a/Master/texmf-dist/doc/latex/xymtex/xymman.sty b/Master/texmf-dist/doc/latex/xymtex/xymman.sty deleted file mode 100644 index efe164c419e..00000000000 --- a/Master/texmf-dist/doc/latex/xymtex/xymman.sty +++ /dev/null @@ -1,63 +0,0 @@ -% xymman.sty 23-Nov-93 Shinsaku Fujita -% For XyMTeX document -% Copyright (C) 1993 by Shinsaku Fujita, all rights reserved. -% This style file is created for submitting a manuscript to -% Journal of the American Chemical Society. -% This style file is to be contained in the ``chemist'' directory -% which is an input directory for TeX. -% Copying of this file is authorized only if either -% (1) you make absolutely no changes to your copy, including name and -% directory name -% (2) if you do make changes, -% (a) you name it something other than the names included in the -% ``chemist'' directory and -% (b) you acknowledge the original name. -% This restriction ensures that all standard styles are identical. -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\def\j@urnalname{xymman} -\def\versi@ndate{November 24, 1993} -\def\versi@nno{ver1.00} -\def\copyrighth@lder{SF} % Shinsaku Fujita -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\typeout{Option Style `\j@urnalname' (\versi@nno) <\versi@ndate>\space -[\copyrighth@lder]} -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\textwidth=16cm -\textheight=22cm -\topmargin-.3in -\oddsidemargin=-0.1cm -\evensidemargin=-0.1cm -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\def\markleft#1{{\let\protect\noexpand - \let\label\relax \let\index\relax - \expandafter\@markleft\@themark - {#1}\mark{\@themark}}% - \if@nobreak\ifvmode\nobreak\fi\fi} -\def\@markleft#1#2#3{\gdef\@themark{{#3}{#2}}} -\def\LEFTmark{\expandafter\@leftmark\botmark} -% -\def\ps@headings{\let\@mkboth\markboth -\def\@oddfoot{}\def\@evenfoot{} -\def\@evenhead{\underline{% -\hbox to\textwidth{\rm \thepage\hfil \sl\LEFTmark}}}% -\def\@oddhead{\underline{\hbox to\textwidth{% -\vphantom{\TeX}\sl\rightmark\hfil\rm\thepage}}}% -\def\chaptermark##1{\markboth {FUJITA S.: \protect\XyMTeX{}}% -{\uppercase{\ifnum \c@secnumdepth>\m@ne% - \@chapapp\ \thechapter. \ \fi ##1}}}% -\def\sectionmark##1{\markleft{FUJITA Shinsaku: \protect\XyMTeX{}}}} -\ps@headings -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\@ifundefined{XyMTeX}{\def\UPSILON{\char'7}% -\def\XyM{X\kern-.30em\smash{\raise.50ex\hbox{\UPSILON}}\kern-.30em{M}}% -\def\XyMTeX{\XyM\kern-.1em\TeX}}{}% -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\newenvironment{xymspec}{\begin{center}\begingroup\origpttrue}% -{\endgroup\end{center}} -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\@ifundefined{shiftii}{% -\newcount\shiftii -\newcount\shifti -\newcount\noshift -\noshift=0 \shiftii=400 \shifti=240\relax}{} - \ No newline at end of file diff --git a/Master/texmf-dist/doc/latex/xymtex/xymtex2.doc b/Master/texmf-dist/doc/latex/xymtex/xymtex2.doc deleted file mode 100644 index 91a2b797172..00000000000 --- a/Master/texmf-dist/doc/latex/xymtex/xymtex2.doc +++ /dev/null @@ -1,94 +0,0 @@ -xymtex2.doc -On-line document for XyMTeX in English -Copyright (C) 1993, 1996, 1998 by Shinsak Fujita. All rights reserved. -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -renamed and revised: xymtex1.doc -Copyright (C) 1993, 1996 by Shinsak Fujita. All rights reserved. -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -`XyMTeX' is a macro package for drawing chemical structural formulas. - -(1) Setting up - - This package has been frozen with LHA. Let the frozen package - (xymtex2.lzh) be placed in the b: directory. To melt the frozen package - in the a:\tex directory, please input the following statement in the - command line of your display. - - a:\tex>lha x b:\xymtex2 - - Thereby, the directory <\xymtex> is automatically created as the - subdirectory of the a:\tex directory; and the following hierarchy of - directories and files is generated. - - a---\tex---\xymtex --- hetaromh.sty, hetarom.sty, ccycle.sty, - | | | chemstr.sty, carom.sty, lowcycl.sty, aliphat.sty, - | hcycle.sty, locant.sty, polymers.sty, chemist.sty - | methylen.sty, fusering.sty - | - | (dtx files) - | - |--\drvdvi---drv files, dvi files - | - |--\doc200--- xymtx200.tex, xymtx200.dvi, - | xymyl.tex, xymadd.tex - | (other files for the document preparation) - | - |---xymtex2.doc (this document) - | - |---xymtex2.jpn (on-line document in Japanes) - | - |---readme2.doc (notes in English) - | - |---readme2.jpn (notes in Japanese) - - The package (sty) files in the \xymtex directory contains the macro - codes of XymTeX commands. The specification of XyMTeX commands and - examples of using these commands are included in the xymtex.dvi file of - the \doc directory. - - The xymtx200.dvi file is a dvi file that is a manual for utilizing - XyMTeX (about 100 pages). The processed dvi file can be obtained in the same - directory of this distribution. It can be printed with an appropriate - printer driver (lips3dvi, dviprt, or others) and can be displayed with an - appropriate previewer (dviout, etc.). - - The xymtx200.tex is the main file of the manuscript for creating the - xymtx200.dvi. The other tex files in the \doc200 directory are input files - which are read by the main file. - -(2) Designating a serach path - - In order to set a search path for using XyMTeX, please add the directory - name to the TEXINPUTS line in \texmf.cnf, which is stored in the - \tex\texmf\web2c directory (for a standard distribution of LaTeX2e). - For example, you add - - platex2e_inputs = .;$TEXMF/tex/platex2e//;$TEXMF/tex/latex2e//; - $TEXMF/tex//;a:/tex/inputs//; - a:/tex/chem//;a:/tex/xymtex//;a:/tex/opsty// - ~~~~~~~~~~~~~~~ <---- to be added - -(3) Writing your manuscript - - Each command of XyMTeX can be used if you add the name of the - corresponding style file to the option list at the top of your - manuscript file, e.g. - - \documentclass{article} - \usepackage{epic,hetarom,hetaromh} - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - where the underlined names are XyMTeX package files containing your - requisite commands. If all of the XyMTeX commands are required, - the short-cut declaration - - \documentclass{article} - \usepackage{xymtex} - - can be used for simplicity. - -(4) Running LaTeX2e or pLaTeX2e - - You should use XyMTeX commands within LaTeX. - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%(END) - \ No newline at end of file diff --git a/Master/texmf-dist/doc/latex/xymtex/xymtx200.dvi b/Master/texmf-dist/doc/latex/xymtex/xymtx200.dvi deleted file mode 100644 index c9b596e907e..00000000000 Binary files a/Master/texmf-dist/doc/latex/xymtex/xymtx200.dvi and /dev/null differ diff --git a/Master/texmf-dist/doc/latex/xymtex/xymtx200.tex b/Master/texmf-dist/doc/latex/xymtex/xymtx200.tex deleted file mode 100644 index fd7de31385c..00000000000 --- a/Master/texmf-dist/doc/latex/xymtex/xymtx200.tex +++ /dev/null @@ -1,56 +0,0 @@ -%xymtx200.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' for drawing chemical structural formulas. -%This file is not permitted to be translated into Japanese and any other -%languages. -\typeout{``xymtx200.tex''--- -This file is a part of xymtex.tex that is the manual of the macro % -package `XyMTeX'. 1998/12/25 S. Fujita} -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\documentclass{book} -%\usepackage{xymtex} -\usepackage{carom} -\usepackage{hetaromh} -\usepackage{aliphat} -\usepackage{hcycle} -\usepackage{fusering} -\usepackage{methylen} -\usepackage{locant} -\usepackage{lowcycle} -\usepackage{epic} -\usepackage{xymman} -% -\begin{document} -\mbox{} -\thispagestyle{empty} -\vfill -\begin{center} -{\LARGE\bfseries \protect\XyMTeX{} for -Typesetting Chemical Structural Formulas. -Enhanced Functions for Version 2.00} - -\vspace*{2cm} -{\Large\bfseries Shinsaku Fujita} - -\vspace*{1cm} -Department of Chemistry and Materials Technology, \\ -Kyoto Institute of Technology, \\ -Matsugasaki, Sakyoku, Kyoto, 606 Japan -\par\vspace*{1cm} -December 25, 1998 (Version 2.00) \\ -(revised March 20, 1999) -\end{center} -\vfill\mbox{} -% -\newpage -\tableofcontents -% -\input{xymyl} -\input{xymadd} - -\end{document} - - - \ No newline at end of file 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} - - \ No newline at end of file -- cgit v1.2.3