IUPAC For Peer Review Only Nomenclature for Rotaxanes IUPAC Provisional Recommendations Journal: Pure and Applied Chemistry Manuscript ID: PAC-REC-05-12-09 Manuscript Type: Recommendation Date Submitted by the 16-Dec-2005 Author: Complete List of Authors: Yerin, Andrey; Advanced Chemistry Development Metanomski, W. Val; Chemical Abstracts Service Moss, Gerard; Queen Mary College, University of London, Department of Chemistry Wilks, Edward S.; N/A Harada, Aika; Osaka University, Graduate School of Science Chemical Nomenclature and Structure Representation Division, Keywords: nomenclature, rotaxanes, molecular shuttles, threading component, threadable ring, rotaxane isomerism, rotaxane stereoisomerism P.O. 13757, Research Triangle Park, NC (919) 485-8700 Page 1 of 43 DRAFT 16 Dec 2005 Page 1 of 42 IUPAC 1 2 INTRODUCTORY NOTES 3 for IUPAC Provision al Recommendations 4 "NOMENCLATURE FOR ROTAXANES" 5 6 7 The first IUPAC recommendations for naming of rotaxanes provide a method for 8 unambiguous description of composition and structure of various types of rotaxanes and 9 inclu de the following main parts: 10 1. Definitions of terms used in rotaxanes: 11 12 a. rotaxane itself , 13 b. rotaxane components, 14 i. threading component and linear section, 15 ii. macrocyclic component and threadable ring, 16 c. molecularFor shuttles Peer and recognition Review sites. Only 17 2. History of the nomenclat ure of rotaxanes . 18 19 3. Classification of rotaxane types . 20 4. Generic name format for rotaxanes. 21 5. Types of rotaxane isomerism and description of the location of simple macrocyclic 22 components at different linear sections of a complex threading component and 23 location o f simple threading components in macrocyclic components with several 24 IUPAC Provisional Recommendations 25 threadable rings . 26 6. Types and specification of rotaxane stereoisomerism – orientation of rotaxane 27 components in relation to each other. 28 7. Examples of rotaxanes and recommended names. 29 30 The rec ommended generic name format is: 31 32 33 prefix -[v]{[ w1](TC 1)-[w2](TC 2)-…-rotaxa -[x1](MC 1)-[x2](MC 2)-... } 34 where: 35 TC n – names of threading components, 36 rotaxa - a connect or to join the names of the thread ing and macrocyclic 37 38 components, 39 MC n – names of macrocyclic co mponents, 40 wn and xn – number s of specific threading and macrocyclic components 41 respectively , 42 v – total number of rotaxane components – sum of wn and xn, 43 44 prefix – description of position and orientation of rotaxane components with respect 45 to each other if v ariants are possible . 46 47 The recommended name format allows use of retained names and abbreviations for 48 components in rotaxane names for general use, but chemical names created according to 49 IUPAC nomenclature recommendations are preferred in systematic nom enclature. 50 51 52 The recommendations provide principles to specify isomerism for the following 53 basic types of rotaxanes: 54 - rotaxanes composed of simple threading components and simple macrocyclic 55 components, 56 57 - rotaxanes composed of several simple macrocyclic compo nents and a single 58 threading component with several linear sections, 59 - rotaxanes composed of a single complex macrocyclic component with several 60 threadable rings and several simple threading components - molecular shuttles . For specification of positional iso merism in rotaxanes that include macrocyclic components with several threading rings, the prefix includes the number of threading P.O. 13757, Research Triangle Park, NC (919) 485-8700 DRAFT 16 Dec 2005 Page 2 of 43 IUPAC Page 2 of 42 1 2 components positioned in each threadable ring. For example, the following two isomeric 3 [4]rotaxane s will have the following generic names: 4 E E 5 E 6 7 E E 8 E 9 10 E E 11 E E 12 E E 13 2:1:0 -[4]{[3](TC) -rotaxa - 14 1:1:1 -[4]{[3](TC) -rotaxa -(MC)} 15 (MC)} 16 For Peer Review Only 17 Rotaxanes composed of several macrocyclic components and one threading 18 component with several threading sections are named accor ding to the same principles: 19 20 21 E E E E 22 23 24 1:1: 0-[3][IUPAC(TC) -rotaxa Provisional- Recommendations1:0:1-[3][(TC) -rotaxa - 25 [2](MC)] [2](MC) ] 26 27 To define stereoisomers of rotaxanes , the following types of asymmetry of rotaxane 28 components are ta ken into account: 29 - threading component direction, 30 31 - threadable ring direction, and 32 - nonequivalence of threadable ring sides. 33 34 Several types of stereoisomerism and the procedures to define specific 35 stereoisomer s in a rotaxane name are recommended. For example , the reported cases of 36 37 "cyclochirality" are unambiguously defined by means of A and C descriptors that 38 correspond to anticlockwise and clockwise orientation of a macrocyclic component in 39 relation to unsymmetrical threading components or to another macrocy clic component. 40 E E 41 B B 42 A C 43 44 E EA A 45 46 A-[2][(TC) -rotaxa -(MC) ] C-[2][(TC) -rotaxa -(MC) ] 47 48 EE EE 49 50 51 C,A -[3][(TC) -rotaxa -[2](MC)] A,C -[3][(TC) -rotaxa -[2](MC)] 52 53 The p rocedures to assign direction in threading and ma crocyclic components are 54 55 based on Cahn -Ingold -Prelog sequence rules. 56 57 The recommended procedures are defined for many reported types of rotaxanes 58 and can be expanded to more complex types. 59 December 2005 60 P.O. 13757, Research Triangle Park, NC (919) 485-8700 Page 3 of 43 DRAFT 16 Dec 2005 Page 3 of 42 IUPAC IUPAC Rotaxanes 2002-007-1-800E December 2005 PROVISIONAL 1 2 Project 2002-007-1-800-E 3 4 INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY 5 6 7 CHEMICAL NOMENCLATURE AND STRUCTURE 8 REPRESENTATION DIVISION 9 10 NOMENCLATURE FOR ROTAXANES 11 12 (IUPAC Recommendations 2005) 13 14 Prepared by a Working Group Consisting of 15 16 A.For HARADA Peer (Japan), W. V.Review METANOMSKI (USA),Only G. P. MOSS (UK), 17 E. S. WILKS (USA), and A. YERIN (Russia) 18 19 20 CONTENTS 21 22 INTRODUCTION........................................................................................................................................................ 1 23 ROT-1. GLOSSARY ............................................................................................................................................. 2 24 ROT-1.1. RotaxaneIUPAC (generic) Provisional........................................................................................................................ Recommendations 2 25 ROT-1.2. Macrocyclic molecule .................................................................................................................. 33 26 ROT-1.3. Threading component (generic) ................................................................................................ 33 27 ROT-1.4. Pseudorotaxane (generic) .......................................................................................................... 44 28 ROT-1.5. Recognition site............................................................................................................................ 55 29 ROT-1.6. Molecular shuttle.......................................................................................................................... 55 30 ROT-2. HISTORY OF THE NOMENCLATURE OF ROTAXANES ............................................................. 55 31 ROT-3. TYPES OF ROTAXANES .................................................................................................................... 66 32 ROT-4. GENERAL PRINCIPLES OF ROTAXANE NOMENCLATURE...................................................... 88 33 ROT-4.1. Name styles.................................................................................................................................. 88 34 ROT-4.2. Name generation ......................................................................................................................... 88 ROT-5. SPECIFICATION OF ISOMERISM OF ROTAXANES 35 ................................................................ 1212 ROT-5.1. Types of isomerism in rotaxanes................................................................................................ 1212 36 ROT-5.2. Position of threading components in several threadable rings (Types 3 and 4) ............ 1313 37 ROT-5.3. Position of Macrocyclic Components on Several Linear Sections (Types 5-8).............. 1414 38 ROT-5.4. Position of threading components for catenarotaxanes of Type 11................................. 1616 39 ROT-5.5. Positions and an order of nonequivalent components of the same type......................... 1617 40 ROT-6. ROTAXANES WITH UNSYMMETRICAL COMPONENTS......................................................... 1919 41 ROT-6.1. Asymmetry of rotaxane components .................................................................................... 1919 42 ROT-6.2. Stereoisomers of rotaxanes ................................................................................................... 2424 43 ROT-7. EXAMPLES OF ROTAXANES AND THEIR SYSTEMATIC NAMES........................................ 3232 44 REFERENCES ....................................................................................................................................................... 3940 45 46 47 Abstract: Expanded definitions of rotaxanes, their components, and other terms 48 concerning rotaxanes are given. The classification of rotaxanes and nomenclature 49 principles for naming of different types of rotaxanes are described and illustrated 50 with examples. Recommendations are provided for unambiguous description