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Paper No and Title Paper 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No and Module 15: Catenanes and Rotaxanes Title Module Tag CHE_P1_M15
CHEMISTRY Paper No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 15: Catenanes and Rotaxanes
TABLE OF CONTENTS 1. Learning Outcomes 2. Introduction 3. Chemical Topology of Catenanes and Rotaxanes 4. Nomenclature of Catenanes and Rotaxanes 5. Stereochemistry of Catenanes and Rotaxanes 6. Properties and Applications of Catenanes and Rotaxanes 7. Summary
CHEMISTRY Paper No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 15: Catenanes and Rotaxanes
1. Learning Outcomes After studying this module, you shall be able to Learn about the basic knowledge of catenanes and rotaxanes Understand the nomenclature of rotaxanes and catenanes Analyze the chemical topology of rotaxanes and catenanes Know to determine stereochemistry of rotaxanes and catenanes Learn about the properties and applications of rotaxanes and catenanes 2. Introduction In the late 1970s, emerged a new branch of chemistry, called supramolecular chemistry, and it has managed to expand very rapidly, consecrated by the award of the Nobel Prize in Chemistry which was conferred upon C. J. Pedersen, D. J. Cram, and J. -M. Lehn in 1987. Catenanes and rotaxanes differ from all other organic compounds synthesized to this date in a way that molecular subunits are linked mechanically. Catenane is a compound consisting of two or more rings that are interlocked mechanically without there being necessarily any chemical interaction/bond between the two. Generally, without breaking a chemical bond, the rings cannot be separated. Catenane is derived from the Latin catena meaning "chain". In recent times the terminology "mechanical bond" has been coined and it is the connection between the macrocycles of a catenane. Rotaxanes are long, fairly linear molecules consisting of a "dumbbell shaped molecule" threaded through a macrocyclic ring, like cotton threads through the eye of a needle. The name is derived from the Latin for wheel (rota) and axle (axis). Same as catenanes, rotaxanes also cannot decompose into ring and chain without breaking chemical bonds. Hence, the bulky groups terminate the linear, chain part of the molecule and it is too large to fit through the cyclic fragment. Rotaxanes without such physical barriers, in which the thread can leave the needle, are called pseudorotaxanes. Pseudorotaxanes are necessary precursors for both rotaxanes and catenanes.
CHEMISTRY Paper No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 15: Catenanes and Rotaxanes
3. Chemical Topology of Catenanes and Rotaxanes A compound can be usually described, unequivocally, by: 1. The order in which given numbers of atoms are joined 2. The type of bonds which connect them 3. The configuration at asymmetric atoms or rigid centers 4. The conformation 5. The topology Chemical topology deals with the structure and the property differences of compounds which are identical with regard to the aforementioned first three points and which in spite of that cannot be interconverted by conformational changes, such as rotation about an axis or modification of bond angles. Compounds which can be suitably classified in this manner were called as ‘Topological Isomers’ by Frisch and Wasserman. Catenane 1 and the twice threaded catenane 6 are thus topological isomers and for similar reasons as stated above, a rotaxanes is not isomeric with its molecular subunits.
Fig. 1: Consider these catenanes in the figure. Since there is no chemical bond between the two rings Frisch et al call it as a mechanical bond whereas, Frisch and Wasserman suggested topological bond as a name.
4. Nomenclature of Catenanes and Rotaxanes The nomenclature of catenanes is decided by the number of rings, i.e. how many number of rings interlocked to each other, e.g. a [2]-catenane consists of two interlocked rings (fig. 2). Analog ‘ane’ used in the end which is similar to alkanes. A catenane mainly consists of an organic fragment, it rarely consists of hydrocarbon moieties. The terms [n]-catenand and [n]- CHEMISTRY Paper No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 15: Catenanes and Rotaxanes
catenate are also used analogously with cryptand and cryptate, for a metal center which is suitably interlocked in the ring system of a catenane acting as a ligand. The catenand is the free ligand that forms a catenate complex in the presence of metal center. Rotaxanes can be named in an analogous manner too. In the case of unbranched species such a numbering system is not necessary. The names of the rings forming a branch to the main chain are numbered with subscripts and placed together with the ring on which the branching takes place in one bracket.
Fig. 2: Nomenclature of catenanes, rotaxanes and pseudorotaxanes
In catenanes and rotaxanes containing multiple windings it is also necessary to designate the winding number α. The quantity α represents the number of times one macrocycle winds about the other. Catenanes which form a ring with themselves as designated as cyclocatenanes. The examples below will clarify the concept of nomenclature.
CHEMISTRY Paper No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 15: Catenanes and Rotaxanes
Fig. 3: Concept of nomenclature of catenanes and rotaxanes
5. Stereochemistry of Catenanes and Rotaxanes
Stereochemistry of catenanes and rotaxanes is not a very highly explored topic except for discussion on simple structures of catenanes in particular. Rotaxanes have been very minimally dealt with in this area of study. Here we shall discuss all the possible cases of stereochemistry of both catenanes and rotaxanes. Catenanes:
CHEMISTRY Paper No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 15: Catenanes and Rotaxanes
The stereochemistry of simpler carbocyclic [2]-catenanes can be categorized as follows: 1. Catenanes bearing no substituents donot occur as antipodes (antipodes are synonymous with enantiomers or optical isomers) 2. Catenanes having substituents in only one of the two rings are stereochemically related to the corresponding uncatenated macrocycles. 3. Catenanes in which each subunit contains two substituents located on the same ring atom are stereochemically related to allenes and spiro compounds. If each ring has two substituents A and B, as shown in formula in the figure, a necessary and sufficient condition for the occurrence of enantiomers is that A≠B.
Fig. 4: A necessary and sufficient condition for the occurrence of enantiomers in catenanes in which each subunit contains two substituents located on the same ring atom is that A≠B
4. Catenanes where each subunit contains two substituents located on different ring atoms, generally exist as an enantiomeric pair. However, Doornbos pointed out that this may not always be true. Consider catenane shown in the figure as an example. In this catenane, each ring has the same two substituents R on different ring atoms. The segments of the individual rings of the catenane have to be of such a nature that the molecule possesses a fourfold alternating axis of symmetry. In this case the catenane is achiral, although the component rings are dissymmetrical.
CHEMISTRY Paper No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 15: Catenanes and Rotaxanes
Fig. 5: In this catenane, each ring has the same two substituents R on different ring atoms. In this case the catenane is achiral, although the component rings are dissymmetrical
5. A type of enantiomerism closely related catenane mentioned in point 3 was first pointed by Closson, and in more generalized form by Prelog et al and later by Cruse. Consider the following two catenanes which are cycloenantiomers. In order that this difference be pertinent, each ring of a catenane must consist of atleast three different segments, even though every segment may appear in both rings.
Fig. 6: Consider the following two catenanes which are cycloenantiomers. In order that this difference be pertinent, each ring of a catenane must consist of atleast three different segments, even though every segment may appear in both rings
6. Special cases may arise if one of the two rings of a catenane is so small, or has substituents so large, that free rotation of one ring within the other is hindered. This case is shown in the figure below wherein the enantiomers arise because the large substituents A and B prevent free rotation of the rings. CHEMISTRY Paper No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 15: Catenanes and Rotaxanes
As shown in figure, the small ring is fixed on right side by two bulky groups A and B in one enantiomer while in the other enantiomer it is fixed on left side. Both stereoisomers should be separable into antipodes.
Fig. 7: Figure depicting that both stereoisomers should be separable into antipodes
7. The [2]-catenane shown below in the figure having a winding number α=2, is not identical with its mirror image and should therefore be optically active. This isomerism corresponds to the mirror image relation which exists between an α- and β- helices.
Fig. 8: figure showing that this isomerism corresponds to the mirror image relation which exists between an α- and β- helices Stereochemistry of the [3]-catenanes, as well as of higher catenanes, has not been considered, except for some special cases. A possibility to differentiate the [3]- catenanes as depicted in the figure below by means of optically active compounds, was pointed first by Frisch and Wasserman.
CHEMISTRY Paper No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 15: Catenanes and Rotaxanes
Fig. 9: A possibility to differentiate the [3]-catenanes as depicted in the figure below by means of optically active compounds, was pointed first by Frisch and Wasserman
Rotaxanes: The stereochemistry of rotaxanes closely resembles that of catenanes as illustrated with catenane mentioned above in point 3. In the figure of the rotaxanes shown below, R≠R’ and A≠B is achiral, it exhibits geometric isomerism.
Fig. 10: In this figure if, R≠R’ and A≠B is achiral, it exhibits geometric isomerism As in the case of catenanes, rotaxanes may exist as cycloenantiomers. The compounds given below are mirror images, which only differ in the direction of the ring segment sequences.
Fig. 11: The compounds in this figure are mirror images, which only differ in the direction of the ring segment sequences
6. Properties and Applications of Catenanes and Rotaxanes
Catenanes:
CHEMISTRY Paper No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 15: Catenanes and Rotaxanes
An interesting property of many catenanes is the ability of the rings to rotate with respect to one another. This rotational motion of one ring with respect to another can often be detected and measured by NMR spectroscopy, amongst other methods. If in the finished catenane, molecular recognition motifs exist (usually those that were used to synthesize the catenane), the catenane can have one or more thermodynamically preferred positions of the rings with respect to each other. If in case, one recognition site is a switchable moiety, a mechanical molecular switch results. When a catenane is synthesized by coordination of the macrocycles moieties around a metal ion, then removal and re-insertion of the metal ion can switch the free motion of the rings on and off. Thus, they can function as molecular switches.
Fig. 12. Photochemically driven switching systems in catenanes
Catenanes have been synthesized by incorporation of many functional units, including redox- active groups (e.g. viologen, TTF=tetrathiafulvalene) for making redox switches, photoisomerizable groups (e.g.azobenzene) for photo switches, fluorescent groups for fluorescent switches and chiral groups for optical switches. Many of these units have been used to create molecular switches as described above, as well as for the fabrication of molecular electronic devices and molecular sensors.
Rotaxanes: CHEMISTRY Paper No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 15: Catenanes and Rotaxanes
Rotaxane-based molecular machines have been of particular interest for their potential uses in molecular electronics as logical molecular switching elements and also as molecular shuttles. These molecular machines are usually based on the movement of macrocycle on the dumbbell. The macrocycle can rotate around the axis of the dumbbell like a wheel and axle or it can slide along its axis from one site to another as shown in figure 13. By controlling the position of the macrocycle, it allows the rotaxane to function as molecular switch. With each possible location of the macrocycle corresponding to a different state. These rotaxane machines can be manipulated both by chemical and photochemical inputs. Rotaxane based systems have also been demonstrated as molecular muscles. In 2009, "domino effect" was reported from one extremity to the other in a Glycorotaxane Molecular Machine. In this case, 4 1 the C1 or C4 chair-like conformation of the mannopyranoside stopper can be controlled, depending on the localization of the macrocycle. Unique pseudo-macrocycles consisting of double-lasso molecular machines (also called rotamacrocycles) have been reported in Chem. Sci. journal in 2012. These structures can be tightened or loosened depending on varying the pH. A controllable jump rope movement was also observed in these new molecular machines.
Fig. 13: Modes of movement of rotaxanes and catenanes which enables them to function as molecular switches
CHEMISTRY Paper No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 15: Catenanes and Rotaxanes
Fig. 14: Rotaxanes as molecular switches
In the last few years, several examples of molecular machines and motors have been designed and constructed. It should be noted, however, that the molecular level machines described in this module operate in solution, that is, in an incoherent fashion. Apart from more or less futuristic applications, the extension of the concept of a machine to the molecular level is of interest not only for the development of nanotechnology, but also for the growth of basic research. Looking at supramolecular chemistry from the viewpoint of functions with references to devices of the macroscopic world is indeed a very interesting exercise which introduces novel concepts into Chemistry as a scientific discipline.
7. Summary Catenanes and rotaxanes differ from all other organic compounds synthesized to this date in a way that molecular subunits are linked mechanically. Catenane is a compound consisting of two or more rings that are interlocked mechanically without there being necessarily any chemical interaction/bond between the two. Rotaxanes consist of a long, fairly linear molecule threaded through a macrocyclic ring, like cotton through the eye of a needle. Chemical topology deals with the structure and the property differences of compounds which are identical with regard to the aforementioned first three points and which in spite of that cannot be interconverted by conformational changes, such
CHEMISTRY Paper No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 15: Catenanes and Rotaxanes
as rotation about an axis or modification of bond angles. In this module we have classified catenanes and rotaxanes according to their chemical topology. Stereochemistry of catenanes and rotaxanes is not a very highly explored topic except for discussion on simple structures of catenanes in particular. Rotaxanes have been very minimally dealt with in this area of study. In this module, we have discussed all possible cases of stereochemistry of catenanes and rotaxanes.
Catenanes have been synthesized by incorporation of many functional units, including redox-active groups (e.g., viologen, TTF = tetrathiafulvalene), photoisomerizable groups (e.g., azobenzene), fluorescent groups and chiral groups. Many of these units have been used to create molecular switches as described above, as well as for the fabrication of molecular electronic devices and molecular sensors.
Rotaxane-based molecular machines have been of particular interest for their potential uses in molecular electronics as logical molecular switching elements and also as molecular shuttles.
CHEMISTRY Paper No. 1: ORGANIC CHEMISTRY- I (Nature of Bonding and Stereochemistry) Module No. 15: Catenanes and Rotaxanes