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Abstract
Molecular composite knots have been prepared from transition metal-assembled precursors via a Glaser acetylenic coupling reaction. The templating metal is copper(I), and the coordinating fragments incorporated into the final structure are 1,10-phenanthroline-type chelates. The compounds are composite knots as opposed to prime knots such as the classical trefoil knot. By combining two tied open-chain fragments in a cyclodimerization reaction, the simplest composite knots are obtained as a mixture of two topological diastereomers. The minimum number of crossing points used to represent the molecules in a plane is six. Due to the complexity of the entangled precursors and to the several cyclization possibilities, the formation yield of composite knots is only modest (3%). On the other hand, the compound has been fully characterized by ES-MS (molecular weight, 4037.8) and by 1H NMR spectroscopy, including 2D NMR (NOESY).
... The study of this kind of molecules has gained attention because it constitutes a new kind of synthetic chemistry [7] which will yield important results in the study of topological stereochemistry [14] and the possible applications are beginning to be noted [15]. Rotaxanes, catenanes, knots and borromean rings have been successfully synthetized via template methods where the metal ions play an important role. ...
... The electronic structure of a molecule with nine-crossing composite knots 9 7 3 link has been studied. The large cavity within this complex-1 opens the opportunity to study many potential applications. ...
Anticancer drug delivery is becoming a central scientific defy since it allows locating drug release near the tumor cell and circumventing secondary side effects. Based on density functional theory (DFT) calculations, adsorption of most abundant melphalan anticancer drug specie at physiological pH on a series of small 24 atoms nanoclusters (C24, B12N12 and carbon doped boron nitride molecules: B12C6N6, B6C12N6 and B6C6N12), was carried out both in vacuum and solvent (water) environment conditions at B3LYP-D3(BJ)/6-31G(d,p) level of theory. The most stable chemisorption state for melphalan was through oxygen atom onto all nanocluster under study, in comparison with chlorine and nitrogen atoms and comparing both environments, the computed results indicate that the adsorption of melphalan in the solvent environment is in general more stable. According to our results, boron nitride and some of its mixed nanoclusters may serve as potential drug delivery nanovehicles for melphalan drug. The results from this work are expected to motivate further inquiries concerning these systems, using both theoretical and experimental approaches, in order to validate their versatility as nanovehicles.
... The study of this kind of molecules has gained attention because it constitutes a new kind of synthetic chemistry [7] which will yield important results in the study of topological stereochemistry [14] and the possible applications are beginning to be noted [15]. Rotaxanes, catenanes, knots and borromean rings have been successfully synthetized via template methods where the metal ions play an important role. ...
... The electronic structure of a molecule with nine-crossing composite knots 9 7 3 link has been studied. The large cavity within this complex-1 opens the opportunity to study many potential applications. ...
The electronic structure of a molecule with nine-crossing composite knots 973 link denoted by the Alexander-Briggs notation (complex-1) are studied by means of theoretical methods (DFT). The most interesting feature of this kind of molecules is their capability to capture anion spices inside the cage. Stability and chemical reactivity were evaluated taking advantage of the criteria chemical hardness and chemical potential. The simulation of the infrared spectra is also included and shows the characteristic signal of the molecule in a range 1000-1600 cm-1. The frontier molecular orbitals were also analyzed. Whereas the capability to capture chlorine ion into the cavity of the complex-1 is explored by means the analysis of bond energy. Also, the electron density distribution of the chlorine complex was studied by means the quantum theory of atoms in molecules (QTAIM) formalism in order to stablish its bonding properties as well as the electron transfer between chlorine ion and complex-1 which was approached by the natural bonding orbital (NBO) and Hirshfeld charge. Ours results revels semiconductor behaviors for both compounds.
... The dimerization of racemic open trefoil knot precursor 49 by Glaser coupling gave trace amounts of a product that was assigned to be a mixture of granny and square knots 50 and 51 (Scheme 19). [113] ...
... If two complexes of the same handedness are combined, a granny knot is obtained, while the combination of two complexes of opposing handedness yields a square knot. [113] been studied by circular dichroism (Figure 22), and the spectrum of enantiopure trefoil knot 15 b shows a greater ellipticity than the corresponding topologically isomeric macrocycle. This finding suggests that the topological chirality of the knot has a significant effect on the asymmetry of the chromophore environment. ...
The first synthetic molecular trefoil knot was prepared in the late 1980s. However, it is only in the last few years that more complex small-molecule knot topologies have been realized through chemical synthesis. The steric restrictions imposed on molecular strands by knotting can impart significant physical and chemical properties, including chirality, strong and selective ion binding, and catalytic activity. As the number and complexity of accessible molecular knot topologies increases, it will become increasingly useful for chemists to adopt the knot terminology employed by other disciplines. Here we give an overview of synthetic strategies towards molecular knots and outline the principles of knot, braid, and tangle theory appropriate to chemistry and molecular structure.
... Despite the fact that Frisch and Wasserman had first suggested the possibility of using Möbius strips to direct trefoil knot formation in 1961 [243], it was not until 1989 that the first molecular trefoil knot was synthesised [244]. Excluding DNA-based knotted molecules [245,246] and composite knots [247], to date, only three different types of knots have been synthesised. These are the trefoil knot (3 1 ), figure-of-eight knot (4 1 ) and pentafoil knot (5 1 ). ...
... However, it was not until the introduction of efficient catalysts for ring-closing olefin metathesis (RCM) that the best yield for a molecular trefoil knot (74%) was achieved ( figure 14(a)) [253]. This successful approach was then extended to the preparation of composite knots, details of which can be found in [247]. In another case, the same group used octahedral iron(II) ions reacted with terpyridine-based ligands to template the synthesis of a trefoil knot [254]. ...
Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance and prevalence of molecular knots have been increasingly recognised by scientists from different disciplines. In this review, we provide an overview on the various molecular knots found in naturally occurring biological systems (DNA, RNA and proteins), and those created by synthetic chemists. We discuss the current knowledge in these fields, including recent developments in experimental and, in some cases, computational studies which are beginning to shed light into the complex interplay between the structure, formation and properties of these topologically intricate molecules.
... Key synthetic papers have switched pictures of the configurations of knots with the same optical chirality. [27,28] Older papers [29] that recent researchers [12] have cited use a definition for signs of crossings which is the opposite of topologists and the majority of chemists today. [24] Even though an S 4 structure has an improper rotation axis and is achiral, oriented structures or crystals of such a symmetry are indeed optically active in some directions [30] and we have made calculations [31][32][33] and measurements [34,35] of the orientational dependencies of OA of a variety of non-enantiomorphous structures. ...
The electronic origins of the computed optical rotations of the simplest chiral and achiral chemical knots with comparatively simple compositions and large, anticipated magnetoelectric polarizabilities are provided. Linear response theory (LRT) is used to calculate the gyration at 1064 nm of two knotted polyyne chains, topological stereoisomers of cyclo[60]carbon. One isomer is analogous to the trefoil knot with approximate D3 symmetry and the other to the figure eight knot with approximate S4 symmetry. The response in each case can be attributed largely to the magnetic dipole term that arises in a near degenerate E‐like excited state. An oriented achiral figure eight knot is as optically active in some directions as the chiral knot in any direction, and its absolute eigenvalues are larger.
... 20 However, such syntheses require linear synthetic schemes that may be lengthy and result in low overall yields. 19,20 A useful synthetic strategy for rapidly assembling complexity from simple building blocks is self-sorting. 22 Self-sorting systems can either be narcissistic 23 �each component preferring to interact with others like themselves�or social, 24 whereby a compound has greater affinity for components within a system that are different from itself. ...
We report the synthesis of molecular prime and composite knots by social self-sorting of 2,6-pyridinedicarboxamide (pdc) ligands of differing topicity and stereochemistry. Upon mixing achiral monotopic and ditopic pdc-ligand strands in a 1:1:1 ratio with Lu(III), a well-defined heteromeric complex featuring one of each ligand strand and the metal ion is selectively formed. Introducing point-chiral centers into the ligands leads to single-sense helical stereochemistry of the resulting coordination complex. Covalent capture of the entangled structure by ring-closing olefin metathesis then gives a socially self-sorted trefoil knot of single topological handedness. In a related manner, a heteromeric molecular granny knot (a six-crossing composite knot featuring two trefoil tangles of the same handedness) was assembled from social self-sorting of ditopic and tetratopic multi-pdc strands. A molecular square knot (a six-crossing composite knot of two trefoil tangles of opposite handedness) was assembled by social self-sorting of a ditopic pdc strand with four (S)-centers and a tetratopic strand with two (S)- and six (R)-centers. Each of the entangled structures was characterized by 1H and 13C NMR spectroscopy, mass spectrometry, and circular dichroism spectroscopy. The precise control of composition and topological chirality through social self-sorting enables the rapid assembly of well-defined sequences of entanglements for molecular knots.
... However, delicate synthetic protocols and low overall yields have hindered detailed investigations until today. The current development of new methodologies to direct the for-mation of more and more complex interlocked structures, using metal-templation [23][24][25][26][27][28][29][30][31][32][33] and other supramolecular interactions, [34][35][36][37][38][39][40] has recently enabled the first studies on the potential use of complex molecular knots and links as catalysts, [41][42][43] anion receptors, [44][45][46] molecular switches, [47] and anti-cancer agents. [48] These studies demonstrate that many important applications can emerge from the field of molecular topology. ...
Complex molecular knots and links are still difficult to synthesize and the properties arising from their topology are mostly unknown. Here, we report on a comparative photophysical study carried out on a family of closely related quinolinium‐based knots and links to determine the impact exerted by topology on the molecular backbone. Our results indicate that topology has a negligible influence on the behavior of loosely braided molecules, which mostly behave like their unbraided equivalents. On the other hand, tightly braided molecules display distinct features. Their higher packing density results in a pronounced ability to resist deformation, a significant reduction in the solvent‐accessible surface area and favors close‐range π–π interactions between the quinolinium units and neighboring aromatics. Finally, the sharp alteration in behavior between loosely and tightly braided molecules sheds light on the factors contributing to braiding tightness.
... This allowed ring closure by a metathesis reaction and gave knotane yields of up to 74%. More complex systems such as the double knotane compound shown in figure 10.10 which, since each individual knot is chiral, can exist in three forms, two enantiomers plus a meso form 27 . ...
Within this chapter we will initially discuss a few other molecular systems that we feel of interest but that have not been subjects of enough research to warrant chapters of their own. Following this we will then expand on the potential functionalities of the molecular systems discussed within this book and report on the strides that are being made in the fields of molecular machines and motors, along with other nanotechnological applications. Finally we will conclude with an overview of this work and briefly discuss the visions of the future that macrocyclic chemistry has the potential to make possible.
... Herein we report on the designed synthesis of one of the topologies missing from the molecular lexicon, a6 2 3 link, via a2 2interwoven grid. Also formed is a3 1 #3 1 [18] (granny) composite [10,19] knot. The6 2 3 link [13] consists of two constitutionally identical macrocycles involving six crossings,the same number as aStar of David catenane (6 2 1 link) but with ad ifferent crossing pattern. ...
A molecular 6_3^2 link (a six crossing, doubly interlocked, [2]catenane with twisted rings) and a 31#31 granny knot (a composite knot made up of two trefoil tangles of the same handedness) were constructed by ring‐closing olefin metathesis of an iron(II)‐coordinated 2×2 interwoven grid. The connections were directed by pendant phenyl groups to be between proximal ligand ends on the same faces of the grid. The 6_3^2 link was separated from the topoisomeric granny knot by recycling size‐exclusion chromatography. The identity of each topoisomer was determined by tandem mass spectrometry and the structure of the 6_3^2 link confirmed by X‐ray crystallography, which revealed two 82‐membered macrocycles, each in figure‐of‐eight conformations, linked through both pairs of loops.
... Herein we report on the designed synthesis of one of the topologies missing from the molecular lexicon, a6 2 3 link, via a2 2interwoven grid. Also formed is a3 1 #3 1 [18] (granny) composite [10,19] knot. The6 2 3 link [13] consists of two constitutionally identical macrocycles involving six crossings,the same number as aStar of David catenane (6 2 1 link) but with ad ifferent crossing pattern. ...
A molecular 6_3^2 link (a six crossing, doubly interlocked, [2]catenane with twisted rings) and a 31#31 granny knot (a composite knot made up of two trefoil tangles of the same handedness) were constructed by ring-closing olefin metathesis of an iron(II)-coordinated 2×2 interwoven grid. The connections were directed by pendant phenyl groups to be between proximal ligand ends on the same faces of the grid. The 6_3^2 link was separated from the topoisomeric granny knot by recycling size-exclusion chromatography. The identity of each topoisomer was determined by tandem mass spectrometry and the structure of the 6_3^2 link confirmed by X-ray crystallography, which revealed two 82-membered macrocycles, each in figure-of-eight conformations, linked through both pairs of loops.
... [3][4][5] In the last few decades, there has been a significant increase in the publications describing the preparation and properties of supramolecular materials such as catenanes, rotaxanes, knots, helicates, dendrimers, racks, grids, boxes, and macrocycles. [6][7][8][9][10][11][12][13] Most result from the self-assembly of molecules that act as building units through self-recognition elements. In metal complexes, these elements correspond to particular features of the ligands and metals, which act synergistically as preorganizers of the supramolecular arrangements. ...
The Cu(I) complex {[CuI(biq)2]ClO4-biq} with biq = 2,2-biquinoline, was prepared, fully characterized and its properties compared with those of the well-known [CuI(biq)2]ClO4 complex. The crystal structures were obtained for both complexes (crystal structure for [CuI(biq)2]ClO4 has not been previously reported). Complex [CuI(biq)2]ClO4 crystallizes as a racemate where each enantiomer has a different τ4 value while compound {[CuI(biq)2]ClO4-biq} crystallizes as a non-chiral supramolecular aggregate with an uncoordinated biq molecule forming a π-π stacking interaction with a coordinated biq. The ¹H-NMR spectroscopy in non-coordinating solvents reveals that structures in solution are similar to those in the solid phase, confirming the presence of a supramolecular arrangement for compound {[CuI(biq)2]ClO4-biq} . Stability of the non-covalent aggregate in solutions of {[CuI(biq)2]ClO4-biq} causes significant differences between the spectroscopic and electrochemical properties of {[CuI(biq)2]ClO4-biq} and [CuI(biq)2]ClO4.
... [111,112] Bis heute beschränkt sich die Synthese von zusammengesetzten Knoten auf Sauvages Bericht über die Synthese eines Gemisches von zusammengesetzten Knoten in geringer Ausbeute.D imerisierung des racemischen offenen Knotens 49 mittels Glaser-Kupplung gab Spuren eines Produkts,d as als Gemisch von Altweiber-u nd Kreuzknoten 50 und 51 interpretiert wurde (Schema 19). [113] ...
The first synthetic molecular trefoil knot was prepared in the late 1980s. However, it is only in the last few years that more complex small-molecule knot topologies have been realized through chemical synthesis. The steric restrictions imposed on molecular strands by knotting can impart significant physical and chemical properties, including chirality, strong and selective ion binding and catalytic activity. As the number and complexity of accessible molecular knot topologies increases it will become increasingly useful for chemists to adopt the knot terminology employed by other disciplines. Here we review synthetic strategies towards molecular knots and outline the principles of knot, braid and tangle theory appropriate to chemistry and molecular structure.
... [2] The chemical realm, in comparison, comprises to date only a few of the simplest structures. Excluding DNA-based structures, chemists were able to synthesize three different types of knots: trefoil knots, [3,4] composite knots, [5] and a pentafoil knot. [6,7] The following types of links have also been reported: a range of [n]catenanes, [7] Borromean rings, [8] and Solomon links. ...
The synthesis of topologically complex structures, such as links and knots, is one of the current challenges in supramolecular chemistry. The so-called Solomon link consists of two doubly interlocked rings. Despite being a rather simple link from a topological point of view, only few molecular versions of this link have been described so far. Here, we report the quantitative synthesis of a giant molecular Solomon link from 30 subcomponents. The highly charged structure is formed by assembly of 12 cis-blocked Pt2+ complexes, six Cu+ ions, and 12 rigid N-donor ligands. Each of the two interlocked rings is composed of six repeating Pt(ligand) units, while the six Cu+ ions connect the two rings. With a molecular weight of nearly 12 kDa and a diameter of 44.2 Å, this complex is the largest non-DNA-based Solomon link described so far. Furthermore, it represents a molecular version of a “stick link”.
Entangling strands in a well-ordered manner can produce useful effects, from shoelaces and fishing nets to brown paper packages tied up with strings. At the nanoscale, non-crystalline polymer chains of sufficient length and flexibility randomly form tangled mixtures containing open knots of different sizes, shapes and complexity. However, discrete molecular knots of precise topology can also be obtained by controlling the number, sequence and stereochemistry of strand crossings: orderly molecular entanglements. During the last decade, substantial progress in the nascent field of molecular nanotopology has been made, with general synthetic strategies and new knotting motifs introduced, along with insights into the properties and functions of ordered tangle sequences. Conformational restrictions imparted by knotting can induce allostery, strong and selective anion binding, catalytic activity, lead to effective chiral expression across length scales, binding modes in conformations efficacious for drug delivery, and facilitate mechanical function at the molecular level. As complex molecular topologies become increasingly synthetically accessible they have the potential to play a significant role in molecular and materials design strategies. We highlight particular examples of molecular knots to illustrate why these are a few of our favourite things.
In this chapter, we examine how catenanes, rotaxanes, and molecular knots can be considered and were effectively used as chiral building blocks in diverse molecular architectures. We first gave few elements of molecular topology and a definition of topological chirality. Then, we showed that it is topological chirality that made the chirality of some chiral catenanes and molecular knots unique by comparison with other chiral molecules. By contrast, rotaxanes, which are constituted of separable components, display the more common inherent chirality. Finally, the use of catenanes, rotaxanes, and knots as chiral building blocks (although they were not qualified as such in the literature) was reviewed and illustrated by several examples, from seminal to more recent ones. In a word, the concept of topologically chiral building blocks is useful in that it constitutes the basis of topological diastereomerism.
A new demetallation method for Cu(I)‐bound catenanes that contain a strong binding bis(phenanthroline) cavity using the bidentate ethylenediamine is reported. Cu(I) extraction using the organic diamine is mild, convenient and efficient, and the metal can be removed from the kinetically stable catenane complexes in various solvents within 5 minutes, offering an alternative strategy to the use of toxic cyanide in competing for the Cu(I) coordination.
Metal‐free and metal‐containing molecular trefoil knots are fascinating ensembles that are usually covalently assembled, the latter requiring the rational design of di‐ or multidentate/multipodal ligands as connectors. In this work, we describe the self‐assembly of pentadecanuclear AuI trefoil knots [Au15(C≡CR)15] from monoalkynes HC≡CR (R=9,9‐X2‐fluorenyl with X=nBu, n‐hexyl) and [AuI(THT)Cl]. Hetero‐bimetallic counterparts [Au9M6(C≡CR)15] (M=Cu/Ag) were self‐assembled by reactions of [Au15(C≡CR)15] with [Cu(MeCN)4]⁺/AgNO3 and HC≡CR. The type of pentadecanuclear trefoil knots described herein is characterized by X‐ray crystallography, 2D NMR and HR‐ESI‐MS. [Au9Cu6(C≡CR)15] is relatively stable in hexane; its excited state properties were investigated. DFT calculations revealed that non‐covalent metal–metal and metal–ligand interactions, together with longer alkyl chain‐strengthened inter‐ligand dispersion interactions, govern the stability of the trefoil knot structures.
Metal‐free and metal‐containing molecular trefoil knots are fascinating ensembles that are usually covalently assembled, the latter requiring the rational design of di‐ or multidentate/multipodal ligands as connectors. In this work, we describe the self‐assembly of pentadecanuclear Au I trefoil knots [Au 15 (C≡CR) 15 ] from monoalkynes HC≡CR (R = 9,9‐X 2 ‐fluorenyl with X = n Bu, n ‐hexyl) and [Au I (THT)Cl]. Hetero‐bimetallic counterparts [Au 9 M 6 (C≡CR) 15 ] (M = Cu/Ag) were self‐assembled by reactions of [Au 15 (C≡CR) 15 ] with [Cu(MeCN) 4 ] + /AgNO 3 and HC≡CR. The type of pentadecanuclear trefoil knots described herein is characterized by X‐ray crystallography, 2D NMR and HR‐ESI‐MS. [Au 9 Cu 6 (C≡CR) 15 ] is relatively stable in hexane; its excited state properties were investigated. DFT calculations revealed that non‐covalent metal‐metal and metal‐ligand interactions, together with longer alkyl chain‐strengthened inter‐ligand dispersion interactions, govern the stability of the trefoil knot structures.
Anion‐coordination‐driven assembly (ACDA) is showing increasing power in the construction of anionic supramolecular architectures. Herein, by expanding the anion centers from oxoanion (phosphate or sulfate) to organic tris‐carboxylates, an Archimedean solid (truncated tetrahedron) and a highly entangled, double‐walled tetrahedron featuring a ravel topology have been assembled with tris‐bis(urea) ligands. The results demonstrate the promising ability of tris‐carboxylates as new anion coordination centers in constructing novel topologies with increasing complexity and diversity compared to phosphate or sulfate ions on account of the modifiable size and easy functionalization character of these organic anions.
Anion-coordination-driven assembly (ACDA) is showing increasing power in the construction of anionic supramolecular architectures. Herein, by expanding the anion centers from oxoanion (phosphate or sulfate) to organic tris-carboxylates, an Archimedean solid (truncated tetrahedron) and a highly entangled, double-walled tetrahedron featuring a ravel topology have been assembled with tris-bis(urea) ligands. The results demonstrate the promising ability of tris-carboxylates as new anion coordination “centers” in constructing novel topologies with increasing complexity and diversity compared to phosphate or sulfate ions on account of the modifiable size and easy functionalization character of these organic anions.
Mechanically Interlocked Molecules (MIMs), such as catenanes, knots, and rotaxanes, are a class of molecules that possess mechanical bonds. These bonds constitute an entanglement in space between components of the MIMs that cannot be separated without breaking a participating covalent bond. Although it is possible to synthesize chiral MIMs with covalent stereogenic centers, this new bond opens up the possibilities of axial, planar and helical chirality, as well as topologically chiral compounds. A growing number of chiral MIMs have been investigated and employed in numerous applications, ranging from sensing to catalysis. While the investigation of the properties of MIMs is highly developed, it is also essential to study their chiroptical properties. In this review, we focus on the chiroptical properties of chiral MIMs. We discuss their electronic circular dichroism (ECD) since these properties have been analyzed in some detail in relation to their structures and stereochemistry. Although only a few examples have been described to date, we discuss the encouraging circularly polarized luminescence (CPL) properties of MIMs. The review also includes a recent study of vibrational circular dichroism (VCD) in mechanically planar chiral rotaxanes suggesting that this technique is a promising tool for analyzing the structures of MIMs. The study of the chiroptical properties of MIMs can have a large impact on their use in materials science or as catalysts. One of the key advantage of chiral MIMs is that they provide a means of generating efficient chiroptical switches that have a bright future in the context of multiple applications.
The self‐assembly of nanostructures is dominated by a limited number of strong coordination elements. Here, we found that metal–acetylene π‐coordination of a tripodal ligand (L) with acetylene spacers gave an M 3 L 2 double‐propeller motif [M = Cu(I) or Ag(I)], which dimerized into an M 6 L 4 interlocked cage [M = Cu(I)]. Higher (M 3 L 2 ) n oligomers were also selectively obtained: an M 12 L 8 truncated tetrahedron [M = Cu(I)] and an M 18 L 12 truncated trigonal prism [M = Ag(I)], both of which contain the same double‐propeller motif. The higher oligomers exhibit multiply entangled facial structures that are classified as a trefoil knot and a Solomon link. The inner cavities of the structures encapsulate counter anions, revealing a potential new strategy toward the synthesis of functional hollow structures that is powered by molecular entanglements.
The self‐assembly of nanostructures is dominated by a limited number of strong coordination elements. Herein, we show that metal–acetylene π‐coordination of a tripodal ligand (L) with acetylene spacers gave an M3L2 double‐propeller motif (M=CuI or AgI), which dimerized into an M6L4 interlocked cage (M=CuI). Higher (M3L2)n oligomers were also selectively obtained: an M12L8 truncated tetrahedron (M=CuI) and an M18L12 truncated trigonal prism (M=AgI), both of which contain the same double‐propeller motif. The higher oligomers exhibit multiply entangled facial structures that are classified as a trefoil knot and a Solomon link. The inner cavities of the structures encapsulate counteranions, revealing a potential new strategy towards the synthesis of functional hollow structures that is powered by molecular entanglements.
We report on the stereoselective synthesis of trefoil knots of single topological handedness in up to 90 % yield (over two steps), through the formation of trimeric circular helicates from ligand strands containing either imine or, unexpectedly, amide chelating units and metal ion templates of the appropriate coordination character (zinc(II) for imines; cobalt(III) for amides). The coordination stereochemistry of the octahedral metal complexes is determined by asymmetric carbon centers in the strands, ulti-mately translating into trefoil knots that are a single enantiomer, both physically and in terms of their fundamental topology. Both the imine-zinc and amide-cobalt systems display self-sorting behavior, with racemic ligands forming knots that individually contain only building blocks of the same chirality. The knots and the corresponding trimeric circular helicate intermediates (Zn(II)3 com-plex for the imine ligands; Co(III)3 complex for the amide ligands) were characterized by NMR spectroscopy, mass spectrometry and X-ray crystallography. The latter confirms the trefoil knots as 84-membered macrocycles with each of the metal ions sited at crossing points for three parts of the strand. The stereochemistry of the octahedral coordination centers impart alternating crossings of the same handedness. The expression of chirality of the knotted molecules was probed by circular dichroism: the topological handedness of the demetallated knots was found to have a greater effect on the CD response than the Euclidean chirality of individual chiral centers.
We report on the stereoselective synthesis of both molecular granny and square knots through the use of lanthanide-complexed overhand knots of specific handedness as three-crossing ‘entanglement synthons’. The composite knots are assembled by combining two entanglement synthons (of the same chirality for a granny knot; of opposite handedness for a square knot) in three synthetic steps: First, a CuAAC reaction joins together one end of each overhand knot. Ring-closing olefin metathesis (RCM) then affords the closed-loop knot, locking the topology. This allows the lanthanide ions necessary for stabilizing the entangled conformation of the synthons to subsequently be removed. The composite knots were characterized by 1H and 13C NMR spectroscopy and mass spectrometry, and the chirality of the knot stereoisomers compared by circular dichroism. The synthetic strategy of combining building blocks of defined stereochemistry (here overhand knots of Λ- or Δ-handed entanglement) is reminiscent of the chiron approach of using minimalist chiral synthons in the stereoselective synthesis of molecules with multiple asymmetric centers.
Knots have been rigorously studied since the 1860s, but only in the past 30 years have they been made in the laboratory in molecular form. Now, the most complex small-molecule examples so far — a composite knot and an isomeric link, each with nine crossings — have been prepared.
The simultaneous synthesis of a molecular nine-crossing composite knot that contains three trefoil tangles of the same handedness and a [Formula: see text] link (a type of cyclic [3]catenane topologically constrained to always have at least three twists within the links) is reported. Both compounds contain high degrees of topological writhe (w = 9), a structural feature of supercoiled DNA. The entwined products are generated from the cyclization of a hexameric Fe(II) circular helicate by ring-closing olefin metathesis, with the mixture of topological isomers formed as a result of different ligand connectivity patterns. The metal-coordinated composite knot was isolated by crystallization, the topology unambiguously proven by tandem mass spectrometry, with X-ray crystallography confirming that the 324-atom loop crosses itself nine times with matching handedness (all Δ or all Λ) at every metal centre within each molecule. Controlling the connectivity of the ligand end groups on circular metal helicate scaffolds provides an effective synthetic strategy for the stereoselective synthesis of composite knots and other complex molecular topologies.
Conventional approaches to the synthesis of molecular knots and links mostly rely on metal-templation. We present here an alternative strategy that uses the hydrophobic effect to drive the formation of complex interlocked structures in water. We designed an aqueous dynamic combinatorial system that can generate knots and links. In this system, the self-assembly of a topologically complex macrocycle is thermodynamically favored only if an optimum packing of all its components minimizes the hydrophobic surface area in contact with water. Therefore, the size, geometry and rigidity of the initial building blocks can be exploited to control the formation of a specific topology. We illustrate the validity of this concept with the syntheses of a Hopf link, a Solomon link and a trefoil knot. This latter molecule, whose self-assembly is templated by halides, binds iodide with high affinity in water. Overall, this work brings a fresh perspective on the synthesis of topologically complex molecules: solvophobic effects can be intentionally harnessed to direct the efficient and selective self-assembly of knots and links.
A helically chiral [2]rotaxane featuring two ammonium ion recognition sites in the dumbbell-like component and a calix-bis-crown ether as the macrocyclic component was synthesized, but with no chirality in either individual component. The enantiomeric nature of the isomers, separated through chiral HPLC, was apparent in their CD spectra, which were mirror images for all wavelengths.
We report on a rotaxane‐like architecture secured by the in situ tying of an overhand knot in the tris(2,6‐pyridyldicarboxamide) region of the axle through complexation with a lanthanide ion (Lu3+). The increase in steric bulk caused by the knotting entanglement locks a crown ether onto the thread. Removal of the lutetium ion unties the knot and, if the axle binding site for the ring is deactivated, the macrocycle spontaneously de‐threads. If the binding interaction is switched on again, the crown ether re‐threads over the 10 nm length of the untangled strand. The overhand knot can be re‐tied, re‐locking the threaded structure, by adding lutetium ions once again.
We report on a rotaxane‐like architecture secured by the in situ tying of an overhand knot in the tris(2,6‐pyridyldicarboxamide) region of the axle through complexation with a lanthanide ion (Lu3+). The increase in steric bulk caused by the knotting entanglement locks a crown ether onto the thread. Removal of the lutetium ion unties the knot and, if the axle binding site for the ring is deactivated, the macrocycle spontaneously de‐threads. If the binding interaction is switched on again, the crown ether re‐threads over the 10 nm length of the untangled strand. The overhand knot can be re‐tied, re‐locking the threaded structure, by adding lutetium ions once again.
Knot theory is a branch of pure mathematics, but it is increasingly being applied in a variety of sciences. Knots appear in chemistry, not only in synthetic molecular design, but also in an array of materials and media, including some not traditionally associated with knots. Mathematics and chemistry can now be used synergistically to identify, characterise and create knots, as well as to understand and predict their physical properties. This tutorial review provides a brief introduction to the mathematics of knots and related topological concepts in the context of the chemical sciences. We then survey the broad range of applications of the theory to contemporary research in the field.
The production of chemical compounds composed of mechanically interlocked molecules (MIMs) by acts of templation are hand-me-downs from the science of chemistry beyond the molecule, which affords molecular recognition free rein to exercise its special powers of organization in marshaling the component parts of the MIMs prior to their being transported back into the molecular world by the formation of chemical bonds. Intersecting the fields of supramolecular chemistry and chemical topology is the discipline of mechanostereochemistry. A mechanical bond is an entanglement in space between two or more component parts, such that they cannot be separated without breaking or distorting chemical bonds between atoms. It follows that a mechanical bond is as strong as the weakest participating chemical bond. Catenanes and rotaxanes are a subset of MIMs that possess mechanical bonds. While mechanomolecules have found their way into switches and motors, the molecules themselves have led to a renaissance in molecular aesthetics.
An over-view of the major developments in inorganic chemistry since its modern origin in Europe in the late eighteenth century up to the present are broadly covered in this article, with mention of only notable contributions by chemists, omitting much of technical details for which the cited references be consulted. Emergence of the Modern Indian school is briefly presented.
In this review, a comprehensive summary of supramolecular transformations within discrete coordination-driven supramolecular architectures, including helices, metallacycles, metallacages, etc., is presented. Recent investigations have demonstrated that coordination-driven self-assembled architectures provide an ideal platform to study supramolecular transformations mainly due to the relatively rigid yet dynamic nature of the coordination bonds. Various stimuli have been extensively employed to trigger the transformation processes of metallosupramolecular architectures, such as solvents, concentration, anions, guests, change in component fractions or chemical compositions, light, and post-modification reactions, which allowed for the formation of new structures with specific properties and functions. Thus, it is believed that supramolecular transformations could serve as another highly efficient approach for generating diverse metallosupramolecular architectures. Classified by the aforementioned various stimuli used to induce the interconversion processes, the emphasis in this review will be on the transformation conditions, structural changes, mechanisms, and the output of specific properties and functions upon induction of structural transformations.
Active metal template Glaser coupling has been used to synthesize a series of rotaxanes consisting of a polyyne, with up to 24 contiguous sp-hybridized carbon atoms, threaded through a variety of macrocycles. Cadiot-Chodkiewicz cross-coupling affords higher yields of rotaxanes than homo-coupling. This methodology has been used to prepare [3]rotaxanes with two polyyne chains locked through the same macrocycle. The crystal structure of one of these [3]rotaxanes shows that there is extremely close contact between the central carbon atoms of the threaded hexayne chains (C···C distance 3.29 Å vs. 3.4 Å for the sum of van der Waals radii) and that the bond-length-alternation is perturbed in the vicinity of this contact. However, despite the close interaction between the hexayne chains, the [3]rotaxane is remarkably stable under ambient conditions, probably because the two polyynes adopt a crossed geometry. In the solid state, the angle between the two polyyne chains is 74°, and this crossed geometry appears to be dictated by the bulk of the 'supertrityl' end groups. Several rotaxanes have been synthesized to explore gem-dibromoethene moieties as 'masked' polyynes. However, the reductive Fritsch-Buttenberg-Wiechell rearrangement to form the desired polyyne rotaxanes has not yet been achieved. X-ray crystallographic analysis on six [2]rotaxanes and two [3]rotaxanes provides insight into the non-covalent interactions in these systems. Differential scanning calorimetry (DSC) reveals that the longer polyyne rotaxanes (C16, C18 and C24) decompose at higher temperatures than the corresponding unthreaded polyyne axles. The stability enhancement increases as the polyyne becomes longer, reaching 60 °C in the C24 rotaxane.
Introduction
Cyclophanes with One Aromatic System and Aliphatic Chain
Cyclophanes with More than One Aromatic Ring
Napthalenophanes and Other Aromatic Systems
Cyclophanes Containing Heteroaromatic Systems
Ferrocenophanes
Knots and ravels are complicated molecular forms and topologies that can be made with relative ease using noncovalent interactions. The orthogonal arrangement of molecular fragments, leading to the formation of “entanglements,” can be promoted by their coordination to metal ions as well as by hydrogen bonding between amides in a suitably rigid arrangement, or the perpendicular stacking of aromatic rings. In the area of nanometer-scale science, the amazing achievements reached in the formation of knotted structures based on DNA provide inspiration and challenging benchmarks for purely synthetic systems. The resolution of the molecular knots into their enantiomers — topological enantiomers — has been achieved, although the full potential of the compounds as materials for any purpose awaits exploitation.Keywords:knot;topology;chirality;coordination chemistry;hydrogen bonding
We give explicit deformations of embeddings of abstractly planar graphs that
lie on the standard torus $T^2 \subset \mathbb{R}^3$ and that contain neither a
nontrivial knot nor a nonsplit link into the plane. It follows that ravels do
not embed on the torus. Our results provide general insight into properties of
molecules that are synthesized on a torus.
The synthesis of topologically complex structures, such as links and knots, is one of the current challenges in supramolecular chemistry. The so-called Solomon link consists of two doubly interlocked rings. Despite being a rather simple link from a topological point of view, only few molecular versions of this link have been described so far. Here, we report the quantitative synthesis of a giant molecular Solomon link from 30 subcomponents. The highly charged structure is formed by assembly of 12 cis-blocked Pt2+ complexes, six Cu+ ions, and 12 rigid N-donor ligands. Each of the two interlocked rings is composed of six repeating Pt(ligand) units, while the six Cu+ ions connect the two rings. With a molecular weight of nearly 12 kDa and a diameter of 44.2 Å, this complex is the largest non-DNA-based Solomon link described so far. Furthermore, it represents a molecular version of a “stick link”.
In this paper, there is an attempt to review the developments in the design and synthesis of pyridine containing [1+1] and [2+2] macrocyclic Schiff-base ligands, formed by condensations of 2,6-diacylpyridine or 2,6-diformylpyridine and appropriate polyamines, which utilize the templating capability of different metal ions to direct the synthetic pathway. The reduction of the cyclic Schiff-bases to their related amine derivatives is also considered since this leads to more flexible ligands capable of structural elaboration through donor groups. Attention is mainly paid to the synthetic and structural aspects of the resulting metal complexes, particularly to the role of the coordination preferences of the different metal ions in directing the synthesis totally or preferentially towards mono-, di- or poly-nuclear entities. The preparation of functionalized ligands, containing pendant arms, capable of promoting rapid complexation and decomplexation and their use in selective metal ion transportation and separation are also paid attention to. Furthermore, a summary of the new approach of these compounds such as mechanically interlocked molecules, catalytic properties and cofactors and artificial metalloenzymes is reviewed.
A homochiral naphthalenediimide-based building block forms in water a disulfide library of macrocycles containing topological isomers. We attempted to identify each of these isomers, and explored the mechanisms leading to their formation. The two most abundant species of the library were assigned as a topologically chiral Solomon link (60%) and a topologically achiral figure eight knot (18%), competing products with formally different geometries but remarkably four-fold symmetries. In contrast, a racemic mixture of building blocks gives the near-quantitative formation of another new and more stable structure, assigned as a meso figure eight knot. Taken together, these results demonstrate a correlation between the chirality of the building block used and the topological chirality of the major structure formed. These and the earlier dis-covery of a trefoil knot, also suggest that the number of rigid components in the building block may translate into corre-sponding knot symmetry and sets the basis of a new strategy for constructing complex topologies.
Mehr als ein Vierteljahrhundert nach der ersten Metalltemplatsynthese eines [2]Catenans in Straßburg existiert nun eine Fülle an Strategien zum Aufbau mechanisch verbundener und verflochtener Strukturen auf molekularer Ebene. Catenane, Rotaxane, Knoten und Borromäische Ringe sind alle erfolgreich über Methoden zugänglich, in denen Metallionen eine Schlüsselrolle spielen. Ursprünglich wurden Metallionen ausschließlich aufgrund ihrer Koordinationschemie verwendet, indem sie entweder die einzelnen Bausteine auf eine Weise anordneten, die durch anschließende Reaktionen die Erzeugung der verschlungenen Produkte ermöglichte, oder indem sie selbst als wesentlicher Bestandteil der Ringe oder als “Stopper” dienten. Vor kurzem wurde die Rolle des Metalls auch auf die Katalyse ausgedehnt: Die Metallionen ordnen die Bausteine nicht nur zu einer verflochtenen oder eingefädelten Struktur an, sondern fördern auch aktiv die Strukturbildung durch kovalenten Einfangen. Dieser Aufsatz fasst die Strategien zur Bildung mechanisch verbundener Molekülstrukturen mit Metallionen zusammen und diskutiert die Taktiken, die zum Aufbau von Überkreuzungen, zur Maximierung der Ausbeuten verschlungener und nichtverschlungener Produkte und zur Bildung eingefädelter oder verflochtener Intermediate durch kovalenten Einfang zur Verfügung stehen.
In this note we indicate the manner in which synchronization criteria may be developed for master-slave connected Lur'e systems. For flexibility we incorporate linear, static state feedback. The criteria presented are based on the generation of Lur'e–Postnikov type Lyapunov functions for the error system.
A new strategy has been developed for synthesizing catenanes; it is based on a generalized template effect, as shown in Figure 1. The first example of a novel class of molecules, the , has been obtained in good yield : it contains copper (I) and macrocyclic phenanthroline derivatives.
A dicopper(I) trefoil knot is synthesized in 30% yield by the use of 1,3-phenylene spacers, the double stranded helical precursor complex being formed quantitatively.
A [3]-catenate is prepared in 58% yield by double acetylenic oxidative coupling from a terminal diyne compound thread into a ring.
Linking two bipyridine units by a 1,3-phenylene spacer has provided a novel class of ligand which promotes the spontaneous self-assembly of double helicates upon reaction with transition-metal ions. Interaction with copper(I) or silver(I) resulted in dinuclear double-helical complexes with the metal ions occupying pseudo-tetrahedral co-ordination sites. Reaction with cobalt(II) or nickel(II) acetates gave similar dinuclear double-helical structures with a didentate acetate ligand completing the co-ordination sphere of each metal to give a pseudo-octahedral geometry. The crystal structure of [Ni2L22(O2CMe)2][PF6]2[L2= 1,3-bis(4-methylthio-2,2′-bipyridin-6-yl)benzene] has been determined. The two metal centres are separated by 5.875 Å. In contrast to the helicates formed by the linear oligopyridines, no significant π-stacking interactions are observed between pyridine moieties on the helical strands.
Vinylisch und an Aromaten gebundenes Brom läßt sich quantitativ mit zweifachem molarem Überschuß an tert-Butyllithium gegen Lithium austauschen. Das entstehende tert-Butylbromid wird selbst bei tiefen Temperaturen von tert-Butyllithium rasch zu Isobuten dehydrohalogeniert. Die Überführung von 1-Brom-1-cycloocten und -1-cycloneone in Vinylthioäther 1d, e und i über die Lithiumderivate ist in hoher Ausbeute möglich und eröffnet einen einfachen Weg von Dibromcarbenaddukten an Olefine zu ringerweiterten Ketonen. Am Beispiel der Brombenzole 2a und 3a wird gezeigt, daß der hier beschriebene Br/Li-Austausch nicht von Arin-Bildung begleitet und auch in Gegenwart der empfindlichen benzylischen CH2-Gruppe von 3 durchführbar ist.
Bromine/Lithium Exchange in Vinyl and Aryl Bromides with tert-Butyl Lithium. On the Ring Enlargement via Dibromocarbene Adducts
Twofold molar excess of tert-butyl lithium replaces vinylic and arylic bromine by lithium. The tert-butyl bromide formed is dehydrohalogenated rapidly to isobutene by tert-butyl lithium even at very low temperatures. Transformation of 1-bromo-1-cyclooctene and - cyclononene via the lithium derivatives to vinyl thioethers 1d, e, and i in high yields opens up a simple alternative route from olefin dibromocarbene adducts to ring enlarged ketones. The bromobenzenes 2a and 3a reveal that the Br/Li-exchange described here is not accompanied by arine formation; it is feasible even in the presence of sensitive benzylic CH2-groups as present in 3.
A new type of potentially helical ligand is represented by 1. The twist of the molecule's chain required to form double helical complexes by self-organization occurs at the CC bonds between the arene rings. Ligand 1 forms double helical complexes with Cu+, Ag+, and Ni2+ salts. A crystal structure analysis of the complex [Ni2(OAc)2(lb)2](PF6)2 revealed neither intermetallic interactions nor stacking interactions between almost coplanar rings.
Molecular knots have long been the subject of speculation. Now, for the first time, it has been possible to synthesize a “knotted” molecule having the topological chirality of a trefoil knot. Compound 1 was synthesized via a double‐helix complex by exploiting the template effect of CuI ions. The chirality of 1 could be demonstrated by ¹H NMR spectroscopy. The “unraveled” topological isomer of 1 was also synthesized. (Figure Presented.)
The syntheses of adrenaline-15-crown-5 and adrenaline-18-crown-6 starting from acetovanillone are reported, together with the properties of these compounds. Alkali and alkaline-earth metal complexes of these ligands have been prepared. A method of separating crown ethers based on their preferential complexation of barium is discussed.
Results of research on two novel problems in organic stereochemistry are described: 1) Topological stereochemistry; and 2) Design and synthesis of novel organic optoelectronic materials. In the topological stereochemistry project, new methods for understanding the symmetries of topologically complex molecular structures have been developed, and the total synthesis of several such structures has been achieved. New strategies for the synthesis of the first molecular knotted ring, a long sought but still illusive target, have been tested and are under development. In the optoelectronic materials project, work has focussed on design and synthesis of new ferroelectric liquid crystals (FLCs), a novel class of fluid materials possessing polar symmetry. Such materials have important potential utility in flat panel video and devices for optical computing. A predictive model for the molecular origins of the ferroelectric polarization in FLCs has been developed and demonstrated, and several new FLC classes have been invented. Also, the model is being applied to design of the first liquid phases with high second order hyperpolarizability for ultra fast electro-optic applications.
DNA winds about itself in a right-handed or left-handed fashion at several structural levels. The double helix is generally right-handed and is given a (+) sign by convention, whereas supercoiling of the helix axis is always (−) in the cell1,2. The winding in higher -order forms such as knots and catenanes is unknown, and this has impeded elucidation of the mechanisms of their formation and resolution by replication, recombination and topoisomerase action3–6. We introduce here a procedure for determining the handedness of DNA winding by inspection of electron micrographs of DNA molecules coated with Escherichia coli RecA protein. We demonstrate the validity of the method and show that DNA topoisomerase I of E. coli
7 generates an equal mixture of (+) and (−) duplex DNA knots, and that one product of recombination by resolvase of transposon Tn3 (refs 8, 9) is a catenane of uniquely (+) sign.
The concept of topological isomerism of cyclic molecules is introduced, e.g., the isomerism between a knotted and unknotted loop and between interlocked and non-interlocked rings. The application to various chemical systems such as knots, chains and Möbius' strips is discussed. Calculations are given for the probability of formation and the stability of these materials.
Synthese d'un catenane comprenant 2 macrocycles imbriques (ce macrocycle etant un hexaoxa [16] paracyclo [0] phenanthrolino-1,10 [0] paracyclophane) a partir de diiodo-1,14 tetraoxa-3,6,9,12tetradecane, de bis-[hydroxy-4 phenyl]-2,9 phenanthroline-1,10 et de Cu(CH 3 CN) 4 + •BF 4 − suivie de demetallation du cuprocatenane obtenu. Proprietes du cuprocatenane
[3]-Catenates have been prepared in good yield by double acetylenic oxidative coupling from a terminal diyne threaded into a preformed ring. The central macrocyle is a 44-membered ring, whereas the peripheral subunits consist of 27- or 30-membered rings; the dicopper [3]-catenates are obtained. Besides these molecular systems containing three interlocked rings, a significant proportion of [4]-catenates was also isolated, the overall yield of interlocking cyclic products thus amounting to 80%. The corresponding [3]-catenands could be prepared by removal of the templating copper(I) centers by KCN. Remetalation of a [3]-catenand by various transition metals (Ag + , Zn 2+ , Co 2+ , or Ni 2+ ) led to new symetrical dimetallic species. These complexes were fully characterized
A covalently closed molecular complex whose double-helical edges have the connectivity of a truncated octahedron has been assembled from DNA on a solid support. This three-connected Archimedean solid contains six squares and eight hexagons, formed from 36 edges arranged about 24 vertices. The vertices are the branch points of four-arm DNA junctions, so each vertex has an extra exocyclic arm associated with it. The construct contains six single-stranded cyclic DNA molecules that form the squares and the extra arms; in addition, there are eight cyclic strands that correspond to the eight hexagons. The molecule contains 1440 nucleotides in the edges and 1110 in the extra arms; the estimated molecular weight for the 2550 nucleotides in the construct is 790 kDa. Each edge contains two turns of double-helical DNA, so that the 14 strands form a catenated structure in which each strand is linked twice to its neighbors along each edge. Synthesis is proved by demonstrating the presence of each square in the object and then by confirming that the squares are flanked by tetracatenane substructures, corresponding to the hexagons. The success of this synthesis indicates that this technology has reached the stage where the control of topology is in hand, in the sense of both helix axis connectivity and strand linkage.
Five new dicopper(I) knots have been synthesized as well as their face-to-face isomers. The knots range from 80- to 90-membered rings, and their preparation yields depend crucially on structural parameters such as number of methylene fragments linking the two chelating units and length of the poly(ethyleneoxy) unit used in the cyclization reaction. The best yield was obtained for an 84-membered knotted ring with a -(CH2)6- connector: this relatively long fragment allows pronounced winding of the double-helix precursor and is thus favorable to the knotting reaction. The face-to-face complexes were in some instances the major products, being obtained in yields amounting to 24% in the case of the dicopper(I) bis(43-membered-ring) system. The electrochemical properties of the copper complexes also depend on their structure. The redox potential values of the Cu(II)/Cu(I) couple span over a wide range (approximately 0.5-0.75 V vs SCE), the most electrochemically stable copper(I) complex being the 84-membered knotted compound. In CH2Cl2 solution, both the Cu2 knots and their face-to-face isomers exhibit metal-to-ligand charge-transfer absorption bands in the visible region and emission bands in the red spectral region. The profile of the absorption spectra and the luminescence properties (lambda(max) quantum yield, lifetime, and rate of excited-state quenching by acetone) depend on the length of the connectors. In agreement with the electrochemical results, the -(CH2)6- linker has a pronounced shielding effect on the metal center as well as a special ability to impose geometrical constraint.
The ligand 1,3-bis(1-methylbenzimidazol-2-yl)benzene (mbzimbe, L3) reacts with copper(I) to give [Cu2(L3)2](ClO4)2. The crystal structure of this compound (Cu2C44H36N8Cl2O8, a = 13.661 (1) angstrom, b = 19.829 (3) angstrom, c = 15.413 (2) angstrom, orthorhombic, Pbca, Z = 4) shows a dinuclear centrosymmetrical nonhelical structure in which each copper is linearly coordinated by a benzimidazole group of each ligand. The complex displays a weak intramolecular stacking interaction between the benzene groups. This complex can be considered as a stereoconformer of the double-helical complex [Cu2(L1)2](ClO4)2 (L1; 2,6-bis(1-methylbenzimidazol-2-yl)pyridine). Conductivity measurements and UV-visible spectra show that the dimeric structures are maintained in solution in polar aprotic solvents. H-1 NMR measurements show that [Cu2(L1)2]2+ retains its helical structure in solution. Comparison of helical and nonhelical structures with those formed by Cu(I) with related ligands allows discussion of the factors favoring the formation of self-assembled dinuclear complexes.
A large number of organic halides was used in the double titration method of analysis for organolithium compounds. I,2-Dibromoethane has been found to give a satisfactory analysis for alkyllithium compounds and phenyllithium. Titration employing the dibromoethane is recommended for general analytical use, although I,I,2-tribromoethane probably gives a slightly more accurate analysis for fresh preparations of phenyl- and methyllithium. The use of allyl bromide in titrations of n-butyllithium in diethyl ether and hexane was also found to afford reliable results.
A method for partitioning topologically chiral knots into mutually heterochiral classes has been developed, based on the principle that for such knots there exist no diagrams whose vertex-bicolored graphs are composed of equivalent black and white subgraphs. The method, which introduces the concept ofwrithe profiles, is successfully applied to alternating as well as non-alternating prime and composite knots, and works in cases where the Jones and Kauffman polynomials fail to recognize the knot's chirality. It is shown that writhe profiles are sensitive indicators of diagram similarity.
Treatment of single-stranded circular phage fd DNA with Escherichia coli ω protein yields a new species which sediments 1.2 to 1.5 times faster than the untreated DNA in an alkaline medium. The infectivity of this species in spheroplast assays, after purification of the DNA by zone sedimentation in an alkaline sucrose gradient, is only slightly lower than that of untreated fd DNA. The formation of this species requires Mg(II) and is strongly dependent on salt concentration and temperature. At 37 °C, over 85% of the input DNA can be converted to this form when incubation is carried out in media containing 0.15 to 0.25 m-salt. The yield decreases with increasing temperature or decreasing salt concentration. The increase in sedimentation coefficient of fd DNA in an alkaline medium following treatment with ω is not due to protein binding, as no change was observed upon treatment of the product with phenol or Pronase. Furthermore, neither the buoyant density of this new species in neutral CsCl nor its sedimentation coefficient in a neutral medium is significantly different from the corresponding properties of untreated fd DNA. Examination by electron microscopy shows that the new form has the appearance of a knotted ring of about the same contour length as an untreated monomeric single-stranded fd DNA. The new form can be converted to full-length linear fd DNA by treatment with pancreatic DNAase I. The rate of conversion is approximately the same as that of untreated circular fd DNA to the linear form. These results show that the new form of fd DNA is a novel topological isomer: a knotted single-stranded DNA ring. It is also found that further treatment of the knotted DNA rings with ω at low ionic strength can reverse the reaction, i.e. the knotted DNA rings can be converted back to simple DNA rings indistinguishable from fd DNA from the phage. At intermediate ionic strength the two forms are interconvertible and form an equilibrium mixture. Results similar to those obtained for fd DNA have also been observed for single-stranded circular φX174 DNA. A mechanism based on the known activity of ω protein on double-stranded DNA, the secondary structure of a single-stranded circular DNA, and the experimental results described here is proposed.
A principal goal of biotechnology is the assembly of novel biomaterials for analytical, industrial and therapeutic purposes. The advent of stable immobile nucleic acid branched junctions makes DNA a good candidate for building frameworks to which proteins or other functional molecules can be attached and thereby juxtaposed. The addition of single-stranded 'sticky' ends to branched DNA molecules converts them into macromolecular valence clusters that can be ligated together. The edges of these frameworks are double-helical DNA, and the vertices correspond to the branch points of junctions. Here, we report the construction from DNA of a covalently closed cube-like molecular complex containing twelve equal-length double-helical edges arranged about eight vertices. Each of the six 'faces' of the object is a single-stranded cyclic molecule, doubly catenated to four neighbouring strands, and each vertex is connected by an edge to three others. Each edge contains a unique restriction site for analytical purposes. This is the first construction of a closed polyhedral object from DNA.
Processes of DNA rearrangement such as recombination or replication frequently have as products different subsets of the limitless
number of distinguishable catenanes or knots. The use of gel electrophoresis and electron microscopy for analysis of these
topological isomers has made it possible to deduce physical and geometric features of DNA structure and reaction mechanisms
that are otherwise experimentally inaccessible. Quantitative as well as qualitative characterization is possible for any pathway
in which the fate of a circular DNA can be followed. The history, theory, and techniques are reviewed and illustrative examples
from recent studies are presented.
Oligomer forms of circular mitochondrial DNA have been identified in mitochondrial extracts of human leukaemic leucocytes. The oligomers occur as circular dimers with a contour length of 10µ and catenanes made up of interlocked 5µ monomers.
Closed circular mitochondrial DNA molecules which are catenated, or connected like the links in a chain, have been identified in extracts of HeLa cells.