Interlocked Rings Research Articles

ChemInform Abstract: Synthesis and Structure Elucidation of a New (2)-Catenane.

A supramolecular self-assembly process has lead to the synthesis of new type of [2]-catenane. A 34% yield of catenane was obtained from a one-pot double macrocyclization reaction. Its three-dimensional structure was determined structure was determined by using two-dimensional 1 H NMR spectroscopy. This structure agrees well the predictions of molecular mechanics calculations, altough there is some ambiguity in the orientation of one of the amide bonds. The molecule is locked into a well-defined conformation by several intermacrocycle H-bonds and π-π interactions and it is these interactions that template the assembly of the interlocked ring system. The dynamic properties of the catenane were investigated by variable-temperature 1 H NMR

Magnetic-field decay of three interlocked flux rings with zero linking number

The resistive decay of chains of three interlocked magnetic flux rings is considered. Depending on the relative orientation of the magnetic field in the three rings, the late-time decay can be either fast or slow. Thus, the qualitative degree of tangledness is less important than the actual value of the linking number or, equivalently, the net magnetic helicity. Our results do not suggest that invariants of higher order than that of the magnetic helicity need to be considered to characterize the decay of the field.

TbPIF1, a Trypanosoma brucei Mitochondrial DNA Helicase, Is Essential for Kinetoplast Minicircle Replication

Kinetoplast DNA, the trypanosome mitochondrial genome, is a network of interlocked DNA rings including several thousand minicircles and a few dozen maxicircles. Minicircles replicate after release from the network, and their progeny reattach. Remarkably, trypanosomes have six mitochondrial DNA helicases related to yeast PIF1 helicase. Here we report that one of the six, TbPIF1, functions in minicircle replication. RNA interference (RNAi) of TbPIF1 causes a growth defect and kinetoplast DNA loss. Minicircle replication intermediates decrease during RNAi, and there is an accumulation of multiply interlocked, covalently closed minicircle dimers (fraction U). In studying the significance of fraction U, we found that this species also accumulates during RNAi of mitochondrial topoisomerase II. These data indicate that one function of TbPIF1 is an involvement, together with topoisomerase II, in the segregation of minicircle progeny.

Synthesis of Interlocked 56‐Membered Rings by Dynamic Self‐Templating

Synthesis of Interlocked 56‐Membered Rings by Dynamic Self‐Templating

Synthesis of Interlocked 56‐Membered Rings by Dynamic Self‐Templating

Synthesis of Interlocked 56‐Membered Rings by Dynamic Self‐Templating

On sublinks and their connections within the graphs of the mechanically bound molecules

The concept of sublinks has been further developed and has been used in the new form for the analysis of the graphs of complex mechanically bound molecules. This analysis is additionally supported by the Brunnian numbers M, µ for topologically non-trivial and their complements L and λ for topologically trivial systems (like (n)-rotaxanes). The detailed topological analysis has been thus performed for more than thirty topologically different structures. The different orders of (sub)links, single and multiple mechanical bonds ought to be discerned to analyze connections within the larger structures. The new nomenclature recommendations developed suggest to indicate the number of the mechanical bonds, their (highest) multiplicities together with the number of covalent units and the number of interlocked rings or rings and dumbbells.

Large double minutes with ring-shape and rod-shape

High incidence of large double minutes (DM) was characteristic of one subline of the SEWA mouse ascites tumor. This subline, SEWA1R, was the one in which the new C-bandless chromosomes (CM) appeared. The incidence of large DM was associated with low incidence of DM per cell, low incidence of DM-carrying cells, and high incidence of CM-carrying cells. The large DM were either round or elongated (rod-shaped). Many of the former kind were suggestive of ring-shape and a few of the largest obviously constituted pairs of rings, free or interlocked. One configuration of 4 interlocked rings was evidently in its second mitotic generation; in the same cell another configuration of 2 pairs of interlocked rings had developed from 1 pair of free rings in the preceding generation. Possible relations between CM and large DM are considered.

P166, a link between the trypanosome mitochondrial DNA and flagellum, mediates genome segregation

Kinetoplast DNA (kDNA), the trypanosome mitochondrial genome, is a giant network containing several thousand interlocked DNA rings. Within the mitochondrion, kDNA is condensed into a disk-shaped structure positioned near the flagellar basal body. The disk is linked to the basal body by a remarkable transmembrane filament system named the tripartite attachment complex (TAC). Following kDNA replication, the TAC mediates network segregation, pulling the progeny networks into the daughter cells by their linkage to the basal bodies. So far TAC has been characterized only morphologically with no known protein components. By screening an RNAi library, we discovered p166, a protein localizing between the kDNA and basal body in intact cells and in isolated flagellum-kDNA complexes. RNAi of p166 has only small effects on kDNA replication, but it causes profound defects in network segregation. For example, kDNA replication without segregation causes the networks to grow to enormous size. Thus, p166 is the first reported molecular component of the TAC, and its discovery will facilitate study of kDNA segregation machinery at the molecular level.

Toward Mechanical Switching of Surface-Adsorbed [2]Catenane by in Situ Copper Complexation

Using scanning tunneling microscopy (STM), electrospray ionization mass spectrometry (ESI-MS), and X-ray photoelectron spectroscopy (XPS), we demonstrate that a free [2]catenane consisting of two interlocking 30-membered rings (cat-30) can be deposited on a Ag(111) surface by vacuum sublimation without decomposition. The deposited cat-30 molecules self-organize as ordered dimer chain structures at the surface, presumably via intermolecular pi-pi stacking. An in situ addition of Cu atoms to the surface-adsorbed catenanes induces a drastic change in the molecular organization, i.e., from the dimer chain structure to isolated species. The nitrogen core level spectra suggest that the cat-30 phenanthroline units coordinate with Cu, indicating that the free catenane has been transformed into a Cu-complexed [2]catenane. Since it is known that the two interlocked macrocyclic rings of the free ligand cat-30 completely rearrange, i.e., circumrotate, upon complexation to copper, our results reveal that when adsorbed on the silver surface, the two macrocyclic rings of the free [2]catenane can glide within one another so as to generate the corresponding copper complex by in situ Cu complexation.

Calix[4]arene‐Based Bis[2]catenanes: Synthesis and Chiral Resolution

The exclusive formation of hydrogen-bonded dimers between tetraaryl and tetratosylurea calix[4]arenes has been used to prepare a series of ten "bisloop" tetraurea calix[4]arenes 3, in which adjacent phenylurea groups are covalently linked through alpha,omega-dioxyalkane chains. This dimerization with tetratosylurea 2 as template preorganizes the alkenyl residues of tetra(m-alkenyloxyphenyl) ureas 1 and enables their selective connection in high yield (up to 95 %) by olefin metathesis followed by hydrogenation. The "bisloop" calixarenes 3 also exclusively form heterodimers with 1. Thus, in a separated metathesis/hydrogenation sequence, a series of 14 cyclic bis[2]catenanes 4, in which two calix[4]arenes are connected through their wide rims by two pairs of interlocked rings (total size 29 to 41 atoms), were prepared in yields of up to 97 %. Optical resolution of these chiral bis[2]catenanes was studied by HPLC on chiral stationary phases. The single-crystal X-ray structure of one example (4(P,10)) confirmed the interlocking rings and revealed that the hydrogen-bonded dimeric capsule of the calix[4]arene can be "completely" opened.

Synthesis and crystal structures of extremely crowded oligophenylenes as model precursors to ‘cubic graphite’

By using drastic conditions for a Diels–Alder cycloaddition reaction, it was possible to synthesize an oligophenylene with an extremely dense packing of the benzene rings. Crystallographic data could be obtained and a projection of the structure on the plane of the central phenyl ring reveals that the molecule retained its theoretical threefold symmetry with only minor deviations. Due to its dense packing of interlocked benzene rings, this oligophenylene could be furthermore used as a suitable precursor for constructing a subunit of ‘cubic graphite’.

Complexes of Ag(i), Hg(i) and Hg(ii) with multidentate pyrazolyl-pyridine ligands: from mononuclear complexes to coordination polymers via helicates, a mesocate, a cage and a catenate

The coordination chemistry of a series of di- and tri-nucleating ligands with Ag(I), Hg(I) and Hg(II) has been investigated. Most of the ligands contain two or three N,N'-bidentate chelating pyrazolyl-pyridine units pendant from a central aromatic spacer; one contains three binding sites (2 + 3 + 2-dentate) in a linear sequence. A series of thirteen complexes has been structurally characterised displaying a wide range of structural types. Bis-bidentate bridging ligands react with Ag(I) to give complexes in which Ag(I) is four-coordinate from two bidentate donors, but the complexes can take the form of one-dimensional coordination polymers, or dinuclear complexes (mesocate or helicate). A tris-bidentate triangular ligand forms a complicated two-dimensional coordination network with Ag(I) in which Ag...Ag contacts, as well as metal-ligand coordination bonds, play a significant role. Three dinuclear Hg(I) complexes were isolated which contain an {Hg2}2+ metal-metal bonded core bound to a single bis-bidentate ligand which can span both metal ions. Also characterised were a series of Hg(II) complexes comprising a simple mononuclear four-coordinate Hg(II) complex, a tetrahedral Hg(II)4 cage which incorporates a counter-ion in its central cavity, a trinuclear double helicate, and a trinuclear catenated structure in which two long ligands have spontaneously formed interlocked metallomacrocyclic rings thanks to cyclometallation of two of the Hg(II) centres.

Molecular design of Goldberg polyhedral links

A new method for understanding the construction of polyhedral links has been developed on the basis of the novel structure of HK97 capsid and the classification of Goldberg polyhedra. Polyhedral links, the interlinked and interlocked architectures, have been solved by analyzing and characterizing the topological structure of the two types of polyhedral links, which are R n+1 = R n +10(2 n+1) and R n+1 = R n +20 n. Where, n=1,2,…, R 1=12 and R represents the number of the interlocked rings. Our results show that these two types of polyhedral links both have I symmetry and therefore are said to possess chirality.

Bovine Mitochondrial Peroxiredoxin III Forms a Two-Ring Catenane

A crystal structure is reported for the C168S mutant of a typical 2-Cys peroxiredoxin III (Prx III) from bovine mitochondria at a resolution of 3.3 A. Prx III is present as a two-ring catenane comprising two interlocking dodecameric toroids that are assembled from basic dimeric units. Each ring has an external diameter of 150 A and encompasses a central cavity that is 70 A in width. The concatenated dodecamers are inclined at an angle of 55 degrees, which provides a large contact surface between the rings. Dimer-dimer contacts involved in toroid formation are hydrophobic in nature, whereas the 12 areas of contact between interlocked rings arise from polar interactions. These two major modes of subunit interaction provide important insights into possible mechanisms of catenane formation.

Fellowship of the rings: the replication of kinetoplast DNA

Kinetoplastid protozoa such as trypanosomes and Leishmania are important because they cause human disease. These parasites are named after one of their most unusual features, a mitochondrial DNA known as kinetoplast DNA (kDNA). Unlike all other DNA in nature, kDNA comprises a giant network of interlocked DNA rings with a topology resembling that of medieval chain mail. The replication of the kDNA network is more complex than previously thought, and the discovery of new proteins involved in this process is currently the best approach for illuminating the replication mechanism.

Nanoscale Borromean Rings

AbstractFor Abstract see ChemInform Abstract in Full Text.

Nanoscale Borromean Rings

The molecular expression of topologically interesting structures represents a formidable challenge for synthetic chemists. The nontrivial link known as the Borromean rings has long been regarded as one of the most ambitious targets in this field. Of ancient provenance, this symbol comprises three interlocked rings in an inseparable union, but cut any one of the rings and the whole assembly unravels into three separate pieces. This Account delineates different strategies that can be applied to the formation of molecules possessing this distinctive topology, culminating with two successful syntheses of such compounds, thus cutting the Gordian knot of topological chemistry.

Sampling protein conformations and pathways.

Protein flexibility and rigidity can be analyzed using constraint theory, which views proteins as 3D networks of constraints involving covalent bonds and also including hydrophobic interactions and hydrogen bonds. This article describes an algorithm, ROCK (Rigidity Optimized Conformational Kinetics), which generates new conformations for these complex networks with many interlocked rings while maintaining the constraints. These new conformations are tracked for the flexible regions of a protein, while leaving the rigid regions undisturbed. An application to HIV protease demonstrates how large the flap motion can be. The algorithm is also used to generate conformational pathways between two distinct protein conformations. As an example, directed trajectories between the closed and the occluded conformations of the protein dihydrofolate reductase are determined.

The Refined Structure of a Protein Catenane: The HK97 Bacteriophage Capsid at 3.44 Å Resolution

The HK97 bacteriophage capsid is a unique example of macromolecular catenanes: interlocked rings of covalently attached protein subunits. The chain mail organization of the subunits stabilizes a particle in which the maximum thickness of the protein shell is 18Å and the maximum diameter is 550Å. The electron density has the appearance of a balloon illustrating the extraordinary strength conferred by the unique subunit organization. The refined structure shows novel qualities of the HK97 shell protein, gp5 that, together with the protease gp4, guides the assembly and maturation of the virion. Although gp5 forms hexamers and pentamers and the subunits exist in different structural environments, the tertiary structures of the seven protein molecules in the viral asymmetric unit are closely similar. The interactions of the subunits in the shell are exceptionally complex with each subunit interacting with nine other subunits. The interactions of the N-terminus released after gp5 cleavage appear important for organization of the loops that become crosslinked to the core of a neighboring subunit at the maturation. A comparison with a model of the Prohead II structure revealed that the surfaces of non-covalent contact between the monomers that build up hexamers/pentamers are completely redefined during maturation.

Cover Picture: Chem. Eur. J. 2/2003

The cover picture conveys the concise message that a fixed element of axial chirality residing in one ring of a catenane can induce chirality of a helical nature within a dynamic setting in the other (interlocked) ring. The overwhelming preference for one enantiomeric pair within a bipartite set of diastereoisomers relating to the particular [2]catenane, presented as its X-ray crystal structure in the circular inset, becomes more and more pronounced as its 1,4-dioxybenzene units are replaced, one at a time, by 1,5-dioxynaphthalene ones, with their concomitant planar chiralities. The very high levels of induction of dynamic helical and planar chiralities by a fixed source of axial chirality in a simple catenane conjures up a number of scenarios where this approximately cubic nanometer of programmable information might be put to good use. For more details concerning these tiny stereochemical wonders with no stereogenic center in sight, see the article on p. 543 ff by J. F. Stoddart and D. J. Williams and the wizards that work their magic for them.