Molecular Helices Research Articles

Artificial Molecular Double‐Stranded Helices

Artificial Molecular Double‐Stranded Helices

Origin of strong chiroptical activities in films of nonafluorenes with a varying extent of pendant chirality.

Novel nonafluorenes with a varying extent of pendant chirality were synthesized for an investigation of the origins of chiroptical activities in neat films. Thermal annealing of 4-microm-thick sandwiched films and of 90-nm-thick spin-cast films, all on surface-treated substrates, produced monodomain glassy films characterized as a right-handed cholesteric stack with a helical pitch length ranging from 180 to 534 nm and from 252 to 1151 nm, respectively. The observed strong circular dichroism (CD) and g(e) as functions of helical pitch length in single-substrate monodomain glassy cholesteric films were quantitatively interpreted with a circularly polarized fluorescence theory accounting for light absorption, emission, and propagation in a cholesteric stack. Although intertwined molecular helices were likely to be present, cholesteric stacking of rodlike molecules seemed to be the predominant contributor to the strong chiroptical activities. All the cholesteric stacks comprising a polydomain glassy film on an untreated substrate were found to contribute to CD and g(e) largely to the same extent as in a monodomain film. A circularly polarized blue organic light-emitting diode containing a nonafluorene film resulted in a g(e) of 0.35 with a luminance yield of 0.94 cd/A at 20 mA/cm(2), the best performance to date.

The Use of Non-Covalent Interactions in the Assembly of Metal/Organic Supramolecular Arrays

The design and synthesis of molecules that can organize into specific supramolecular assemblies in the solid state is an area of considerable interest, since incorporation of specific structural components into a crystal lattice may lead to new materials with desirable chemical and physical properties. However, it is still difficult to reliably predict crystal structures especially those in non-centrosymmetric space groups. To develop compounds whose assembly is more controlled and predictable, we are investigating the formation of supramolecular assemblies from C 2 - and C 3 -symmetric molecular species. The C 2 -symmetric systems use a rigid template to control the orientation of appended groups. Using hydrogen bonds and weak metal-ligand interactions as the key forces to control molecular structure, a variety of helical forming compounds can be isolated. The assembly of these compounds was monitored in the crystalline phase and shown to yield a diverse group of lattice architectures. Molecular helices have produced i) microporous networks, ii) extended helices in the lattice and iii) chiral arrays that assemble enantioselectively during crystallization. The use of C 3 -symmetric compounds in supramolecular assembly is illustrated by a chiral tripodal system that forms non-centrosymmetric crystal lattices. A Ni(II)-F salt of this tripod has a lattice that is noteworthy for its six-fold symmetric open framework structure and the alignment of all the molecular Ni-F bonds along a crystallographic axis.

Helical molecular programming: folding of oligopyridine-dicarboxamides into molecular single helices.

Molecular strands composed of alternating 2,6-diaminopyridine and 2,6-pyridinedicarbonyl units have been designed to self-organize into single stranded helical structures upon forming intramolecular hydrogen bonds. Pentameric strands 11, 12, and 14, heptameric strands 1 and 20, and undecameric strand 15 have been synthesized using stepwise convergent strategies. Single helical conformations have been characterized in the solid state by single crystal X-ray diffraction analysis for four of these compounds. Helices from pentameric strands 12 and 14 extend over one turn, and helices from heptameric 20 and undecameric 15 species extend to one and a half and two and a half turns, respectively. Intramolecular hydrogen bonds are responsible for the strong bending of the strands. 1H NMR shifts both in polar and nonpolar organic solvents indicate intramolecular overlap between the peripheral aromatic groups. Thus, helical conformations also predominate in solution. Molecular stochastic dynamic simulations of strand folding starting from a high energy extended linear conformer show a rapid (600 ps at 300 K) conversion into a stable helical conformation.

Comparative Supramolecular Chemistry of Coronene and Hexahelicene: Helix Alignment in Crystalline Complexes with Trimesic Acid (=Benzene-1,3,5-tricarboxylic Acid) andπ-Acceptor Compounds

The crystallization of the molecular complex (TMA)2⋅COR is reported, and evidence is produced that its structure is built up of planar hexagonal, H-bonded TMA honeycomb sheets, the large pores of which accommodate the almost perfectly complementary COR molecules by means of favorable straight C−H⋅⋅⋅O contacts. The detailed crystal structure of (TMA)2⋅COR could, however, not be unravelled by X-ray means, probably due to sheet stacking disorder. On the other hand, the crystals of the corresponding (racemic) complex (TMA)2⋅HEL, engineered by exploiting the geometric similarities of HEL and COR, are fully ordered and have an analogous structure, although the HEL-filled TMA honeycomb sheets are puckered for improved `helix following' via C−H⋅⋅⋅O contacts. The absence of stacking disorder is ascribed to the non-planarity of the HEL molecules protruding out of the mean plane of the TMA sheets. Further remarkable structural features of (TMA)2⋅HEL comprise: substantial helix flattening of HEL, perfect helix alignment (parallel helix axes of HEL molecules), TMA sheets with homochiral HEL guests, opposite chirality of HEL molecules in neighboring sheets, striking non-natural example of a mutually induced-fit molecular recognition process. In the ordered crystals of the racemic π donor-acceptor complexes HEL⋅TNB (two crystal forms), HEL⋅DNBA, HEL⋅TCNQ, and (NIPA)2⋅HEL, the molecular helices of the HEL molecules are also well aligned, and, except for HEL⋅TNB, arranged in homochiral sheets. In these HEL sheets, some helix flattening is again observed, as well as head-to-tail contacts among the HEL molecules via protrusion into their molecular clefts. The crystal structure of (NIPA)2⋅HEL is particularly amazing and may be characterized as an elegant triply interpenetrating, distorted diamond architecture involving H-bonded NIPA zig-zag chains, which embrace the HEL molecules by means of C−H⋅⋅⋅O contacts with almost perfect `helix following'. Simultaneously, good π donor-acceptor contacts between HEL and NIPA molecules are enabled, upon which the diamondoid model may also be based. Alternatively, the solid-state structure of (NIPA)2⋅HEL can also be viewed as a system of stacked, triply concatenated `molecular fences' of the crossed lath-and-hinge type, with the laths representing the NIPA zig-zag chains and the HEL molecules providing the hinges. Both models account well for the alignment and chirality characteristics of the HEL sheets in (NIPA)2⋅HEL. The crystal structure of the adduct PHEN⋅NIPA is also presented, which has architectural elements in common with (NIPA)2⋅HEL, (TMA)2⋅HEL, and (TMA)2⋅COR. Apparently, PHEN⋅NIPA owes its stability in substantial measure to favorable C−H⋅⋅⋅O contacts (`C−H⋅⋅⋅O assisted π donor-acceptor complex'). Furthermore, the crystal architecture of PHEN⋅NIPA involves remarkably close intermolecular H⋅⋅⋅H contacts between neighboring PHEN molecules, which may be estimated as short as 1.86 A, i.e., more than 0.5 A smaller than the van der Waals diameter of H. Finally, the crystal structures of the complexes COR⋅TNB and COR⋅DNBA are briefly reported and compared to the analogous HEL adducts. The COR molecules are twofold orientationally disordered in these molecular compounds, which involve the usual donor-acceptor π stacks, but with only limited alignment of the COR molecular disks. The complex (NIPA)2⋅COR could be crystallized, but resisted X-ray structure solution efforts, probably again due to substantial disorder phenomena. The corresponding pairs of COR and HEL molecular complexes studied generally agree in their stoichiometries, but differ conspicuously as regards their crystal-structural order, which is significantly perturbed if the perfectly circular, disk-shaped COR molecules are involved. The results are evaluated as regards the following prospects: recovery of COR from PAH mixtures, scanning-probe microscopic applications, extreme chiroptic and non-linear optical (NLO) properties of helix-aligned HEL molecular complexes, extension to crystalline adducts of other (higher) helicenes. Emphasis is laid on the stimulation of future attempts to engineer crystalline helix-aligned molecular complexes of optically active helicenes, which may be expected to bring forth particularly intriguing, useful, and extreme material properties.

Structures and related properties of AgX bearing 3,3'-thiobispyridine (X- = NO3-, BF4-, CLO4-, and PF6-.

Infinite molecular helices [Ag(3,3'-Py2S)]X (3,3'-Py2S = 3,3'-thiobispyridine; X- = BF4-, ClO4-, and PF6-) have been rationally constructed or induced. Crystallographic characterization (X- = BF-, monoclinic P2(1)/n, a = 8.946(3) A, b = 14.130(2) A, c = 10.124(2) A, beta = 107.83(2) degrees, V = 1218.3(5) A3, Z = 4, R = 0.0351; X- = ClO4-, monoclinic P2(1)/n, a = 8.884(1) A, b = 14.305(3) A, c = 10.110(1) A, beta = 106.78(1) degrees, V = 1230.1(3) A3, Z = 4, R = 0.0417; X- = PF6-, monoclinic P2(1)/c, a = 10.959(2) A, b = 9.808(2) A, c = 14.065(3) A, beta = 112.03(2) degrees, V = 1401.4(5) A3, Z = 4, R = 0.0442) reveals that the skeletal structure is an oblong cylindrical cationic helix consisting of alternating Ag(I) and 3,3'-Py2S species and that its counteranions are pinched in two columns inside each helix. The formation of the helical coordination polymer appears to be primarily associated with a suitable combination of the skewed conformer of 3,3'-Py2S and the potential linear geometry of the N-Ag(I)-N bond. However, the framework of the nitrate analogue [Ag(3,3'-Py2S)NO3] (monoclinic P2(1)/c, a = 8.177(2) A, b = 10.291(1) A, c = 14.771(2) A, beta = 102.19(1) degrees, V = 1214.9(4) A3, Z = 4, R = 0.0300) is a two-dimensional network consisting of an 18-membered ring unit, where each 3,3'-Py2S acts as a N,N',S- tridentate ligand connecting three tetrahedral silver(I) ions with the monodentate nitrate weakly bonded to the silver (Ag.O = 2.65(1) A) rather than acting as a counteranion. The anion exchange of [Ag(3,3'-Py2S)NO3] with BF4-, ClO4-, or PF6- has been accomplished in aqueous media. The two-dimensional networks are easily converted into the helices via the anion exchange, but the reverse anion exchange proceeds slightly. Thermal analyses indicate a relationship between the thermal stabilities and the structural properties.

Interconversion of single and double helices formed from synthetic molecular strands.

Synthetic single-helical conformations are quite common, but the formation of double helices based on recognition between the two constituent strands is relatively rare. Known examples include duplex formation through base-pair-specific hydrogen bonding and stacking, as found in nucleic acids and their analogues, and polypeptides composed of amino acids with alternating L and D configurations. Some synthetic polymers and self-assembled fibres have double-helical winding induced by van der Waals interactions. A third mode of non-covalent interaction, coordination of organic ligands to metal ions, can give rise to double, triple and quadruple helices, although in this case the assembly is driven by the coordination geometry of the metal and the structure of the ligands, rather than by direct inter-strand complementarity. Here we describe a family of oligomeric molecules with bent conformations, which exhibit dynamic exchange between single and double molecular helices in solution, through spiral sliding of the synthetic oligomer strands. The bent conformations leading to the helical shape of the molecules result from intramolecular hydrogen bonding within 2'-pyridyl-2-pyridinecarboxamide units, with extensive intermolecular aromatic stacking stabilizing the double-stranded helices that form through dimerization.

Self-assembled dinuclear molecular box [Ag2L2]2+ and triple helicates [Co2L3]4+, [Ni2L3]4+ {L = bis[4-(2-pyridylmethyleneamino)phenyl] ether}

The self-assembly and structural characterization of the new silver(I) molecular box [Ag2L2]2+ and cobalt(II), and nickel(II) molecular helices [Co2L3]4+ and [Ni2L3]4+ have been achieved. These complexes are derived from an inexpensive and easy-to-prepare bis-bidentate Schiff base ligand bis[4-(2-pyridylmethyleneamino)phenyl] ether (L). The cage-like cation [Ag2L2]2+ is located at an inversion center with two tetrahedrally co-ordinated silver(I) atoms and two ether oxygen atoms in the corner of a box. The edge length Ag⋯O is ca. 7.1 A. Each silver(I) center is bound to two pyridylimine units, one from each ligand. One ligand passes above the silver(I)–silver(I) axis, while the other passes beneath, giving a non-helical metallo-cyclophane with Ag⋯Ag separation ca. 12.3 A. Both triple helical [Co2L3]4+ and [Ni2L3]4+ cations contain two metal atoms and three ligands. Each metal center is bound to three pyridylimine units to attain a pseudo-octahedral co-ordination geometry. The ligand wraps in a helical arrangement around the two metal ions. Edge-to-face and face-to-face π–π interactions play important roles in the metal-assisted self-assembling process.

The crystal structure ofBombyx mori silk fibroin at the air–water interface

A new crystalline polymorph of Bombyx mori silk, which forms at the air–water interface, has been characterized. A previous study found this structure to be trigonal, and to be distinctly different than the two previously observed silk crystal structures, silk I and silk II. This new structure was named silk III. Identification of this new silk polymorph was based on evidence from transmission electron microscopy and electron diffraction, coupled with molecular modeling. In the current paper, additional data enables us to refine our model of the silk III structure. Some single crystal electron diffraction patterns indicate a deviation in symmetry away from a perfect trigonal unit cell to monoclinic unit cell. The detailed shape of the powder diffraction peaks also supports a monoclinic cell. The monoclinic crystal structure has an nonprimitive unit cell incorporating a slightly distorted hexagonal packing of silk molecular helices. The chains each assume a threefold helical conformation, resulting in a crystal structure similar to that observed for polyglycine II, but with some additional sheet-like packing features common to the threefold helical crystalline forms of many glycine-rich polypeptides. © 1997 John Wiley & Sons, Inc. Biopoly 42: 705–717, 1997

Collagen: the organic matrix of bone.

Collagen is the principal organic matrix in bone. The triple helical region of the molecule is 1014 amino acids long. In fibrils these molecules are staggered axially by integers of 234 residues or 68 nm (D). This axial shift occurs by self-assembly and can be understood in terms of a periodicity in the occurrence of apolar and polar residues in the amino acid sequence. Because the molecular length L = 4.47 D, there are gaps 1.5 X 36.5 nm regularly arrayed throughout the fibrils. The three-dimensional molecular arrangement is a quasi-hexagonal lattice with three distinct values for the principal interplanar spacings. Analysis of the intensity distribution in the medium-angle X-ray diffraction patterns from tendons has produced the following picture of the molecular arrangement in fibrils (Fraser et al. 1983). The molecular helices have a coherent length of 32 nm and are tilted parallel to a specific place within the lattice. A regular azimuthal interaction exists between these helices. This crystalline region could be the overlap region with a non-crystalline gap region. However, the gap is still regular axially and the molecular helices retain their structure; their lateral packing is perturbed although they retain a 'gap'. Neutron and X-ray scattering experiments have shown that calcium hydroxyapatite crystals occur in the gap and are nucleated at a specific though unknown location within the gap. The c-axis of the apatite crystals is parallel to the fibril axis and its length c = 0.688 nm is close to the axial periodicity in a protein with an extended beta-conformation. If the telopeptides at the end of a collagen molecule do have this conformation they would either have a highly heterogeneous conformation or exist in a folded manner because the overall length of the telopeptides is shorter than a regular collagen repeat of 0.029 nm would allow.

Irregular conformations of poly-4-vinylpyridine

Additive approximation involving the use of atom-atom potentials provided the means of calculating the irregular conformations of iso- and syndiotactic chain fragments of poly-4-vinylpyridine (P-4VP) as well as the most stable conformations of atactic P-4VP for dddl, ddld, dlld and ddll, i.e. independent tetrads of asymmetrical centres. It was found that the most stable conformations were 3 1 -type helical segments of similar rotational sign for the iso-configuration of asymmetrical centres, and 2 1 -molecular helices for the syndio-configuration, and these conformations link up without any sort of energy losses, while helical segments of dissimilar rotational sign link up successfully via a trans-zigzag“buffer” structure. It is shown that the conformational structures of heterotactic P-4VP may be made up of sequences of regular conformations of chain fragments. A model is proposed for the orientation of macromolecules of non-stereospecific P-4VP. In this model dichroism is brought about by chain segments with a syndiotactic sequence of asymmetrical centres in the trans-zigzag conformation.