The electronic factor in Bergman cyclization

Through-bond interactions in 1,4-dehydrobenzene preferentially stabilize the out-of-phase combination of the radical hydrids, The resultant splitting between the frontier orbitals is crucial in making Bergman cyclization a symmetry-allowed process. Orbital symmetry also inhibits the radical centers from forming a C-C bond, enabling the biradical to survive as a local minimum capable of intermolecular hydrogen abstraction, Both these factors, which are important in the design of DNA cleaving molecules, are confirmed through calculations on biradicals formed from diynes in which through-bond interactions stabilize the in-phase combination of hybrids at the radical centers.

Structure of bis(thiocyanato-N)bis(thiosemicarbazide-N1,S)nickel(II): a redetermination

[Ni(NCS)2(CHsN3S)2], Mr = 356.7, monoclinic, P21/c , a = 5-297 (1), b = 7.869 (1), c - 16-078 (2) A,/3 = 91.53 (1) °, V-= 669.9 A 3, Z= 2, Om = 1"76, Dx = 1"771 g cm -3, A(Mo Ka) = 0-71069 ]k, /.~ = 19"9 cm-l, F(000) = 364, T = 295 K, final R = 0.026 for 1576 significant [F > 10g(F)] reflections. The complex lies on a crystallographic centre of symmetry. The Ni atom is octahedrally coordinated by two thiocyanates (through N atoms) and by two thiosemicarbazide molecules (through hydrazinic N and S atoms). The crystal structure is stabilized by N--H...S hydrogen bonds. Early work on this structure [Garaj & Dunaj-Jurco (1968). Chem. Commun. p. 518] used photographic data and was refined to R = 0-13 for 512 reflections.

Electron cryo-microscopy studies of bacteriophage phi8 and archaeal virus SH1

Symmetry is a key principle in viral structures, especially the protein capsid shells. However, symmetry mismatches are very common, and often correlate with dynamic functionality of biological significance. The three-dimensional structures of two isometric viruses, bacteriophage phi8 and the archaeal virus SH1 were reconstructed using electron cryo-microscopy. Two image reconstruction methods were used: the classical icosahedral method yielded high resolution models for the symmetrical parts of the structures, and a novel asymmetric in-situ reconstruction method allowed us to resolve the symmetry mismatches at the vertices of the viruses. Evidence was found that the hexameric packaging enzyme at the vertices of phi8 does not rotate relative to the capsid. The large two-fold symmetric spikes of SH1 were found not to be responsible for infectivity. Both virus structures provided insight into the evolution of viruses. Comparison of the phi8 polymerase complex capsid with those of phi6 and other dsRNA viruses suggests that the quaternary structure in dsRNA bacteriophages differs from other dsRNA viruses. SH1 is unusual because there are two major types of capsomers building up the capsid, both of which seem to be composed mainly of single beta-barrels perpendicular to the capsid surface. This indicates that the beta-barrel may be ancestral to the double beta-barrel fold.

Metal-Nucleotide Interactions: Crystal Structures of Alkali (Li+, Na+, K+) and Alkaline Earth (Ca2+, Mg2+) Metal Complexes of Adenosine 2'-Monophosphate

Crystal structures of lithium, sodium, potassium, calcium and magnesium salts of adenosine 2'-monophosphate (2'-AMP) have been obtained at atomic resolution by X-ray crystallographic methods. 2'-AMP.Li belongs to the monoclinic space group P21 with a = 7.472(3)Å, b = 26.853(6) Å, c = 9.184(1)Å, b = 113.36(1)Å and Z= 4. 2'-AMP.Na and 2'-AMP.K crystallize in the trigonal space groups P31 and P3121 with a = 8.762(1)Å, c = 34.630(5)Å, Z= 6 and a = 8.931(4), Åc = 34.852(9)Å and Z= 6 respectively while 2'-AMP.Ca and 2'-AMP.Mg belong to space groups P6522 and P21 with cell parameters a = 9.487(2), c = 74.622(13), Z = 12 and a = 4.973(1), b = 10.023(2), c = 16.506(2), beta = 91.1(0) and Z = 2 respectively. All the structures were solved by direct methods and refined by full matrix least-squares to final R factors of 0.033, 0.028, 0.075, 0.069 and 0.030 for 2'-AMP.Li, 2'-AMP.Na, 2'- AMP.K, 2'-AMP.Ca and 2'-AMP.Mg, respectively. The neutral adenine bases in all the structures are in syn conformation stabilized by the O5'-N3 intramolecular hydrogen bond as in free acid and ammonium complex reported earlier. In striking contrast, the adenine base is in the anti geometry (cCN = -156.4(2)°) in 2'-AMP.Mg. Ribose moieties adopt C2'-endo puckering in 2'-AMP.Li and 2'-AMP.Ca, C2'-endo-C3'-exo twist puckering in 2'-AMP.Na and 2'-AMP.K and a C3'-endo-C2'-exo twist puckering in 2'-AMP.Mg structure. The conformation about the exocyclic C4'-C5' bond is the commonly observed gauche-gauche (g+) in all the structures except the gauche- trans (g-) conformation observed in 2'-AMP.Mg structure. Lithium ions coordinate with water, ribose and phosphate oxygens at distances 1.88 to 1.99Å. Na+ ions and K+ ions interact with phosphate and ribose oxygens directly and with N7 indirectly through a water oxygen. A distinct feature of 2'-AMP.Na and 2'-AMP.K structures is the involvement of ribose O4' in metal coordination. The calcium ion situated on a two-fold axis coordinates directly with three oxygens OW1, OW2 and O2 and their symmetry mates at distances 2.18 to 2.42Å forming an octahedron. A classic example of an exception to the existence of the O5'-N3 intramolecular hydorgen bond is the 2'-AMP.Mg strucure. Magnesium ion forms an octahedral coordination with three water and three phosphate oxygens at distances ranging from 2.02 to 2.11Å. A noteworthy feature of its coordination is the indirect link with N3 through OW3 oxygen resulting in macrochelation between the base and the phosphate group. Greater affnity of metal clays towards 5' compared to 2' and 3' nucleotides (J. Lawless, E. Edelson, and L. Manring, Am. Chem. Soc. Northwest Region Meeting, Seattle. 1978) due to macrochelation infered from solution studies (S. S. Massoud, H. Sigel, Eur. J. Biochem. 179, 451-458 (1989)) and interligand hydrogen bonding induced by metals postulated from metal-nucleotide structures in solid state (V. Swaminathan and M. Sundaralingam, CRC. Crit. Rev. Biochem. 6, 245-336 (1979)) are borne out by our structures also. The stacking patterns of adenine bases of both 2'-AMP.Na and 2'-AMP.K structures resemble the 2'-AMP.NH4 structure reported in the previous article. 2'-AMP.Li, 2'-AMP.Ca and 2'-AMP.Mg structures display base-ribose O4' stacking. An overview of interaction of monovalent and divalent cations with 2' and 5'-nucleotides has been presented.

Theoretical calculations of base-base interactions in nucleic acids: I Stacking interactions in free bases

Stacking interactions in free bases were computed on the basis of molecular association. The results of the calculations were compared with the stacking patterns observed in a few single crystals of nucleic acid components as examples. The following are the conclusions: (i) there can be two types of stacking pattern classified as normal and inverted types for any two interacting bases and both can be energetically favourable (ii) in both the types the stacking interaction is a combined effect of the overlap of the interacting bases and relative positions and orientations of the atomic centres of the two bases (iii) crystal symmetry and H-bonding interaction may influence stacking patterns.

Synthesis, structural and ferromagnetic properties of La1-xKxMnO3 (0.0 <= x <= 0.25) phases by solution combustion method

We describe the solution combustion synthesis and characterization of La1-xKxMnO3 (0.0 <= x <= 0.25) perovskite phases, which is a low temperature initiated, rapid route to prepare metal oxides. As-synthesized compounds are amorphous in nature; crystallinity was observed on heating at 800 degrees C for 5 min. Structural parameters were determined by the Rietveld refinement method using powder XRD data. Parent LaMnO3 compound crystallizes in the orthorhombic structure (space group Pbnm, No. 62). Potassium substituted compounds were crystallized with rhombohedral symmetry (space group R-3c, No. 167). The ratio of the Mn3+/Mn4+ was determined by the iodometric titration. The Fourier transform infrared spectrum (FTIR) shows two absorption bands for Mn-O stretching vibration (v, mode), Mn-O-Mn deformation vibration (v(b) mode) around 600 cm(-1) and 400 cm(-1) for the compositions, x = 0.0, 0.05 and 0-10. Four-probe electrical resistivity measurements reveal a composition controlled metal to insulator transition (TM-1), the maximum TM-1 was observed for the composition La0.85K0.15MnO3 at 287 K. Room temperature vibrating sample magnetometer data indicate that for the composition up to x = 0-10, the compounds are paramagnetic whereas composition with x = 0.15, 0.20 and 0.25 show magnetic moments of 27, 29 and 30 emu/g, respectively.

Simulation of laminar flow in a three-dimensional lid-driven cavity by lattice Boltzmann method

Purpose - The purpose of this paper is to apply lattice Boltzmann equation method (LBM) with multiple relaxation time (MRT) model, to investigate lid-driven flow in a three-dimensional (3D), rectangular cavity, and compare the results with flow in an equivalent two-dimensional (2D) cavity. Design/methodology/approach - The second-order MRT model is implemented in a 3D LBM code. The flow structure in cavities of different aspect ratios (0.25-4) and Reynolds numbers (0.01-1000) is investigated. The LBM simulation results are compared with those from numerical solution of Navier-Stokes (NS) equations and with available experimental data. Findings - The 3D simulations demonstrate that 2D models may predict the flow structure reasonably well at low Reynolds numbers, but significant differences with experimental data appear at high Reynolds numbers. Such discrepancy between 2D and 3D results are attributed to the effect of boundary layers near the side-walls in transverse direction (in 3D), due to which the vorticity in the core-region is weakened in general. Secondly, owing to the vortex stretching effect present in 3D flow, the vorticity in the transverse plane intensifies whereas that in the lateral plane decays, with increase in Reynolds number. However, on the symmetry-plane, the flow structure variation with respect to cavity aspect ratio is found to be qualitatively consistent with results of 2D simulations. Secondary flow vortices whose axis is in the direction of the lid-motion are observed; these are weak at low. Reynolds numbers, but become quite strong at high Reynolds numbers. Originality/value - The findings will be useful in the study of variety of enclosed fluid flows.

Trifurcated (four-center) hydrogen bond in solid state crystal structure of 5'-amino-5'-deoxyadenosine p-toluenesulfonate

The crystal structure of 5'-amino-5'-deoxyadenosine (5'-Am.dA) p-toluenesulfonate has been determined by X-ray crystallographic methods. It belongs to the orthorhombic space group P2(1)2(1)2(1) with a = 7.754(3)Angstrom, b = 8.065(1)Angstrom and c = 32.481(2)Angstrom. This nucleoside side shows a syn conformation about the glycosyl bond and C2'-endo-C3'-exo puckering for the ribose sugar. The orientation of N5' atom is gauche-trans about the exocyclic C4'-C5' bond. The amino nitrogen N5' forms a trifurcated hydrogen bond with N3, O9T and O4' atoms. Adenine bases form A.A.A triplets through hydrogen bonding between N6, N7 and N1 atoms of symmetry related nucleoside molecules.

Computing magnetic anisotropy constants of single molecule magnets

We present here a theoretical approach to compute the molecular magnetic anisotropy parameters, D (M) and E (M) for single molecule magnets in any given spin eigenstate of exchange spin Hamiltonian. We first describe a hybrid constant M (S) valence bond (VB) technique of solving spin Hamiltonians employing full spatial and spin symmetry adaptation and we illustrate this technique by solving the exchange Hamiltonian of the Cu6Fe8 system. Treating the anisotropy Hamiltonian as perturbation, we compute the D (M)and E(M) values for various eigenstates of the exchange Hamiltonian. Since, the dipolar contribution to the magnetic anisotropy is negligibly small, we calculate the molecular anisotropy from the single-ion anisotropies of the metal centers. We have studied the variation of D (M) and E(M) by rotating the single-ion anisotropies in the case of Mn12Ac and Fe-8 SMMs in ground and few low-lying excited states of the exchange Hamiltonian. In both the systems, we find that the molecular anisotropy changes drastically when the single-ion anisotropies are rotated. While in Mn12Ac SMM D (M) values depend strongly on the spin of the eigenstate, it is almost independent of the spin of the eigenstate in Fe-8 SMM. We also find that the D (M)value is almost insensitive to the orientation of the anisotropy of the core Mn(IV) ions. The dependence of D (M) on the energy gap between the ground and the excited states in both the systems has also been studied by using different sets of exchange constants.

Transcriptional activation of the Escherichia coli bgl operon: negative regulation by DNA structural elements near the promoter

The bgl operon of Escherichia coil is transcriptionally inactive in wild-type cells. DNA insertion sequences (IS) constitute a major class of spontaneous mutations that activate the cryptic bgl promoter. In an attempt to study the molecular mechanism of activation mediated by insertion sequences, transcription of the bgl promoter was carried out in vitro. Stimulation of transcription is observed when a plasmid containing an insertionally activated bgl promoter is used as a template in the absence of proteins other than RNA polymerase. Deletions that remove sequences upstream of the bgl promoter, and insertion of a 1.2 kb DNA fragment encoding resistance to kanamycin, activate the promoter. Point mutations within a region of dyad symmetry upstream of the promoter, which has the potential to extrude into a cruciform structure under torsional stress, also lead to activation, Introduction of a sequence with dyad symmetry, upstream of an activated bgl promoter carrying a deletion of upstream sequences, results in a fourfold reduction in transcription, These results suggest that the cryptic nature of the bgl promoter is because of the presence of DNA structural elements near the promoter that negatively affect transcription.

Microneurovascular free muscle transfer with cross-over nerve grafts in facial reanimation

Microneurovascular free muscle transfer with cross-over nerve grafts in facial reanimation Loss of facial symmetry and mimetic function as seen in facial paralysis has an enormous impact on the psychosocial conditions of the patients. Patients with severe long-term facial paralysis are often reanimated with a two-stage procedure combining cross-facial nerve grafting, and 6 to 8 months later with microneurovascular (MNV) muscle transfer. In this thesis, we recorded the long-term results of MNV surgery in facial paralysis and observed the possible contributing factors to final functional and aesthetic outcome after this procedure. Twenty-seven out of forty patients operated on were interviewed, and the functional outcome was graded. Magnetic resonance imaging (MRI) of MNV muscle flaps was done, and nerve graft samples (n=37) were obtained in second stage of the operation and muscle biopsies (n=18) were taken during secondary operations.. The structure of MNV muscles and nerve grafts was evaluated using histological and immunohistochemical methods ( Ki-67, anti-myosin fast, S-100, NF-200, CD-31, p75NGFR, VEGF, Flt-1, Flk-1). Statistical analysis was performed. In our studies, we found that almost two-thirds of the patients achieved good result in facial reanimation. The longer the follow-up time after muscle transfer the weaker was the muscle function. A majority of the patients (78%) defined their quality of life improved after surgery. In MRI study, the free MNV flaps were significantly smaller than originally. A correlation was found between good functional outcome and normal muscle structure in MRI. In muscle biopsies, the mean muscle fiber diameter was diminished to 40% compared to control values. Proliferative activity of satellite cells was seen in 60% of the samples and it tended to decline with an increase of follow-up time. All samples showed intramuscular innervation. Severe muscle atrophy correlated with prolonged intraoperative ischaemia. The good long-term functional outcome correlated with dominance of fast fibers in muscle grafts. In nerve grafts, the mean number of viable axons amounted to 38% of that in control samples. The grafted nerves characterized by fibrosis and regenerated axons were thinner than in control samples although they were well vascularized. A longer time between cross facial nerve grafting and biopsy sampling correlated with a higher number of viable axons. P75Nerve Growth Factor Receptor (p75NGFR) was expressed in every nerve graft sample. The expression of p75NGFR was lower in older than in younger patients. A high expression of p75NGFR was often seen with better function of the transplanted muscle. In grafted nerve Vascular Endothelial Growth Factor (VEGF) and its receptors were expressed in nervous tissue. In conclusion, most of the patients achieved good result in facial reanimation and were satisfied with the functional outcome. The mimic function was poorer in patients with longer follow-up time. MRI can be used to evaluate the structure of the microneurovascular muscle flaps. Regeneration of the muscle flaps was still going on many years after the transplantation and reinnervation was seen in all muscle samples. Grafted nerves were characterized by fibrosis and fewer, thinner axons compared to control nerves although they were well vascularized. P75NGFR and VEGF were expressed in human nerve grafts with higher intensity than in control nerves which is described for the first time.

Shrinking Violets

Description of the work Shrinking Violets is comprised of two half scale garments in laser cut silk organza, developed with a knotting device to allow for disassembly and reassembly. The first is a jacket in layered red organza including black storm flap details. The second is a vest in jade organza with circles of pink organza attached through a pattern of knots. Research Background This practice-led fashion design research sits within the field of Design for Sustainability (DfS) in fashion that seeks to mitigate the environmental and ethical impacts of fashion consumption and production. The research explores new systems of garment construction for DfS, and examines how these systems may involve ‘designing’ new user interactions with the garments. The garments’ construction system allows them to be disassembled and recycled or reassembled by users to form a new garment. Conventional garment design follows a set process of cutting and construction, with pattern pieces permanently machine-stitched together. Garments typically contain multiple fibre types; for example a jacket may be constructed from a shell of wool/polyester, an acetate lining, fusible interlinings, and plastic buttons. These complex inputs mean that textile recycling is highly labour intensive, first to separate the garment pieces and second to sort the multiple fibre types. This difficulty results in poor quality ‘shoddy’ comprised of many fibre types and unsuitable for new apparel, or in large quantities of recyclable textile waste sent to landfill (Hawley 2011). Design-led approaches that consider the garment’s end of life in the design process are a way of addressing this problem. In Gulich’s (2006) analysis, use of single materials is the most effective way to ensure ease of recycling, with multiple materials that can be detached next in effectiveness. Given the low rate of technological innovation in most apparel manufacturing (Ruiz 2011), a challenge for effective recycling is how to develop new manufacturing methods that allow for garments to be more easily disassembled at end-of-life. Research Contribution This project addresses the research question: How can design for disassembly be considered within the fashion design process? I have employed a practice-led methodology in which my design process leads the research, making use of methods of fashion design practice including garment and construction research, fabric and colour research, textile experimentation, drape, patternmaking, and illustration as well as more recent methods such as laser cutting. Interrogating the traditional approaches to garment construction is necessarily a technical process; however fashion design is as much about the aesthetic and desirability of a garment as it is about the garment’s pragmatics or utility. This requires a balance between the technical demands of designing for disassembly with the aesthetic demands of fashion. This led to the selection of luxurious, semi-transparent fabrics in bold floral colours that could be layered to create multiple visual effects, as well as the experimentation with laser cutting for new forms of finishing and fastening the fabrics together. Shrinking Violets makes two contributions to new knowledge in the area of design for sustainability within fashion. The first is in the technical development of apparel modularity through the system of laser cut holes and knots that also become a patterning device. The second contribution lies in the design of a system for users to engage with the garment through its ability to be easily reconstructed into a new form. Research Significance Shrinking Violets was exhibited at the State Library of Queensland’s Asia Pacific Design Library, 1-5 November 2015, as part of The International Association of Societies of Design Research’s (IASDR) biannual design conference. The work was chosen for display by a panel of experts, based on the criteria of design innovation and contribution to new knowledge in design. References Gulich, B. (2006). Designing textile products that are easy to recycle. In Y. Wang (Ed.), Recycling in Textiles (pp. 25-37). London: Woodhead. Hawley, J. M. (2011). Textile recycling options: exploring what could be. In A. Gwilt & T. Rissanen (Eds.), Shaping Sustainable Fashion: Changing the way we make and use clothes (pp. 143 - 155). London: Earthscan. Ruiz, B. (2014). Global Apparel Manufacturing. Retrieved 10 August 2014, from http://clients1.ibisworld.com/reports/gl/industry/default.aspx?entid=470

Quantum Interference in Coherent Molecular Conductance

Coherent electronic transport through individual molecules is crucially sensitive to quantum interference. We investigate the zero-bias and zero-temperature conductance through pi-conjugated annulene molecules weakly coupled to two leads for different source-drain configurations, finding an important reduction for certain transmission channels and for particular geometries as a consequence of destructive quantum interference between states with definite momenta. When translational symmetry is broken by an external perturbation we find an abrupt increase of the conductance through those channels. Previous studies concentrated on the effect at the Fermi energy, where this effect is very small. By analyzing the effect of symmetry breaking on the main transmission channels we find a much larger response thus leading to the possibility of a larger switching of the conductance through single molecules.

Adducts of bis(acetylacetonato)zinc(II) with 1,10-phenanthroline and 2,2'-bipyridine

In each of the zinc(II) complexes bis(acetylacetonato-kappa(2)O,O')(1,10-phenanthroline-kappa(2)N,N')zinc(II), [Zn(C(5)H(7)O(2))(2)(C(12)H(8)N(2))], (I), and bis(acetylacetonato-kappa(2)O,O')(2,2'-bipyridine-kappa(2)N,N')zinc(II), [Zn(C(5)H(7)O(2))(2)(C(10)H(8)N(2))], (II), the metal center has a distorted octahedral coordination geometry. Compound (I) has crystallographically imposed twofold symmetry, with Z' = 0.5. The presence of a rigid phenanthroline group precludes intramolecular hydrogen bonding, whereas the rather flexible bipyridyl ligand is twisted to form an intramolecular C-H...O interaction [the chelated bipyridyl ligand is nonplanar, with the pyridyl rings inclined at an angle of 13.4 (1) degrees]. The two metal complexes are linked by dissimilar C-H...O interactions into one-dimensional chains. The present study demonstrates the distinct effects of two commonly used ligands, viz. 1,10-phenanthroline and 2,2'-bipyridine, on the structures of metal complexes and their assembly.

Apparent shortening of the Csp(3)-Csp(3) bond analysed via a variable-temperature X-ray diffraction study in racemic 1,1 '-binaphthalene-2,2 '-diyl diethyl bis(carbonate)

Crystal structure determination at room temperature [292 (2) K] of racemic 1,1'-binaphthalene-2,2'-diyl diethyl bis(carbonate), C26H22O6, showed that one of the terminal carbon-carbon bond lengths is very short [Csp(3)-Csp(3) = 1.327 (6) angstrom]. The reason for such a short bond length has been analysed by collecting data sets on the same crystal at 393, 150 and 90 K. The values of the corrected bond lengths clearly suggest that the shortening is mainly due to positional disorder at two sites, with minor perturbations arising as a result of thermal vibrations. The positional disorder has been resolved in the analysis of the 90 K data following the changes in the unit-cell parameters for the data sets at 150 and 90 K, which appear to be an artifact of a near centre of symmetry relationship between the two independent molecules in the space group P (1) over bar at these temperatures. Indeed, the unit cell at low temperature (150 and 90 K) is a supercell of the room-temperature unit cell.