HELANAL: A program to characterise helix geometry in proteins,

A detailed analysis of structural and position dependent characteristic features of helices will give a better understanding of the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies the geometry of helices in proteins on the basis of their C-alpha atoms alone. The Fortran program HELANAL can extract the helices from the PDB files and then characterises the overall geometry of each helix as being linear, curved or kinked, in terms of its local structural features, viz. local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes. Even helices with large radius of curvature are unambiguously identified as being linear or curved. The program can also be used to differentiate a kinked helix and other motifs, such as helix-loop-helix or a helix-turn-helix (with a single residue linker) with the help of local bending angles. In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures.

Nature of Cl center dot center dot center dot Cl Intermolecular Interactions via Experimental and Theoretical Charge Density Analysis:Correlation of Polar Flattening Effects with Geometry

The experimental charge density distribution in three compounds, 2-chloro-3-quinolinyl methanol, 2-chloro-3-hydroxypyridine, and 2-chloro-3-chloromethyl-8-methylquinoline, has been obtained using high-resolution X-ray diffraction data collected at 100 K based on the aspherical multipole modeling of electron density. These compounds represent type I (cis), type I (trans), and type II geometries, respectively, as defined for short Cl center dot center dot center dot Cl interactions. The experimental results are compared with the theoretical charge densities using theoretical structure factors obtained from a periodic quantum calculation at the B3LYP/6-31G** level. The topological features derived from the Bader's theory of atoms in molecules (AIM) approach unequivocally suggest that both cis and trans type I geometries show decreased repulsion, whereas type II geometry is attractive based on the nature of polar flattening of the electron density around the Cl atom.

Role of Surface Texture, Roughness, and Hardness on Friction During Unidirectional Sliding

In the present investigation, experiments were conducted by unidirectional sliding of pins made of FCC metals (Pb, Al, and Cu) with significantly different hardness values against the steel plates of various surface textures and roughness using an inclined pin-on-plate sliding apparatus in ambient conditions under both the dry and lubricated conditions. For a given material pair, it was observed that transfer layer formation and the coefficient of friction along with its two components, namely adhesion and plowing, are controlled by the surface texture of the harder mating surfaces and are less dependent of surface roughness (R (a)) of the harder mating surfaces. The effect of surface texture on the friction was attributed to the variation of the plowing component of friction for different surfaces. It was also observed that the variation of plowing friction as a function of hardness depends on surface textures. More specifically, the plowing friction varies with hardness of the soft materials for a given type of surface texture and it is independent of hardness of soft materials for other type of surface texture. These variations could be attributed to the extent of plane strain conditions taking place at the asperity level during sliding. It was also observed that among the surface roughness parameters, the mean slope of the profile, Delta (a), correlated best with the friction. Furthermore, dimensionless quantifiable roughness parameters were formulated to describe the degree of plowing taking place at the asperity level.

Formation of a single, rotated-Brass (1 1 0)< 5 5 6 > texture by hot cross-rolling of an Al-Zn-Mg-Cu-Zr alloy

The present work describes the evolution of a strong, single-component rotated-Brass ((1 1 0) < 5 5 6 >) texture in an Al-Zn-Mg-Cu-Zr alloy by an uneven hot cross-rolling with frequent interpass annealing. This texture development is unique because hot rolling of aluminum alloys results in orientation distribution along the ``beta-fibre''. It has been demonstrated that the deformation by cross-rolling of a partially recrystallized grain structure having rotated-Cube and Goss orientations, and the recrystallization resistance of near-Brass-oriented elongated grains play a critical role in development of this texture. (C) 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Texture evolution and operative mechanisms during large-strain deformation of nanocrystalline nickel

The large-strain deformation of nanocrystalline nickel was investigated at room temperature and cryogenic (liquid N-2) temperature. Deformation mechanisms ranging from grain boundary sliding to slip, operate due to a wide distribution of grain sizes. These mechanisms leave their finger print in the deformation texture evolution during rolling of nanocrystalline nickel. The occurrence and severance of different mechanisms is understood by a thorough characterization of the deformed samples using X-ray diffraction, X-ray texture measurements, electron back-scattered diffraction and transmission electron microscopy. Crystal plasticity-based viscoplastic self-consistent simulations were used to further substantiate the experimental observations. Thus, a comprehensive understanding of deformation behavior of nanocrystalline nickel, which is characterized by simultaneous operation of dislocation-dominated and grain boundary-mediated mechanisms, has been developed.

Texture evolution in commercially pure titanium after warm equal channel angular extrusion

Texture development in commercially pure titanium during equal channel angular extrusion (ECAE) through Routes A, Be and C has been studied up to three passes at 400 C. Textures were measured using X-ray diffraction, while the microstructural analyses were performed using electron back-scattered diffraction as well as transmission electron microscopy. Occurrences of dynamic restoration processes (recovery and recrystallization) were clearly noticed at all levels of deformations. Finally, the textures were simulated using a viscoplastic polycrystal self-consistent (VPSC) model. Simulations were performed incorporating basal, prismatic and pyramidal slip systems as well as tensile and compressive twinning. The simulated textures corroborate well with experimental textures in spite of the occurrence of dynamic restoration processes. (C) 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Geometry and quadratic nonlinearity of charge transfer complexes in solution using depolarized hyper-Rayleigh scattering

We report large quadratic nonlinearity in a series of 1:1 molecular complexes between methyl substituted benzene donors and quinone acceptors in solution. The first hyperpolarizability, beta(HRS), which is very small for the individual components, becomes large by intermolecular charge transfer (CT) interaction between the donor and the acceptor in the complex. In addition, we have investigated the geometry of these CT complexes in solution using polarization resolved hyper-Rayleigh scattering (HRS). Using linearly (electric field vector along X direction) and circularly polarized incident light, respectively, we have measured two macroscopic depolarization ratios D = I-2 omega,I-X,I-X/I-2 omega,I-Z,I-X and D' = I-2 omega,I-X,I-C/I-2 omega,I-Z,I-C in the laboratory fixed XYZ frame by detecting the second harmonic scattered light in a polarization resolved fashion. The experimentally obtained first hyperpolarizability, beta(HRS), and the value of macroscopic depolarization ratios, D and D', are then matched with the theoretically deduced values from single and double configuration interaction calculations performed using the Zerner's intermediate neglect of differential overlap self-consistent reaction field technique. In solution, since several geometries are possible, we have carried out calculations by rotating the acceptor moiety around three different axes keeping the donor molecule fixed at an optimized geometry. These rotations give us the theoretical beta(HRS), D and D' values as a function of the geometry of the complex. The calculated beta(HRS), D, and D' values that closely match with the experimental values, give the dominant equilibrium geometry in solution. All the CT complexes between methyl benzenes and chloranil or 1,2-dichloro-4,5-dicyano-p-benzoquinone investigated here are found to have a slipped parallel stacking of the donors and the acceptors. Furthermore, the geometries are staggered and in some pairs, a twist angle as high as 30 degrees is observed. Thus, we have demonstrated in this paper that the polarization resolved HRS technique along with theoretical calculations can unravel the geometry of CT complexes in solution. (C) 2011 American Institute of Physics. doi:10.1063/1.3514922]

Geometry and quadratic nonlinearity of charge transfer complexes in solution: A theoretical study

In this paper, we have computed the quadratic nonlinear optical (NLO) properties of a class of weak charge transfer (CT) complexes. These weak complexes are formed when the methyl substituted benzenes (donors) are added to strong acceptors like chloranil (CHL) or di-chloro-di-cyano benzoquinone (DDQ) in chloroform or in dichloromethane. The formation of such complexes is manifested by the presence of a broad absorption maximum in the visible range of the spectrum where neither the donor nor the acceptor absorbs. The appearance of this visible band is due to CT interactions, which result in strong NLO responses. We have employed the semiempirical intermediate neglect of differential overlap (INDO/S) Hamiltonian to calculate the energy levels of these CT complexes using single and double configuration interaction (SDCI). The solvent effects are taken into account by using the self-consistent reaction field (SCRF) scheme. The geometry of the complex is obtained by exploring different relative molecular geometries by rotating the acceptor with respect to the fixed donor about three different axes. The theoretical geometry that best fits the experimental energy gaps, beta(HRS) and macroscopic depolarization ratios is taken to be the most probable geometry of the complex. Our studies show that the most probable geometry of these complexes in solution is the parallel displaced structure with a significant twist in some cases. (C) 2011 American Institute of Physics. doi:10.1063/1.3526748]

Crystallography of solid-liquid interface and evolution of texture during directional solidification of Tb0.3Dy0.7Fe1.95 alloy

The effect of growth texture on the magnetostriction of ternary Tb0.3Dy0.7Fe1.95 was studied by conducting unidirectional solidification experiments using a zoning set-up. Detailed texture evolutions were studied using X-ray diffraction on samples obtained by varying growth rates from 18 to 72 cm/h, under a temperature gradient of 100 degrees C/cm. The estimated texture co-efficient and pole figures of the samples indicate that during the onset of the solidification, < 110 > and < 331 >/'rotated < 110 >' texture components nucleate and grow in all the samples. However, as the solidification progresses, < 112 > texture component becomes dominant at higher growth rate. This results in an improvement of magnetostriction from 1000 to 1300 microstrains for samples grown at growth rates of 18 and 72 cm/h respectively. The transition of preferred growth direction occurs through intermediate orientations < 123 >. An attempt has been made in this paper to explain the occurrence of different growth texture by considering the stability of growing interface, its planar packing fraction and atomic stacking sequence of several low index planes. (C) 2010 Elsevier Ltd. All rights reserved.

Lattice embedding and equilibrium geometry of metal-halogen chains in the two-band extended Hubbard model

Two-band extended Hubbard model studies show that the shift in optical gap of the metal-halogen (MX) chain upon embedding in a crystalline environment depends upon alternation in the site-diagonal electron-lattice interaction parameter (epsilon(M)) and the strength of electron-electron interactions at the metal site (U(M)). The equilibrium geometry studies on isolated chains show that the MX chains tend to distort for alternating epsilon(M) and small U(M) values.

Geometry of proline-containing alpha-helices in proteins

Crystal structure analysis of proline-containing alpha-helices in proteins has been carried out. High resolution crystal structures were selected from the Protein Data Bank. Apart from the standard internal parameters, some parameters which are specifically related to the bend in the helix due to proline have been developed and analyzed. Finally the position and nature of these helices and their interactions with the rest of the protein have been analyzed.

Influence of initial texture on the microstructural instabilities during compression of commercial ?-Titanium at 25 °C to 400 °C

Cylindrical specimens of textured commercial pure alpha-titanium plate, cut with the cylinder axis along the rolling direction for one set of experiments and in the long transverse direction for the other set, were compressed at strain rates in the range of 0.001 to 100 s-1 and temperatures in the range of 25-degrees-C to 400-degrees-C. At strain rates greater-than-or-equal-to 1 s-1, both sets of specimens exhibited adiabatic shear bands, but the intensity of shear bands was found to be higher in the rolling direction specimens than in the long transverse direction specimens. At strain rates -0.1 s-1, the material deformed in a microstructurally inhomogeneous fashion. For the rolling direction specimens, cracking was observed at 100-degrees-C and at strain rates -0.1 s-1. This is attributed to dynamic strain aging. Such cracking was not observed in the long transverse specimens. The differences in the intensity of adiabatic shear bands and that of dynamic strain aging between the two sets of test specimens are attributed to the strong crystallographic texture present in these plates.

Texture Evolution in Boron Modified Ti-6Al-4V Alloy

Owing to their high strength-to-weight ratio, excellent mechanical properties and corrosion resistance, titanium (Ti) and its alloys, especially (alpha+beta) alloys like Ti-6Al-4V is the backbone materials for aerospace, energy, and chemical industries. Trace boron addition (similar to 0.1 wt. %) to the alloy Ti-6Al-4V produces a reduction in as-cast grain size by roughly an order of magnitude resulting in enhanced ductility, higher stiffness, strength and good fracture resistance. Boron addition could also affect the evolution of texture and microstructure in the material. The solidification microstructures of Boron free as well as Boron containing Ti-6Al-4V are found to be almost homogeneous from periphery towards the center of as-cast ingot in terms of both alpha-colony size and distribution. Boron addition substantially reduces alpha-colony size (similar to 50-80 mu m). A gradual change in alpha texture from periphery towards the center has been observed with orientations close to specific texture components suggesting the formation of texture zones. The mechanism of texture evolution can be visualized as a result of variant selection during solidification through (alpha+beta) phase field.

Evolution of Transformation Texture in a Metastable B - Titanium Alloy

Texture evolution in h. c. p. (alpha) phase derived from aging of a differently processed metastable b.c.c. (beta) titanium alloy was investigated. The study was aimed at examining (i) the effect of different b. c. c. cold rolling textures and (ii) the effect of different defect structures on the h. c. p transformation texture. The alloy metastable beta alloy Ti-10V-4.5Fe-1.5Al was rolled at room temperature by unidirectional (UDR) and multi-step cross rolling (MSCR). A piece of the as-rolled materials were subjected to aging in order to derive the h. c. p. (alpha) phase. In the other route, the as-rolled materials were recrystallized and then aged. Textures were measured using X-ray as well as Electron Back Scatter Diffraction. Rolling texture of beta phase, as characterized by the presence of a strong gamma fibre, was found stronger in M S C R compared to UDR, although they were qualitatively similar. The stronger texture of MSCR sample could be attributed to the inhomogeneous deformation taking place in the sample that might contribute to weakening of texture. Upon recrystallization in beta phase field close to beta-transus. the textures qualitatively resembled the corresponding beta deformation textures; however, they got strengthed. The aging of differently beta rolled samples resulted in the product alpha-phase with different textures. The (UDR + Aged) sample had a stronger texture than (MSCR + Aged) sample, which could be due to continuation of defect accumulation in UDR sample, thus providing more potential sites for the nucleation of alpha phase. The trend was reversed in samples recrystallized prior to aging. The (MSCR + Recrystallized + Aged) sample showed stronger texture of alpha phase than the (UDR + Recrystallized + Aged) sample. This could be attributed to extensive defect annihilation in the UDR sample on recrystallization prior to aging. The (MSCR + Aged) sample exhibited more alpha variants when compared to (MSCR + Recrystallized + Aged) sample. This has been attributed to the availability of more potential sites for nucleation of alpha phase in the former. It could be concluded that alpha transformation texture depends mainly on the defect structure of the parent phase.