Raman spectroscopy explores molecular structural signatures of hidden materials in depth: Universal Multiple Angle Raman Spectroscopy

Non-invasive 3D imaging in materials and medical research involves methodologies such as X-ray imaging, MRI, fluorescence and optical coherence tomography, NIR absorption imaging, etc., providing global morphological/density/absorption changes of the hidden components. However, molecular information of such buried materials has been elusive. In this article we demonstrate observation of molecular structural information of materials hidden/buried in depth using Raman scattering. Typically, Raman spectroscopic observations are made at fixed collection angles, such as, 906, 1356, and 1806, except in spatially offset Raman scattering (SORS) (only back scattering based collection of photons) and transmission techniques. Such specific collection angles restrict the observations of Raman signals either from or near the surface of the materials. Universal Multiple Angle Raman Spectroscopy (UMARS) presented here employs the principle of (a) penetration depth of photons and then diffuse propagation through non-absorbing media by multiple scattering and (b) detection of signals from all the observable angles.

Syntheses and structural investigation of some alkali metal ion-mediated (LVO2-)-O-V (L2- = tridentate ONO ligands) species: DNA binding, photoinduced DNA cleavage and cytotoxic activities

Eight alkali metal ion-mediated dioxidovanadium(V), {(VO2L1-6)-O-V} A(H2O)n]proportional to, complexes for A = Li+, Na+, K+ and Cs+, containing tridentate aroylhydrazonate ligands coordinating via ONO donor atoms, are described. All the synthesised ligands and the metal complexes were successfully characterised by elemental analysis, IR, UV-Vis and NMR spectroscopy. X-ray crystallographic investigation of 3, 5-7 shows the presence of distorted NO4 coordination geometries for LVO2- in each case, and varying mu-oxido and/ or mu-aqua bridging with interesting variations correlated with the size of the alkali metal ions: with small Li+, no bridging-O is found but four ion aggregates are found with Na+, chains for K+ and finally, layers for Cs+. Two (5) or three-dimensional (3, 6 and 7) architectures are consolidated by hydrogen bonding. The dioxidovanadium(V) complexes were found to exhibit DNA binding activity due to their interaction with CT-DNA by the groove binding mode, with binding constants ranging from 10(3) to 10(4) M-1. Complexes 1-8 were also tested for DNA nuclease activity against pUC19 plasmid DNA which showed that 6 and 7 had the best DNA binding and photonuclease activity; these results support their good protein binding and cleavage activity with binding constants ranging from 104 to 105 M-1. Finally, the in vitro antiproliferative activity of all complexes was assayed against the HeLa cell line. Some of the complexes (2, 5, 6 and 7) show considerable activity compared to commonly used chemotherapeutic drugs. The variation in cytotoxicity of the complexes is influenced by the various functional groups attached to the aroylhydrazone derivative.

THE LEGACY OF GN RAMACHANDRAN AND THE DEVELOPMENT OF STRUCTURAL BIOLOGY IN INDIA

G.N. Ramachandran is among the founding fathers of structural molecular biology. He made pioneering contributions in computational biology, modelling and what we now call bioinformatics. The triple helical coiled coil structure of collagen proposed by him forms the basis of much of collagen research at the molecular level. The Ramachandran map remains the simplest descriptor and tool for validation of protein structures. He has left his imprint on almost all aspects of biomolecular conformation. His contributions in the area of theoretical crystallography have been outstanding. His legacy has provided inspiration for the further development of structural biology in India. After a pause, computational biology and bioinformatics are in a resurgent phase. One of the two schools established by Ramachandran pioneered the development of macromolecular crystallography, which has now grown into an important component of modern biological research in India. Macromolecular NMR studies in the country are presently gathering momentum. Structural biology in India is now poised to again approach heights of the kind that Ramachandran conquered more than a generation ago.

Influence of sputter power on structural and electrical properties of TiO2 films for Al/TiO2/Si gate capacitors

Titanium dioxide (TiO2) thin films were deposited onto p-Si substrates held at room temperature by reactive Direct Current (DC) magnetron sputtering at various sputter powers in the range 80-200W. The as-deposited TiO2 films were annealed at a temperature of 1023K. The post-annealed films were characterized for crystallographic structure, chemical binding configuration, surface morphology and optical absorption. The electrical and dielectric properties of Al/TiO2/p-Si structure were determined from the capacitance-voltage and current-voltage characteristics. X-ray diffraction studies confirmed that the as-deposited films were amorphous in nature. After post-annealing at 1023K, the films formed at lower powers exhibited anatase phase, where as those deposited at sputter powers >160W showed the mixed anatase and rutile phases of TiO2. The surface morphology of the films varied significantly with the increase of sputter power. The electrical and dielectric properties on the air-annealed Al/TiO2/p-Si structures were studied. The effect of sputter power on the electrical and dielectric characteristics of the structure of Al/TiO2/p-Si (metal-insulator-semiconductor) was systematically investigated. Copyright (c) 2014 John Wiley & Sons, Ltd.

Role of DNA sequence based structural features of promoters in transcription initiation and gene expression

D Regulatory information for transcription initiation is present in a stretch of genomic DNA, called the promoter region that is located upstream of the transcription start site (TSS) of the gene. The promoter region interacts with different transcription factors and RNA polymerase to initiate transcription and contains short stretches of transcription factor binding sites (TFBSs), as well as structurally unique elements. Recent experimental and computational analyses of promoter sequences show that they often have non-B-DNA structural motifs, as well as some conserved structural properties, such as stability, bendability, nucleosome positioning preference and curvature, across a class of organisms. Here, we briefly describe these structural features, the differences observed in various organisms and their possible role in regulation of gene expression.

Local structural distortions and their role in superconductivity in SmFeAsO1-xFx superconductors

EXAFS studies at the As K edge as a function of temperature were carried out in SmFeAsO1-xFx (x = 0 and 0.2) compounds to understand the role of local structural distortions in superconductivity observed in F-doped compounds. A significant correlation between the thermal variation of local structural parameters such as anion height and superconducting onset is found in the fluorinated compounds. Such a variation in anion height is absent in the non-superconducting compound. An increase in the Fe-As bond distance just below the superconducting onset temperature indicates a similarity between the distortions observed in the high-T-C cuprates and these Fe-based superconductors.

Automatic finite element formulation and assembly of hyperelastic higher order structural models

The formulation of higher order structural models and their discretization using the finite element method is difficult owing to their complexity, especially in the presence of non-linearities. In this work a new algorithm for automating the formulation and assembly of hyperelastic higher-order structural finite elements is developed. A hierarchic series of kinematic models is proposed for modeling structures with special geometries and the algorithm is formulated to automate the study of this class of higher order structural models. The algorithm developed in this work sidesteps the need for an explicit derivation of the governing equations for the individual kinematic modes. Using a novel procedure involving a nodal degree-of-freedom based automatic assembly algorithm, automatic differentiation and higher dimensional quadrature, the relevant finite element matrices are directly computed from the variational statement of elasticity and the higher order kinematic model. Another significant feature of the proposed algorithm is that natural boundary conditions are implicitly handled for arbitrary higher order kinematic models. The validity algorithm is illustrated with examples involving linear elasticity and hyperelasticity. (C) 2013 Elsevier Inc. All rights reserved.

Comparison of structural and luminescence properties of Dy2O3 nanopowders synthesized by co-precipitation and green combustion routes

Dysprosium oxide (Dy2O3) nanopowders were prepared by co-precipitation (CP) and eco-friendly green combustion (GC) routes. SEM micrographs prepared by CP route show smooth rods with various lengths and diameters while, GC route show porous, agglomerated particles. The results were further confirmed by TEM. Thermoluminescence (TL) responses of the nanopowder prepared by both the routes were studied using gamma-rays. A well resolved glow peak at 353 degrees C along with less intense peak at 183 degrees C was observed in GC route while, in CP a single glow peak at 364 degrees C was observed. The kinetic parameters were estimated using Chen's glow peak route. Photoluminescence (PL) of Dy2O3 shows peaks at 481, 577,666 and 756 nm which were attributed to Dy3+ transitions of F-4(9/2)-H-6(15/2), H-6(11/2), H-6(11/2) and H-6(9/2), respectively. Color co-ordinate values were located in the white region as a result the product may be useful for the fabrication of WLED'S. (C) 2014 Elsevier Ltd. All rights reserved.

Structural refinement, optical and electrical properties of Ba1-x Sm-2x/3](Zr0.05Ti0.95)O-3 ceramics

Samarium doped barium zirconate titanate ceramics with general formula Ba1-x Sm-2x/3](Zr0.05Ti0.95)O-3 x = 0, 0.01, 0.02, and 0.03] were prepared by high energy ball milling method. X-ray diffraction patterns and micro-Raman spectroscopy confirmed that these ceramics have a single phase with a tetragonal structure. Rietveld refinement data were employed to model BaO12], SmO12], ZrO6], and TiO6] clusters in the lattice. Scanning electron microscopy shows a reduction in average grain size with the increase of Sm3+ ions into lattice. Temperature-dependent dielectric studies indicate a ferroelectric phase transition and the transition temperature decreases with an increase in Sm3+ ion content. The nature of the transition was investigated by the Curie-Weiss law and it is observed that the diffusivity increases with Sm3+ ion content. The ferroelectric hysteresis loop illustrates that the remnant polarization and coercive field increase with an increase in Sm3+ ions content. Optical properties of the ceramics were studied using ultraviolet-visible diffuse reflectance spectroscopy.

Eco-friendly green synthesis, structural and photoluminescent studies of CeO2:Eu3+ nanophosphors using E. tirucalli plant latex

The investigation involves preparation and photoluminescence properties of CeO2:Eu3+ (1-11 mol%) nano phosphors by eco-friendly green combustion route using Euphorbia tirucalli plant latex as fuel. The final product was characterized by powder X-ray diffraction (PXRD), Scanning electron microcopy (SEM) and Transmission electron microscopy (TEM). The PXRD and SEM results reveals cubic fluorite phase with flaky structure. The crystallite size obtained from TEM was found to be similar to 20-25 nm, which was comparable to W-H plots and Scherrer's method. Photoluminescence (PL) emission of all the Eu3+ doped samples shows characteristic bands arising from the transitions of D-5(0) -> F-5(J) (J = 0, 1, 2, 3, 4) manifolds under excitation at 373 and 467 nm excitation. The D-5(0) -> F-7(2) (613 nm) transition often dominate the emission spectra, indicating that the Eu3+ cations occupy a site without inversion center. The highest PL intensity was recorded for 9 mol% Eu3+ ions with 5 ml latex. PL quenching was observed upon further increase in Eu3+ concentration. The international commission on illumination (CIE) chromaticity co-ordinates were calculated from emission spectra, the values (x, y) were very close to national television system committee (NTSC) standard values of pure red emission. The results demonstrate that the synthesized phosphor material could be very useful for display applications. Further, the phosphor material prepared by this method was found to be non toxic, environmental friendly and could be a potential alternative to economical routes. (C) 2014 Elsevier B.V. All rights reserved.

Self-assembly of Chloro-Bridged Arene-Ruthenium Based Rectangle: Synthesis, Structural Characterization and Sensing Study

Self-assembly of a chloro-bridged half-sandwich p-cymene ruthenium(II) complex Ru-2(mu-Cl-2)(eta(6)-p-cymene)(2)Cl-2] 1 with linear ditopic donor L; trans-1,2-bis(4-pyridyl) ethylene] in presence of 2 eq. AgNO3 in CH3CN yielded a chloro-bridged molecular rectangle 2. The rectangle 2 was isolated as nitrate salt in high yield (90 %) and characterized by infra-red, H-1 NMR spectroscopy including ESI-MS analyses. Molecular structure of 2 was determined by single crystal X-ray diffraction study The diffraction analysis shows that 2 adopts a tetranuclear rectangular geometry with the dimensions of 5.51 angstrom x 13.29 angstrom and forming an infinite supramolecular chain with large internal porosity arising through multiple pi-pi and CH-pi interactions between the adjacent rectangles. Furthermore, rectangle 2 is used as selective receptor for phenolic-nitroaromatic compounds such as picric acid, dinitrophenol and nitrophenol.

Comprehending the Formation of Eutectics and Cocrystals in Terms of Design and Their Structural Interrelationships

The phenomenon of cocrystallization, which encompasses the art of making multicomponent organic solids such as cocrystals, solid solutions, eutectics, etc. for novel applications, has been less studied in terms of reliably and specifically obtaining a desired cocrystallization product and the issues that govern their formation. Further, the design, structural, and functional aspects of organic eutectics have been relatively unexplored as compared to solid solutions and cocrystals well-established by crystal engineering principles. Recently, eutectics were proposed to be designable materials on par with cocrystals, and herein we have devised a systematic approach, based on the same crystal engineering principles, to specifically and desirably make both eutectics and cocrystals for a given system. The propensity for strong homomolecular synthons over weak heteromolecular synthons and vice versa during supramolecular growth was successfully utilized to selectively obtain eutectics and cocrystals, respectively, in two model systems and in two drug systems. A molecular level understanding of the formation of eutectics and cocrystals and their structural interrelationships which is significant from both fundamental and application viewpoints is discussed. On the other hand, the obscurity in establishing a low melting combination as a eutectic or a cocrystal is resolved through phase diagrams.

Re-analysis of cryoEM data on HCV IRES bound to 40S subunit of human ribosome integrated with recent structural information suggests new contact regions between ribosomal proteins and HCV RNA

In this study, we combine available high resolution structural information on eukaryotic ribosomes with low resolution cryo-EM data on the Hepatitis C Viral RNA (IRES) human ribosome complex. Aided further by the prediction of RNA-protein interactions and restrained docking studies, we gain insights on their interaction at the residue level. We identified the components involved at the major and minor contact regions, and propose that there are energetically favorable local interactions between 40S ribosomal proteins and IRES domains. Domain II of the IRES interacts with ribosomal proteins S5 and S25 while the pseudoknot and the downstream domain IV region bind to ribosomal proteins S26, S28 and S5. We also provide support using UV cross-linking studies to validate our proposition of interaction between the S5 and IRES domains II and IV. We found that domain IIIe makes contact with the ribosomal protein S3a (S1e). Our model also suggests that the ribosomal protein S27 interacts with domain IIIc while S7 has a weak contact with a single base RNA bulge between junction IIIabc and IIId. The interacting residues are highly conserved among mammalian homologs while IRES RNA bases involved in contact do not show strict conservation. IRES RNA binding sites for S25 and S3a show the best conservation among related viral IRESs. The new contacts identified between ribosomal proteins and RNA are consistent with previous independent studies on RNA-binding properties of ribosomal proteins reported in literature, though information at the residue level is not available in previous studies.

Local Structural and Environmental Factors Define the Efficiency of an RNA Pseudoknot Involved in Programmed Ribosomal Frameshift Process

In programmed -1 ribosomal frameshift, an RNA pseudoknot stalls the ribosome at specific sequence and restarts translation in a new reading frame. A precise understanding of structural characteristics of these pseudoknots and their PRF inducing ability has not been clear to date. To investigate this phenomenon, we have studied various structural aspects of a -1 PRF inducing RNA pseudoknot from BWYV using extensive molecular dynamics simulations. A set of functional and poorly functional forms, for which previous mutational data were available, were chosen for analysis. These structures differ from each other by either single base substitutions or base-pair replacements from the native structure. We have rationalized how certain mutations in RNA pseudoknot affect its function; e.g., a specific base substitution in loop 2 stabilizes the junction geometry by forming multiple noncanonical hydrogen bonds, leading to a highly rigid structure that could effectively resist ribosome-induced unfolding, thereby increasing efficiency. While, a CG to AU pair substitution in stem 1 leads to loss of noncanonical hydrogen bonds between stems and loop, resulting in a less stable structure and reduced PRF inducing ability, inversion of a pair in stem 2 alters specific base-pair geometry that might be required in ribosomal recognition of nucleobase groups, negatively affecting pseudoknot functioning. These observations illustrate that the ability of an RNA pseudoknot to induce -1 PRF with an optimal rate depends on several independent factors that contribute to either the local conformational variability or geometry

Depalladation of Neutral Monoalkyne- and Dialkyne-Inserted Palladacycles and Alkyne Insertion/Depalladation Reactions of Cationic Palladacycles Derived from N,N `,N `'-Triarylguanidines as Facile Routes for Guanidine-Containing Heterocycles/Carbocycles: Synthetic, Structural, and Mechanistic Aspects

Depalladation of the monoalkyne-inserted cyclopalldated guanidines (kappa 2(C,N)Pd(2,6-Me2C5H3N)Br] (I and II) in PhCl under reflux conditions and that of the dialkyne-inserted cyclopalladated guanidine kappa(2)(C,N):eta(2)(C=C)PdBr] (III) in pyridine under reflux conditions afforded a guanidine-containing indole (1), imidaziondole (2), and benzazepine (3) in 80%, 67%, and 76%, yields, respectively. trans-L2PdBr2] species (L = 2,6-Me2C5H3N, C5H5N) were also isolated in the aforementioned reactions in 35%, 42%, and 40% yields. Further , the reaction of the cyclopalladated guanidine kappa(2)(C,N)Pd(mu-Br)](2) (IV) with AgBF4 in a CH2Cl2/MeCN mixture afforded the cationic pincer type cyclopalladated guanidine kappa(3)(C,N,O)Pd(MeCN)]BF4] (4) in 85% yield and this palladacycle upon crystallization in MeCN and the reaction of kappa(2)(C,N)Pd(mu-Br)](2) (V) with AgBf(4) in a CH2Cl2/MeCN mixture afforded the cationic palladacycles {kappa(2)(C,N)Pd(MeCN)(2)]BF4](5 and 6) in 89% and 91% yields, respectively. The separate reactions of 4 with 2 equiv of methyl phenylpropiolate (MPP) or diphenylacetylene (DPA) and the reaction of 5 with 2 equiv of MPP in PhCl at 110 degrees C afforded the guanidine-containing quinazolinium tetrafluoroborate 7 in 25-32% yields. The reaction of 6 with 2 equiv of DPA under otherwise identical conditions afforded the unsymmetrically substituted guanidinium tetrafluoroborate 8, containing a highly substituted naphthalene unit, in 82% yield. Compounds 1-8 were characterized by analytical and spectroscopic techniques, and all compounds except 4 were characterized by single-crystal X-ray diffraction. The Molecular structure of 2 and 3 are nove, as the framework in the former arises due to the formation of two C-N bonds upon depalladation while the butadienyl unit in the latter revealed cis,cis stereochemistry, a-feature unprecedented in alkyne insertion chemistry. Plausible pathways for the formation of heterocycles/carbocycles are proposed. the influence of substitutents on the aryl rings fo the cyclopalladated guanidine moiety and those on alkynes upon the nature of the products in addressed. Heterocycles 1 and 7 revealed the presence of two rotamers in about a 1.00:0.43 ratio in CDCl3 and in about a 1.00:0.14 ratio in CD3OD, respectively, as detected by H-1 NMR spectroscopy while in CD3CN and DMSO-d(6) (1) and CD3CN and CDCl3 (7), these heterocycles revealed the presence of a single rotamer. These spectral features are attributed to the restricted C-N single-bond rotation of the CN3 unit of the guanidine moiety, which possibly arises from steric constraint due to the formation of a N-H center dot center dot center dot Cl hydrogen bond with CDCl3 (1) and N-H center dot center dot center dot O and O-D center dot center dot center dot O hydrogen bonds with CD3OD (7).