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Shiv Nadar University

(SoNS) School of Natural Sciences

High throughput in silico methods have offered the tantalizing potential to drastically accelerate the drug discovery process. Yet despite significant efforts expended by academia, national labs and industry over the years, many of these methods have not lived up to their initial promise of reducing the time and costs associated with the drug discovery enterprise, a process that can typically take over a decade and cost hundreds of millions of dollars from conception to final approval and marketing of a drug. Nevertheless structure-based modeling has become a mainstay of computational biology and medicinal chemistry, helping to leverage our knowledge of the biological target and the chemistry of protein-ligand interactions. While ligand-based methods utilize the chemistry of molecules that are known to bind to the biological target, structure-based drug design methods rely on knowledge of the three-dimensional structure of the target, as obtained through crystallographic, spectroscopic or bioinformatics techniques. Here we review recent developments in the methodology and applications of structure-based and ligand-based methods and target-based chemogenomics in Virtual High Throughput Screening (VHTS), highlighting some case studies of recent applications, as well as current research in further development of these methods. The limitations of these approaches will also be discussed, to give the reader an indication of what might be expected in years to come. © 2011 Bentham Science Publishers.

Chemistry

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Fulltext

Combinatorial Chemistry and High Throughput Screening

Current trends in virtual high throughput screening using ligand-based and structure-based methods

Computational Approaches in Cheminformatics and Bioinformatics

Molecular Descriptors for Biological Systems

The multipolar atom model, constructed by transferring the charge-density parameters from an experimental or theoretical database, is considered to be an easy replacement of the widely used independent atom model. The present study on a new crystal structure of quercetin monohydrate [2-(3,4-dihydroxyphenyl)-3,5, 7-trihydroxy-4H-chromen-4-one monohydrate], a plant flavonoid, determined by X-ray diffraction, demonstrates that the transferred multipolar atom model approach greatly improves several factors: the accuracy of atomic positions and the magnitudes of atomic displacement parameters, the residual electron densities and the crystallographic figures of merit. The charge-density features, topological analysis and electrostatic interaction energies obtained from the multipole models based on experimental database transfer and periodic quantum mechanical calculations are found to compare well. This quantitative and comparative study shows that in the absence of high-resolution diffraction data, the database transfer approach can be applied to the multipolar electron density features very accurately. © 2011 International Union of Crystallography Printed in Singapore - all rights reserved.

Acta Crystallographica Section B: Structural Science

Structural analysis and multipole modelling of quercetin monohydrate - A quantitative and comparative study

An equimolar mixture of Ni(NO3)2.6H3O and pyridine-2-aldehyde with two equivalents of NaN3 in methanol in the presence of NaOMe resulted in the formation of light green precipitate which upon crystallization from dimethylformamide (DMF) yielded light green single crystals [{Ni2Na2(pic)4(N3) 2(H2O)2(MeOH)}.MeOH.3H2O]n (1) and [{Ni2Na2(pic)4(N3) 2(H2O)4}.2DMF.H2O]n (2) (pic = pyridine-2-carboxylate) at room temperature and high temperature (100°C), respectively. Variable temperature magnetic studies revealed the existence of overall ferromagnetic behaviour with J ̃ +10 cm-1 and D ̃ -2 to -7 cm-1 for 1 and 2, respectively. Negative D values as well as variation of D upon slight distortion of structure by varying reaction temperature were observed. The X-band Electron Paramagnetic Resonance (EPR) spectra of both 2 and 3 were recorded below 50 K. The structural distortion was also implicated from the EPR spectra. Density Functional Theory (DFT) calculations on both complexes were performed in two different ways to corroborate the magnetic results. Considering only NiII2 dimeric unit, results were J = +20.65 cm-1 and D = -3.16 cm -1 for 1 and J =+24.56 cm-1 and D =-4.67 cm-1 for 2. However, considering NiII2 NaI2 cubane as magnetic core the results were J =+16.35 cm-1 (1), +19.54 cm-1 (2); D =-3.05 cm-1 (1), -4.25 cm-1 (2). {\textcopyright} Indian Academy of Sciences.

Journal of Chemical Sciences

Two new 1D chains of Ni2Na2 heterometallic double half-cubane building units: Synthesis, structures and variable temperature magnetic study

Synthesis of a series of two-dimensional metallamacrocycles via coordination-driven self-assembly of a shape-selective PtII2-molecular building unit incorporating carbazole-ethynyl functionality is described. An equimolar (1:1) combination of a Pt II2-organometallic 90° acceptor, 1, with rigid linear ditopic donors (La and Lb) afforded [4 + 4] self-assembled octanuclear molecular squares, 2 and 3, in quantitative yields, respectively [La = 4,4′-bipyridine; Lb = trans-1,2-bis(4-pyridyl) ethylene]. Conversely, a similar treatment of 1 with an amide-based unsymmetrical flexible ditopic donor, Lc, resulted in the formation of a [2 + 2] self-sorted molecular rhomboid (4a) as a single product [L c = N-(4-pyridyl)isonicotinamide]. Despite the possibility of several linkage isomeric macrocycles (rhomboid, triangle and square) due to the different connectivity of Lc, the formation of a single and symmetrical molecular rhomboid (4a) as the only product is an interesting observation. All the self-assembled macrocycles (2, 3 and 4a) were fully characterized by multinuclear NMR (1H and 31P) and ESI-MS analysis. Further structural insights about the size and shape of the macrocycles were obtained through energy minimization using density functional theory (DFT) calculations. Decoration of the starting carbazole building unit with Pt-ethynyl functionality enriches the assemblies to be more $\pi$-electron rich and luminescent in nature. Macrocycles 2 and 3 could sense the presence of electron deficient nitroaromatics in solution by quenching of the initial intensity upon gradual addition of picric acid (PA). They exhibited the largest quenching response with high selectivity for nitroaromatics compared to several other electron deficient aromatics tested. {\textcopyright} 2011 The Royal Society of Chemistry.

Dalton Transactions

Coordination-driven self-assembly of 2D-metallamacrocycles using a shape-selective PtII2-organometallic 90° acceptor: Design, synthesis and sensing study

Fluorescence dynamics of a polar solute probe in molten (CH 3CONH2 + Ca(NO3)2·4.37H 2O) mixtures have been measured in order to probe the solute-medium interactions in such complex systems. Steady state and time-resolved measurements bear no signatures of mega-value of the static dielectric constant, strong heterogeneity and extremely slow relaxation times reported in dielectric relaxation experiments for these molten mixtures. Subsequent applications of a semi-molecular theory reveal both the solute-medium dipole-dipole and ion-dipole interactions contribute significantly to the measured Stokes' shifts. Calculated average solvation times in the underdamped and overdamped limits of frictional solvent response agree semi-quantitatively with those from time-resolved measurements. © 2010 Elsevier B.V. All rights reserved.

Chemical Physics Letters

Fluorescence dynamics in supercooled (acetamide + calcium nitrate) molten mixtures

InAs with an extremely high electron mobility (up to 40000 cm2/V s) seems to be the most suitable candidate for better electronic devices performance. Here we present a synthesis of inverted crystalline InAs nanopyramids (NPs) in silicon using a combined hot ion implantation and millisecond flash lamp annealing techniques. Conventional selective etching was used to form the InAs/Si heterojunction. The current-voltage measurement confirms the heterojunction diode formation with the ideality factor of η = 4.6. Kelvin probe force microscopy measurements indicate a type-II band alignment of n-type InAs NPs on p-type silicon. The main advantage of our method is its integration with large-scale silicon technology, which also allows applying it for Si-based electronic devices. © 2011 American Chemical Society.

Physics

Nano Letters

N-InAs nanopyramids fully integrated into silicon

Using scanning transmission electron microscopy and aberration-corrected high-resolution transmission electron microscopy the existence of Er around Ge nanocrystals (NCs) is established. In fact, Ge NCs with Er-rich graded interfaces are proposed experimentally and validated by theoretical modeling using a supercell structure that consists of compounds determined by x-ray diffraction. The local electronic structure of the proposed interface geometry is found to be in accordance with the hypothesis behind the inverse energy transfer process from the Er3+ to Ge related oxygen-deficiency centers. © 2011 American Physical Society.

Physical Review B - Condensed Matter and Materials Physics

Microstructure analysis at the interface of Er decorated Ge nanocrystals in SiO2

Electrochemical impedance spectroscopy measurements of pulsed laser deposited single crystal anatase TiO2 thin films with various concentrations of Ta substituting for Ti were carried out. The qualities of the films were characterized by X-ray diffraction and Rutherford back scattering-channeling measurements. UV-visible measurements show a systematic increase of the bandgap with Ta incorporation. Corresponding Mott-Schottky plot was applied to obtain a continuous shift of the flat band potential with increasing free charge carrier (provided by Ta) concentration. This was verified theoretically by ab initio calculation which shows that extra Ta d-electrons occupy Ti t2g orbital with increasing Ta concentration, thereby pushing up the Fermi level. The Mott-Schottky results were consistent when compared with Hall effect and temperature dependent resistivity measurements. From the measured deviation of carrier densities from Hall and Mott-Schottky measurements we have estimated the static dielectric constant of the TiO 2 as a function of Ta incorporation, not possible from capacitive measurements. © 2011 Author(s).

AIP Advances

Scaling of flat band potential and dielectric constant as a function of Ta concentration in Ta-TiO2 epitaxial films

The use of graphene electronics in space will depend on the radiation hardness of graphene. The damage threshold of graphene samples, subjected to 2 MeV H+ irradiation, was found to increase with layer number and also when the graphene layer was supported by a substrate. The thermal properties of graphene as a function of the number of layers or as influenced by the substrate argue against a thermal model for the production of damage by the ion beam. We propose a model of intense electronically-stimulated surface desorption of the atoms as the most likely process for this damage mechanism. © 2010 Elsevier Ltd. All rights reserved.