Chemistry

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Facile synthesis of ultrasmall gold nanoclusters of size <2 nm dispersible in water using a novel quaternary ammonium ligand is reported. Further, arrays of these nanoclusters are encapsulated in monodisperse silica nanospheres of size 25-30 nm. The photophysical characteristics of the clusters are found to be intact upon encapsulation, rendering the resulting composite material ideal for fluorescence imaging applications. We have further shown the utilization of these materials in catalysis as precursors for Au nanoparticles encapsulated in porous silica. © 2011 American Chemical Society.

World University root node

(SoNS) School of Natural Sciences

Journal of Physical Chemistry C

Ultrasmall gold cluster arrays encapsulated in silica nanospheres: Applications in fluorescence imaging and catalysis

The kinetics of the irreversible photoinduced switch in polarisation (p) observed in single crystals of a fullerene derivative possessing hydrogen-bonding barbiturate units were investigated using confocal fluorescence microscopy. In the samples investigated, it was found that the maximum luminescence polarisation (p = 0.78) is obtained for an orientation of ca. 60°from the long axis of the crystal. Upon irradiation at 385 nm, the maximum luminescence polarisation undergoes a rotation of ca. 70°with respect to the initial orientation and reaches a new value of p = 0.40. The results indicate that the process is not dependent on the orientation of the incident polarised excitation beam and that it is not accompanied by a noticeable change in the photophysical properties of the crystal. Based on these observations, a mechanism is proposed in which photoinduced dimerisation occurs from the lowest energy emissive excimer-like state that acts as a sink for the excitation energy. © 2012 the Owner Societies.

Fulltext

Physical Chemistry Chemical Physics

Effect of hydrogen-bonding on the excited-state reactivity of fullerene derivatives and its impact on the control of the emission polarisation from photopolic single crystals

A Matter of Density: Exploring the Electron Density Concept in the Chemical, Biological, and Materials Sciences

Does God Play Dice?

The Electron Density

Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, which are the fundamental in protecting the cell from recombination and degradation. Telomeric DNA sequences can form four stranded quadruplex structures, which are involved in the structure of telomere ends. The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadrulex as an attractive target for cancer therapeutic intervention. Molecular dynamic simulation offers the prospects of detailed description of the dynamical structure with ion and water at molecular level. In this work we have taken a oligomeric part of human telomeric DNA, d(TAGGGT) to form different monomeric quadruplex structures d(TAGGGT) 4. Here we report the relative stabilities of these structures under K+ ion conditions and binding interaction between the strands, as determined by molecular dynamic simulations followed by energy calculation. We have taken locked nucleic acid (LNA) in this study. The free energy molecular mechanics Poission Boltzman surface area calculations are performed for the determination of most stable complex structure between all modified structures. We calculated binding free energy for the combination of different strands as the ligand and receptor for all structures. The energetic study shows that, a mixed hybrid type quadruplex conformation in which two parallel strands are bind with other two antiparallel strands, are more stable than other conformations. The possible mechanism for the inhibition of the cancerous growth has been discussed. Such studies may be helpful for the rational drug designing. © Springer Science+Business Media B.V. 2012.

Journal of Computer-Aided Molecular Design

Stability and free energy calculation of LNA modified quadruplex: A molecular dynamics study

Abl kinase plays a decisive role in the mechanism of the most fatal human pathogen chronic mylogenous leukemia (CML). Here, we have carried out a comprehensive study about the conformational flexibility, role of salt bridge and the protein- ligand interaction for this kinase with its well-known inhibitor, Imatinib. We have performed molecular dynamics simulations for conformational behavior, investigated the salt bridges and calculated the binding free energy of Imatinib with MM-PB/SA method for Abl kinase complex. We also explored the role of salt-bridge in the kinase complex and its effect on binding activity of inhibitors. Furthermore, to investigate the importance of those residues which form salt bridges, we mutated them by Alanine with the help of Alanine scanning program. We noticed significant variations in total free energy of Imatinib in all possible mutations. The binding free energy of ligand for kinase receptor was analyzed by molecular mechanics Poission Boltzmann surface area (MM-PB/SA) method. These results suggest that conserved glutamic acid and lysine are necessary for stability of complex. © Springer-Verlag 2011.

Journal of Molecular Modeling

Conformational flexibility, binding energy, role of salt bridge and alanine-mutagenesis for c-Abl kinase complex

The vast amounts of chemical and biological data available through robotic high-throughput assays and micro-array technologies require computational techniques for visualization, analysis, and predictive-modeling. Predictive cheminformatics and bioinformatics employ statistical methods to mine this data for hidden correlations and to retrieve molecules or genes with desirable biological activity from large databases, for the purpose of drug development. While many statistical methods are commonly employed and widely accessible, their proper use involves due consideration to data representation and preprocessing, model validation and domain of applicability estimation, similarity assessment, the nature of the structure-activity landscape, and model interpretation. This chapter seeks to review these considerations in light of the current state of the art in statistical modeling and to summarize the best practices in predictive cheminformatics. © 2012 Springer Science+Business Media New York.

Methods in Molecular Biology

Predictive cheminformatics in drug discovery: Statistical modeling for analysis of micro-array and gene expression data

Imidazole, a subunit of histidine, plays a crucial role in proton-relay processes that are important for various biological activities, such as metal efflux, viral replication and photosynthesis. We show here how an imidazolyl ring incorporated into a rotary switch based on a hydrazone enables a switching cascade that involves proton relay between two different switches. The switching process starts with a single input, zinc(II), that initiates an E/Z isomerization in the hydrazone system through a coordination-coupled proton transfer. The resulting imidazolium ring is unusually acidic and, through proton relay, activates the E/Z isomerization of a non-coordinating pyridine-containing hydrazone switch. We hypothesize that the reduction in the acid dissociation constant of the imidazolium ring results from a combination of electrostatic and conformational effects, the study of which might help elucidate the proton-coupled electron-transfer mechanism in photosynthetic bacteria. © 2012 Macmillan Publishers Limited. All rights reserved.

Nature Chemistry

A switching cascade of hydrazone-based rotary switches through coordination-coupled proton relays

Chemical and biological network analysis has recently garnered intense interest from the perspective of drug design and discovery. While graph theoretic concepts have a long history in chemistry - predating quantum mechanics - and graphical measures of chemical structures date back to the 1970s, it is only recently with the advent of public repositories of information and availability of high-throughput assays and computational resources that network analysis of large-scale chemical networks, such as protein-protein interaction networks, has become possible. Drug design and discovery are undergoing a paradigm shift, from the notion of 'one target, one drug' to a much more nuanced view that relies on multiple sources of information: genomic, proteomic, metabolomic and so on. This holistic view of drug design is an incredibly daunting undertaking still very much in its infancy. Here, we focus on current developments in graph- and network-centric approaches in chemical and biological informatics, with particular reference to applications in the fields of SAR modeling and drug design. Key insights from the past suggest a path forward via visualization and fusion of multiple sources of chemical network data. © 2012 Future Science Ltd.

Future Medicinal Chemistry

Graphs and networks in chemical and biological informatics: Past, present and future

In the presence of tert-butyl iodide, alkyl azides are converted into the corresponding iodides at room temperature, whereas, N-t-Bu anilines are obtained from aryl azides under the same experimental conditions. A mechanism is proposed to explain this unusual reactivity. {\textcopyright} 2012 Elsevier Ltd. All rights reserved.