Chemistry

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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.

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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

The tris-chelate formed by biguanide, H2NC(NH)NHC(NH)NH 2, and Mn(IV) is one of the rarely encountered examples of water-stable mononuclear complexes of this oxidation state. This cation is reduced in aqueous acid by both V(II) and V(III). In contrast to the kinetically straightforward bimolecular reduction by V(II) in 0.5 M HClO4 (k = 7.4 × 103 M-1 s-1 at 22 °C), reductions by excess V(III) yield profiles which are linear (zero-order in MnIV) until the last few percent reaction. Analyses of these composite curves are consistent with the sequences2VIIIk-1k1(VIII)2(VIII) 2+MnIV→k22VIV+MnIIin which reaction is initiated by slow and reversible conversion of VIII to an activated dimeric species (VIII)2 Treatment of data in terms of this sequence yields a value of k1 1.9 × 10-3 M-1 s-1 and a ratio k2/k -1 2 × 106. This activated route for (VIII)2 appears to be preferred over a remarkably slow electron transfer from monomeric V(III) to the Mn(IV) center, reflecting an unusually high barriet to V(III/IV) self-exchange. © 2010 Elsevier B.V. All rights reserved.

Inorganica Chimica Acta

Electron transfer. Part 169 [1]. Delayed reduction of mononuclear manganeses(IV) using vanadium(III)

We report a facile diversity oriented synthesis of α- and β-amino acids, by utilizing the pluripotent α-methylene group in a chiral bicyclic lactam as our key point of transformation. © 2011 Elsevier Ltd. All rights reserved.

Tetrahedron Letters

Diversity-oriented synthesis of amino acids using chiral enolates

Computational techniques are widely used in the chemoinformatics and bioinformatics. Most of the drugs produce their effect by interacting with the target molecules via different interactions. However, these interactions are tough to be calculated without use of robotics techniques. The potentials of these drugs depend upon their binding affinity. Due to huge number of such drugs, the measurement of their relative potency is a hard task. In present chapter the authors have discussed about some most common techniques which are widely used in bioinformatics and chemoinformatics. © 2012, IGI Global.

Advanced Methods and Applications in Chemoinformatics: Research Progress and New Applications

Computational techniques in binding affinity prediction of drugs

Anthracene monolayers covalently bound to hydrogen-terminated n-type Si(100) surfaces have been prepared from the attachment of an amine-substituted anthracene derivative to a preassembled acid-terminated alkyl monolayer using carbodiimide coupling. The anthracene headgroups were then used as anchoring sites for C60 following [4 + 2] Diels-Alder cycloaddition. After cycloaddition of C60 on the anthracene layer, the surface roughness determined by atomic force microscopy increased from 3.0 ± 0.7 to 5.0 ± 1.0 Å and the morphology showed uniformly distributed globular features a few nanometers high. Cyclic voltammograms of the anthracene-modified monolayer in the dark were characterized by an ill-defined reversible system at E°′ = -2.05 V vs saturated calomel electrode (SCE), which compares well with the value determined for the anthracene derivative in solution on a platinum electrode. Furthermore, the surface coverage of attached anthracene units was estimated to be (4.6 ± 0.3) × 10-10 mol cm-2, which is consistent with a densely packed monolayer. In contrast, the voltammogram of the C60-modified monolayer did not show multiple reversible one-electron transfers characteristic of the anthracene:C60 adduct. Instead, one irreversible cathodic peak at -1.50 V followed by a reversible system at -2.15 V was observed. These electrochemical differences between surface-confined and dissolved species are assigned to reduced charge transfer kinetics between the underlying semiconductor and bound C60 within a certain potential range. This hypothesis is consistent with the flat band potential Efb value of -0.80 ± 0.05 V vs SCE, determined from capacitance measurements. Moreover, scanning electrochemical microscopy (SECM) measurements in feedback mode provided clear evidence for the electroactive properties of bound C 60. The SECM approach curves suggest that both the anthracene and anthracene:C60 layers displayed good conductivity, presumably by electron hopping between adjacent redox sites. © 2011 American Chemical Society.

Journal of Physical Chemistry C

Anthracene and anthracene:C60 adduct-terminated monolayers covalently bound to hydrogen-terminated silicon surfaces

The entry of dengue viruses is mediated by pH triggering in the host cells. Here we have studied the DENV E protein stability and binding of its units at low and normal pH using MD and MM-PB/SA method for the first time. To investigate the role of pH in dissociation of dimeric protein, we have performed a concise study of hydrogen bonding and other interactions between units of dimer at low and normal pH. The Generalized Born calculation connotes that dimeric unit was relatively less stable and less proned for dimerisation at low pH. Our results provide a theoretical verification for previous assumptions of pH triggering mechanism of dengue envelope protein. During the pH alteration, we found a large decrement in salt bridges which were observed at normal pH. We also compared the flexibility of each unit and found that they exhibit different fluctuations during molecular dynamics simulations. © 2011 Elsevier B.V. All Rights Reserved.

Biochimica et Biophysica Acta - Proteins and Proteomics

Role of pH on dimeric interactions for DENV envelope protein: An insight from molecular dynamics study

We report a Quantum mechanics/Molecular Mechanics-Poisson-Boltzmann/ Surface Area (QM/MM-PB/SA) method to calculate the binding free energy of c-Abl human tyrosine kinase by combining the QM and MM principles where the ligand is treated quantum mechanically and the rest of the receptor by classical molecular mechanics. To study the role of entropy and the flexibility of the protein ligand complex in a solvated environment, molecular dynamics calculations are performed using a hybrid QM/MM approach. This work shows that the results of the QM/MM approach are strongly correlated with the binding affinity. The QM/MM interaction energy in our reported study confirms the importance of electronic and polarization contributions, which are often neglected in classical MM-PB/SA calculations. Moreover, a comparison of semi-empirical methods like DFTB-SCC, PM3, MNDO, MNDO-PDDG, and PDDG-PM3 is also performed. The results of the study show that the implementation of a DFTB-SCC semi-empirical Hamiltonian that is derived from DFT gives better results than other methods. We have performed such studies using the AMBER molecular dynamic package for the first time. The calculated binding free energy is also in agreement with the experimentally determined binding affinity for c-Abl tyrosine kinase complex with Imatinib. © 2010 Springer Science+Business Media B.V.

Journal of Biological Physics

Binding free energy calculation with QM/MM hybrid methods for Abl-Kinase inhibitor

Highly luminescent micrometre-sized fine particles of a Zn(ii) metal-organic framework (MOF) of a new $\pi$-electron rich tricarboxylate dispersed in ethanol is demonstrated as a selective sensory material for the detection of nitroaromatic explosives via a fluorescence quenching mechanism. {\textcopyright} The Royal Society of Chemistry 2011.

Chemical Communications

Fluorescent metal-organic framework for selective sensing of nitroaromatic explosives

Four new neutral copper azido polymers, [Cu 4(N 3) 8(L 1)2] n (1), [Cu 4(N 3) 8(L 2)2] n (2), [Cu 4(N 3) 8(L 3)2] n (3) and [Cu9(N3)18(L 4)4]n (4) [L 1-4 are formed in situ by reacting pyridine-2-carboxaldehyde with 2-[2-(methylamino)ethyl]pyridine (mapy, L 1), N,N-dimethylethylenediamine (N,N-dmen, L 2), N,Ndiethylethylenediamine (N,N-deen, L 3) and N,N,2,2- tetramethylpropanediamine (N,N,2,2-tmpn, L 4)], have been synthesized by using 0.5 mol equiv of the chelating tridentate ligands with Cu- (NO 3) 2 33H 2O and an excess of NaN 3. Single-crystal X-ray structures show that the basic unit of these complexes, especially 1-3, contains very similar Cu II4 building blocks. The overall structure of 3 is two-dimensional, while the other three complexes are one-dimensional in nature.Complex 1 represents a unique example containing hemiaminal ether arrested by copper(II). Complexes 1 and 2 have a rare bridging azido pathway: both end-on and end-to-end bridging azides between a pair of Cu II centers. Cryomagnetic susceptibility measurements over a wide range of temperature exhibit dominant ferromagnetic behavior in all four complexes. Density functional theory calculations (B3LYP functional) have been performed on complexes 1-3 to provide a qualitative theoretical interpretation of their overall ferromagnetic behavior. {\textcopyright} 2011 American Chemical Society.

Inorganic Chemistry

Synthesis, structures and magnetic behavior of a series of copper(II) azide polymers of Cu 4 building clusters and isolation of a new hemiaminal ether as the metal complex