Designing specific inhibitors against dihydrofolate reductase of W. bancrofti towards drug discovery for lymphatic filariasis

Structural Chemistry - Lymphatic filariasis (LF) is one among the leading neglected diseases caused by mosquitoe-borne parasite Wuchereria bancrofti to humans. Though drugs are available for the...     

Collective vibrations in cluster models for semiconductor surfaces: vibrational spectra of acetylenyl and methylacetylenyl functionalized Si(111)

The geometries and harmonic vibrational frequencies of the acetylenyl and methylacetylenyl functionalized Si(111) surfaces are investigated using quantum chemical calculations. The vibrational spectra are computed using a previously introduced method whereby the collective vibrational modes that correspond to the vibrations of the infinite periodic system are derived from modest sized cluster models. Our predictions should be useful for the interpretation of the experimental spectra when they become available. The symmetry elements of the methylacetylenyl Si(111) surface that are derived from the space group of the optimized structure and a vibrational mode resulting from photon-adsorbate coupling are explored.     

Gaussian-4 theory using reduced order perturbation theory

Two modifications of Gaussian-4 (G4) theory [L. A. Curtiss et al., J. Chem. Phys. 126, 084108 (2007)] are presented in which second- and third-order perturbation theories are used in place of fourth-order perturbation theory. These two new methods are referred to as G4(MP2) and G4(MP3), respectively. Both methods have been assessed on the G3/05 test set of accurate experimental data. The average absolute deviation from experiment for the 454 energies in this test set is 1.04 kcalmol for G4(MP2) theory and 1.03 kcalmol for G4(MP3) theory compared to 0.83 kcalmol for G4 theory. G4(MP2) is slightly more accurate for enthalpies of formation than G4(MP3) (0.99 versus 1.04 kcalmol), while G4(MP3) is more accurate for ionization potentials and electron affinities. Overall, the G4(MP2) method provides an accurate and economical method for thermochemical predictions. It has an overall accuracy for the G3/05 test set that is much better than G3(MP2) theory (1.04 versus 1.39 kcalmol) and even better than G3 theory (1.04 versus 1.13 kcalmol). In addition, G4(MP2) does better for challenging hypervalent systems such as H(2)SO(4) and for nonhydrogen species than G3(MP2) theory.     

Two methanes are better than one: a density functional theory study of the reactions of Mo2Oy- (y = 2-5) with methane

The mechanisms of chemical reactions of molybdenum suboxide clusters Mo(2)O(n)- (n = 2-5) with methane are investigated using B3LYP hybrid density functional theory and polarized basis sets. In particular, we focus on the reactions of the most stable structural isomers of Mo(2)O(2,3,4,5)- that lead to single molybdenum species such as HMoO(2)CH(3)-, as seen in the recent experimental study of Jarrold and co-workers. We find that, while all experimentally observed products are unfavorable due to the high amount of energy required to cleave the metal oxide, the formation of HMoO(2)CH(3)- is least endothermic. Even in this case, the thermodynamics of these reactions is very unfavorable when a single methane is reacted with the metal oxide. However, we find that the sequential addition of two methanes produces HMoO(2)CH(3)- (and another neutral molecule whose identity depends on the number of oxygens in the metal oxide) at a much lower thermodynamic cost. Further, the overall reaction barriers are much lower when the second methane adds prior to the Mo(2)O(2,3,4,5)- cleavage. The methane addition at each metal center oxidizes the metals to produce a species that is then stable enough to afford the Mo-Mo cleavage.     

QM:QM electronic embedding using Mulliken atomic charges: energies and analytic gradients in an ONIOM framework

An accurate first-principles treatment of chemical reactions for large systems remains a significant challenge facing electronic structure theory. Hybrid models, such as quantum mechanics:molecular mechanics (QM:MM) and quantum mechanics:quantum mechanics (QM:QM) schemes, provide a promising avenue for such studies. For many chemistries, including important reactions in materials science, molecular mechanics or semiempirical methods may not be appropriate, or parameters may not be available (e.g., surface chemistry of compound semiconductors such as indium phosphide or catalytic chemistry of transition metal oxides). In such cases, QM:QM schemes are of particular interest. In this work, a QM:QM electronic embedding model within the ONIOM (our own N-layer integrated molecular orbital molecular mechanics) extrapolation framework is presented. To define the embedding potential, we choose the real-system low-level Mulliken atomic charges. This results in a set of well-defined and unique embedding charges. However, the parametric dependence of the charges on molecular geometry complicates the energy gradient that is necessary for the efficient exploration of potential energy surfaces. We derive an efficient form for the forces where a single set of self-consistent field response equations is solved. Initial tests of the method and key algorithmic issues are discussed.     

Synthesis and characterization of nitroglycerin‐functionalized polystyrene

The synthesis and characterization of diethyl oxomalonate‐, glycerol‐, and nitroglycerin‐functionalized polystyrene (DPS, GPS, and NGPS) from polystyrene (PS) by the chemical‐modification route were explored. DPS was synthesized by the Friedel–Crafts acylation of PS with diethyl oxomalonate in the presence of SnCl₄ by a batchwise‐addition process. Proton NMR studies indicate that the acylation was essentially quantitative. IR spectroscopy was additionally used to confirm the transformation. The reduction of DPS was carried out using various reduction agents and reaction conditions. The sodium hydride reduction in tetrahydrofuran resulted in a quantitative conversion to GPS as estimated by ¹H NMR spectroscopy. Treatment of GPS with a nitrating mixture of nitric and sulfuric acids results in the formation of NGPS. All the polymers were characterized using gel permeation chromatography, IR, UV, ¹H spectroscopic techniques, pyrolysis‐mass spectrometry, and thermogravimetric analysis. This is the first investigation on the syntheses of DPS, GPS, and NGPS. © 2001 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 39: 1203–1215, 2001     

Ambient temperature Atom Transfer Radical copolymerization of tetrahydrofurfuryl methacrylate and methyl methacrylate: Reactivity ratio determination

Tetrahydrofurfuryl methacrylate (THFMA), a heterocyclic monomer was polymerized by ambient temperature Atom Transfer Radical Polymerization (AT ATRP) using CuX/PMDETA/EBiB system. THFMA was found to undergo very rapid polymerization, in bulk. For a target DP > 200, bulk polymerization results in cross-linking as evidenced by (CH₂)_n,wag peaks (IR spectroscopy). Atom Transfer Radical copolymerization (ATRcP) of THFMA with MMA was performed and the reactivity ratios were calculated from the copolymer composition, as determined by ¹H NMR, using Fineman–Ross and Kelen–Tudos methods. The reactivity ratios determined for ATRP were found to be significantly different from the literature values for conventional free radical polymerization (CFRP). This may be due to the coordination of copper catalytic system with the oxygen atom of the tetrahydrofurfuryl group that could lead to the variation in reactivity ratios. ¹H NMR evidence for catalyst–monomer interaction is also provided.     

Controlled radical polymerization of tert‐butyl acrylate at ambient temperature: Effect of initiator structure and synthesis of amphiphilic block copolymers

Controlled and very rapid ambient temperature polymerization of tert‐butyl acrylate (tBA) via atom transfer radical polymerization (ATRP) and single electron transfer living radical polymerization (SET‐LRP) conditions is reported. Two initiators, one that would generate a secondary radical and another that would generate a primary radical, upon activation, are used. A very active catalyst CuBr/Me₆TREN was found to initiate rapid polymerization whether it was the primary or the secondary initiator. The polymerization was well controlled and very rapid. The initiator that produces secondary initiating site is found to result in more rapid polymerization than the one that produces primary initiating site. To explore the possibility of rapid ambient temperature polymerization through the SET‐LRP mechanism, the polymerization was also carried out in the presence of DMSO. It was found that the polymerization was much faster compared to the bulk ATRP, without loss of control. Styrene was block copolymerized from PtBA macroinitiators and vice versa. In both the cases, block copolymers with controlled molecular weights were obtained. The tBA block of the polymer was selectively hydrolyzed to get amphiphilic block copolymers. This amphiphilic block copolymer was found to be useful in preparing stable cadmium sulfide (CdS) nanoparticulate dispersion. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Synthesis of graft copolymers onto styrenic polymer backbone via “grafting from” raft process

A new synthetic methodology is developed for preparing graft copolymers via RAFT polymerization method by the “R group approach” onto styrenic polymers. In this approach, latent sites of the styrenic polymer was brominated first and then converted into macro‐RAFT agents with pyrazole and thio dodecyl as the Z groups. This was used to synthesize graft copolymer such as polystyrene‐graft‐polymethyl methacrylate (PS‐g‐PMMA), polystyrene‐graft‐poly(isobornyl acrylate), polystyrene‐graft‐poly[2‐(acetoacetoxy)ethyl methacrylate] (PS‐g‐PAEMA), and poly(para‐methoxystyrene)‐graft‐polystyrene (P(p‐MS)‐g‐PS). The polymers are characterized by gel permeation chromatography, ¹H NMR, IR, and atomic force microscopy (AFM). The morphology of PS‐g‐PMMA in THF was investigated using AFM and island‐like features were noticed. The AFM studies of the PS‐g‐PAEMA graft copolymers revealed the formation of globules and ribbon‐like morphological features. The PS‐g‐PAEMA graft copolymers form complex with Fe(III) in dimethylformamide and the AFM studies suggest the formation of globular superstructures. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Performance analysis of an eight channel demultiplexer using a 2D-photonic crystal quasi square ring resonator

Recent years, the design of photonic crystal (PC) based optical devices is receiving keen interest in research and scientific community. In this paper, two dimensional (2D) PC based eight channel demultiplexer is proposed and designed and the functional characteristics of demultiplexer namely resonant wavelength, transmission efficiency, quality factor, spectral width, channel spacing and crosstalk are investigated. The demultiplexer is designed to drop the wavelength centred at 1537.6 nm, 1538.5 nm, 1539.4 nm, 1540.4 nm, 1541.2 nm, 1541.9 nm, 1542.6 nm and 1543.1 nm. The proposed demultiplexer is primarily composed of bus waveguide, drop waveguide and quasi square ring resonator. The quasi square ring resonator and square ring micro cavity (inner rods) are playing a vital role for a desired channel selection. The operating range of the devices is identified through a photonic band gap (PBG) which is obtained using a plane wave expansion (PWE) method. The functional characteristics of the proposed demultiplexer are attained using a 2D finite difference time domain (FDTD) method. The proposed device offers low crosstalk and high transmission efficiency with ultra-compact size, hence, it is highly desirable for DWDM applications.