Diffusion constant of a nonspecifically bound protein undergoing curvilinear motion along DNA

The mechanism of a protein's diffusion along a DNA segment is a subject of much current interest because of the involvement of this diffusion in numerous biological processes, including the recognition of DNA sequences and chemical modifications of DNA. In this work we present a theoretical derivation of the diffusion coefficient of a nonspecifically bound protein, assuming that the protein follows a helical track along the DNA. It is shown that, for protein-sized molecules, the principal contribution to the total translational friction comes from the curvilinear motion along the helix, and this contribution is given by 6pietaRR(oc)(2) + 8pietaR(3), where R is the protein radius, ROC is the distance of separation between the center of mass of the protein and the helical axis of DNA, and eta is the viscosity of the medium. The translational diffusion of the protein along the helical track of DNA is thus predicted to have a nearly R(-3) size dependence, not the R(-1) dependence characterizing simple translational diffusion. It is shown that this expression gives rather good estimates of the translational diffusion coefficient measured in single molecule experiments.     

Boron-Thioketonates: A New Class of S,O-Chelated Boranes as Acceptors in Optoelectronic Devices

Development of new n-type semiconductors with tunable band gap and dielectric constant has significant implication in dissociating bound charge carrier relevant for demonstrating high performance optoelectronic devices. Boron-β-thioketonates (MTDKB), analogues to boron-β-diketonates containing a sulfur atom in the framework of β-diketones were synthesized. Bulk transport measurement exhibited an outstanding bulk electron mobility of ≈0.003 cm² V⁻¹ s⁻¹, which is among the best values reported till date in these class of semiconducting materials and correspondingly a single junction photo responsivity of upto 6 mA W⁻¹ was obtained. This new family of O,S-chelated boron compounds exhibited luminescence in the far red/near-infrared region. The remarkable red shift of 89 nm (fluorescence) observed for 4 a in comparison with analogues boron-β-diketonate signifies the importance of sulfur in these molecules. MTDKBs with amine functionality have also been investigated as an ON/OFF fluorescent sensor.     

Vibrational phase relaxation of O–H stretch in bulk water: Role of large amplitude angular jumps and negative cross-correlations among the forces on the O–H bond

The ultrafast vibrational phase relaxation of O–H stretch in bulk water is investigated in molecular dynamics simulations. The dephasing time (T₂) of the O–H stretch in bulk water calculated from the frequency fluctuation time correlation function (C_ω(t)) is in the range of 70–80 femtosecond (fs), which is comparable to the characteristic timescale obtained from the vibrational echo peak shift measurements using infrared photon echo [W.P. de Boeij, M.S. Pshenichnikov, D.A. Wiersma, Ann. Rev. Phys. Chem. 49 (1998) 99]. The ultrafast decay of C_ω(t) is found to be responsible for the ultrashort T₂ in bulk water. Careful analysis reveals the following two interesting reasons for the ultrafast decay of C_ω(t). (A) The large amplitude angular jumps of water molecules (within 30–40 fs time duration) provide a large scale contribution to the mean square vibrational frequency fluctuation and gives rise to the rapid spectral diffusion on 100 fs time scale. (B) The projected force, due to all the atoms of the solvent molecules on the oxygen (F_O(t)) and hydrogen (F_H(t)) atom of the O–H bond exhibit a large negative cross-correlation (NCC). We further find that this NCC is partly responsible for a weak, non-Arrhenius temperature dependence of the dephasing rate.     

Mono-oxo bis(dithiolene) Mo(IV)/W(IV) complexes as building blocks for sulfide bridged Bi- and Tri-nuclear complexes

A new electron precise, six-electron, sulfide-bicapped trinuclear cluster complex [Et4N]4[Mo(IV)3(mu3-S)2(mnt)6] (1) has been synthesized, where each Mo(IV) atom is seven coordinated. Identical reaction conditions yielded a dimeric complex, [PNP]2[W(V)2(mu2-S)2(mnt)4] (2) from the starting W(IV) analogue due to oxidation by sulfur formed by the auto-oxidation of H2S. Two stepwise reversible reductions and no oxidation of 2 as observed by cyclic voltammetry are correlated with the nonbonding nature of the lowest unoccupied molecular orbital and deeply buried highest occupied molecular orbital by theoretical calculations at the density-functional theory level.     

Comparative study of temperature dependent orientational relaxation in a model thermotropic liquid crystal and in a model supercooled liquid

Recent optical Kerr effect experiments have revealed a power law decay of the measured signal with a temperature independent exponent at short-to-intermediate times for a number of liquid crystals in the isotropic phase near the isotropic-nematic transition and supercooled molecular liquids above the mode coupling theory critical temperature. In this work, the authors investigate the temperature dependence of short-to-intermediate time orientational relaxation in a model thermotropic liquid crystal across the isotropic-nematic transition and in a binary mixture across the supercooled liquid regime in molecular dynamics simulations. The measure of the experimentally observable optical Kerr effect signal is found to follow a power law decay at short-to-intermediate times for both systems in agreement with recent experiments. In addition, the temperature dependence of the power law exponent is found to be rather weak. As the model liquid crystalline system settles into the nematic phase upon cooling, the decay of the single-particle second-rank orientational time correlation function exhibits a pattern that is similar to what has been observed for supercooled liquids.     

Truncated harmonic oscillator and parasupersymmetric quantum mechanics

We discuss in detail the parasupersymmetric quantum mechanics of arbitrary order where the parasupersymmetry is between the normal bosons and those corresponding to the truncated harmonic oscillator. We show that even though the parasusy algebra is different from that of the usual parasusy quantum mechanics, still the consequences of the two are identical. We further show that the parasupersymmetric quantum mechanics of arbitrary orderp can also be rewritten in terms ofp supercharges (i.e. all of which obeyQ _i ² =0). However, the Hamiltonian cannot be expressed in a simple form in terms of thep supercharges except in a special case. A model of conformal parasupersymmetry is also discussed and it is shown that in this case, thep supercharges, thep conformal supercharges along with HamiltonianH, conformal generatorK and dilatation generatorD form a closed algebra.     

A concise synthesis of 2-benzoyl-1-indanones and 1-indanones from 2-aryl-1-tetralones

Abstract

Methyl-2-(3-oxo-3-aryl) benzoates derived from acid catalyzed air oxidative fragmentation of 2-aryl-1-tetralones were efficiently undergone intramolecular-Claisen condensation in the presence of potassium tertiary butoxide. The resulting 2-benzoyl-1-indanones formed in two-step ring contractions were further subjected to indium triflate mediated retro-Claisen condensation to get 1-indanones.     

Water extract of red mud: an efficient and renewable medium for environmentally benign synthesis of 2-amino-4H-chromenes

Molecular Diversity - In this study, an efficient and convenient domino Michael addition/intramolecular cyclization protocol is presented for the synthesis of biologically relevant...