Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy coinciding with the native binding site. The representative structure of the most stable cluster reproduced the experimental binding configuration, but an interesting conformational change in Hsp90 could be observed. The combined effects of solvation and ligand binding shift the equilibrium from a preferred loop-in conformation in the unbound state to an α-helical one in the bound state for the flexible lid region of Hsp90. Thus, our dynamic docking method is effective at predicting the native binding site while exhaustively sampling a wide configurational space, modulating the protein structure upon binding.     

Amperometric Folic Acid Quantification Using a Supramolecular Tetraruthenated Nickel Porphyrin µ‐Peroxo‐Bridged Matrix Modified Electrode Associated to Batch Injection Analysis

A supramolecular Nickel (II) porphyrin complex containing four pyridyl‐bis(2,2′‐bipyridyl)chloro ruthenium meso substituents was submitted to successive voltammetric cycles in high alkaline media to produce a supramolecular matrix with Nickel centers linked by µ‐peroxo bridges, producing a highly stable thin film able to act as redox mediator for electrocatalytic oxidation of folic acid. The characterization of electrode surface material was performed by Scanning Electron Microscopy and Electrochemical Impedance Spectroscopy. The modified electrode was inserted into a batch injection electrochemical cell used for the rapid and precise quantification of folic acid in pharmaceutical products. The favorable hydrodynamic conditions provided by amperometry‐BIA association allowed a very high throughput with good linear range (1 to 200 µmol L^?1) and low detection limit (7.37×10^?7 mol L^?1). The electrochemical method was applied to the quantification of folic acid in different tablet samples. The results were comparable with values indicated by the manufacturer and those found using high HPLC according to the Brazilian Pharmacopoeia; commercial samples were submitted to a procedure in order to remove lactose of tablets, since carbohydrates act as interfering species. This procedure together with the electrochemical method showed to be simple, rapid, efficient and an appropriate alternative for quantifying this compound in real samples.     

Time-harmonic BEM for 2-D piezoelectricity applied to eigenvalue problems

We will derive the fundamental generalized displacement solution, using the Radon transform, and present the direct formulation of the time-harmonic boundary element method (BEM) for the two-dimensional general piezoelectric solids. The fundamental solution consists of the static singular and the dynamics regular parts; the former, evaluated analytically, is the fundamental solution for the static problem and the latter is given by a line integral along the unit circle. The static BEM is a component of the time-harmonic BEM, which is formulated following the physical interpretation of Somigliana’s identity in terms of the fundamental generalized line force and dislocation solutions obtained through the Stroh–Lekhnitskii (SL) formalism. The time-harmonic BEM is obtained by adding the boundary integrals for the dynamic regular part which, from the original double integral representation over the boundary element and the unit circle, are reduced to simple line integrals along the unit circle.The BEM will be applied to the determination of the eigen frequencies of piezoelectric resonators. The eigenvalue problem deals with full non-symmetric complex-valued matrices whose components depend non-linearly on the frequency. A comparative study will be made of non-linear eigenvalue solvers: QZ algorithm and the implicitly restarted Arnoldi method (IRAM). The FEM results whose accuracy is well established serve as the basis of the comparison. It is found that the IRAM is faster and has more control over the solution procedure than the QZ algorithm. The use of the time-harmonic fundamental solution provides a clean boundary only formulation of the BEM and, when applied to the eigenvalue problems with IRAM, provides eigen frequencies accurate enough to be used for industrial applications. It supersedes the dual reciprocity BEM and challenges to replace the FEM designed for the eigenvalue problems for piezoelectricity.     

Synthesis of a “molecular rope curtain”: Preparation and characterization of a sliding graft copolymer with grafted poly(ethylene glycol) side chains by the “grafting onto” strategy

A sliding graft copolymer (SGC) with poly(ethylene glycol) (PEG) side chains was prepared by ester formation between terminal carboxyl groups of oxidized PEG methyl ether with molecular weight of 2000 (mPEG2000‐COOH) and hydroxyl groups of a polyrotaxane consisting of PEG and cyclodextrins (CDs). Formation of the SGC structure was confirmed by ¹H NMR, attenuated total reflectance Fourier‐transformed infrared, and gel permeation chromatography. The SGC was soluble in good solvents of PEG and insoluble in poor solvents of PEG. Estimation of the number of grafted mPEG chains suggested a “rope‐curtain” like structure, in which an mPEG chain is connected to each CD ring. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

Controllable Electronic Structures and Photoinduced Processes of Bay‐Linked Perylenediimide Dimers and a Ferrocene‐Linked Triad

A series of perylene‐3,4,9,10‐bis(dicarboximide) (PDI) dimers linked through the bay regions was systematically synthesized to examine the electronic structures and photophysical properties in dependence on the distance and orientation between the two PDI units. The spectroscopic and electrochemical measurements suggested that the coupling value of a directly linked PDI dimer (PDI)₂ is much larger than those of para‐ and meta‐phenylene‐bridged PDI dimers p‐(PDI)₂ and m‐(PDI)₂. The width of Davydov splitting was quantitatively evaluated to compare the coupling values between the two PDI units in these dimers by absorption spectroscopy in frozen 2‐methyl‐THF. Excimer formation of PDI dimers induced the strong fluorescence quenching and large red‐shifts. Femtosecond transient absorption revealed a broad absorption derived from an excimer in the range from about 600 nm to the near‐IR region. The rate constants of formation and decay of the excimer are strongly dependent on the coupling values. Time‐resolved measurements on ferrocene‐linked p‐(PDI)₂ revealed a competition between the photoinduced processes of electron transfer and excimer formation in PhCN, which is in sharp contrast with the sole electron‐transfer process in toluene.     

Triangular ruthenium acetate clusters containing the bis(pyridyl)propane ligand and their inclusion chemistry with β-cyclodextrin

The triruthenium carboxylate cluster [Ru₃O(OAc)₆(py)₂(bpp)]⁺ (OAc = acetate) containing the bridging 1,3-bis(4-pyridyl)propane (bpp) ligand, and its dimeric species [{Ru₃O(OAc)₆(py₂)}₂(μ-bpp)]²⁺ were synthesized in order to investigate their inclusion compounds with β-cyclodextrin (β-CD). Characterization of the complexes was carried out based on spectroscopic, electrochemical and spectroelectrochemical techniques, while the formation of inclusion complexes was evaluated using ¹H NMR/NOESY spectroscopy. Since bpp is a flexible ligand, a DFT study was carried out in order to characterize its conformational isomers and their possible role in the host–guest chemistry with β-CD. Instead of observing the formation of inclusion compounds with different stoichiometries, we observed the formation of 1:1 bpp/β-CD compounds in which the bpp ligand assumes different conformations. The assembly of polymetallic rotaxane species was successfully demonstrated by monitoring the ¹H NMR spectra of the monomeric cluster species in the presence of aquapentacyanoferrate(II) ions and β-CD.     

Efficient Light-Harvesting Antennae Resulting from the Dense Organization of Dyes into DNA Junctions through d-Threoninol

Herein we report the construction of efficient light-harvesting antennae by hybridization of DNA oligonucleotides containing high densities of fluorophores into DNA junctions through d -threoninol. Six pyrene donors could be incorporated into each arm without self-quenching. A perylene acceptor was located at the center of the junction. Antenna effects of a duplex and three- to eight-way junctions were systematically compared. Six- and eight-way junctions had the highest antenna effects, and their effective absorption coefficients were 8.5 times higher than that of perylene. Interestingly, even-numbered junctions had higher efficiencies than odd-numbered junctions. Nondenaturing gel analyses and fluorescence lifetime measurements demonstrated that the strong odd–even effects were derived from differences in the stability of junctions. The results presented will guide the design of efficient artificial photosynthetic systems.     

Synthetic study of kosinostatin aglycone: synthesis of BCDE rings using alkoxycarbonylmethylation of diazonaphthoquinone

A synthetic study of kosinostatin aglycone is reported. Synthesis of key intermediate lactone 3, which corresponds to the BCDE ring fragment, was accomplished, and the precursor BCD ring fragment 5 was synthesized via two routes. First, 5 was synthesized from 2,5-dimethoxybenzaldehyde 16 by the combination of typical known transformations including efficient application of non-aqueous OsO₄ oxidation in the presence of PhB(OH)₂. However the synthesis required 15 long steps, and its main difficulty was ortho-alkoxycarbonylmethylation of 1-naphthol. Next we attempted to apply our recently developed alkoxycarbonylmethylation of diazonaphthoquinone for the synthesis of 5, and 5 was successfully synthesized in 9 steps from the same starting compound 16. Finally, 5 was stereoselectively converted to lactone 3 via trifluoroacetic acid-mediated cyclization of the 3,4-epoxycylohexanecarboxylic acid derivative.