Hybrid and biohybrid silicate based materials: molecular vs. block-assembling bottom-up processes

This critical review introduces a discussion on the influence of preparative procedures (nanofabrication) of nanostructured hybrids and biohybrids, comparing their structural and textural characteristics that determine the properties of the resulting materials. Selected examples of silicate-based hybrids of analogous compositions prepared by both molecular and blocks-assembly bottom-up strategies are discussed to show advantages and inconveniences of each methodology (341 references).     

Crucial importance of the water-entropy effect in predicting hot spots in protein-protein complexes

"Hot spots" are residues accounting for the majority of the protein-protein binding free energy (BFE) despite that they comprise only a small fraction of the protein-protein interface. A hot spot can be found experimentally by measuring the BFE change upon mutating it to alanine: the mutation gives rise to a significantly large increase in the BFE. Theoretical prediction of hot spots is an enthusiastic subject in biophysics, biochemistry, and bioinformatics. For the development of a reliable prediction method, it is essential to understand the physical origin of hot spots. To this end, we calculate the water-entropy gains upon binding both for a wild-type complex and for its mutant complex using a hybrid method of the angle-dependent integral equation theory applied to a molecular model for water and the morphometric approach. We note that this type of calculation has never been employed in the previously reported methods. The BFE change due to alanine mutation is evaluated only from the change in the water-entropy gain with no parameters fitted to the experimental data. It is shown that the overall performance of predicting hot spots in our method is higher than that in Robetta, a standard free-energy-based method using fitting parameters, when the most widely used criterion for defining an actual hot spot is adopted. This result strongly suggests that the water-entropy effect we calculate is the key factor governing basic physics of hot spots.     

Improvement of in vitro-transcribed amber suppressor tRNAs toward higher suppression efficiency in wheat germ extract

In vitro-transcribed, unmodified, and non-aminoacylated amber suppressor tRNAs that are recognized by natural aminoacyl-tRNA synthetase were improved toward higher suppression efficiency in batch-mode cell-free translation in wheat germ extract. The suppression efficiency of the suppressor obtained through four sequence optimization steps (anticodon alteration of natural tRNAs (the first generation); chimerization of the efficient suppressors in the first generation; investigation and optimization of the effective parts in the second generation; combination of the optimized parts in the third generation) and by the terminal tuning was approximately 60%, which was 2.4-fold higher than that of the best suppressor in the first generation. In addition, an eRF1 aptamer further increased the efficiency up to 85%. This highly efficient suppression system also functioned well in a dialysis-based large-scale protein synthesis.     

Multinuclear Pd/Zn complex-catalyzed asymmetric alkylative ring-opening reaction of oxabicyclic alkenes

A multinuclear palladium catalyst can be used to realize the efficient catalytic asymmetric alkylative ring-opening reaction of oxabicyclic alkenes using dimethylzinc. The use of (R)-BINOL-PHOS bearing bisphosphine and diol moieties is essential for achieving excellent catalytic performance; the corresponding monophosphine and hydroxy-protected derivatives showed lower catalytic activities and/or enantioselectivities. The generation of Pd/Zn-multinuclear complexes is a key feature of the present catalysis.     

Dialkyl bisphosphonate platinum(II) complex as a potential drug for metastatic bone tumor

Bisphosphonates have high affinity for hydroxyapatite (HA), which is abundantly present in bone. Also, platinum complexes are known that have a wide spectrum of antitumor activities. The conjugate of bisphosphonate and a platinum complex might have HA affinity and antitumor activity, and become a drug for metastatic bone tumor. In this study, the authors synthesized platinum complexes that had dialkyl bisphosphonic acid as a ligand, and evaluated the possibility of the synthesized complexes as a drug for metastatic bone tumor. The synthesized dialkyl bisphosphonate platinum(II) complex was characterized, and its stability in an aqueous solution was also confirmed. The synthesized platinum complex showed higher HA affinity than other platinum complexes such as cisplatin and carboplatin in an experiment of adsorption to HA. In vitro, the platinum complex showed tumor growth inhibitory effect stronger than or equal to cisplatin, which is the most commonly used antitumor agent. Moreover, the platinum complex showed a bone absorption inhibitory effect on the osteoclast. These results suggest potential of dialkyl bisphosphonate platinum(II) complexes as a drug for metastatic bone tumor.     

SYNTHESES AND SOME PROPERTIES OF SULFOXIDES,SULFILIMINES, AMINOSULFONIUM SALTS AND SULFOXIMINES CONTAINING PYRIDINE NUCLEI

Abstract

Several 2-pyridyl sulfides (1) (e.g., methyl (1a), ethyl (1b), isopropyl (1c), benzyl (1d), 1-phenylethyl (1e), l-menthyl (If) 2-pyridyl sulfides; and bis(2-pyridylthio)methane (1g), and methyl 2-(N-oxy-pyridyl) sulfide (1h) were prepared by the usual method. Sulfoxides (2) were prepared by oxidation of the corresponding sulfides with m-chloroperbenzoic acid in good yields. A few sulfoxides were found to work as phase-transfer catalysts for some typical nucleophilic reactions in nonpolar solvents such as benzene, and in two-phase systems such as benzene-water. S-2-Pyridyl-N-(p-toluenesulfonyl) sulfilimines (3) were prepared upon treatment of sulfides with Chloramine-T. Hydrolysis of N-(p-toluenesulfonyl)-2-pyridyl-o-tolylsulfilimine (3i) with conc. sulfuric acid gave the corresponding free sulfilimine in a moderate yield. S-2-Pyridyl sulfoximines (4) were not obtained by the general method from the sulfoxides and hydrazoic acid. Alkyl-2-pyridyl sulfoximines, however, were obtained by oxidation of the free sulfilimines derived from the corresponding aminosulfonium salts (5) prepared by reaction of the sulfides with mesitylene-sulfonylhydroxylamine (MSH). These free sulfilimines and sulfoximines thus prepared were found to give adducts with a few copper salts.     

Syntheses of Metallaphosphorane Complexes and Berry Pseudorotation

Iron-, ruthenium-phosphoranes Cp'(CO) 2 M{P(OC 7 H 6 O) 2 }(Cp' = m 5 -C 5 H 5 , m 5 -C 5 Me 5 ; M = Ru, Fe), and cobalt-phosphoranes L(CO) 3 Co-{P(OC 7 H 6 O) 2 }(L = PPh 3 , PPh 2 Me) were prepared. From the variable-temperature 31 P NMR studies, the activation parameters for Berry pseudorotation were determined.     

Synthesis and Properties of Carbocyclic 5′- Nor Oligodeoxynucleotides as Potential Antisense Molecules

We have synthesized carbocyclic 5'-nor oligodeoxynucleotides with a shortened overall chain length lacking the 5'-methylene. Their hybridization properties with DNA and RNA were investigated by UV and CD melting curves. These oligomers formed unstable duplexes with DNA, but formed stable duplexes with RNA selectively. In addition, these oligomers were very stable against nucleases.     

Resolving double disulfide bond patterns in SNAP25B using liquid chromatography–ion trap mass spectrometry

Complex disulfide bond patterns in synaptosomal‐associated protein of 25 kD B (SNAP25B) are thought to regulate neurotransmitter release in response to oxidative stress. However, the steric feasibility of each possible disulfide pattern in SNAP25B has not been assessed. To assess the steric feasibility of hypothesized closely spaced complex disulfide patterning in SNAP25B and also the feasibility of identifying complex disulfide bond patterns with MS, we have developed a novel probabilistic analysis to unambiguously resolve complex double disulfide bond patterns by using an ion trap mass spectrometer. We analyzed fragmentation patterns of singly linked peptides to determine likely fragmentation events in an ion trap mass spectrometer and observed double and single backbone cleavage along with heterolytic cleavage of the disulfide bond. We modeled these same events in the doubly disulfide linked SNAP25B peptide and used a cumulative hypergeometric distribution with top–down scoring to both identify and differentiate these bonding patterns. Because of the presence of unique MS/MS peaks, two of the bonding patterns were directly identified. The third was assigned on the basis of full chromatographic separation and confirmed by modeling triple breakage fragments. In total, this work demonstrates the feasibility – and also limitations – of identification of complex intradisulfide patterns by using ion trap‐based collision‐induced dissociation‐based fragmentation methods. Copyright © 2013 John Wiley & Sons, Ltd.     

Non-markovian dynamics of spectral narrowing for excitons in the layered semiconductor GaSe observed using optical four-wave mixing spectroscopy

We have investigated non-markovian dephasing by using time-resolved and spectrally resolved four-wave mixing measurements in a layered semiconductor GaSe. When the time interval between the first and second excitation pulses is increased, photon echo spectra exhibit narrowing only in a regime of a few picoseconds. In the initial dephasing of these signals, fast damping is observed. The narrowing of the spectrally resolved signal is consistent with the Fourier transformation of the time-resolved signals. Spectral narrowing is crucial evidence of the transition from non-markovian to markovian dynamics. By comparing experimental data with calculation results based on the non-markovian theory, we have found that the correlation time of the exciton-phonon interaction is 1.1 ps.