Hydration Structure Around the Carboxyl Group Studied by Neutron Diffraction with 12C/13C and H/D Isotopic Substitution Methods

Time-of-Flight (TOF) neutron diffraction measurements have been carried out on aqueous 8 mol% sodium acetate solutions in D₂O. Scattering cross sections that were observed for sample solutions involving ¹²C/¹³C and H/D isotopically substituted acetate ions were used to derive the first-order difference functions, Δ_H(Q) and Δ_C(Q), and corresponding distribution functions, G _H(r;r) and G _C(r;r), which describe the environmental structure around the methyl and the carboxyl groups within the acetate ion, respectively. Structural parameters concerning the first hydration shell of the carboxyl group within the acetate ion were obtained through the least squares fit to the observed intermolecular difference function, Δ_C ^inter(Q). The nearest neighbor C _O...D _W1 (C_O: carboxyl carbon atom, D_W1: water deuterium atom) distance, r(C _O...D _W1 ), and the angle, ∠ C _O ...D _W1 -O _W (O _W : water oxygen atom), were determined to be 2.63(1) Å and 120(1)°, respectively. The coordination number, n(C _O ...D _W1 ), was obtained to be 4.0(1). These results are consistent with the hydration structure in which water molecules in the first hydration shell of the carboxyl group are hydrogen-bonded with oxygen atoms of the carboxyl group.     

New features in the catalytic cycle of cytochrome P450 during the formation of compound I from compound 0

Density functional theory (DFT) is applied to the dark section of the catalytic cycle of the enzyme cytochrome P450, namely, the formation of the active species, Compound I (Cpd I), from the ferric-hydroperoxide species (Cpd 0) by a protonation-assisted mechanism. The chosen 96-atom model includes the key functionalities deduced from experiment: Asp(251), Thr(252), Glu(366), and the water channels that relay the protons. The DFT model calculations show that (a) Cpd I is not formed spontaneously from Cpd 0 by direct protonation, nor is the process very exothermic. The process is virtually thermoneutral and involves a significant barrier such that formation of Cpd I is not facile on this route. (b) Along the protonation pathway, there exists an intermediate, a protonated Cpd 0, which is a potent oxidant since it is a ferric complex of water oxide. Preliminary quantum mechanical/molecular mechanical calculations confirm that Cpd 0 and Cpd I are of similar energy for the chosen model and that protonated Cpd 0 may exist as an unstable intermediate. The paper also addresses the essential role of Thr(252) as a hydrogen-bond acceptor (in accord with mutation studies of the OH group to OMe).     

Mechanisms of ATPases--a multi-disciplinary approach

ATPases are important molecular machines that convert the chemical energies stored in ATP to mechanical actions within the cell. ATPases are among the most abundant proteins with diverse functions involved in almost every cellular pathway. The well characterised ATPases include the various motor proteins responsible for cargo transfers, cell motilities, and muscle contractions; the protein degradation machinery - the proteasome; the ATP synthase, F-ATPase; and the chaperone systems. Other ATPases include DNA helicases and DNA replication complex; proteins responsible for protein/complex disassembly; and certain gene regulators. It is beyond the scope of this review to cover the complete range of ATPases. Instead, we will focus on a few representative ATPases, chosen based on their diverse mechanisms and properties. Furthermore, this review is by no means trying to cover comprehensively the literature for each ATPase nor the historical aspects in each field. We will focus on describing the various techniques being employed to derive the mechanisms and properties of the chosen ATPases. Among them, high and low resolution structural studies combined with biochemical assays seem to be the dominant technical advances adapted to reveal mechanisms for most of the ATPases except the bacterial sigma54 activators, whose mechanism of action is mostly derived from large amount of biochemical studies. A number of them, especially the F-ATPase and motor proteins, have been studied successfully by various single molecule and imaging techniques. We will therefore discuss them in greater details in order to describe the wide range techniques being utilised.     

Palladium-catalyzed oxidation of alcohols via their allyl carbonates under neutral conditions

Treatment of alkyl allyl carbonates derived from various alcohols with a palladium catalyst in MeCN affords ketones and aldehydes in high yields. This new method of oxidation of alcohols can be applied to various alcohols except simple primary alcohols.     

Solid sampling technique for direct detection of condensed tannins in bark by matrix-assisted laser desorption/ionization mass spectrometry

A novel method for the direct analysis of condensed tannin components in bark was developed on the basis of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) combined with a simple solid sampling technique. The MALDI mass spectra obtained from the wood (bark) powder sample clearly showed a series of peaks corresponding to the sodium ion adducts of condensed tannin oligomers up to around m/z 3000. The results indicate that the condensed tannins in the bark sample used in this work mostly consist of combinations of flavan-3-ol units such as profisetinidin (PF), prorobinetinidin (PR) and prodelphinidin (PD), at least up to 10-mers (m/z approximately 3000).     

Cobalt-catalyzed cross-coupling reactions of alkyl halides with allylic and benzylic Grignard reagents and their application to tandem radical cyclization/cross-coupling reactions

Details of cobalt-catalyzed cross-coupling reactions of alkyl halides with allylic Grignard reagents are disclosed. A combination of cobalt(II) chloride and 1,2-bis(diphenylphosphino)ethane (DPPE) or 1,3-bis(diphenylphosphino)propane (DPPP) is suitable as a precatalyst and allows secondary and tertiary alkyl halides--as well as primary ones--to be employed as coupling partners for allyl Grignard reagents. The reaction offers a facile synthesis of quaternary carbon centers, which has practically never been possible with palladium, nickel, and copper catalysts. Benzyl, methallyl, and crotyl Grignard reagents can all couple with alkyl halides. The benzylation definitely requires DPPE or DPPP as a ligand. The reaction mechanism should include the generation of an alkyl radical from the parent alkyl halide. The mechanism can be interpreted in terms of a tandem radical cyclization/cross-coupling reaction. In addition, serendipitous tandem radical cyclization/cyclopropanation/carbonyl allylation of 5-alkoxy-6-halo-4-oxa-1-hexene derivatives is also described. The intermediacy of a carbon-centered radical results in the loss of the original stereochemistry of the parent alkyl halides, creating the potential for asymmetric cross-coupling of racemic alkyl halides.     

Homogeneous palladium catalyst suppressing Pd black formation in air oxidation of alcohols

In homogeneous catalyst systems, there is the persistent problem that metal aggregation and precipitation cause catalyst decomposition and considerable loss of catalytic activity. Pd black formation is a typical example. Pd catalysts are known to easily aggregate and form Pd black, although they realize a wide variety of useful reactions in organic synthesis. In order to overcome this intrinsic problem of homogeneous Pd catalysis, we explored a new class of Pd catalyst by adopting aerobic oxidation of alcohols as a probe reaction. Herein we report a new catalyst system that suppresses the Pd black formation even under air and with a high substrate to catalyst molar ratio (S/C: more than 1000) in oxidation of alcohols. The novel pyridine derivatives having a 2,3,4,5-tetraphenylphenyl substituent and its higher dendritic unit at the 3-position of the pyridine ring were found to be excellent ligands with Pd(OAc)2 in the palladium-catalyzed air (balloon) oxidation of alcohols in toluene at 80 degrees C. Comparison with structurally related pyridine ligands revealed that introduction of the 2,3,4,5-tetraphenylphenyl substituent at the 3-position of pyridine ring effectively suppresses the Pd black formation, maintaining the catalytic activity for a long time to give aldehydes or ketones as products in high yields.     

CpRuIIPF6/quinaldic acid-catalyzed chemoselective allyl ether cleavage. A simple and practical method for hydroxyl deprotection

A cationic CpRu(II) complex in combination with quinaldic acid shows high reactivity and chemoselectivity for the catalytic deprotection of hydroxyl groups protected as allyl ethers. The catalyst operates in alcoholic solvents without the need for any additional nucleophiles, satisfying the practical requirements of operational simplicity, safety, and environmental friendliness. The wide applicability of this deprotection strategy to a variety of multifunctional molecules, including peptides and nucleosides, may provide new opportunities in protective group chemistry. [structure: see text]