Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

We have developed a two‐dimensional replica‐exchange method for the prediction of protein–ligand binding structures. The first dimension is the umbrella sampling along the reaction coordinate, which is the distance between a protein binding pocket and a ligand. The second dimension is the solute tempering, in which the interaction between a ligand and a protein and water is weakened. The second dimension is introduced to make a ligand follow the umbrella potential more easily and enhance the binding events, which should improve the sampling efficiency. As test cases, we applied our method to two protein‐ligand complex systems (MDM2 and HSP 90‐alpha). Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank much faster with the improved sampling efficiency than the replica‐exchange umbrella sampling method that we have previously developed. © 2013 Wiley Periodicals, Inc.     

Vinyl Polymerization by Metal Complexes. XXXIII. Polymerization of Acrylonitrile Initiated by Triazole-Copper(II) Complex in Dimethylsulfoxide Solution

Polymerization of acrylonitrile initiated by triazole-copper(II) complexes was studied in dimethylsulfoxide solution. It was found that the polymerization proceeds by a free radical mechanism; however, the complexes can hardly homopolymerize methyl methacrylate and styrene. Ability of the complexes to initiate polymerization seems to depend on the substituents of triazole, the sort of solvents, and the counterions of copper(n) salts. From the data of visible spectroscopy and the spin trapping, the initiation mechanism was discussed in terms of reduction of copper(II) followed by forming active species.     

Functional Monomers and Polymers. 145. Synthetic Application Based on the Tautomerism of Polymer-Bound Purine and Pyrimidine Bases

Polymer-bound alkylthiopurine and -pyrimidine bases were prepared and used as the polymeric reagents for the reactions of nitrile, olefin, and enone formation. The corresponding low molecular weight compounds were also prepared for comparison. Differences in the reactivity of these reagents were related to the change in tautomerism of the purine and pyrimidine moieties.     

The Synthesis of L-aminosugar and the studies of L-pyranoses on the ring III of pyranmycins

The synthesis of a novel class of aminoglycoside, pyranmycin, and a convenient method for the preparation of 6-amino-L-idopyranosides were reported. One of the members in the reported pyranmycin families, TC010, has prominent activity against Escherichia coli, Staphylococcus aureus, and Bacillus megaterium. We also discovered that the (4)C(1) chair conformation on ring III of pyranmycin is essential for the antibacterial activity. [reaction: see text]     

Chemo-enzymatic synthesis of 2′,3′-dideoxy-3′-fluoro-β-d-guanosine via 2,3-dideoxy-3-fluoro-α-d-ribose 1-phosphate

2,3-Dideoxy-3-fluoro-α-d-ribose 1-phosphate 2 was stereoselectively synthesized and converted to 2′,3′-dideoxy-3-fluoro-β-d-guanosine 1 by enzymatic reaction using purine nucleoside phosphorylase. This chemo-enzymatic strategy was first applied to the synthesis of 1.     

Total synthesis of (±)-erythravine based on ring closing dienyne metathesis

The first total synthesis of (±)-erythravine was achieved in thirteen steps from 3,4-dimethoxyphenethylamine using ring closing dienyne metathesis as the key step.     

Photoelectrochemical decomposition of water on nanocrystalline BiVO4 film electrodes under visible light

The nanocrystalline BiVO4 film electrode on conducting glass showed an excellent efficiency (IPCE = 29% at 420 nm) for the decomposition of water under visible light.     

Divergent and Chemoselective Transformations of Thioamides with Designed Carbene Equivalents

The reactions of thioamides with ortho-nitro-substituted iodonium ylides proceeded under mild conditions to give enaminones or thiazoles, depending on the iodonium ylide used. This protocol allowed the use of protic solvents, including aqueous solutions, and therefore coupling reactions with complex molecules such as peptides or steroids were possible. A mild and efficient method for the synthesis of various iodonium ylides was established. DFT calculations suggested that the halogen bonding between a thioamide and iodonium ylide was important in this chemoselective coupling reaction. The potential use of enaminones conjugated with pharmaceuticals as prodrugs was also demonstrated.     

A Hydroperoxide-Mediated Decarboxylation of α-Ketoacids Enables the Chemoselective Acylation of Amines

Strategies for the formation of amide bonds, that is, one of the most basic and important transformations in organic synthesis, have so far focused predominantly on dehydration reactions. Herein, we report and demonstrate the practical utility of a novel decarboxylative amidation of α-ketoacids by using inexpensive tert-butyl hydroperoxide (TBHP), which is characterized by high yields, a broad substrate scope, mild reaction conditions, and a unique chemoselectivity. These features enable the synthesis of peptides from amino acid derived α-ketoacids under preservation of the stereochemical information.