Nickel-catalyzed enantio- and diastereoselective three-component coupling of 1,3-dienes, aldehydes, and silanes using chiral N-heterocyclic carbenes as ligands

Nickel(0)-catalyzed asymmetric three-component coupling of 1,3-dienes, aldehydes, and silanes has been realized utilizing a chiral N-heterocyclic carbene as a ligand. On the basis of the screening of various NHC precursors, an imidazolium salt having 1-(2,4,6-trimethylphenyl)propyl groups on the nitrogen was designed and synthesized. In this reaction, various coupling products were produced in good yields with high regio-, diastereo- (anti selective in the case of the internal 1,3-diene), and enantioselectivities (up to 97% ee).     

β-Galactosidase fluorescence probe with improved cellular accumulation based on a spirocyclized rhodol scaffold

We identified a rhodol bearing a hydroxymethyl group (HMDER) as a suitable scaffold for designing fluorescence probes for various hydrolases. HMDER shows strong fluorescence at physiological pH, but phenolic O-alkylation of HMDER results in a strong preference for the spirocyclic form, which has weak fluorescence. As a proof of concept, we utilized this finding to develop a new fluorescence probe for β-galactosidase. This probe has favorable characteristics for imaging in biological samples: it has good cellular permeability, and its hydrolysis product is well-retained intracellularly. It could rapidly and clearly visualize β-galactosidase activity in cultured cells and in Drosophila melanogaster tissue, which has rarely been achieved with previously reported fluorescence probes.     

Distribution of the cationic state over the chlorophyll pair of the photosystem II reaction center

The reaction center chlorophylls a (Chla) of photosystem II (PSII) are composed of six Chla molecules including the special pair Chla P(D1)/P(D2) harbored by the D1/D2 heterodimer. They serve as the ultimate electron abstractors for water oxidation in the oxygen-evolving Mn(4)CaO(5) cluster. Using the PSII crystal structure analyzed at 1.9 ? resolution, the redox potentials of P(D1)/P(D2) for one-electron oxidation (E(m)) were calculated by considering all PSII subunits and the protonation pattern of all titratable residues. The E(m)(Chla) values were calculated to be 1015-1132 mV for P(D1) and 1141-1201 mV for P(D2), depending on the protonation state of the Mn(4)CaO(5) cluster. The results showed that E(m)(P(D1)) was lower than E(m)(P(D2)), favoring localization of the charge of the cationic state more on P(D1). The P(D1)(?+)/P(D2)(?+) charge ratio determined by the large-scale QM/MM calculations with the explicit PSII protein environment yielded a P(D1)(?+)/P(D2)(?+) ratio of ~80/~20, which was found to be due to the asymmetry in electrostatic characters of several conserved D1/D2 residue pairs that cause the E(m)(P(D1))/E(m)(P(D2)) difference, e.g., D1-Asn181/D2-Arg180, D1-Asn298/D2-Arg294, D1-Asp61/D2-His61, D1-Glu189/D2-Phe188, and D1-Asp170/D2-Phe169. The larger P(D1)(?+) population than P(D2)(?+) appears to be an inevitable fate of the intact PSII that possesses water oxidation activity.     

Ruthenium‐catalyzed cyclizations of enynes via a ruthenacyclopentene intermediate: Development of three novel cyclizations controlled by a substituent on alkyne of enyne

Three novel ruthenium‐catalyzed cyclizations of enynes were developed. In each cyclization, a ruthenacyclopentene derived from enyne and Cp*RuCl(cod) is a common intermediate. When an enyne having an alkyl, an ester, or a formyl group on an alkyne was reacted with Cp*RuCl(cod) under ethylene gas, ethylene was inserted into the ruthenium‐sp² carbon bond of ruthenacyclopentene to afford ruthenacycloheptene, and β‐hydrogen elimination followed by reductive elimination occurred to give a cyclic compound having a 1,3‐diene moiety. When an acyl group was placed on the alkyne, the carbonyl oxygen coordinated to the ruthenium metal of ruthenacyclopentene to produce a ruthenium carbene complex, which reacted with ethylene to give a cyclic compound having a cyclopropane ring on the substituent. On the other hand, when the substituent on the alkyne was pent‐4‐enyl, insertion of an alkene part into ruthenacyclopentene followed by reductive elimination gave a tricyclic compound by a ruthenium‐catalyzed [2 + 2 + 2] cyclization of diene and an alkyne. DOI 10.1002/tcr.201100003     

Protein assemblies by site-specific avidin-biotin interactions

Exploiting self-assembly systems with biological building blocks is of significant interest in the fabrication of advanced biomaterials. We assessed the potential use of site-specific ligand labeling of protein building blocks in designing functional protein self-assemblies by combining site-specifically biotinylated bacterial alkaline phosphatase (as a bidentate or tetradentate ligand unit) and streptavidin (as a tetrameric receptor).     

Regio- and stereoselective synthesis of 2-amino-1,3-diene derivatives by ruthenium-catalyzed coupling of ynamides and ethylene

A ruthenium-catalyzed hydrovinylation-type cross-coupling of ynamides and ethylene proceeds via ruthenacyclopentene to give 2-aminobuta-1,3-diene derivatives in a highly regioselective manner. It was also demonstrated that 2-aminobuta-1,3-diene derivatives reacted with various dienophiles or singlet oxygen to give a cyclic enamide derivative.     

Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water

Trivial trajectory parallelization of multicanonical molecular dynamics (TTP-McMD) explores the conformational space of a biological system with multiple short runs of McMD starting from various initial structures. This method simply connects (i.e., trivially parallelizes) the short trajectories and generates a long trajectory. First, we theoretically prove that the simple trajectory connection satisfies a detailed balance automatically. Thus, the resultant long trajectory is regarded as a single multicanonical trajectory. Second, we applied TTP-McMD to an alanine decapeptide with an all-atom model in explicit water to compute a free-energy landscape. The theory imposes two requirements on the multiple trajectories. We have demonstrated that TTP-McMD naturally satisfies the requirements. The TTP-McMD produces the free-energy landscape considerably faster than a single-run McMD does. We quantitatively showed that the accuracy of the computed landscape increases with increasing the number of multiple runs. Generally, the free-energy landscape of a large biological system is unknown a priori. The current method is suitable for conformational sampling of such a large system to reduce the waiting time to obtain a canonical ensemble statistically reliable.     

Structure of the catalytic, inorganic core of oxygen-evolving photosystem II at 1.9 Å resolution

The catalytic center for photosynthetic water-splitting consists of 4 Mn atoms and 1 Ca atom and is located near the lumenal surface of photosystem II. So far the structure of the Mn(4)Ca-cluster has been studied by a variety of techniques including X-ray spectroscopy and diffraction, and various structural models have been proposed. However, its exact structure is still unknown due to the limited resolution of crystal structures of PSII achieved so far, as well as possible radiation damages that might have occurred. Very recently, we have succeeded in solving the structure of photosystem II at 1.9 ?, which yielded a detailed picture of the Mn(4)CaO(5)-cluster for the first time. In the high resolution structure, the Mn(4)CaO(5)-cluster is arranged in a distorted chair form, with a cubane-like structure formed by 3 Mn and 1 Ca, 4 oxygen atoms as the distorted base of the chair, and 1 Mn and 1 oxygen atom outside of the cubane as the back of the chair. In addition, four water molecules were associated with the cluster, among which, two are associated with the terminal Mn atom and two are associated with the Ca atom. Some of these water molecules may therefore serve as the substrates for water-splitting. The high resolution structure of the catalytic center provided a solid basis for elucidation of the mechanism of photosynthetic water splitting. We review here the structural features of the Mn(4)CaO(5)-cluster analyzed at 1.9 ? resolution, and compare them with the structures reported previously.     

Synthetic protocol for diarylethenes through Suzuki-Miyaura coupling

The synthesis of a variety of diarylethenes through the Suzuki-Miyaura coupling reaction of 1,2-dichlorohexafluorocyclopentene with arylboronic acids and esters has been developed. Thiophenes with various substituents such as cyano and ester functionalities can be incorporated.