Luminescence of tris(2,2'-bipyridine)ruthenium(II) cations ([Ru(bpy)(3)]2+) adsorbed in mesoporous silicas modified with sulfonated phenethyl group

The adsorption of tris(2,2'-bipyridine)ruthenium(II) ([Ru(bpy)(3)]2+) complex cation into modified mesoporous silicas was investigated. In order to immobilize [Ru(bpy)(3)]2+, the mesopore surface was modified with sulfonic acid groups by the reactions between MCM-41 and phenethyl(dichloro)methylsilane and the subsequent sulfonation of the attached phenethyl groups with chlorosulfonic acid. The modified mesoporous silicas effectively adsorbed [Ru(bpy)(3)]2+ from ethanol solution. It was thought that the effective adsorption was the cause of the cooperative effects of the electrostatic interactions between [Ru(bpy)(3)]2+ cation and sulfonic acid group and the interactions between the phenyl rings on the mesopore surface and the bipyridine rings of the complex. The variation of the position and the intensity of the luminescence of [Ru(bpy)(3)]2+ suggested that the average distance between the adjacent [Ru(bpy)(3)]2+ changed with the loading amounts.     

New pi-conjugated system with a rigid framework of 1,8-anthrylene-ethynylene cyclic dimer and its monoanthraquinone analogue

Two types of pi-conjugated compounds were synthesized by Sonogashira coupling, and their structures and properties were investigated by X-ray analysis and spectroscopic measurements. The monoanthraquinone compound features an out-of-plane deformation of the inner carbonyl moiety and dimer formation in crystals and solution.     

Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme

We have developed a parallelized integral-direct code of the perturbative doubles correction for configuration interaction with singles, proposed as CIS(D) by Head-Gordon et al. (Chem Phys Lett 219:21, 1994). The CIS(D) method provides the energy corrections both of the relaxation and differential correlation for the respective CIS excited states. The implementation of CIS(D) is based on our original algorithm for the second-order Møller–Plesset perturbation (MP2) calculations (Mochizuki et al. in Theor Chem Acc 112:442, 2004). There is no need to communicate bulky intermediate data among worker processes of the parallelized execution. This CIS(D) code is then incorporated into a developer version of ABINIT-MP program, in order to improve the overestimation in excitation energies calculated by the CIS method in conjunction with the multilayer fragment molecular orbital scheme (MLFMO-CIS) (Mochizuki et al. in Chem Phys Lett 406:283, 2005). The MLFMO-CIS(D) method is first used in evaluating the lowest n\(\pi^{*}\) excitation energy of the hydrated formaldehyde. The photoactive yellow protein (PYP) is the second target of MLFMO-CIS(D) calculation. Through these applications, it is shown that the CIS(D) correction improves the CIS results favorably.     

Ring-closing reaction of allenic/propargylic anions generated by base treatment of sulfonylallenes

The intramolecular trapping of allenyl/propargyl anions generated by base treatment of sulfonylallenes was investigated. Treatment of 1-(omega-iodoalkyl)-1-(phenylsulfonyl)allenes with TBAF or NaH in DMF efficiently produced three- to seven-membered 1-ethynyl-1-(phenylsulfonyl) substituted carbocycles. The allenyl/propargyl anions could also be intramolecularly trapped using a terminal aldehyde or alpha,beta-unsaturated ester. The phenylsulfonyl group was found to be replaced by other electron-withdrawing functionalities like ketone and ester groups but not by an alkyl group for this novel ring-closing reaction.     

Identification of the druggable concavity in homology models using the PLB index

Identification of the druggable concavity, in which drug-like molecules are highly inclined to bind, is an important step in structure-based drug design. We previously proposed an index named PLB (propensity for ligand binding), which is based on the amino acid composition characteristically observed at the small molecule binding sites in the X-ray structures of the complexes between proteins and drug-like small molecules. The PLB index was proven to be useful in identifying the druggable concavities in the quality X-ray structures of proteins. Here, we apply the PLB to predicting the druggable concavity in target proteins using the structures of homologous proteins constructed by homology modeling. In this study, we assembled a set of reference proteins that were accurately determined by X-ray analysis in forms of complexes with drug-like small molecules. Homology models for the reference protein were constructed using multiple homologous proteins as templates. The PLB index was then used to predict the druggable concavity. If the template protein in a complex with a drug-like small molecule was used, the druggable concavity was predicted well, with a prediction rate of 78%. When only the apo protein was available as the template, the practical prediction rate was 71%. Interestingly, even when the percent sequence identity between the reference and template proteins was lower than 30, the PLB index could successfully identify the druggable concavity in some cases. This study demonstrates the practical value of applying the PLB index to identifying the drugabble concavity in the homology model.     

How and Why Does Ni0 Promote Smooth Etheric CO Bond Cleavage and CC Bond Formation? A Theoretical Study

Ni‐catalyzed cross‐coupling between aryl alkyl ethers (ArOR) and Grignard reagents (RMgBr), known since 1979, proceeds under mild conditions in many cases. Although the reaction routes of various synthetic protocols involving transition‐metal‐catalyzed C?O bond activation have been elucidated, the mechanism of this etheric Kumada–Tamao–Curriu reaction remains enigmatic. This is because oxidative addition of inert etheric C?O to Ni⁰ is thermodynamically and kinetically unfavorable, making it hard to explain the observed high reactivity of ether toward Ni catalysts. In this work, we used DFT calculations to identify a plausible reaction pathway by the Ni⁰‐ate complex, which enables smooth C?O bond cleavage and R‐group transfer with reasonable activation barriers; this mechanism also accounts for the ineffectiveness of Pd catalysts. These results throw new light on both C?O activation and cross‐coupling, and should be valuable for further rational development of the methodologies.     

Label-Free Imaging of Intracellular Temperature by Using the O−H Stretching Raman Band of Water

We propose a label-free method for measuring intracellular temperature using a Raman image of a cell in the O−H stretching band. Raman spectra of cultured cells and the medium were first measured at various temperatures using a Raman microscope and the intensity ratio of the two regions of the O−H stretching band was calculated. The intensity ratio varies linearly with temperature in both the medium and cells, and the resulting calibration lines allow simultaneous visualization of both intracellular and extracellular temperatures in a label-free manner. We applied this method to the measurement of temperature changes after the introduction of FCCP (carbonyl cyanide-p-trifluoromethoxyphenylhydrazone) in living cells. We observed a temperature rise in the cytoplasm and succeeded in obtaining an image of the change in intracellular temperature after the FCCP treatment.