Self-aggregation behavior of dimeric chlorophyll-a derivatives linked with ethynylene and m-phenylene moieties.

Chlorophyll(Chl)-a derivatives inserting an ethynylene-m-phenylene group between a zinc chlorin ring and a hydroxymethyl group, in which various substituents were introduced on the benzene spacer, were prepared as model compounds for the light-harvesting antennae (chlorosomes) of photosynthetic green bacteria. These compounds were synthesized from a C3-ethynylated Chl-a derivative via sequential Sonogashira cross-coupling reaction, and the effects of the substituents on the phenylene linker on their self-aggregation behaviors were investigated by electronic absorption, circular dichroism, and infrared absorption spectroscopic measurements. These studies exhibited that some compounds gave the disordered self-assemblies including several species; however, the zinc complex of the dimeric Chl-a derivative primarily allowed a single J-aggregate species in an aqueous Triton X-100 micellar solution. Additional control experiments revealed that its self-assembly was constructed through the hydrogen and coordination bonding involving the hydroxymethyl group on benzene ring, keto-carbonyl group at C13-position, and central zinc atom, and this is consistent with a conventional chlorosomal manner.

Synthesis and Self-Aggregation of Chlorophyll-a Derivatives Possessing a Hydroxymethyl Group in the C20-Substituent with Ethynylene and/or Phenylene Linkers.

Chlorophyll(Chl)-a derivatives containing some rigid linkers in the C20 substituents, which were inserted between a hydroxymethyl group and the chlorin π-skeleton, were synthesized and their self-aggregation abilities were investigated. Measurements of electronic absorption, circular dichroism and infrared absorption spectra revealed that the zinc complex of a Chl-a derivative bearing a (p-ethynyl)benzyl alcoholic moiety at the C20-position gave its J-aggregates in an aqueous micellar solution through the hydrogen and coordination bonding. These results exhibited the potential of Chl-a derivatives bearing a hydroxyl group in the C20 substituents as the model compounds for chlorosomal light-harvesting antennas.

Aryl/Heteroaryl Substituted Boron-Difluoride Complexes Bearing 2-(Isoquinol-1-yl)pyrrole Ligands Exhibiting High Luminescence Efficiency with a Large Stokes Shift.

A series of 2-(isoquinol-1-yl)pyrrole-boron complexes possessing (hetero)aryl substituents on the pyrrole and/or isoquinoline moiety were prepared. These compounds exhibited the fluorescence emission character in both solution and solid state. In most cases, the large Stokes shift and high fluorescence quantum yield in the solution were compatible. Furthermore, the structural diversity allowed the precise tuning of emitting colors from light blue to red with strong emission intensity. The present paper describes their comprehensive optical characteristics dependent on the type and position of the substituted aryl groups by the experimental and computational studies.

Synthesis and Optical Properties of Thiazolo-Chlorin and Porphyrin Skeletons.

Macrocyclic π-skeletons containing a thiazole moiety were synthesized via MacDonald [3 + 1]-type condensation. The construction of thiazolochlorin 1a and thiazoloporphyrin 1b depended on the conformation of the thiazole moieties, and their 18π-systems expanded along the molecular y and x axes, respectively. In particular, the structure of thiazolochlorin 1a was studied in detail using 2D nuclear magnetic resonance methods. The optical properties in solution were measured and discussed based on both experimental data and computational studies.

Synthesis and Characterization of Boron Difluoride Complexes Bearing π-Expanded Pyridine Ligands as Organic Fluorochromes.

Novel boron complexes bearing pyrrole and π-expanded pyridine structures, such as quinoline, isoquinoline, and phenanthridine, were prepared. These compounds showed the fluorescence emission characters in both solution and solid state. Particularly, several complexes in solution exhibited high fluorescence quantum yield with Stokes shift values being four to five times larger than that of boron dipyrromethenes (BODIPYs). The present paper describes the optical properties of these novel boron complexes as well as their halogenated derivatives from the results of both experimental and computational studies.

Different morphologies of human embryonic kidney 293T cells in various types of culture dishes.

Human embryonic kidney 293T (HEK293T) cells are used in various biological experiments and researches. In this study, we investigated the effect of cell culture environments on morphological and functional properties of HEK293T cells. We used several kinds of dishes made of polystyrene or glass for cell culture, including three types of polystyrene dishes provided from different manufacturers for suspension and adherent cell culture. In addition, we also investigated the effect of culturing on gelatin-coated surfaces on the cell morphology. We found that HEK293T cells aggregated and formed into three-dimensional (3-D) multicellular spheroids (MCS) when non-coated polystyrene dishes were used for suspension culture. In particular, the non-coated polystyrene dish from Sumitomo bakelite is the most remarkable characteristic for 3-D MCS among the polystyrene dishes. On the other hand, HEK293T cells hardly aggregated and formed 3-D MCS on gelatin-coated polystyrene dishes for suspension culture. HEK293T cells adhered on the non- or gelatin-coated polystyrene dish for adherent culture, but they did not form 3-D MCS. HEK293T cells also adhered to non- or gelatin-coated glass dishes and did not form 3-D MCS in serum-free medium. These results suggest that HEK293T cells cultured on non-coated polystyrene dish may be useful for the tool to analyze the characteristics of 3D-MCS.

Palladium-Catalyzed Acylation of Terminal Alkynes toward 3-Ynone-Linked Chlorophyll-a Derivatives and Their Optical Properties.

The Pd-catalyzed acylation reactions of terminal 3-ethynyl moieties of chlorophyll-a (Chl-a) derivatives are described herein. Both acyl chlorides and acid anhydrides were valuable reagents for the coupling, resulting in the formation of π-conjugation extended Chl-a derivatives possessing a carbonyl-ethynyl group at the C3-position. The ultraviolet-visible absorption and fluorescence emission data were obtained in solution to evaluate the optical properties of the 3-ynone-linked Chl-a derivatives.

Silver-Catalyzed Allylation of Ketones and Intramolecular Cyclization through Carbene Intermediates from Cyclopropenes Under Ambient Conditions.

Tandem C-C bond formation was achieved through silver-catalyzed ring-opening of cyclopropenes via carbene intermediates. The reaction of cyclopropenes in the presence of a silver catalyst gave indene derivatives under ambient conditions. In contrast, the insertion of organozinc reagents to silver carbene or allylic cation intermediates afforded allylmetal intermediates for the tandem allylation of carbonyl compounds.

Hydrodynamic consideration of the finite size effect on the self-diffusion coefficient in a periodic rectangular parallelepiped system.

In the present study, we use molecular dynamics (MD) simulations to provide an insight into the system size effect on the self-diffusion coefficient of liquids in the periodic rectangular parallelepiped system, from the hydrodynamic perspective. We have previously shown that in the rectangular box system, the diffusivity exhibits anomalous behaviors, i.e., the diffusion tensor appears to be anisotropic despite the bulk liquid simulation and the diffusion component in the direction along the short side of rectangular box with a high aspect ratio exceeding the diffusivity in the infinite system [Kikugawa et al., J.Chem. Phys. 142, 024503 (2015)]. So far, the size effect on the diffusivity has been intensively studied in the cubic system and has been interpreted quite well by the theoretical considerations employing the hydrodynamic interaction. Here, we have extended the hydrodynamic theory to be applied to periodic rectangular box systems and compared the theoretical predictions with MD simulation results. As a result, the diffusivity predicted by the hydrodynamic theory shows good agreement with the MD results. In addition, the system size effect was examined in a rod-shaped rectangular box in which the two shorter side lengths were equivalent and a film-type rectangular box in which the two longer side lengths were equivalent. It is of interest that we found that the aspect ratio, at which the diffusivity coincides with that in the infinite system, is a universal constant independent of the cross-sectional area for the rod system or the thickness for the film system. By extracting the universal structure in the hydrodynamic description, we also suggested a simplified approximate model to accurately predict the size effect on the diffusivity over a practical range of aspect ratios.

(Z)-Selective Enol Triflation of α-Alkoxyacetoaldehydes: Application to Synthesis of (Z)-Allylic Alcohols via Cross-Coupling Reaction and [1,2]-Wittig Rearrangement.

The stereoselective transformation of α-alkoxyacetoaldehydes to the corresponding (Z)-vinyl triflates was achieved by treatment with phenyl triflimide and DBU. The stereochemistry was explained by the "syn-effect," which was attributed primarily to an σ → π* interaction. The ß-alkoxy vinyl triflates obtained were applied to the stereoselective synthesis of structurally diverse (Z)-allylic alcohols via transition metal-catalyzed cross-coupling reaction and [1,2]-Wittig rearrangement.

Effect of the computational domain size and shape on the self-diffusion coefficient in a Lennard-Jones liquid.

In the present study, molecular dynamics (MD) simulations on the monatomic Lennard-Jones liquid in a periodic boundary system were performed in order to elucidate the effect of the computational domain size and shape on the self-diffusion coefficient measured by the system. So far, the system size dependence in cubic computational domains has been intensively investigated and these studies showed that the diffusion coefficient depends linearly on the inverse of the system size, which is theoretically predicted based on the hydrodynamic interaction. We examined the system size effect not only in the cubic cell systems but also in rectangular cell systems which were created by changing one side length of the cubic cell with the system density kept constant. As a result, the diffusion coefficient in the direction perpendicular to the long side of the rectangular cell significantly increases more or less linearly with the side length. On the other hand, the diffusion coefficient in the direction along the long side is almost constant or slightly decreases. Consequently, anisotropy of the diffusion coefficient emerges in a rectangular cell with periodic boundary conditions even in a bulk liquid simulation. This unexpected result is of critical importance because rectangular fluid systems confined in nanospace, which are present in realistic nanoscale technologies, have been widely studied in recent MD simulations. In order to elucidate the underlying mechanism for this serious system shape effect on the diffusion property, the correlation structures of particle velocities were examined.

Catalytic tandem C-C bond formation/cleavage of cyclopropene for allylzincation of aldehydes or aldimine using organozinc reagents.

The tandem allylation of aldehydes or an aldimine with allylzinc intermediates derived from organozinc reagents and cyclopropenes is described. The present three-component reaction involves carbozincation of cyclopropene and sequential cleavage of a cyclopropylzinc intermediate in situ without a transition-metal catalyst. The allylzinc intermediates generated in situ, which is an α,ß-unsaturated acylanion equivalent, gave the corresponding homoallylic alcohols or amine in good yields.

Stereoselective synthesis of (2Z,4E)-2,4-pentadien-1-ols via sequential 1,4-elimination reaction and [1,2]-Wittig rearrangement starting from (E)-4-alkoxy-2-butenyl benzoates.

The sequential 1,4-elimination reaction of (E)-4-alkoxy-2-butenyl benzoates and [1,2]-Wittig rearrangement gave (2Z,4E)-2,4-pentadien-1-ols stereoselectively. Z-Selective formation of intermediary vinyl ethers, whose stereochemistry was well elucidated by the "syn-effect", was achieved by treatment of the 2-butenyl benzoates with KOH in the presence of Pd catalyst. The subsequent [1,2]-Wittg rearrangement by use of n-BuLi proceeded with retention of the stereochemistry of the intermediary vinyl ethers.

A molecular dynamics study on heat conduction characteristics in DPPC lipid bilayer.

In this paper, nonequilibrium molecular dynamics simulations were performed on a single component 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine lipid bilayer in order to investigate the thermal conductivity and its anisotropy. To evaluate the thermal conductivity, we applied a constant heat flux to the lipid bilayer along and across the membrane with ambient water. The contribution of molecular interaction to the heat conduction was also evaluated. Along the bilayer plane, there is little transfer of thermal energy by the interaction between lipid molecules as compared with the interaction between water molecules. Across the bilayer plane, the local thermal conductivity depends on the constituents (i.e., water, head group, and tail group of lipid molecule) that occupy the domain. Although the intramolecular transfer of thermal energy in the tail groups of lipid molecules works efficiently to promote high local thermal conductivity in this region, the highest thermal resistance appears at the center of lipid bilayer where acyl chains of lipid molecules face each other due to a loss of covalent-bond and low number density. The overall thermal conductivities of the lipid bilayer in the directions parallel and perpendicular to the lipid membrane have been compared, and it was found that the thermal conductivity normal to the membrane is higher than that along the membrane, but it is still smaller than that of bulk water.

Contribution of inter- and intramolecular energy transfers to heat conduction in liquids.

The molecular dynamics expression of heat flux, originally derived by Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] for pairwise potentials, is generalized in this paper for systems with many-body potentials. The original formula consists of a kinetic part and a potential part, and the latter term is found in the present study to be expressible as a summation of contributions from all the many-body potentials defined in the system. The energy transfer among a set of sites for which a many-body potential is defined is discussed and evaluated by the rate of increase in the kinetic energy of each site due to the potential, and its accumulation over all the potentials in the system is shown to make up the potential part of the generalized expression. A molecular dynamics simulation for liquid n-octane was performed to demonstrate the applicability of the new expression obtained in this study to measure the heat flux and to elucidate the contributions of inter- and intramolecular potentials to heat conduction.