Comparative molecular dynamics study of ether- and ester-linked phospholipid bilayers

The lipid membranes found in archaea have high bilayer stability and low permeability. The molecular structure of their constituent lipids is characterized by ether-linked, branched hydrophobic chains, whereas the conventional lipids obtained from eukaryotic or eubacterial sources have ester linked straight chains. In order to elucidate the influence of the ether linkage, instead of an ester one, on the physical properties of the lipid bilayers, we have carried out comparative 10 ns molecular dynamics simulations of diphytanyl phosphatidylcholine (ether-DPhPC) and diphytanoyl phosphatidylcholine (ester-DPhPC) bilayers in water, respectively. We analyze bilayer structures, hydration of the lipids, membrane dipole potentials, and free energy profiles of water and oxygen across the bilayers. We observe that the membrane dipole potential for the ether-DPhPC bilayer, which arises mainly from the ether linkage, is about half of that of the ester-DPhPC. The calculated free energy barrier for a water molecule in the ether-DPhPC bilayer system is slightly higher than that in the ester-DPhPC counterpart, which is in accord with experimental data.     

An application of the novel quantum mechanical/molecular mechanical method combined with the theory of energy representation: An ionic dissociation of a water molecule in the supercritical water

A novel quantum chemical approach recently developed has been applied to an ionic dissociation of a water molecule (2H(2)O-->H(3)O(+)+OH(-)) in ambient and supercritical water. The method is based on the quantum mechanical/molecular mechanical (QM/MM) simulations combined with the theory of energy representation (QM/MM-ER), where the energy distribution function of MM solvent molecules around a QM solute serves as a fundamental variable to determine the hydration free energy of the solute according to the rigorous framework of the theory of energy representation. The density dependence of the dissociation free energy in the supercritical water has been investigated for the density range from 0.1 to 0.6 g/cm(3) with the temperature fixed at a constant. It has been found that the product ionic species significantly stabilizes in the high density region as compared with the low density. Consequently, the dissociation free energy decreases monotonically as the density increases. The decomposition of the hydration free energy has revealed that the entropic term (-TDeltaS) strongly depends on the density of the solution and dominates the behavior of the dissociation free energy with respect to the variation of the density. The increase in the entropic term in the low density region can be attributed to the decrease in the translational degrees of freedom brought about by the aggregation of solvent water molecules around the ionic solute.     

Strong convergence of approximated sequences for nonexpansive mappings in Banach spaces

In this paper, we study the convergence of the sequence defined by

where and is a nonexpansive mapping from a closed convex subset of a Banach space into itself.

     

Spin and orbital excitations in perovskite Mn oxides

An effective Hamiltonian of perovskite type LaMnO₃ is derived by taking into account the degeneracy ofe _g orbitals, Hund coupling and strong Coulomb interactions betweend-electrons in Mn ions. Spin and orbital excitations are calculated by using the effective Hamiltonian.     

Introduction of clutch function into a molecular gear system by silane-silicate interconversion

Introduction of the clutch-declutch mechanism into a new gear system, bis(4-methyl-9-triptycyl)difluorosilane 1, is achieved by the reversible attachment of fluoride ion giving the corresponding fluorosilicate 2. Although the phase isomers of 1 (1(dl) and 1(meso)) cannot be separated because of the equilibrium via a slow gear slippage process (DeltaH(double dagger) = 17.2 +/- 0.2 kcal x mol(-1) and DeltaS(double dagger) = 0.9 +/- 0.9 cal x mol(-1) x K(-1)), 1 works as meshed molecular gears in solution at room temperature. On the other hand, silicate 2 in the solid state has quite an unusual TBP structure having two organic triptycyl groups at the apical positions and three electronegative fluorine atoms at the equatorial positions against the Muetterties rule. Rotation of the two triptycyl groups around Si-C bonds in 2 is facile and independent to each other in solution. Silicate 2 is reverted to the corresponding silane mixture by treating with excess water.     

Carboxylation of a Palladacycle Formed via C(sp3)−H Activation: Theory-Driven Reaction Design

Theory-driven organic synthesis is a powerful tool for developing new organic transformations. A palladacycle(II), generated from 8-methylquinoline via C(sp³)−H activation, is frequently featured in the scientific literature, albeit that the reactivity toward CO₂, an abundant, inexpensive, and non-toxic chemical, remains elusive. We have theoretically discovered potential carboxylation pathways using the artificial force induced reaction (AFIR) method, a density-functional-theory (DFT)-based automated reaction path search method. The thus obtained results suggest that the reduction of Pd(II) to Pd(I) is key to promote the insertion of CO₂. Based on these computational findings, we employed various one-electron reductants, such as Cp*₂Co, a photoredox catalyst under blue LED irradiation, and reductive electrolysis ((+)Mg/(−)Pt), which afforded the desired carboxylated products in high yields. After screening phosphine ligands under photoredox conditions, we discovered that bidentate ligands such as dppe promoted this carboxylation efficiently, which was rationally interpreted in terms of the redox potential of the Pd(II)-dppe complex as well as on the grounds of DFT calculations. We are convinced that these results could serve as future guidelines for the development of Pd(II)-catalyzed C(sp³)−H carboxylation reactions with CO₂.     

Nanostructured molybdenum oxides and their catalytic performance in the alkylation of arenes

We report for the first time that nanostructured MoO(3) is an excellent catalyst for the alkylation of a wide range of arenes with substituted benzyl alcohols as alkylating agents.     

de novo design and synthesis of N-benzylanilines as new candidates for VEGFR tyrosine kinase inhibitors

N-Benzylanilines were designed and synthesized as vascular endothelial growth factor (VEGF)-2 inhibitors using de novo drug design systems based on the X-ray structure of VEGFR-2 kinase domain. Among compounds synthesized, compound showed the most potent inhibitory activity toward VEGFR-2 (KDR) tyrosine kinase and its IC(50) value was 0.57 microM.