Mixing parameters for geometry optimization using the Hamiltonian algorithm

We study the mixing parameters for the search of an optimal geometry using the Hamiltonian algorithm (HA) combined with ab initio molecular orbital calculations. We choose the C?CC?CC?CC dihedral angle of the butane molecule as an example. HF/3-21G level calculations are employed as the molecular orbital calculations. The distributions of the eigenvalues of mixing coefficients are fitted with the linear, quadratic, and quartic functions. Analyses of HA calculations both up to 2,000 and 60,000 iterative calculations show a possibility that the mixing process reduces the number of iterations. The low energy HF/3-21G, B3LYP/6-31G**, and PCM B3LYP/aug-cc-pVDZ optimized structures of the N-acetyl l-histidine N??-methyl amide and four water molecule supermolecule were also determined using the HA optimization method and compared to the recently determined thought to be global minimum energy structure.     

SmI2-mediated reduction of gamma,gamma-difluoro-alpha,beta-enoates with application to the synthesis of functionalized (Z)-fluoroalkene-type dipeptide isosteres

A samarium diiodide (SmI(2))-mediated reduction of gamma,gamma-difluoro-alpha,beta-enoates (15, 29, and 34) was successfully applied to the synthesis of (Z)-fluoroalkene dipeptide isosteres (23, 30, and 35), which have served as potential dipeptide mimetics. Reduction of the gamma,gamma-difluoro-alpha,beta-enoates by SmI(2) proceeded via successive two-electron transfers to form dienolate species which upon kinetically controlled trapping with t-BuOH yielded Xaa-Gly-type fluoroalkene isosteres exemplified by 23, 30, and 35. Replacement of the t-BuOH kinetic trapping agent with aldehydes or ketones provided access to alpha-substituted fluoroalkene isosteres (43 and 45) through aldol reactions of Sm-dienolates with the carbonyl compounds. Of particular note, the use of the SmI(2)-HCHO reagent system with chiral enoate 34 provided D-Phe-psi[(Z)-CF[double bond]CH]-D/L-Ser isosteres (45), which could be converted to enantiomerically pure isosteres (49-52) that bore a variety of side chain functionalities at the alpha-position. This was achieved by a sequence of manipulations consisting of beta-lactone formation followed by chromatographic separation and ring-opening with soft nucleophiles. Included in the present work is the first utilization of a Rh-catalyzed Reformatsky reaction of chiral imines for the stereoselective preparation of alpha,alpha-difluoro-beta-amino acid derivatives (28 and 33). The appropriate choice of reagents (carbonyl compounds for kinetic trapping or ring-opening nucleophiles and imines for Reformatsky reactions) allows the presented methodology to yield various fluoroalkene isosteres possessing a wide range of side chain functionalities.     

OBSERVATION OF THE PICOSECOND TIME-RESOLVED SPECTRUM OF SQUID BATHORHODOPSIN AT ROOM TEMPERATURE

Difference spectra between squid rhodopsin and its bathorhodopsin at room temperature were measured ca. 150 ps and ca. 500 ps after the excitation at 347.2 nm by a double-beam picosecond time-resolved spectrometer. The spectra measured showed a red shift of the isosbestic point between squid rhodopsin and its bathorhodopsin and a lower ΔA_max/ΔA_min value compared with those measured at low temperatures by conventional spectrophotometry.     

Reaction optimization using solid-phase catalysis-CD HTS: Nb-imidazoline-Cu(I)-catalyzed asymmetric benzoylation of 1,2-diols

Catalytic asymmetric benzoylation of 1,2-diols has been developed using a solid-phase asymmetric catalyst. The reaction conditions were optimized by the screening of different metal salts, solvents, bases, and temperatures. High-throughput screening was performed using circular dichroism detection, and the results revealed that Nb-imidazoline-copper(I) in combination with diisopropylethylamine was able to catalyze with high enantioselectivity, giving the monobenzoylated products in high yields and excellent enantiomeric excesses of up to 95% ee. [reaction: see text]     

Sandwich-shaped silver(I) metallomacrocycles encapsulating a XF6(2-) (X = Si, Ge and Sn) anion

A series of sandwich-shaped complexes based on two square tetranuclear Ag(I) metallomacrocycles, [[Ag4(pprd)4]2(XF6)]-(BF4)6.8MeNO2 (pprd = 4-(2-pyridyl)pyrimidine; X = Si, Ge and Sn), in which a XF6(2-) anion is encapsulated, were prepared and their structures were characterized both in the solid state and solution.     

The Electronic State of Hydrogen in the α Phase of the Hydrogen‐Storage Material PdH(D)x: Does a Chemical Bond Between Palladium and Hydrogen Exist?

The palladium–hydrogen system is one of the most famous hydrogen‐storage systems. Although there has been much research on β‐phase PdH(D)_x, we comprehensively investigated the nature of the interaction between Pd and H(D) in α‐phase PdH(D)_x (x<0.03 at 303 K), and revealed the existence of Pd?H(D) chemical bond for the first time, by various in situ experimental techniques and first‐principles theoretical calculations. The lattice expansion, magnetic susceptibility, and electrical resistivity all provide evidence. In situ solid‐state ¹H and ²H NMR spectroscopy and first‐principles theoretical calculations revealed that a Pd?H(D) chemical bond exists in the α phase, but the bonding character of the Pd?H(D) bond in the α phase is quite different from that in the β phase; the nature of the Pd?H(D) bond in the α phase is a localized covalent bond whereas that in the β phase is a metallic bond.     

Analytical optimization of exponent values in protonic and deuteronic Gaussian‐type functions by elimination of translational and rotational motions from multi‐component molecular orbital scheme

To optimize the exponent values in protonic and deuteronic Gaussian‐type functions (GTF) by the elimination of translational and rotational motions, we have proposed the new scheme of an analytical gradient formula with respect to the exponent values in the multi‐component molecular orbital scheme, which can take into account the quantum effects of protons and deuterons, under the Hartree‐Fock level of theory. Numerical assessment of H₂ and D₂ molecules confirms that there is a clear difference between distributions of protonic and deuteronic orbitals following the elimination of translational and rotational motions. In particular, the d‐type GTF in the protonic orbital drastically improves the total energy. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

The Gibbs Energies of Activation of Lysozyme for Viscous Flow in Water + Dimethyl Sulfoxide Solutions at 298.15 K

Gibbs energies of activation for viscous flow of binary water (1) + dimethyl sulfoxide (2) mixtures, Δμ ₁₂^○, and of lysozyme (3) in corresponding ternary mixtures, Δμ ₃^○, were determined at 298.15 K. The binary mixtures have a maximum in the value of the excess quantity for Δμ ₁₂^○ at a dimethyl sulfoxide mole fraction of x ₂≈0.31. The values of Δμ ₃^○ are larger than Δμ ₁₂^○ at all values of x ₂, even when normalized by their molar volumes, suggesting that the solvents interact more strongly with lysozyme than with themselves. The values of Δμ ₃^○ significantly increased in the range of x ₂=0.3 to 0.4 because of an increase in solvent-lysozyme interactions, which resulted from an increase in the accessible surface area of lysozyme that was exposed by its unfolding. The mean value obtained for Δμ ₃^○ per amino acid of lysozyme at x ₂=0.2 is greater than that for hydrophobic amino acids, indicating that the solvent interacts with hydrophilic amino acids more strongly than with hydrophobic ones.     

Transmission electron microscopy study of an AlN nucleation layer for the growth of GaN on a 7-degree off-oriented (0 0 1) Si substrate by metalorganic vapor phase epitaxy

We have investigated the morphology of the high-temperature-grown AlN nucleation layer and its role in the early stage of GaN growth, by means of transmission electron microscopy. The nitride was selectively grown on a 7-degree off-oriented (0 0 1) patterned Si substrate by metalorganic vapor phase epitaxy. AlN was deposited on the inclined unmasked (1 1 1) facet in the form of islands. The size of the islands varied along the slope, which is attributable to the diffusion of the growth species in the vapor phase. The GaN nucleation occurred at the region where rounded AlN islands formed densely. The threading dislocations were observed to generate in the GaN nucleated region.