A new hierarchical parallelization scheme: generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO)

A two-level hierarchical scheme, generalized distributed data interface (GDDI), implemented into GAMESS is presented. Parallelization is accomplished first at the upper level by assigning computational tasks to groups. Then each group does parallelization at the lower level, by dividing its task into smaller work loads. The types of computations that can be used with this scheme are limited to those for which nearly independent tasks and subtasks can be assigned. Typical examples implemented, tested, and analyzed in this work are numeric derivatives and the fragment molecular orbital method (FMO) that is used to compute large molecules quantum mechanically by dividing them into fragments. Numeric derivatives can be used for algorithms based on them, such as geometry optimizations, saddle-point searches, frequency analyses, etc. This new hierarchical scheme is found to be a flexible tool easily utilizing network topology and delivering excellent performance even on slow networks. In one of the typical tests, on 16 nodes the scalability of GDDI is 1.7 times better than that of the standard parallelization scheme DDI and on 128 nodes GDDI is 93 times faster than DDI (on a multihub Fast Ethernet network). FMO delivered scalability of 80-90% on 128 nodes, depending on the molecular system (water clusters and a protein). A numerical gradient calculation for a water cluster achieved a scalability of 70% on 128 nodes. It is expected that GDDI will become a preferred tool on massively parallel computers for appropriate computational tasks.     

Novel unsymmetrical PCP′ pincer ligands and their palladium(II) complexes

Synthetic routes towards novel PCP′ pincer ligands were devised. Ligand 1-(Pr₂ⁱPOCH₂)-3-(Bu₂^tPCH₂)(C₆H₄) is prepared in a three step synthesis from 1,3-benzenedimethanol and 1-(Pr₂ⁱPO)-3-(Bu₂^tPCH₂)(C₆H₄) is accessible in three steps from 3-hydroxybenzylalcohol. Both their palladium(II) complexes are prepared in good yields but are distinctly different since [PdCl{(C₆H₃)(OPPr₂ⁱ)-2-(CH₂PBu₂^t)-6}] possesses two five-membered palladacycles, whereas [PdCl{(C₆H₃)(CH₂PBu₂^t)-2-(CH₂OPPr₂ⁱ)-6}] is unusual for a pincer complex in that it contains both five- and six-membered palladacycles. Both compounds also represent the first examples of pincer complexes where one donor is a phosphinite and the other is a phosphine. The X-ray structures of these complexes were solved and are discussed. The data reveal that an increase in the metallacycle ring-size leads to changes in bond lengths, but more importantly to significant increases in the bond angles.     

Simultaneous Determination of Ultratrace Prostaglandins in Biological Samples with High-Performance Liquid-Chromatography/Laser-Induced Fluorometry

A newly developed analytical technique to extract, derivatize, and simultaneously determine trace prostaglandins (PGs) in practical biological samples is described. Trace PGs were extracted by a column separation technique and derivatized by 9-anthryldiazomethane (ADAM). The conventional chemical procedure for determination of carboxylic acids using ADAM was reinvestigated to get separation of trace PGs from enormous amounts of coexisting biological substances and by- and decomposition products of ADAM. The PG derivatives were separated by high-performance liquid chromatography and detected by laser-induced fluorometry (HPLC/LIF). The minimum detectable absolute quantity of the HPLC/LIF system was 0.5 pg (1.3 fmol) per injection. For the overall chemical procedure, sub-nanogram per milliliter levels of PGs in human urine were determined simultaneously.     

Raman spectroscopic verification of fac-Sc(PMBP)3 by solid and solute spectra and density functional method calculation

Two kinds of solids were obtained for Sc(PMBP)₃ by precipitation from different solvents. They were light-yellow crystal and yellowish-white powder, and their melting points were 209 and 217 °C, respectively. Raman spectra of six anhydrous samples prepared from these materials were measured and classified into two types of spectral patterns. Raman solute spectra of these two materials were measured in a dilute solution of dichloromethane, in which the solute is a free molecule in a solvent cage. Their spectra were considerably similar to each other, but they indicated clear differences in some pairs of bands. One of these two molecules was concluded to be a facial form of Sc(PMBP)₃, because the other constituent has been established to be a meridional form of Sc(PMBP)₃ by X-ray analysis of a single crystal. Structural optimization for mer- and fac-Sc(PMBP)₃ and their vibrational calculation of frequencies and intensities were carried out with the density functional method of B3LYP/6-31G**. Their computed Raman spectra were well coincident with their observed spectra. The existence of fac-Sc(PMBP)₃ has been established by thermal analysis, Raman spectroscopy and ab initio calculation.     

Molecular-dynamics simulation of crystallization in helical polymers

The molecular mechanism of crystallization in helical polymers is a fascinating but very difficult subject of research. We here report our recent efforts toward better understanding of the crystallization in helical polymers by use of molecular-dynamics simulation. With straightforward approaches to the problem being quite difficult, we adopt a different strategy of categorizing the helical polymers into two distinct types: one type is a simple bare helix which is essentially made of backbone atomic groups only and has smoother molecular contours, and the other is a more general helix having large side groups that would considerably hamper molecular motion and crystallization. Both types of helical polymers are here constructed by use of the united atom model, but they show quite distinct crystallization behavior; the crystallization of the former-type polymer is rather fast, while that of the latter-type polymer is extremely slow. We find that the bare helix, when rapidly cooled in free three-dimensional space, freezes into partially ordered state with limited intramolecular and intermolecular orders, and that remarkable improvement of order and growth of an ordered chain-folded crystallite occurs by very long-time annealing of the partially ordered state around the apparent freezing temperature. We also study crystallization of the bare helix upon a growth surface; the crystallization in this case proceeds much faster through highly cooperative process of the intermolecular and the intramolecular degrees of freedom. On the other hand, crystallization of the realistic model of isotactic polypropylene (iPP) having pendant methylene groups is found to be extremely sluggish. By restricting the spatial dimension of the system thereby fully disentangling the chain, we observe that the molecule of iPP crystallizes very quickly onto the crystal substrate made of the same iPP chain. Quite remarkable is that the molecule of iPP strictly recognizes the helical sense of the substrate chain and efficiently selects its chirality during crystallization.     

Validity of <Emphasis Type="Italic">B</Emphasis>-splines as a universal basis set for atomic Hartree–Fock–Roothaan calculations

The validity of B-splines as a universal basis set for atomic Hartree–Fock–Roothaan calculations is studied. In order to accomplish our aim, the ground-state energies of neutral atoms He–Xe, cations Li ⁺–Xe ⁺, and anions H ^-–I ^- with the nuclear charge Z=54 are calculated by the Hartree–Fock–Roothaan method with the B-spline sets. All radial functions of the atoms and singly charged ions are expanded by common B-spline sets regardless of atomic systems and symmetries of atomic orbitals. The energies obtained by the best B-spline set are in excellent agreement with ten-digit numerical Hartree–Fock results.     

An interesting inclusion phenomenon with (S)-1-(hydroxydiphenylmethyl)-5-azoniaspiro[4.4]nonane bromide and (S)-1-(hydroxydiphenylmethyl)-5-azoniaspiro[4.5]decane bromide and optical resolution of binaphthyl and biphenanthyl diols by inclusion crystallization with these optically active ammonium salts

Recrystallization of the spiro-pyrrolidinium salts (S)-1-(hydroxydiphenyl methyl)-5-azoniaspiro[4.4]nonane bromide or (S)-1-(hydroxydiphenylmethyl)-5-azoniaspiro[4.5] decane bromide from chloroform afforded a crystalline spiro-pyrrolidinium salt including two molecules of chloroform which was determined by 'H nmr elemental analysis, and X-ray analysis. Racemic 2.2-dihydroxy-1, 1-binaphthyl and 10, 10-dihydroxy-9,9-biphenanthryl have been resolved effectively by inclusion crystallization using these chiral ammonium salts.     

Crystallization of In2O3 by vapor reaction

Crystallization of In₂O₃ occured in closed porcelain crucibles in air at 960–1200°C by vapor phase reaction of In₂O or In vapor with the oxygen diffusing into the system. The In₂O or In vapors were thermally generated from mixtures such as graphite/In₂O₃, graphite/In, In₂O₃/In and graphite/In₂O₃/In. The graphite/In₂O₃ system at a mole ratio of 30/1 and 1000°C produced yellow, transparent needle crystals with a maximum size of 0.5 X 0.5 X 8 mm and electrical resistivity of 5.5 X 10^-2 ω cm at 25°C.     

Bound states of the nucleon-monopole system

The energy spectrum of the bound states of the nucleon-monopole system is determined, the monopole harmonics Y_q,l,m are related to Wigner's functions D _m,m ^(L) of the rotation matrix, and the scattering wave functions of the proton in the dyon source field are calculated.     

Absolute asymmetric photocyclization of isopropylbenzophenone derivatives using a cocrystal approach involving single-crystal-to-single-crystal transformation

Absolute asymmetric photocyclization of isopropylbenzophenone derivatives was achieved by means of a cocrystal approach. Three chiral salt crystals formed by carboxylic acid derivatives with achiral amines could be prepared by spontaneous crystallization. In the M-crystal of 4-(2,5-diisopropylbenzoyl)benzoic acid with 2,4-dichlorobenzylamine, a twofold helical arrangement occurs in a counterclockwise direction to generate the crystal chirality. Conversely, the clockwise helix exists alone in the P-crystal. Irradiation of the M-crystal at >290 nm caused highly enantioselective Norrish type II cyclization to give the (R,R)-cyclopentenol, (R)-cyclobutenol, and (R)-hydrol in a 6:3:1 molar ratio, resulting in successful absolute asymmetric synthesis, while irradiation at around 350 nm afforded the (R,R)-cyclopentenol as the sole product. The reaction proceeded via single-crystal-to-single-crystal transformation, and therefore the reaction path producing the (R,R)-cyclopentenol could be traced by X-ray crystallographic analysis before and after irradiation.