Theoretical investigation on electron transport through an organic molecule: effect of the contact structure

Knowing how the contact geometry influences the conductance of a molecular wire junction requires both a precise determination of the molecule/metallic-electrode interface structure and an evaluation of the conductance for different contact geometries with a fair accuracy. With a greatly improved method to solve the Lippmann-Schwinger equation, we are able to include at least one atomic layer of each electrode into the extended molecule. The artificial effect of the jellium model used for the electrodes is therefore significantly reduced. Our first-principles calculations on the transport properties of a single benzene dithiolate molecule sandwiched between Au(111) surfaces show that the transmission of the bridge site contact, which is the most stable adsorption configuration in equilibrium, displays different features from those of other configurations, and that the inclusion of the surface layers of Au electrodes into the extended molecule shifts and broadens the transmission peaks due to a stronger and more realistic S-Au bonding. We discuss the geometry dependence of the transport properties by analyzing the density of states of the molecular orbitals.     

Fern constituents: triterpenoids from Adiantum capillus-veneris

Two new migrated hopane triterpenoids, viz. 4alpha-hydroxyfilican-3-one and fern-9(11)-en-12beta-ol, and olean-18-en-3-one and olean-12-en-3-one as the first example of oleanane compounds from Adiantum ferns were isolated along with many other known triterpenoids from Adiantum capillus-veneris of China and Egypt. Their structures were elucidated by spectroscopic analyses.     

2,3-di-O-methoxymethyl-6-O-tert-butyldimethylsilyl-beta-cyclodextrin, a useful stationary phase for gas chromatographic separation of enantiomers

Heptakis(2,3-di-O-methoxymethyl-6-O-tert-butyldimethylsilyl)-beta-cyclodextrin (2,3-MOM-6-TBDMS-beta-CD), synthesized by using methoxymethylchloride (MOM-Cl) as derivatization reagent, was used for capillary gas chromatographic separation of enantiomers. The new chiral stationary phase proved to be suitable for the enantiodifferentiation of volatiles from various chemical classes. Compared to the corresponding gamma-CD derivative (2,3-MOM-6-TBDMS-gamma-CD), the spectrum of compounds for which enantiomers could be separated was more limited and the enantioseparation achieved was generally less pronounced. Unusually high separation factors were observed for 2-alkyl esters of short chain acids (C2-C6). Phenomena underlying the enantioseparation of 2-pentyl acetate (alpha: 4.31; 35 degrees C) were investigated by determining thermodynamic parameters. Data show that only one enantiomer is retained significantly on the chiral stationary phase whereas the other one behaves like the hydrocarbons used as references.     

Highly saddle shaped (porphyrinato)iron(III) iodide with a pure intermediate spin state

Combined analyses using NMR, EPR and M?ssbauer spectroscopy as well as SQUID magnetometry have revealed that highly saddle shaped Fe(OETPP)I adopts an essentially pure intermediate spin state in spite of the coordination of an iodide ligand.     

Gingipains, the major cysteine proteinases and virulence factors of Porphyromonas gingivalis: structure, function and assembly of multidomain protein complexes

Gingipains, extracellular cysteine proteinases of Porphyromonas gingivalis, constitute the major virulence factor of this periodontopathogenic bacterium. They are the product of three genes, two coding for an Arg-specific (RgpA and RgpB) and one for a Lys-specific proteinase (Kgp). Proteinase domains of RgpA and RgpB are virtually identical; however, the gene encoding the former enzyme is missing a large segment coding for hemaglutinin / adhesin (HA) domains. The latter domains are present also in Kgp. The tertiary structure of RgpB revealed that the proteinase domain of gingipains has a protein fold referred to as the caspase-hemoglobinase fold. On this basis, they are also evolutionary related to other highly specific proteinases including clostripain, caspases, legumains and separase (clan CD of cysteine peptidases). Gingipains are produced as large preproproteins and are subject to elaborate, not yet fully understood, secretion, glycosylation, activation, and maturation processes. How they traverse the outer membrane is unknown, although it can be hypothesized that they use an autotransporter pathway. Apparently during transport through the periplasm the LPS-like glycan moiety is added at the conserved C-terminal portion of progingipains. At the cell surface pro-gingipains fold into partially active, single-chain zymogens and undergo autocatalytic, intermolecular processing. Two sequential cleavages within the profragment domain enhance zymogen activity and in the case of RgpA and Kgp are followed by excision of the individual HA domains. These domains are further truncated at the C-terminus by concerted action of Kgp and carboxypeptidase and form a non-covalent multidomain, multifunctional complex anchored into the outer membrane by the glycated, C-terminal HA domain. This hypothetical scenario is a reasonable explanation for the occurrence of many forms of gingipains.     

Preparation of polysiloxanes from silicic acid. VII. Effects of the degree of esterification and alkyl groups on condensations of silicic acid esters and formation of fibrous silica

Silicic acid esters were prepared by the reaction of the silicic acid in tetrahydrofuran with various alcohols such as such as methanol, ethanol, 2-propanol, 1-butanol, 2-methyl-2-propanol and 1-octanol, using an esterification apparatus designed especially to allow the preparation of silicic acid esters from alcohols with low boiling points or appreciable steric hindrance. With the intent of obtaining a spinnable ester solution by condensation of silicic acid esters, the effects of the degree of esterification (DE) and alkyl group on gel time and spinnability are investigated. An increase in the DE and the size of the alkyl group led to an increase in the gel time of the esters. Esters solutions with a good spinnability were prepared from n-butyl and isopropyl esters with DEs of 40–50%. In addition, the gel permeation chromatography of condensing esters with low DEs showed a rapid increase in molecular weight. The results showed that spinnability depended on DE and the ester's alkyl group. Fibers could be formed with length of about 10–100 cm from ethyl, isopropyl, and n-butyl esters with DEs 40–50% and with length of 10 cm from octyl ester with DE 26%.     

Molecular structures of five-coordinated halide ligated iron(III) porphyrin,porphycene, and corrphycene complexes

Molecular structures of 12 porphyrin analogues, Fe(III)(EtioP)X(1(a)-1(d)), Fe(III)(EtioCn)X(2(a)-2(d)), and Fe(III)(Etio-Pc)X(3(a)-3(d)), where X = F (a), Cl (b), Br (c), and I (d), are determined on the basis of X-ray crystallography. Combined analyses using M?ssbauer, (1)H NMR, and EPR spectroscopy as well as SQUID magnetometry have revealed that 3(d) exhibits a quite pure S = 3/2 spin state with a small amount of an S = 5/2 spin admixture. In contrast, all the other complexes show the S = 5/2 spin state with a small amount of the S = 3/2 spin admixture. The structural and spectroscopic data indicate a strong correlation between the spin states of the complexes and the core geometries such as Fe-N bond lengths, cavity areas, and DeltaFe values.     

Syntheses of arbutin-alpha-glycosides and a comparison of their inhibitory effects with those of alpha-arbutin and arbutin on human tyrosinase

The effects of 4-hydroxyphenyl alpha-glucopyranoside (alpha-arbutin) and 4-hydroxyphenyl beta-glucopyranoside (arbutin) on the activity of tyrosinase from human malignant melanoma cells were examined. The inhibitory effect of alpha-arbutin on human tyrosinase was stronger than that of arbutin. The K(i) value for alpha-arbutin was calculated to be 1/20 that for arbutin. We then synthesized arbutin-alpha-glycosides by the transglycosylation reaction of cyclomaltodextrin glucanotransferase using arbutin and starch, respectively, as acceptor and donor molecules. The structural analyses using 13C- and 1H-NMR proved that the transglycosylated products were 4-hydroxyphenyl beta-maltoside (beta-Ab-alpha-G1) and 4-hydroxyphenyl beta-maltotrioside (beta-Ab-alpha-G2). These arbutin-alpha-glycosides exhibited competitive type inhibition on human tyrosinase, and their K(i) values were calculated to be 0.7 mM and 0.9 mM, respectively. These arbutin-alpha-glycosides possessed stronger inhibitory activity than arbutin, but less activity than alpha-arbutin. These results suggested that the alpha-glucosidic linkage of hydroquinone-glycosides plays an important role in the inhibitory effect on human tyrosinase.     

Torsion potential works in rhodopsin

We investigate the role of protein environment of rhodopsin and the intramolecular interaction of the chromophore in the cis-trans photoisomerization of rhodopsin by means of a newly developed theoretical method. We theoretically produce modified rhodopsins in which a force field of arbitrarily chosen part of the chromophore or the binding pocket of rhodopsin is altered. We compare the equilibrium conformation of the chromophore and the energy stored in the chromophore of modified rhodopsins with those of native rhodopsins. This method is called site-specific force field switch (SFS). We show that this method is most successfully applied to the torsion potential of rhodopsin. Namely, by reducing the twisting force constant of the C11=C12 of 11-cis retinal chromophore of rhodopsin to zero, we found that the equilibrium value of the twisting angle of the C11=C12 bond is twisted in the negative direction down to about -80 degrees. The relaxation energy obtained by this change amounts to an order of 10 kcal/mol. In the case that the twisting force constant of the other double bond is reduced to zero, no such large twisting of the bond happens. From these results we conclude that a certain torsion potential is applied specifically to the C11=C12 bond of the chromophore in the ground state of rhodopsin. This torsion potential facilitates the bond-specific cis-trans photoisomerization of rhodopsin. This kind of the mechanism is consistent with our torsion model proposed by us more than a quarter of century ago. The origin of the torsion potential is analyzed in detail on the basis of the chromophore structure and protein conformation, by applying the SFS method extensively.     

CCSD calculations on C(14), C(18), and C(22) carbon clusters

The structure and energetics of the ring isomers of C(4n+2) (n=3-5) carbon clusters were studied by using coupled-cluster singles and doubles excitation theory to overcome the vast differences existing in the literature. The results obtained in the present study clearly indicate that C(14), C(18), and C(22) carbon rings have bond-length and bond-angle alternated acetylenic minimum energy structures. Contrarily, density functional theory calculations were unable to predict these acetylenic-type structures and they ended up with the cumulenic structures. It is found from the coupled-cluster studies that the lowest-energy ring isomer for the first two members of C(4n+2) series is a bond-angle alternated cumulenic D((2n+1)h) symmetry structure while the same for the remaining members is a bond-length and bond-angle alternated C((2n+1)h) symmetry structure. In C(4n+2) carbon rings, Peierls-type distortion, transformation from bond-angle alternated to bond-length alternated minimum energy structures, occurs at C(14) carbon ring.