Performance of the general amber force field in modeling aqueous POPC membrane bilayers

The aim of this work was to answer the question of whether the general amber force field (GAFF) is good enough to simulate fully hydrated POPC membrane bilayers. The test system contained 128 POPC and 2985 TIP3P water molecules. The equilibration was carried out in a nonarbitrary manner to reach the stable liquid-crystalline phase. The simulations were performed by using particle mesh Ewald electrostatics implemented in molecular dynamics packages Amber8 (NPT ensembles) and NAMD2 (NPgammaT ensembles). The computational results were assessed against the following experimental membrane properties: (i) area per lipid, (ii) area compressibility modulus, (iii) order parameter, (iv) gauche conformations per acyl chain, (v) lateral diffusion coefficients, (vi) electron density profile, and (vii) bound water at the lipid/water interface. The analyses revealed that the tested force field combination approximates the experimental values at an unexpectedly good level when the NPgammaT ensemble is applied with a surface tension of 60 mN m(-1) per bilayer. It is concluded that the GAFF/TIP3P combination can be utilized for aqueous membrane bilayer simulations, as it provides acceptable accuracy for biomolecular modeling.     

IPy2BF4-mediated transformation of n-pentenyl glycosides to glycosyl fluorides: a new pair of semiorthogonal glycosyl donors

Bis(pyridinium) iodonium(I) tetrafluoroborate (IPy2BF4), a solid and stable reagent, can be used to transform n-pentenyl orthoesters (NPOEs) and n-pentenyl glycosides (NPGs) into glycosyl fluorides. The latter pair constitutes a new set of semiorthogonal glycosyl donors that can be used in glycosylation strategies, alone or in combination with NPOEs.     

Structure and bonding in first-row transition metal dicarbide cations MC2+

A theoretical study of the first-row transition metal dicarbide cations MC2+ (M=Sc-Zn) has been carried out. Predictions for different molecular properties that could help in their eventual experimental detection have been made. Most MC2+ compounds prefer a C2v symmetric arrangement over the linear geometry. In particular, the C2v isomer is specially favored for early transition metals. Only for CuC2+ is the linear isomer predicted to be the global minimum, although by only 1 kcal/mol. In all cases the isomerization barrier between cyclic and linear species seems to be very small (below 2 kcal/mol). The topological analysis of the electronic density shows that most C2v isomers are T-shaped structures. In general, MC2+ compounds for early transition metals have larger dissociation energies than those formed by late transition metals. In most cases the dissociation energies for MC2+ compounds are much smaller than those obtained for their neutral analogues. An analysis of the bonding in MC2+ compounds in terms of the interactions between the valence orbitals of the fragments helps to interpret their main features.     

Water-soluble carbosilane dendrimers protect phosphorothioate oligonucleotides from binding to serum proteins

Treatment of dendriplexes formed between water-soluble carbosilane dendrimers and phosphorothioate oligodeoxynucleotides (ODN) with the anionic detergent sodium dodecyl sulfate disrupted the complexes indicating that the nature of the union in such dendriplexes is merely electrostatic. However, dendriplexes were not dissociated by serum proteins like bovine or human serum albumins, as assessed by gel electrophoresis and fluorescence experiments. This would imply a dendrimer-mediated protective effect able to prevent ODN interactions with serum proteins and additionally could translate into a reduction of the ODN doses needed to achieve the biological effects. The employment of carbosilane dendrimers as carriers may solve the problem of ODN kidnapping by plasmatic proteins as a key drawback for therapeutics involving ODNs. As examples, transfection processes on normal primary peripheral blood cells and diagnosis of HIV infection in the presence of serum have been assayed.     

Copper acetylacetonate anchored onto amine-functionalised clays

Copper (II) acetylacetonate was immobilised directly onto two clays, laponite (Lap) and K10-montmorillonite (K10), and after their amine functionalisation with (3-aminopropyl)triethoxysilane (APTES). All the materials were characterised by nitrogen adsorption isotherms at -196 degrees C, elemental analysis, TG-DSC, XRD, and IR spectroscopy. The K10-based materials were also characterised by XPS. The APTES-functionalised K10 showed higher copper loading than K10, indicating that the clay functionalisation enhanced the complex immobilisation; on the contrary, in Lap-based materials higher metal content was obtained by direct complex anchoring, probably due to the delaminated nature of Lap which induced the particles aggregation on functionalisation with APTES. All the results pointed out that the Cu complex was anchored onto the amine-functionalised clays by Schiff condensation between the amine groups of anchored APTES and the carbonyl groups of the acetylacetonate ligand, whereas direct immobilisation proceeded mostly through interaction between the metal centre and the clay surface hydroxyl groups.     

Effect of peracylation of beta-cyclodextrin on the molecular structure and on the formation of inclusion complexes: an X-ray study.

The molecular structures of peracylated beta-cyclodextrins (CDs)--heptakis(2,3,6-tri-O-acetyl)-beta-CD (TA), heptakis(2,3,6-tri-O-propanoyl)-beta-CD (TP), and heptakis(2,3,6-tri-O-butanoyl)-beta-CD (TB)--have been determined by single crystal X-ray structure analysis. Due to the lack of O2...O3' hydrogen bonds between adjacent glucose units of the peracylated CDs, the macrocycles are elliptically distorted into nonplanar boat-shaped structures. The glucose units are tilted with respect to the O4 plane to relieve steric hindrance between adjacent acyl chains. In TB, all glucose units adopt the common (4)C(1)-chair conformation and one butanoyl chain intramolecularly penetrates the cavity, whereas, in TA and TP, one glucose unit each occurs in (O)S(2)-skew-boat conformation and one acyl chain closes the O6 side like a lid. In each of the three homologous molecules the intramolecular self-inclusion and lidlike orientation of acyl chains forces the associated O5-C5-C6-O6 torsion angle into a trans-conformation never observed before for unsubstituted CD; the inclusion behavior of TA, TP, and TB in solution has been studied by circular dichroism spectroscopy with the drug molsidomine and several organic compounds. No inclusion complexes are formed, which is attributed to the intramolecular closure of the molecular cavity by one of the acyl chains.     

Determination of haloacetic acids in aqueous environments by solid-phase extraction followed by ion-pair liquid chromatography-electrospray ionization mass spectrometric detection.

Haloacetic acids (HAAs) were determined in different water samples by a new, fast and simple analysis method based on enrichment of 50-ml water samples at pH 1.8 by solid-phase extraction (SPE) followed by liquid chromatography (LC) separation and electrospray ionization mass spectrometric detection in the negative ionization mode. Deprotonated (M-H)-haloacetates and decarboxylated (M-COOH)- ions were detected. Different polymeric SPE sorbents were tested, and LiChrolut EN was found to be the best material for the extraction. Complete LC separation of all compounds could only be achieved by ion-pair chromatography using triethylamine as volatile ion-pairing reagent. The detection limits were in the low microg/l range. High microg/l concentration levels for the chlorinated and brominated haloacetates were found in drinking water from a drinking water treatment plant in Barcelona, and the corresponding tap water. In swimming pool water samples from Catalonia mg/l levels and in surface river water from Portugal microg/l values were detected. These results confirm other recent reports on the ubiquitous occurrence of HAAs in aqueous environments.     

电喷雾串联质谱分析附子炮制中的化学成分变化

利用电喷雾质谱方法(ESI-MS)分析了附子加辅料(甘草)炮制前后水煎液中二萜类生物碱在种类和含量方面的变化,通过加入内标化合物,建立了电喷雾质谱的半定量分析方法。此方法具有快速、准确、灵敏的特点,能够更加全面地反映中药配伍炮制过程中多种化学成分的含量变化,并能根据电喷雾串联质谱的分析结果鉴定配伍后产生的新的化学成分,在共煎液中的次乌头碱、中乌头碱和乌头碱的相对含量分别是单煎液中的5.67%、4.05%和4.88%。通过研究附子与甘草的单煎液、共煎液以及药渣中化学成分的变化,揭示了甘草作为辅料,在炮制过程中对附子减毒作用机理。     

Mono- and dinuclear five-coordinate cyclometalated palladium(II) compounds

Reaction of cyclometalated halide-bridged Pd(II) complexes 1-4 with the tertiary triphosphine ligand (Ph2PCH2CH2)2PPh (triphos) yielded complexes [((Ph2PCH2CH2)2PPh-P,P,P)Pd(N(Cy)=(H)C)C6H2(C(H)=N(Cy))Pd((Ph2PCH2CH2)2PPh-P,P,P)][ClO4]2 5, [Pd(C6H4-N=NC6H5)((Ph2PCH2CH2)2PPh-P,P,P)][ClO4] 6, and [Pd(R-C6H3C(H)=NCy)((Ph2PCH2CH2)2PPh-P,P,P)][ClO4] (7; R = 4-CHO, 8; 3-CHO). Spectroscopic and analytic data suggest five-coordination on the palladium atom, which, for complexes 5, 6, and 7, was confirmed by X-ray crystallography. The geometry around palladium may be view as a distorted trigonal bipyramid, with the palladium, nitrogen, and terminal phosphorus atoms in the equatorial plane. Compound 5 is the first doubly cyclometalated palladium(II) compound with two pentacoordinated metal centers. The structure of 6 comprises two discrete cations with slightly different geometries, showing the importance of crystal packing forces in order to determine the coordination arrangement.     

Pt- (and Co-) Promoted Molybdena-Alumina Catalysts: Analysis of the Impregnation Steps

The equilibrium parameters for the adsorption of Mo(VI) on gamma-Al(2)O(3) and of Co(II) and Pt(IV) on MoO(3)/gamma-Al(2)O(3) were determined. The adsorption isotherms were performed from aqueous solutions of the corresponding precursors on two different alumina supports. According to the classification given by Giles, L-type-shaped, subgroup 2, adsorption curves were found for the system Mo on gamma-Al(2)O(3), L-type, subgroup 1, for the Pt on MoO(3)/gamma-Al(2)O(3), and S-type for Co on the MoO(3)/gamma-Al(2)O(3) system. Numerical calculations were carried out for all the isotherms to find the equilibrium parameters. These constants are being used to model the development of Pt, Co, and Mo profiles on MoO(3)/gamma-Al(2)O(3) or gamma-Al(2)O(3) extrudates, respectively, which belong to the new generation of noble-metal-MoO(3)/gamma-Al(2)O(3)-supported catalysts to be used in oil-refining processes. Copyright 2001 Academic Press.