Hydration free energies and entropies for water in protein interiors

Free energy calculations for the transfer of a water molecule from the pure liquid to an interior cavity site in a protein are presented. Two different protein cavities, in bovine pancreatic trypsin inhibitor (BPTI) and in the I76A mutant of barnase, represent very different environments for the water molecule: one which is polar, forming four water-protein hydrogen bonds, and one which is more hydrophobic, forming only one water-protein hydrogen bond. The calculations give very different free energies for the different cavities, with only the polar BPTI cavity predicted to be hydrated. The corresponding entropies for the transfer to the interior cavities are calculated as well and show that the transfer to the polar cavity is significantly entropically unfavorable while the transfer to the nonpolar cavity is entropically favorable. For both proteins an analysis of the fluctuations in the positions of the protein atoms shows that the addition of a water molecule makes the protein more flexible. This increased flexibility appears to be due to an increased length and weakened strength of protein-protein hydrogen bonds near the cavity.     

Structural determination of neutral O-linked oligosaccharide alditols by negative ion LC-electrospray-MS<Superscript>n</Superscript>.

Neutral O-linked oligosaccharides released from the salivary mucin MUC5B were separated and detected by negative ion LC-MS and LC-MS(2). The resolution of the chromatography and the information obtained from collision induced dissociation of detected [M - H](-) ions were usually sufficient to identify the sequence of individual oligosaccharides, illustrated by the fact that 50 different oligosaccharides ranging from disaccharides to nonasaccharides could be assigned from the sample. Fragmentation was shown to yield mostly reducing end sequence fragments (Z(i) and Y(i)), enabling primary sequence assignment. Specific fragmentation pathways or patterns were also detected giving specific linkage information. The reducing end core (Gal/GlcNAcbeta1-3GalNAcol or Gal/GlcNAcbeta1-3(GlcNAcbeta1-6)GalNAcol) could be deduced from the pronounced glycosidic C-3 cleavage and A(i) type cleavages of the reducing end GalNAcol, together with the non reducing end fragment from the loss of a single substituted GalNAcol. Substitution patterns on GlcNAc residues were also found, indicative for C-4 substitution ((0,2)A(i) - H(2)O cleavage) and disubstitution of C-3 and C-4 (Z(i)/Z(i) cleavages). This kind of fragmentation can be used for assigning the mode of chain elongation (Galbeta1-3/4GlcNAcbeta1-) and identification of Lewis type antigens like Lewis a/x and Lewis b/y on O-linked oligosaccharides. In essence, negative ion LC-MS(2) was able to generate extensive data for understanding the overall glycosylation pattern of a sample, especially when only a limited amount of material is available.     

Sodium hexadecanoate micellar aggregation number

The diffusion coefficient of sodium hexadecanoate micelles was studied by polarography at 63°C, and the size and aggregation number of the micelles was computed. At concentrations above 0.01 mol·L^–1 rodlike micelles exist, which become flexible at 0.040 mol·L^–1 and entangle at 0.043 mol·L^–1     

Effect of NaOH and NaCl on the disodiumn-decane phosphonate micellar aggregation number

The diffusion coefficient of disodiumn-decane phosphonate micelles was studied by polarography at 25°C in NaCl and in NaOH solutions, and the size and aggregation number of the micelles was computed as a function of Na⁺ concentration. All other conditions being equal, the addition of NaCl produces micelles with an aggregation number one order of magnitude larger than the NaOH addition. This is due to the increase of the effective charge per micellized head group produced by the reaction of OH- with the hydrolized head groups which are mainly present as-PO₃H- in the micellar Stern layer.     

Micro raman spectroscopy on a single carbon fibre under stress

An example is given for the application of Raman spectroscopy in material characterization. Raman spectra of carbonaceous materials obtained with the microscope attachment have been used to study orientation of graphite planes in a single carbon fibre under stress with a lateral resolution of 1 m.Dedicated to Professor Dr. H. Kriegsmann on the occasion of his 70th birthday     

Reactive scattering of sodium clusters with molecular oxygen

The first reactive differential scattering study for atomic clusters is reported. Oxidation of Na _x (x8) with O₂ is investigated in a crossed beam apparatus. Sodium oxide (Na _n O,n4) and sodium dioxide (Na _n O₂,n6) are produced with a total reactive cross section from 50 to 80 Ų, depending on the cluster size. The excess energies for these reactions are estimated by an SCF type ab initio calculation and range from 0.5 to 5 eV. The large cross section may then be understood quantitatively in terms of a harpooning mechanism as a first step in the reaction path. Angular distributions have been determined for the most abundant products, showing strong forward scattering. Two different schemes are discussed for the reaction: while the dioxides Na _n O₂ may be formed by an evaporative cooling process from a highly excited collision complex, formation of Na _n O appears to originate from a direct process. In both cases the experimental data suggest that most of the exothermicity remains in the reaction products.     

Binary pnictogen azides--an experimental and theoretical study: [As(N3)4]-, [Sb(N3)4]-, and [Bi(N3)5(dmso)]2-

[PPh(4)][EI(4)] (E=As, Sb, Bi) salts were reacted with four and five equivalents of AgN(3) to form tetraazidopnictates and pentaazidopnictates of the type [PPh(4)][E(N(3))(4)] and [PPh(4)](2)[E(N(3))(5)], respectively. The synthesis of [PPh(4)][P(N(3))(4)] was also attempted from the reaction of P(N(3))(3) with [PPh(4)]N(3), but it yielded only the starting materials. Herein, we report the synthesis and structure elucidation of [PPh(4)][E(N(3))](4) (E=As, Sb) and pentaazidobismuthate, stabilized as the dimethyl sulfoxide (DMSO) anion adduct, [PPh(4)](2)[Bi(N(3))(5)(dmso)]. Successive anion formation along the series E(N(3))(3)+nN(3)(-) (n=1-3) and E(N(3))(5)+N(3)(-) was studied by density functional theory.     

Formation of N719 dye multilayers on dye sensitized solar cell photoelectrode surfaces investigated by direct determination of element concentration depth profiles

The structure of the dye layer adsorbed on the titania substrate in a dye-sensitized solar cell is of fundamental importance for the function of the cell, since it strongly influences the injection of photoelectrons from the excited dye molecules into the titania substrate. The adsorption isotherms of the N719 ruthenium-based dye were determined both with a direct method using the depth profiling technique neutral impact collision ion scattering spectroscopy (NICISS) and with the standard indirect solution depletion method. It is found that the dye layer adsorbed on the titania surface is laterally inhomogeneous in thickness and there is a growth mechanism already from low coverage levels involving a combination of monolayers and multilayers. It is also found that the amount of N719 adsorbed on the substrate depends on the titania structure. The present results show that dye molecules in dye-sensitized solar cells are not necessarily, as presumed, adsorbed as a self-assembled monolayer on the substrate.     

Cluster size selectivity in the product distribution of ethene dehydrogenation on niobium clusters

Ethene reactions with niobium atoms and clusters containing up to 25 constituent atoms have been studied in a fast-flow metal cluster reactor. The clusters react with ethene at about the gas-kinetic collision rate, indicating a barrierless association process as the cluster removal step. Exceptions are Nb8 and Nb10, for which a significantly diminished rate is observed, reflecting some cluster size selectivity. Analysis of the experimental primary product masses indicates dehydrogenation of ethene for all clusters save Nb10, yielding either Nb(n)C2H2 or Nb(n)C2. Over the range Nb-Nb6, the extent of dehydrogenation increases with cluster size, then decreases for larger clusters. For many clusters, secondary and tertiary product masses are also observed, showing varying degrees of dehydrogenation corresponding to net addition of C2H4, C2H2, or C2. With Nb atoms and several small clusters, formal addition of at least six ethene molecules is observed, suggesting a polymerization process may be active. Kinetic analysis of the Nb atom and several Nb(n) cluster reactions with ethene shows that the process is consistent with sequential addition of ethene units at rates corresponding approximately to the gas-kinetic collision frequency for several consecutive reacting ethene molecules. Some variation in the rate of ethene pick up is found, which likely reflects small energy barriers or steric constraints associated with individual mechanistic steps. Density functional calculations of structures of Nb clusters up to Nb(6), and the reaction products Nb(n)C2H2 and Nb(n)C2 (n = 1...6) are presented. Investigation of the thermochemistry for the dehydrogenation of ethene to form molecular hydrogen, for the Nb atom and clusters up to Nb6, demonstrates that the exergonicity of the formation of Nb(n)C2 species increases with cluster size over this range, which supports the proposal that the extent of dehydrogenation is determined primarily by thermodynamic constraints. Analysis of the structural variations present in the cluster species studied shows an increase in C-H bond lengths with cluster size that closely correlates with the increased thermodynamic drive to full dehydrogenation. This correlation strongly suggests that all steps in the reaction are barrierless, and that weakening of the C-H bonds is directly reflected in the thermodynamics of the overall dehydrogenation process. It is also demonstrated that reaction exergonicity in the initial partial dehydrogenation step must be carried through as excess internal energy into the second dehydrogenation step.