Computer optimization of small atomic clusters

We have successfully identified stable configurations of both rare-gas and NaCl clusters with a new optimization procedure. An initial cluster configuration is prepared in a so-called shoot-and-stay process. Its total energy is then minimized with respect to the atomic coordinates. To prevent the system from being locked in local minima, the step size of each move is chosen as the width of the energy well at a higher level. As the system evolves, the global minimum is contained in the volume bounded by the decreasing value of step sizes. We have also carried out the optimization of NaCl clusters by the simulated annealing technique, for comparison. The results show that for such heterogeneous systems, the latter method cannot always find the global minimum, because of large energy gaps between different catchment regions in phase space.     

Syntheses totales et etudes de lignanes biologiquement actifs—I : Application de la reaction d'ullmann a la synthese de biaryles precurseurs de lignanes bisbenzocyclooctadienes

Several biaryls bearing various substituents on both rings were synthesized in a preparative fashion, and in yields up to 88% by a technical improvement on the classical Ullmann reaction. All these biaryls bear reactive functional groups (i.e. formyl, methoxycarbonyl, dimethoxycarbonylpropyl and butanolidylmethyl) in both the o and o′ positions. The biaryls 9, 13, 21 and 26–33 are plausible synthons for bisbenzocyclooctadiene lignans such as schizandrin and steganacin.     

Evaluation of enzymatic digestion and liquid chromatography-mass spectrometry peptide mapping of the integral membrane protein bacteriorhodopsin

A method for the complete peptide mapping of the model integral membrane protein bacteri-orhodopsin is demonstrated. Utilizing more effective enzymatic digestion, procedures with capillary liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) and tandem mass spectrometry (MS/MS), all predicted tryptic digestion products were detected, as well as peptides from all previously reported post-translational modifications of bacteriorhodopsin. A significant contribution of chymotryptic-like digestion products was also observed. A characterization of the behavior of hydrophobic integral membrane peptides in a reversed-phase liquid chromatographic separation is also provided. The method reported here offers improved compatibility of the solubilizing reagents with both the chromatography and mass spectrometry, rendering it suitable for high-throughput proteomic applications.     

Studies of chromium cages and wheels

Studies of two distinct classes of chromium(III) cage complexes are discussed. The first are compact oxo- and carboxylate cages, made by heating precursors to high temperature under a flow of nitrogen. One of these cages, [Cr₁₂O₉(OH)₃(O₂CCMe₃)₁₅], has an S = 6 spin ground state which proves a very interesting subject for study by EPR and MCD spectroscopy. Use of other carboxylates leads to other octa- and dodeca-nuclear complexes. The second class of compounds are homo- and hetero-metallic wheels and chains bridged by fluoride and carboxylates. These include the first heterometallic anti-ferromagnetically coupled ring systems and are being widely studied in areas as diverse as magnetic cooling and quantum information processing. The mechanism by which these unusual cyclic and acyclic structures form is discussed.     

A biological process for the reclamation of flue gas desulfurization gypsum using mixed sulfate-reducing bacteria with inexpensive carbon sources

A combined chemical and biological process for the recycling of flue gas desulfurization (FGD) gypsum into calcium carbonate and elemental sulfur is demonstrated. In this process, a mixed culture of sulfate-reducing bacteria (SRB) utilizes inexpensive carbon sources, such as sewage digest or synthesis gas, to reduce FGD gypsum to hydrogen sulfide. The sulfide is then oxidized to elemental sulfur via reaction with ferric sulfate, and accumulating calcium ions are precipitated as calcium carbonate using carbon dioxide. Employing anaerobically digested municipal sewage sludge (AD-MSS) medium as a carbon source, SRBs in serum bottles demonstrated an FGD gypsum reduction rate of 8 mg/L/h (10⁹ cells)^-1. A chemostat with continuous addition of both AD-MSS media and gypsum exhibited sulfate reduction rates as high as 1.3 kg FGD gypsum/m³d. The increased biocatalyst density afforded by cell immobilization in a columnar reactor allowed a productivity of 152 mg SO₄ ^-2/Lh or 6.6 kg FGD gypsum/m³d. Both reactors demonstrated 100% conversion of sulfate, with 75–100% recovery of elemental sulfur and chemical oxygen demand utilization as high as 70%. Calcium carbonate was recovered from the reactor effluent on precipitation using carbon dioxide. It was demonstrated that SRBs may also use synthesis gas (CO, H₂, and CO₂ in the reduction of gypsum, further decreasing process costs. The formation of two marketable products—elemental sulfur and calcium carbonate—from FGD gypsum sludge, combined with the use of a low-cost carbon source and further improvements in reactor design, promises to offer an attractive alternative to the landfilling of FGD gypsum.

     

Relative molecular mass information from aliphatic nitro compounds: A chemical ionization study

The mass spectra of a number of aliphatic nitro compounds have been studied using electron Ionization (EI) and a variety of chemical Ionization (CI) techniques in attempts to obtain relative molecular mass information. The use of positive ion ammonia chemical Ionization techniques gave very satisfactory results, providing abundant [M + NH4]⁺ ions, not only from both primary and secondary nitro compounds, but also from the much more labile tertiary nitro compounds. However, the use of methane and isobutane positive ion CI or EI conditions resulted in facile fragmentation with little relative molecular mass information being made available. Negative ion CI using methane, isobutane or ammonia as moderating gases all gave abundant [M ? 1]^? ions with primary and secondary nitro compounds but at much reduced sensitivity.     

Mechanism of UV photoreactivity of alkylsiloxane self-assembled monolayers

A molecular level understanding of the photoreactivity of self-assembled monolayers (SAMs) becomes increasingly important as the spatial resolution starts to be limited by the size of the resist and the spatial extent of the photochemical reactions in photoresist micropatterning. To this end, a number of surface characterization techniques were combined to understand the reactive agents, reactive sites, kinetics, and reaction pathways in the UV photoreactivity of octadecylsiloxane (ODS) SAMs. Quantitative analysis of our results provides evidence that ground state atomic oxygen is the primary reactive agent for the UV degradation of ODS SAMs. UV degradation, which follows zero-order kinetics, results in the scission of alkyl chains instead of the siloxane headgroups. Our results suggest that the top of the ODS SAMs is the preferential reactive site. Using a novel, highly surface sensitive technique, fluorescence labeling of surface species, we identified the presence of submonolayer quantities chemical functional groups formed by the UV degradation. These groups are intermediates in a proposed mechanism based on hydrogen abstraction.     

Quantum correspondence to classical chaos

A simple analysis of the competition between the alternative channels of atom and excitation transfer in collisions of metastable rare-gas atoms with halogens is presented. The intervention of potential surfaces correlating with highly excited Rydberg states lying just below the limit of the molecular cation as well as those which correlate with the anion provides a qualitative rationale for much current experimental data.     

Assessing the efficiency of free energy calculation methods

The efficiencies of two recently developed methods for calculating free energy changes along a generalized coordinate in a system are discussed in the context of other, related approaches. One method is based on Jarzynski's identity [Phys. Rev. Lett. 78, 2690 (1997)]. The second method relies on thermodynamic integration of the average force and is called the adaptive biasing force method [Darve and Pohorille, J. Chem. Phys. 115, 9169 (2001)]. Both methods are designed such that the system evolves along the chosen coordinate(s) without experiencing free energy barriers and they require calculating the instantaneous, unconstrained force acting on this coordinate using the formula derived by Darve and Pohorille. Efficiencies are analyzed by comparing analytical estimates of statistical errors and by considering two numerical examples-internal rotation of hydrated 1,2-dichloroethane and transfer of fluoromethane across a water-hexane interface. The efficiencies of both methods are approximately equal in the first but not in the second case. During transfer of fluoromethane the system is easily driven away from equilibrium and, therefore, the performance of the method based on Jarzynski's identity is poor.     

Thin film platinum cuff electrodes for neurostimulation: in vitro approach of safe neurostimulation parameters

Thin film technology takes more and more importance in the development of biomedical devices dedicated to functional neurostimulation. Our research about the design of implant neurostimulating electrode is oriented toward thin film cuff electrodes based on a polyimide substrate covered by a chromium/gold/Pt film. The chromium/gold sputtered film serves as adhesion layer and current collector whereas platinum acts as an electrochemical actuator. The electrode surface has been designed to obey safe stimulation criteria (i.e. chemically inert noble metal, low electrode-electrolyte impedance, high electrochemical reversibility, high corrosion stability). The electrochemical behaviour of such platinum electrodes has been assessed and compared to a foil of platinum. Extensive in vitro characterisations of the both electrode types were carried out using AFM, SEM and electrochemical techniques. The role of enhanced surface roughness enabling high double layer capacitances to be achieved was clearly highlighted. The obtained results are discussed, with particular reference to thin film electrodes stability under in vitro electrical stimulation in NaCl 0.9% (physiological serum). Therefore, these thin film devices showed reversible PtOH formation and decomposition making them potentially attractive for the fabrication of implant stimulation cuff electrodes.