No description available.

No description available.

We have developed a novel computational approach to functional de novo protein design using gradient based continuous optimization techniques. Motivated by many engineering applications in which a cost function is optimized subject to a set of constraints, we pose a functional protein design task as a continuous optimization problem to search sequence and conformation spaces simultaneously. The methods used in sequence-space search are analogous to the material-design formulations in the topology optimization of structures, whereas the conformation search techniques are similar to mechanical-link like models and modal analysis of structures. Computationally efficient techniques such as the nonlinear conjugate gradient and interior point optimization are used to solve optimization problems. Both the sequence and conformation search techniques are individually validated with real proteins. Coarse-grained as well as atomistic potentials are used to model the energy. Finally, we combine the sequence and conformation search methods and propose a new strategy for a simultaneous search in sequence and conformation spaces for designing functional de novo proteins. In view of the lack of experimental resources, the proposed computational scheme is validated by re-designing an existing protein, the hen-egg white lysozyme. Since the thrust of this method is on developing computationally efficient models, we developed an amino acid grouping scheme based on metric multi-dimensional scaling. Some structure-prediction problems are also solved using Graphics Processing Unit (GPU) based Compute Unified Device Architecture (CUDA) programming.

The 207Pb and 119Sn NMR chemical shift were used to study the effect of temperature on Ph3MCl (M= Pb and Sn) adducts in the presence of 10% excess pyridine. The 207Pb and 119Sn chemical shift indicate a slow exchange at low temperatures below -90 0C and a significant exchange at higher temperatures above 10 0C. A plot of temperature against 207Pb or 119Sn chemical shift showed a curve with gentle slope at lower and a steep slope at higher temperatures. A good linear correlation (coefficient. of 0.95) between Hammett substituent constant and 207Pb or 119Sn chemical shift of para-substituted derivatives of Ph3MCl.py* (py* = NMe2, OMe, Me, Ph, H, Br, COPh and COMe; at -90 0C in CD2Cl2/CH2Cl2) was found. Both 207Pb and 119Sn chemical shift ranges are characteristic of five coordinate systems resolving into trigonal bipyramidal geometry as shown by X-ray crystal structures. New complexes of the type [CpFe(CO)(SnPh3)L] (L = PPh3, PBu3, PCy3, PMe3, P(NMe2)3, PMePh2, PMe2Ph, P(p-FC6H5)3, P(p-OMeC6H4)3, P(p-tolyl)3, P(OMe)3, and P(OPh)3 were synthesized by ultraviolet irradiation of [CpFe(CO)2(SnPh3)] and the appropriate phosphine or phosphite ligand. 57Fe NMR studies of the complexes showed an increasing linear relationship with Tolman’s steric parameter, whereas with Tolman’s electronic parameter the 57Fe chemical shift showed a decrease. The X-ray crystallographic profile of the selected new piano stool type complexes shows a significant correlation to the NMR data (solution state), i.e. Fe-Sn, Fe-P bond length and Sn-Fe-P bond angle against chemical shifts of 207Pb and 119Sn. Disubstituted complexes of the type [CpFe(SnPh3)L2] (L = PMe3, PMe2Ph, P(OMe)3 and P(OPh)3 were synthesized under similar conditions as monosubstituted compounds. The correlation trends between the NMR data and X-ray crystallographic profiles are similar to those found for monocarbonylated complexes. Tungsten phosphine complexes of the type [W(CO)5(PR3)] (prepared from [W(CO)6] under thermal conditions) and [W(CO)4(NCMe)(PR3)] (prepared from [W(CO)5(PR3)] by use of Me3NO-promoted decarbonylation) were synthesized and characterized by, among other methods X-ray diffraction techniques (R = Ph, p-tolyl, p-OMeC6H4, p-FC6H4, p-CF3C6H4, and NMe2). The tungsten complexes [W(CO)4(NCMe)(PR3)] react with [(dppp)Pt{C≡C-C5H4N}2] at room temperature to form new complexes of the type [(dppe)Pt{C≡C-C5H4N-W(CO)4(PR3)}2] which were characterized unambiguously by NMR spectroscopy. There is a fair correlation between 195Pt and 183W NMR chemical shifts and Tolman’s electronic parameter which indicates a fair influence by the substituents of the phosphorus atom on both metal centres. Tungsten complexes of the type [W(CO)4(NCMe)(L)] (L= PPh3, P(p-FC6H4)3, P(p-OMeC6H4)3, P(p-tolyl)3, P(p-CF3C6H4)3, PMePh2, and PPh2(C6F5) react with [(PPh3)2Rh(H)2(pytca)] (pytca = 2-(4-pyridyl)thiazole-4-carboxylate) to form new complexes of the type [(PPh3)2Rh(H)2(pytca)- W(CO)4(L)] under mild conditions. These complexes were characterized principally by NMR spectroscopy and X-Ray crystallography (L = P(p-tolyl)3). Crystallographic evidence was found for π-π-π interactions involving two phenyl rings, one of the two phosphines bonded to rhodium atom, one of the three phosphines bonded to tungsten and the pyridyl ring of the thiazole corboxylate group. A second π-π interaction is found between a thiazole and a phenyl ring of the phosphine ligand bonded to the rhodium atom. A fair correlation was found between the rhodium and tungsten chemical shift measured from this series of complexes as a result of varied paraphenyl substituent of phosphine ligand bonded to the tungsten atom. This therefore implies the possible existence of electronic communication between the two bridged metal centres.

No description available.

We discuss the role of symmetries in the dissociative recombinations (DR) of three polyatomic ions, namely the linear HCO+ (formyl) ion and the two highly symmetric H+3 and H3O+ (hydronium) molecular ions. Regarding the HCO+ ion, we apply a quantum mechanical treatment using the Multi-channel Quantum Defect Theory (MQDT) formalism to describe the ion-electron scattering process. Our study takes into account the Renner-Teller effect in order to model the non Born-Oppenheimer vibronic coupling in linear polyatomic ions. The coupling has shown to represent the main mechanism responsible for electronic capturing in highly excited Rydberg states associated with excited vibrational levels of the ionic core. We consider all internal degrees of freedom of HCO+ and obtain the dissociative cross section as a function of the incident electron kinetic energy. We have also improved the theoretical approach by including the large permanent dipole moment of HCO+ using a generalization of the MQDT formalism. To our knowledge, this is the rst time the permanent dipole moment of an ion is included in a DR study. The obtained results are in good agreement with experimental data. We also study the DR of H+3 and H3O+ symmetric ions using a simpli ed theoretical treatment, which focuses on the key ingredient of the DR process, the electron capture in the rst excited degenerate vibrational normal mode of the ions through non Born-Oppenheimer Jahn-Teller coupling. For both ions the obtained cross sections are in very good agreement with the available experimental data. Moreover, in the case of H+3 , the results reproduce previous calculations from two independent theoretical studies. Finally, we investigate the role of symmetries in few body ultra-cold collisions by considering both three and four identical atoms systems. We derive allowed rearrangements of different fragments of the system, satisfying the complete symmetry of the molecular Hamiltonian. For that purpose we establish a correspondence between constants of motion of the system in di erent large-distance con gurations and irreducible representations of the total symmetry group. Selection rules (forbidden transitions) and allowed states, which depend on the fermionic or bosonic nature of the atoms, can be derived from these results.

No description available.

The investigation of the rotational spectra of fluoroformyliminosulfur difluoride, SF2NCOF, and pentafluorosulfanyliminosulfur difluoride, SF2NSF5 , was undertaken to determine, from the experimental moments Q.f inertia, the number and type of positional isomers and the bonding parameters. SF2NCOF and SF2NSF5 are the first iminosulfur difluorides (RN=SF2) to be investigated by microwave spectroscopy. The iminosulfur difluorides are characterized by a nitrogen-sulfur double bond with nonbonding pairs of electrons in an sp2 hybridized orbital on the nitrogen atom and in an sp3 hybridized orbital on the sulfur atom. This bonding scheme is expected to impart a unique charge distribution in the vicinity of the SF2 fluorines. In SF2NCOF the nitrogen-carbon bond may acquire some partial double bond character which can be described through resonance involving the S, N, C, and 0 atoms. The extent of this resonance would be expected to affect the length of the NC bond and to influence the height of the barrier to rotation about this bond. For SF2NCOF and SF2NSF51 the question of cis-trans conformation about the nitrogen-sulfur double bond will be considered. Additionally, several rotameric forms of SF2NCOF which can arise from rotation about the nitrogen-carbon axis and which cannot be definitely precluded by presumptive reasoning will also be examined. / Ph. D.

The interphase region at modified polymer surfaces or at polymer\ metal interfaces may be critical in determining the strength and durability in adhesive applications. Methods to investigate these regions are limited however and this research has focused on the use of infrared reflection absorption spectroscopy (IRRAS) and x-ray photoelectron spectroscopy (XPS) to investigate the molecular structure of both modified and unmodified thin films. The optical constants of polyphenylene sulfide (PPS) were determined and exact optical theory was utilized to simulate spectra for a variety of reflectance techniques. This method was also utilized to confirm the ordered state of thin spin coated PPS films. The surface modification of polystyrene, polyphenylene sulfide, and poly(arylene ether) phosphine oxides was also examined by these techniques and optical theory used to optimize experimental conditions. Results after plasma treatment indicated a very thin modified surface layer (< 10 nm) where the thickness and specific surface chemistry depended on the polymer and plasma gas used. The interaction of an epoxy resin with a surface modified PPS film showed that while most of the modified surface layer is removed after this treatment, a remaining amount can serve to cross-link a thin adsorbed epoxy film. Results for the oxygen plasma treatment of poly(arylene ether) phosphine oxides showed the formation of a surface phosphate layer that inhibited further plasma etching. The kinetics of formation and the particular chemistry involved were examined in detail. A new technique, variable temperature reflection absorption spectroscopy (VTRAS) was developed as a method to investigate the reorganization of thin PPS films on a variety of substrates. Both the crystallization and melting temperatures could be determined for quenched coatings on a variety of substrates. While degradation under vacuum was not observed on chromium and aluminum surfaces, PPS films on copper surfaces showed a loss in crystallizability, and did not return to the original ordered state after exposure to temperatures near 300°C. Loss of cuprous oxide was also observed, and chain scission mechanisms were postulated. Additional measurements on thin sputtered cuprous oxide films showed less degradation for the same temperature treatments, emphasizing the role of the underlying metal in the degradation process. Spin coated films of polyetherimide were shown to be oriented after spin coating, and the relaxation to a more random state could also be observed by the VTRAS technique. Degradation of PPS films in air was examined and the diffusion of copper species into the bulk of the film with the formation of copper carboxylates was observed. The use of the VTRAS technique in air also was useful in determining the temperature needed for the onset of degradation. Bonded PPS/copper laminates were investigated and results showed that the particular surface chemistry was crucial in determining the peel strength observed. After a simple thermal! oxidation pretreatment for copper foil, an increase in the peel strength of almost one order of magnitude was observed over non-oxidized foils. Chemical oxidation with alkaline persulfate solutions resulted in a needle-like surface oxide morphology, and bond strengths were also increased by this pretreatment method. Failure surface analysis and model interaction studies with PPS tetramer showed that the formation of excess cuprous sulfide at the interface was the most probable cause of poor adhesion in these systems. Foil pretreatment by thermal oxidation gave the highest peel strength, and also exhibited the lowest amount of interfacial cuprous sulfide. / Ph. D.

No / The synthesis of 1,1-thiodisaccharide trehalose analogues in good to excellent yields by a Lewis acid (BF(3).Et(2)O)-catalysed coupling of sugar per-O-acetate with thiosugar is described. The reactivity of different sugar per-O-acetates and thiosugars is explored.