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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.

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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.

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.

Yes / Ionic systems with enhanced proton conductivity are widely viewed as promising electrolytes in fuel cells and batteries. Nevertheless, a major challenge toward their commercial applications is determination of the factors controlling the fast proton hopping in anhydrous conditions. To address this issue, we have studied novel proton-conducting materials formed via a chemical reaction of lidocaine base with a series of acids characterized by a various number of proton-active sites. From ambient and high pressure experimental data, we have found that there are fundamental differences in the conducting properties of the examined salts. On the other hand, DFT calculations revealed that the internal proton hopping within the cation structure strongly affects the pathways of mobility of the charge carrier. These findings offer a fresh look on the Grotthuss-type mechanism in protic ionic glasses as well as provide new ideas for the design of anhydrous materials with exceptionally high proton conductivity.