Free energy perturbation approach to the critical assessment of selective cyclooxygenase-2 inhibitors

The discovery of selective cyclooxygenase-2 (COX-2) inhibitors represents a major achievement of the efforts over the past few decades to develop therapeutic treatments for inflammation. To gain insights into designing new COX-2-selective inhibitors, we address the energetic and structural basis for the selective inhibition of COX isozymes by means of a combined computational protocol involving docking experiment, force field design for the heme prothetic group, and free energy perturbation (FEP) simulation. We consider both COX-2- and COX-1-selective inhibitors taking the V523I mutant of COX-2 to be a relevant structural model for COX-1 as confirmed by a variety of experimental and theoretical evidences. For all COX-2-selective inhibitors under consideration, we find that free energies of binding become less favorable as the receptor changes from COX-2 to COX-1, due to the weakening and/or loss of hydrogen bond and hydrophobic interactions that stabilize the inhibitors in the COX-2 active site. On the other hand, COX-1-selective oxicam inhibitors gain extra stabilization energy with the change of residue 523 from valine to isoleucine because of the formations of new hydrogen bonds in the enzyme-inhibitor complexes. The utility of the combined computational approach, as a valuable tool for in silico screening of COX-2-selective inhibitors, is further exemplified by identifying the physicochemical origins of the enantiospecific selective inhibition of COX-2 by -substituted indomethacin ethanolamide inhibitors.     

Extremality and the global Markov property II: The global markov property for non-FKG maximal Gibbs measures

We give a condition on a Gibbs measure for an attractive Markov specification, which assures extremality and the global Markov property. As an example of application we consider the class of attractive Markov specifications defined on a compact configuration space over a two-dimensional lattice by the interaction Hamiltonians (assumed to have a finite set of periodic ground configurations) satisfying Peierl's condition. We prove that each extremal Gibbs measure for such a specification, at sufficiently low temperature, has the global Markov property.On leave of absence from the Institute of Theoretical Physics, University of Wrocaw, Poland.     

AFM of adsorbed polyelectrolytes on cellulose I surfaces spin-coated on silicon wafers

Thin layers of cellulose I nanocrystals were spin-coated onto silicon wafers to give a flat model cellulose surface. A mild heat treatment was required to stabilize the cellulose layer. Interactions of this surface with polyelectrolyte layers and multilayers were probed by atomic force microscopy in water and dilute salt solutions. Deflection–distance curves for standard silicon nitride tips were measured for silicon, cellulose-coated silicon, and for polyelectrolytes adsorbed on the cellulose surface. Transfer of polymer to the tip was checked by running deflection–distance curves against clean silicon. Deflection–distance curves were relatively insensitive to adsorbed polyelectrolyte, but salt addition caused transfer of cationic polyelectrolyte to the tip, and swelling of the polyelectrolyte multilayers.     

A force field study of diacetylene molecule by kinetic constant method

The potential constants of diacetylene molecule has been evaluated using kinetic constants. The other molecular constants such as the generalised vibrational mean amplitudes, shrinkage constants, Coriolis coupling constants and centrifugal distortion constants are also calculated using the vibrational frequencies and the results discussed.     

Reduced parabolic model for radical addition reactions

The transition state of addition of free radicals and atoms to multiple bonds is considered as a result of intersecting of two parabolic potential curves. One of them characterizes the stretching vibration of the attacked multiple bond, and another curve characterizes the stretching vibration of the bond formed in the transition state. The force constant of the latter is calculated by an empirical equation that correlates the force constant with the bond dissociation energy. In the framework of this model, the thermally neutral activation energy (E _e0) and the elongation of the attacked and formed bonds (r _e) in the transition state were calculated from the experimental data (activation energy (E _e) and enthalpy of reaction (H _e)) for the addition of an H atom and methyl, alkoxyl, aminyl, triethylsilyl, and peroxyl radicals to the C=C bond and the addition of H and CH₃ to the C=O and CC bonds. Analysis of the data obtained showed that E _e0 depends linearly on the |H _e| + E_e sum, i.e., E_e0/kJ mol^–1 = 14.2 + 0.61 · (E_e – H _e), and the bond elongation in the transition state for addition of the most part of radicals to ethylene and acetylene vary within (0.65–0.87)·10_–10 m. The factors affecting the activation energy of the radical addition reactions are discussed.Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1542–August, 2004.     

Measurement of attachment force of microbial cells

A parallel-plate flow chamber consisting of two transparent electro-conductive glass plates was constructed. The two glass plates were set parallel to each other and connected to a potentiostat apparatus to regulate the strength of the electric field between the plates. A microbial cell suspension was flowed through the chamber. This system enabled the application of an electrostatic force to suspend charged particles, e.g. microbial cells, existing between the two plates. The time course of the cell attachment of Pseudomonas syringae pv. atropurpurea NIAES 1309 suspended in 10 mM phosphate buffer solution (pH 7.0) to the glass plate was investigated at various electric field strengths ranging from −4.2 to +4.1 V cm⁻¹. The attachment rate and the maximum number of attached cells increased linearly with the increase in the strength of the positive electric field. In contrast, the rate and the number of cells decreased linearly with the decrease in the strength of the negative electric field. These linear relations gave a specific value for the strength of the electric field (−5.9 ± 0.7 V cm⁻¹) where the electrostatic repulsion and the microbial attachment force were thought to be equal, resulting in no cell attachment. From this value, the electrostatic repulsion, i.e. the microbial attachment force, was calculated to be 5.0 × 10⁻¹¹ N cell⁻¹ for cells of average size.     

Lattice Thermal Transport in the Homogeneous Cage-Like Compounds Cu3VSe4 and Cu3NbSe4: Interplay between Phonon-Phase Space,Anharmonicity, and Atomic Mass

Understanding the correlation between crystal structure and thermal conductivity in semiconductors is very important for designing heat-transport-related devices, such as high-performance thermoelectric materials and heat dissipation in micro-nano-scale devices. In this work, the lattice thermal conductivity ( ) of the cage-like compounds Cu₃VSe₄ and Cu₃NbSe₄ was investigated by experimental measurements and first-principles calculations. The experimental of Cu₃NbSe₄ is approximately 25 % lower than that of Cu₃VSe₄ at 300 K. The relevant important physical parameters, including the sound velocity, heat capacity, weighted phonon phase space (W), and third-order force constants along with atomic mass were theoretically analyzed. It is found that W is the dominant parameter in determining the , and the other factors only play a minor role. The physical origin is the relatively “soft” lattice of Cu₃NbSe₄ with heavier atomic mass. This research provides deep insight into the correlation between the thermal conductivity and crystal structure and paves the way for discovering high-performance thermal management device and thermoelectric materials with intrinsically low .     

Structure inhomogeneities of medium-range order in fluorozirconate glasses

Images of cleaved surfaces were obtained for 53ZrF₄-20BaF₂-4LaF₃-3AlF₃-20NaF (ZBLAN) glasses and fused quartz using an NTMDT atomic force microscope. It is shown that the scatter of particle size depends on the cooling rate and is 21–48.5 Å for the cleaved surface of ZBLAN glass obtained by very fast cooling and 68–172 Å for the cleaved surface of ZBLAN after slow cooling. For cleaved fused quartz, the range is 25-18 Å.     

聚乙二醇在高真空条件下的单链弹性

在过去二十年间，高分子的单链弹性已经得到了广泛的研究.然而由于环境和高分子之间往往有着复杂的相互作用，实验中很难得到高分子在严格无扰状态下的单链弹性（即本征弹性）.为此，利用单分子力谱技术研究了高真空条件下聚乙二醇（PEG）的单链弹性.结果表明，由于高真空条件下溶剂分子的干扰被消除，PEG在这一准无扰状态下呈现其本征弹性.在非极性有机溶剂中，由于溶剂分子和PEG之间只有微弱的范德华力作用，PEG表现出和高真空中基本一致的弹性.然而，在不同环境中，力曲线的低力区（F<100 pN）存在着细微的差异.这一现象可归因于不同条件下基底与PEG链之间的吸附力不同.采用的高真空力谱可用于研究其他高分子单链在准无扰状态下的本征弹性.