The configurational dependence of binding free energies: A Poisson–Boltzmann study of Neuraminidase inhibitors

The linear finite difference Poisson-Boltzmann (FDPB) equation is applied to the calculation of the electrostatic binding free energies of a group of inhibitors to the Neuraminidase enzyme. An ensemble of enzyme-inhibitor complex conformations was generated using Monte Carlo simulations and the electrostatic binding free energies of subtly different configurations of the enzyme-inhibitor complexes were calculated. It was seen that the binding free energies calculated using FDPB depend strongly on the configuration of the complex taken from the ensemble. This configurational dependence was investigated in detail in the electrostatic hydration free energies of the inhibitors. Differences in hydration energies of up to 7 kcal mol^–1 were obtained for root mean square (RMS) structural deviations of only 0.5 Å. To verify the result, the grid size and parameter dependence of the calculated hydration free energies were systematically investigated. This showed that the absolute hydration free energies calculated using the FDPB equation were very sensitive to the values of key parameters, but that the configurational dependence of the free energies was independent of the parameters chosen. Thus just as molecular mechanics energies are very sensitive to configuration, and single-structure values are not typically used to score binding free energies, single FDPB energies should be treated with the same caution.     

Changes in calmodulin main-chain dynamics upon ligand binding revealed by cross-correlated NMR relaxation measurements

The fast dynamics of protein backbones are often investigated by nuclear magnetic relaxation experiments that report on the degree of spatial restriction of the amide bond vector. By comparing calmodulin in the peptide-bound and peptide-free states with these classical methods, we observe little difference in the dynamics of the polypeptide main chain (average order parameter decrease of 0.01 unit upon binding). However, when using NMR methods that monitor the mobility of the CO-Calpha bond vector, we reveal a significant reduction of dynamics of the protein main chain (average order parameter decrease of 0.048 units). Previous investigations have suggested that the side-chain dynamics is reduced by an average of 0.07 order parameter units upon ligand binding (Lee, A. L.; Kinnear, S. A.; Wand, A. J. Nat. Struct. Biol. 2000, 7, 72-77). The current findings suggest that the change of the CO-Calpha bond vector dynamics is intermediate between the changes in NH and side-chain dynamics and report a previously undetected loss of main-chain entropy. Weak site-to-site correlations between the different motional indicators are also observed.     

Fully imidized soluble polyimides based on a novel dianhydride: 2,2′-dichloro-4,4′,5,5′-benzophenone tetracarboxylic dianhydride

We have synthesized a novel dianhydride, 2,2′-dichloro-4,4′,5,5′-benzophenone tetracarboxylic dianhydride (DCBTDA). Polyimides were synthesized with DCBTDA or 3,3′,4,4′-benzophenone tetracarboxylic dianhydride (BTDA) and several relatively rigid meta- and para- substituted mononuclear diamines. The BTDA based systems were insoluble in dipolar, aprotic solvents whereas the DCBTDA based polymers displayed enhanced solubility in these solvents. The thermal stability of these polyimides was excellent as measured by 5% weight loss decomposition. The T_g's of the polymers were all above 290°C.     

Novel species in the electrochemical reduction of a metalmetal bond bridged by a bidentate fluorophosphine

The purple bridged bimetallic complex [CH₃N(PF₂)₂]₃Co₂(CO)₂ undergoes successive chemically and electrochemically reversible one-electron reductions to the corresponding green radical anion and pale-yellow dianion. The radical anion is relatively unreactive towards oxygen and methyl iodide. The dianion is not only reactive towards oxygen and methyl iodide but also captures small positively charged species (e.g. Li⁺ and H⁺) with significant alteration of its chemical properties.     

Clar valence bond representation of pi-bonding in carbon nanotubes

The application of the Clar aromatic sextet valence bond (VB) model to extended, defect-free single-walled carbon nanotubes (CNTs) with roll-up vectors (m, n) provides a real space model of their electronic structure. If m - n = 3k, where k is an integer, then all pi-electrons can be represented by aromatic sextets, and the CNT is fully benzenoid; the converse is also true. Since m - n = 3k is known to be a necessary criterion for conductivity in CNTs, only fully benzenoid CNTs are metallic, and only potentially metallic CNTs are fully benzenoid. This behavior contrasts with that of planar polycyclic aromatic hydrocarbons, in which the fully benzenoid structures are known to have large HOMO-LUMO gaps. For CNTs that are not fully benzenoid, e.g., m - n = 3k + l, where l = 1 or 2 and k is an integer, a seam of double bonds wraps about an otherwise benzenoid CNT at the chiral angle - 60 degrees or the chiral angle, respectively. Nucleus-independent chemical shift calculations on hydrogen-terminated CNT segments support this, and show that the magnetic manifestation of aromatic sextets is not due to electron correlation. The resonance hybrid of the Clar VB structures corresponds to patterns occasionally observed in scanning tunneling microscopy images of CNTs.     

Gradient corrections in density functional theory calculations for surfaces: Co on Pd{110}

Ab initio total energy calculations have been performed for CO chemisorption on Pd{110}. Local density approximation (LDA) calculations yield chemisorption energies which are significantly higher than experimental values but inclusion of the generalised gradient approximation (GGA) gives better agreement. In general, sites with higher coordination of the adsorbate to surface atoms lead to a larger degree of overbinding with LDA, and give larger corrections with GGA. The reason is discussed using a first-order perturbation approximation. It is concluded that this may be a general failure of LDA for chemisorption energy calculations. This conclusion may be extended to many surface calculations, such as potential energy surfaces for diffusion.     

Thermal analysis of PMMA/gel silica glass composites

Thermal analysis of poly-methylmethacrylate (PMMA) impregnated porous gel silica glasses confirms that the PMMA chains form hydrogen bonds with the pore surface silanol groups. The adopted conditions for the insitu polymerisation result in about 4% of residual monomers trapped in the polymer, most of them in the amorphous structure. The polymer and monomer mixture takes up the whole of the free pore volume. Most of the residual monomer polymerises during the DSC scans above the glass transition temperature providing an excellent probe for the weak glass transition. Polymerisation in the gel silica glass medium affects the glass transition temperature, the length of polymer chains, and the degree of polymerisation.     

Mass spectra of organometallic compounds: XIV—Some monometallic olefing manganese tricarbonyl derivatives

The metastable ion supported fragmentation process in the mass spectra of the cyclohexadienyl derivative C₆H₇Mn(CO)₃, the cycloheptadienyl derivative C₇H₉Mn(CO)₃, the 1,2,3,4,5-and 1,2,3,5,6-pentahaptocyclootadienyl derivatives C₈H₁₁Mn(CO)₃, the cyclooctatrienyl derivative C₈H₉Mn(CO)₃ and the substituted cyclopentadienyl derivative (CH₃)₂NCH₂C₅H₄Mn(CO)₃, are described. Losses of carbonyl groups, generally stepwise, from the molecular ions to give the corresponding [M – 3CO]⁺· ions are first observed. Further fragmentation of the carbonyl-free [M – 3CO]⁺· ions can involve a variety of processes such as the following: (a) elimination of a neutral manganese atom to give a hydrocarbon fragment; (b) elimination of a neutral hydrocarbon fragment to give an [MnH]⁺· ion; (c) dehydrogenation; (d) elimination of a 2-carbon C₂H₂ or C₂H₄ fragment; (e) elimination of a C₃H₄ or C₃H₆ fragment as a neutral species when it is bridging two carbon atoms bonded to manganese, as in C₈H₉Mn(CO)₃ and 1,2,3,4,5,h⁵-C₈H₁₁Mn(CO)₃, respectively. Fragmentation of the [M – 3CO]⁺· ion in (CH₃)₂NCH₂C₅H₄Mn(CO)₃ presents the following additional features: (a) elimination of C₆H₆ with a nitrogen shift from carbon to manganese; (b) elimination of a neutral dimethylamino fragment to give [C₆H₆Mn]⁺·, which then loses neutral C₆H₆, C₆H₅ or Mn fragments and thus is formulated tentatively as [(fulvene)Mn]⁺· or [C₆H₅MnH]⁺· rather than [(benzene)Mn]⁺·.     

Development of a systems analysis approach for resolving the structure of biodegrading soil systems

An experimental and mathematical method is developed for the microbial systems analysis of polyaromatic hydrocarbon (PAH)-degrading mixed cultures in PAH-contaminated “town gas” soil systems. Frequency response is the primary experimental and data analysis tool used to probe the structure of these complicated systems. The objective is to provide a fundamental protocol for evaluating the performance of specific mixed microbial cultures on specific soil systems by elucidating the salient system variables and their interactions. Two well-described reactor systems, a constant volume stirred tank reactor (CSTR) and a plug flow differential volume reactor, are used in order to remove performance effects that are related to reactor type as opposed to system structure. These two reactor systems are well-defined systems that can be described mathematically and represent the two extremes of one potentially important system variable, macroscopic mass transfer. The experimental and mathematical structure of the protocol is described, experimental data is presented, and data analysis is demonstrated for the stripping, sorption, and biodegradation of napththalene.