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.     

Sparsely substituted chlorins as core constructs in chlorophyll analogue chemistry. I. Synthesis

Five routes to stable chlorins bearing 0 or 1 meso substituents have been investigated, among which reaction of a 9-bromo-1-formyldipyrromethane and 2,3,4,5-tetrahydro-1,3,3-trimethyldipyrrin proved most effective. Application of this route afforded metallochlorins [Cu(II), Zn(II), and Pd(II)] including the chlorin lacking any β-pyrrole and meso substituents.     

Stereoselective synthesis of erythro-β-hydroxy carboxylic acids via iron acyl complexes

β-Hydroxy acyl ligands bound to (η⁵-C₅H₅)Fe(CO)(PPh₃) are stereoselectively alkylated on the α-carbon to give after decomplexation erythro-β-hydroxy carboxylic acids.     

The application of symbolic computing to chemical kinetic reaction schemes

Given a reaction mechanism we show how a symbolic computation approach can be used to develop the kinetic equations by identifying the reaction scheme with an equivalent matrix. Our method is also applicable in cases where the stoichiometric matrix approach fails. The specific algorithm that is written applies to schemes where individual reactions are at most ternary, but the way to generalize the procedure is also discussed. By using symbolic computing it is possible to determine general properties of the system. We demonstrate this by showing how to use the matrix to determine the system's conservation laws, which in turn can be used to reduce the number of equations in the system. As another application it is shown how to determine some of the species which have a zero equilibrium state. To illustrate the procedure, example reaction schemes are investigated.     

De novo synthesis of stable tetrahydroporphyrinic macrocycles: bacteriochlorins and a tetradehydrocorrin

[structures: see text] Bacteriochlorins (tetrahydroporphyrins) are attractive for diverse photochemical applications owing to their strong absorption in the near-infrared spectral region, as exemplified by the bacterial photosynthetic pigment bacteriochlorophyll a, yet often are labile toward dehydrogenation to give the chlorin. Tetradehydrocorrins (ring-contracted tetrahydroporphyrins) are attractive for studies of catalysis analogous to that of vitamin B12. An eight-step synthesis toward such tetrahydroporphyrinic macrocycles begins with p-tolualdehyde and proceeds to a dihydrodipyrrin-acetal (1) bearing a geminal dimethyl group and a p-tolyl substituent. Self-condensation of 1 in CH3CN containing BF3 x OEt2 at room temperature afforded a readily separable mixture of two free base bacteriochlorins and a free base B,D-tetradehydrocorrin. Each bacteriochlorin contains two geminal dimethyl groups to lock-in the bacteriochlorin hydrogenation level, p-tolyl substituents at opposing (2,12) beta-positions, and the absence (H-BC) or presence (MeO-BC) of a methoxy group at the 5- (meso) position. The B,D-tetradehydrocorrin (TDC) lies equidistant between the hydrogenation levels of corrin and corrole, is enantiomeric, and contains two geminal dimethyl groups, 2,12-di-p-tolyl substituents, and an acetal group at the pyrroline-pyrrole junction. Examination of the effect of the concentrations of 1 (2.5-50 mM) and BF3 x OEt2 (10-500 mM) revealed a different response surface for each of H-BC, MeO-BC, and TDC, enabling relatively selective preparation of a given macrocycle. The highest isolated yield of each was 49, 30, and 66%, respectively. The macrocycles are stable to routine handling in light and air. The bacteriochlorins display characteristic spectral features; for example, H-BC exhibits near-IR absorption (lambda(Qy) = 737 nm, epsilon(Qy) = 130,000 M(-1) cm(-1)) and emission (lambda(em) = 744 nm, phi(f) = 0.14). In summary, this simple entry to stable bacteriochlorins and tetradehydrocorrins should facilitate a wide variety of applications.     

Particle circulation and oxygen mass transfer in an immobilized cell bioreactor

Two important considerations in the design of an aerobic particulate immobilized cell bioreactor are the provision of sufficient oxygen to maintain the desired metabolism of the immobilized organism, and the biomass holdup (which is proportional to the number of immobilized cell particles in the reactor). The Circulating Bed Reactor, a reactor developed for use with those forms of immobilization that result in particles of essentially neutral buoyancy, operates with an expanded bed of circulating particles. The particle number density attainable in such a reactor has been found to be dependent upon the circulation cell aspect ratio, the individual particle properties, the static bed voidage of the particles, and the superficial gas velocity. The oxygen mass transfer characteristics have been found to be dependent upon the circulatory nature of the system, the particle (solids) holdup, the particle porosity, and the superficial gas velocity.     

Experimental measurement and prediction of hydrate forming conditions in the nitrogen-propane-water system

Experimental data on initial hydrate formation conditions have been obtained for the nitrogen-propane-water system in the L₁HG, L₁L₂H, and L₁L₂HG regions, where L₁ is the water rich liquid phase, L₂ is the hydrocarbon rich liquid phase, H is the hydrate and the G is the vapor phase. The measurements covered a range of temperatures from about 275 to 293 K and pressures from about 0.3 to 17.0 MPa. The concentrations covered for the L₁HG region extended from 0.94 to 75.0 mole percent propane in the gas phase, and for the L₁L₂H region they extended from 83.1 to 99.0 mole percent in the condensed liquid phase. Four-phase measurements were made at concentrations of propane from 18.1 to 71.1 mole percent in the gas phase.The experimental data were used to find a fitted binary interaction parameter for predicting hydrate formation in systems containing nitrogen and propane.     

Application of the energy gap law to the decay of charge transfer excited states,solvent effects

Values of non-radiative decay rate constants (k_nr) and emission energies (E_cm) have been obtained for Os(Phen₃)²⁺ in a series of solvents and the results are consistent with the energy gap law. For hydroxylic solvents like water or methanol related studies suggest the existence of strong, specific contributions to the vibrational trapping energy of the solvent.     

An Education in Robustness

A case study is presented of the application of robustness analysis to the choice of examination subjects to be made by a 14-year-old girl. The analysis is conducted in terms of the desirable future career options which may be preserved by different combinations of subjects, and also of the balance with topics selected for their intrinsic interest. The approach, which employs very limited technical apparatus, is justified on a number of grounds-in particular, the crucial importance of uncertainty, and the need for understanding and acceptance by a "client" very unlike the corporate manager. Some tentative conclusions are reached on the extension of such methods to other cases of decision-makers with little, if any, resources to control except their own lives.     

Decoupling the effects of hydrophilic and hydrophobic moieties at the neuron–nanofibre interface

Peptide-based nanofibres are a versatile class of tunable materials with applications in optoelectronics, sensing and tissue engineering. However, the understanding of the nanofibre surface at the molecular level is limited. Here, a series of homologous dilysine–diphenylalnine tetrapeptides were synthesised and shown to self-assemble into water-soluble nanofibres. Despite the peptide nanofibres displaying similar morphologies, as evaluated through atomic force microscopy and neutron scattering, significant differences were observed in their ability to support sensitive primary neurons. Contact angle and labelling experiments revealed that differential presentation of lysine moieties at the fibre surface did not affect neuronal viability; however the mobility of phenylalanine residues at the nanofibre surface, elucidated through solid- and gel-state NMR studies and confirmed through tethered bilayer lipid membrane experiments, was found to be the determining factor in governing the suitability of a given peptide as a scaffold for primary neurons. This work offers new insights into characterising and controlling the nanofibre surface at the molecular level.

The mobility of hydrophobic moieties at a peptide nanofibre surface determines its suitability as a scaffold for sensitive primary cells.