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.     

A twenty-four membered mixed-metal macrocycle; synthesis and structure of cyclo-[(3-Me-1,2-C6H3O2)2SbNa(THF)2]6

The first example of a twenty-four membered mixed p-/s-block macrocycle, cyclo-[(3-Me-1,2-C6H3O2)2SbNa(THF)2]6 1 has been synthesised and structurally characterised from the reaction between 3-Me-1,2-C6H3(OH)(ONa) and (Me2N)2Sb(CH2)3Sb(NMe2)2.     

Structural studies of ammonia and metallic lithium-ammonia solutions

The technique of hydrogen/deuterium isotopic substitution has been used to extract detailed information concerning the solvent structure in pure ammonia and metallic lithium-ammonia solutions. In pure ammonia we find evidence for approximately 2.0 hydrogen bonds around each central nitrogen atom, with an average N-H distance of 2.4 A. On addition of alkali metal, we observe directly significant disruption of this hydrogen bonding. At 8 mol % metal there remains only around 0.7 hydrogen bond per nitrogen atom. This value decreases to 0.0 for the saturated solution of 21 mol % metal, as all ammonia molecules have then become incorporated into the tetrahedral first solvation spheres of the lithium cations. In conjunction with a classical three-dimensional computer modeling technique, we are now able to identify a well-defined second cationic solvation shell. In this secondary shell the nitrogen atoms tend to reside above the faces and edges of the primary tetrahedral shell. Furthermore, the computer-generated models reveal that on addition of alkali metal the solvent molecules form voids of approximate radius 2.5-3.0 A. Our data therefore provide new insight into the structure of the polaronic cavities and tunnels, which have been theoretically predicted for lithium-ammonia solutions.     

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.     

In vivo microdialysis determination of collagen-induced serotonin release in rat blood

We developed a sensitive microbore HPLC method coupled with an on-line microdialysis system to simultaneously measure endogenous 5-hydroxytryptamine (serotonin; 5-HT) and its major metabolite 5-hydroxyindoleacetic acid (5-HIAA) in the rat blood in vivo. A dialysis tube was placed in the right jugular vein. The validity of the procedure is demonstrated because analysis of the aggregating agents, collagen (I mg/kg) plus epinephrine (0.3 mg/kg) after intravenous injection, showed that they induced an increase in 5-HT and 5-HIAA levels in the jugular vein of the rat.     

Synthesis of 3,5,7-Trioxapentacyclo[7.2.1.02,8.04,11.06,10]dodecane. A Novel Diacetal Trioxa-Cage

3,5,7-Trioxapentacyclo[7.2.1.0^2,8.0^4,11.0^6,10]dodecane, the parent compound of novel diacetal trioxa-cages, was synthesized from maleic anhydride cyclopentadiene adduct 1 by a four-step sequence. Attempts for the synthesis of monoaza dioxa-cage 12 failed. Ozonolysis of compound 9 in CH₂Cl₂-EtOH(1:1) at ?78°C followed by reduction with Me₂S gave 13 in 65% yield.     

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.     

1, n-Triorganosilyl migrations in the rearrangements of silyl-substituted organolithium compounds

Under the agency of the potent lithiating agent, n-butyllithium in TMEDA, an array of organosilanes was found to undergo 1, n-silyl rearrangements via carbanionic intermediates. Unambiguous 1, 2-, 1, 3- and 1, 4-silyl shifts were uncovered in 1-trimethylsilyl-1, 1, 2-triphenylethane, 1, 1-bis(trimethylsilyl)-1-phenylalkanes and 1, 2-bis(trimethylsilyl)-1, 2-diphenylethane, respectively. Cross-over and competition experiments established that these rearrangements generally are intramolecular and occur with decreasing ease in the order, 1, 2 > 1, 3 > 1, 4. In other compounds, such as 1, 1-bis(trimethylsilyl)-1, 2-diphenylethane, 1, n-bis(trimethylsilyl)benzenes and triphenyl(trimethylsilyl)methane, competing 1, n-silyl shifts occurred. Attack of the organolithium intermediates on solvent and silicon—lithium exchange were significant side reactions in some instances. 1-Trimethylgermyl-1, 1, 2-triphenylgermane underwent no discernible rearrangement but rather gave the product expected from germanium—lithium exchange. By conducting time and competition studies, it was shown that lithiation is the product-determining step in these rearrangements and that dual pathways, namely 1, 3-versus consecutive 1, 2- 1, 4-pathways, are operative in certain rearrangements.     

Polyarylates. III. Kinetic studies of interfacial polycondensation

The kinetics of interfacial polycondensation of bisphenol A with isophthaloyl chloride and terephthaloyl chloride in dichloromethane with triethylbenzylammonium chloride (TEBAC) as the catalyst was investigated via measurements of bisphenolate concentration by UV. The reaction was found to be second order with respect to bisphenolate. The dependence of the rate constant on stirring speed, amount of TEBAC, and reaction temperature was studied. The rate constant was increased with an increase of stirring speed, quantity of TEBAC added, as well as the reaction temperature. The activation energy was found to be 7.7 kcal/mol at a stirring speed of 700 rpm in the presence of 0.160 of TEBAC. The role of TEBAC was found to be interesting. It did not alter the equilibrium (the partition coefficient remained the same in the presence of TEBAC), but it did enhance the transfer rate of bisphenolate.