Determination of enthalpies of formation of organic free radicals from bond dissociation energies 2. Halosubstituted radicals

The enthalpies of formation (ΔH _f ^o) for 23 halosubstituted radicals were determined from the published data on bond dissociation energies. The ΔH _f ^o values of the corresponding molecules necessary for the calculation of ΔH _f ^o of the radicals were taken from handbooks or calculated by the additive-group method. The conjugation energies of the radicals are calculated, and the effect of substituents at the π-system on these values was shown. Errors of determination of the ΔH _f ^o values of the radicals were estimated. For Part 1, see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 643–646, April, 1998.     

Transition state geometry in radical abstraction reactions: comparison of interatomic distances in the intersecting parabolas and Morse curves models with quantum-chemical calculations

Interatomic distances in the transition state were estimated for the reactions of radical abstraction: H^· + H₂, H^· + HCl, H^· + CH₄, N^·H₂ + NH₃, HO^· + H₂O, HO₂ ^· + HOOH, and C^·H₃ + SiH₄. The calculation was performed by the quantum-chemical density functional method or coupled clusters method (QCH), as well as by the methods of intersecting parabolas (IPM) and Morse curves (IMM), using experimental data (activation energies and reaction enthalpies). The results of the latter two methods are close to the quantum-chemical calculation and differ only by the increment a: r(IPM or IMM) = a + r(QCH), where a = –4.5·10^–12 m for IPM and a = +1.9·10^–12 m for IMM.     

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.     

Importance of the Debye interaction in organic solutions: Henry's law constants for polar liquids in nonpolar solvents and vice versa

Henry's law constants have been determined for -butyrolactone (BL), ethyl acetate (EA), and 2-methyl-3-pentanol (MEP) in mixtures of iso-octane (ISO) and toluene (TOL), for BL, EA, TOL, and ISO in cinnamaldehyde (CIN) and for TOL and ISO in each other and in BL. From these data and published vapor pressures, the activity coefficients at infinite dilution and the standard molar Gibbs free energy of transfer, G ₂ ⁰ of the solutes from dilute solution in ISO to dilute solution in each solvent medium have been calculated. The different behavior patterns of BL and EA are attributed to differences in their abilities to exist in different conformations possessing different dipole moments. For polar solutes, G ₂ ⁰ decreases with increasing polarizability of the solvent and with increasing dipole moment of the solute, suggesting increased contributions from dipole-induced dipole (Debye) interactions. The sigmoidal plot of G ₂ ⁰ against the change in pair potential energy calculated from the classical expressions suggests that G ₂ ⁰ seriously underestimates the strength of the Debye interactions in comparison with the London interactions.     

STUDIES OF ELECTRON SPIN RESONANCE ON BILIRUBIN FREE RADICALS

The nature of ESR signals derived from bilirubin-Ⅸα has been studied by focusing onthe samples treated with free radical generating and inhibiting systems, i.e. X-XOD, Fe/EDTA, SOD, mannitol/ascorbate, CO, KCN, etc. In all the cases, the stable signals comprisethose originated from semiquinone radical (g = 2.0012) and superoxide free radical (g_∥=2.041, g_⊥= 2.0040). The superoxide is shown binding with certain metal ions chelated bybilirubin. The free radical scavengers are able to destroy these radicals. The kinetic curveof the regeneration of bilirubin radicals has been determined and the reaction follows azero order mechanism. It is likely that both the physiological and toxic actions of bilirubinare related to the characters of its free radicals. Bilirubin is discussed as "active oxygensink" in mammalians.     

Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SASbur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, deltaGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC5o without reparametrization.     

Aerobic oxidation assisted by ligand-free palladium catalysts

Aerobic oxidation of electron-rich benzylic and phenyl allylic alcohols was achieved with high yields with only 0.1 mol.% of Pd(OAc)2 catalyst in the absence of any ligand. This procedure was expected to be valuable for realistic industrial-scale applications from both economic as well as environmental points of view.     

The free loop space and the algebraic k-theory of spaces

Let A(X) be the space defined by Waldhausen whose homotopy groups define the algebraic K-groups of the space X and let . Here (X) denotes the free loop space of X and Q denotes the functor . For X = Y, the suspension of a connected space Y, we shall prove that the homotopy fibers Ã(X), B(X) of the maps A(X) A (point), B(X) B (point) are equivalent as infinite loop spaces.     

Gap exponents for percolation processes with triangle condition

A study is made of the gap exponents for percolation processes with the triangle condition in the subcritical region. It is show that the gaps are given by _t =2 fort=2, 3,. Scaling theory predicts thatP _p (¦C ₀¦S(p))–(p _c –p) andE _p (1/¦C ₀¦; ¦C ₀¦S(p))–(p _c –p)³, whereS(p) is the typical cluster size. It is found that (p _c –p)P _p (|C ₀S(p) ^1–)(p _c –p)^1–2 and (p _c –p)³E _p (1/|C ₀|;|C ₀|S(p) ^1–))(p _c –p)^3–4.     

Photochemistry of molecules relevant to the atmosphere: photodissociation of nitric acid in the gas phase.

This Minireview gives an account of the photochemical decay of nitric acid HNO3 in the gas phase, which has been well investigated under bulk and molecular-beam conditions. Due to the importance of this molecule in atmospheric chemistry, attention was paid to the irradiation regions around 300 and 200 nm, where solar photolysis of HNO3 is expected to be particularly efficient. While the low-energy region is characterized by the products OH and NO2, the high-energy region gives rise to a variety of photochemical decay pathways, dominated by channels which lead to the products HONO + O in different electronic states.