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.     

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.     

Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method

A complete cycle of chemical transformations for the serine protease prototype reaction is modeled following calculations with the flexible effective fragment quantum mechanical/molecular mechanical (QM/MM) method. The initial molecular model is based on the crystal structure of the trypsin–bovine pancreatic trypsin inhibitor complex including all atoms of the enzyme within approximately 15–18 Å of the oxygen center O of the catalytic serine residue. Several selections of the QM/MM partitioning are considered. Fractions of the side chains of the residues from the catalytic triad (serine, histidine and aspartic acid) and a central part of a model substrate around the C–N bond to be cleaved are included into the QM subsystem. The remaining part, or the MM subsystem, is represented by flexible chains of small effective fragments, whose potentials explicitly contribute to the Hamiltonian of the QM part, but the corresponding fragment–fragment interactions are described by the MM force fields. The QM/MM boundaries are extended over the C–C bonds of the peptides assigned to the QM subsystem in the enzyme, C–C and C–N bonds in model substrates. Multiple geometry optimizations have been performed by using the RHF/6-31G method in the QM part and OPLSAA or AMBER sets of MM parameters, resulting in a series of stationary points on the complex potential-energy surfaces. All structures generally accepted for the serine protease catalytic cycle have been located. Energies at the stationary points found have been recomputed at the MP2/6-31+G^* level for the QM part in the protein environment. Structural changes along the reaction path are analyzed with special attention to hydrogen-bonding networks. In the case of a model substrate selected as a short peptide CH₃(NHCO-CH₂)₂ – HN–CO–(CH₂–NHCO)CH₃ the computed energy profile for the acylation step shows too high activation energy barriers. The energetics of this rate-limiting step is considerably improved, if more realistic model for the substrate is considered, following the motifs of the ThrI11–GlyI12–ProI13-–CysI14–LysI15–AlaI16–ArgI17–IleI18–IleI19 sequence of the bovine pancreatic trypsin inhibitor.     

Aspects of thermal conductivity relative to heat flow

Summary The various techniques and methodologies of thermal conductivity measurement have been conventionally based on the determination of the rate of directional heat flow through a material having a unit temperature differential between its opposing faces. The constancy of this rate depends on the material density, its thermal resistance and the heat flow path itself. The last of these variables contributes most significantly to the true value of steady-state axial and radial heat dissipation depending on the magnitude of transient thermal diffusivity along these directions. The purpose of this paper is to exemplify the above features by defined parameters of heat flow measurement by existing methodologies. No new method is proposed here. Importantly, the relationship between the rate of heat transfer, total heat transferred and thermal conductivity at a given temperature under steady-state conditions for a fixed heat flow path will be illustrated.     

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.     

Thermodynamic properties of electrolyte solutions: An EMF study of the activity coefficients of KCl in the system KCl−KNO3−H2O at 25, 35 and 45°C

Electromotive force measurements were carried out on the system KCl–KNO₃–H₂O at constant total ionic strengths of 0.5, 1.0, 2.0 and 3.0 mol-kg^–1 and at 25, 35 and 45°C using a cell consisting of a potassium ionselective electrode and a Ag/AgCl electrode. The Harned coefficients and the Pitzer binary and ternary interaction parameters for the system have been evaluated at each temperature. The osmotic coefficients, excess free energies of mixing and heats of mixing of the system have been predicted at each of the experimental temperatures and ionic strengths. The solubility data at 25°C are also interpreted.     

极性非质子溶剂与甲醇或1,2-二氯乙烷的汽液平衡

使用双沸点仪测定了丙酮、乙酸乙酯、对二氧六环、乙腈或三乙胺与甲醇或1,2→二氯乙烷以及二者混合物等十一组二元体系在99.3 kPa下的汽液平衡数据(T,x,p), 计算了有关体系的过量吉布斯自由能。结果表明, 六种非质子溶剂与甲醇组成的二元系GE>0; 乙腈或三乙胺与1,2-二氯乙烷组成的二元系GE>0, 而丙酮、乙酸乙酯或对二氧六环与1,2-二氯乙烷的二元混合物GE<0。从同种分子间或不同种分子间的缔合作用对上述结果进行了讨论。本文还在固定极性非质子溶剂(第三组分)物质的量浓度的条件下, 测定了非质子溶剂+1,2-二氯乙烷+甲醇三元混合物的汽液平衡数据, 考察了非质子溶剂的加入对甲醇+1,2-二氯乙烷二元系GE的影响。