Thermodynamics and kinetics of the hydride-transfer cycles for 1-aryl-1,4-dihydronicotinamide and its 1,2-dihydroisomer

Five 1-(p-substituted phenyl)-1,4-dihydronicotinamides (GPNAH-1,4-H(2)) and five 1-(p-substituted phenyl)-1,2-dihydronicotinamides (GPNAH-1,2-H(2)) were synthesized, which were used to mimic NAD(P)H coenzyme and its 1,2-dihydroisomer reductions, respectively. When the 1,4-dihydropyridine (GPNAH-1,4-H(2)) and the 1,2-dihydroisomer (GPNAH-1,2-H(2)) were treated with p-trifluoromethylbenzylidenemalononitrile (S) as a hydride acceptor, both reactions gave the same products: pyridinium derivative (GPNA(+)) and carbanion SH(-) by a hydride one-step transfer. Thermodynamic analysis on the two reactions shows that the hydride transfer from the 1,2-dihydropyridine is much more favorable than the hydride transfer from the corresponding 1,4-dihydroisomer, but the kinetic examination displays that the former reaction is remarkably slower than the latter reaction, which is mainly due to much more negative activation entropy for the former reaction. When the formed pyridinium derivative (GPNA(+)) was treated with SH(-), the major reduced product was the corresponding 1,4-dihydropyridine along with a trace of the 1,2-dihydroisomer. Thermodynamic and kinetic analyses on the hydride transfer from SH(-) to GPNA(+) all suggest that the 4-position on the pyridinium ring in GPNA(+) is much easier to accept the hydride than the 2-position, which indicates that when the 1,4-dihydropyridine is used the hydride donor to react with S, the formed pyridinium derivative GPNA(+) may return to the 1,4-dihydropyridine by a hydride transfer cycle; but when the 1,2-dihydropyridine is used as the hydride donor, the formed pyridinium derivative can not return to the 1,2-dihydropyridine by the hydride reverse transfer from SH(-) to GPNA(+). These results clearly show that the hydride-transfer cycle is favorable for the 1,4-dihydronicotinamides, but unfavorable for the corresponding 1,2-dihydroisomers.     

Scoring functions: A view from the bench

Computational approaches to drug design are presently hindered by the complexity of the physical chemistry which underlies weak, non- covalent interactions between protein targets and small molecule ligands. Although a number of programs are now available for the design of novel potential ligands, it remains a key problem to rank these rapidly and reliably by estimated binding affinity. Such a step is necessary to select only the most promising candidates for synthesis and experimental characterisation. To calculate ligand affinity quickly and reliably is an extremely difficult problem, but it may well prove possible to estimate sufficiently accurately given an appropriate set of parameters to score individual protein–ligand interactions. Improvements in the situation will require a wider set of thermodynamically characterised systems than is currently available.     

Synthesis of porous vinylnaphthalene/divinylnaphthalene copolymers and their sorptive properties towards phenol and its derivatives

Four porous vinylnaphthalene/divinylnaphthalene (VN/DVN) polymers having three different nominal crosslinking degrees (60, 80 and 100 wt.%) have been synthesized using the suspension polymerization method in the presence of toluene and decane.The use of various crosslinking levels and inert diluents was aimed at changing the extent of polymeric network-diluent interactions. The resultant polymers have specific surface area in the range 450-700 m²/g depending on the DVN content. Two sets of pores were detected in all resins: one with the diameter of ≈2 nm and the second one in the range of 30-40 nm. Their sorptive properties have been studied using dilute (0.5 mmol/l) solutions of phenol and its derivatives (o-chlorophenol, 2-methylphenol, o-nitrophenol, m-nitrophenol and p-nitrophenol). It has been found that sorption, at low equilibrium concentration, follows the order: o-nitrophenol > o-chlorophenol > m-nitrophenol > o-methylphenol > p-nitrophenol > phenol. Full characteristics of the porous structure of resultant polymers was obtained by nitrogen adsorption at 77 K and their surface properties analyzed using Inverse Gas Chromatography.     

Excess enthalpies of solution of some primary and secondary alcohols in sodium dodecylsulfate micellar solutions

The exces enthalpies of solution of some primary and secondary alcohols in aqueous sodium dodecylsulfate micellar solutions were measured and the results were explained by considering the distribution of alcohols between aqueous and micellar phases. The distribution constant and the enthalpy of transfer (and the standard free energy and entropy of transfer) were obtained. The thermodynamic parameters for the transfer of secondary alcohols from the aqueous to the sodium dodecylsulfate (NaDS) micellar phase differ slightly from those of the corresponding primary alcohols. For both series of alcohols the additivity rule holds for free energies of transfer whereas enthalpies and entropies display convex curves. The present data are compared to those for the transfer of the same solutes from the aqueous to the dodecyldimethylamine oxide (DDAO) and dodecyltrimethylammonium bromide (DTAB) micellar phases. The role of the hydrophilic interactions between the OH group and the micelles' head groups is formulated. The thermodynamics of the branched methyl group were determined. Furthermore, the thermodynamics of solvation of primary alcohols in water, in NaDS micelles, and in octane have been calculated using reference states based on the assumption that the empty space around alcohols in the initial and final states is the same. It is shown that the solvation of alcohols in NaDS micellar phase is enthalpy driven and that the thermodynamic properties of solvation vs. the length of the alcohol tail is the same for water and NaDS micelles whereas it is different for octane. A possible explanation for this difference is that the alkyl chain of alcohols folds in octane.     

Criteria for local equilibrium in a system with transport of heat and mass

Nonequilibrium molecular dynamics is used to compute the coupled heat and mass transport in a binary isotope mixture of particles interacting with a Lennard-Jones/spline potential. Two different stationary states are studied, one with a fixed internal energy flux and zero mass flux, and the other with a fixed diffusive mass flux and zero temperature gradient. Computations are made for one overall temperature,T=2, and three overall number densities,n=0.1, 0.2, and 0.4. (All numerical values are given in reduced, Lennard-Jones units unless otherwise stated.) Temperature gradients are up to T=0.09 and weight-fraction gradients up to w ₁=0.007. The flux-force relationships are found to be linear over the entire range. All four transport coefficients (theL-matrix) are determined and the Onsager reciprocal relationship for the off-diagonal coefficients is verified. Four different criteria are used to analyze the concept of local equilibrium in the nonequilibrium system. The local temperature fluctuation is found to be T0.03T and of the same order as the maximum temperature difference across the control volume, except near the cold boundary. A comparison of the local potential energy, enthalpy, and pressure with the corresponding equilibrium values at the same temperature, density, and composition also verifies that local equilibrium is established, except near the boundaries of the system. The velocity contribution to the BoltzmannH-function agrees with its Maxwellian (equilibrium) value within 1%, except near the boundaries, where the deviation is up to 4%. Our results do not support the Eyring-type transport theory involving jumps across energy barriers; we find that its estimates for the heat and mass fluxes are wrong by at least one order of magnitude.     

Inclusion complexes of alcohols with α-cyclodextrin

Calorimetric studies of the inclusion complexes of straight and branched alcohols and of diols with alpha-cyclodextrin (-CD) have been carried out in water solvent. The data suggest that straight and branched chain alcohols enter the cavity of -CD alkyl end first. The hydroxyl group hydrogen bonds to the outer oxygen ring of the cyclodextrin. For branched chain alcohols the longer alkyl part of the molecule penetrates the -CD cavity up to the hydroxyl group. Diols form two hydrogen bonds to the outer oxygen ring of the cyclodextrin with some penetration into its interior.     

Intermolecular contact interactions and their temperature dependence

A model, based on inverse gas chromatography experiments, has been developed for intermolecular interaction and its temperature dependence. The model ascribes to each substance a four-component solubility parameter; the four components reflect the van der Waals, polar, electron donor, and electron acceptor interactive properties. Their values depend on temperature in the same manner as does the cohesive energy. The latter was found to depend only on the critical temperature, the acentric factor, and the reduced temperature. The model was used for evaluation of the solubility parameters from polymer-solvent interaction coefficients and their temperature dependence with high accuracy. For binary solventsolvent mixtures, the free energy of mixing and its temperature dependence, as well as enthalpy of mixing can be derived from this model with a good accuracy.     

Thermodynamics of natural selection

It is shown that biological-natural-selection-like behavior can occur, as a general type of time evolution, in a statistical system where detailed balance is violated owing to the presence of metastable energy states. A model of a non-equilibrium phase transition corresponding to the spontaneous origin of self-reproduction in the system is suggested. After a phase transition, the system passes from one quasistationary distribution of self-reproducing subsystems to another, with an increase in the total organization, as long as the growth of the energy flow through the system or a reduction of energy dissipation in the system is possible. The entropy production is calculated for this process in terms of selective values of Eigen's theory for self-organization in autocatalytic systems. Correspondence of the extremal principle of Eigen's theory with the criterion of evolution in Prigogine's thermodynamics is established.     

Thermodynamics for Coulomb systems: A problem at vanishing particle densities

In this paper I combine techniques recently developed by Charles Fefferman with the well-known methods of Joel Lebowitz and Elliott Lieb to resolve some technical problems left unsettled by Lebowitz and Lieb's fundamental 1972 paper The constitution of matter: Existence of thermodynamics for systems composed of electrons and nuclei.