From anisole to 1,2,4,5‐tetramethoxybenzene: Theoretical study of the factors that determine the conformation of methoxy groups on a benzene ring

Unhindered ortho‐dimethoxy‐substituted phenyl rings often display a coplanar conformation. A theoretical study of a series of methoxybenzenes consisting of methoxybenzene (anisole), the three dimethoxybenzenes, and 1,2,4,5‐tetramethoxybenzene, at the DFT/B3LYP/6‐311++G** level of theory, allows us to identify the factors influencing the conformational preference and attribute the coplanarity of such methoxy groups to mesomeric effects. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

The Role of Binary and Many-centre Molecular Interactions in Spin Crossover in the Solid State. Part I. Equation for Free Energy

Summary. A formalism has been developed that describes spin crossover equilibrium in the solid state by taking into account the effects of n nearest neighbours of a given molecule on its partition function. In this way binary and many-body interactions of the order n + 1 are included into the theoretical model and represented by non-ideality parameters connected with the splitting of free energy levels. Binary interactions are characterised by the main splittings whereas higher order interactions manifest themselves in asymmetries of splittings within multiplets. The contribution of molecular interactions can also be written in terms of formal excess free energies of the second, third, fourth and higher orders. Simple relationships between excess free energies and parameters of multiplets have been found for binary, ternary and quaternary interactions. This formalism is reduced to that of the model of binary interactions when effects of surroundings are additive leading to equidistant free energy multiplets. Higher order interactions may cause an abrupt spin crossover but in a limited range of compositions around the transition point. The regression of experimental transition curves of one-step spin crossover may yield estimates of excess energies up to the fifth order.     

Solute-solute-solvent interactions in dilute aqueous solutions of aliphatic diols. Excess enthalpies and gibbs free energies

The heats of dilution and the osmotic coefficients for some aliphatic diols (1,3-propanediol; 1,2-butanediol; 1,3-butanediol; 1,4-butanediol; 2,3-butanediol; 1,5-pentanediol; 1,6-hexanediol) in water at 25°C are reported. The experimental free energy and enthalpy pairwise interaction coefficients were evaluated and are discussed in terms of the hydrophobic-hydrophilic properties of the solutes. The effect of the mutual position of the polar hydrophilic groups in the molecule on the experimental interaction coefficients transposed to the McMillan-Mayer (MM) state is emphasized. The Sawage-Wood additivity of groups (SWAG) approach has been used and critically discussed.Paper presented at J.C.A.T. '86-Ferrara 27–30 Ottobre 1986.     

Thermodynamic molecular switch in sequence‐specific hydrophobic interactions

This communication will demonstrate the existence of a thermodynamic molecular switch in the pairwise, sequence‐specific hydrophobic interaction of Ile–Ile, Leu–Ile, Val–Leu, or Ala–Leu over the temperature range of 273–333 K reported by Nemethy and Scheraga in 1962. Based on Chun's development of the Planck–Benzinger methodology, the change in inherent chemical bond energy at 0 K, ΔH°(T₀), is 3.0 kcal mol^?1 for Ile–Ile, 2.4 for Leu–Ile, 1.8 for Val–Leu, and 1.2 kcal mol^?1 for Ala–Leu. The value of ΔH°(T₀) decreases as the length of the hydrophobic side chain decreases. It is clear that the strength and stability of the hydrophobic interaction is determined by the packing density of the side chains, with Ala–Leu being the most stable. At 〈T_m〉, the thermal agitation energy, $\int^{T}_{0}\Delta Cp^{\circ}(T)\,dT$, is about five times greater than ΔH°(T₀) in each case. Additionally, the thermal agitation energy for the same series, evaluated at 〈T_m〉, decreases in the same order, that is, as the length of the side chain decreases. This pairwise, sequence‐specific hydrophobic interaction is highly similar in its thermodynamic behavior to that of other biological systems, except that the negative Gibbs free energy change minimum at 〈T_s〉 occurs at a considerably higher temperature, 355 K compared to about 300 K. The melting temperature, 〈T_m〉, is also high, 470 K compared to 343 K in a biological system. The implication is that the negative Gibbs free energy minimum at a well‐defined 〈T_s〉 has it origin in the hydrophobic interactions, which are highly dependent on details of molecular structure. In addition to the four specific dipeptide interactions described, we have shown in our unpublished work the existence of a thermodynamic molecular switch in the interactions of 32 dipeptides wherein a change of sign in ΔCp°(T)_reaction leads to a true negative minimum in the Gibbs free energy of reaction, and hence, a maximum in the related K_eq. Indeed, all interacting biological systems that we have thus far examined using the Planck–Benzinger approach point to the universality of thermodynamic molecular switches. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Dynamic light-scattering analysis of the electrostatic interaction of hexahistidine-tagged cytochrome P450 enzyme with semiconductor quantum dots.

Currently, there is great interest in the development of methods suitable for determining the stoichiometry of biomolecules attached to nanoparticles. We describe the use of the dynamic light-scattering technique (DLS) to determine the stoichiometry of the protein cytochrome P450(BSbeta) attached to CdS and CdSe quantum dots (QDs). The enzyme-conjugated QDs have different diffusion characteristics compared to the QD and enzyme precursors, expressed in their size, scattering intensity as well as zeta-potential values. The significant enhancement of the scattering intensity of QDs observed upon conjugation with the P450(BSbeta) due to the refractive-index increment and the systematic variation in zeta potential resulting from charge neutralization of the anionic QDs by the cationic histidine-tagged P450(BSbeta) have been used for stoichiometry determination.     

Thermodynamics of molecular interactions in ethyl iodide+toluene mixtures

The excess Gibb's free energy of mixing, G^E, for ethyl iodide+toluene at 25°C have been obtained from the measured vapor pressuure data. The H^E and G^E values for ethyl iodide+toluene are positive throughout the ethyl iodide concentration range and G^E>H^E. The results have been analyzed in terms of Flory and ideal associated model theory of nonelectrolyte solutions. It has been observed that the ideal associated model approach which assumes the presence of AN and A₂B molecular species describes well (within±10 J-mol^–1 in the worst case) the general dependence of H^E on X_A (mole fraction of ethyl iodide) over the whole composition range for ethyl iodide+toluene mixtures. The equilibrium constants for A+A AB and 2A+BA₂B reactions along with the enthalpies of formation of AB and A₂B molecular species have been calculated.     

Zur Chemie der Pyrrolpigmente, 54. Mitt.: Phytochrommodellstudien: Ein 2,3-Dihydrobilatrien-abc-3-Cholesterylderivat

The diastereomeric 2,3-Dihydrobilatrienes-abc derivatives (4Z, 9Z, 15Z)-7 and (4Z, 9Z, 15E)-7 bearing a cholesterylacetate moiety in position 3 of the chromophore are prepared. The reaction sequence contains an isomerisation step providing quantitative enantioselective formation of the chiral center in position 3. Configurations and conformations of the diastereomers are elucidated using¹H- and¹³C-NMR spectra, NOE-difference spectra, 2D-NMR experiments (NOESY) and arguments from UV-VIS and CD data. It is concluded that the hydrophobic interactions between chromophore and cholesteryl-fragment yield a compact conformation where the two substructures are in close contact with each other. On the other hand these interactions seem to be too weak to induce significant changes in the chemistry, absorption spectra and conformational characterics of the bile pigment chromophore. Therefore hydrophobic interactions between chromophor and apolar amino acid residues of the protein in phytochrome should be of minor relevance for determining spectroscopic shifts.

     

Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

Excess enthalpies of aqueous solutions of polyols at 25°

The excess enthalpies of aqueous solutions of nine polyols were determined at 25°C and reported in the virial form. The most interesting and new feature of this family of solutes is that the sign of the enthalpic pair interaction coefficients h_xx is positive for the first members of the series and negative for the higher homologues. Other points are the large differences found among the values of h_xx for stereoisomers, whereas pairs of enantiomers show the same values within experimental errors. An application of the group additivity method is also discussed.