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.     

Heats of solution of gaseous hydrocarbons in water at 25°C

The heats of solution at 25°C for a number of hydrocarbon gases are reported as measured by a calorimetric method. There is excellent agreement between the standard enthalpy changes of solution measured calorimetrically and those derived from high precision temperature dependent solubility measurements. However the calorimetrically determined standard enthalpies of solution of a number of gases are greatly improved over values obtained from low precision temperature dependent solubility measurements. A method is presented to readily estimate the standard errors in the standard enthalpy change for any process derived from the temperature dependence of the equilibrium constant for the process. Comparison of the standard enthalpies and entropies of solution of hydrocarbon gases in water shows that the standard free energies of solution for all hydrocarbon gases investigated are dominated by unfavorable entropy contributions. A strong linear correlation between the standard entropy of solution and the number of hydrogens in the hydrocarbon molecule is found. This correlation suggests that the hydrocarbon hydrophobic effect is regulated by the number of allowable configurations of a water molecule in contact with each C–H group.     

Molecular structure of di-aryl-aldimines by multinuclear magnetic resonance and X-ray diffraction

The complete ¹H, ¹³C and ¹⁵N NMR analyses for a series of 25 diaryl-aldimines containing phenyl, pyridyl, pyrazolone and furanyl moieties are described herein. Detailed evaluation of substituent chemical shift and coupling constant effects showed that interaction between the lone pair of the pyrazolone carbonyl group or the nitrogen of 2-substitued pyridines with the aldimine hydrogen increases the value and shifts the resonance signal for this hydrogen to high frequency, in the ¹H NMR spectra. The X-ray crystal structure analysis of pyrazolone substituted aldimines evidenced the planarity of the aryl groups which are conjugated with the CN double bond. In the case of the N-(2-pyridinemethylene)-1,5-dimethyl-2-phenyl-1,2-dihydro-pyrazol-3-one, two rotamers were observed in the same unit cell.     

Calculations of concentration dependences of chemical shifts for acrylamide in water—DMSO mixed solvent

The lattice model of associated solutions was used to calculate the concentration dependences of the chemical shifts of¹³C magnetic nuclei in the acrylamide molecule in water—DMSO solvent. Each pair of bonds between the acrylamide group containing a magnetic nucleus and the neighboring solvent molecule was assumed to additively contribute to the change in the chemical shift of the nucleus in question. The new approach affords the same accuracy in describing the experimental data at any ratios of the solution components. It was shown that the chemical shifts and the excess heat of mixing of the water—DMSO binary solution can be simultaneously described using the same set of energy parameters of the model. The model makes it possible to employ experimental data on chemical shifts for studying intermolecular interactions in solutions. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1983–1987, October, 1998.     

Optimization of on-chip elongation for fabricating double-stranded DNA microarrays

The sequence-specific recognitions between DNA and proteins are playing important roles in many biological functions. The double-stranded DNA microarrays (dsDNA microarrays) can be used to study the sequence-specific recognitions between DNAs and proteins in highly parallel way. In this paper, two different elongation processes in forming dsDNA from the immobilized oligonucleotides have been compared in order to optimize the fabrication of dsDNA microarrays: (1) elongation from the hairpins formed by the self-hybridized oligonucleatides spotted on a glass; (2) elongation from the complementary primers hybridized on the spotted oligonucleatides. The results suggested that the dsDNA probes density produced by the hybridized-primer extension was about four times lower than those by the self-hybridized hairpins. Meanwhile, in order to reduce the cost of dsDNA microarrays, we have replaced the Klenow DNA polymerase with Taq DNA polymerase, and optimized the reaction conditions of on-chip elongation. Our experiements showed that the elongation temperature of 50 °C and the Mg²⁺ concentration of 2.5 mM are the optimized conditions in elongation with Taq DNA polymerase. A dsDNA microarray has been successfully constructed with the above method to detect NF-kB protein.