Solubility and preferential solvation of acetaminophen in methanol + water mixtures at 298.15 K

The equilibrium solubility of acetaminophen in methanol + water binary mixtures at 298.15 K was determined and correlated with the Jouyban–Acree model. Preferential solvation parameters by methanol (δx_1,3) were derived from their thermodynamic solution properties by means of the inverse Kirkwood–Buff integrals method. δx_1,3 values are negative in water-rich mixtures but positive in compositions from 0.32 in mole fraction of methanol to pure methanol. It is conjecturable that in the former case, the hydrophobic hydration around non-polar groups plays a relevant role in the solvation. The higher solvation by methanol in mixtures of similar cosolvent compositions and methanol-rich mixtures could be explained in terms of the higher basic behavior of this cosolvent.     

Hybrid molecular dynamics-quantum mechanics simulations of solute spectral properties in the condensed phase: evaluation of simulation parameters

We have explored the impact of a number of basic simulation parameters on the results of a recently developed hybrid molecular dynamics-quantum mechanics (MD-QM) method (Mercer et al., J Phys Chem B 1999, 103, 7720). The method utilizes MD simulations to explore the ground-state configuration space of the system and QM evaluation of those structures to yield the time-dependent electronic transition energy, which is transformed into the optical line-broadening function using the second-order cumulant expansion. Both linear and nonlinear optical spectra can then be generated for comparison to experiment. The dependence of the resulting spectra on the length of the MD trajectory, the QM sampling rate, and the QM model chemistry have all been examined. In particular, for the system of oxazine-4 in methanol studied here, at least 20 ps of MD trajectory are needed for qualitative convergence of linear spectral properties, and >100 ps is needed for quantitative convergence. Surprisingly, little difference is found between the 3-21G and 6-31G(d) basis sets, and the CIS and TD-B3LYP methods yield remarkably similar spectra. The semiempirical INDO/s method yields the most accurate results, reproducing the experimental Stokes shift to within 5% and the FWHM to within 20%. Nonlinear 3-pulse photon echo peak shift (3PEPS) decays have also been simulated. Decays are generally poorly reproduced, though the initial peak shift which depends on the overall coupling of motions to the solute transition energy is within 15% of experiment for all model chemistries other than those using the STO-3G basis.     

Common system setup for the entire catalytic cycle of cytochrome P450(cam) in quantum mechanical/molecular mechanical studies

We describe a system setup that is applicable to all species in the catalytic cycle of cytochrome P450(cam). The chosen procedure starts from the X-ray coordinates of the ferrous dioxygen complex and follows a protocol that includes the careful assignment of protonation states, comparison between different conceivable hydration schemes, and system preparation through a series of classical minimizations and molecular dynamics (MD) simulations. The resulting setup was validated by quantum mechanical/molecular mechanical (QM/MM) calculations on the resting state, the pentacoordinated ferric and ferrous complexes, Compound I, the transition state and hydroxo intermediate of the C--H hydroxylation reaction, and the product complex. The present QM/MM results are generally consistent with those obtained previously with individual setups. Concerning hydration, we find that saturating the protein interior with water is detrimental and leads to higher structural flexibility and catalytically inefficient active-site geometries. The MD simulations favor a low water density around Asp251 that facilitates side chain rotation of protonated Asp251 during the conversion of Compound 0 to Compound I. The QM/MM results for the two preferred hydration schemes (labeled SE-1 and SE-4) are similar, indicating that slight differences in the solvation close to the active site are not critical as long as camphor and the crystallographic water molecules preserve their positions in the experimental X-ray structures.     

Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface

In this study we investigated the interaction behavior between thirteen different small peptides and a hydrophobic surface using three progressively more complex methods of representing solvation effects: a united-atom implicit solvation method [CHARMM 19 force field (C19) with Analytical Continuum Electrostatics (ACE)], an all-atom implicit solvation method (C22 with GBMV), and an all-atom explicit solvation method (C22 with TIP3P). The adsorption behavior of each peptide was characterized by the calculation of the potential of mean force as a function of peptide-surface separation distance. The results from the C22/TIP3P model suggest that hydrophobic peptides exhibit relatively strong adsorption behavior, polar and positively-charged peptides exhibit negligible to relatively weak favorable interactions with the surface, and negatively-charged peptides strongly resist adsorption. Compared to the TIP3P model, the ACE and GBMV implicit solvent models predict much stronger attractions for the hydrophobic peptides as well as stronger repulsions for the negatively-charged peptides on the CH(3)-SAM surface. These comparisons provide a basis from which each of these implicit solvation methods may be reparameterized to provide closer agreement with explicitly represented solvation in simulations of peptide and protein adsorption to functionalized surfaces.     

Ab initio quantum mechanics-based free energy perturbation method for calculating relative solvation free energies

A free energy perturbation (FEP) method was developed that uses ab initio quantum mechanics (QM) for treating the solute molecules and molecular mechanics (MM) for treating the surroundings. Like our earlier results using AM1 semi empirical QMs, the ab initio QM/MM-based FEP method was shown to accurately calculate relative solvation free energies for a diverse set of small molecules that differ significantly in structure, aromaticity, hydrogen bonding potential, and electron density. Accuracy was similar to or better than conventional FEP methods. The QM/MM-based methods eliminate the need for time-consuming development of MM force field parameters, which are frequently required for drug-like molecules containing structural motifs not adequately described by MM. Future automation of the method and parallelization of the code for Linux 128/256/512 clusters is expected to enhance the speed and increase its use for drug design and lead optimization.     

One-dimensional Ising-like systems: an analytical investigation of the static and dynamic properties, applied to spin-crossover relaxation

We investigate the dynamical properties of the 1-D Ising-like Hamiltonian taking into account short and long range interactions, in order to predict the static and dynamic behavior of spin crossover systems. The stochastic treatment is carried out within the frame of the local equilibrium method [1]. The calculations yield, at thermodynamic equilibrium, the exact analytic expression previously obtained by the transfer matrix technique [2]. We mainly discuss the shape of the relaxation curves: (i) for large (positive) values of the short range interaction parameter, a saturation of the relaxation curves is observed, reminiscent of the behavior of the width of the static hysteresis loop [3]; (ii) a sigmoidal (self-accelerated) behavior is obtained for large enough interactions of any type; (iii) the relaxation curves exhibit a sizeable tail (with respect to the mean-field curves) which is clearly associated with the transient onset of first-neighbor correlations in the system, due to the effect of short-range interactions. The case of negative short-range interaction is briefly discussed in terms of two-step properties. Received 29 October 1999 and Received in final form 30 December 1999     

Kinetics of shape equilibration for two dimensional islands

We study the relaxation to equilibrium of two dimensional islands containing up to 20 000 atoms by Kinetic Monte Carlo simulations. We find that the commonly assumed relaxation mechanism - curvature-driven relaxation via atom diffusion - cannot explain the results obtained at low temperatures, where the island edges consist in large facets. Specifically, our simulations show that the exponent characterizing the dependence of the equilibration time on the island size is different at high and low temperatures, in contradiction with the above cited assumptions. Instead, we propose that - at low temperatures - the relaxation is limited by the nucleation of new atomic rows on the large facets: this allows us to explain both the activation energy and the island size dependence of the equilibration time. Received 7 December 1998 and Received in final form 18 March 1999     

Curvature autocorrelations in domain growth dynamics

We show how the interface curvature autocorrelation function (ICAF) and associated structure factor (ICSF), of relevance in non-equilibrium pattern-formation problems where sharp interfaces are present, provide new and interesting information on domain structure, as yet not visible via the order-parameter structure factor (OPSF). This is done by discussing numerical simulations of model A (non-conserved relaxational phase-ordering kinetics) in two-dimensional systems. The ICAF is Gaussian over short distances and exhibits dynamical scaling and t ^1/2 power-law growth. We use it to show what the typical length-scale in the model A dynamics corresponds to physically and how it can be obtained uniquely, rather than simply within a multiplicative constant. Experimental methods to measure the ICAF and/or ICSF are still needed at this point. Received 22 April 1998     

Solvatochromic studies on the hydrogen-bond donating and dipolarity/polarizability properties of the polyethylene oxide/silica interface

The polarity of the polyethylene oxide(PEO)/silica interface in 1,2-dichloroethane as solvent is classified by means of linear solvation energy (LSE) relationships . The properties of the bare silica particle surface and the silica/PEO interface is expressed by two terms: the dipolarity/polarizability (π*) of the interface and the hydrogen-bond donating ability (α) of the surface silanols. These terms can be defined by using the Kamlet–Taft solvent parameters α and π* as a reference system. The interfacial polarity parameters α and π* were calculated by means of correlation analyses of the energy of the UV/vis absorption maxima of the surface polarity indicators: di-cyano-bis(1,10-phenanthroline) iron II, bis-4,4′-(N,N-dimethylamino) benzophenone, and 2,6-diphenyl-4-(2,4,6-triphenyl-N-pyridino)phenolate when adsorbed onto the PEO/silica particle surface. The experimental values of the E _T(30) parameter of the PEO/silica interface are compared with independently calculated values employing specific LSE relations derived for well-behaved regular solvents and functionalized silicas. PEO adsorption on silica causes a decrease in the value of the α parameter of the silica surface and an evident increase in the dipolarity/polarizability of the interface. Received: 16 December 1998 Accepted in revised form: 8 January 1999     

The short-time critical behaviour of the Ginzburg-Landau model with long-range interaction

The renormalisation group approach is applied to the study of the short-time critical behaviour of the d-dimensional Ginzburg-Landau model with long-range interaction of the form in momentum space. Firstly the system is quenched from a high temperature to the critical temperature and then relaxes to equilibrium within the model A dynamics. The asymptotic scaling laws and the initial slip exponents and of the order parameter and the response function respectively, are calculated to the second order in . Received 9 June 2000 and Received in final form 2 August 2000