Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen

The choice of solvent is key in the manufacturing of solution-grown crystals due to the critical effect it can exert on their morphology. Here we set out to investigate the dynamics and thermodynamics of solvent molecules at the crystal-solution interface for the morphologically dominant crystal faces of ibuprofen. In particular, we evaluate how thermodynamically favourable the desorption of a solvent molecule is and estimate the rate of exchange of adsorbed solvent molecules with molecules from the bulk solution. This analysis is carried out for all four morphologically dominant crystal faces of ibuprofen {100}, {002}, {011} and {110}, and ten solvents, i.e. water, 1-butanol, toluene, cyclohexanone, cyclohexane, acetonitrile, trichloromethane, methanol, ethyl acetate and ethanol. Our work reveals that the structure of the solution and the exchange dynamics can be strongly dependent on both the crystal face and the solvent, i.e. the same solvent can show radically different structure when in contact with different faces, alternatively the same face can induce different structuring in different solvents. Moreover, we find particularly strong surface-solvent interactions for the {002} and {100} crystal faces in several of the solvents examined. We conclude that the role of desolvation in the growth process is solvent- and face-specific, and therefore it has the potential of impacting the crystal shape anisotropy. We provide a framework to rationalise this effect based on molecular simulations of the crystal/solution interface

Oxygen radical-mediated oxidation reactions of an alanine peptide motif - density functional theory and transition state theory study

<p>Abstract</p> <p>Background</p> <p>Oxygen-base (O-base) oxidation in protein backbone is important in the protein backbone fragmentation due to the attack from reactive oxygen species (ROS). In this study, an alanine peptide was used model system to investigate this O-base oxidation by employing density functional theory (DFT) calculations combining with continuum solvent model. Detailed reaction steps were analyzed along with their reaction rate constants.</p> <p>Results</p> <p>Most of the O-base oxidation reactions for this alanine peptide are exothermic except for the bond-breakage of the C_α-N bond to form hydroperoxy alanine radical. Among the reactions investigated in this study, the activated energy of OH α-H abstraction is the lowest one, while the generation of alkylperoxy peptide radical must overcome the highest energy barrier. The aqueous situation facilitates the oxidation reactions to generate hydroxyl alanine peptide derivatives except for the fragmentations of alkoxyl alanine peptide radical. The C_α-C_βbond of the alkoxyl alanine peptide radical is more labile than the peptide bond.</p> <p>Conclusion</p> <p>the rate-determining step of oxidation in protein backbone is the generation of hydroperoxy peptide radical via the reaction of alkylperoxy peptide radical with HO₂. The stabilities of alkylperoxy peptide radical and complex of alkylperoxy peptide radical with HO₂are crucial in this O-base oxidation reaction.</p

Recent Progress in Density Functional Methodology for Biomolecular Modeling

International audienceDensity Functional Theory (DFT) has become the workhorse of applied computational chemistry. DFT has grown in a number of different directions depending on the applications concerned. In this chapter, we provide a broad review of a number of DFT and DFT-based methods, having in mind the accurate description of biological systems and processes. These range from pure "cluster" DFT studies of the structure, properties, and reactions of biochemical species (such as enzymatic catalysts) using either straight DFT or dispersion-corrected functionals (DFT-D), to Born-Oppenheimer-DFT dynamics of systems containing up to a hundred atoms or more (such as glycero-lipids), to hybrid DFT/Molecular Mechanical Molecular Dynamics methods which include protein and solvent environments (for enzymes or ion channels, for example), to constrained-DFT (working within the Marcus framework for electron-transfer reactions), to Interpretational-DFT (which provides the interpretational benefits of the Kohn-Sham DFT methodology)