Optimized intermolecular potential for nitriles based on Anisotropic United Atoms model

An extension of the Anisotropic United Atoms intermolecular potential model is proposed for nitriles. The electrostatic part of the intermolecular potential is calculated using atomic charges obtained by a simple Mulliken population analysis. The repulsion-dispersion interaction parameters for methyl and methylene groups are taken from transferable AUA4 literature parameters [Ungerer et al., J. Chem. Phys., 2000, 112, 5499]. Non-bonding Lennard-Jones intermolecular potential parameters are regressed for the carbon and nitrogen atoms of the nitrile group (–C≡N) from experimental vapor-liquid equilibrium data of acetonitrile. Gibbs Ensemble Monte Carlo simulations and experimental data agreement is very good for acetonitrile, and better than previous molecular potential proposed by Hloucha et al. [J. Chem. Phys., 2000, 113, 5401]. The transferability of the resulting potential is then successfully tested, without any further readjustment, to predict vapor-liquid phase equilibrium of propionitrile and n-butyronitrile

Density-scaling exponents and virial potential-energy correlation coefficients for the (2n, n) Lennard-Jones system

This paper investigates the relation between the density-scaling exponent $\gamma$ and the virial potential-energy correlation coefficient $R$ at several thermodynamic state points in three dimensions for the generalized $(2n,n)$ Lennard-Jones (LJ) system for $n=4, 9, 12, 18$, as well as for the standard $n=6$ LJ system in two, three, and four dimensions. The state points studied include many low-density states at which the virial potential-energy correlations are not strong. For these state points we find the roughly linear relation $\gamma\cong 3nR/d$ in $d$ dimensions. This result is discussed in light of the approximate "extended inverse power law" description of generalized LJ potentials [N. P. Bailey et al., J. Chem. Phys. 129, 184508 (2008)]. In the plot of $\gamma$ versus $R$ there is in all cases a transition around $R\approx 0.9$, above which $\gamma$ starts to decrease as $R$ approaches unity. This is consistent with the fact that $\gamma\rightarrow 2n/d$ for $R\rightarrow 1$, a limit that is approached at high densities and/or temperatures at which the repulsive $r^{-2n}$ term dominates the physics

Microemulsions as a Novel Toolfor Enhancing the Bioremediation of Xenobiotics

Bioremediation is an advantageous and sustainable technology to remediate contaminated environments since it is cost-effective and environmentally safe.However, some pollutants such as most organochlorine pesticides and hydrocarbons are poorly soluble in water and thus tend to adhere tightly to soil particles. Therefore, the degradation of hydrophobic compounds is usually slow and frequently unsatisfactory due to the difficulties related to their transfer from soil particles to the aqueous phase, where these compounds are more available for degradative microorganisms. In this relation, a fundamental issue for the bioremediation processes is to overcome the limited accessibility of these hydrophobic pollutants for the microorganisms. As an alternative to synthetic surfactants, which are usually introduced into bioremediation processes with the aim of enhancing the bioavailability of hydrophobic pollutants, microemulsions have attained increasing significance both in basic research and environmental applications. Microemulsions consist of a combination of surfactants, co-surfactants, and oil phase and have demonstrated to be promising candidates due to its much higher solubilization capacity.Fil: Sáez, Juliana María. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; ArgentinaFil: Casillas García, Verena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Polti, Marta Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; ArgentinaFil: Benimeli, Claudia Susana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; Argentina. Universidad Nacional de Catamarca; Argentin

Coarse-Grained Strategy for Modeling Protein Stability in Concentrated Solutions. III: Directional Protein Interactions

We extend our coarse-grained modeling strategy described in parts I and II of this investigation to account for nonuniform spatial distributions of hydrophobic residues on the solvent-exposed surfaces of native proteins. Within this framework, we explore how patchy surfaces can influence the solvent-mediated protein-protein interactions, and the unfolding and self-assembly behaviors of proteins in solution. In particular, we compare the equilibrium unfolding and self-assembly trends for three model proteins that share the same overall sequence hydrophobicity, but exhibit folded configurations with different solvent-exposed native-state surface morphologies. Our model provides new insights into how directional interactions can affect native-state protein stability in solution. We find that strongly-directional attractions between native molecules with patchy surfaces can help stabilize the folded conformation through the formation of self-assembled clusters. In contrast, native proteins with more uniform surfaces are destabilized by protein-protein attractions involving the denatured state. Finally, we discuss how the simulation results provide insights into the experimental solution behaviors of several proteins that display directional interactions in their native states

Coarse-Grained Strategy for Modeling Protein Stability in Concentrated Solutions

We present a coarse-grained approach for modeling the thermodynamic stability of single-domain globular proteins in concentrated aqueous solutions. Our treatment derives effective protein-protein interactions from basic structural and energetic characteristics of the native and denatured states. These characteristics, along with the intrinsic (i.e., infinite dilution) thermodynamics of folding, are calculated from elementary sequence information using a heteropolymer collapse theory. We integrate this information into Reactive Canonical Monte Carlo simulations to investigate the connections between protein sequence hydrophobicity, protein-protein interactions, protein concentration, and the thermodynamic stability of the native state. The model predicts that sequence hydrophobicity can affect how protein concentration impacts native-state stability in solution. In particular, low hydrophobicity proteins are primarily stabilized by increases in protein concentration, whereas high hydrophobicity proteins exhibit richer nonmonotonic behavior. These trends appear qualitatively consistent with the available experimental data. Although factors such as pH, salt concentration, and protein charge are also important for protein stability, our analysis suggests that some of the nontrivial experimental trends may be driven by a competition between destabilizing hydrophobic protein-protein attractions and entropic crowding effects