Generating Excess Protons in Microsolvated Acid Clusters under Ambient Conditions: An Issue of Configurational Entropy versus Internal Energy

Acid dissociation, and thus liberation of excess protons in small water droplets, impacts on diverse fields such as interstellar, atmospheric or environmental chemistry. At cryogenic temperatures below 1 K, it is now well established that as few as four water molecules suffice to dissociate the generic strong acid HCl, yet temperature-driven recombination sets in simply upon heating that cluster. Here, the fundamental question is posed of how many more water molecules are required to stabilize a hydrated excess proton at room temperature. Ab initio path integral simulations disclose that not five, but six water molecules are needed at 300 K to allow for HCl dissociation independently from nuclear quantum effects. In order to provide the molecular underpinnings of these observations, the classical and quantum free energy profiles were decomposed along the dissociation coordinate in terms of the corresponding internal energy and entropy profiles. What decides in the end about acid dissociation, and thus ion pair formation, in a specific microsolvated water cluster at room temperature is found to be a fierce competition between classical configurational entropy and internal energy, where the former stabilizes the undissociated state whereas the latter favors dissociation. It is expected that these are generic findings with broad implications on acid–base chemistry depending on temperature in small water assemblies.     

The differentiation operator in the space of uniformly convergent Dirichlet series

Continuity, compactness, the spectrum and ergodic properties of the differentiation operator are investigated, when it acts in the Fréchet space of all Dirichlet series that are uniformly convergent in all half-planes for each . The properties of the formal inverse of the differentiation are also investigated.     

A comparison of different approaches to integrate flamelet tables with presumed-shape PDF in flamelet models for turbulent flames

Flamelet models for turbulent combustion modelling make use of presumed-shape probability density functions (PDFs) for integrating laminar flamelet solutions to obtain an integrated flamelet table that can readily be used for turbulent flame calculations. The existence of non-unique approaches for such an integration has rarely been investigated before. For the first time, this work studies systematically the non-uniqueness of the flamelet table integration approaches. A flamelet model called the flamelet/progress variable model is used in the study, although the issue exists generally in many other flamelet models. Two classes of table integration approaches are investigated, one preserving the laminar flamelet structures during integration and the other not. Three different table integration approaches are examined and compared in detail to provide a thorough understanding of the different approaches. A partially stirred reactor is used as a test case for examining the different approaches. A method based on the transported PDF method is also employed to provide a reference for the assessment of the different flamelet table integration approaches. It is found in general that the flamelet preserving integration approach yields a more reasonable joint PDF of the mixture fraction and the progress variable, and the prediction results are closer to the referenced transported PDF results.     

Dynamics of trailing vortices in the wake of a generic high-speed train

The three-dimensional dynamics of a pair of counter-rotating streamwise vortices that are present in the wake of an ICE3 high-speed train typical of modern, streamlined vehicles in operation, is investigated in a 1/10th-scale wind-tunnel experiment. Velocity mapping, frequency analysis, phase-averaging and proper orthogonal decomposition of data from high-frequency multi-hole dynamic pressure probes, two-dimensional total pressure arrays and one-dimensional multi-hole arrays was performed. Sinusoidal, antisymmetric motion of the pair of counter-rotating streamwise vortices in the wake is observed. These unsteady characteristics are proposed to be representative of full-scale operational high-speed trains, in spite of the experimental limitations: static floor, reduced model length and reduced Reynolds number. This conclusion is drawn from favourable comparisons with numerical literature, and the ability of the identified characteristics to explain phenomena established in full-scale and scaled moving-model experiments.     

Well/Ill Posedness for the Euler-Korteweg-Poisson System and Related Problems

We consider a general Euler-Korteweg-Poisson system in R ³, supplemented with the space periodic boundary conditions, where the quantum hydrodynamics equations and the classical fluid dynamics equations with capillarity are recovered as particular examples. We show that the system admits infinitely many global-in-time weak solutions for any sufficiently smooth initial data including the case of a vanishing initial density - the vacuum zones. Moreover, there is a vast family of initial data, for which the Cauchy problem possesses infinitely many dissipative weak solutions, i.e. the weak solutions satisfying the energy inequality. Finally, we establish the weak-strong uniqueness property in a class of solutions without vacuum. In this paper we show that, even in presence of a dispersive tensor, we have the same phenomena found by De Lellis and Székelyhidi.     

FEW: A workflow tool for free energy calculations of ligand binding

In the later stages of drug design projects, accurately predicting relative binding affinities of chemically similar compounds to a biomolecular target is of utmost importance for making decisions based on the ranking of such compounds. So far, the extensive application of binding free energy approaches has been hampered by the complex and time‐consuming setup of such calculations. We introduce the free energy workflow (FEW) tool that facilitates setup and execution of binding free energy calculations with the AMBER suite for multiple ligands. FEW allows performing free energy calculations according to the implicit solvent molecular mechanics (MM‐PB(GB)SA), the linear interaction energy, and the thermodynamic integration approaches. We describe the tool's architecture and functionality and demonstrate in a show case study on Factor Xa inhibitors that the time needed for the preparation and analysis of free energy calculations is considerably reduced with FEW compared to a fully manual procedure. © 2013 Wiley Periodicals, Inc.     

Comparative assessment of computational methods for the determination of solvation free energies in alcohol‐based molecules

The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson–Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane‐alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM‐based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane‐alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane‐alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug‐binding in computer‐aided drug design. © 2013 Wiley Periodicals, Inc.