Thermodynamics of water modeled using ab initio simulations

We regularize the potential distribution framework to calculate the excess free energy of liquid water simulated with the BLYP-D density functional. The calculated free energy is in fair agreement with experiments but the excess internal energy and hence also the excess entropy are not. Our work emphasizes the importance of thermodynamic characterization in assessing the quality of electron density functionals in describing liquid water and hydration phenomena

Ab initio RNA folding

RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.Comment: 28 pages, 18 figure

Microscopic dynamics of charge separation at the aqueous electrochemical interface

We have used molecular simulation and methods of importance sampling to study the thermodynamics and kinetics of ionic charge separation at a liquid water-metal interface. We have considered this process using canonical examples of two different classes of ions: a simple alkali-halide pair, Na$^+$I$^-$, or classical ions, and the products of water autoionization, H$_3$O$^+$OH$^-$, or water ions. We find that for both ion classes, the microscopic mechanism of charge separation, including water's collective role in the process, is conserved between the bulk liquid and the electrode interface. Despite this, the thermodynamic and kinetic details of the process differ between these two environments in a way that depends on ion type. In the case of the classical ion pairs, a higher free energy barrier to charge separation and a smaller flux over that barrier at the interface, results in a rate of dissociation that is 40x slower relative to the bulk. For water ions, a slightly higher free energy barrier is offset by a higher flux over the barrier from longer lived hydrogen bonding patters at the interface, resulting in a rate of association that is similar both at and away from the interface. We find that these differences in rates and stabilities of charge separation are due to the altered ability of water to solvate and reorganize in the vicinity of the metal interface.Comment: 6 pages, 3 figures + S

Simulation and Theory of Ions at Atmospherically Relevant Aqueous Liquid-Air Interfaces

Chemistry occurring at or near the surfaces of aqueous droplets and thin films in the atmosphere influences air quality and climate. Molecular dynamics simulations are becoming increasingly useful for gaining atomic-scale insight into the structure and reactivity of aqueous interfaces in the atmosphere. Here we review simulation studies of atmospherically relevant aqueous liquid-air interfaces, with an emphasis on ions that play important roles in the chemistry of atmospheric aerosols. In addition to surveying results from simulation studies, we discuss challenges to the refinement and experimental validation of the methodology for simulating ion adsorption to the air-water interface, and recent advances in elucidating the driving forces for adsorption. We also review the recent development of a dielectric continuum theory that is capable of reproducing simulation and experimental data on ion behavior at aqueous interfaces

How Water's Properties Are Encoded in Its Molecular Structure and Energies.

How are water's material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth's living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies-water's solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions-hydroxide and protons-diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water's molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water's orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties

Ideal, Defective, and Gold--Promoted Rutile TiO2(110) Surfaces: Structures, Energies, Dynamics, and Thermodynamics from PBE+U

Extensive first principles calculations are carried out to investigate gold-promoted TiO2(110) surfaces in terms of structure optimizations, electronic structure analyses, ab initio thermodynamics calculations of surface phase diagrams, and ab initio molecular dynamics simulations. All computations rely on density functional theory in the generalized gradient approximation (PBE) and account for on-site Coulomb interactions via inclusion of a Hubbard correction, PBE+U, where U is computed from linear response theory. This approach is validated by investigating the interaction between TiO2(110) surfaces and typical probe species (H, H2O, CO). Relaxed structures and binding energies are compared to both data from the literature and plain PBE results. The main focus of the study is on the properties of gold-promoted titania surfaces and their interactions with CO. Both PBE+U and PBE optimized structures of Au adatoms adsorbed on stoichiometric and reduced TiO2 surfaces are computed, along with their electronic structure. The charge rearrangement induced by the adsorbates at the metal/oxide contact are also analyzed and discussed. By performing PBE+U ab initio molecular dynamics simulations, it is demonstrated that the diffusion of Au adatoms on the stoichiometric surface is highly anisotropic. The metal atoms migrate either along the top of the bridging oxygen rows, or around the area between these rows, from one bridging position to the next along the [001] direction. Approximate ab initio thermodynamics predicts that under O-rich conditions, structures obtained by substituting a Ti5c atom with an Au atom are thermodynamically stable over a wide range of temperatures and pressures.Comment: 20 pages, 12 figures, accepted for publication in Phys. Rev.

On the Impact of Solvation on a Au/TiO2 Nanocatalyst in Contact with Water

Water, the ubiquitous solvent, is also prominent in forming liquid solid interfaces with catalytically active surfaces, in particular with promoted oxides. We study the complex interface of a gold nanocatalyst, pinned by an F center on titania support, and water. The ab initio simulations uncover the microscopic details of solvent-induced charge rearrangements at the metal particle. Water is found to stabilize charge states differently from the gas phase as a result of structure specific charge transfer from to the solvent, thus altering surface reactivity. The metal cluster is shown to feature both cationic and anionic solvation, depending on fluctuation and polarization effects in the liquid, which creates novel active sites. These observations open up an avenue toward solvent engineering in liquid-phase heterogeneous catalysis

Hydrogen and vacancy clustering in zirconium

The effect of solute hydrogen on the stability of vacancy clusters in hexagonal closed packed zirconium is investigated with an ab initio approach, including contributions of H vibrations. Atomistic simulations within the density functional theory evidence a strong binding of H to small vacancy clusters. The hydrogen effect on large vacancy loops is modeled through its interaction with the stacking faults. A thermodynamic modeling of H segregation on the various faults, relying on ab initio binding energies, shows that these faults are enriched in H, leading to a decrease of the stacking fault energies. This is consistent with the trapping of H by vacancy loops observed experimentally. The stronger trapping, and thus the stronger stabilization, is obtained for vacancy loops lying in the basal planes, i.e. the loops responsible for the breakaway growth observed under high irradiation dose.Comment: submitte

Molecular modeling for physical property prediction

Multiscale modeling is becoming the standard approach for process study in a broader framework that promotes computer aided integrated product and process design. In addition to usual purity requirements, end products must meet new constraints in terms of environmental impact, safety of goods and people, specific properties. This chapter adresses the use of molecular modeling tools for the prediction of physical property usefull for chemical engineering practice