Ali A. Hassanali

Proton transfer through the water gossamer

The diffusion of protons through water is understood within the framework of the Grotthuss mechanism, which requires that they undergo structural diffusion in a stepwise manner throughout the water network. Despite long study, this picture oversimplifies and neglects the complexity of the supramolecular structure of water. We use first-principles simulations and demonstrate that the currently accepted picture of proton diffusion is in need of revision. We show that proton and hydroxide diffusion occurs through periods of intense activity involving concerted proton hopping followed by periods of rest. The picture that emerges is that proton transfer is a multiscale and multidynamical process involving a broader distribution of pathways and timescales than currently assumed. To rationalize these phenomena, we look at the 3D water network as a distribution of closed directed rings, which reveals the presence of medium-range directional correlations in the liquid. One of the natural consequences of this feature is that both the hydronium and hydroxide ion are decorated with proton wires. These wires serve as conduits for long proton jumps over several hydrogen bonds.

On the recombination of hydronium and hydroxide ions in water.

The recombination of hydronium and hydroxide ions following water ionization is one of the most fundamental processes determining the pH of water. The neutralization step once the solvated ions are in close proximity is phenomenologically understood to be fast, but the molecular mechanism has not been directly probed by experiments. We elucidate the mechanism of recombination in liquid water with ab initio molecular dynamics simulations, and it emerges as quite different from the conventional view of the Grotthuss mechanism. The neutralization event involves a collective compression of the water-wire bridging the ions, which occurs in approximately 0.5 ps, triggering a concerted triple jump of the protons. This process leaves the neutralized hydroxide in a hypercoordinated state, with the implications that enhanced collective compressions of several water molecules around similarly hypercoordinated states are likely to serve as nucleation events for the autoionization of liquid water.

Aqueous solutions: state of the art in ab initio molecular dynamics

The simulation of liquids by ab initio molecular dynamics (AIMD) has been a subject of intense activity over the last two decades. The significant increase in computational resources as well as the development of new and efficient algorithms has elevated this method to the status of a standard quantum mechanical tool that is used by both experimentalists and theoreticians. As AIMD computes the electronic structure from first principles, it is free of ad hoc parametrizations and has thus been applied to a large variety of physical and chemical problems. In particular, AIMD has provided microscopic insight into the structural and dynamical properties of aqueous solutions which are often challenging to probe experimentally. In this review, after a brief theoretical description of the Born–Oppenheimer and Car–Parrinello molecular dynamics formalisms, we show how AIMD has enhanced our understanding of the properties of liquid water and its constituent ions: the proton and the hydroxide ion. Thereafter, a broad overview of the application of AIMD to other aqueous systems, such as solvated organic molecules and inorganic ions, is presented. We also briefly describe the latest theoretical developments made in AIMD, such as methods for enhanced sampling and the inclusion of nuclear quantum effects.

Anomalous water diffusion in salt solutions

Significance Liquid water remains one of the most important environments in which physical, chemical, and biological processes occur. One such process involves the solvation of ions. Understanding the perturbation that ions make on the hydrogen bond network of water remains an open question. Here, using state-of-the-art simulation methods, we show that treating the electronic degrees of freedom explicitly is required to reproduce the experimentally observed water diffusion trends in CsI and NaCl solutions, where ab initio water is characterized by dynamic heterogeneity. We find that the ions do not disrupt the network in any significant manner and provide some nuances to classical ideas in physical chemistry regarding the “structure-making” and “structure-breaking” properties of ions. The dynamics of water exhibits anomalous behavior in the presence of different electrolytes. Recent experiments [Kim JS, Wu Z, Morrow AR, Yethiraj A, Yethiraj A (2012) J Phys Chem B 116(39):12007–12013] have found that the self-diffusion of water can either be enhanced or suppressed around CsI and NaCl, respectively, relative to that of neat water. Here we show that unlike classical empirical potentials, ab initio molecular dynamics simulations successfully reproduce the qualitative trends observed experimentally. These types of phenomena have often been rationalized in terms of the “structure-making” or “structure-breaking” effects of different ions on the solvent, although the microscopic origins of these features have remained elusive. Rather than disrupting the network in a significant manner, the electrolytes studied here cause rather subtle changes in both structural and dynamical properties of water. In particular, we show that water in the ab initio molecular dynamics simulations is characterized by dynamic heterogeneity, which turns out to be critical in reproducing the experimental trends.

The water–amorphous silica interface: Analysis of the Stern layer and surface conduction

To explain why dynamical properties of an aqueous electrolyte near a charged surface seem to be governed by a surface charge less than the actual one, the canonical Stern model supposes an interfacial layer of ions and immobile fluid. However, large ion mobilities within the Stern layer are needed to reconcile the Stern model with surface conduction measurements. Modeling the aqueous electrolyte-amorphous silica interface at typical charge densities, a prototypical double layer system, the flow velocity does not vanish until right at the surface. The Stern model is a good effective model away from the surface, but cannot be taken literally near the surface. Indeed, simulations show no ion mobility where water is immobile, nor is such mobility necessary since the surface conductivity in the simulations is comparable to experimental values.

Proton Transfer and Structure-Specific Fluorescence in Hydrogen Bond-Rich Protein Structures.

Protein structures which form fibrils have recently been shown to absorb light at energies in the near UV range and to exhibit a structure-specific fluorescence in the visible range even in the absence of aromatic amino acids. However, the molecular origin of this phenomenon has so far remained elusive. Here, we combine ab initio molecular dynamics simulations and fluorescence spectroscopy to demonstrate that these intrinsically fluorescent protein fibrils are permissive to proton transfer across hydrogen bonds which can lower electron excitation energies and thereby decrease the likelihood of energy dissipation associated with conventional hydrogen bonds. The importance of proton transfer on the intrinsic fluorescence observed in protein fibrils is signified by large reductions in the fluorescence intensity upon either fully protonating, or deprotonating, the fibrils at pH = 0 or 14, respectively. Thus, our results point to the existence of a structure-specific fluorophore that does not require the presence of aromatic residues or multiple bond conjugation that characterize conventional fluorescent systems. The phenomenon may have a wide range of implications in biological systems and in the design of self-assembled functional materials.

The Fuzzy Quantum Proton in the Hydrogen Chloride Hydrates

The motion of the excess proton is understood as a process involving interconversion between two limiting states, namely, the Eigen and Zundel cations. Nuclear quantum effects (NQE) and the organization of the surrounding solvent play a significant role in this process. However, little is known about how these factors can change the limiting state in molecular systems and the physicochemical properties of its surrounding hydrogen-bond environment. In this work we use state of the art ab initio molecular dynamics simulations to examine the role of NQE on the nature of the proton in four hydrogen chloride hydrates. We demonstrate that NQE significantly alter the phase space properties of the proton and that the local electronic structure of the proton is an exquisitely sensitive indicator of the limiting state in each of the crystals. We evaluate both the proton momentum distribution and the proton chemical shifts and demonstrate that deep inelastic neutron scattering and solid-state nuclear magnetic resonance experiments can serve as complementary techniques for probing the quantum nature of the proton in hydrogen-bonding systems. We believe that the rich and insightful information we obtain for these acid hydrates provides a motivation for new experimental studies.

The Dissociated Amorphous Silica Surface: Model Development and Evaluation

At pH 7, amorphous silica has a characteristic negative charge due to the deprotonation of silanol groups on the surface. Electrokinetic phenomena and transport of biomolecules in devices depend sensitively on the surface morphology, distribution of ions and solvent, and adsorption properties of solutes close to the surface in the electrical double layer region. Hence, simulation of these phenomena requires detailed atomistic models of the double layer region. In this Article, we extend our undissociated silica surface model [J. Phys. Chem. B 2007, 111, 11181-11193] to include dissociated Si-O(-) groups, which interact with both water and salt (Na(+) and Cl(-)). We have also conducted ab initio molecular dynamics (AIMD) simulations of a smaller system consisting of a hydrated silica slab. The radial distribution functions predicted by the empirical model are in qualitative agreement with those from the AIMD simulations. The hydrophobic and hydrophilic nature of silanol-poor and silanol-rich regions of the amorphous silica surface observed in our empirical model is reproduced in the AIMD simulations of the smaller slab. In the initial stages of our AIMD simulations, we observe various chemical processes that represent different hydroxylation mechanisms of the surface.

Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab Initio Molecular Dynamics Simulations

The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab initio molecular dynamics simulations in conjunction with an instantaneous surface definition [Willard, A. P.; Chandler, D. J. Phys. Chem. B 2010, 114, 1954]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface.

The Role of Quantum Effects on Structural and Electronic Fluctuations in Neat and Charged Water

In this work, we revisit the role of nuclear quantum effects on the structural and electronic properties of the excess proton in bulk liquid water using advanced molecular dynamics techniques. The hydronium ion is known to be a weak acceptor of a hydrogen bond which gives it some hydrophobic character. Quantum effects reduce the degree of this hydrophobicity which facilitates the fluctuations of the protons along the wires compared to the classical proton. Although the Eigen and Zundel species still appear to be dominant motifs, quantum fluctuations result in rather drastic events where both transient autoionization and delocalization over extended proton wires can simultaneously occur. These wild fluctuations also result in a significant change of the electronic properties of the system such as the broadening of the electronic density of states. An analysis of the Wannier functions indicate that quantum fluctuations of neat water molecules result in transient charging with subtle similarities and differences to that of the excess proton.