Damián A. Scherlis

Density functional theory in transition-metal chemistry: a self-consistent Hubbard U approach.

Transition-metal centers are the active sites for a broad variety of biological and inorganic chemical reactions. Notwithstanding this central importance, density-functional theory calculations based on generalized-gradient approximations often fail to describe energetics, multiplet structures, reaction barriers, and geometries around the active sites. We suggest here an alternative approach, derived from the Hubbard U correction to solid-state problems, that provides an excellent agreement with correlated-electron quantum chemistry calculations in test cases that range from the ground state of Fe2 and Fe2- to the addition elimination of molecular hydrogen on FeO+. The Hubbard U is determined with a novel self-consistent procedure based on a linear-response approach.

Freezing, melting and structure of ice in a hydrophilic nanopore

The nucleation, growth, structure and melting of ice in 3 nm diameter hydrophilic nanopores are studied through molecular dynamics simulations with the mW water model. The melting temperature of water in the pore was T(m)(pore) = 223 K, 51 K lower than the melting point of bulk water in the model and in excellent agreement with experimental determinations for 3 nm silica pores. Liquid and ice coexist in equilibrium at the melting point and down to temperatures as low as 180 K. Liquid water is located at the interface of the pore wall, increasing from one monolayer at the freezing temperature, T(f)(pore) = 195 K, to two monolayers a few degrees below T(m)(pore). Crystallization of ice in the pore occurs through homogeneous nucleation. At the freezing temperature, the critical nucleus contains approximately 75 to 100 molecules, with a radius of gyration similar to the radius of the pore. The critical nuclei contain features of both cubic and hexagonal ice, although stacking of hexagonal and cubic layers is not defined until the nuclei reach approximately 150 molecules. The structure of the confined ice is rich in stacking faults, in agreement with the interpretation of X-ray and neutron diffraction experiments. Though the presence of cubic layers is twice as prevalent as hexagonal ones, the crystals should not be considered defective Ic as sequences with more than three adjacent cubic (or hexagonal) layers are extremely rare in the confined ice.

A unified electrostatic and cavitation model for first-principles molecular dynamics in solution

The electrostatic continuum solvent model developed by [Fattebert and Gygi J. Comput. Chem. 23, 662 (2002); Int. J. Quantum Chem. 93, 139 (2003)] is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon.

Modeling heme proteins using atomistic simulations

Heme proteins are found in all living organisms, and perform a wide variety of tasks ranging from electron transport, to the oxidation of organic compounds, to the sensing and transport of small molecules. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of several relevant issues in heme proteins chemistry: (i) conformational analysis, ligand migration, and solvation effects studied using classical molecular dynamics simulations; (ii) electronic structure and spin state energetics of the active sites explored using quantum-mechanics (QM) methods; (iii) the interaction of heme proteins with small ligands studied through hybrid quantum mechanics-molecular mechanics (QM-MM) techniques; (iv) and finally chemical reactivity and catalysis tackled by a combination of quantum and classical tools.

A Surface Effect Allows HNO/NO Discrimination by a Cobalt Porphyrin Bound to Gold

Nitroxyl (HNO) is a small short-lived molecule for which it has been suggested that it could be produced, under certain cofactors conditions, by nitric oxide (NO) synthases. Biologically relevant targets of HNO are heme proteins, thiols, molecular oxygen, NO, and HNO itself. Given the overlap of the targets and reactivity between NO and HNO, it is very difficult to discriminate their physiopathological role conclusively, and accurate discrimination between them still remains critical for interpretation of the ongoing research in this field. The high reactivity and stability of cobalt(II) porphyrins toward NO and the easy and efficient way of covalently joining porphyrins to electrodes through S-Au bonds prompted us to test cobalt(II) 5,10,15,20-tetrakis[3-(p-acetylthiopropoxy)phenyl]porphyrin [Co(P)], as a possible candidate for the electrochemical discrimination of both species. For this purpose, first, we studied the reaction between NO, NO donors, and commonly used HNO donors, with Co(II)(P) and Co(III)(P). Second, we covalently attached Co(II)(P) to gold electrodes and characterized its redox and structural properties by electrochemical techniques as well as scanning tunneling microscopy, X-ray photoelectron spectroscopy, and solid-state density functional theory calculations. Finally, we studied electrochemically the NO and HNO donor reactions with the electrode-bound Co(P). Our results show that Co(P) is positioned over the gold surface in a lying-down configuration, and a surface effect is observed that decreases the Co(III)(P) (but not Co(III)(P)NO(-)) redox potential by 0.4 V. Using this information and when the potential is fixed to values that oxidize Co(III)(P)NO(-) (0.8 V vs SCE), HNO can be detected by amperometric techniques. Under these conditions, Co(P) is able to discriminate between HNO and NO donors, reacting with the former in a fast, efficient, and selective manner with concomitant formation of the Co(III)(P)NO(-) complex, while it is inert or reacts very slowly with NO donors.

Melting and crystallization of ice in partially filled nanopores

We investigate the melting and formation of ice in partially filled hydrophilic and hydrophobic nanopores of 3 nm diameter using molecular dynamics simulations with the mW water model. Above the melting temperature, the partially filled nanopores contain two water phases in coexistence: a condensed liquid plug and a surface-adsorbed phase. It has been long debated in the literature whether the surface-adsorbed phase is involved in the crystallization. We find that only the liquid plug crystallizes on cooling, producing ice I with stacks of hexagonal and cubic layers. The confined ice is wetted by a premelted liquid layer that persists in equilibrium with ice down to temperatures well below its melting point. The liquid-ice transition is first-order-like but rounded. We determine the temperature and enthalpy of melting as a function of the filling fraction of the pore. In agreement with experiments, we find that the melting temperature of the nanoconfined ice is strongly depressed with respect to the bulk T(m), it depends weakly on the filling fraction and is insensitive to the hydrophobicity of the pore wall. The state of water in the crystallized hydrophilic and hydrophobic pores, however, is not the same: the hydrophobic pore has a negligible density of the surface-adsorbed phase and higher fraction of water in the ice phase than the hydrophilic pore. The widths of the ice cores are nevertheless comparable for the hydrophobic and hydrophilic pores, and this may explain their almost identical melting temperatures. The enthalpy of melting ΔH(m), when normalized by the actual amount of ice in the pore, is indistinguishable for the hydrophobic and hydrophilic pores, insensitive to the filling fraction, and within the error bars, the same as the difference in enthalpy between bulk liquid and bulk ice evaluated at the temperature of melting of ice in the nanopores.

First-principles molecular dynamics simulations at solid-liquid interfaces with a continuum solvent

Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such a continuum approach in a density functional theory framework using plane-wave basis sets and periodic boundary conditions. Our work stems from a recent model designed for Car-Parrinello simulations of quantum solutes in a dielectric medium [D. A. Scherlis et al., J. Chem. Phys. 124, 074103 (2006)], for which the permittivity of the solvent is defined as a function of the electronic density of the solute. This strategy turns out to be inadequate for systems extended in two dimensions: the dependence of the dielectric function on the electronic density introduces a new term in the Kohn-Sham potential, which becomes unphysically large at the interfacial region, seriously affecting the convergence of the self-consistent calculations. If the dielectric medium is properly redefined as a function of the atomic coordinates, a good convergence is obtained and the constant of motion is conserved during the molecular dynamics simulations. The Poisson problem is solved using a multigrid method, and in this way Car-Parrinello molecular dynamics simulations of solid-liquid interfaces can be performed at a very moderate computational cost. This scheme is employed to investigate the acid-base equilibrium at the TiO(2)-water interface. The aqueous behavior of titania surfaces has stimulated a large amount of experimental research, but many open questions remain concerning the molecular mechanisms determining the chemistry of the interface. Here we make an attempt to answer some of them, putting to the test our continuum model.

Vapor Pressure of Water Nanodroplets

Classical thermodynamics is assumed to be valid up to a certain length-scale, below which the discontinuous nature of matter becomes manifest. In particular, this must be the case for the description of the vapor pressure based on the Kelvin equation. However, the legitimacy of this equation in the nanoscopic regime can not be simply established, because the determination of the vapor pressure of very small droplets poses a challenge both for experiments and simulations. In this article we make use of a grand canonical screening approach recently proposed to compute the vapor pressures of finite systems from molecular dynamics simulations. This scheme is applied to water droplets, to show that the applicability of the Kelvin equation extends to unexpectedly small lengths, of only 1 nm, where the inhomogeneities in the density of matter occur within spatial lengths of the same order of magnitude as the size of the object. While in principle this appears to violate the main assumptions underlying thermodynamics, the density profiles reveal, however, that structures of this size are still homogeneous in the nanosecond time-scale. Only when the inhomogeneity in the density persists through the temporal average, as it is the case for clusters of 40 particles or less, do the macroscopic thermodynamics and the molecular descriptions depart from each other.

Water filling of hydrophilic nanopores

Molecular dynamics simulations of water in cylindrical hydrophilic pores with diameters of 1.5 and 3 nm were performed to explore the phase behavior and the nucleation dynamics of the confined fluid as a function of the percentage of volume filled f. The interactions of water with the pore wall were considered to be identical to the interactions between water molecules. At low water contents, all the water is adsorbed to the surface of the pore. A second phase consisting of a liquid plug appears at the onset filling for capillary condensation, f(onset)=27% and 34% for the narrow and wide pores, respectively. In agreement with experimental results for silica pores, the liquid phase appears close to the equilibrium filling f(eq) in the 1.5 nm pore and under conditions of strong surface supersaturations for the 3 nm pore. After condensation, two phases, a liquid plug and a surface-adsorbed phase, coexist in equilibrium. Under conditions of phase coexistence, the water surface density Gamma(coex) was found to be independent of the water content and the diameter of the pore. The value of Gamma(coex) found in the simulations (approximately 3 nm(-2)) is in good agreement with experimental results for silica pores, suggesting that the interactions of water with silica and with itself are comparable. The surface-adsorbed phase at coexistence is a sparse monolayer with a structure dominated by small water clusters. We characterize the density and structure of the liquid and surface phases, the nucleation mechanism of the water plug, and the effect of surface hydrophilicity on the two-phase equilibrium and hysteresis. The results are discussed in light of experiments and previous simulations.

Selenium-Based Self-Assembled Monolayers: The Nature of Adsorbate−Surface Interactions

In recent years, self-assembled monolayers (SAMs) of selenols have been characterized using electrochemistry, scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), thermal desorption spectroscopy, and other experimental approaches. Interest in the relative stability and conductance of the Se-Au interface as compared to S-Au prompted different investigations which have led to contradictory results. From the theoretical side, on the other hand, the study of selenol-based SAMs has concentrated on the investigation of the electron transport across the Se-Au contact, whereas the structural and the thermodynamic features of the monolayer were essentially neglected. In this Article, we examine the binding of selenols to the Au(111) surface using density functional theory with plane wave basis sets and periodic boundary conditions. Our calculations provide insights on the geometry of the headgroup, the stability of the monolayer, and the electronic properties of the bond. In particular, we propose that the presence of a conjugated backbone might be a major factor determining the relative conductance at the monolayer, by differentially enhancing the intramolecular electron transport in selenols with respect to thiols. This surmise, if confirmed, would explain the conflictive data coming from the available experiments.