ZundEig: The Structure of the Proton in Liquid Water from Unsupervised Learning.

The structure of the excess proton in liquid water has been the subject of lively debate on both experimental and theoretical fronts for the last century. Fluctuations of the proton are typically interpreted in terms of limiting states referred to as the Eigen and Zundel species. Here, we put these ideas under the microscope, taking advantage of recent advances in unsupervised learning that use local atomic descriptors to characterize environments of acidic water combined with advanced clustering techniques. Our agnostic approach leads to the observation of only one charged cluster and two neutral ones. We demonstrate that the charged cluster involving the excess proton is best seen as an ionic topological defect in water's hydrogen bond network, forming a single local minimum on the global free-energy landscape. This charged defect is a highly fluxional moiety, where the idealized Eigen and Zundel species are neither limiting configurations nor distinct thermodynamic states. Instead, the ionic defect enhances the presence of neutral water defects through strong interactions with the network. We dub the combination of the charged and neutral defect clusters as ZundEig, demonstrating that the fluctuations between these local environments provide a general framework for rationalizing more descriptive notions of the proton in the existing literature.

Water Self-Dissociation is Insensitive to Nanoscale Environments.

Nanoconfinement effects on water dissociation and reactivity remain controversial, despite their importance to understand the aqueous chemistry at interfaces, pores, or aerosols. The pKw in confined environments has been assessed from experiments and simulations in a few specific cases, leading to dissimilar conclusions. Here, with the use of carefully designed ab initio simulations, we demonstrate that the energetics of bulk water dissociation is conserved intact to unexpectedly small length-scales, down to aggregates of only a dozen molecules or pores of widths below 2 nm. The reason is that most of the free-energy involved in water autoionization comes from breaking the O-H covalent bond, which has a comparable barrier in the bulk liquid, in a small droplet of nanometer size, or in a nanopore in the absence of strong interfacial interactions. Thus, dissociation free-energy profiles in nanoscopic aggregates or in 2D slabs of 1 nm width reproduce the behavior corresponding to the bulk liquid, regardless of whether the corresponding nanophase is delimited by a solid or a gas interface. The present work provides a definite and fundamental description of the mechanism and thermodynamics of water dissociation at different scales with broader implications on reactivity and self-ionization at the air-liquid interface.

Shared Hydrogen Atom Location and Chemical Composition in Picolinic Acid and Pyridoxal Hydrochloride Derivatives Determined by X-ray Crystallography.

Three new single-crystal structures were isolated for picolinic acid (2), the trifluoroacetate salt of picolinic acid (1), and pyridoxal hydrochloride (3). These compounds displayed unconventional crystallographic features that must be considered when structural refinements are carried out. Thus, the generated Fourier differences map obtained with the diffraction data collected at 100 K was crucial to visualize electron densities, which were balanced by either one hydrogen atom or a hydrogen atom with an occupancy factor of 1/2 located between either two carboxylate moieties, two phenolic oxygen atoms, or two pyridinic nitrogen atoms. Moreover, NMR studies were conducted to analyze the bulk chemical composition of single crystals of 2-pyridinecarboxylic acid obtained from the gem-diol/hemiacetal forms and the polymerization products after the treatment of 2-pyridinecarboxaldehyde with TFA:H2O (1) or a diluted Cu(NO3)2 solution (2). The quantitative yield of the pyridoxal hydrochloride crystalline material (3) obtained from a diluted CuCl2 solution was exhaustively characterized by solid-state NMR methods. These methods allowed the resolution of the signals corresponding to the protons of the hydroxyl moiety of the intramolecular hemiacetal group and the phenolic hydrogen. Theoretical calculations using DFT methods were done to complement the atomic location of the hydrogen atoms obtained from the X-ray analysis.

Solid-State Characterization of Acetylpyridine Copper Complexes for the Activation of H2 O2 in Advanced Oxidation Processes.

This work describes the synthesis of 4-(4-AcPy) and 3-acetylpyridine (3-AcPy) copper soluble complexes for the activation of hydrogen peroxide and the concomitant generation of reactive oxygen species (ROS). Given the paramagnetic effects of copper ions in the Nuclear Magnetic Resonance (NMR) lines, we aimed at demonstrating that the combination of high-resolution 2D solid-state NMR experiments, Electron Paramagnetic Resonance (EPR), single-crystal X-ray crystallography and Density Functional Theory (DFT) calculations allows a detailed study of the chemical structure of the ligands and the surrounding metal ions. The copper complexes synthesized with CuCl2 were useful for the activation of H2 O2 during which the only ROS was the hydroxyl one, as demonstrated by EPR experiments. A removal of methyl orange (MO) azo-dye higher than 85 % was achieved in 200 minutes, combining 1.7 mM of copper complexes with 60 mM of H2 O2 and 40 µM of MO.

Paramagnetic solid-state NMR assignment and novel chemical conversion of the aldehyde group to dihydrogen ortho ester and hemiacetal moieties in copper(ii)- and cobalt(ii)-pyridinecarboxaldehyde complexes.

The complex chemical functionalization of aldehyde moieties in Cu(ii)- and Co(ii)-pyridinecarboxaldehyde complexes was studied. X-ray studies demonstrated that the aldehyde group (RCHO) of the four pyridine molecules is converted to dihydrogen ortho ester (RC(OCH3)(OH)2) and hemiacetal (RCH(OH)(OCH3)) moieties in both 4-pyridinecarboxaldehyde copper and cobalt complexes. In contrast, the aldehyde group is retained when the 3-pyridinecarboxaldehyde ligand is complexed with cobalt. In the different copper complexes, similar paramagnetic 1H resonance lines were obtained in the solid state; however, the connectivity with the carbon structure and the 1H vicinities were done with 2D 1H-13C HETCOR, 1H-1H SQ/DQ and proton spin diffusion (PSD) experiments. The strong paramagnetic effect exerted by the cobalt center prevented the observation of 13C NMR signals and chemical information could only be obtained from X-ray experiments. 2D PSD experiments in the solid state were useful for the proton assignments in both Cu(ii) complexes. The combination of X-ray crystallography experiments with DFT calculations together with the experimental results obtained from EPR and solid-state NMR allowed the assignment of NMR signals in pyridinecarboxaldehyde ligands coordinated with copper ions. In cases where the crystallographic information was not available, as in the case of the 3-pyridinecarboxaldehyde Cu(ii) complex, the combination of these techniques allowed not only the assignment of NMR signals but also the study of the functionalization of the substituent group.

Does Acid Rain Alter the Leaf Anatomy and Photosynthetic Pigments in Urban Trees?

Megapolis such as Mexico City, have atmospheric pollutants that interact with the humidity and solar radiation. The topography of this city promotes air stagnation, generating atmospheric pollutants and episodes of acid rain, a phenomenon well recorded since the end of the 1980s. However, little we know about how urban trees respond to acid rain in the city. Here we present how simulated acid rain causes anatomical and changes in photosynthetic pigments in two of the most abundant urban trees in Mexico City: Liquidambar styraciflua L. and Fraxinus uhdei (Wenz.) Lingelsh. We first described the leaf anatomy of both species. Then, we used one-year-old trees sprayed with sulfuric acid solutions at pH 2.5 and 3.8, and evaluated visible leaf damage, anatomical alterations, and chlorophyll contents. In both species, the pH 2.5 caused cuticle alterations and areas of total tissue destruction. L. styraciflua showed greater sensitivity, but we discuss some of the tolerance mechanisms. Finally, acid rain also reduced the chlorophyll contents. These results contribute toward a catalogue of urban tree species to describe pollution-induced damages, and the identification of tolerant species useful for short- and mid-term detection of environmental crisis, in cities with similar environmental conditions and urban tree composition.

Temperature dependent spectroscopic and excited state dynamics of 3-hydroxychromones with electron donor and acceptor substituents.

We have studied the photophysical and photochemical behavior of three compounds derived from 3-hydroxychromone (3-HC), capable of undergoing excited state proton transfer (ESIPT). The compounds have two substituents, located in positions 2 and 7, one on each ring of the 3-HC heterocycle. The substituent pattern shows different electron donating and acceptor features. The compounds were studied by absorption and emission spectroscopy, steady state anisotropy, and time resolved emission spectroscopy (TRES) as a function of temperature. Results were interpreted using time dependent density functional theory calculations. Compared to reference compounds of 3-HC substituted only in the 2 position, the compounds show similar absorption and emission spectra, shifted 20-30 nm to higher wavelengths due to extended conjugation. TRES shows the existence of ESIPT in the thermodynamic equilibrium regime. This process is endothermic in all three compounds. The different behavior compared to monosubstituted 3-HC is attributed to the extended conjugation and to the electron donor acceptor character of the substituents, which has a more pronounced effect when the electron acceptor is located in position 2.

A quantum-mechanics molecular-mechanics scheme for extended systems.

We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car-Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions. With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO2 anatase (1 0 1) solid-liquid interface. This investigation suggests that the inclusion of a second monolayer of H2O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces.

Adsorption of R-OH molecules on TiO2 surfaces at the solid-liquid interface.

The exploration of TiO2 surface reactivity from first-principles calculations has been almost always limited to the gas phase, even though most of the chemically relevant applications of this interface involve the solid-liquid boundary. The reason for this limitation is the complexity of the solid-liquid interface, which poses a serious challenge to standard ab initio methodologies as density functional theory (DFT). In this work we study the interaction of H2O, CH3OH, H2O2, and HCO2H with anatase (101) and rutile (110) surfaces in aqueous solution, employing a continuum solvation model in a DFT framework in periodic boundary conditions [ J. Chem. Phys. 2009 , 131 , 174108 ]. Different adsorption configurations were analyzed, examining the effect of the first water monolayer explicitly included in the simulation. For water and methanol, molecular adsorption was found to be the most stable in the presence of the solvent, while for hydrogen peroxide the preferred configuration depended on the surface. The explicit inclusion of the first water monolayer turns out to be important since it may play a role in the stabilization of the adsorbates at the interface. In general, the slightly positive adsorption energy values obtained (with respect to water) suggest that CH3OH and H2O2 will poorly adsorb from an aqueous solution at the titania surface. Among the three species investigated other than water, the formic acid was the only one to exhibit a higher affinity for the surface than H2O.

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.