In this work, a range of van der Waals type density functionals are applied to the H2O/NaCl(001) and H2O/MgO(001) interface systems to explore the effect of an explicit dispersion treatment. The functionals we use are the self-consistent vdW functionals vdW-DF, vdW-DF2, optPBE-vdW, optB88-vdW, optB86b-vdW, and vdW-DF-cx, as well as the dispersion-corrected PBE-TS and PBE-D2 methods; they are all compared with the standard PBE functional. For both NaCl(001) and MgO(001), we find that the dispersion-flavoured functionals stabilize the water-surface interface by approximately 20%-40% compared to the PBE results. For NaCl(001), where the water molecules remain intact for all overlayers, the dominant contribution to the adsorption energy from "density functional theory dispersion" stems from the water-surface interactions rather than the water-water interactions. The optPBE-vdW and vdW-DF-cx functionals yield adsorption energies in good agreement with available experimental values for both NaCl and MgO. To probe the strengths of the perturbations of the adsorbed water molecules, we also calculated water dipole moments and found an increase up to 85% for water at the MgO(001) surface and 70% at the NaCl(001) surface, compared to the gas-phase dipole moment.

Combining classical force fields for the Hartree-Fock (HF) part and the method of increments for post-HF contributions, we calculate the cohesive energy of the ordered and randomly disordered nitrous oxide (N2 O) solid. At 0 K, ordered N2 O is most favorable with a cohesive energy of -27.7 kJ/mol. At temperatures above 60 K, more disordered structures become compatible and a phase transition to completely disordered N2 O is predicted. Comparison with experiment in literature suggests that experimentally prepared N2 O crystals are mainly disordered due to a prohibitively high activation energy of ordering processes. © 2015 Wiley Periodicals, Inc.

We assess the consequences of the interface model—embedded‐cluster or periodic‐slab model—on the ability of DFT calculations to describe charge transfer (CT) in a particularly challenging case where periodic‐slab calculations indicate a delocalized charge‐transfer state. Our example is Cu atom adsorption on ZnO(10 0), and in fact the periodic slab calculations indicate three types of CT depending on the adsorption site: full CT, partial CT, and no CT. Interestingly, when full CT occurs in the periodic calculations, the calculated Cu atom adsorption energy depends on the underlying ZnO substrate supercell size, since when the electron enters the ZnO it delocalizes over as many atoms as possible. In the embedded‐cluster calculations, the electron transferred to the ZnO delocalizes over the entire cluster region, and as a result the calculated Cu atom adsorption energy does not agree with the value obtained using a large periodic supercell, but instead to the adsorption energy obtained for a periodic supercell of roughly the same size as the embedded cluster. Different density functionals (of GGA and hybrid types) and basis sets (local atom‐centered and plane‐waves) were assessed, and we show that embedded clusters can be used to model Cu adsorption on ZnO(10 0), as long as care is taken to account for the effects of CT. © 2015 Wiley Periodicals, Inc.

We assess the consequences of the interface model-embedded-cluster or periodic-slab model-on the ability of DFT calculations to describe charge transfer (CT) in a particularly challenging case where periodic-slab calculations indicate a delocalized charge-transfer state. Our example is Cu atom adsorption on ZnO(10 (1) over bar0), and in fact the periodic slab calculations indicate three types of CT depending on the adsorption site: full CT, partial CT, and no CT. Interestingly, when full CT occurs in the periodic calculations, the calculated Cu atom adsorption energy depends on the underlying ZnO substrate supercell size, since when the electron enters the ZnO it delocalizes over as many atoms as possible. In the embedded-cluster calculations, the electron transferred to the ZnO delocalizes over the entire cluster region, and as a result the calculated Cu atom adsorption energy does not agree with the value obtained using a large periodic supercell, but instead to the adsorption energy obtained for a periodic supercell of roughly the same size as the embedded cluster. Different density functionals (of GGA and hybrid types) and basis sets (local atom-centered and plane-waves) were assessed, and we show that embedded clusters can be used to model Cu adsorption on ZnO(10 (1) over bar0), as long as care is taken to account for the effects of CT. (C) 2015 Wiley Periodicals, Inc.

Using hybrid density functional theory, we investigate structural and electronic properties of small Cu-n clusters (with n <= 9) adsorbed on the nonpolar ZnO(10 (1) over bar0) surface. The Cu clusters grow in a planar fashion up to a size of six atoms, after which the clusters take on a polyhedral shape. We find even odd alternations with respect to both duster stability (for n = 1-6) and cluster charge, as a function of the number of atoms. Even-numbered dusters are always charge-neutral, while odd-numbered clusters can become positively charged by donation of an electron to the ZnO conduction band, which can be traced back to the fact that the ionization energies of odd-numbered gas-phase Cu dusters are lower than for even-numbered ones. The most stable adsorbed odd-numbered clusters are neutral and planar for n <= 3 and positively charged and polyhedral for n >= 7. For n = 5, both neutral planar and positively charged polyhedral configurations are similarly stable.

Molecular dynamics simulations is an important application in theoretical chemistry, and with the large high-performance computing resources available today the programs also generate huge amounts of output data. In particular in life sciences, with complex biomolecules such as proteins, simulation projects regularly deal with several terabytes of data. Apart from the need for more cost-efficient storage, it is increasingly important to be able to archive data, secure the integrity against disk or file transfer errors, to provide rapid access, and facilitate exchange of data through open interfaces. There is already a whole range of different formats used, but few if any of them (including our previous ones) fulfill all these goals. To address these shortcomings, we present Trajectory Next Generation (TNG)a flexible but highly optimized and efficient file format designed with interoperability in mind. TNG both provides state-of-the-art multiframe compression as well as a container framework that will make it possible to extend it with new compression algorithms without modifications in programs using it. TNG will be the new file format in the next major release of the GROMACS package, but it has been implemented as a separate library and API with liberal licensing to enable wide adoption both in academic and commercial codes. (c) 2013 Wiley Periodicals, Inc.

The interaction between water molecules and small Cu clusters (up to a size of four atoms) adsorbed on the nonpolar ZnO(10 (1) over bar0) surface has been studied using hybrid density functional theory. We find that the water molecules can give rise to different scenarios: (i) In contrast to water adsorption on the clean ZnO(10 (1) over bar0) surface, which occurs molecularly, the first water molecule often preferentially dissociates upon adsorption on the Cu cluster, which may be a key step in the watergas shift reaction. (ii) While the adsorption of the first water molecule on the adsorbed Cu clusters is always more favorable than the adsorption on the bare ZnO surface, the opposite is true for the second molecule. (iii) As a water molecule adsorbs on the adsorbed Cu atom, it induces charge transfer between the Cu and the ZnO, so that an electron from the Cu atom populates the ZnO conduction band (giving an oxidized Cu species). (iv) Water molecule adsorption on the adsorbed Cu trimer results in a spontaneous dissociation of the Cu trimer into an adsorbed dimer and an adsorbed atom, after which the water molecule adsorbs on the atom, again resulting in the Cu-ZnO charge transfer. We also show that the use of a hybrid density functional gives qualitatively different results as compared to a semilocal density functional for this system, and we explain this in terms of the underestimation of the ZnO band gap obtained with the semilocal functional.

Hellström, M. 2015. Chemistry and Physics of Cu and H2O on ZnO Surfaces. Electron Transfer, Surface Triangles, and Theory. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1207. 50 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-9111-6. This thesis discusses the chemistry and physics of Cu and H2O on ZnO surfaces, based primarily on results from quantum chemical calculations. The underlying context is heterogeneous catalysis, where Cu/ZnO-mixtures are used in the industrial synthesis of methanol and in the water gas shift reaction. Electron transfer between small Cu clusters and ZnO is central to this thesis, as are the design and use of models that can describe realistic and very large-scale ZnO surface structures while still retaining the electronic nature of the system. Method and model enhancements as well as tests and validations constitute a large part of this thesis. The thesis demonstrates that the charges of small Cu clusters, adsorbed on the non-polar ZnO(1010) surface, depend on whether the Cu clusters contain an even or odd number of atoms, and whether water is present (water can induce electron transfer from Cu to ZnO). On the polar Zn-terminated ZnO(0001) surface, Cu becomes negatively charged, which causes it to attract positively charged subsurface defects and to wet the ZnO(0001) surface at elevated temperatures. When a Cu cluster on a ZnO surface becomes positively charged, this happens because it donates an electron to the ZnO conduction band. Hence, it is necessary to use a method which describes the ZnO band gap correctly, and we show that a hybrid density functional, which includes a fraction of Hartree-Fock exchange, fulfills this requirement. When the ZnO conduction band becomes populated by electrons from Cu, band-filling occurs, which affects calculated adsorption energy under periodic boundary conditions to the zero coverage (isolated adsorbate, infinite supercell) limit. A part of this thesis concerns the parameterization of the computationally very efficient SCC-DFTB method (density functional based tight binding with self-consistent charges), in a multi-scale modeling approach. Our findings suggest that the SCC-DFTB method satisfactorily describes the interaction between ZnO surfaces and water, as well as the stabilities of different surface reconstructions (such as triangularly and hexagonally shaped pits) at the polar ZnO(0001) and ZnO(0001) surfaces.

Interactions between the group XII metals Zn2+ and Cd2+ and amino acid residues play an important role in biology due to the prevalence of the first and the toxicity of the second. Estimates of the interaction energies between the ions and relevant residues in proteins are however difficult to obtain. This study reports on calculated interaction energy curves for small complexes of Zn2+ or Cd2+ and amino acid mimics (acetate, methanethiolate, and imidazole) or water. Given that many applications and models (e.g., force fields, solvation models, etc.) begin with and rely on an accurate description of gas-phase interaction energies, this is where our focus lies in this study. Four density functional theory (DFT)-functionals and MP2 were used to calculate the interaction energies not only at the respective equilibrium distances but also at a relevant range of ion-ligand separation distances. The calculated values were compared with those obtained by CCSD(T). All DFT-methods are found to overestimate the magnitude of the interaction energy compared to the CCSD(T) reference values. The deviation was analyzed in terms of energy components from localized molecular orbital energy decomposition analysis scheme and is mostly attributed to overestimation of the polarization energy. MP2 shows good agreement with CCSD(T) [root mean square error (RMSE)=1.2 kcal/mol] for the eight studied complexes at equilibrium distance. Dispersion energy differences at longer separation give rise to increased deviations between MP2 and CCSD(T) (RMSE=6.4 kcal/mol at 3.0 angstrom). Overall, the results call for caution in applying DFT methods to metalloprotein model complexes even with closed-shell metal ions such as Zn2+ and Cd2+, in particular at ion-ligand separations that are longer than the equilibrium distances. (c) 2013 Wiley Periodicals, Inc.

We present a simple method, the "band-filling correction", to calculate accurate adsorption energies (Eads) in the low coverage limit from finite-size supercell slab calculations using DFT. We show that it is necessary to use such a correction if charge transfer takes place between the adsorbate and the substrate, resulting in the substrate bands either filling up or becoming depleted. With this correction scheme, we calculate Eads of an isolated Cu atom adsorbed on the ZnO(101̅0) surface. Without the correction, the calculated Eads is highly coverage-dependent, even for surface supercells that would typically be considered very large (in the range from 1 nm × 1 nm to 2.5 nm × 2.5 nm). The correction scheme works very well for semilocal functionals, where the corrected Eads is converged within 0.01 eV for all coverages. The correction scheme also works well for hybrid functionals if a large supercell is used and the exact exchange interaction is screened.

The formation of Cu dimers on the ZnO(10$\overline{1}$0) surface has been studied using hybrid density functional theory. Depending on the adsorption site, Cu atoms are found to adsorb with either oxidation state 0 or $+$1. In the latter case, the Cu atom has donated an electron to the ZnO conduction band. The two modes of adsorption display similar stability at low coverages, while at higher coverages the neutral species is more stable. Single Cu atoms diffuse across the ZnO(10$\overline{1}$0) surface with small barriers of migration (0.3--0.4 eV) along ZnO[1$\overline{2}$10], repeatedly switching their oxidation states, while the barrier along ZnO[0001] is significantly higher ($>$1.5 eV). The formation of a Cu dimer from two adsorbed Cu atoms is energetically favorable with two competing structures of similar stability, both being charge neutral. The minimum energy paths for Cu atom diffusion and dimer formation are characterized by at least one of the two Cu atoms being in oxidation state 0.

We report the observation of sequential Penning ionization of dopants by metastable helium atoms in helium nano-droplets resulting in doubly charged ions. Strong charge induced dipole-interaction between the excited helium atom and the target ion provides a high probability for the transfer of the internal energy of the excited helium atom to the dopant ion. This process may also lead subsequently to a Coulomb explosion of molecular or cluster dopants.

The formation of Cu dimers on the ZnO(10 (1) over bar0) surface has been studied using hybrid density functional theory. Depending on the adsorption site, Cu atoms are found to adsorb with either oxidation state 0 or +1. In the latter case, the Cu atom has donated an electron to the ZnO conduction band. The two modes of adsorption display similar stability at low coverages, while at higher coverages the neutral species is more stable. Single Cu atoms diffuse across the ZnO(10 (1) over bar0) surface with small barriers of migration (0.3-0.4 eV) along ZnO[1 (2) over bar 10], repeatedly switching their oxidation states, while the barrier along ZnO[0001] is significantly higher (>1.5 eV). The formation of a Cu dimer from two adsorbed Cu atoms is energetically favorable with two competing structures of similar stability, both being charge neutral. The minimum energy paths for Cu atom diffusion and dimer formation are characterized by at least one of the two Cu atoms being in oxidation state 0.

In the quest towards coarse-grained potentials and new water models, we present an extension of the force matching technique to parameterize an all-atom force field for rigid water. The methodology presented here allows to improve the matching procedure by first optimizing the weighting exponents present in the objective function. A new gauge for unambiguously evaluating the quality of the fit has been introduced; it is based on the root mean square difference of the distributions of target properties between reference data and fitted potentials. Four rigid water models have been parameterized; the matching procedure has been used to assess the role of the ghost atom in TIP4P-like models and of electrostatic damping. In the former case, burying the negative charge inside the molecule allows to fit better the torques. In the latter, since short-range interactions are damped, a better fit of the forces is obtained. Overall, the best performing model is the one with a ghost atom and with electrostatic damping. The approach shown in this paper is of general validity and could be applied to any matching algorithm and to any level of coarse graining, also for non-rigid molecules.

Recently many various research groups have devoted a huge effort to develop a realistic classical force field for ions in water. The parametrization techniques used could be gathered into two classes: (i) fit of the ab initio potential energy surface for clusters at gas phase, and (ii) fit of experimental properties. For both classes of force fields, a high level of accuracy has been achieved, which has led to important improvements in the modeling of ion–water systems. In this paper a new, complementary, approach is proposed to overcome the limitations and to get a deeper insight into the atomistic description of ion–water interactions. We use the recently developed force matching method to parametrize classical halide–water force fields for three different water models. Here we discuss both methodological issues and the level of agreement between the results obtained using this method to Car–Parrinello simulation results.

We study how the ultrafast intermolecular hopping of electrons excited from the water O1s core level into unoccupied orbitals depends on the local molecular environment in liquid water. Our probe is the resonant Auger decay of the water O1s core hole (lifetime ∼3.6 fs), by which we show that the electron-hopping rate can be significantly reduced when a first-shell water molecule is replaced by an atomic ion. Decays resulting from excitations at the O1s post-edge feature (∼540 eV) of 6 m LiBr and 3 m MgBr(2) aqueous solutions reveal electron-hopping times of ∼1.5 and 1.9 fs, respectively; the latter represents a 4-fold increase compared to the corresponding value in neat water. The slower electron-hopping in electrolytes, which shows a strong dependence on the charge of the cations, can be explained by ion-induced reduction of water-water orbital mixing. Density functional theory electronic structure calculations of solvation geometries obtained from molecular dynamics simulations reveal that this phenomenon largely arises from electrostatic perturbations of the solvating water molecules by the solvated ions. Our results demonstrate that it is possible to deliberately manipulate the rate of charge transfer via electron-hopping in aqueous media.

The hydroxylation structural features of the first adsorption layer and its connection to proton transfer reactivity have been studied for the ZnO-liquid water interface at room temperature. Molecular dynamics simulations employing the ReaxFF forcefield were performed for water on seven ZnO surfaces with varying step concentrations. At higher water coverage a higher level of hydroxylation was found, in agreement with previous experimental results. We have also calculated the free energy barrier for transferring a proton to the surface, showing that stepped surfaces stabilize the hydroxylated state and decrease the water dissociation barrier. On highly stepped surfaces the barrier is only 2 kJ/mol or smaller. Outside the first adsorption layer no dissociation events were found during almost 100 ns of simulation time; this indicates that these reactions are much more likely if catalyzed by the metal oxide surface. Also, when exposed to a vacuum, the less stepped surfaces stabilize adsorption beyond monolayer coverage.