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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.

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 (N2O) solid. At 0 K, ordered N2O 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 N2O is predicted. Comparison with experiment in literature suggests that experimentally prepared N2O crystals are mainly disordered due to a prohibitively high activation energy of ordering processes.

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.

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.

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.

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 Å). 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.

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.

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 local electronic structure of glycine in neutral, basic, and acidic aqueous solution is studied experimentally by X-ray photoelectron spectroscopy and theoretically by molecular dynamics simulations accompanied by first-principle electronic structure and spectrum calculations. Measured and computed nitrogen and carbon is binding energies are assigned to different local atomic environments, which are shown to be sensitive to the protonation/deprotonation of the amino and carboxyl functional groups at different pH values. We report the first accurate computation of core-level chemical shifts of an aqueous solute in various protonation states and explicitly show how the distributions of photoelectron binding energies (core-level peak widths) are related to the details of the hydrogen bond configurations, i.e. the geometries of the water solvation shell and the associated electronic screening. The comparison between the experiments and calculations further enables the separation of protonation-induced (covalent) and solvent-induced (electrostatic) screening contributions to the chemical shifts in the aqueous phase. The present core-level line shape analysis facilitates an accurate interpretation of photoelectron spectra from larger biomolecular solutes than glycine.

The hydroxylation structural features of the first adsorption layer and its connection to proton transfer reactivity has 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 concentration. 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 stabilizes the hydroxylated state and decreases 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 observed during almost 100 ns of simulation time; this indicates that these reactions are much more likely if catalysed by the metal oxide surface. Also, when exposed to a vacuum, the less stepped surfaces stabilizes adsorption beyond monolayer coverage.

We study how the ultrafast electron transfer between H2O molecules in liquid water upon absorption of soft X-ray radiation depends on the local molecular binding environment. Our probe is the resonant Auger-decay of the water O1s core-hole (~3.6 fs), by which we show that efficiency for electron delocalization 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 6m LiBr and 3m MgBr2 aqueous solutions reveal electron hopping-times of approximately 1.5 and 1.9 fs, respectively – the latter represents a four-fold increase compared to the corresponding value in neat water. The slower electron delocalization 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 (DFT) electronic structure calculations of solvation geometries obtained from molecular dynamics simulations reveal that this phenomenon largely arises from electrostatic perturbations of ions on the solvating water molecules. Our results demonstrate that it is possible to deliberately manipulate charge-transfer rates in aqueous media.

Molecular dynamics and electric field strength simulations are performed in order to quantify the structural, dynamic, and vibrational properties of non-H-bonded (dangling) OH groups in the hydration shell of neopentane, as well as in bulk water. The results are found to be in good agreement with the experimentally observed high-frequency (similar to 3660 cm(-1)) OH band arising from the hydration shell of neopentanol dissolved in HOD/D2O, obtained by analyzing variable concentration Raman spectra using multivariate curve resolution (Raman-MCR). The simulation results further indicate that hydration shell dangling OH groups preferentially point toward the central carbon atom of neopentane to a degree that increases with the lifetime of the dangling OH.

The OH− ion in water is studied using a CPMD/BLYP + QMelectronic + QMvibrational approach. The ion resides in a cage of water molecules, which are H-bonded among each other, and pinned by H-bonding to the ion’s O atom. The water network keeps the ‘on-top’ water in place, despite the fact that this particular ion-water pair interaction is non-binding. The calculated OH− vibrational peak maximum is at ∼3645 cm−1 (experiment ∼3625 cm−1) and the shift with respect to the gas-phase is ∼ +90 cm−1 (experiment +70 cm−1). The waters molecules on each side of the ion (O and H) induce a substantial OH− vibrational blueshift, but the net effect is much smaller than the sum. A parabolic ‘frequency-field’ relation qualitatively explains this non-additivity. The calculated ‘in-liquid’ ν(OH−) anharmonicity is 85 cm−1.

The anharmonic OH stretching vibrational frequencies, nu(OH), for the first-shell water molecules around the Li+, Ca2+, Mg2+, and Al3+ ions in dilute aqueous solutions have been calculated based on classical molecular dynamics (MD) simulations and quantum-mechanical (QM) calculations. For Li+(aq), Ca2+(aq), Mg2+(aq), and Al3+(aq), our calculated IR frequency shifts, Delta nu(OH), with respect to the gas-phase water frequency, are about -300, -350, -450, and -750 cm(-1), compared to -290, -290, -420, and -830 cm(-1) from experimental infrared (IR) studies. The agreement is thus quite good, except for the order between Li+ and Ca2+. Given that the polarizing field from the Ca2+ ion ought to be larger than that from Li+(aq), our calculated result seems reasonable. Also the absolute OH frequencies agree well with experiment. The method we used is a sequential four-step procedure: QM(electronic) to make a force field+MD simulation +QM(electronic) for point-charge-embedded Mn+ (H2O)(x)(first shell) (H2O)(y)(second shell) (H2O)(z)(third shell) clusters+QM(vibrational) to yield the OH spectrum. The many-body Ca2+-water force-field presented in this paper is new. IR intensity-weighting of the density-of-states frequency distributions was carried out by means of the squared dipole moment derivatives.

We report the observation of the ejection of electrons caused by collisions of excited atoms with ions, rather than neutrals, leading to the production of doubly charged ions. Doping superfluid He droplets with methyl iodide and exposing them to electrons enhances the formation of doubly charged iodine atoms at the threshold for the production of two metastable He atoms. These observations point toward a novel ionization process where doubly charged ions are produced by sequential Penning ionization. In some cases, depending on the neutral target, the process also leads to a subsequent Coulomb explosion of the dopant.

The surface structures of ZnO surfaces and ZnO nanoparticles, with and without water, were studied with a ReaxFF reactive force field (FF) and molecular dynamics (MD) simulations. The force field parameters were fitted to a training set of data points (energies, geometries, charges) derived from quantum-mechanical DFT/B3LYP calculations. The ReaxFF model predicts structures and reactions paths at a fraction of the computational cost of the quantum-mechanical calculations and as such allows dynamical simulations of reactive process for large (>>1000 atoms) and long (> 100 ps) timescales. Our simulations give the following results for the (10 (1) over bar0) surface. (i) The alternating H-bond pattern of Meyer et al. for a single monolayer coverage is reproduced by our simulations. This pattern is maintained at elevated temperatures (COOK). (ii) At coverages beyond one water monolayer we observe enhanced ZnO hydroxylation at the expense of ZnO hydration. (iii) This is achieved through an entirely new H-bond pattern mediated via the water molecules in the second layer above the ZnO surface. (iv) During a water desorption simulation at T=300K we observe that the desorption rate slows significantly when two monolayers remain. (v) Simulations of nanoparticles in the presence and absence of water suggest that water plays a key role in the determination of nanoparticle shape by catalyzing surface reconstruction reactions and stabilizing specific surface structures., Dep. of Materials Chemistry, The Ångström Laboratory, Uppsala University, Box 538, S-75121 Uppsala, Sweden

The surface structures of ZnO surfaces and ZnO nanoparticles, with and without water, were studied with a reactive force field (FF) within the ReaxFF framework, and molecular dynamics (MD) simulations. The force field parameters were fitted to a training set of data points (energies, geometries, charges) derived from quantum-mechanical B3LYP calculations. The ReaxFF model predicts structures and reactions paths at a fraction of the computational cost of the quantum-mechanical calculations. Our simulations give the following results for the (10-10) surface. (i) The alternating H-bond pattern of Meyer et al. for one monolayer coverage is reproduced and maintained at higher temperatures. (ii) Coverages beyond one water monolayer enhances ZnO hydroxylation at the expense of ZnO hydration. (iii) This is achieved through an entirely new H-bond pattern mediated via the water molecules in the second layer above the ZnO surface. (iv) During a desorption process, the desorption rate slows significantly when two monolayers remain. Simulations of nanoparticles in water suggest that these conclusions are relevant also in the nano case.

The oxygen self-diffusion in partially reduced CeO2 has been investigated by large-scale Molecular Dynamics simulations, in the temperature range between 800 and 2200 K. Simulation boxes with ~ 4100 and ~ 33,000 ions were investigated for randomly distributed oxygen vacancies and Ce3+ ions. Our calculated self-diffusion coefficients vary between 10−8 and 10−6 cm2/s in the temperature range studied. The activation energy and D0 values are also reported. The oxygen diffusion mechanism has also been analyzed: only a 100 vacancy mechanism is observed.

The optimized geometry, energetics, and vibrational properties of Al(D2O) clusters, with n=1,2,4, and 6, have been studied using plane waves, different local basis sets, different methodologies [density-functional theory, MP2, CCSD(T)], and different functionals (BLYP, PBE). Moreover, Car-Parrinello molecular-dynamics (MD) simulations using the BLYP functional, plane waves, and the Vanderbilt ultrasoft pseudopotentials have been performed for an aqueous Al3+ solution with 1 ion and 32 D2O molecules in a periodic box at room temperature, studied for 10 ps. The cluster calculations were performed to pinpoint possible shortcomings of the electronic structure description used in the Car-Parinello MD (CPMD) simulation. For the clusters, the hydration structure and interaction energies calculated with the `BLYP/plane-wave' approach agree well with high-level ab initio methods but the exchange-correlation functional introduces errors in the OD stretching frequencies (both in the absolute values and in the ion-induced shifts). For the aqueous solution, the CPMD simulation yields structural properties in good agreement with experimental data. The CPMD-simulated OD stretching vibrational band for the first-shell water molecules around Al3+ is strongly downshifted by the influence of the ion and is compared with experimental data from the literature. To make such a comparison meaningful, the influences of a number of systematic effects have been addressed, such as the exchange-correlation functional, the fictitious electron mass, anharmonicity effects, and the small box size in the simulation. Each of these factors (except the last one) is found to affect the OD frequency by 100 cm–1 or more. The final "corrected" frequencies agree with experiment within ~30 cm–1 for bulk water but are too little downshifted for the first-shell Al3+(aq) water molecules (by ~200 cm–1).

The solvation shell structure and dynamics of a single Cu2+ ion in a periodic box with 32 water molecules under ambient conditions has been investigated using Car–Parrinello molecular dynamics simulations in a time-window of 18 ps. Five-fold coordination with four equidistant equatorial water molecules at 2.00 and one axial water molecule at 2.45 from the Cu2+ ion is found. A hole without water molecules is found on the opposite side of the axial water. The ion–water bonding character for the equatorial water molecules is different from that of the axial water molecules, as shown by a localized orbital analysis of the electronic structure. Moreover, the calculated OD stretching vibrational band for the equatorial water molecules lies ca. 175 cm–1 below the axial-water band, in good agreement with experimental data. The equatorial-water band lies below, and the axial-water band above, the pure liquid D2O band, also in agreement with experimental data.

The optimized geometry and energetic properties of Fe(D2O)n3+ clusters, with n = 4 and 6, have been studied with density-functional theory calculations and the BLYP functional, and the hydration of a single Fe3+ ion in a periodic box with 32 water molecules at room temperature has been studied with Car-Parrinello molecular dynamics and the same functional. We have compared the results from the CPMD simulation with classical MD simulations, using a flexible SPC-based water model and the same number of water molecules, to evaluate the relative strengths and weaknesses of the two MD methods. The classical MD simulations and the CPMD simulations both give Fe-water distances in good agreement with experiment, but for the intramolecular vibrations, the classical MD yields considerably better absolute frequencies and ion-induced frequency shifts. On the other hand, the CPMD method performs considerably better than the classical MD in describing the intramolecular geometry of the water molecule in the first hydration shell and the average first shell···second shell hydrogen-bond distance. Differences between the two methods are also found with respect to the second-shell water orientations. The effect of the small box size (32 vs 512 water molecules) was evaluated by comparing results from classical simulations using different box sizes; non-negligible effects are found for the ion-water distance and the tilt angles of the water molecules in the second hydration shell and for the O-D stretching vibrational frequencies of the water molecules in the first hydration shell.

The average OH stretching vibrational frequency for the water molecules in the first hydration shell around a Li+ ion in a dilute aqueous solution was calculated by a hybrid molecular dynamics + quantum-mechanical ("MD + QM") approach. Using geometry configurations from a series of snapshots from an MD simulation, the anharmonic, uncoupled OH stretching frequencies were calculated for 100 first-shell OH oscillators at the B3LYP and HF/6-31G(d,p) levels of theory, explicitly including the first shell and the relevant second shell water molecules into charge-embedded supermolecular QM calculations. Infrared intensity-weighting of the density-of-states (DOS) distributions by means of the squared dipole moment derivatives (which vary by a factor of 20 over the OH stretching frequency band at the B3LYP level), changes the downshift from approximately -205 to -275 cm-1 at the B3LYP level. Explicit inclusion of relevant third-shell water molecules in the supermolecular cluster leads to a further downshift by approximately -30 cm-1. Our final estimated average downshift is approximately -305 cm-1. The experimental value lies somewhere in the range between -290 and -420 cm-1. Also, the absolute (OH) frequency is well reproduced in our calculations. "In-liquid" instantaneous correlation curves between (OH) and various typical H-bond strength parameters such as R(O···O), R(H···O), the intramolecular OH bond length, and the IR intensity are presented. Some of these correlations are robust and persist also for the rather distorted instantaneous geometries in the liquid; others are less so.

We report the soft-X-ray absorption and emission studies of NaCl, MgCl2, and AlCl3 in water solutions. The influences of cations on the water molecular structure can be seen as the absorption threshold edge shifted to high energy in the X-ray absorption spectra; the mixing of molecular orbital in 3a1 symmetry is reinforced as the intensity of 3a1 is further reduced; and the 1b1-emission peak shows the broadening and shift differently for Na+, Mg2+, and Al3+ water solutions, which indicates that the charge difference of the cations may not be the only playing role being responsible to the interactions between the cations and water molecules.

Molecular dynamics simulations of single-ion Fe2+(aq) and Fe3+(aq) solutions have been performed with two rigid-water models (SPC and SPC/E) and a newly constructed SPC-based flexible-water model (SPC+CCL). The SPC+CCL water model in combination with effective Fe2+ and Fe3+ ion-water potentials manages to reproduce many experimental structural and dynamical properties of the solutions. Special attention is given to the large ion-induced frequency shifts of the OH stretching bands, which are also well reproduced by the SPC+CCL model.

Many-body potentials for the aqueous Li+, Na+, Mg2+, and Al3+ ions have been constructed from ab initio cluster calculations. Pure pair, effective pair, effective three-body, and effective polarizable models were created and used in subsequent molecular dynamics simulations. The structures of the first and second solvation shells were studied using radial distribution functions and angular-radial distribution functions. The effective three-body and polarizable potentials yield similar first-shell structures, while the contraction of the O–O distances between the first and second solvation shells is more pronounced with the polarizable potentials. The definition of the tilt angle of the water molecules around the ions is discussed. When a proper definition is used, it is found that for Li+, Mg2+, and Al3+ the water molecules prefer a trigonal orientation, but for Na+ a tetrahedral orientation (ion in lone-pair direction) is preferred. The self-diffusion coefficients for the water molecules and the ions were calculated; the ionic values follow the order obtained from experiment, although the simulated absolute values are smaller than experiment for Mg2+ and Al3+.