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  • 1.
    Ahlstrand, Emma
    et al.
    Linnæus University Centre for Biomaterials Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Friedman, Ran
    Interaction Energies Between Metal Ions (Zn2+ and Cd2+) and Biologically Relevant Ligands2013In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, no 23, p. 2554-2562Article in journal (Refereed)
    Abstract [en]

    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.

  • 2.
    Amira, Sami
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Derivation and evaluation of a flexible SPC model for liquid water2004In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 303, no 3, p. 372-334Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations of a new flexible water model are presented. The potential function is based on the simple point charge (SPC) model combined with an accurate experimental quartic intramolecular potential (CCL). This potential not only reproduces the key structural, dynamical and thermodynamical properties of liquid water, but also generates the correct values for both the absolute O–H vibrational frequency and the gas-to-liquid frequency shift. Thus, the model yields a value of ca. 3420 cm−1 for the peak maximum of the anharmonic OH stretching band for liquid water (experiment 3400 cm−1) and a corresponding gas-to-liquid downshift of −300 cm−1 (experiment −310 cm−1). The paper also emphasizes the importance of parameterizing correctly both the harmonic and anharmonic force constants in the gas-phase when developing flexible water models to be used in the liquid state.

  • 3.
    Amira, Sami
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Distorted fivefold coordination of Cu2+(aq) from a Car-Parrinello Molecular Dynamics Simulation2005In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 7, no 15, p. 2874-2880Article in journal (Refereed)
    Abstract [en]

    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.

  • 4.
    Amira, Sami
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    OD vibrations and hydration structure in an Al3+(aq) solution from a Car-Parrinello Molecular Dynamics Simulation2006In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 124, no 10, p. 104501-Article in journal (Refereed)
    Abstract [en]

    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).

  • 5.
    Amira, Sami
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Probst, Michael
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Molecular Dynamics simulation of Fe2+(aq) and Fe3+(aq)2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 1, p. 496-502Article in journal (Refereed)
    Abstract [en]

    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.

  • 6.
    Amira, Sami
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Zelin, Viktor
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Probst, Michael
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Car-Parrinello Molecular Dynamics simulation of Fe3+(aq)2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 29, p. 14235-14242Article in journal (Refereed)
    Abstract [en]

    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.

  • 7.
    Gotte, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Baudin, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Molecular dynamics study of oxygen self-diffusion in reduced CeO22007In: Solid State Ionics, ISSN 0167-2738, E-ISSN 1872-7689, Vol. 178, no 25-26, p. 1421-1427Article in journal (Refereed)
    Abstract [en]

    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.

  • 8. Guo, Jinghua
    et al.
    Augustsson, Andreas
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Materials Chemistry, Structural Chemistry. Department of Physics and Materials Science, Physics II.
    Kashtanov, S
    Spångberg, Daniel
    Chemistry, Department of Materials Chemistry, Structural Chemistry. Department of Physics and Materials Science, Physics II. strukturkemi.
    Nordgren, Joseph
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Materials Chemistry, Structural Chemistry. Department of Physics and Materials Science, Physics II.
    Hermansson, Kersti
    Chemistry, Department of Materials Chemistry, Structural Chemistry. Department of Physics and Materials Science, Physics II. strukturkemi.
    Luo, Yi
    The interaction of cations and liquid water studied by resonant soft-X-ray absorption and emission spectroscopy2005In: Journal of Electron Spectroscopy and Related Phenomena, Vol. 144-147, p. 287-290Article in journal (Refereed)
    Abstract [en]

    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.

  • 9.
    Hellström, Matti
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Broqvist, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Band-Filling Correction Method for Accurate Adsorption Energy Calculations: A Cu/ZnO Case Study2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 11, p. 4673-4678Article in journal (Refereed)
    Abstract [en]

    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.

  • 10.
    Hellström, Matti
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Broqvist, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Cu dimer formation mechanism on the ZnO(10(1)over-bar0) surface2012In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 86, no 23, p. 235302-Article in journal (Refereed)
    Abstract [en]

    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.

  • 11.
    Hellström, Matti
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Broqvist, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Small Cu Clusters Adsorbed on ZnO(10(1)over-bar0) Show Even-Odd Alternations in Stability and Charge Transfer2014In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, no 12, p. 6480-6490Article in journal (Refereed)
    Abstract [en]

    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.

  • 12.
    Hermansson, Kersti
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Pejov, Ljupco
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    PHYS 74-OH vibrational frequencies of hydration water in ionic aqueous solutions: A QM plus MD plus QM plus QM approach2008Conference paper (Refereed)
  • 13. Jalilehvand, F.
    et al.
    Spångberg, Daniel
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry, Structural Chemistry. strukturkemi.
    Lindqvist-Reis, P.
    Hermansson, Kersti
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry, Structural Chemistry. strukturkemi.
    Persson, I.
    Sandström, M.
    The hydration of the calcium ion. An EXAFS, large-angle X-ray scattering and molecular dynamics study.2001In: J. Amer. Chem. Soc., Vol. 123, p. 431-Article in journal (Refereed)
  • 14.
    Kebede, Getachew G.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Mitev, Pavlin D.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Broqvist, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Comparing van der Waals DFT methods for water on NaCl(001) and MgO(001)2017In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 146, article id 064703Article in journal (Other (popular science, discussion, etc.))
  • 15.
    Kersti, Hermansson
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Bopp, Philippe A.
    Department of Chemistry, Université Bordeaux 1, 351, Cours de la Libération Bld. A12, F-33405 Talence CEDEX, France.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Pejov, Ljupco
    Institute of Chemistry, Faculty of Science, Sts. Cyril and Methodius University, P.O. Box 162, 1000 Skopje, Republic of Macedonia.
    Mitev, Pavlin D.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    The vibrating hydroxide ion in water2011In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 514, no 1-3, p. 1-15Article in journal (Refereed)
    Abstract [en]

    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.

  • 16. Lundborg, Magnus
    et al.
    Apostolov, Rossen
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Gardenäs, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Lindahl, Erik
    An Efficient and Extensible Format, Library, and API for Binary Trajectory Data from Molecular Simulations2014In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, no 3, p. 260-269Article in journal (Refereed)
    Abstract [en]

    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. 

  • 17.
    Ottosson, Niklas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Børve, Knut
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Bergersen, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Saethre, Leif
    Faubel, Manfreg
    Pokapanich, Wandared
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Ohrwall, Gunnar
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Winter, Bernd
    On the Origins of Core-Electron Chemical Shifts of Small Biomolecules in Aqueous Solution: Insights from Photoemisson and ab Initio Calculations of Glycine(aq)2011In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 133, no 9, p. 3120-3130Article in journal (Refereed)
    Abstract [en]

    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.

  • 18.
    Ottosson, Niklas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Odelius, Michael
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Pokapanich, Wandared
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Svantqvist, Mattias
    Öhrwall, Gunnar
    Winter, Bernd
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Cations Strongly Reduce Electron Hopping-Times in Aqueous Solutions2011In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 133, no 34, p. 13489-13495Article in journal (Refereed)
    Abstract [en]

    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.

  • 19. Pejov, Ljupco
    et al.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Al3+, Ca2+, Mg2+, and Li+ in aqueous solution: Calculated first-shell anharmonic OH vibrations at 300 K2010In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 133, no 17, p. 174513-Article in journal (Refereed)
    Abstract [en]

    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.

  • 20. Pejov, Ljupco
    et al.
    Spångberg, Daniel
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry, Structural Chemistry. strukturkemi.
    Hermansson, Kersti
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry, Structural Chemistry. strukturkemi.
    Using MD Snapshots in ab Initio and DFT Calculations: OH Vibrations in the First Hydration Shell around Li+(aq)2005In: J. Phys. Chem. A, Vol. 109, no 23, p. 5144-5152Article in journal (Refereed)
    Abstract [en]

    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.

  • 21.
    Raymand, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Edvinsson, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Inorganic Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    van Duin, Adri
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Water adsorption beyond monolayer coverage on ZnO surfaces and nanoclusters2008In: SOLAR HYDROGEN AND NANOTECHNOLOGY III / [ed] Westin, G, 2008, Vol. 7044, p. E440-E440Conference paper (Refereed)
    Abstract [en]

    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.

  • 22.
    Raymand, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    van Duin, Adri
    Department of Mechanical and Nuclear Engineering, Penn State University, USA.
    Goddard III, William A.
    Materials and Process Simulation Center (MSC), California Institute of Technology, USA.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Hydroxylation Structure and Proton Transfer Reactivity at the Zinc Oxide-Water Interface2011In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 115, no 17, p. 8573-8579Article in journal (Refereed)
    Abstract [en]

    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.

  • 23.
    Raymand, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    van Duin, Adri
    Department of Mechanical and Nuclear Engineering, Penn State University, USA.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Goddard III, William A.
    Materials and Process Simulation Center (MSC), California Institute of Technology, USA.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Water adsorption on stepped ZnO surfaces from MD simulation2010In: Surface Science, ISSN 0039-6028, E-ISSN 1879-2758, Vol. 604, no 9-10, p. 741-752Article in journal (Refereed)
    Abstract [en]

    This work presents a ReaxFF reactive force-field for use in molecular dynamics simulations of the ZnO–water system. The force-field parameters were fitted to a data-set of energies, geometries and charges derived from quantum-mechanical B3LYP calculations. The presented ReaxFF model provides a good fit to the QM reference data for the ZnO–water system that was present in the data-set. The force-field has been used to study how water is adsorbed, molecularly or dissociatively, at monolayer coverage on flat and stepped ZnO surfaces, at three different temperatures (10 K, 300 K, and 600 K). The stepped surfaces were created by introducing steps along the (0 0 0 1)-direction on the -surface. Equilibrium between molecular and dissociated water was observed on the terraces, resulting in a half dissociated, half molecular water monolayer. The equilibrium between dissociated and molecular water on the surface was found to be reached quickly (<10 ps). When water molecules desorb and the coverage falls, the 1:1 water–hydroxyl ratio is maintained on terraces, while steps remain largely hydroxylated. The results show that structures that promote hydrogen bonding are favored and that the presence of steps promotes an increased level of hydroxylation in the water monolayers.

  • 24. Sala, Jonas
    et al.
    Guardia, Elvira
    Marti, Jordi
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Masia, Marco
    Fitting properties from density functional theory based molecular dynamics simulations to parameterize a rigid water force field2012In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 136, no 5, p. 054103-Article in journal (Refereed)
    Abstract [en]

    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.

  • 25. Sandström, M
    et al.
    Persson, I
    Jalilehvand, F
    Lindqvist-Reis, P.
    Spångberg, Daniel
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry, Structural Chemistry. strukturkemi.
    Hermansson, Kersti
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry, Structural Chemistry. strukturkemi.
    Hydration of some large and highly charged metal ions.2001In: J. Synchrotron Rad., Vol. 8, p. 657-Article in journal (Refereed)
  • 26. Schoebel, Harald
    et al.
    Bartl, Peter
    Leidlmair, Christian
    Daxner, Matthias
    Zoettl, Samuel
    Denifl, Stephan
    Maerk, Tilmann D.
    Scheier, Paul
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Mauracher, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Bohme, Diethard K.
    Sequential Penning Ionization: Harvesting Energy with Ions2010In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 105, no 24, p. 243402-Article in journal (Refereed)
    Abstract [en]

    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.

  • 27.
    Spångberg, Daniel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Guardia, Elvira
    Masia, Marco
    Aqueous halide potentials from force matching of Car-Parrinello data2012In: Computational and Theoretical Chemistry, ISSN 2210-271X, Vol. 982, p. 58-65Article in journal (Refereed)
    Abstract [en]

    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.

  • 28.
    Spångberg, Daniel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Effective three-body potentials for Li+(aq) and Mg2+(aq)2003In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 119, no 14, p. 7263-Article in journal (Refereed)
    Abstract [en]

    A method for the extraction of effective three-body potential parameters from high-level ab initio cluster calculations is presented and compared to effective pair potentials extracted at the same level. Dilute Li+(aq) and Mg2+(aq) solutions are used as test cases and long molecular-dynamics simulations using these newly developed potentials were performed. Resulting thermodynamical, structural, and dynamical properties are compared to experiment as well as to the empirical effective pair potentials of Åqvist. Moreover, a new time-saving method for the correction of cluster energies computed with a relatively cheap ab initio method, to yield expensive, high-level ab initio energies, is presented. The effective pair approach is shown to give inconsistent results when compared to the effective three-body potentials. The performance of three different charge compensation methods (uniform charge plasm, Bogusz net charge correction, and counter ions) is compared for a large number of different system sizes. For most properties studied here, the system-size dependence is found to be small for system sizes with 256 water molecules or more. However, for the self-diffusion coefficients, a 1/L dependence is found, i.e., a very large system-size dependence. A very simple method for correcting for this deficiency is proposed. The results for most properties are found to compare reasonably well to experiment when using the effective three-body potentials.

  • 29.
    Spångberg, Daniel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Many-body potentials for aqueous Li+, Na+, Mg2+ and Al3+: Comparison of effective three-body potentials and poliarizable models2004In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 120, no 10, p. 4829-4843Article in journal (Refereed)
    Abstract [en]

    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+.

  • 30.
    Spångberg, Daniel
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry, Structural Chemistry. strukturkemi.
    Hermansson, Kersti
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry, Structural Chemistry. strukturkemi.
    The solvation of Li+ and Na+ in acetonitrile from ab initio-derived many-body ion-solvent potentials2004In: Chemical Physics, Vol. 300, p. 165-176Article in journal (Refereed)
    Abstract [en]

    Several Li+- and Na+-acetonitrile models were derived from ab initio calculations at the counterpoise-corrected MP2/TZV++(d,p) level for distorted ion-(MeCN)n clusters with n=1, 4 and 6. Two different many-body ion-acetonitrile models were constructed: an effective three-body potential for use with the six-site effective pair model of Böhm et al., and an effective polarizable many-body model. The polarizable acetonitrile model used in the latter model is a new empirical model which was also derived in the present paper. Mainly for comparative purposes, two ion-acetonitrile pair potentials were also constructed from the ab initio cluster calculations: one pure pair potential and one effective pair potential. Using all these potential models, MD simulations in the NPT ensemble were performed for the pure acetonitrile liquid and for Li+(MeCN) and Na+(MeCN) solutions with 1 ion in 512 solvent molecules and with a simulation time of at least 120 ps per system. Thermodynamic properties, solvation-shell structure and the self-diffusion coefficient of the ions and of the solvent molecules were calculated and compared between the different models and with experimental data, where available. The Li+ ion is found to be four-coordinated when the new many-body potentials are used, in contrast to the six-coordinated structure obtained for the pure pair and effective pair potentials. The coordination number of Na+ is close to six for all the models derived here, although the coordination number becomes slightly smaller with the many-body potentials. For both ions, the solvent molecules in the first shell point their nitrogen ends towards the cation, while in the second shell the opposite orientation is the most common.

  • 31.
    Spångberg, Daniel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Larsson, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Trajectory NG: portable, compressed, general molecular dynamics trajectories2011In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 17, no 10, p. 2669-2685Article in journal (Refereed)
    Abstract [en]

    We present general algorithms for the compression of molecular dynamics trajectories. The standard ways to store MD trajectories as text or as raw binary floating point numbers result in very large files when efficient simulation programs are used on supercomputers. Our algorithms are based on the observation that differences in atomic coordinates/velocities, in either time or space, are generally smaller than the absolute values of the coordinates/velocities. Also, it is often possible to store values at a lower precision. We apply several compression schemes to compress the resulting differences further. The most efficient algorithms developed here use a block sorting algorithm in combination with Huffman coding. Depending on the frequency of storage of frames in the trajectory, either space, time, or combinations of space and time differences are usually the most efficient. We compare the efficiency of our algorithms with each other and with other algorithms present in the literature for various systems: liquid argon, water, a virus capsid solvated in 15 mM aqueous NaCl, and solid magnesium oxide. We perform tests to determine how much precision is necessary to obtain accurate structural and dynamic properties, as well as benchmark a parallelized implementation of the algorithms. We obtain compression ratios (compared to single precision floating point) of 1:3.3-1:35 depending on the frequency of storage of frames and the system studied.

  • 32.
    Spångberg, Daniel
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry, Structural Chemistry. strukturkemi.
    Lindqvist-Reis, P
    Jalilehvand, F
    Persson, I
    Hermansson, Kersti
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry, Structural Chemistry. strukturkemi.
    Model EXAFS spectra from MD data for hydrated Ca 2+ and A13+ ions2000In: J. Phys. Chem., Vol. B104, p. 1046-Article in journal (Refereed)
  • 33.
    Spångberg, Daniel
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry, Structural Chemistry. strukturkemi.
    Rey, R
    Hynes, J. T
    Hermansson, Kersti
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry, Structural Chemistry. strukturkemi.
    Rate and mechanisms for water exchange around Li+(aq) from MD simulations2003In: Physical Chemistry B, Vol. 107, no 18, p. 4470-4477Article in journal (Refereed)
  • 34. Tomlinson-Phillips, Jill
    et al.
    Davis, Joel
    Ben-Amotz, Dor
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Pejov, Ljupco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Structure and Dynamics of Water Dangling OH Bonds in Hydrophobic Hydration Shells: Comparison of Simulation and Experiment2011In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 115, no 23, p. 6177-6183Article in journal (Refereed)
    Abstract [en]

    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.

  • 35. Zöttl, S.
    et al.
    Schöbel, H.
    Bartl, P.
    Leidlmair, C.
    Daxner, M.
    Denifl, S.
    Märk, T. D.
    Scheier, P.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Mauracher, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Bohme, D. K.
    Energy harvesting in doped helium nano-droplets2012In: Journal of Physics, Conference Series, ISSN 1742-6588, E-ISSN 1742-6596, Vol. 388, no 13, p. 132003-Article in journal (Refereed)
    Abstract [en]

    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.

1 - 35 of 35
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