37 results on '"Daniel Spångberg"'
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2. Treatment of delocalized electron transfer in periodic and embedded cluster DFT calculations: The case of Cu on ZnO (10 1¯0).
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Matti Hellström, Daniel Spångberg, and Kersti Hermansson
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- 2015
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3. An efficient and extensible format, library, and API for binary trajectory data from molecular simulations.
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Magnus Lundborg, Rossen Apostolov, Daniel Spångberg, Anders Gärdenäs, David van der Spoel, and Erik Lindahl
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- 2014
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4. Water-Induced Oxidation and Dissociation of Small Cu Clusters on ZnO(101̅0)
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Peter Broqvist, Matti Hellström, Kersti Hermansson, and Daniel Spångberg
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General Energy ,Adsorption ,Chemistry ,Inorganic chemistry ,Molecule ,Physical and Theoretical Chemistry ,Photochemistry ,Dissociation (chemistry) ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials - Abstract
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 th ...
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- 2015
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5. Small Cu Clusters Adsorbed on ZnO(101̅0) Show Even–Odd Alternations in Stability and Charge Transfer
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Daniel Spångberg, Peter Broqvist, Matti Hellström, and Kersti Hermansson
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Chemistry ,Charge (physics) ,Stability (probability) ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Transfer (group theory) ,General Energy ,Adsorption ,Planar ,Computational chemistry ,Chemical physics ,Density functional theory ,Physical and Theoretical Chemistry ,Electronic properties - Abstract
Using hybrid density functional theory, we investigate structural and electronic properties of small Cu-n clusters (with n = 7. For n = 5, both neutral planar and positively charged polyhedral conf ...
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- 2014
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6. Interaction energies between metal ions (Zn2+ and Cd2+ ) and biologically relevant ligands
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Ran Friedman, Daniel Spångberg, Emma Ahlstrand, and Kersti Hermansson
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inorganic chemicals ,Cadmium ,animal structures ,Metal ions in aqueous solution ,chemistry.chemical_element ,Zinc ,Condensed Matter Physics ,Atomic and Molecular Physics, and Optics ,chemistry ,Computational chemistry ,Theoretical chemistry ,Density functional theory ,Physical and Theoretical Chemistry ,Amino acid residue ,circulatory and respiratory physiology - Abstract
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 ...
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- 2013
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7. Comparing van der Waals DFT methods for water on NaCl(001) and MgO(001)
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Getachew G. Kebede, Pavlin D. Mitev, Peter Broqvist, Daniel Spångberg, and Kersti Hermansson
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Chemistry ,General Physics and Astronomy ,Thermodynamics ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,symbols.namesake ,Dipole ,Adsorption ,Computational chemistry ,Yield (chemistry) ,0103 physical sciences ,Teoretisk kemi ,symbols ,Theoretical chemistry ,Molecule ,Density functional theory ,Physical and Theoretical Chemistry ,van der Waals force ,010306 general physics ,0210 nano-technology ,Dispersion (chemistry) ,Theoretical Chemistry - Abstract
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.
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- 2017
8. The vibrating hydroxide ion in water
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Imre Bakó, Daniel Spångberg, Kersti Hermansson, Philippe A. Bopp, Pavlin D. Mitev, and Ljupčo Pejov
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Car–Parrinello molecular dynamics ,010304 chemical physics ,Chemistry ,Inorganic chemistry ,Anharmonicity ,Analytical chemistry ,General Physics and Astronomy ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Ion ,Blueshift ,chemistry.chemical_compound ,0103 physical sciences ,Atom ,Molecule ,Hydroxide ,Physical and Theoretical Chemistry - Abstract
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.
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- 2011
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9. Hydroxylation Structure and Proton Transfer Reactivity at the Zinc Oxide−Water Interface
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Kersti Hermansson, Daniel Spångberg, Adri C. T. van Duin, William A. Goddard, and David Raymand
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Chemistry ,Inorganic chemistry ,Oxide ,Photochemistry ,Dissociation (chemistry) ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Catalysis ,Hydroxylation ,Metal ,chemistry.chemical_compound ,General Energy ,Adsorption ,visual_art ,Monolayer ,visual_art.visual_art_medium ,Physical and Theoretical Chemistry ,ReaxFF - Abstract
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.
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- 2011
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10. Trajectory NG: portable, compressed, general molecular dynamics trajectories
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Daniel Spångberg, Daniel S. D. Larsson, and David van der Spoel
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Floating point ,Chemistry ,Organic Chemistry ,Binary number ,Molecular Dynamics Simulation ,Data Compression ,Huffman coding ,Catalysis ,Single-precision floating-point format ,Computer Science Applications ,Inorganic Chemistry ,symbols.namesake ,Computational Theory and Mathematics ,Computational chemistry ,Compression (functional analysis) ,Compression ratio ,Trajectory ,Benchmark (computing) ,symbols ,Physical and Theoretical Chemistry ,Algorithm ,Algorithms - Abstract
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.
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- 2011
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11. Water adsorption on stepped ZnO surfaces from MD simulation
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Daniel Spångberg, Kersti Hermansson, William A. Goddard, Adri C. T. van Duin, and David Raymand
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Work (thermodynamics) ,Chemistry ,Hydrogen bond ,Surfaces and Interfaces ,Condensed Matter Physics ,Surfaces, Coatings and Films ,Molecular dynamics ,Adsorption ,Chemical physics ,Desorption ,Monolayer ,Materials Chemistry ,Molecule ,Physical chemistry ,ReaxFF - Abstract
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 (0001)-direction on the (1010)-surface. Equilibrium between molecular and dissociated water was observed on the (1010) 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 (
- Published
- 2010
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12. Potential energy surface and molecular dynamics simulation of gold(I) in liquid nitromethane
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Tamás Radnai, Daniel Spångberg, Szabolcz Balint, Michael Probst, Tuende Megyes, Jumras Limtrakul, Natcha Injan, and Imre Bakó
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Nitromethane ,Condensed Matter Physics ,Molecular physics ,Quantum chemistry ,Potential energy ,Atomic and Molecular Physics, and Optics ,Electronic, Optical and Magnetic Materials ,Ion ,chemistry.chemical_compound ,Molecular dynamics ,Solvation shell ,chemistry ,Potential energy surface ,Materials Chemistry ,Molecule ,Physical and Theoretical Chemistry ,Atomic physics ,Spectroscopy - Abstract
Potential energy functions for Au(I)-nitromethane (NM, CH 3 NO 2 ) and NM–NM interactions were calculated by fitting analytical expressions to quantum chemically derived energies. These functions were then used in a molecular dynamics simulation of one Au(I) cation in 499 nitromethane molecules in the NVT ensemble at room temperature. A comparative simulation with a generic NM–NM potential energy function was also performed for comparison and gave the same results with respect to the calculated properties. It was found that the first solvation shell around the gold ion contains 9–10 nitromethane molecules in an environment with no strong symmetry. Complementary, cluster calculations on AuNM n + were performed. The especially strong binding of nitromethane in AuNM 2 + and the validity of the pair approximation are discussed.
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- 2009
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13. Molecular dynamics study of oxygen self-diffusion in reduced CeO2
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Daniel Spångberg, Kersti Hermansson, Michael Baudin, and Anders Gotte
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Self-diffusion ,Materials science ,Diffusion ,Inorganic chemistry ,chemistry.chemical_element ,General Chemistry ,Atmospheric temperature range ,Condensed Matter Physics ,Oxygen ,Catalysis ,Molecular dynamics ,chemistry ,Chemical physics ,General Materials Science ,Yttria-stabilized zirconia - Abstract
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 ~ 410 ...
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- 2007
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14. Treatment of delocalized electron transfer in periodic and embedded cluster DFT calculations: The case of Cu on ZnO (10(1)0)
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Kersti Hermansson, Matti Hellström, and Daniel Spångberg
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Computational Mathematics ,Delocalized electron ,Adsorption ,Chemistry ,Atom ,Supercell (crystal) ,Cluster (physics) ,Charge (physics) ,General Chemistry ,Substrate (electronics) ,Electron ,Atomic physics - Abstract
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)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(1)0), as long as care is taken to account for the effects of CT.
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- 2015
15. Car−Parrinello Molecular Dynamics Simulation of Fe3+(aq)
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Viktor Zelin, Kersti Hermansson, Daniel Spångberg, Sami Amira, and M. Probst
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Canonical ensemble ,Aqueous solution ,Optimized geometry ,Liquid water ,Chemistry ,Ab initio ,Surfaces, Coatings and Films ,Molecular dynamics ,Electron transfer ,Solvation shell ,Chemical physics ,Computational chemistry ,Materials Chemistry ,Physical and Theoretical Chemistry - Abstract
The optimized geometry and energetic properties of Fe(D2O)n 3+ clusters, with n = 4 and 6, have been studied with density-functional theory calculations and the BLYP functional, and the hydration of a single Fe 3+ 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.
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- 2005
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16. Derivation and evaluation of a flexible SPC model for liquid water
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Daniel Spångberg, Kersti Hermansson, and Sami Amira
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Molecular dynamics ,Liquid water ,Chemistry ,Computational chemistry ,Point particle ,Quartic function ,Water model ,General Physics and Astronomy ,Function (mathematics) ,Statistical physics ,Physical and Theoretical Chemistry - Abstract
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 int ...
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- 2004
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17. The solvation of Li+ and Na+ in acetonitrile from ab initio-derived many-body ion–solvent potentials
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Daniel Spångberg and Kersti Hermansson
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Chemistry ,Coordination number ,Ab initio ,Solvation ,General Physics and Astronomy ,Ion ,Molecular dynamics ,Computational chemistry ,Ab initio quantum chemistry methods ,Standard electrode potential ,Physical chemistry ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Pair potential - Abstract
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 Bohm 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.
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- 2004
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18. Many-body potentials for aqueous Li+, Na+, Mg2+, and Al3+: Comparison of effective three-body potentials and polarizable models
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Daniel Spångberg and Kersti Hermansson
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Aqueous solution ,Chemistry ,Ab initio ,Solvation ,General Physics and Astronomy ,Ionic bonding ,Molecular physics ,Ion ,Molecular dynamics ,Ab initio quantum chemistry methods ,Physics::Atomic and Molecular Clusters ,Density functional theory ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Atomic physics - Abstract
Many-body potentials for the aqueous Li(+), Na(+), Mg(2+), and Al(3+) 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(+), Mg(2+), and Al(3+) 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 Mg(2+) and Al(3+).
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- 2004
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19. Molecular Dynamics Simulation of Fe2+(aq) and Fe3+(aq)
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M. Probst, Daniel Spångberg, Sami Amira, and Kersti Hermansson
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Solvent ,Electron transfer ,Molecular dynamics ,Aqueous solution ,Chemistry ,Chemical physics ,Computational chemistry ,Metal ions in aqueous solution ,Materials Chemistry ,Physical and Theoretical Chemistry ,Force field (chemistry) ,Surfaces, Coatings and Films - Abstract
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 ( ...
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- 2003
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20. Effective three-body potentials for Li+(aq) and Mg2+(aq)
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Daniel Spångberg and Kersti Hermansson
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Free energy perturbation ,Molecular dynamics ,Lennard-Jones potential ,Chemistry ,Ab initio quantum chemistry methods ,Yield (chemistry) ,Ab initio ,General Physics and Astronomy ,Physical chemistry ,Density functional theory ,Physical and Theoretical Chemistry ,Molecular physics ,Ion - Abstract
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 Aqvist. 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.
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- 2003
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21. Hydration of the Calcium Ion. An EXAFS, Large-Angle X-ray Scattering, and Molecular Dynamics Simulation Study
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Patric Lindqvist-Reis, Magnus Sandström, Kersti Hermansson, Farideh Jalilehvand, Daniel Spångberg, and Ingmar Persson
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Coordination sphere ,Molecular Structure ,Absorption spectroscopy ,Extended X-ray absorption fine structure ,Chemistry ,Coordination number ,Analytical chemistry ,Water ,Hydrogen Bonding ,General Chemistry ,Crystal structure ,Biochemistry ,Catalysis ,Bond length ,Molecular dynamics ,Crystallography ,Colloid and Surface Chemistry ,Body Water ,Nonlinear Dynamics ,X-Ray Diffraction ,Humans ,Calcium ,Computer Simulation ,Extracellular Space ,Spectroscopy - Abstract
The structure of the hydrated calcium(II) ion in aqueous solution has been studied by means of extended X-ray absorption fine structure spectroscopy (EXAFS), large-angle X-ray scattering (LAXS), and molecular dynamics (MD) methods. The EXAFS data displayed a broad and asymmetric distribution of the Ca-O bond distances with the centroid at 2.46(2) A. LAXS studies on four aqueous calcium halide solutions (1.5-2 mol dm(-)(3)) gave a mean Ca-O bond distance of 2.46(1) A. This is consistent with a hydration number of 8 determined from correlations between mean distances and coordination numbers from crystal structures. The LAXS studies showed a second coordination sphere with a mean Ca.O(II) distance of 4.58(5) A, and for the hydrated halide ions the distances Cl.O 3.25(1) A, Br.O 3.36(1) A, and I.O 3.61(1) A were obtained. Molecular dynamics simulations of CaCl(2)(aq) were performed using three different Ca(2+)-OH(2) pair potentials. The potential from the GROMOS program gave results in agreement with experiments, i.e., a coordination number of 8 and an average Ca-O distance of 2.46 A, and was used for further comparisons. Theoretical EXAFS oscillations were computed for individual MD snapshots and showed very large variations, though the simulated average spectrum from 2000 snapshots gave satisfactory agreement with the experimental EXAFS spectra. The effect of thermal motions of the coordinated atoms is inherent in the MD simulation method. Thermal disorder parameters evaluated from simulated spatial atom distribution functions of the oxygen atoms coordinated to the calcium ion were in close agreement with those from the current LAXS and EXAFS analyses. The combined results are consistent with a root-mean-square displacement from the mean Ca-O distance of 0.09(2) A in aqueous solution at 300 K.
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- 2000
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22. Model Extended X-ray Absorption Fine Structure (EXAFS) Spectra from Molecular Dynamics Data for Ca2+ and Al3+ Aqueous Solutions
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Ingmar Persson, Magnus Sandström, Patric Lindqvist-Reis, Daniel Spångberg, Farideh Jalilehvand, and Kersti Hermansson
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Molecular dynamics ,Molecular geometry ,Extended X-ray absorption fine structure ,Chemistry ,Scattering ,Materials Chemistry ,Analytical chemistry ,Ab initio ,Physical and Theoretical Chemistry ,Absorption (chemistry) ,Spectral line ,Surfaces, Coatings and Films ,Ion - Abstract
Theoretical extended X-ray absorption fine structure (EXAFS) spectra have been computed from molecular dynamics (MD) simulation data. Based on MD-generated molecular geometries, EXAFS spectra were generated with the FEFF6 program, commonly used in the analysis of experimental EXAFS spectra. The effects of multiple scattering and second-shell neighbors on the theoretical spectra were evaluated for CaCl2(aq) and AlCl3(aq), i.e., for two solutions with very different cation hydration structures. The effects are significantly larger for the more structured Al3+ solution, The theoretical Ca2+(aq) spectra are compared with new experimental EXAFS data.
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- 2000
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23. Pressure dependence and activation volume for the water exchange mechanism in NaCl(aq) from MD simulations
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Daniel Spångberg, Kersti Hermansson, and Mark Wojcik
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chemistry.chemical_classification ,General Physics and Astronomy ,Thermodynamics ,Water exchange ,Pressure dependence ,Ion ,External pressure ,Divalent ,Solvent ,Molecular dynamics ,Volume (thermodynamics) ,chemistry ,Physical chemistry ,Physical and Theoretical Chemistry - Abstract
The influence of an external pressure on the solvent exchange mechanisms around the Na+ ion in a dilute NaCl(aq) solution has been investigated through MD simulations at 0 and 200 MPa. At zero pressure most of the exchange processes (≈ 75%) can be classified in terms of associative 6-7-6 mechanisms. At 200 MPa the exchange rate is 20% higher and the mechanistic processes become more involved. The activation volume for the 6-7-6 exchange process at zero pressure was calculated from the MD simulation using Voronoi polyhedra, and gives a negative sign for ΔV#. This supports the prevailing notion that a negative activation volume is indicative of an associative exchange mechanism.
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- 1997
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24. An efficient and extensible format, library, and API for binary trajectory data from molecular simulations
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Daniel Spångberg, Magnus Lundborg, Rossen Apostolov, Erik Lindahl, David van der Spoel, and Anders Gärdenäs
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Theoretical computer science ,Computer science ,Binary number ,Molecular Dynamics Simulation ,010402 general chemistry ,01 natural sciences ,Extensibility ,Computational science ,Ribonucleases ,2-Naphthylamine ,0103 physical sciences ,Acetamides ,Kv1.2 Potassium Channel ,Animals ,Zebrafish ,Electronic Data Processing ,010304 chemical physics ,Ethanol ,General Chemistry ,Zebrafish Proteins ,File format ,0104 chemical sciences ,Computational Mathematics ,Trajectory ,Algorithms ,Software - Abstract
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.
- Published
- 2013
25. Cu dimer formation mechanism on the ZnO(101¯0) surface
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Daniel Spångberg, Peter Broqvist, Matti Hellström, and Kersti Hermansson
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Surface (mathematics) ,Crystallography ,chemistry.chemical_compound ,Adsorption ,Chemistry ,Dimer ,Density functional theory ,Condensed Matter Physics ,Mechanism (sociology) ,Electronic, Optical and Magnetic Materials - Abstract
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 o ...
- Published
- 2012
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26. Fitting properties from density functional theory based molecular dynamics simulations to parameterize a rigid water force field
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Jonàs Sala, Jordi Martí, Elvira Guàrdia, Marco Masia, Daniel Spångberg, Universitat Politècnica de Catalunya. Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya. SIMCON - First-principles approaches to condensed matter physics: quantum effects and complexity, and Universitat Politècnica de Catalunya. SIMCON - Grup de Recerca de Simulació per Ordinador en Matèria Condensada
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Funcional de densitat, Teoria del ,Física [Àrees temàtiques de la UPC] ,Chemistry ,General Physics and Astronomy ,Parameterized complexity ,Water ,Molecular Dynamics Simulation ,Molecular dynamics ,Force field (chemistry) ,Weighting ,Water model ,Torque ,Statistical physics ,Granularity ,Dinàmica molecular ,Physical and Theoretical Chemistry ,Blossom algorithm ,Density functionals - Abstract
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.
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- 2012
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27. Aqueous halide potentials from force matching of Car-Parrinello data
- Author
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Elvira Guàrdia, Daniel Spångberg, Marco Masia, Universitat Politècnica de Catalunya. Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya. SIMCON - First-principles approaches to condensed matter physics: quantum effects and complexity, and Universitat Politècnica de Catalunya. SIMCON - Grup de Recerca de Simulació per Ordinador en Matèria Condensada
- Subjects
Physics ,Research groups ,Aqueous solution ,Física [Àrees temàtiques de la UPC] ,Ab initio ,Halide ,Water ,Condensed Matter Physics ,Biochemistry ,Force field (chemistry) ,Halides ,Aigua ,Halurs ,Force matching ,Quantum mechanics ,Potential energy surface ,Forcematching ,Water model ,Force field ,Statistical physics ,Physical and Theoretical Chemistry ,Car parrinello molecular dynamics - Abstract
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.
- Published
- 2012
- Full Text
- View/download PDF
28. Cations strongly reduce electron-hopping rates in aqueous solutions
- Author
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Olle Björneholm, Michael Odelius, Daniel Spångberg, Niklas Ottosson, Mattias Svanqvist, Wandared Pokapanich, Gunnar Öhrwall, and Bernd Winter
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Aqueous solution ,Chemistry ,Astrophysics::High Energy Astrophysical Phenomena ,technology, industry, and agriculture ,Molecular binding ,Water ,Electrons ,General Chemistry ,Radiation ,Molecular Dynamics Simulation ,Biochemistry ,Catalysis ,Electron hopping ,Electron transfer ,Colloid and Surface Chemistry ,Chemical physics ,Cations ,Molecule ,Physics::Chemical Physics ,Absorption (chemistry) ,Ultrashort pulse - Abstract
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.
- Published
- 2011
29. On the origins of core-electron chemical shifts of small biomolecules in aqueous solution: insights from photoemission and ab initio calculations of glycine(aq)
- Author
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Olle Björneholm, Daniel Spångberg, Leif J. Sæthre, Henrik Bergersen, Bernd Winter, Wandared Pokapanich, Manfred Faubel, Niklas Ottosson, Knut J. Børve, and Gunnar Öhrwall
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Quantitative Biology::Biomolecules ,Aqueous solution ,Chemistry ,Chemical shift ,Photoelectron Spectroscopy ,Binding energy ,Glycine ,Water ,Protonation ,Electrons ,General Chemistry ,Electronic structure ,Hydrogen-Ion Concentration ,Molecular Dynamics Simulation ,Biochemistry ,Catalysis ,Molecular dynamics ,Colloid and Surface Chemistry ,Solvation shell ,Ab initio quantum chemistry methods ,Physical chemistry - Abstract
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 1s 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.
- Published
- 2011
30. Structure and dynamics of water dangling OH bonds in hydrophobic hydration shells. Comparison of simulation and experiment
- Author
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Joel G. Davis, Jill Tomlinson-Phillips, Dor Ben-Amotz, Ljupčo Pejov, Kersti Hermansson, and Daniel Spångberg
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Inorganic chemistry ,02 engineering and technology ,Molecular Dynamics Simulation ,010402 general chemistry ,01 natural sciences ,chemistry.chemical_compound ,symbols.namesake ,Molecular dynamics ,Electric field ,Molecule ,Physical and Theoretical Chemistry ,Multivariate curve resolution ,Molecular Structure ,Hydroxyl Radical ,Water ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,Solvation shell ,chemistry ,Neopentane ,symbols ,Physical chemistry ,Thermodynamics ,Hydroxyl radical ,0210 nano-technology ,Raman spectroscopy ,Hydrophobic and Hydrophilic Interactions - Abstract
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 (∼3660 cm(-1)) OH band arising from the hydration shell of neopentanol dissolved in HOD/D(2)O, 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.
- Published
- 2011
- Full Text
- View/download PDF
31. Sequential Penning Ionization: Harvesting Energy with Ions
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Harald Schöbel, Paul Scheier, Daniel Spångberg, Peter Bartl, Stephan Denifl, Tilmann D. Märk, Samuel Zöttl, Matthias Daxner, Christian Leidlmair, A. Mauracher, and Diethard K. Bohme
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Materials science ,Coulomb explosion ,General Physics and Astronomy ,Electron ,Ion ,chemistry.chemical_compound ,chemistry ,Penning ionization ,Excited state ,Ionization ,Physics::Atomic and Molecular Clusters ,Physics::Atomic Physics ,Atomic physics ,Electron ionization ,Methyl iodide - Abstract
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.
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- 2010
- Full Text
- View/download PDF
32. Using MD snapshots in ab initio and DFT calculations: OH vibrations in the first hydration shell around Li+(aq)
- Author
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Kersti Hermansson, Ljupčo Pejov, and Daniel Spångberg
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Bond length ,Dipole ,Solvation shell ,Chemistry ,Computational chemistry ,Intramolecular force ,Molecular vibration ,Anharmonicity ,Ab initio ,Physical and Theoretical Chemistry ,Molecular physics ,Ion - Abstract
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 nu(OH) frequency is well reproduced in our calculations. "In-liquid" instantaneous correlation curves between nu(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.
- Published
- 2006
33. Distorted five-fold coordination of Cu2+(aq) from a Car-Parrinello molecular dynamics simulation
- Author
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Daniel Spångberg, Sami Amira, and Kersti Hermansson
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Aqueous solution ,Chemistry ,Cations, Divalent ,Solvation ,Ab initio ,General Physics and Astronomy ,Water ,Electronic structure ,Ion ,Oxygen ,Molecular dynamics ,Solvation shell ,Models, Chemical ,Chemical physics ,Computational chemistry ,Molecule ,Computer Simulation ,Physical and Theoretical Chemistry ,Deuterium Oxide ,Algorithms ,Copper - Abstract
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 A and one axial water molecule at 2.45 A 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.
- Published
- 2005
34. Hydration of some large and highly charged metal ions
- Author
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Patric Lindquist-Reis, Farideh Jalilehvand, Daniel Spångberg, Kersti Hermansson, Magnus Sandström, and Ingmar Persson
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Nuclear and High Energy Physics ,Radiation ,Aqueous solution ,Metal ions in aqueous solution ,Inorganic chemistry ,Analytical chemistry ,chemistry.chemical_element ,Spectrometry, X-Ray Emission ,Water ,Yttrium ,Ion ,Bond length ,Solutions ,chemistry ,Metals ,Cations ,Lanthanum ,Molecule ,Scandium ,Instrumentation - Abstract
EXAFS studies of metal ions with hydration numbers higher than six in aqueous solution, often show asymmetric distribution of the metal-oxygen bond distances. The hydration number can be determined from a correlation with the bond distance. The mean Ca-O distance 2.46(1) Å shows the calcium(II) ion to be eight-hydrated in a wide asymmetric distribution. Theoretically calculated EXAFS oscillations for individual snapshots from an MD simulation show large variations. The scandium(III) ion is surrounded by two groups of about eight water molecules, with the mean Sc-O distance 2.185(6) Å. The yttrium(III) ion coordinates eight waters in an asymmetric distribution at 2.368(5) Å, and the lanthanum(III) ion 6 + 3 water molecules at 2.52(2) and 2.65(3) Å, respectively. For the the uranium(IV) and thorium(IV) ions, the M-O distances 2.42(1) and 2.45(1) Å, respectively, indicate hydration numbers close to 10.
- Published
- 2001
35. Energy harvesting in doped helium nano-droplets
- Author
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Paul Scheier, Harald Schöbel, Stephan Denifl, Tilmann D. Märk, Peter Bartl, Matthias Daxner, Samuel Zöttl, Daniel Spångberg, Christian Leidlmair, A. Mauracher, and Diethard K. Bohme
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History ,Internal energy ,Helium atom ,Coulomb explosion ,chemistry.chemical_element ,Computer Science Applications ,Education ,Ion ,chemistry.chemical_compound ,chemistry ,Penning ionization ,Excited state ,Physics::Atomic and Molecular Clusters ,Physics::Atomic Physics ,Atomic physics ,Antiprotonic helium ,Helium - Abstract
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.
- Published
- 2012
- Full Text
- View/download PDF
36. Al3+, Ca2+, Mg2+, and Li+ in aqueous solution: Calculated first-shell anharmonic OH vibrations at 300 K
- Author
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Daniel Spångberg, Kersti Hermansson, and Ljupčo Pejov
- Subjects
Spectrophotometry, Infrared ,General Physics and Astronomy ,Infrared spectroscopy ,Lithium ,Molecular Dynamics Simulation ,Vibration ,Ion ,Molecular dynamics ,Cations ,Hydroxides ,Molecule ,Magnesium ,Physical and Theoretical Chemistry ,Aqueous solution ,Chemistry ,Anharmonicity ,Temperature ,Solvation ,Water ,Solutions ,Quantum Theory ,Physical chemistry ,Calcium ,Solvent effects ,Algorithms ,Aluminum - Abstract
The anharmonic OH stretching vibrational frequencies, ν(OH), for the first-shell water molecules around the Li(+), Ca(2+), Mg(2+), and Al(3+) ions in dilute aqueous solutions have been calculated based on classical molecular dynamics (MD) simulations and quantum-mechanical (QM) calculations. For Li(+)(aq), Ca(2+)(aq), Mg(2+)(aq), and Al(3+)(aq), our calculated IR frequency shifts, Δν(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 Ca(2+). Given that the polarizing field from the Ca(2+) 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 M(n+) (H(2)O)(y) (second shell) (H(2)O)(z) (third shell) clusters+QM(vibrational) to yield the OH spectrum. The many-body Ca(2+)-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.
- Published
- 2010
- Full Text
- View/download PDF
37. Distorted five-fold coordination of Cu2+(aq) from a Car–Parrinello molecular dynamics simulation.
- Author
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Sami Amira, Daniel Spångberg, and Kersti Hermansson
- Published
- 2005
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