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  • 1.
    Adamovic, Nadja
    et al.
    TU Wien, ISAS, Vienna, Austria..
    Asinari, Pietro
    Politecn Torino, Dept Energy, Turin, Italy..
    Goldbeck, Gerhard
    Goldbeck Consulting Ltd, St Johns Innovat Ctr, Cambridge, England..
    Hashibon, Adham
    Fraunhofer Inst Mech Mat IWM, Freiburg, Germany..
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hristova-Bogaerds, Denka
    DPI, Eindhoven, Netherlands..
    Koopmans, Rudolf
    Koopmans Consulting GmbH, Zurich, Switzerland..
    Verbrugge, Tom
    Dow Benelux BV, Hoek, Netherlands..
    Wimmer, Erich
    Mat Design, Le Mans, France..
    European Materials Modelling Council2017In: Proceedings Of The 4Th World Congress On Integrated Computational Materials Engineering (Icme 2017) / [ed] Mason, P Fisher, CR Glamm, R Manuel, MV Schmitz, GJ Singh, AK Strachan, A, Springer Publishing Company, 2017, p. 79-92Conference paper (Refereed)
    Abstract [en]

    The aim of the European Materials Modelling Council (EMMC) is to establish current and forward looking complementary activities necessary to bring the field of materials modelling closer to the demands of manufacturers (both small and large enterprises) in Europe. The ultimate goal is that materials modelling and simulation will become an integral part of product life cycle management in European industry, thereby making a strong contribution to enhance innovation and competitiveness on a global level. Based on intensive efforts in the past two years within the EMMC, which included numerous consultation and networking actions with representatives of all stakeholders including Modellers, Software Owners, Translators and Manufacturers in Europe, the EMMC identified and proposed a set of underpinning and enabling actions to increase the industrial exploitation of materials modelling in Europe. EMMC will pursue the following overarching objectives in order to bridge the gap between academic innovation and industrial application: enhance the interaction and collaboration between all stakeholders engaged in different types of materials modelling, including modellers, software owners, translators and manufacturers, facilitate integrated materials modelling in Europe building on strong and coherent foundations, coordinate and support actors and mechanisms that enable rapid transfer of materials modelling from academic innovation to the end users and potential beneficiaries in industry, achieve greater awareness and uptake of materials modelling in industry, in particular SMEs, elaborate Roadmaps that (i) identify major obstacles to widening the use of materials modelling and (ii) elaborate strategies to overcome them.

  • 2.
    Ahlstrand, Emma
    et al.
    Linnus Univ, Dept Chem & Biomed Sci, S-39182 Kalmar, Sweden.;Linnus Univ, Ctr Biomat Chem, S-39182 Kalmar, Sweden..
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Friedman, Ran
    Linnus Univ, Dept Chem & Biomed Sci, S-39182 Kalmar, Sweden.;Linnus Univ, Ctr Biomat Chem, S-39182 Kalmar, Sweden..
    Interaction Energies in Complexes of Zn and Amino Acids: A Comparison of Ab Initio and Force Field Based Calculations2017In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 121, no 13, p. 2643-2654Article in journal (Refereed)
    Abstract [en]

    Zinc plays important roles in structural stabilization of proteins, eniyine catalysis, and signal transduction. Many Zn binding sites are located at the interface between the protein and the cellular fluid. In aqueous solutions, Zn ions adopt an octahedral coordination, while in proteins zinc can have different coordinations, with a tetrahedral conformation found most frequently. The dynainics of Zn binding to proteins and the formation of complexes that involve Zn are dictated by interactions between Zn and its binding partners. We calculated the interaction energies between Zn and its ligands in complexes that mimic protein binding sites and in Zn complexes of water and one or two amino acid moieties, using quantum mechanics (QM) and molecular mechanics (MM). It was found that MM calculations that neglect or only approximate polarizability did not reproduce even the relative order of the QM interaction energies in these complexes. Interaction energies calculated with the CHARMM-Diode polarizable force field agreed better with the ab initio results,:although the deviations between QM and MM were still rather large (40-96 kcallmol). In order to gain further insight into Zn ligand interactions, the free energies of interaction were estimated by QM calculations with continuum solvent representation, and we performed energy decomposition analysis calculations to examine the characteristics of the different complexes. The ligand-types were found to have high impact on the relative strength of polarization and electrostatic interactions. Interestingly, ligand ligand interactions did not play a significant role in the binding of Zn. Finally) analysis of ligand exchange energies suggests that carboxylates could be exchanged with water molecules, which explains the flexibility in Zn:binding dynamics. An exchange between earboxylate (Asp/Glii) and imidazole (His) is less likely.

  • 3.
    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.

  • 4. Alfredsson, M
    et al.
    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.
    Hartree-Fock and DFT calculations of quadrupole coupling constants in water clusters and ice1999In: CHEMICAL PHYSICS, ISSN 0301-0104, Vol. 242, no 2, p. 161-175Article in journal (Other scientific)
    Abstract [en]

    Periodic ab initio calculations of the O-17 and H-2 quadrupole coupling constants (QCC) and their shifts have been performed for ice VIII and ice IX. Cluster calculations were done for smaller water clusters and chains. The ice Vm crystal structure was op

  • 5.
    Alfredsson, M
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    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.
    OH frequency calculations for the hydroxylated MgO(001) surface2002In: Molecular Simulation, Vol. 28, p. 663-Article in journal (Refereed)
  • 6.
    Alfredsson, M
    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.
    Dovesi, R
    Periodic ab initio calculations of the spontaneous polarisation in ferroelectric NaNO2(s).2002In: Phys. Chem. Chem.Phys., p. 4204-Article in journal (Refereed)
  • 7. Alfredsson, Maria
    et al.
    Ojamae, Lars
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry. strukturkemi.
    A comparison of Hartree-Fock, MP2, and DFT results for the HCN dimer and crystal1996In: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Vol. 60, no 3, p. 767-777Article in journal (Refereed)
    Abstract [en]

    A number of hydrogen-bond related quantities-geometries, interaction energies, dipole moments, dipole moment derivatives, and harmonic vibrational frequencies-were calculated at the Hartree-Fock, MP2, and different DFT levels for the HCN dimer and the pe

  • 8.
    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.

  • 9.
    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.

  • 10.
    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).

  • 11.
    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.

  • 12.
    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.

  • 13. Bakker, A
    et al.
    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.
    Lindgren, Jan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry, Structural Chemistry. strukturkemi.
    Probst, M
    Bopp, Ph
    A molecular dynamics simulation of an aqueous aluminium (III) chloride solution with three-body interactions.2000In: Int. J. Quantum Chem., Vol. 80, p. 892-Article in journal (Refereed)
  • 14. BAKKER, ALBERT
    et al.
    GEJJI, SHRIDHAR
    LINDGREN, JAN
    HERMANSSON, KERSTI
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    PROBST, MICHAEL M
    CONTACT ION-PAIR FORMATION AND ETHER OXYGEN COORDINATION IN THE POLYMER ELECTROLYTES M[N(CF3SO2)(2)](2)PEO(N) FOR M=MG, CA, SR AND BA1995In: Polymer, ISSN 0032-3861, E-ISSN 1873-2291, Vol. 36, no 23, p. 4371-4378Article in journal (Refereed)
    Abstract [en]

    The polymer electrolytes M[N(CF3SO2)(2)](2)PEO(n) for M = Mg, Ca, Sr and Ba have been investigated using infra-red spectroscopy, differential scanning calorimetry and impedance spectroscopy. The effects of varying concentration (n = 6-40) and temperature (25-95 degrees C) on the contact ion pair formation and cation coordination have been studied. Contact ion pairs are only found for the most concentrated samples (n < 9). Ion pairs occur with two types of structures: one type is found far samples containing Mg2+ and the other for samples with Ca2+, Sr2+ and Ba2+. The conductivities of the samples are discussed in terms of radii and coordination numbers of the cations.

  • 15. Bakker, Albert
    et al.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Lindgren, Jan
    Probst, Michael M
    Bopp, Philippe A
    Interaction of aluminum(III) with water. An ab initio study1999In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 75, no 4-5, p. 659-669Article in journal (Refereed)
    Abstract [en]

    Hydrated Al(3+) ions [Al(H(2)O)(n)](3+), n = 1-6, were examined with ab Initio self-consistent field (SCF) calculations. The relative contributions of two-, three-, and higher-body terms to the total interaction energy for an [Al(H(2)O)(6)](3+) complex were calculated The sum of all three-body contributions amounts to - 30% of the sum of all pair-additive contributions and is opposite in sign. The three-body energy contributions were also derived for two types of [Al(H(2)O)(2)](3+) complexes. in the first type, both water molecules reside in the first hydration shell of Al(3+) and in the second type there is one in the first shell and one in the second. Altogether 15,500 triplets were investigated and analytical two- and three-body potential energy functions were derived via a fitting procedure. (C) 1999 John Wiley & Sons, Inc.

  • 16. Bakker, Albert
    et al.
    Lindgren, Jan
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    Polymer electrolytes based on triblock-copoly(oxyethylene/oxypropylene/oxyethylene) systems1996In: Polymer, ISSN 0032-3861, E-ISSN 1873-2291, Vol. 37, no 10, p. 1871-1878Article in journal (Refereed)
    Abstract [en]

    Polymer electrolytes based on triblock copolymers of ethylene oxide (EO)/propylene oxide (PO)/ethylene oxide of moderate molecular weight and narrow block-length distributions, doped with M(CF3SO3)(2) and M[N(CF3SO2)(2)](2) (M = Mg, Ca, Sr and Ba), LiCF3SO3 and LiN(CF3SO2)(2) have been investigated using infrared spectroscopy, differential scanning calorimetry and conductivity measurements. The effects of varying the EO/PO block length, composition and temperature on the phase behaviour, ion-pair formation and conductivity of the polymer electrolytes have been studied. A two-phase microstructure has been observed. Ion pairing occurs for the triflate salts and the amount was found to be sensitive to the relative block sizes rather than the molecular weight of the copolymer. Copyright (C) 1996 Elsevier Science Ltd.

  • 17.
    Bakó, Imre
    et al.
    Hungarian Academy of Sciences, Budapest, Hungary.
    Lábas, Anikó
    Budapest University of Technology and Economics, Budapest, Hungary.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Oláh, Julianna
    Budapest University of Technology and Economics, Budapest, Hungary.
    How can we detect hydrogen bond local cooperativity in liquid water: A simulation study2017In: Journal of Molecular Liquids, ISSN 0167-7322, E-ISSN 1873-3166, Vol. 245, p. 140-146Article in journal (Refereed)
    Abstract [en]

    The significant cooperative effect between water molecules substantially affects the properties of liquid water. The cooperativity of hydrogen bonds means that the hydrogen bond strength is influenced by the neighboring water molecules. Another descriptor related to cooperativity is degree correlation (or static correlation) describing the probability of hydrogen-bonded molecule pairs participating in additional hydrogen-bonds. Herein we analyze the latter one in liquid water at various temperatures and densities in a series of molecular dynamics simulations with the help of knowledge from network science. We investigated how the applied hydrogen bond criteria (energetic or geometric) influence the obtained results, and showed that the energetic criterion is much more rigorous and reliable, therefore should be used for similar studies. We found that the structure of the subsystems of water molecules with 3 and 4 hydrogen-bonds is distinctly different at low temperature, 3‑hydrogen-bonded water molecules form branched chain structures at all temperature. Deconvolution of the descriptors of the mixing pattern of water molecules according to their donor and acceptor numbers showed that species with complementary hydrogen bonding properties are likely to correlate and form H-bonds with each other, while species with similar H-bond pattern tend to avoid each other. Pearson's coefficient (global descriptor of the local cooperativity) of the studied networks suggests that at normal density the H-bonded network in liquid water can be described by an uncorrelated network.

  • 18.
    Baudin, M
    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.
    Wojcik, M
    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.
    Dynamics, structure and energetics of the (001), (011) and (111) surfaces of ceria.2000In: Surf. Sci., Vol. 468, p. 51-Article in journal (Refereed)
  • 19.
    Baudin, Micael
    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.
    Metal oxide surface dynamics from MD simulations: The alfa-alumina (0001) surface.2001In: Surf. Sci., Vol. 474, p. 107-Article in journal (Refereed)
  • 20.
    Baudin, Micael
    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.
    Wojcik, M.
    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.
    MD simulations of an A12O3(ppp1,010)/CeO2(011,011) interface system.2001In: Thin Solid Films, Vol. 401, p. 159-Article in journal (Refereed)
  • 21.
    Baudin, Micael
    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.
    Wojcik, M
    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.
    Palmqvist, AEC
    Muhammed, M
    MD simulations of a doped ceria surface - very large surface ion motion2001In: CHEMICAL PHYSICS LETTERS, ISSN 0009-2614, Vol. 335, no 5-6, p. 517-523Article in journal (Refereed)
    Abstract [en]

    Mean-square displacements (MSDs) and individual-ion square-displacements (ISDs) for the different constituents in Ca-doped CeO2(0 1 1) slabs at 300 K have been studied as a function of depth from the surface. Constant pressure-constant temperature MD simu

  • 22. Baudin, Micael
    et al.
    Wojcik, Mark
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    A molecular dynamics study of MgO(111) slabs1997In: Surface Science, ISSN 0039-6028, E-ISSN 1879-2758, Vol. 375, no 2-3, p. 374-384Article in journal (Refereed)
    Abstract [en]

    Constant stress - constant temperature molecular dynamics simulations are reported for 30 Angstrom thick crystalline MgO (111) slabs with 2-D periodicity in the temperature range 10-1100 K. The 10 K run was 3.75 ps, the 300 K run was 41.25 ps while the others were 11.25 ps. The shell-model potential was used and the long-range interaction was taken into account with the 2-D Ewald summation technique. Two different models have been used in order to achieve the necessary charge compensation for the polar (111) surface. The relaxation of the surface structure and its temperature dependence have been investigated and compared with bulk MgO. The average coordination number in the surface layer and the surface energy are presented. The dynamics in the slab system is presented in terms of atomic mean-square displacements and vibrational density-of-states curves as a function of depth from the surface. (C) 1997 Elsevier Science B.V.

  • 23. Bischof, Gerhard
    et al.
    Silbernagl, Alexander
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    Probst, Michael
    Quantum chemical study of the molecular dynamics of hydrated Li+ and Be2+ cations1997In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 65, no 5, p. 803-816Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations of clusters of Li+ and Be2(+) cations with up to 12 water molecules were performed calculating the particle trajectories using Hartree-Fock-derived forces. It was found that independent of the starting configuration tetrahedral clusters are obtained in less than 1 ps. Only for Li+ clusters, transition states with five and three water molecules are found. We discuss the structures of the clusters and the vibrational dynamics of the water molecules and compare them with other ab initio simulations, with simulations using analytical potential functions, and with static calculations. Water-dissociation (hydrogen transfer) reactions which take place at elevated temperatures were investigated. (C) 1997 John Wiley & Sons, Inc.

  • 24.
    Broqvist, Peter
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Kullgren, Jolla
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Wolf, Matthew J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    van Duin, Adri C. T.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    ReaxFF Force-Field for Ceria Bulk, Surfaces, and Nanoparticles2015In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 119, no 24, p. 13598-13609Article in journal (Refereed)
    Abstract [en]

    We have developed a reactive force-field of the ReaxFF type for stoichiometric ceria (CeO2) and partially reduced ceria (CeO2-x). We describe the parametrization procedure and provide results validating the parameters in terms of their ability to accurately describe the oxygen chemistry of the bulk, extended surfaces, surface steps, and nanoparticles of the material. By comparison with our reference electronic structure method (PBE+U), we find that the stoichiometric bulk and surface systems are well reproduced in terms of bulk modulus, lattice parameters, and surface energies. For the surfaces, step energies on the (111) surface are also well described. Upon reduction, the force-field is able to capture the bulk and surface vacancy formation energies (E-vac), and in particular, it reproduces the E-vac variation with depth from the (110) and (111) surfaces. The force-field is also able to capture the energy hierarchy of differently shaped stoichiometric nanoparticles (tetrahedra, octahedra, and cubes), and of partially reduced octahedra. For these reasons, we believe that this force-field provides a significant addition to the method repertoire available for simulating redox properties at ceria surfaces.

  • 25.
    Broqvist, Peter
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Kullgren, Jolla
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Zhang, Chao
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Du, Dou
    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.
    Kebede, Getachew
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Rafieefar, Ali
    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.
    Chemistry of Complex Materials2017Conference paper (Other academic)
  • 26. Carrasco, J
    et al.
    Illas, F
    Lopez, N
    Kotomin, E.A.
    Zhukovskii, Yu.F.
    Piskunov, S
    Maier, J
    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.
    First principles simulations of F centers in cubic SrTiO32005In: physica status solidi (c), Vol. 2, no 1, p. 153-158Article in journal (Refereed)
    Abstract [en]

    Atomic and electronic structure of regular and O-deficient SrTiO3 have been studied. Several types of first principles atomistic simulations: Hartree-Fock method, Density Functional Theory, and hybrid HF-DFT functionals, have been applied to periodic models that consider supercells of different sizes (ranging between 40 and 240 atoms). We confirm the ionic character of the Sr-O bonds and the high covalency of the Ti-O2 substructure. For the stoichiometric cubic crystal; the lattice constant and bulk modulus correctly reproduce the experimental data whereas the band gap is only properly obtained by the B3PW functional. The relaxed geometry around the F center shows a large expansion of the two nearest Ti ions. Moreover, the vacancy formation energy is extremely sensitive to the size and the shape of the supercell as well as the calculation method. The electronic density map indicates the redistribution of two electrons of the missing O atom between the vacancy and 3d atomic orbitals of the two nearest Ti ions, in contrast to the F centers in ionic oxides where the charge centroid does not change.

  • 27.
    Castleton, Christopher
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Kullgren, Jolla
    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.
    Tuning LDA+U for electron localization and structure at oxygen vacancies in ceria2007In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 127, no 24, p. 244704-244704-11Article in journal (Refereed)
    Abstract [en]

    We examine the real space structure and the electronic structure (particularly Ce4f electron localization) of oxygen vacancies in CeO2 (ceria) as a function of U in density functional theory studies with the rotationally invariant forms of the LDA+U and GGA+U functionals. The four nearest neighbor Ce ions always relax outwards, with those not carrying localized Ce4f charge moving furthest. Several quantification schemes show that the charge starts to become localized at U~3 eV and that the degree of localization reaches a maximum at ~6 eV for LDA+U or at ~5.5 eV for GGA+U. For higher U it decreases rapidly as charge is transferred onto second neighbor O ions and beyond. The localization is never into atomic corelike states; at maximum localization about 80-90% of the Ce4f charge is located on the two nearest neighboring Ce ions. However, if we look at the total atomic charge we find that the two ions only make a net gain of (0.2-0.4)e each, so localization is actually very incomplete, with localization of Ce4f electrons coming at the expense of moving other electrons off the Ce ions. We have also revisited some properties of defect-free ceria and find that with LDA+U the crystal structure is actually best described with U=3-4 eV, while the experimental band structure is obtained with U=7-8 eV. (For GGA+U the lattice parameters worsen for U>0 eV, but the band structure is similar to LDA+U.) The best overall choice is U~6 eV with LDA+U and ~5.5 eV for GGA+U, since the localization is most important, but a consistent choice for both CeO2 and Ce2O3, with and without vacancies, is hard to find.

  • 28.
    Castleton, Christopher
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Nokbin, Somkiat
    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.
    Charge transfer and adhesion in Rh/MgO(001)2008In: Proceedings of the 17th international vacuum congress/13th international conference on surface science/international conference on nanoscience and technology / [ed] Johansson LSO; Andersen JN; Gothelid M; Helmersson U; Montelius L; Rubel M; Setina J; Wernersson LE, 2008, Vol. 100, no 8, p. 082027-Conference paper (Refereed)
    Abstract [en]

    Ab initio density functional calculations are reported for Rh adlayers on MgO(001) at coverages of 1, 1/2 and 1/8 monolayers. It is shown that charge is transferred from oxide surface to the Rh adatoms. The transfer ranges from 0.06 e to 0.27 e, depending upon adsorption site and coverage. In comparison, transfers of 0.08 e from adatom to surface and 0.32 e surface to adatom are found for monolayer coverages of Mg and O, respectively. With the Rh adatoms, significant charge polarization of both Rh and the surface are also seen, but it is never-the-less found that the adhesion energy is linearly related to the charge transfer, with the most stable adsorption site at any particular coverage being the one at which the charge transfer is a maximum.

  • 29.
    Castleton, Christopher
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Nokbin, Somkiat
    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.
    Correlations between magnetic properties and bond formation in Rh–MgO(0 0 1)2007In: Surface Science, ISSN 0039-6028, E-ISSN 1879-2758, Vol. 601, no 5, p. 1218-1230Article in journal (Refereed)
    Abstract [en]

    We present the results of first principles calculations for the magnetism of Rh adlayers on MgO(0 0 1), at three different adsorption sites and three different coverages, corresponding to 1, 1/2 and 1/8 monolayers. Finite magnetization is found in all cases except that of one Rh monolayer above the oxygen site, which is also the most stable. We examine how the magnetization changes as a function of the Rh–surface distance and relate this to changes in the real-space charge density and in the density of states (DOS) as the Rh adlayer interacts with the surface. We find that increasing either the Rh–Rh interaction strength or the Rh–surface interaction strength leads to reduced magnetization, while increasing the former drives a crossover from localized (atomic) to itinerant magnetism. Neither the magnetic transition itself, nor the localized-to-itinerant magnetism crossover, is found to be directly related to the formation of Rh–surface bonds. From a practical point of view, we predict that magnetism in the Rh–MgO(0 0 1) system is most likely to be found experimentally at reduced coverages and at low temperatures.

  • 30. de Carolis, Stefano
    et al.
    Pascual, Jose Luis
    Pettersson, Lars G.M.
    Baudin, Micael
    Wojcik, Mark
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Palmqvist, Anders E.C.
    Muhammed, Mamoun
    Structure and electronic properties of Ca-doped CeO2 and implications on catalytic activity: An experimental and theoretical study1999In: J PHYS CHEM B, ISSN 1089-5647, Vol. 103, no 36, p. 7627-7636Article in journal (Refereed)
    Abstract [en]

    Doping CeO2 with for example, Ca gives an enhanced reactivity toward reduction of SO2 by CO, and total combustion of methane. Theoretical modeling using static minimizations and molecular dynamics (MD) simulations of the doped (110) face in combination with ab initio quantum chemical cluster models shows large effects on the Ce(IV)/Ce(III) balance due to the doping. Computed oxygen-to-cerium charge-transfer energies are strongly reduced as a result of the introduction of defects and oxygen vacancies, but not sufficiently to explain the observed reactivities. The structures resulting from the MD simulations for both the doped and undoped material are in good agreement with recent experimental pulsed neutron scattering results.

  • 31.
    Dennis Larsson, Ernst
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Kullgren, Jolla
    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.
    DFT studies of CO2 hydrogenation on Ru/TiO2(101)2017Conference paper (Other academic)
  • 32. Dennis Larsson, Ernst
    et al.
    Pazoki, Meysam
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry. 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.
    Kullgren, Jolla
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Computational Green Chemistry2017Conference paper (Other academic)
  • 33. Duan, Sai
    et al.
    Xu, Xin
    Luo, Yi
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Tian, Zhong-Qun
    Thermal effects on electronic properties of CO/Pt(111) in water2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 32, p. 13619-13627Article in journal (Refereed)
    Abstract [en]

    Structure and adsorption energy of carbon monoxide molecules adsorbed on the Pt(111) surfaces with various CO coverages in water as well as work function of the whole systems at room temperature of 298 K were studied by means of a hybrid method that combines classical molecular dynamics and density functional theory. We found that when the coverage of CO is around half monolayer, i.e. 50%, there is no obvious peak of the oxygen density profile appearing in the first water layer. This result reveals that, in this case, the external force applied to water molecules from the CO/Pt(111) surface almost vanishes as a result of the competitive adsorption between CO and water molecules on the Pt(111) surface. This coverage is also the critical point of the wetting/non-wetting conditions for the CO/Pt(111) surface. Averaged work function and adsorption energy from current simulations are consistent with those of previous studies, which show that thermal average is required for direct comparisons between theoretical predictions and experimental measurements. Meanwhile, the statistical behaviors of work function and adsorption energy at room temperature have also been calculated. The standard errors of the calculated work function for the water-CO/Pt(111) interfaces are around 0.6 eV at all CO coverages, while the standard error decreases from 1.29 to 0.05 eV as the CO coverage increases from 4% to 100% for the calculated adsorption energy. Moreover, the critical points for these electronic properties are the same as those for the wetting/non-wetting conditions. These findings provide a better understanding about the interfacial structure under specific adsorption conditions, which can have important applications on the structure of electric double layers and therefore offer a useful perspective for the design of the electrochemical catalysts.

  • 34. Dungrikaew, Virasak
    et al.
    Limtrakul, Jumras
    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.
    Probst, Michael
    Comparison of Methods for Point-charge Representation of Electrostatic Fields2004In: Int. Journ. Quant. Chem., Vol. 96, p. 17-22Article in journal (Refereed)
    Abstract [en]

    The calculation of the electrostatic potential resulting from an infinite or extended array of charges in the interior of a region of interest is a frequent task in computational chemistry. In case of a periodic potential this can, for example, be done by Ewald summation or by multipole methods. An important alternative are those methods where arrays of auxiliary point charges are optimized with respect to charge and/or position to reproduce the original electrostatic potential. In the literature different variations are reported. We compare the performance of some of these with respect to their ability to reproduce the original potential and the computational effort required. Between (1) surface charges determined by the conductor-boundary condition, (2) optimized surface charges, and (3) surface charges floating on the surface we find that (2) offers good quality with small computational costs involved.

  • 35.
    Eriksson, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    Analysis of the thermal parameters of the water molecule in crystalline hydrates studied by neutron diffraction1983In: Acta Crystallographica Section B: Structural Science, ISSN 0108-7681, E-ISSN 1600-5740, Vol. B39, p. 703-711Article in journal (Refereed)
    Abstract [en]

    A survey is given of the thermal parameters of 150 water molecules in crystalline hydrates determined by neutron diffraction. The accuracy of the thermal parameters has been examined and rigid-bond tests revealed systematic errors for approximately 25% of the molecules. Considering only the most precise and accurate studies, good agreement is obtained between vibrational amplitudes derived from diffraction and spectroscopy. The influence of the immediate environment on the vibrations of the water molecule has also been investigated. A positive correlation is found between H...O hydrogen-bond distances and librational amplitudes. The coordination geometry around the O atom is shown to influence the vibrational amplitudes of the O atom.

  • 36. Eriksson, Anders
    et al.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    Lindgren, Jan
    Thomas, John O.
    The use of spectroscopic data in the least-squares refinement of diffraction-obtained structure parameters. An example: K 2C 2O 4.H 2O1982In: Acta Crystallogr. A, Cryst. Phys. Diffr. Theor. Gen. Crystallogr. (Denmark), ISSN 0567-7394, Vol. A38, p. 138-142Article in journal (Refereed)
    Abstract [en]

    A method is presented in which parameters obtained from vibrational spectroscopy are used in the least-squares refinement of positional and thermal parameters obtained from diffraction data. The method involves the calculation of those contributions to the temperature factors not well described by the second-rank tensor approximation conventionally used in crystal structure determinations. Expressions are given for the temperature-factor contributions from vibrational motion on an arc and from anharmonic linear motion. The method is applied to the water molecule in dipotassium oxalate monohydrate, 2K +.C 2O 4-.H 2O. Refinements using vibrational data are compared with a conventional refinement; the latter are shown to give considerable systematic errors in the geometrical parameters for the water molecule.

  • 37. Gajewski, Grzegorz
    et al.
    Mitev, Pavlin D.
    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.
    2D calculation of anharmonic OH vibrations in a layered hydroxide crystal2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 129, no 6, p. 064502-Article in journal (Refereed)
    Abstract [en]

    Anharmonicvibrational frequencies for the Raman-active (A1g) and the IR-active (A2u)modes have been calculated for the LiOH crystal within aplane-wave density functional theory (DFT) framework. We find that atwo-dimensional quantum-mechanical vibrational approach, allowing for anharmonic coupling between symmetricand antisymmetric OH stretching modes, produces OH frequencies—both absolute frequenciesand gas-to-solid frequency shifts—in good agreement with experiment. Remaining errorsin the absolute frequencies are largely a consequence of theDFT model chosen. A one-dimensional normal-mode following vibrational treatment, onthe other hand, fails to reproduce both absolute anharmonic frequenciesand gas-to-solid frequency shifts.

  • 38. Gassner, Helmut
    et al.
    Probst, Michael
    Lauenstein, Albert
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    Representation of intermolecular potential functions by neural networks1998In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 102, no 24, p. 4596-4605Article in journal (Refereed)
    Abstract [en]

    We have investigated how a neural network representation of intermolecular potential functions can be used to elevate some of the problems commonly encountered during fitting and application of analytical potential functions in computer simulations. For this purpose we applied feed-forward networks of various sizes to reproduce the three-body interaction energies in the system H(2)O-Al(3+)-H(2)O. In this highly polarizable system the three-body interaction terms are necessary for an accurate description of the system, and it proved difficult to fit an analytical function to them. Subsequently we performed Monte Carlo simulations on an Al(3+ )ion dissolved in water and compared the results obtained using the neural network type potential function with those using a conventional analytical potential. The performance and results of our calculations lead to the conclusion that, for suitable systems, the advantages of a neural network type representation of potential functions as a model-independent and "semiautomatic" potential function outweigh the disadvantages in computing speed and lack of interpretability.

  • 39. GEJJI, SHRIDHAR P
    et al.
    HERMANSSON, KERSTI
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    LINDGREN, JAN
    ABINITIO VIBRATIONAL FREQUENCIES OF THE TRIFLATE ION, (CF3SO3)-1993In: J PHYS CHEM-US, ISSN 0022-3654, Vol. 97, no 15, p. 3712-3715Article in journal (Refereed)
    Abstract [en]

    The optimized geometry, harmonic vibrational frequencies and infrared intensities of the trifluoromethanesulfonate (triflate) ion, CF3SO3-, have been determined with ab initio self-consistent Hartree-Fock theory by using 3-21G* and 6-31G* Gaussian basis sets. Second-order Moller-Plesset perturbation calculations were also carried out with 6-31G* basis. A normal mode analysis shows that the vibrations assigned as symmetric and antisymmetric CF3 stretching involve other internal coordinates as well, viz., CF3 bending and CS stretching. The corresponding SO3 stretching modes, on the other hand, are almost entirely described with SO stretching coordinates. The assignments of the symmetric and antisymmetric SO3 and CF3 stretching vibrations from Moller-Plesset theory are seen to be different from those reported in the literature. Recent infrared spectroscopic experiments of the triflate ion coordinated to the zinc or lead ion in poly(ethylene oxide) complexes support the conclusions from second-order perturbation theory. The vibrational frequencies and infrared intensities show a strong dependence on basis set and electron correlation.

  • 40. GEJJI, SHRIDHAR P
    et al.
    HERMANSSON, KERSTI
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    LINDGREN, JAN
    AB-INITIO VIBRATIONAL FREQUENCIES OF THE TRIFLIC ACID MOLECULE1993In: J PHYS CHEM-US, ISSN 0022-3654, Vol. 97, no 27, p. 6986-6989Article in journal (Refereed)
    Abstract [en]

    The optimized geometry, harmonic vibrational frequencies, and infrared intensities of the trifluoromethanesulfonic (triflic) acid, CF3SO2OH, have been determined by ab initio self-consistent Hartree-Fock calculations and second-order Moller-Plesset perturbation theory with 6-31G** and lower basis sets. The optimized geometry of the triflic acid molecule is in good agreement with that reported from electron diffraction experiments. The overall symmetry for the molecule, however, is C1, and not C(s) as suggested from the experiments. The symmetric CF3 and SO2 stretching vibrational modes of the triflic acid are seen to be reversed compared to the assignment from the infrared spectra, reported earlier in the literature. The CF3 stretchings and the O=S=O bending normal modes include strong couplings of different internal coordinates. The vibrational frequencies and the infrared intensities are sensitive to the basis set choice as well as to electron correlation effects.

  • 41. GEJJI, SHRIDHAR P
    et al.
    HERMANSSON, KERSTI
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    LINDGREN, JAN
    STRUCTURE AND VIBRATIONAL FREQUENCIES OF THE MOLECULAR TRICHLOROMETHANESULFONIC ACID AND ITS ANION FROM AB-INITIO CALCULATIONS1994In: J PHYS CHEM-US, ISSN 0022-3654, Vol. 98, no 35, p. 8687-8692Article in journal (Refereed)
    Abstract [en]

    The equilibrium structure, vibrational frequencies, and the infrared intensities of the trichloromethanesulfonic acid molecule and its anion have been investigated using the ab initio self-consistent Hartree-Fock method and second-order Moller-Plesset perturbation theory with the 6-31G** and lower basis sets. A normal mode analysis shows that, unlike CCl3 stretchings, the SO3 stretching vibrations in the CCl3SO3- anion are pure normal modes comprised of S-O stretching coordinates only. The molecular point group for the trichloromethanesulfonic acid molecule is C-1 and not C-s. The vibrational frequencies and the infrared intensities are sensitive to the basis set choice as well as to the electron correlation effects.

  • 42. GEJJI, SHRIDHAR P
    et al.
    HERMANSSON, KERSTI
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    TEGENFELDT, JÖRGEN
    LINDGREN, JAN
    GEOMETRY AND VIBRATIONAL FREQUENCIES OF THE LITHIUM TRIFLATE ION-PAIR - AN AB-INITIO STUDY1993In: J PHYS CHEM-US, ISSN 0022-3654, Vol. 97, no 44, p. 11402-11407Article in journal (Refereed)
    Abstract [en]

    The optimized geometry, harmonic vibrational frequencies, and infrared absorption intensities of the lithium trifluoromethanesulfonate (triflate) ion pair, CF3SO3-Li have been investigated using the ab initio self-consistent Hartree-Fock and correlated second-order Moller-Plesset perturbation theory with the 6-31G* and lower basis sets. In the optimized structure the lithium cation is bound to two of the oxygens of the SO3 group forming a bidentate complex with C(s) symmetry. A local minimum with a monodentate structure was obtained in the HF/3-21G* calculations. The energy difference between the mono- and bidentate structures of the complex is predicted to be nearly 39 kJ mol-1 in this basis. A splitting of 230 and 158 cm-1 is obtained for the antisymmetric SO3 stretching for the bi- and monodentate coordination of the lithium cation with the free anion, respectively. The infrared spectrum of lithium triflate in poly(propylene oxide) shows a splitting of 43 cm-1. The strong interaction of the metal cation with the anion in the 1:1 complex thus overemphasizes the ''splitting behavior'' observed for lithium triflate dissolved in polymers. In the bidentate (MP2/6-31G*) complex the symmetric SO3 stretching shows a downshift of 38 cm-1, in contrast to an upshift of 47 cm-1 for the monodentate complex. The different signs of these frequency shifts have a purely geometric origin. The dependence of this frequency shift on the position of the Li+ ion is discussed.

  • 43.
    Gotte, Anders
    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.
    Baudin, Micael
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Materials Chemistry, Structural Chemistry. strukturkemi.
    Molecular Dynamics simulations of reduced CeO2: bulk and surface2004In: Surface Science, Vol. 552, p. 273-Article in journal (Refereed)
    Abstract [en]

    Results from molecular dynamics simulations for bulk and the (0 1 1) surface of reduced and unreduced CeO2 at 300 K are reported. The presence of vacancies in reduced ceria is found to give rise to many different local structural arrangements, and to a significant broadening of the peaks in the pair-distribution function. This broadening is mainly due to the appearance of these new structural arrangements, and it is not due to the increased ionic motions in the reduced systems.

  • 44.
    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.

  • 45. 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.

  • 46.
    Gyoeroek, Michael
    et al.
    Univ Innsbruck, Inst Ion Phys & Appl Phys, Technikerstr 25, A-6020 Innsbruck, Austria.
    Kaiser, Alexander
    Univ Innsbruck, Inst Ion Phys & Appl Phys, Technikerstr 25, A-6020 Innsbruck, Austria.
    Sukuba, Ivan
    Comenius Univ, Dept Nucl Phys & Biophys, Fac Math Phys & Informat, SK-84248 Bratislava, Slovakia.
    Urban, Jan
    Comenius Univ, Dept Nucl Phys & Biophys, Fac Math Phys & Informat, SK-84248 Bratislava, Slovakia.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Probst, Michael
    Univ Innsbruck, Inst Ion Phys & Appl Phys, Technikerstr 25, A-6020 Innsbruck, Austria. ; VISTEC, Wangchan 20210, Rayong, Thailand.
    Surface binding energies of beryllium/tungsten alloys2016In: Journal of Nuclear Materials, ISSN 0022-3115, E-ISSN 1873-4820, Vol. 472, p. 76-81Article in journal (Refereed)
    Abstract [en]

    Binding energies of beryllium and tungsten atoms on surfaces of the alloys Be2W and Be12W were obtained from density functional theory calculations. Values of 4.08–5.63 eV for beryllium and 6.81–10.04 eV for tungsten were obtained. An analytical force field agrees for beryllium, but its tungsten surface atoms are too strongly bound. The surface binding energies of Be and W on Be12W surfaces is slightly smaller than on the pure Be and W surfaces, respectively. For higher tungsten content, i.e. for Be2W, the situation is more complicated. For some surfaces of this alloy the surface binding energies are enhanced while for others they are diminished, compared to the pure metal surfaces. The dependency of the cohesive energy on the mole fraction follows a linear relationship.

  • 47.
    Hellström, Matti
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Beinik, Igor
    Aarhus Univ, Interdisciplinary Nanosci Ctr iNANO, Aarhus, Denmark..
    Broqvist, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Lauritsen, Jeppe V.
    Aarhus Univ, Interdisciplinary Nanosci Ctr iNANO, Aarhus, Denmark..
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Subsurface hydrogen bonds at the polar Zn-terminated ZnO(0001) surface2016In: PHYSICAL REVIEW B, ISSN 2469-9950, Vol. 94, no 24, article id 245433Article in journal (Refereed)
    Abstract [en]

    The role of hydrogen and other defects in the stabilization of polar oxide interfaces is a matter of significant fundamental and practical interest. Using experimental (scanning tunneling microscopy, x-ray photoelectron spectroscopy) and theoretical (density functional theory) surface science techniques, we find that the polar Zn-terminated ZnO(0001) surface becomes excessively Zn deficient during high-temperature annealing (780 K) in ultrahigh vacuum (UHV). The Zn vacancies align themselves into rows parallel to the [10 (1) over bar 10] direction, and the remaining surface Zn ions alternately occupy wurtzite (hcp) and zinc-blende (fcc) lattice positions, giving a characteristic "striped" c(root 12 x root 12) R30 degrees surface morphology with three types of rows: wurtzite Zn, zinc-blende Zn, and Zn vacancies. Interstitial H plays a central role in such a reconstruction, as it helps to compensate the excessive Zn deficiency. We propose a model in which hydrogen occupies positions in half of the vacancy rows to form hydroxide ions that can participate in hydrogen bonds in the O subsurface layer as a result of the mixed wurtzite/zinc-blende stacking.

  • 48.
    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.
    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.
    Water-Induced Oxidation and Dissociation of Small Cu Clusters on ZnO(101̅0)2015In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 119, no 3, p. 1382-1390Article in journal (Refereed)
    Abstract [en]

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

  • 49.
    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. Uppsala Univ, Dept Chem Angstrom, SE-75121 Uppsala, Sweden..
    Treatment of Delocalized Electron Transfer in Periodic and Embedded Cluster DFT Calculations: The Case of Cu on ZnO (10(1)over-bar0)2015In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 36, no 32, p. 2394-2405Article in journal (Refereed)
    Abstract [en]

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

  • 50.
    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.

12345 1 - 50 of 214
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