Tag Archives: Daniel Spångberg

Comparing van der Waals DFT methods for water on NaCl(001) and MgO(001)

Authors: Getachew G. Kebede, Daniel Spångberg, Pavlin D. Mitev, Peter Broqvist, and   Kersti Hermansson

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.

The Journal of Chemical Physics 146, 064703 (2017);
doi: http://dx.doi.org/10.1063/1.4971790

Treatment of delocalized electron transfer in periodic and embedded cluster DFT calculations: The case of Cu on ZnO (10-10)

Authors: Matti Hellström, Daniel Spångberg, and Kersti Hermansson

mattiPaperWe 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 inline image0), 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(10inline image0), as long as care is taken to account for the effects of CT.

 J. Comput. Chem. 2015, 36,23942405.
DOI: 10.1002/jcc.24219

Calculation of the stability of nonperiodic solids using classical force fields and the method of increments: N2O as an example

Authors: Carsten Müller and Daniel Spångberg

jcc23939-fig-0005Combining classical force fields for the Hartree–Fock (HF) part and the method of increments for post-HF contributions, we calculate the cohesive energy of the ordered and randomly disordered nitrous oxide (N2O) solid. At 0 K, ordered N2O is most favorable with a cohesive energy of −27.7 kJ/mol. At temperatures above 60 K, more disordered structures become compatible and a phase transition to completely disordered N2O is predicted. Comparison with experiment in literature suggests that experimentally prepared N2O crystals are mainly disordered due to a prohibitively high activation energy of ordering processes.

J. Comput. Chem., 36, (2015), 1420–1427
DOI: 10.1002/jcc.23939

Water-Induced Oxidation and Dissociation of Small Cu Clusters on ZnO(101̅0)

Authors: Matti Hellström, Daniel Spångberg, Peter Broqvist, and Kersti Hermansson

matti1

The interaction between water molecules and small Cu clusters (up to a size of four atoms) adsorbed on the nonpolar ZnO(101̅0) 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(101̅0) 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 water–gas 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.

J. Phys. Chem. C, 2015119 (3), pp 1382–1390 

DOI: 10.1021/jp509501z

Small Cu Clusters Adsorbed on ZnO(101̅0) Show Even–Odd Alternations in Stability and Charge Transfer

Authors: Matti Hellström, Daniel Spångberg, Kersti Hermansson and Peter Broqvist

jp-2013-12694y_0009

Using hybrid density functional theory, we investigate structural and electronic properties of small Cun clusters (with n ≤ 9) adsorbed on the nonpolar ZnO(101̅0) surface. The Cu clusters grow in a planar fashion up to a size of six atoms, after which the clusters take on a polyhedral shape. We find even–odd alternations with respect to both cluster stability (for n = 1–6) and cluster charge, as a function of the number of atoms. Even-numbered clusters are always charge-neutral, while odd-numbered clusters can become positively charged by donation of an electron to the ZnO conduction band, which can be traced back to the fact that the ionization energies of odd-numbered gas-phase Cu clusters are lower than for even-numbered ones. The most stable adsorbed odd-numbered clusters are neutral and planar forn ≤ 3 and positively charged and polyhedral for n ≥ 7. For n = 5, both neutral planar and positively charged polyhedral configurations are similarly stable.

J. Phys. Chem. C, 2014, 118 (12), pp 6480–6490

DOI: 10.1021/jp412694y

An efficient and extensible format, library, and API for binary trajectory data from molecular simulations

Authors: Magnus Lundborg, Rossen Apostolov, Daniel Spångberg, Anders Gärdenäs, David van der Spoel, and Erik Lindahl

tng_file_structure

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.

Journal of Computational Chemistry 2013, DOI: 10.1002/jcc.23495

Band-Filling Correction Method for Accurate Adsorption Energy Calculations: A Cu/ZnO Case Study

Authors: Matti Hellström, Daniel Spångberg, Kersti Hermansson and Peter Broqvist

We present a simple method, the “band-filling correction”, to calculate accurateadsorption energies (Eads) in the low coverage limit from finite-size supercell slab calculations using DFT.

band-filling

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.

J. Chem. Theory Comput. 9, 4673 (2013).

DOI: 10.1021/ct400645v

Interaction energies between metal ions (Zn2+ and Cd2+) and biologically relevant ligands

Authors: Emma Ahlstrand, Daniel Spångberg, Kersti Hermansson, Ran Friedman

allmols

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.

International Journal of Quantum Chemistry Volume 113, Issue 23, pages 2554–2562, 5 December 2013

DOI: 10.1002/qua.24506

Cu dimer formation mechanism on the ZnO(101̅ 0) surface

Matti Hellström, Daniel Spångberg, Kersti Hermansson, and Peter Broqvist

The formation of Cu dimers on the ZnO(101̅ 0) surface has been studied using hybrid density functional theory. Depending on the adsorption site, Cu atoms are found to adsorb with either oxidation state 0 or +1. In the latter case, the Cumatti atom has donated an electron to the ZnO conduction band. The two modes of adsorption display similar stability at low coverages, while at higher coverages the neutral species is more stable. Single Cu atoms diffuse across the ZnO(101̅ 0) surface with small barriers of migration (0.3–0.4 eV) along ZnO[12̅ 10], repeatedly switching their oxidation states, while the barrier along ZnO[0001] is significantly higher (>1.5 eV). The formation of a Cu dimer from two adsorbed Cu atoms is energetically favorable with two competing structures of similar stability, both being charge neutral. The minimum energy paths for Cu atom diffusion and dimer formation are characterized by at least one of the two Cu atoms being in oxidation state 0.

Phys. Rev. B, 2012, 86,  235302
DOI: 10.1103/PhysRevB.86.235302

Aqueous halide potentials from force matching of Car–Parrinello data

Authors: Daniel Spångberg, Elvira Guàrdia, Marco Masia

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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.

Computational and Theoretical Chemistry, 982: 58-65

DOI: 10.1016/j.comptc.2011.12.011