Mostrar el registro sencillo del ítem

dc.creatorDohn A.O., Jónsson E.O., Levi G., Mortensen J.J., Lopez-Acevedo O., Thygesen K.S., Jacobsen K.W., Ulstrup J., Henriksen N.E., Møller K.B., Jónsson H.spa
dc.date.accessioned2018-04-13T16:34:49Z
dc.date.available2018-04-13T16:34:49Z
dc.date.created2017spa
dc.identifier.issn15499618spa
dc.identifier.urihttp://hdl.handle.net/11407/4568
dc.description.abstractA multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H2O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt2(P2O5H2)4]4- complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 Å from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2% from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex. © 2017 American Chemical Society.eng
dc.language.isoengspa
dc.publisherAmerican Chemical Societyspa
dc.relation.isversionofhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85038262208&doi=10.1021%2facs.jctc.7b00621&partnerID=40&md5=6905c4c34f6d486b8f9975cd410f32ddspa
dc.sourceScopusspa
dc.titleGrid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complexspa
dc.typeArticlespa
dc.typeinfo:eu-repo/semantics/publishedVersionspa
dc.typeinfo:eu-repo/semantics/articlespa
dc.rights.accessRightsinfo:eu-repo/semantics/restrictedAccessspa
dc.contributor.affiliationFaculty of Physical Sciences and Science Institute, University of Iceland, Reykjavĺk, Iceland; Department of Chemistry, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark; CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark; Department of Applied Physics, Aalto University, Espoo, Finland; Facultad de Ciencias Baśicas, Universidad de Medellín, Carrera 87 No. 30-65, Medellín, Colombiaspa
dc.identifier.doi10.1021/acs.jctc.7b00621spa
dc.publisher.facultyFacultad de Ciencias Básicasspa
dc.abstractA multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H2O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt2(P2O5H2)4]4- complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 Å from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2% from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex. © 2017 American Chemical Society.eng
dc.source.bibliographicCitationWarshel, A., Levitt, M., Theoretical Studies of Enzymatic Reactions: Dielectric, Electrostatic and Steric Stabilization of the Carbonium Ion in the Reaction of Lysozyme (1976) J. Mol. Biol., 103, pp. 227-249; Field, M.J., Bash, P.A., Karplus, M., A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations (1990) J. Comput. Chem., 11, pp. 700-733; Bakowies, D., Thiel, W., Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches (1996) J. Phys. Chem., 100, pp. 10580-10594; Antes, I., Thiel, W., Gao, J., On the Treatment of Link Atoms in Hybrid Methods (1998) Combined Quantum Mechanical and Molecular Mechanical Methods, 712, pp. 50-65. , ACS Symposium Series, No. American Chemical Society: Washington, DC, Chapter 4; Bentzien, J., Florián, J., Glennon, T.M., Warshel, A., Quantum Mechanical-Molecular Mechanical Approaches for Studying Chemical Reactions in Proteins and Solution (1998) Combined Quantum Mechanical and Molecular Mechanical Methods, 712, pp. 16-34. , ACS Symposium Series, No. American Chemical Society: Washington, DC, Chapter 2; Merz, K.M., Jr., (1998) Combined Quantum Mechanical and Molecular Mechanical Methods, 712, pp. 2-15. , ACS Symposium Series, No. American Chemical Society: Washington, DC, Chapter 1; Mordasini, T.Z., Thiel, W., Computational Chemistry Column: Combined Quantum Mechanical and Molecular Mechanical Approaches (1998) CHIMIA Int. J. Chem., 52, pp. 288-291; Woo, T., Margl, P., Deng, L., Cavallo, L., Ziegler, T., Combined QM/MM and Ab Initio Molecular Dynamics Modeling of Homogeneous Catalysis (1999) Transition State Modeling for Catalysis, 721, pp. 173-186. , ACS Symposium Series, No. American Chemical Society: Washington, DC, Chapter 14; Monard, G., Merz, K.M., Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems (1999) Acc. Chem. Res., 32, pp. 904-911; Hillier, I.H., Chemical reactivity studied by hybrid QM/MM methods (1999) J. Mol. Struct.: THEOCHEM, 463, pp. 45-52; Morokuma, K., New challenges in quantum chemistry: Quests for accurate calculations for large molecular systems (2002) Philos. Trans. R. Soc., A, 360, pp. 1149-1164; Gao, J., Truhlar, D.G., Quantum mechanical methods for enzyme kinetics (2002) Annu. Rev. Phys. Chem., 53, pp. 467-505; Lin, H., Truhlar, D.G., QM/MM: What have we learned, where are we, and where do we go from here? (2007) Theor. Chem. Acc., 117, p. 185; Senn, H.M., Thiel, W., QM/MM methods for biomolecular systems (2009) Angew. Chem., Int. Ed., 48, pp. 1198-1229; Kirchner, B., Vrabec, J., Multiscale Molecular Methods in Applied Chemistry (2012) Topics in Current Chemistry, 307. , Springer: Berlin, Heidelberg, Germany; Van Der Kamp, M.W., Mulholland, A.J., Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology (2013) Biochemistry, 52, pp. 2708-2728; Brunk, E., Rothlisberger, U., Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States (2015) Chem. Rev., 115, pp. 6217-6263; Pezeshki, S., Lin, H., Recent Advances in the Molecular Simulation of Chemical Reactions (2015) Mol. Simul., 41, pp. 168-189; Zheng, M., Waller, M.P., Adaptive quantum mechanics/molecular mechanics methods (2016) Wiley Interdiscip. Rev. Comput. Mol. Sci., 6, pp. 369-385; Sousa, S.F., Ribeiro, A.J.M., Neves, R.P.P., Brás, N.F., Cerqueira, N.M.F.S.A., Fernandes, P.A., Ramos, M.J., Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms (2017) Wiley Interdiscip. Rev. Comput. Mol. Sci., 7, p. e1281; Scanlon, D.O., Dunnill, C.W., Buckeridge, J., Shevlin, S.A., Logsdail, A.J., Woodley, S.M., Catlow, C.R.A., Sokol, A.A., Band alignment of rutile and anatase TiO2 (2013) Nat. Mater., 12, pp. 798-801; Smirnov, I.V., Golovin, A.V., Chatziefthimiou, S.D., Stepanova, A.V., Peng, Y., Zolotareva, O.I., Belogurov, A.A., Lerner, R.A., Robotic QM/MM-driven maturation of antibody combining sites (2016) Sci. Adv., 2, p. e1501695; Barends, T.R.M., Foucar, L., Ardevol, A., Nass, K., Aquila, A., Botha, S., Doak, R.B., Schlichting, I., Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation (2015) Science, 350, pp. 445-450; Senn, H.M., Thiel, W., QM/MM Methods for Biomolecular Systems (2009) Angew. Chem., Int. Ed., 48, pp. 1198-1229; Warshel, A., Sharma, P.K., Kato, M., Xiang, Y., Liu, H., Olsson, M.H.M., Electrostatic basis for enzyme catalysis (2006) Chem. Rev., 106, pp. 3210-3235; Zheng, F., Xue, L., Hou, S., Liu, J., Zhan, M., Yang, W., Zhan, C.-G., A highly efficient cocaine-detoxifying enzyme obtained by computational design (2014) Nat. Commun., 5, p. 3457; Knorr, J., Sokkar, P., Schott, S., Costa, P., Thiel, W., Sander, W., Sanchez-Garcia, E., Nuernberger, P., Competitive solvent-molecule interactions govern primary processes of diphenylcarbene in solvent mixtures (2016) Nat. Commun., 7, p. 12968; Mortensen, J., Hansen, L., Jacobsen, K.W., Real-space grid implementation of the projector augmented wave method) (2005) Phys. Rev. B: Condens. Matter Mater. Phys., 71, p. 035109; Enkovaara, J., Rostgaard, C., Mortensen, J.J., Chen, J., Dulak, M., Ferrighi, L., Gavnholt, J., Jacobsen, K.W., Electronic structure calculations with GPAW: A real-space implementation of the projector augmented-wave method (2010) J. Phys.: Condens. Matter, 22, p. 253202; Dohn, A.O., Jónsson, E.O., Kjær, K.S., Van Driel, T.B., Nielsen, M.M., Jacobsen, K.W., Henriksen, N.E., Møller, K.B., Direct Dynamics Studies of a Binuclear Metal Complex in Solution: The Interplay between Vibrational Relaxation, Coherence, and Solvent Effects (2014) J. Phys. Chem. Lett., 5, pp. 2414-2418; Dohn, A.O., Henriksen, N.E., Møller, K.B., (2014) Transient Changes in Molecular Geometries and How to Model Them, , Springer International Publishing: Cham, Switzerland; Dohn, A.O., Kjær, K.S., Harlang, T.B., Canton, S.E., Nielsen, M.M., Møller, K.B., Electron Transfer and Solvent-Mediated Electronic Localization in Molecular Photocatalysis (2016) Inorg. Chem., 55, pp. 10637-10644; Canton, S.E., Kjær, K.S., Vankó, S.E., Van Driel, G., Adachi, T.B., Bordage, S.-I., Bressler, A., Nielsen, M.M., Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses (2015) Nat. Commun., 6, p. 6359; Van Driel, T.B., Kjær, K.S., Hartsock, R.W., Dohn, A.O., Harlang, T., Chollet, M., Christensen, M., Gaffney, K.J., Atomistic characterization of the active-site solvation dynamics of a model photocatalyst (2016) Nat. Commun., 7, p. 13678; Blöchl, P.E., Projector Augmented-Wave Method (1994) Phys. Rev. B: Condens. Matter Mater. Phys., 50, p. 17953; Blöchl, P.E., Först, C.J., Schimpl, J., Projector Augmented Wave Method: Ab Initio Molecular Dynamics with Full Wave Functions (2003) Bull. Mater. Sci., 26, p. 33; Bahn, S.R., Jacobsen, K.W., An object-oriented scripting interface to a legacy electronic structure code (2002) Comput. Sci. Eng., 4, pp. 56-66; Hjorth Larsen, A., Mortensen, J.J., Blomqvist, J., Castelli, I., Christensen, R., Dulak, M., Friis, J., Jacobsen, K.W., The Atomic Simulation Environment - A Python library for working with atoms (2017) J. Phys.: Condens. Matter, 29, p. 273002; Laino, T., Mohamed, F., Laio, A., Parrinello, M., An Efficient Real Space Multigrid QM/MM Electrostatic Coupling (2005) J. Chem. Theory Comput., 1, pp. 1176-1184; Laino, T., Mohamed, F., Laio, A., Parrinello, M., An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations (2006) J. Chem. Theory Comput., 2, pp. 1370-1378; Lim, H.-K., Lee, H., Kim, H., A Seamless Grid-Based Interface for Mean-Field QM/MM Coupled with Efficient Solvation Free Energy Calculations (2016) J. Chem. Theory Comput., 12, pp. 5088-5099; Sanz-Navarro, C.F., Grima, R., García, A., Bea, E.A., Soba, A., Cela, J.M., Ordejón, P., An efficient implementation of a QM-MM method in SIESTA (2011) Theor. Chem. Acc., 128, pp. 825-833; Golze, D., Iannuzzi, M., Nguyen, M.-T., Passerone, D., Hutter, J., Simulation of Adsorption Processes at Metallic Interfaces: An Image Charge Augmented QM/MM Approach (2013) J. Chem. Theory Comput., 9, pp. 5086-5097; Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L., Comparison of simple potential functions for simulating liquid water (1983) J. Chem. Phys., 79, pp. 926-935; Jorgensen, W.L., Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water (1981) J. Am. Chem. Soc., 103, pp. 335-340; Rizzato, S., Bergès, J., Mason, S.A., Albinati, A., Kozelka, J., Dispersion-driven hydrogen bonding: Predicted hydrogen bond between water and platinum(II) identified by neutron diffraction (2010) Angew. Chem., Int. Ed., 49, pp. 7440-7443; Andrić, J.M., Janjić, G.V., Ninković, D.B., Zarić, S.D., The influence of water molecule coordination to a metal ion on water hydrogen bonds (2012) Phys. Chem. Chem. Phys., 14, pp. 10896-10898; Gray, H.B., Záliš, S., Vlček, A., Electronic structures and photophysics of d8-d8 complexes (2017) Coord. Chem. Rev., 345, p. 297; Peterson, J.R., Kalyanasundaram, K., Energy- and Electron-Transfer Processes of the Lowest Triplet Excited State of Tetrakis(diphosphito)diplatinate(II) (1985) J. Phys. Chem., 89, pp. 2486-2492; Roundhill, M.D., Gray, H.B., Che, C., Pyrophosphito-bridged diplatinum chemistry (1989) Acc. Chem. Res., 22, pp. 55-61; Christensen, M., Haldrup, K., Bechgaard, K., Feidenhans'l, R., Kong, Q., Cammarata, M., Russo, M.L., Nielsen, M.M., Time-Resolved X-ray Scattering of an Electronically Excited State in Solution. Structure of the 3A2u State of Tetrakis-pyrophosphitodiplatinate(II) (2009) J. Am. Chem. Soc., 131, pp. 502-508; Van Der Veen, R.M., Cannizzo, A., Van Mourik, F., Vlček, A.J., Chergui, M., Vibrational relaxation and intersystem crossing of binuclear metal complexes in solution (2011) J. Am. Chem. Soc., 133, pp. 305-315; Penfold, T.J., Curchod, B.F.E., Tavernelli, I., Abela, R., Rothlisberger, U., Chergui, M., Simulations of X-ray absorption spectra: The effect of the solvent (2012) Phys. Chem. Chem. Phys., 14, p. 9444; Kong, Q., Kjær, K.S., Haldrup, K., Sauer, S.P.A., Van Driel, T.B., Christensen, M., Nielsen, M.M., Wulff, M., Theoretical study of the triplet excited state of PtPOP and the exciplexes M-PtPOP (M = Tl, Ag) in solution and comparison with ultrafast X-ray scattering results (2012) Chem. Phys., 393, pp. 117-122; Zipp, A.P., The behavior of the tetra-pyrophosphito-diplatinum(II) ion Pt2(P2O5H2)44 and related species (1988) Coord. Chem. Rev., 84, pp. 47-83; Motobayashi, K., Árnadóttir, L., Matsumoto, C., Stuve, E.M., Jónsson, H., Kim, Y., Kawai, M., Adsorption of Water Dimer on Platinum(111): Identification of the OH···Pt Hydrogen Bond (2014) ACS Nano, 8, pp. 11583-11590; Friedrich, J., Yu, H., Leverentz, H.R., Bai, P., Siepmann, J.I., Truhlar, D.G., Water 26-mers Drawn from Bulk Simulations: Benchmark Binding Energies for Unprecedentedly Large Water Clusters and Assessment of the Electrostatically Embedded Three-Body and Pairwise Additive Approximations (2014) J. Phys. Chem. Lett., 5, pp. 666-670. , (PMID: 26270834); Isegawa, M., Wang, B., Truhlar, D.G., Electrostatically Embedded Molecular Tailoring Approach and Validation for Peptides (2013) J. Chem. Theory Comput., 9, pp. 1381-1393. , (PMID: 26587600); Olsen, J.M.H., Steinmann, C., Ruud, K., Kongsted, J., Polarizable Density Embedding: A New QM/QM/MM-Based Computational Strategy (2015) J. Phys. Chem. A, 119, pp. 5344-5355; Kratz, E.G., Walker, A.R., Lagardère, L., Lipparini, F., Piquemal, J.-P., Andrés Cisneros, G., LICHEM: AQM/MM program for simulations with multipolar and polarizable force fields (2016) J. Comput. Chem., 37, pp. 1019-1029; Loco, D., Polack, E., Caprasecca, S., Lagardère, L., Lipparini, F., Piquemal, J.-P., Mennucci, B., A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State to Electronic Excitations (2016) J. Chem. Theory Comput., 12, pp. 3654-3661; Ganguly, A., Boulanger, E., Thiel, W., Importance of MM Polarization in QM/MM Studies of Enzymatic Reactions: Assessment of the QM/MM Drude Oscillator Model (2017) J. Chem. Theory Comput., 13, pp. 2954-2961; Wang, B., Truhlar, D.G., Geometry optimization using tuned and balanced redistributed charge schemes for combined quantum mechanical and molecular mechanical calculations (2011) Phys. Chem. Chem. Phys., 13, pp. 10556-10564; Marques, M.A., Oliveira, M.J., Burnus, T., Libxc: A library of exchange and correlation functionals for density functional theory (2012) Comput. Phys. Commun., 183, pp. 2272-2281; Laio, A., VandeVondele, J., Rothlisberger, U., A Hamiltonian Electrostatic Coupling Scheme for Hybrid Car-Parrinello Molecular Dynamics Simulations (2002) J. Chem. Phys., 116, p. 6941; Cisneros, G.A., Tholander, S.N.-I., Parisel, O., Darden, T.A., Elking, D., Perera, L., Piquemal, J.-P., Simple formulas for improved point-charge electrostatics in classical force fields and hybrid quantum mechanical/molecular mechanical embedding (2008) Int. J. Quantum Chem., 108, pp. 1905-1912; Yoo, S., Xantheas, S.S., Communication: The effect of dispersion corrections on the melting temperature of liquid water (2011) J. Chem. Phys., 134, p. 121105; Klimeš, J., Bowler, D.R., Michaelides, A., Chemical accuracy for the van der Waals density functional (2010) J. Phys.: Condens. Matter, 22, p. 022201; Berland, K., Cooper, V.R., Lee, K., Schröder, E., Thonhauser, T., Hyldgaard, P., Lundqvist, B.I., Van der Waals forces in density functional theory: A review of the vdW-DF method (2015) Rep. Prog. Phys., 78, p. 066501; Todorova, T., Seitsonen, A.P., Hutter, J., Kuo, I.W., Mundy, C.J., Molecular Dynamics Simulation of Liquid Water: Hybrid Density Functionals (2006) J. Phys. Chem. B, 110, pp. 3685-3691; Møgelhøj, A., Kelkkanen, A.K., Wikfeldt, K.T., Schiøtz, J., Mortensen, J.J., Pettersson, L.G.M., Lundqvist, B.I., Nørskov, J.K., Ab Initio van der Waals Interactions in Simulations of Water Alter Structure from Mainly Tetrahedral to High-Density-Like (2011) J. Phys. Chem. B, 115, pp. 14149-14160; Groenenboom, M.C., Keith, J.A., Explicitly Unraveling the Roles of Counterions, Solvent Molecules,and Electron Correlation in Solution Phase Reaction Pathways (2016) J. Phys. Chem. B, 120, pp. 10797-10807; Larsen, A.H., Vanin, M., Mortensen, J.J., Thygesen, K.S., Jacobsen, K.W., Localized Atomic Basis Set in the Projector Augmented Wave Method (2009) Phys. Rev. B: Condens. Matter Mater. Phys., 80, p. 195112; Andersen, H.C., Rattle: A "velocity" version of the shake algorithm for molecular dynamics calculations (1983) J. Comput. Phys., 52, p. 24; Jurečka, P., Šponer, J., Černý, J., Hobza, P., Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs (2006) Phys. Chem. Chem. Phys., 8, pp. 1985-1993; Rappe, A.K., Casewit, C.J., Colwell, K.S., Goddard, W.A., Skiff, W.M., UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations (1992) J. Am. Chem. Soc., 114, pp. 10024-10035; Gillan, M.J., Alfè, D., Michaelides, A., Perspective: How good is DFT for water? (2016) J. Chem. Phys., 144, p. 130901; Head-Gordon, T., Hura, G., Water Structure from Scattering Experiments and Simulation (2002) Chem. Rev., 102, pp. 2651-2670; Horn, H.W., Swope, W.C., Pitera, J.W., Madura, J.D., Dick, T.J., Hura, G.L., Head-Gordon, T., Development of an Improved Four-Site Water Model for Biomolecular Simulations: TIP4P-Ew (2004) J. Chem. Phys., 120, p. 9665; Bates, D.M., Tschumper, G.S., CCSD(T) Complete Basis Set Limit Relative Energies for Low-Lying Water Hexamer Structures (2009) J. Phys. Chem. A, 113, pp. 3555-3559; Temelso, B., Archer, K.A., Shields, G.C., Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections (2011) J. Phys. Chem. A, 115, pp. 12034-12046; Becke, A.D., Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior (1988) Phys. Rev. A: At., Mol., Opt. Phys., 38, p. 3098; Lee, C., Yang, W., Parr, R.G., Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density (1988) Phys. Rev. B: Condens. Matter Mater. Phys., 37, pp. 785-789; Schwenk, C.F., Rode, B.M., Extended ab initio quantum mechanical/molecular mechanical molecular dynamics simulations of hydrated Cu2+ (2003) J. Chem. Phys., 119, pp. 9523-9531; Pham, V., Tavernelli, I., Milne, C., Van Der Veen, R., D'Angelo, P., Bressler, C., Chergui, M., The solvent shell structure of aqueous iodide: X-ray absorption spectroscopy and classical, hybrid QM/MM and full quantum molecular dynamics simulations (2010) Chem. Phys., 371, pp. 24-29; Uhlig, F., Marsalek, O., Jungwirth, P., Unraveling the Complex Nature of the Hydrated Electron (2012) J. Phys. Chem. Lett., 3, pp. 3071-3075; Hitzenberger, M., Ratanasak, M., Parasuk, V., Hofer, T.S., Optimizing link atom parameters for DNA QM/MM simulations (2016) Theor. Chem. Acc., 135, p. 47; Melander, M., Jónsson, E.O., Mortensen, J.J., Vegge, T., Garcia Lastra, J.M., Implementation of Constrained DFT for Computing Charge Transfer Rates within the Projector Augmented Wave Method (2016) J. Chem. Theory Comput., 12, p. 5367; Schmidt, J., VandeVondele, J., Kuo, I.-F.W., Sebastiani, D., Siepmann, J.I., Hutter, J., Mundy, C.J., Isobaric-Isothermal Molecular Dynamics Simulations Utilizing Density Functional Theory: An Assessment of the Structure and Density of Water at Near-Ambient Conditions (2009) J. Phys. Chem. B, 113, pp. 11959-11964; Lin, I., Seitsonen, A.P., Tavernelli, I., Rothlisberger, U., Structure and Dynamics of Liquid Water from ab Initio Molecular Dynamics - Comparison of BLYP, PBE, and revPBE Density Functionals with and without van der Waals Corrections (2012) J. Chem. Theory Comput., 8, pp. 3902-3910; Plimpton, S., Fast Parallel Algorithms for Short-Range Molecular Dynamics (1995) J. Comput. Phys., 117, pp. 1-19; Wernet, P., Nordlund, D., Bergmann, U., Cavalleri, M., Odelius, M., Ogasawara, H., Näslund, L.A., Nilsson, A., The Structure of the First Coordination Shell in Liquid Water (2011) Science, 304, pp. 995-999; Lee, H.-S., Tuckerman, M.E., Structure of liquid water at ambient temperature from ab initio molecular dynamics performed in the complete basis set limit (2006) J. Chem. Phys., 125, p. 154507; Mantz, Y.A., Chen, B., Martyna, G.J., Temperature-dependent water structure: Ab initio and empirical model predictions (2005) Chem. Phys. Lett., 405, pp. 294-299; Mantz, Y.A., Chen, B., Martyna, G.J., Structural correlations and motifs in liquid water at selected temperatures: Ab initio and empirical model predictions (2006) J. Phys. Chem. B, 110, pp. 3540-3554; Chandler, D., (1987) Introduction to Modern Statistical Mechanics, , Oxford University Press: Oxford, U.K; Huber, K.P., Herzberg, G., (1979) Constants of Diatomic Molecules Molecular Spectra and Molecular Structure, 4. , Van Nostrand Reinhold: New York; (1997) Copyright IBM Corp. 1990-2015, , http://www.cpmd.org/, CopyrightMPIfür Festkörperforschung, Stuttgart; Fordyce, W.A., Brummer, J.G., Crosby, G.A., Electronic Spectroscopy of a Diplatinum(II) Octaphosphite Complex (1981) J. Am. Chem. Soc., 103, pp. 7061-7064; Pezeshki, S., Davis, C., Heyden, A., Lin, H., Adaptive-Partitioning QM/MM Dynamics Simulations: 3. Solvent Molecules Entering and Leaving Protein Binding Sites (2014) J. Chem. Theory Comput., 10, pp. 4765-4776; Wikfeldt, K.T., Batista, E.R., Vila, F.D., Jónsson, H., A Transferable H2O Interaction Potential Based on a Single Center Multipole Expansion: SCME (2013) Phys. Chem. Chem. Phys., 15, p. 16542; Gavnholt, J., Olsen, T., Engelund, M., Schiøtz, J., Excited-state potential-energy surfaces of metal-adsorbed organic molecules from linear expansion Δ-self-consistent field density-functional theory (ΔSCF-DFT) (2008) Phys. Rev. B: Condens. Matter Mater. Phys., 78, p. 075441; Olsen, T., Gavnholt, J., Schiøtz, J., Hot-electron-mediated desorption rates calculated from excited-state potential energy surfaces (2009) Phys. Rev. B: Condens. Matter Mater. Phys., 79, p. 0354403; Walter, M., Häkkinen, H., Lehtovaara, L., Puska, M., Enkovaara, J., Rostgaard, C., Mortensen, J.J., Time-dependent density-functional theory in the projector augmented-wave method (2008) J. Chem. Phys., 128, p. 244101; Yan, J., Mortensen, J.J., Jacobsen, K.W., Thygesen, K.S., Linear density response function in the projector augmented wave method: Applications to solids, surfaces, and interfaces (2011) Phys. Rev. B: Condens. Matter Mater. Phys., 83, p. 245122spa
dc.creator.affiliationDohn, A.O., Faculty of Physical Sciences and Science Institute, University of Iceland, Reykjavĺk, Iceland; Jónsson, E.O., Faculty of Physical Sciences and Science Institute, University of Iceland, Reykjavĺk, Iceland; Levi, G., Department of Chemistry, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark; Mortensen, J.J., CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark; Lopez-Acevedo, O., Department of Applied Physics, Aalto University, Espoo, Finland, Facultad de Ciencias Baśicas, Universidad de Medellín, Carrera 87 No. 30-65, Medellín, Colombia; Thygesen, K.S., CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark; Jacobsen, K.W., CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark; Ulstrup, J., Department of Chemistry, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark; Henriksen, N.E., Department of Chemistry, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark; Møller, K.B., Department of Chemistry, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark; Jónsson, H., Faculty of Physical Sciences and Science Institute, University of Iceland, Reykjavĺk, Iceland, Department of Applied Physics, Aalto University, Espoo, Finlandspa
dc.relation.ispartofesJournal of Chemical Theory and Computationspa


Ficheros en el ítem

FicherosTamañoFormatoVer

No hay ficheros asociados a este ítem.

Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro sencillo del ítem