1
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Mortensen JJ, Larsen AH, Kuisma M, Ivanov AV, Taghizadeh A, Peterson A, Haldar A, Dohn AO, Schäfer C, Jónsson EÖ, Hermes ED, Nilsson FA, Kastlunger G, Levi G, Jónsson H, Häkkinen H, Fojt J, Kangsabanik J, Sødequist J, Lehtomäki J, Heske J, Enkovaara J, Winther KT, Dulak M, Melander MM, Ovesen M, Louhivuori M, Walter M, Gjerding M, Lopez-Acevedo O, Erhart P, Warmbier R, Würdemann R, Kaappa S, Latini S, Boland TM, Bligaard T, Skovhus T, Susi T, Maxson T, Rossi T, Chen X, Schmerwitz YLA, Schiøtz J, Olsen T, Jacobsen KW, Thygesen KS. GPAW: An open Python package for electronic structure calculations. J Chem Phys 2024; 160:092503. [PMID: 38450733 DOI: 10.1063/5.0182685] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 03/08/2024] Open
Abstract
We review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different wave-function representations, namely real-space grids, plane waves, and numerical atomic orbitals. The three representations are complementary and mutually independent and can be connected by transformations via the real-space grid. This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for the implementation of new features and methodologies. Moreover, it is well integrated with the Atomic Simulation Environment (ASE), providing a flexible and dynamic user interface. In addition to ground-state DFT calculations, GPAW supports many-body GW band structures, optical excitations from the Bethe-Salpeter Equation, variational calculations of excited states in molecules and solids via direct optimization, and real-time propagation of the Kohn-Sham equations within time-dependent DFT. A range of more advanced methods to describe magnetic excitations and non-collinear magnetism in solids are also now available. In addition, GPAW can calculate non-linear optical tensors of solids, charged crystal point defects, and much more. Recently, support for graphics processing unit (GPU) acceleration has been achieved with minor modifications to the GPAW code thanks to the CuPy library. We end the review with an outlook, describing some future plans for GPAW.
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Affiliation(s)
- Jens Jørgen Mortensen
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ask Hjorth Larsen
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Mikael Kuisma
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Aleksei V Ivanov
- Riverlane Ltd., St Andrews House, 59 St Andrews Street, Cambridge CB2 3BZ, United Kingdom
| | - Alireza Taghizadeh
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Andrew Peterson
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
| | - Anubhab Haldar
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Asmus Ougaard Dohn
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark and Science Institute and Faculty of Physical Sciences, VR-III, University of Iceland, Reykjavík 107, Iceland
| | - Christian Schäfer
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Elvar Örn Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Eric D Hermes
- Quantum-Si, 29 Business Park Drive, Branford, Connecticut 06405, USA
| | | | - Georg Kastlunger
- CatTheory, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Gianluca Levi
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Hannu Häkkinen
- Departments of Physics and Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Jakub Fojt
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Jiban Kangsabanik
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Joachim Sødequist
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jouko Lehtomäki
- Department of Applied Physics, Aalto University, P.O. Box 11100, 00076 Aalto, Finland
| | - Julian Heske
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jussi Enkovaara
- CSC-IT Center for Science Ltd., P.O. Box 405, FI-02101 Espoo, Finland
| | - Kirsten Trøstrup Winther
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Marcin Dulak
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Marko M Melander
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Martin Ovesen
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Martti Louhivuori
- CSC-IT Center for Science Ltd., P.O. Box 405, FI-02101 Espoo, Finland
| | - Michael Walter
- FIT Freiburg Centre for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Morten Gjerding
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Olga Lopez-Acevedo
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, 050010 Medellin, Colombia
| | - Paul Erhart
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Robert Warmbier
- School of Physics and Mandelstam Institute for Theoretical Physics, University of the Witwatersrand, 1 Jan Smuts Avenue, 2001 Johannesburg, South Africa
| | - Rolf Würdemann
- Freiburger Materialforschungszentrum, Universität Freiburg, Stefan-Meier-Straße 21, D-79104 Freiburg, Germany
| | - Sami Kaappa
- Computational Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Simone Latini
- Nanomade, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Tara Maria Boland
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Thomas Bligaard
- Department of Energy Conversion and Storage, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Thorbjørn Skovhus
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Toma Susi
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Tristan Maxson
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Tuomas Rossi
- CSC-IT Center for Science Ltd., P.O. Box 405, FI-02101 Espoo, Finland
| | - Xi Chen
- School of Physical Science and Technology, Lanzhou University, Lanzhou, Gansu 730000, China
| | | | - Jakob Schiøtz
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Thomas Olsen
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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2
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Dohn AO, Markmann V, Nimmrich A, Haldrup K, Møller KB, Nielsen MM. Eliminating finite-size effects on the calculation of x-ray scattering from molecular dynamics simulations. J Chem Phys 2023; 159:124115. [PMID: 38127395 DOI: 10.1063/5.0164365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/01/2023] [Indexed: 12/23/2023] Open
Abstract
Structural studies using x-ray scattering methods for investigating molecules in solution are shifting focus toward describing the role and effects of the surrounding solvent. However, forward models based on molecular dynamics (MD) simulations to simulate structure factors and x-ray scattering from interatomic distributions such as radial distribution functions (RDFs) face limitations imposed by simulations, particularly at low values of the scattering vector q. In this work, we show how the value of the structure factor at q = 0 calculated from RDFs sampled from finite MD simulations is effectively dependent on the size of the simulation cell. To eliminate this error, we derive a new scheme to renormalize the sampled RDFs based on a model of the excluded volume of the particle-pairs they were sampled from, to emulate sampling from an infinite system. We compare this new correction method to two previous RDF-correction methods, developed for Kirkwood-Buff theory applications. We present a quantitative test to assess the reliability of the simulated low-q scattering signal and show that our RDF-correction successfully recovers the correct q = 0 limit for neat water. We investigate the effect of MD-sampling time on the RDF-corrections, before advancing to a molecular example system, comprised of a transition metal complex solvated in a series of water cells with varying densities. We show that our correction recovers the correct q = 0 behavior for all densities. Furthermore, we employ a simple continuum scattering model to dissect the total scattering signal from the solvent-solvent structural correlations in a solute-solvent model system to find two distinct contributions: a non-local density-contribution from the finite, fixed cell size in NVT simulations, and a local contribution from the solvent shell. We show how the second contribution can be approximated without also including the finite-size contribution. Finally, we provide a "best-practices"-checklist for experimentalists planning to incorporate explicit solvation MD simulations in future work, offering guidance for improving the accuracy and reliability of structural studies using x-ray scattering methods in solution.
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Affiliation(s)
- A O Dohn
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
- Science Institute and Faculty of Physical Sciences, VR-III, University of Iceland, Reykjavík 107, Iceland
| | - V Markmann
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - A Nimmrich
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - K Haldrup
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - K B Møller
- Department of Chemistry, Technical University of Denmark, 2800 Lyngby, Denmark
| | - M M Nielsen
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
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3
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Abidi N, Steinmann SN. An Electrostatically Embedded QM/MM Scheme for Electrified Interfaces. ACS APPLIED MATERIALS & INTERFACES 2023; 15:25009-25017. [PMID: 37163568 DOI: 10.1021/acsami.3c01430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Atomistic modeling of electrified interfaces remains a major issue for detailed insights in electrocatalysis, corrosion, electrodeposition, batteries, and related devices such as pseudocapacitors. In these domains, the use of grand-canonical density functional theory (GC-DFT) in combination with implicit solvation models has become popular. GC-DFT can be conveniently applied not only to metallic surfaces but also to semiconducting oxides and sulfides and is, furthermore, sufficiently robust to achieve a consistent description of reaction pathways. However, the accuracy of implicit solvation models for solvation effects at interfaces is in general unknown. One promising way to overcome the limitations of implicit solvents is going toward hybrid quantum mechanical (QM)/molecular mechanics (MM) models. For capturing the electrochemical potential dependence, the key quantity is the capacitance, i.e., the relation between the surface charge and the electrochemical potential. In order to retrieve the electrochemical potential from a QM/MM hybrid scheme, an electrostatic embedding is required. Furthermore, the charge of the surface and of the solvent regions has to be strictly opposite in order to consistently simulate charge-neutral unit cells in MM and in QM. To achieve such a QM/MM scheme, we present the implementation of electrostatic embedding in the VASP code. This scheme is broadly applicable to any neutral or charged solid/liquid interface. Here, we demonstrate its use in the context of GC-DFT for the hydrogen evolution reaction (HER) over a noble-metal-free electrocatalyst, MoS2. We investigate the effect of electrostatic embedding compared to the implicit solvent model for three contrasting active sites on MoS2: (i) the sulfur vacancy defect, which is rather apolar; (ii) a Mo antisite defect, where the active site is a surface bound highly polar OH group; and (iii) a reconstructed edge site, which is generally believed to be responsible for most of the catalytic activity. According to our results, the electrostatic embedding leads to almost indistinguishable results compared to the implicit solvent for the apolar system but has a significant effect on polar sites. This demonstrates the reliability of the hybrid QM/MM, electrostatically embedded solvation model for electrified interfaces.
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Affiliation(s)
- Nawras Abidi
- Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, F-69364 Lyon, France
| | - Stephan N Steinmann
- Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, F-69364 Lyon, France
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4
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Katayama T, Choi TK, Khakhulin D, Dohn AO, Milne CJ, Vankó G, Németh Z, Lima FA, Szlachetko J, Sato T, Nozawa S, Adachi SI, Yabashi M, Penfold TJ, Gawelda W, Levi G. Atomic-scale observation of solvent reorganization influencing photoinduced structural dynamics in a copper complex photosensitizer. Chem Sci 2023; 14:2572-2584. [PMID: 36908966 PMCID: PMC9993854 DOI: 10.1039/d2sc06600a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Photochemical reactions in solution are governed by a complex interplay between transient intramolecular electronic and nuclear structural changes and accompanying solvent rearrangements. State-of-the-art time-resolved X-ray solution scattering has emerged in the last decade as a powerful technique to observe solute and solvent motions in real time. However, disentangling solute and solvent dynamics and how they mutually influence each other remains challenging. Here, we simultaneously measure femtosecond X-ray emission and scattering to track both the intramolecular and solvation structural dynamics following photoexcitation of a solvated copper photosensitizer. Quantitative analysis assisted by molecular dynamics simulations reveals a two-step ligand flattening strongly coupled to the solvent reorganization, which conventional optical methods could not discern. First, a ballistic flattening triggers coherent motions of surrounding acetonitrile molecules. In turn, the approach of acetonitrile molecules to the copper atom mediates the decay of intramolecular coherent vibrations and induces a further ligand flattening. These direct structural insights reveal that photoinduced solute and solvent motions can be intimately intertwined, explaining how the key initial steps of light harvesting are affected by the solvent on the atomic time and length scale. Ultimately, this work takes a step forward in understanding the microscopic mechanisms of the bidirectional influence between transient solvent reorganization and photoinduced solute structural dynamics.
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Affiliation(s)
- Tetsuo Katayama
- Japan Synchrotron Radiation Research Institute Kouto 1-1-1, Sayo Hyogo 679-5198 Japan.,RIKEN SPring-8 Center 1-1-1 Kouto, Sayo Hyogo 679-5148 Japan
| | - Tae-Kyu Choi
- XFEL Division, Pohang Accelerator Laboratory Jigok-ro 127-80 Pohang 37673 Republic of Korea
| | | | - Asmus O Dohn
- Science Institute, University of Iceland 107 Reykjavík Iceland .,DTU Physics, Technical University of Denmark Kongens Lyngby Denmark
| | | | - György Vankó
- Wigner Research Centre for Physics, Hungarian Academy of Sciences H-1525 Budapest Hungary
| | - Zoltán Németh
- Wigner Research Centre for Physics, Hungarian Academy of Sciences H-1525 Budapest Hungary
| | | | - Jakub Szlachetko
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University PL-30392 Kraków Poland
| | - Tokushi Sato
- European XFEL Holzkoppel 4, Schenefeld 22869 Germany
| | - Shunsuke Nozawa
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) 1-1 Oho Tsukuba Ibaraki 305-0801 Japan.,Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies 1-1 Oho Tsukuba Ibaraki 305-0801 Japan
| | - Shin-Ichi Adachi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) 1-1 Oho Tsukuba Ibaraki 305-0801 Japan.,Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies 1-1 Oho Tsukuba Ibaraki 305-0801 Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center 1-1-1 Kouto, Sayo Hyogo 679-5148 Japan
| | - Thomas J Penfold
- Chemistry-School of Natural and Environmental Sciences, Newcastle University Newcastle Upon-Tyne NE1 7RU UK
| | - Wojciech Gawelda
- Departamento de Química, Universidad Autónoma de Madrid, Campus Cantoblanco 28047 Madrid Spain.,IMDEA-Nanociencia, Campus Cantoblanco C/Faraday 9 28049 Madrid Spain.,Faculty of Physics, Adam Mickiewicz University 61-614 Poznań Poland
| | - Gianluca Levi
- Science Institute, University of Iceland 107 Reykjavík Iceland
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5
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Kirchhoff B, Jónsson EÖ, Dohn AO, Jacob T, Jónsson H. Elastic Collision Based Dynamic Partitioning Scheme for Hybrid Simulations. J Chem Theory Comput 2021; 17:5863-5875. [PMID: 34460258 DOI: 10.1021/acs.jctc.1c00522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In hybrid simulations, such as the QM/MM approach, the system is partitioned into regions that are treated at different levels of theory. The key question then becomes how to evaluate the interactions between particles on opposite sides of the boundary. One approach is to place the boundary in such a way that particles near the boundary on both sides are of the same type, thus simplifying the evaluation of the interactions. If mobile particles are present, such as solvent molecules, and particles are allowed to cross the boundary, the conservation of energy and atomic forces is problematic unless the computational effort is increased significantly. By preventing particles from crossing the boundary but allowing the boundary to be flexible, an accurate estimate of average thermodynamic properties is obtained in principle as illustrated by the flexible inner region ensemble separator (FIRES) method [C. Rowley and B. Roux, J. Chem. Theory Comput. 2012, 8, 3526]. In FIRES, a harmonic restraint is applied to particles near the boundary. Therefore, it can occur that particle cross the boundary to some extent resulting in anomalies in the particle density. Here, a constraint approach is presented where particles instantaneously scatter from the boundary. This scattering-adapted FIRES (SAFIRES) implementation makes use of a variable-time-step propagation algorithm where the time step is scaled automatically to identify the moment a collision should occur. If the length of the time step is kept constant, this propagator reduces to a regular Langevin dynamics algorithm, and to the velocity Verlet algorithm for conservative dynamics if the friction coefficient is set to zero. Correct average ensemble statistics are obtained as demonstrated in simulations where, for testing purposes, the particles in the two regions are treated at the same level of theory, namely, a homogeneous Lennard-Jones (LJ) liquid and liquid water based on the TIP4P potential function. In order to illustrate this approach in solid-liquid interface simulations, a LJ liquid in contact with the surface of a crystal is also simulated. The simulations using SAFIRES are shown to reproduce the unconstrained reference simulations without significant deviations in the particle density and the dynamics are shown to conserve energy when coupling to the heat bath is turned off.
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Affiliation(s)
- Björn Kirchhoff
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Elvar Örn Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Asmus Ougaard Dohn
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland.,Technical University of Denmark, Lyngby, Denmark
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany.,Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, Helmholtz-Straße 16, 89081 Ulm, Germany.,Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
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6
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Krumland J, Gil G, Corni S, Cocchi C. LayerPCM: An implicit scheme for dielectric screening from layered substrates. J Chem Phys 2021; 154:224114. [PMID: 34241221 DOI: 10.1063/5.0050158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We present LayerPCM, an extension of the polarizable-continuum model coupled to real-time time-dependent density-functional theory, for an efficient and accurate description of the electrostatic interactions between molecules and multilayered dielectric substrates on which they are physisorbed. The former are modeled quantum-mechanically, while the latter are treated as polarizable continua characterized by their dielectric constants. The proposed approach is purposely designed to simulate complex hybrid heterostructures with nano-engineered substrates including a stack of anisotropic layers. LayerPCM is suitable for describing the polarization-induced renormalization of frontier energy levels of the adsorbates in the static regime. Moreover, it can be reliably applied to simulating laser-induced ultrafast dynamics of molecules through the inclusion of electric fields generated by Fresnel-reflection at the substrate. Depending on the complexity of the underlying layer structure, such reflected fields can assume non-trivial shapes and profoundly affect the dynamics of the photo-excited charge carriers in the molecule. In particular, the interaction with the substrate can give rise to strong delayed fields, which lead to interference effects resembling those of multi-pulse-based spectroscopy. The robustness of the implementation and the above-mentioned features are demonstrated with a number of examples, ranging from intuitive models to realistic systems.
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Affiliation(s)
- Jannis Krumland
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Gabriel Gil
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via F. Marzolo 1, 35131 Padova, Italy
| | - Stefano Corni
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via F. Marzolo 1, 35131 Padova, Italy
| | - Caterina Cocchi
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
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7
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Liu H, Siani P, Bianchetti E, Zhao J, Di Valentin C. Multiscale simulations of the hydration shells surrounding spherical Fe 3O 4 nanoparticles and effect on magnetic properties. NANOSCALE 2021; 13:9293-9302. [PMID: 33983352 PMCID: PMC8230581 DOI: 10.1039/d1nr01014j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
Iron oxide magnetic nanoparticles (NPs) are excellent systems in catalysis and in nanomedicine, where they are mostly immersed in aqueous media. Even though the NP solvation by water is expected to play an active role, the detailed structural insight at the nanostructure oxide/water interface is still missing. Here, based on our previous efforts to obtain accurate models of dehydrated Fe3O4 NPs and of their magnetic properties and through multiscale molecular dynamics simulations combining the density functional tight binding method and force field, we unravel the atomistic details of the short range (chemical) and long range (physical) interfacial effects when magnetite nanoparticles are immersed in water. The influence of the first hydration shell on the structural, electronic and magnetic properties of Fe3O4 NPs is revealed by high-level hybrid density functional calculations. Hydrated Fe3O4 NPs possess larger magnetic moment than dehydrated ones. This work bridges the large gap between experimental studies on solvated Fe3O4 NPs and theoretical investigations on flat Fe3O4 surfaces covered with water and paves the way for further study of Fe3O4 NPs in biological environments.
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Affiliation(s)
- Hongsheng Liu
- Laboratory of Materials Modification by Laser, Ion and Electron Beams, Dalian University of Technology, Ministry of Education, Dalian 116024, China and Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, I-20125 Milano, Italy.
| | - Paulo Siani
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, I-20125 Milano, Italy.
| | - Enrico Bianchetti
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, I-20125 Milano, Italy.
| | - Jijun Zhao
- Laboratory of Materials Modification by Laser, Ion and Electron Beams, Dalian University of Technology, Ministry of Education, Dalian 116024, China
| | - Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, I-20125 Milano, Italy.
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8
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Buntov EA, Zatsepin AF. Carbon Bond Breaking under Ar +-Ion Irradiation in Dependence on sp Hybridization: Car–Parrinello, Ehrenfest, and Classical Dynamics Study. J Phys Chem A 2020; 124:9128-9132. [DOI: 10.1021/acs.jpca.0c05739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Evgeny A. Buntov
- Institute of Physics and Technology, Ural Federal University, Ekaterinburg 620002, Russia
| | - Anatoly F. Zatsepin
- Institute of Physics and Technology, Ural Federal University, Ekaterinburg 620002, Russia
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9
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Siani P, Motta S, Ferraro L, Dohn AO, Di Valentin C. Dopamine-Decorated TiO 2 Nanoparticles in Water: A QM/MM vs an MM Description. J Chem Theory Comput 2020; 16:6560-6574. [PMID: 32880452 PMCID: PMC7735700 DOI: 10.1021/acs.jctc.0c00483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
Nanoparticle functionalization
is a modern strategy in nanotechnology
to build up devices for several applications. Modeling fully decorated
metal oxide nanoparticles of realistic size (few nanometers) in an
aqueous environment is a challenging task. In this work, we present
a case study relevant for solar-light exploitation and for biomedical
applications, i.e., a dopamine-functionalized TiO2 nanoparticle
(1700 atoms) in bulk water, for which we have performed an extensive
comparative investigation with both MM and QM/MM approaches of the
structural properties and of the conformational dynamics. We have
used a combined multiscale protocol for a more efficient exploration
of the complex conformational space. On the basis of the results of
this study and of some QM and experimental data, we have defined strengths
and limitations of the existing force field parameters. Our findings
will be useful for an improved modeling and simulation of many other
similar hybrid bioinorganic nanosystems in an aqueous environment
that are pivotal in a broad range of nanotechnological applications.
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Affiliation(s)
- Paulo Siani
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Via Cozzi 55, 20125 Milano, Italy
| | - Stefano Motta
- Dipartimento di Scienze dell'Ambiente e della Terra, Università di Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Lorenzo Ferraro
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Via Cozzi 55, 20125 Milano, Italy
| | - Asmus O Dohn
- Department of Physics, Technical University of Denmark, DK-2800 Lyngby, Denmark.,Faculty of Physical Sciences and Science Institute, University of Iceland, 107 Reykjavík, Iceland
| | - Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Via Cozzi 55, 20125 Milano, Italy
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10
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You P, Chen D, Lian C, Zhang C, Meng S. First‐principles dynamics of photoexcited molecules and materials towards a quantum description. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1492] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Peiwei You
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics Chinese Academy of Sciences Beijing China
- School of Physical Sciences University of Chinese Academy of Sciences Beijing China
| | - Daqiang Chen
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics Chinese Academy of Sciences Beijing China
- School of Physical Sciences University of Chinese Academy of Sciences Beijing China
| | - Chao Lian
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics Chinese Academy of Sciences Beijing China
| | - Cui Zhang
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics Chinese Academy of Sciences Beijing China
- Songshan Lake Materials Laboratory Dongguan China
| | - Sheng Meng
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics Chinese Academy of Sciences Beijing China
- School of Physical Sciences University of Chinese Academy of Sciences Beijing China
- Songshan Lake Materials Laboratory Dongguan China
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11
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Scarbath-Evers LK, Hammer R, Golze D, Brehm M, Sebastiani D, Widdra W. From flat to tilted: gradual interfaces in organic thin film growth. NANOSCALE 2020; 12:3834-3845. [PMID: 31995082 DOI: 10.1039/c9nr06592j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We investigate domain formation and local morphology of thin films of α-sexithiophene (α-6T) on Au(100) beyond monolayer coverage by combining high resolution scanning tunneling microscopy (STM) experiments with electronic structure theory calculations and computational structure search. We report a layerwise growth of highly-ordered enantiopure domains. For the second and third layer, we show that the molecular orbitals of individual α-6T molecules can be well resolved by STM, providing access to detailed information on the molecular orientation. We find that already in the second layer the molecules abandon the flat adsorption structure of the monolayer and adopt a tilted conformation. Although the observed tilted arrangement resembles the orientation of α-6T in the bulk, the observed morphology does not yet correspond to a well-defined surface of the α-6T bulk structure. A similar behavior is found for the third layer indicating a growth mechanism where the bulk structure is gradually adopted over several layers.
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Affiliation(s)
| | - René Hammer
- Martin-Luther University Halle-Wittenberg, Institute of Physics, Halle/Saale, Germany.
| | - Dorothea Golze
- Department of Applied Physics, Aalto University School of Science, FI-00076 Aalto, Finland
| | - Martin Brehm
- Martin-Luther University Halle-Wittenberg, Institute of Chemistry, Halle/Saale, Germany
| | - Daniel Sebastiani
- Martin-Luther University Halle-Wittenberg, Institute of Chemistry, Halle/Saale, Germany
| | - Wolf Widdra
- Martin-Luther University Halle-Wittenberg, Institute of Physics, Halle/Saale, Germany.
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12
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Levi G, Biasin E, Dohn AO, Jónsson H. On the interplay of solvent and conformational effects in simulated excited-state dynamics of a copper phenanthroline photosensitizer. Phys Chem Chem Phys 2020; 22:748-757. [DOI: 10.1039/c9cp06086c] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
QM/MM direct dynamics simulations in acetonitrile reveal the interplay between solvent and conformational effects in the photoinduced ultrafast flattening of a copper photosensitizer.
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Affiliation(s)
- Gianluca Levi
- Science Institute and Faculty of Physical Sciences
- University of Iceland
- Iceland
| | - Elisa Biasin
- PULSE Institute
- SLAC National Accelerator Laboratory
- Menlo Park
- California 94025
- USA
| | - Asmus O. Dohn
- Science Institute and Faculty of Physical Sciences
- University of Iceland
- Iceland
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences
- University of Iceland
- Iceland
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13
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Dohn AO, Jónsson EÖ, Jónsson H. Polarizable Embedding with a Transferable H 2O Potential Function II: Application to (H 2O) n Clusters and Liquid Water. J Chem Theory Comput 2019; 15:6578-6587. [PMID: 31692344 DOI: 10.1021/acs.jctc.9b00778] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The incorporation of polarization in multiscale quantum-mechanics/molecular-mechanics (QM/MM) simulations is important for a variety of applications, for example, charge-transfer reactions. A recently developed formalism based on a density functional theory description of the QM region and a potential energy function for H2O molecules that includes quadrupole as well as dipole polarizability of the MM region is used to simulate liquid water and water clusters. Analysis of the energy, atomic forces, MM polarization, and structure is presented. A quantitative assessment of the QM/MM-MM/MM interaction energy differences of all possible QM/MM configurations of (H2O)n clusters shows that the interquartile range of the distributions of the QM/MM binding energies is never more than 20 meV/molecule higher or lower than the binding energies produced with either of the single-model results. Comparing these interaction energy differences with the QM/MM induction differences show that they are not systematically caused by the induced MM moments of our polarizable embedding scheme. Optimized hexamer geometries as well as the liquid water structure are shown to be improved in comparison with results obtained using point-charge based embedding models neglecting polarization.
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Affiliation(s)
- Asmus Ougaard Dohn
- Science Institute and Faculty of Physical Sciences , University of Iceland , Reykjavík 107 , Iceland
| | - Elvar Örn Jónsson
- Science Institute and Faculty of Physical Sciences , University of Iceland , Reykjavík 107 , Iceland
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences , University of Iceland , Reykjavík 107 , Iceland
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14
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Jónsson EÖ, Dohn AO, Jónsson H. Polarizable Embedding with a Transferable H 2O Potential Function I: Formulation and Tests on Dimer. J Chem Theory Comput 2019; 15:6562-6577. [PMID: 31689104 DOI: 10.1021/acs.jctc.9b00777] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The incorporation of mutual polarization in multiscale simulations where different regions of the system are treated at different level of theory is important in studies of, for example, electronic excitations and charge transfer processes. We present here an energy functional for describing a quantum mechanics/molecular mechanics (QM/MM) scheme that includes reciprocal polarization between the two subsystems. The inclusion of polarization alleviates shortcomings inherent in electrostatic embedding QM/MM models based on point-charge force fields. A density functional theory (DFT) description of the QM subsystem is coupled to a single center multipole expansion (SCME) description of H2O molecules in the MM subsystem that includes anisotropic dipole and quadrupole polarizability as well as static multipoles up to and including the hexadecapole. The energy functional and the coupling scheme is general and can be extended to arbitrary order in terms of both the static and induced moments. Tests of the energy surface for the H2O dimer show that the QM/MM results lie in between the pure DFT and pure SCME values. The consistency of the many-body contributions to the energy and analytical forces is demonstrated for an H2O pentamer.
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Affiliation(s)
- Elvar Örn Jónsson
- Science Institute and Faculty of Physical Sciences, VR-III , University of Iceland , Reykjavík 107 , Iceland
| | - Asmus Ougaard Dohn
- Science Institute and Faculty of Physical Sciences, VR-III , University of Iceland , Reykjavík 107 , Iceland
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, VR-III , University of Iceland , Reykjavík 107 , Iceland
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15
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Vester P, Zaluzhnyy IA, Kurta RP, Møller KB, Biasin E, Haldrup K, Nielsen MM, Vartanyants IA. Ultrafast structural dynamics of photo-reactions observed by time-resolved x-ray cross-correlation analysis. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:024301. [PMID: 30915388 PMCID: PMC6416776 DOI: 10.1063/1.5086374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/10/2019] [Indexed: 05/08/2023]
Abstract
We applied angular X-ray Cross-Correlation analysis (XCCA) to scattering images from a femtosecond resolution X-ray free-electron laser pump-probe experiment with solvated PtPOP {[Pt2(P2O5H2)4]4-} metal complex molecules. The molecules were pumped with linear polarized laser pulses creating an excited state population with a preferred orientational (alignment) direction. Two time scales of 1.9 ± 1.5 ps and 46 ± 10 ps were revealed by angular XCCA associated with structural changes and rotational dephasing of the solvent molecules, respectively. These results illustrate the potential of XCCA to reveal hidden structural information in the analysis of time-resolved x-ray scattering data from molecules in solution.
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Affiliation(s)
- Peter Vester
- Department of Physics, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | | | - Ruslan P Kurta
- European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany
| | - Klaus B Møller
- Department of Chemistry, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | | | - Kristoffer Haldrup
- Department of Physics, Technical University of Denmark, DK-2800 Lyngby, Denmark
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16
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Haldrup K, Levi G, Biasin E, Vester P, Laursen MG, Beyer F, Kjær KS, Brandt van Driel T, Harlang T, Dohn AO, Hartsock RJ, Nelson S, Glownia JM, Lemke HT, Christensen M, Gaffney KJ, Henriksen NE, Møller KB, Nielsen MM. Ultrafast X-Ray Scattering Measurements of Coherent Structural Dynamics on the Ground-State Potential Energy Surface of a Diplatinum Molecule. PHYSICAL REVIEW LETTERS 2019; 122:063001. [PMID: 30822093 DOI: 10.1103/physrevlett.122.063001] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Indexed: 05/21/2023]
Abstract
We report x-ray free electron laser experiments addressing ground-state structural dynamics of the diplatinum anion Pt_{2}POP_{4} following photoexcitation. The structural dynamics are tracked with <100 fs time resolution by x-ray scattering, utilizing the anisotropic component to suppress contributions from the bulk solvent. The x-ray data exhibit a strong oscillatory component with period 0.28 ps and decay time 2.2 ps, and structural analysis of the difference signal directly shows this as arising from ground-state dynamics along the PtPt coordinate. These results are compared with multiscale Born-Oppenheimer molecular dynamics simulations and demonstrate how off-resonance excitation can be used to prepare a vibrationally cold excited-state population complemented by a structure-dependent depletion of the ground-state population which subsequently evolves in time, allowing direct tracking of ground-state structural dynamics.
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Affiliation(s)
- Kristoffer Haldrup
- Technical University of Denmark, Department of Physics, Fysikvej 307, DK-2800 Kongens Lyngby, Denmark
| | - Gianluca Levi
- Technical University of Denmark, Department of Chemistry, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
- Current address: Science Institute of the University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Elisa Biasin
- Technical University of Denmark, Department of Physics, Fysikvej 307, DK-2800 Kongens Lyngby, Denmark
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Peter Vester
- Technical University of Denmark, Department of Physics, Fysikvej 307, DK-2800 Kongens Lyngby, Denmark
| | - Mads Goldschmidt Laursen
- Technical University of Denmark, Department of Physics, Fysikvej 307, DK-2800 Kongens Lyngby, Denmark
| | - Frederik Beyer
- Technical University of Denmark, Department of Physics, Fysikvej 307, DK-2800 Kongens Lyngby, Denmark
| | - Kasper Skov Kjær
- Technical University of Denmark, Department of Physics, Fysikvej 307, DK-2800 Kongens Lyngby, Denmark
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Department of Chemical Physics, Lund University, Box 118, S-22100 Lund, Sweden
| | - Tim Brandt van Driel
- Technical University of Denmark, Department of Physics, Fysikvej 307, DK-2800 Kongens Lyngby, Denmark
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Tobias Harlang
- Technical University of Denmark, Department of Physics, Fysikvej 307, DK-2800 Kongens Lyngby, Denmark
- Department of Chemical Physics, Lund University, Box 118, S-22100 Lund, Sweden
| | - Asmus O Dohn
- Technical University of Denmark, Department of Chemistry, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
- Science Institute of the University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Robert J Hartsock
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Silke Nelson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - James M Glownia
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Henrik T Lemke
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Morten Christensen
- Technical University of Denmark, Department of Physics, Fysikvej 307, DK-2800 Kongens Lyngby, Denmark
| | - Kelly J Gaffney
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Niels E Henriksen
- Technical University of Denmark, Department of Chemistry, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Klaus B Møller
- Technical University of Denmark, Department of Chemistry, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Martin M Nielsen
- Technical University of Denmark, Department of Physics, Fysikvej 307, DK-2800 Kongens Lyngby, Denmark
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17
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Abedi M, Levi G, Zederkof DB, Henriksen NE, Pápai M, Møller KB. Excited-state solvation structure of transition metal complexes from molecular dynamics simulations and assessment of partial atomic charge methods. Phys Chem Chem Phys 2019; 21:4082-4095. [DOI: 10.1039/c8cp06567e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Excited-state solvation structure (radial distribution function) of transition metal complexes by classical and mixed quantum-classical (QM/MM) molecular dynamics simulations.
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Affiliation(s)
- Mostafa Abedi
- Department of Chemistry
- Technical University of Denmark
- 2800 Kongens Lyngby
- Denmark
| | - Gianluca Levi
- Department of Chemistry
- Technical University of Denmark
- 2800 Kongens Lyngby
- Denmark
| | - Diana B. Zederkof
- Department of Physics
- Technical University of Denmark
- 2800 Kongens Lyngby
- Denmark
| | - Niels E. Henriksen
- Department of Chemistry
- Technical University of Denmark
- 2800 Kongens Lyngby
- Denmark
| | - Mátyás Pápai
- Department of Chemistry
- Technical University of Denmark
- 2800 Kongens Lyngby
- Denmark
- Wigner Research Center for Physics
| | - Klaus B. Møller
- Department of Chemistry
- Technical University of Denmark
- 2800 Kongens Lyngby
- Denmark
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18
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Ougaard Dohn A, Selli D, Fazio G, Ferraro L, Mortensen JJ, Civalleri B, Di Valentin C. Interfacing CRYSTAL/AMBER to Optimize QM/MM Lennard⁻Jones Parameters for Water and to Study Solvation of TiO₂ Nanoparticles. Molecules 2018; 23:molecules23112958. [PMID: 30428551 PMCID: PMC6278561 DOI: 10.3390/molecules23112958] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/01/2018] [Accepted: 11/06/2018] [Indexed: 11/28/2022] Open
Abstract
Metal oxide nanoparticles (NPs) are regarded as good candidates for many technological applications, where their functional environment is often an aqueous solution. The correct description of metal oxide electronic structure is still a challenge for local and semilocal density functionals, whereas hybrid functional methods provide an improved description, and local atomic function-based codes such as CRYSTAL17 outperform plane wave codes when it comes to hybrid functional calculations. However, the computational cost of hybrids are still prohibitive for systems of real sizes, in a real environment. Therefore, we here present and critically assess the accuracy of our electrostatic embedding quantum mechanical/molecular mechanical (QM/MM) coupling between CRYSTAL17 and AMBER16, and demonstrate some of its capabilities via the case study of TiO2 NPs in water. First, we produced new Lennard–Jones (LJ) parameters that improve the accuracy of water–water interactions in the B3LYP/TIP3P coupling. We found that optimizing LJ parameters based on water tri- to deca-mer clusters provides a less overstructured QM/MM liquid water description than when fitting LJ parameters only based on the water dimer. Then, we applied our QM/MM coupling methodology to describe the interaction of a 1 nm wide multilayer of water surrounding a spherical TiO2 nanoparticle (NP). Optimizing the QM/MM water–water parameters was found to have little to no effect on the local NP properties, which provide insights into the range of influence that can be attributed to the LJ term in the QM/MM coupling. The effect of adding additional water in an MM fashion on the geometry optimized nanoparticle structure is small, but more evident effects are seen in its electronic properties. We also show that there is good transferability of existing QM/MM LJ parameters for organic molecules–water interactions to our QM/MM implementation, even though these parameters were obtained with a different QM code and QM/MM implementation, but with the same functional.
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Affiliation(s)
- Asmus Ougaard Dohn
- Faculty of Physical Sciences and Science Institute, University of Iceland, 107 Reykjavík, Iceland.
| | - Daniele Selli
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via Cozzi 55, 20125 Milano, Italy.
| | - Gianluca Fazio
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via Cozzi 55, 20125 Milano, Italy.
| | - Lorenzo Ferraro
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via Cozzi 55, 20125 Milano, Italy.
| | - Jens Jørgen Mortensen
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Bartolomeo Civalleri
- Dipartimento di Chimica, Università di Torino and NIS Centre of Excellence, Via P. Giuria 7, I-10129 Torino, Italy.
| | - Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via Cozzi 55, 20125 Milano, Italy.
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19
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Fazio G, Selli D, Ferraro L, Seifert G, Di Valentin C. Curved TiO 2 Nanoparticles in Water: Short (Chemical) and Long (Physical) Range Interfacial Effects. ACS APPLIED MATERIALS & INTERFACES 2018; 10:29943-29953. [PMID: 29950088 PMCID: PMC6188221 DOI: 10.1021/acsami.8b08172] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/28/2018] [Indexed: 05/25/2023]
Abstract
In most technological applications, nanoparticles are immersed in a liquid environment. Understanding nanoparticles/liquid interfacial effects is extremely relevant. This work provides a clear and detailed picture of the type of chemistry and physics taking place at the prototypical TiO2 nanoparticles/water interface, which is crucial in photocatalysis and photoelectrochemistry. We present a multistep and multiscale investigation based on hybrid density functional theory (DFT), density functional tight-binding, and quantum mechanics/molecular mechanics calculations. We consider increasing water partial pressure conditions from ultra-high vacuum up to the bulk water environment. We first investigate single water molecule adsorption modes on various types of undercoordinated sites present on a realistic curved nanoparticle (2-3 nm) and then, by decorating all the adsorption sites, we study a full water monolayer to identify the degree of water dissociation, the Brønsted-Lowry basicity/acidity of the nanoparticle in water, the interface effect on crystallinity, surface energy, and electronic properties, such as the band gap and work function. Furthermore, we increase the water coverage by adding water multilayers up to a thickness of 1 nm and perform molecular dynamics simulations, which evidence layer structuring and molecular orientation around the curved nanoparticle. Finally, we clarify whether these effects arise as a consequence of the tension at the water drop surface around the nanosphere by simulating a bulk water up to a distance of 3 nm from the oxide surface. We prove that the nanoparticle/water interfacial effects go rather long range since the dipole orientation of water molecules is observed up to a distance of 5 Å, whereas water structuring extends at least up to a distance of 8 Å from the surface.
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Affiliation(s)
- Gianluca Fazio
- Dipartimento di
Scienza dei Materiali, Università
di Milano Bicocca, Via R. Cozzi 55, 20125 Milano, Italy
| | - Daniele Selli
- Dipartimento di
Scienza dei Materiali, Università
di Milano Bicocca, Via R. Cozzi 55, 20125 Milano, Italy
| | - Lorenzo Ferraro
- Dipartimento di
Scienza dei Materiali, Università
di Milano Bicocca, Via R. Cozzi 55, 20125 Milano, Italy
| | - Gotthard Seifert
- Institut für
Theoretische Chemie, Technische Universität
Dresden, D-01062 Dresden, Germany
| | - Cristiana Di Valentin
- Dipartimento di
Scienza dei Materiali, Università
di Milano Bicocca, Via R. Cozzi 55, 20125 Milano, Italy
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20
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Zhang YJ, Khorshidi A, Kastlunger G, Peterson AA. The potential for machine learning in hybrid QM/MM calculations. J Chem Phys 2018; 148:241740. [DOI: 10.1063/1.5029879] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Yin-Jia Zhang
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Alireza Khorshidi
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
| | - Georg Kastlunger
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
| | - Andrew A. Peterson
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
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