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Mandal S, Kar R, Meyer B, Nair NN. Hybrid Functional and Plane Waves based Ab Initio Molecular Dynamics Study of the Aqueous Fe 2+ /Fe 3+ Redox Reaction. Chemphyschem 2023; 24:e202200617. [PMID: 36169153 DOI: 10.1002/cphc.202200617] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/27/2022] [Indexed: 02/03/2023]
Abstract
Kohn-Sham density functional theory and plane wave basis set based ab initio molecular dynamics (AIMD) simulation is a powerful tool for studying complex reactions in solutions, such as electron transfer (ET) reactions involving Fe2+ /Fe3+ ions in water. In most cases, such simulations are performed using density functionals at the level of Generalized Gradient Approximation (GGA). The challenge in modelling ET reactions is the poor quality of GGA functionals in predicting properties of such open-shell systems due to the inevitable self-interaction error (SIE). While hybrid functionals can minimize SIE, standard plane-wave based AIMD at that level of theory is typically 150 times slower than GGA for systems containing ∼100 atoms. Among several approaches reported to speed-up AIMD simulations with hybrid functionals, the noise-stabilized MD (NSMD) procedure, together with the use of localized orbitals to compute the required exchange integrals, is an attractive option. In this work, we demonstrate the application of the NSMD approach for studying the Fe2+ /Fe3+ redox reaction in water. It is shown here that long AIMD trajectories at the level of hybrid density functionals can be obtained using this approach. Redox properties of the aqueous Fe2+ /Fe3+ system computed from these simulations are compared with the available experimental data for validation.
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Affiliation(s)
- Sagarmoy Mandal
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), 208016, Kanpur, India.,Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nägelsbachstr. 25, 91052, Erlangen, Germany.,Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Martensstr. 1, 91058, Erlangen, Germany
| | - Ritama Kar
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), 208016, Kanpur, India
| | - Bernd Meyer
- Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nägelsbachstr. 25, 91052, Erlangen, Germany.,Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Martensstr. 1, 91058, Erlangen, Germany
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), 208016, Kanpur, India
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2
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Mudryk KD, Seidel R, Winter B, Wilkinson I. The electronic structure of the aqueous permanganate ion: aqueous-phase energetics and molecular bonding studied using liquid jet photoelectron spectroscopy. Phys Chem Chem Phys 2020; 22:20311-20330. [PMID: 32895669 DOI: 10.1039/d0cp04033a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Permanganate aqueous solutions, MnO4-(aq.), were studied using liquid-micro-jet-based soft X-ray non-resonant and resonant photoelectron spectroscopy to determine valence and core-level binding energies. To identify possible differences in the energetics between the aqueous bulk and the solution-gas interface, non-resonant spectra were recorded at two different probing depths. Similar experiments were performed with different counter ions, Na+ and K+, with the two solutions yielding indistinguishable anion electron binding energies. Our resonant photoelectron spectroscopy measurements, performed near the Mn LII,III- and O K-edges, selectively probed valence charge distributions between the Mn metal center, O ligands, and first solvation shell in the aqueous bulk. Associated resonantly-enhanced solute ionisation signals revealed hybridisation of the solute constituents' atomic orbitals, including the inner valence Mn 3p and O 2s. We identified intermolecular coulombic decay relaxation processes following resonant X-ray excitation of the solute that highlight valence MnO4-(aq.)-H2O(l) electronic couplings. Furthermore, our results allowed us to infer oxidative reorganisation energies of MnO4˙(aq.) and adiabatic valence ionisation energies of MnO4-(aq.), revealing the Gibbs free energy of oxidation and permitting estimation of the vertical electron affinity of MnO4˙(aq.). Finally, the Gibbs free energy of hydration of isolated MnO4- was determined. Our results and analysis allowed a near-complete binding-energy-scaled MnO4-(aq.) molecular orbital and a valence energy level diagram to be produced for the MnO4-(aq.)/MnO4˙(aq.) system. Cumulatively, our mapping of the aqueous-phase electronic structure of MnO4- is expected to contribute to a deeper understanding of the exceptional redox properties of this widely applied aqueous transition-metal complex ion.
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Affiliation(s)
- Karen D Mudryk
- Locally-Sensitive & Time-Resolved Spectroscopy, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany. and Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Robert Seidel
- Operando Interfacial Photochemistry, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany and Fachbereich Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489 Berlin, Germany
| | - Bernd Winter
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Iain Wilkinson
- Locally-Sensitive & Time-Resolved Spectroscopy, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany.
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3
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Giannini S, Ziogos OG, Carof A, Ellis M, Blumberger J. Flickering Polarons Extending over Ten Nanometres Mediate Charge Transport in High‐Mobility Organic Crystals. ADVANCED THEORY AND SIMULATIONS 2020. [DOI: 10.1002/adts.202000093] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Samuele Giannini
- Department of Physics and Astronomy and Thomas Young Centre University College London London WC1E 6BT UK
| | - Orestis George Ziogos
- Department of Physics and Astronomy and Thomas Young Centre University College London London WC1E 6BT UK
| | - Antoine Carof
- Laboratoire de Physique et Chimie Théoriques, CNRS, UMR No. 7019 Université de Lorraine BP 239 Vandœuvre‐lès‐Nancy Cedex 54506 France
| | - Matthew Ellis
- Department of Physics and Astronomy and Thomas Young Centre University College London London WC1E 6BT UK
| | - Jochen Blumberger
- Department of Physics and Astronomy and Thomas Young Centre University College London London WC1E 6BT UK
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4
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Futera Z, Jiang X, Blumberger J. Ergodicity Breaking in Thermal Biological Electron Transfer? Cytochrome C Revisited II. J Phys Chem B 2020; 124:3336-3342. [PMID: 32223243 DOI: 10.1021/acs.jpcb.0c01414] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It was recently suggested that cytochrome c operates in an ergodicity-breaking regime characterized by unusually large energy gap thermal fluctuations and associated reorganization free energies for heme oxidation of up to 3.0 eV. The large fluctuations were reported to lower activation free energy for oxidation of the heme cofactor by almost a factor of 2 compared to the case where ergodicity is maintained. Our group has recently investigated this claim computationally at several levels of theory and found no evidence for such large energy gap fluctuations. Here we address the points of our earlier work that have raised criticism and we also extend our previous investigation by considering a simple linear polarizability model for cytochrome c oxidation. We find very consistent results among all our computational approaches, ranging from classical molecular dynamics, to the linear polarizability model to QM(PMM)/MM to full QM(DFT)/MM electrostatic emdedding. None of them support the notion of very large energy gap fluctuations or ergodicity breaking. The deviation between our simulations and the ones reported in [ J. Phys. Chem. B 2017, 121, 4958] is traced back to rather large electric fields at the Fe site of the heme c cofactor in that study, not seen in our simulations, neither with the AMBER nor with the CHARMM force field. While ergodicity breaking effects may well occur in other biological ET, our numerical evidence suggests that this is not the case for cytochrome c.
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Affiliation(s)
- Zdenek Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Xiuyun Jiang
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, U.K
| | - Jochen Blumberger
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, U.K
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5
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Ahart CS, Blumberger J, Rosso KM. Polaronic structure of excess electrons and holes for a series of bulk iron oxides. Phys Chem Chem Phys 2020; 22:10699-10709. [DOI: 10.1039/c9cp06482f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
With the use of a gap-optimized hybrid functional and large supercells, it is found that while the electron hole polaron generally localises onto a single iron site, the electron polaron localises across two iron sites of the same spin layer.
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Affiliation(s)
- Christian S. Ahart
- Department of Physics and Astronomy
- University College London
- London WC1E 6BT
- UK
| | - Jochen Blumberger
- Department of Physics and Astronomy
- University College London
- London WC1E 6BT
- UK
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6
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Carof A, Giannini S, Blumberger J. How to calculate charge mobility in molecular materials from surface hopping non-adiabatic molecular dynamics - beyond the hopping/band paradigm. Phys Chem Chem Phys 2019; 21:26368-26386. [PMID: 31793569 DOI: 10.1039/c9cp04770k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Charge transport in high mobility organic semiconductors is in an intermediate regime between small polaron hopping and band transport limits. We have recently shown that surface hopping non-adiabatic molecular dynamics is a powerful method for prediction of charge transport mechanisms in organic materials and for near-quantitative prediction of charge mobilities at room temperature where the effects of nuclear zero-point motion and tunneling are still relatively small [S. Giannini et al., Nat. Commun., 2019, 10, 3843]. Here we assess and critically discuss the extensions to Tully's original method that have led to this success: (i) correction for missing electronic decoherence, (ii) detection of trivial crossings and (iii) removal of decoherence correction-induced spurious charge transfer. If any one of these corrections is not included, the charge mobility diverges with system size, each for different physical reasons. Yet if they are included, convergence with system size, detailed balance and good internal consistency are achieved.
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Affiliation(s)
- Antoine Carof
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK.
| | - Samuele Giannini
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK.
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK. and Institute for Advanced Study, Technische Universität München, Lichtenbergstrasse 2 a, D-85748 Garching, Germany
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7
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Jiang X, Futera Z, Blumberger J. Ergodicity-Breaking in Thermal Biological Electron Transfer? Cytochrome C Revisited. J Phys Chem B 2019; 123:7588-7598. [PMID: 31405279 DOI: 10.1021/acs.jpcb.9b05253] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
It was recently suggested that certain redox proteins operate in an ergodicity-breaking regime to facilitate biological electron transfer (ET). A signature for this is a large variance reorganization free energy (several electronvolts) but a significantly smaller Stokes reorganization free energy due to incomplete protein relaxation on the time scale of the ET event. Here we investigate whether this picture holds for oxidation of cytochrome c in aqueous solution, at various levels of theory including classical molecular dynamics with two additive and one electronically polarizable force field, and QM/MM calculations with the QM region treated by full electrostatic DFT embedding and by the perturbed matrix method. Sampling the protein and energy gap dynamics over more than 250 ns, we find no evidence for ergodicity-breaking effects. In particular, the inclusion of electronic polarizability of the heme group at QM/MM levels did not induce nonergodic effects, contrary to previous reports by Matyushov et al. The well-known problem of overestimation of reorganization free energies with additive force fields is cured when the protein and solvent are treated as electronically polarizable. Ergodicity-breaking effects may occur in other redox proteins, and our results suggest that long simulations, ideally on the ET time scale, with electronically polarizable force fields are required to obtain strong numerical evidence for them.
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Affiliation(s)
- Xiuyun Jiang
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
| | - Zdenek Futera
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
| | - Jochen Blumberger
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
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8
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Oberhofer H, Reuter K, Blumberger J. Charge Transport in Molecular Materials: An Assessment of Computational Methods. Chem Rev 2017. [PMID: 28644623 DOI: 10.1021/acs.chemrev.7b00086] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The booming field of molecular electronics has fostered a surge of computational research on electronic properties of organic molecular solids. In particular, with respect to a microscopic understanding of transport and loss mechanisms, theoretical studies assume an ever-increasing role. Owing to the tremendous diversity of organic molecular materials, a great number of computational methods have been put forward to suit every possible charge transport regime, material, and need for accuracy. With this review article we aim at providing a compendium of the available methods, their theoretical foundations, and their ranges of validity. We illustrate these through applications found in the literature. The focus is on methods available for organic molecular crystals, but mention is made wherever techniques are suitable for use in other related materials such as disordered or polymeric systems.
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Affiliation(s)
- Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom.,Institute for Advanced Study, Technische Universität München , Lichtenbergstrasse 2 a, D-85748 Garching, Germany
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9
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Rybkin VV, VandeVondele J. Nuclear Quantum Effects on Aqueous Electron Attachment and Redox Properties. J Phys Chem Lett 2017; 8:1424-1428. [PMID: 28296416 DOI: 10.1021/acs.jpclett.7b00386] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nuclear quantum effects (NQEs) on the reduction and oxidation properties of small aqueous species (CO2, HO2, and O2) are quantified and rationalized by first-principles molecular dynamics and thermodynamic integration. Vertical electron attachment, or electron affinity, and detachment energies (VEA and VDE) are strongly affected by NQEs, decreasing in absolute value by 0.3 eV going from a classical to a quantum description of the nuclei. The effect is attributed to NQEs that lessen the solvent response upon oxidation/reduction. The reduction of solvent reorganization energy is expected to be general for small solutes in water. In the thermodynamic integral that yields the free energy of oxidation/reduction, these large changes enter with opposite sign, and only a small net effect (0.1 eV) remains. This is not obvious for CO2, where the integrand is strongly influenced by NQEs due to the onset of interaction of the reduced orbital with the conduction band of the liquid during thermodynamic integration. We conclude that NQEs might not have to be included in the computation of redox potentials, unless high accuracy is needed, but are important for VEA and VDE calculations.
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Affiliation(s)
- Vladimir V Rybkin
- Nanoscale Simulations, Department of Materials, ETH Zürich , Wolfgang-Pauli-Str. 27, CH-8093 Zürich, Switzerland
| | - Joost VandeVondele
- Nanoscale Simulations, Department of Materials, ETH Zürich , Wolfgang-Pauli-Str. 27, CH-8093 Zürich, Switzerland
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10
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Rubešová M, Jurásková V, Slavíček P. Efficient modeling of liquid phase photoemission spectra and reorganization energies: Difficult case of multiply charged anions. J Comput Chem 2017; 38:427-437. [DOI: 10.1002/jcc.24696] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/25/2016] [Accepted: 11/23/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Martina Rubešová
- Department of Physical Chemistry; University of Chemistry and Technology; Technická 5 Prague 16628 Czech Republic
| | - Veronika Jurásková
- Department of Physical Chemistry; University of Chemistry and Technology; Technická 5 Prague 16628 Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry; University of Chemistry and Technology; Technická 5 Prague 16628 Czech Republic
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11
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Nanoparticle loading effects on the broadband absorption for plasmonic-metal@semiconductor-microsphere photocatalyst. Catal Today 2016. [DOI: 10.1016/j.cattod.2016.01.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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12
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Gaiduk AP, Govoni M, Seidel R, Skone JH, Winter B, Galli G. Photoelectron Spectra of Aqueous Solutions from First Principles. J Am Chem Soc 2016; 138:6912-5. [PMID: 27105336 DOI: 10.1021/jacs.6b00225] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a combined computational and experimental study of the photoelectron spectrum of a simple aqueous solution of NaCl. Measurements were conducted on microjets, and first-principles calculations were performed using hybrid functionals and many-body perturbation theory at the G0W0 level, starting with wave functions computed in ab initio molecular dynamics simulations. We show excellent agreement between theory and experiments for the positions of both the solute and solvent excitation energies on an absolute energy scale and for peak intensities. The best comparison was obtained using wave functions obtained with dielectric-dependent self-consistent and range-separated hybrid functionals. Our computational protocol opens the way to accurate, predictive calculations of the electronic properties of electrolytes, of interest to a variety of energy problems.
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Affiliation(s)
- Alex P Gaiduk
- Institute for Molecular Engineering, The University of Chicago , Chicago, Illinois 60637, United States
| | - Marco Govoni
- Institute for Molecular Engineering, The University of Chicago , Chicago, Illinois 60637, United States.,Materials Science Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Robert Seidel
- Methods for Material Development, Helmholtz-Zentrum Berlin für Materialien und Energie , D-12489 Berlin, Germany
| | - Jonathan H Skone
- Institute for Molecular Engineering, The University of Chicago , Chicago, Illinois 60637, United States
| | - Bernd Winter
- Methods for Material Development, Helmholtz-Zentrum Berlin für Materialien und Energie , D-12489 Berlin, Germany
| | - Giulia Galli
- Institute for Molecular Engineering, The University of Chicago , Chicago, Illinois 60637, United States.,Materials Science Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
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13
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Glinka YD, Babakiray S, Holcomb MB, Lederman D. Effect of Mn doping on ultrafast carrier dynamics in thin films of the topological insulator Bi2Se3. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:165601. [PMID: 27001950 DOI: 10.1088/0953-8984/28/16/165601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Transient reflectivity (TR) measured at laser photon energy 1.51 eV from the indirectly intersurface-coupled topological insulator Bi2-x Mn x Se3 films (12 nm thick) revealed a strong dependence of the rise-time and initial decay-time constants on photoexcited carrier density and Mn content. In undoped samples (x = 0), these time constants are exclusively governed by electron-electron and electron-phonon scattering, respectively, whereas in films with x = 0.013-0.27 ultrafast carrier dynamics are completely controlled by photoexcited electron trapping by ionized Mn(2+) acceptors and their dimers. The shortest decay-time (~0.75 ps) measured for the film with x = 0.27 suggests a great potential of Mn-doped Bi2Se3 films for applications in high-speed optoelectronic devices. Using Raman spectroscopy exploiting similar laser photon energy (1.58 eV), we demonstrate that due to indirect intersurface coupling in the films, the photoexcited electron trapping in the bulk enhances the electron-phonon interaction strength in Dirac surface states.
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Affiliation(s)
- Yuri D Glinka
- Department of Physics and Astronomy, West Virginia University, Morgantown, WV 26506-6315, USA. Institute of Physics, National Academy of Sciences of Ukraine, Kiev 03028, Ukraine
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14
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Seidel R, Winter B, Bradforth SE. Valence Electronic Structure of Aqueous Solutions: Insights from Photoelectron Spectroscopy. Annu Rev Phys Chem 2016; 67:283-305. [PMID: 27023757 DOI: 10.1146/annurev-physchem-040513-103715] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The valence orbital electron binding energies of water and of embedded solutes are crucial quantities for understanding chemical reactions taking place in aqueous solution, including oxidation/reduction, transition-metal coordination, and radiation chemistry. Their experimental determination based on liquid-photoelectron spectroscopy using soft X-rays is described, and we provide an overview of valence photoelectron spectroscopy studies reported to date. We discuss principal experimental aspects and several theoretical approaches to compute the measured binding energies of the least tightly bound molecular orbitals. Solutes studied are presented chronologically, from simple electrolytes, via transition-metal ion solutions and several organic and inorganic molecules, to biologically relevant molecules, including aqueous nucleotides and their components. In addition to the lowest vertical ionization energies, the measured valence photoelectron spectra also provide information on adiabatic ionization energies and reorganization energies for the oxidation (ionization) half-reaction. For solutes with low solubility, resonantly enhanced ionization provides a promising alternative pathway.
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Affiliation(s)
- Robert Seidel
- Institute of Methods for Material Development, Helmholtz-Zentrum Berlin, D-12489 Berlin, Germany; ,
| | - Bernd Winter
- Institute of Methods for Material Development, Helmholtz-Zentrum Berlin, D-12489 Berlin, Germany; ,
| | - Stephen E Bradforth
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482;
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15
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Guerard JJ, Tentscher PR, Seijo M, Samuel Arey J. Explicit solvent simulations of the aqueous oxidation potential and reorganization energy for neutral molecules: gas phase, linear solvent response, and non-linear response contributions. Phys Chem Chem Phys 2016; 17:14811-26. [PMID: 25978135 DOI: 10.1039/c4cp04760e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
First principles simulations were used to predict aqueous one-electron oxidation potentials (Eox) and associated half-cell reorganization energies (λaq) for aniline, phenol, methoxybenzene, imidazole, and dimethylsulfide. We employed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations of the oxidized and reduced species in an explicit aqueous solvent, followed by EOM-IP-CCSD computations with effective fragment potentials for diabatic energy gaps of solvated clusters, and finally thermodynamic integration of the non-linear solvent response contribution using classical MD. A priori predicted Eox and λaq values exhibit mean absolute errors of 0.17 V and 0.06 eV, respectively, compared to experiment. We also disaggregate Eox into several well-defined free energy properties, including the gas phase adiabatic free energy of ionization (7.73 to 8.82 eV), the solvent-induced shift in the free energy of ionization due to linear solvent response (-2.01 to -2.73 eV), and the contribution from non-linear solvent response (-0.07 to -0.14 eV). The linear solvent response component is further apportioned into contributions from the solvent-induced shift in vertical ionization energy of the reduced species (ΔVIEaq) and the solvent-induced shift in negative vertical electron affinity of the ionized species (ΔNVEAaq). The simulated ΔVIEaq and ΔNVEAaq are found to contribute the principal sources of uncertainty in computational estimates of Eox and λaq. Trends in the magnitudes of disaggregated solvation properties are found to correlate with trends in structural and electronic features of the solute. Finally, conflicting approaches for evaluating the aqueous reorganization energy are contrasted and discussed, and concluding recommendations are given.
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Affiliation(s)
- Jennifer J Guerard
- Environmental Chemistry Modeling Laboratory, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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16
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Grell G, Bokarev SI, Winter B, Seidel R, Aziz EF, Aziz SG, Kühn O. Multi-reference approach to the calculation of photoelectron spectra including spin-orbit coupling. J Chem Phys 2015; 143:074104. [PMID: 26298112 DOI: 10.1063/1.4928511] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
X-ray photoelectron spectra provide a wealth of information on the electronic structure. The extraction of molecular details requires adequate theoretical methods, which in case of transition metal complexes has to account for effects due to the multi-configurational and spin-mixed nature of the many-electron wave function. Here, the restricted active space self-consistent field method including spin-orbit coupling is used to cope with this challenge and to calculate valence- and core-level photoelectron spectra. The intensities are estimated within the frameworks of the Dyson orbital formalism and the sudden approximation. Thereby, we utilize an efficient computational algorithm that is based on a biorthonormal basis transformation. The approach is applied to the valence photoionization of the gas phase water molecule and to the core ionization spectrum of the [Fe(H2O)6](2+) complex. The results show good agreement with the experimental data obtained in this work, whereas the sudden approximation demonstrates distinct deviations from experiments.
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Affiliation(s)
- Gilbert Grell
- Institut für Physik, Universität Rostock, D-18051 Rostock, Germany
| | - Sergey I Bokarev
- Institut für Physik, Universität Rostock, D-18051 Rostock, Germany
| | - Bernd Winter
- Helmholtz-Zentrum Berlin für Materialien und Energie, Methods for Material Development, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Robert Seidel
- Helmholtz-Zentrum Berlin für Materialien und Energie, Methods for Material Development, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Emad F Aziz
- Helmholtz-Zentrum Berlin für Materialien und Energie, Methods for Material Development, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Saadullah G Aziz
- Chemistry Department, Faculty of Science, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Oliver Kühn
- Institut für Physik, Universität Rostock, D-18051 Rostock, Germany
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17
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Sun B, Guan X, Fang J, Tratnyek PG. Activation of Manganese Oxidants with Bisulfite for Enhanced Oxidation of Organic Contaminants: The Involvement of Mn(III). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:12414-21. [PMID: 26421879 DOI: 10.1021/acs.est.5b03111] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
MnO4(-) was activated by HSO3(-), resulting in a process that oxidizes organic contaminants at extraordinarily high rates. The permanganate/bisulfite (PM/BS) process oxidized phenol, ciprofloxacin, and methyl blue at pHini 5.0 with rates (kobs ≈ 60-150 s(-1)) that were 5-6 orders of magnitude faster than those measured for permanganate alone, and ∼5 to 7 orders of magnitude faster than conventional advanced oxidation processes for water treatment. Oxidation of phenol was fastest at pH 4.0, but still effective at pH 7.0, and only slightly slower when performed in tap water. A smaller, but still considerable (∼3 orders of magnitude) increase in oxidation rates of methyl blue was observed with MnO2 activated by HSO3(-) (MO/BS). The above results, time-resolved spectroscopy of manganese species under various conditions, stoichiometric analysis of pH changes, and the effect of pyrophosphate on UV absorbance spectra suggest that the reactive intermediate(s) responsible for the extremely rapid oxidation of organic contaminants in the PM/BS process involve manganese(III) species with minimal stabilization by complexation. The PM/BS process may lead to a new category of advanced oxidation technologies based on contaminant oxidation by reactive manganese(III) species, rather than hydroxyl and sulfate radicals.
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Affiliation(s)
- Bo Sun
- State Key Laboratory of Pollution Control and Resources Reuse, Tongji University , Shanghai 20092, People's Republic of China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology , Harbin 150090, People's Republic of China
| | - Xiaohong Guan
- State Key Laboratory of Pollution Control and Resources Reuse, Tongji University , Shanghai 20092, People's Republic of China
| | - Jingyun Fang
- School of Environmental Science and Engineering, Sun Yat-Sen University , Guangzhou 510275, People's Republic of China
| | - Paul G Tratnyek
- Institute of Environmental Health, Oregon Health & Science University , 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
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18
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Blumberger J. Recent Advances in the Theory and Molecular Simulation of Biological Electron Transfer Reactions. Chem Rev 2015; 115:11191-238. [DOI: 10.1021/acs.chemrev.5b00298] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jochen Blumberger
- Department of Physics and
Astronomy, University College London, Gower Street, London WC1E 6BT, U.K
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19
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Kubas A, Gajdos F, Heck A, Oberhofer H, Elstner M, Blumberger J. Electronic couplings for molecular charge transfer: benchmarking CDFT, FODFT and FODFTB against high-level ab initio calculations. II. Phys Chem Chem Phys 2015; 17:14342-54. [PMID: 25573447 DOI: 10.1039/c4cp04749d] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A new database (HAB7-) of electronic coupling matrix elements (Hab) for electron transfer in seven medium-sized negatively charged π-conjugated organic dimers is introduced. Reference data are obtained with spin-component scaled approximate coupled cluster method (SCS-CC2) and large basis sets. Assessed DFT-based approaches include constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), self-consistent charge density functional tight-binding (FODFTB) and the recently described analytic overlap method (AOM). This complements the previously reported HAB11 database where only cationic dimers were considered. The CDFT method in combination with a functional based on PBE and including 50% of exact exchange (HFX) was found to provide best estimates, with a mean relative unsigned error (MRUE) of 8.2%. CDFT couplings systematically increase with decreasing fraction of HFX as a consequence of increasing delocalisation of the SOMO orbital. The FODFT method is found to be very robust underestimating electronic couplings by 28%. The FODFTB and AOM methods, although orders of magnitude more efficient in terms of computational effort than the DFT approaches, perform well with reasonably small errors of 54% and 29%, respectively, translating in errors in the non-adiabatic electron transfer rate of a factor of 2.4 and 1.7, respectively. We discuss carefully various sources of errors and the scope and limitations of all assessed methods taking into account the results obtained for both HAB7- and HAB11 databases.
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Affiliation(s)
- Adam Kubas
- University College London, Department of Physics and Astronomy, Gower Street, London WC1E 6BT, UK.
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20
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Breuer M, Rosso KM, Blumberger J, Butt JN. Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities. J R Soc Interface 2015; 12:20141117. [PMID: 25411412 DOI: 10.1098/rsif.2014.1117] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multi-haem cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometres. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-haem cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-haem cytochromes have attracted much interest and contributed to advances in bioenergy applications and bioremediation of contaminated soils. Looking forward, there are opportunities to engage multi-haem cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence, it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-haem cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-haem cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies.
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Affiliation(s)
- Marian Breuer
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Kevin M Rosso
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Julea N Butt
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK
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21
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Tentscher PR, Seidel R, Winter B, Guerard JJ, Arey JS. Exploring the aqueous vertical ionization of organic molecules by molecular simulation and liquid microjet photoelectron spectroscopy. J Phys Chem B 2014; 119:238-56. [PMID: 25516011 DOI: 10.1021/jp508053m] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
To study the influence of aqueous solvent on the electronic energy levels of dissolved organic molecules, we conducted liquid microjet photoelectron spectroscopy (PES) measurements of the aqueous vertical ionization energies (VIEaq) of aniline (7.49 eV), veratrole alcohol (7.68 eV), and imidazole (8.51 eV). We also reanalyzed previously reported experimental PES data for phenol, phenolate, thymidine, and protonated imidazolium cation. We then simulated PE spectra by means of QM/MM molecular dynamics and EOM-IP-CCSD calculations with effective fragment potentials, used to describe the aqueous vertical ionization energies for six molecules, including aniline, phenol, veratrole alcohol, imidazole, methoxybenzene, and dimethylsulfide. Experimental and computational data enable us to decompose the VIEaq into elementary processes. For neutral compounds, the shift in VIE upon solvation, ΔVIEaq, was found to range from ≈-0.5 to -0.91 eV. The ΔVIEaq was further explained in terms of the influence of deforming the gas phase solute into its solution phase conformation, the influence of solute hydrogen-bond donor and acceptor interactions with proximate solvent molecules, and the polarization of about 3000 outerlying solvent molecules. Among the neutral compounds, variability in ΔVIEaq appeared largely controlled by differences in solute-solvent hydrogen-bonding interactions. Detailed computational analysis of the flexible molecule veratrole alcohol reveals that the VIE is strongly dependent on molecular conformation in both gas and aqueous phases. Finally, aqueous reorganization energies of the oxidation half-cell ionization reaction were determined from experimental data or estimated from simulation for the six compounds aniline, phenol, phenolate, veratrole alcohol, dimethylsulfide, and methoxybenzene, revealing a surprising constancy of 2.06 to 2.35 eV.
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Affiliation(s)
- Peter R Tentscher
- Environmental Chemistry Modeling Laboratory, GR C2 544, Ecole Polytechnique Fédérale de Lausanne , Station 2, CH-1015 Lausanne, Switzerland
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22
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Liu X, Cheng J, Sprik M. Aqueous Transition-Metal Cations as Impurities in a Wide Gap Oxide: The Cu2+/Cu+ and Ag2+/Ag+ Redox Couples Revisited. J Phys Chem B 2014; 119:1152-63. [DOI: 10.1021/jp506691h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Xiandong Liu
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- State Key Laboratory
for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Jun Cheng
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Department
of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - Michiel Sprik
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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23
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Kubas A, Hoffmann F, Heck A, Oberhofer H, Elstner M, Blumberger J. Electronic couplings for molecular charge transfer: benchmarking CDFT, FODFT, and FODFTB against high-level ab initio calculations. J Chem Phys 2014; 140:104105. [PMID: 24628150 DOI: 10.1063/1.4867077] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We introduce a database (HAB11) of electronic coupling matrix elements (H(ab)) for electron transfer in 11 π-conjugated organic homo-dimer cations. High-level ab inito calculations at the multireference configuration interaction MRCI+Q level of theory, n-electron valence state perturbation theory NEVPT2, and (spin-component scaled) approximate coupled cluster model (SCS)-CC2 are reported for this database to assess the performance of three DFT methods of decreasing computational cost, including constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), and self-consistent charge density functional tight-binding (FODFTB). We find that the CDFT approach in combination with a modified PBE functional containing 50% Hartree-Fock exchange gives best results for absolute H(ab) values (mean relative unsigned error = 5.3%) and exponential distance decay constants β (4.3%). CDFT in combination with pure PBE overestimates couplings by 38.7% due to a too diffuse excess charge distribution, whereas the economic FODFT and highly cost-effective FODFTB methods underestimate couplings by 37.6% and 42.4%, respectively, due to neglect of interaction between donor and acceptor. The errors are systematic, however, and can be significantly reduced by applying a uniform scaling factor for each method. Applications to dimers outside the database, specifically rotated thiophene dimers and larger acenes up to pentacene, suggests that the same scaling procedure significantly improves the FODFT and FODFTB results for larger π-conjugated systems relevant to organic semiconductors and DNA.
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Affiliation(s)
- Adam Kubas
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Felix Hoffmann
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Alexander Heck
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Harald Oberhofer
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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24
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Gajdos F, Valner S, Hoffmann F, Spencer J, Breuer M, Kubas A, Dupuis M, Blumberger J. Ultrafast Estimation of Electronic Couplings for Electron Transfer between π-Conjugated Organic Molecules. J Chem Theory Comput 2014; 10:4653-60. [DOI: 10.1021/ct500527v] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Fruzsina Gajdos
- Department
of Physics and Astronomy, University College London, London WC1E 6BT, U.K
| | - Siim Valner
- Department
of Physics and Astronomy, University College London, London WC1E 6BT, U.K
| | - Felix Hoffmann
- Department
of Physics and Astronomy, University College London, London WC1E 6BT, U.K
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität Bochum, Universitätsstrasse
150, 44801 Bochum, Germany
| | - Jacob Spencer
- Department
of Physics and Astronomy, University College London, London WC1E 6BT, U.K
| | - Marian Breuer
- Department
of Physics and Astronomy, University College London, London WC1E 6BT, U.K
| | - Adam Kubas
- Department
of Physics and Astronomy, University College London, London WC1E 6BT, U.K
| | - Michel Dupuis
- Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Jochen Blumberger
- Department
of Physics and Astronomy, University College London, London WC1E 6BT, U.K
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25
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Marenich AV, Ho J, Coote ML, Cramer CJ, Truhlar DG. Computational electrochemistry: prediction of liquid-phase reduction potentials. Phys Chem Chem Phys 2014; 16:15068-106. [PMID: 24958074 DOI: 10.1039/c4cp01572j] [Citation(s) in RCA: 314] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.
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Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455-0431, USA.
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26
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Yepes D, Seidel R, Winter B, Blumberger J, Jaque P. Photoemission Spectra and Density Functional Theory Calculations of 3d Transition Metal–Aqua Complexes (Ti–Cu) in Aqueous Solution. J Phys Chem B 2014; 118:6850-63. [DOI: 10.1021/jp5012389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Diana Yepes
- Departamento
de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Avenida Republica 275, Santiago 8370146, Chile
| | - Robert Seidel
- Department
of Chemistry, University of Southern California, 920 Bloom Walk, Los Angeles, California 90089, United States
| | - Bernd Winter
- Joint
Laboratory for Ultrafast Dynamics in Solutions and at Interfaces (JULiq), Helmholtz−Zentrum Berlin für Materialien und Energie, and BESSY II, Albert−Einstein−Strasse 15, D-12489 Berlin, Germany
| | - Jochen Blumberger
- Department
of Physics and Astronomy, University College London, London WC1E6BT, United Kingdom
| | - Pablo Jaque
- Departamento
de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Avenida Republica 275, Santiago 8370146, Chile
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27
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Tanaka A, Sakaguchi S, Hashimoto K, Kominami H. Preparation of Au/TiO2 with Metal Cocatalysts Exhibiting Strong Surface Plasmon Resonance Effective for Photoinduced Hydrogen Formation under Irradiation of Visible Light. ACS Catal 2012. [DOI: 10.1021/cs3006499] [Citation(s) in RCA: 282] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Atsuhiro Tanaka
- Department of Applied
Chemistry, Faculty of Science
and Engineering, Kinki University, Kowakae,
Higashiosaka, Osaka 577-8502, Japan
| | - Satoshi Sakaguchi
- Department of Applied
Chemistry, Faculty of Science
and Engineering, Kinki University, Kowakae,
Higashiosaka, Osaka 577-8502, Japan
| | - Keiji Hashimoto
- Department of Applied
Chemistry, Faculty of Science
and Engineering, Kinki University, Kowakae,
Higashiosaka, Osaka 577-8502, Japan
| | - Hiroshi Kominami
- Department of Applied
Chemistry, Faculty of Science
and Engineering, Kinki University, Kowakae,
Higashiosaka, Osaka 577-8502, Japan
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28
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Iida K, Sato H. Theoretical study on ionization process in aqueous solution. J Chem Phys 2012; 136:144510. [DOI: 10.1063/1.3700225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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29
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Tipmanee V, Blumberger J. Kinetics of the terminal electron transfer step in cytochrome c oxidase. J Phys Chem B 2012; 116:1876-83. [PMID: 22243050 DOI: 10.1021/jp209175j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome c oxidase (cco) catalyzes the oxygen reduction reaction in most aerobically respiring organisms. Decades of research have uncovered many aspects relating to structure and function of this enzyme. However, the origin of the unusually fast terminal electron transfer step from heme a to heme a(3) in cco has been the subject of intense discussions over recent years. Yet, no satisfactory consensus has been achieved. Carrying out large-scale molecular dynamics simulation of the protein embedded in a solvated membrane, we obtain a reorganization free energy λ = 0.57 eV. Evaluation of the quantized single-mode rate equation using the experimental rate and the computed reorganization free energy gives a value of 1.5 meV for the average electronic coupling (H(ab)) between heme a and heme a(3). Thus, according to our calculations, the nanosecond electron transfer (ET) is due to a small but significant activation barrier (ΔG(‡) = 0.12 eV) in combination with effective electronic coupling between the two cofactors. The activation free energy is caused predominantly by collective reorganization of protein residues. We show that our results are consistent with the weak temperature dependence observed in experiment if one allows for very minor variations in the donor-acceptor distance as the temperature changes.
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Affiliation(s)
- Varomyalin Tipmanee
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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30
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Wang LP, Van Voorhis T. A Polarizable QM/MM Explicit Solvent Model for Computational Electrochemistry in Water. J Chem Theory Comput 2012; 8:610-7. [DOI: 10.1021/ct200340x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lee-Ping Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
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31
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Leung K, Qi Y, Zavadil KR, Jung YS, Dillon AC, Cavanagh AS, Lee SH, George SM. Using Atomic Layer Deposition to Hinder Solvent Decomposition in Lithium Ion Batteries: First-Principles Modeling and Experimental Studies. J Am Chem Soc 2011; 133:14741-54. [DOI: 10.1021/ja205119g] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Kevin Leung
- Sandia National Laboratories, MS 1415 and 0888, Albuquerque, New Mexico 87185, United States
| | - Yue Qi
- General Motors R&D Center, Warren, Michigan 48090, United States
| | - Kevin R. Zavadil
- Sandia National Laboratories, MS 1415 and 0888, Albuquerque, New Mexico 87185, United States
| | - Yoon Seok Jung
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Interdisciplinary School of Green Energy, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798 South Korea
| | - Anne C. Dillon
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
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32
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Seidel R, Thürmer S, Moens J, Geerlings P, Blumberger J, Winter B. Valence Photoemission Spectra of Aqueous Fe2+/3+ and [Fe(CN)6]4–/3– and Their Interpretation by DFT Calculations. J Phys Chem B 2011; 115:11671-7. [DOI: 10.1021/jp203997p] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Robert Seidel
- Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Stephan Thürmer
- Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Jan Moens
- Faculty of Sciences, Department of General Chemistry, Free University of Brussels (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Paul Geerlings
- Faculty of Sciences, Department of General Chemistry, Free University of Brussels (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Bernd Winter
- Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
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33
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Thürmer S, Seidel R, Eberhardt W, Bradforth SE, Winter B. Ultrafast Hybridization Screening in Fe3+ Aqueous Solution. J Am Chem Soc 2011; 133:12528-35. [DOI: 10.1021/ja200268b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stephan Thürmer
- Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Robert Seidel
- Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Wolfgang Eberhardt
- Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Stephen E. Bradforth
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Bernd Winter
- Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
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34
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Mangold M, Rolland L, Costanzo F, Sprik M, Sulpizi M, Blumberger J. Absolute pKa Values and Solvation Structure of Amino Acids from Density Functional Based Molecular Dynamics Simulation. J Chem Theory Comput 2011; 7:1951-61. [PMID: 26596456 DOI: 10.1021/ct100715x] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Absolute pKa values of the amino acid side chains of arginine, aspartate, cysteine, histidine, and tyrosine; the C- and N-terminal group of tyrosine; and the tryptophan radical cation are calculated using a revised density functional based molecular dynamics simulation technique introduced previously [ Cheng , J. ; Sulpizi , M. ; Sprik , M. J. Chem. Phys. 2009 , 131 , 154504 ]. In the revised scheme, acid deprotonation is considered as a dissociation rather than a proton transfer reaction, and a correction term for treating the proton as a hydronium ion is suggested. The acidity constants of the amino acids are obtained from the vertical energy gaps for removal or insertion of the acidic proton and the computed solvation free energy of the proton. The unsigned mean error relative to experimental results is 2.1 pKa units with a maximum error of 4.0 pKa units. The estimated mean statistical uncertainty due to the finite length of the trajectories is ±1.1 pKa units. The solvation structures of the protonated and deprotonated amino acids are analyzed in terms of radial distribution functions, which can serve as reference data for future force field developments.
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Affiliation(s)
- Martina Mangold
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Leslie Rolland
- Departement de Chimie, Ecole Normale Superieure , 24 rue Lhomond, 75231 Paris Cedex 05, France
| | - Francesca Costanzo
- Dipartimento di Chimica Fisica e Inorganica, Universita di Bologna , Viale Risorgimento 4, I-40136 Bologna, Italy
| | - Michiel Sprik
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Marialore Sulpizi
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London , London WC1E 6BT, United Kingdom
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35
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Pollet R, Nair NN, Marx D. Water exchange of a ProHance MRI contrast agent: isomer-dependent free-energy landscapes and mechanisms. Inorg Chem 2011; 50:4791-7. [PMID: 21520891 DOI: 10.1021/ic102403r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The water-exchange reaction in two diastereoisomers of the clinical magnetic resonance imaging contrast agent [Gd(HP-DO3A)(H(2)O)] (also known as ProHance) has been studied using ab initio simulations. On the basis of the molecular-level details of the mechanism derived from these simulations in aqueous solution, we unravel the underlying difference in the free energies and mechanisms of water exchange in the two diastereoisomers. These findings reveal the crucial role played by hydrogen-bonding dynamics and thus suggest their appropriate control in tailoring improved gadolinium-based constrast agents.
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Affiliation(s)
- Rodolphe Pollet
- DSM/IRAMIS/SIS2M (CEA-CNRS UMR3299), Commissariat à l'Énergie Atomique, 91191 Gif-sur-Yvette, France.
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36
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Kirchner B, di Dio PJ, Hutter J. Real-world predictions from ab initio molecular dynamics simulations. Top Curr Chem (Cham) 2011; 307:109-53. [PMID: 21842358 DOI: 10.1007/128_2011_195] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented.
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Affiliation(s)
- Barbara Kirchner
- Wilhelm-Ostwald Institute of Physical and Theoretical Chemistry, University of Leipzig, Linnéstr. 2, 04103 Leipzig, Germany.
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37
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Tipmanee V, Oberhofer H, Park M, Kim KS, Blumberger J. Prediction of Reorganization Free Energies for Biological Electron Transfer: A Comparative Study of Ru-Modified Cytochromes and a 4-Helix Bundle Protein. J Am Chem Soc 2010; 132:17032-40. [DOI: 10.1021/ja107876p] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Varomyalin Tipmanee
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom, and Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology (POSTECH), San 31, Hyojadong, Namgu, Pohang (790-784), Korea
| | - Harald Oberhofer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom, and Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology (POSTECH), San 31, Hyojadong, Namgu, Pohang (790-784), Korea
| | - Mina Park
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom, and Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology (POSTECH), San 31, Hyojadong, Namgu, Pohang (790-784), Korea
| | - Kwang S. Kim
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom, and Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology (POSTECH), San 31, Hyojadong, Namgu, Pohang (790-784), Korea
| | - Jochen Blumberger
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom, and Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology (POSTECH), San 31, Hyojadong, Namgu, Pohang (790-784), Korea
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