1
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Attosecond spectroscopy of size-resolved water clusters. Nature 2022; 609:507-511. [PMID: 35820616 DOI: 10.1038/s41586-022-05039-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 06/28/2022] [Indexed: 11/08/2022]
Abstract
Electron dynamics in water are of fundamental importance for a broad range of phenomena1-3, but their real-time study faces numerous conceptual and methodological challenges4-6. Here, we introduce attosecond size-resolved cluster spectroscopy and build up a molecular-level understanding of the attosecond electron dynamics in water. We measure the effect that the addition of single water molecules has on the photoionization time delays7-9 of water clusters. We find a continuous increase of the delay for clusters containing up to 4-5 molecules and little change towards larger clusters. We show that these delays are proportional to the spatial extension of the created electron hole, which first increases with cluster size and then partially localizes through the onset of structural disorder that is characteristic of large clusters and bulk liquid water. These results suggest a previously unknown sensitivity of photoionization delays to electron-hole delocalization and indicate a direct link between electronic structure and attosecond photoionization dynamics. Our results offer novel perspectives for studying electron/hole delocalization and its attosecond dynamics.
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2
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Christensen EG, Lutz KT, Steele RP. Electronic Structure and Vibrational Signatures of the Delocalized Radical in Hydrated Clusters of Copper("II") Hydroxide CuOH +(H 2O) 0-2. J Phys Chem A 2021; 125:3631-3645. [PMID: 33881321 DOI: 10.1021/acs.jpca.1c01547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The copper hydroxide ion, CuOH+, serves as the catalytic core in several recently developed water-splitting catalysts, and an understanding of its chemistry is critical to determining viable catalytic mechanisms. In spite of its importance, the electronic structure of this open-shell ion has remained ambiguous in the literature. In particular, computed values for both the thermodynamics of hydration and the vibrational signatures of the mono- and dihydrates have shown prohibitively large errors compared to values from recent experimental measurements. In this work, the source of this discrepancy is demonstrated to be the propensity of this ion to exist between traditional Cu(I) and Cu(II) oxidation-state limits. The spin density of the radical is accordingly shown to delocalize between the metal center and surrounding ligands, and increasing the hydration serves to exacerbate this behavior. Equation-of-motion coupled-cluster methods demonstrated the requisite accuracy to resolve the thermodynamic discrepancies. Such methods were also needed for spectral simulations, although the latter also required a direct simulation of the role of the deuterium "tag" molecules that are used in modern predissociation spectroscopy experiments. This nominally benign tag molecule underwent direct complexation with the open-valence metal ion, thereby forming a species akin to known metal-H2 complexes and strongly impacting the resulting spectrum. Thermal populations of this configuration and other more traditional noncovalently bound isomers led to a considerable broadening of the spectral lineshapes. Therefore, at least for the CuOH+(H2O)0-2 hydrates, these benchmark ions should be considered to be delocalized radical systems with some degree of multireference character at equilibrium. They also serve as a cautionary tale for the spectroscopy community, wherein the role of the D2 tag is far from benign.
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Affiliation(s)
- Elizabeth G Christensen
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Kevin T Lutz
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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3
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Harb H, Hratchian HP. ΔSCF Dyson orbitals and pole strengths from natural ionization orbitals. J Chem Phys 2021; 154:084104. [DOI: 10.1063/5.0040454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Hassan Harb
- Department of Chemistry and Chemical Biology and Center for Chemical Computation and Theory, University of California, Merced, California 95343, USA
| | - Hrant P. Hratchian
- Department of Chemistry and Chemical Biology and Center for Chemical Computation and Theory, University of California, Merced, California 95343, USA
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4
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Gozem S, Seidel R, Hergenhahn U, Lugovoy E, Abel B, Winter B, Krylov AI, Bradforth SE. Probing the Electronic Structure of Bulk Water at the Molecular Length Scale with Angle-Resolved Photoelectron Spectroscopy. J Phys Chem Lett 2020; 11:5162-5170. [PMID: 32479725 DOI: 10.1021/acs.jpclett.0c00968] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We report a combined experimental and theoretical study of bulk water photoionization. Angular distributions of photoelectrons produced by ionizing the valence bands of neat water using X-ray radiation (250-750 eV) show a limited (∼20%) decrease in the β anisotropy parameter compared to the gas phase, indicating that the electronic structure of the individual water molecules can be probed. We show that, in the high-energy regime, photoionization of bulk can be described using an incoherent superposition of individual molecules, in contrast to a low-energy regime where photoionization probes delocalized entangled states of molecular aggregates. The two regimes-low versus high energy-are limiting cases where the de Broglie wavelength of the photoelectron is larger or smaller than the intermolecular distance between water molecules, respectively. The comparison of measured and computed anisotropies reveals that the reduction in β at high kinetic energies is mostly due to scattering rather than rehybridization due to solvation.
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Affiliation(s)
- Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Robert Seidel
- Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Strasse 2, D-12489 Berlin, Germany
| | - Uwe Hergenhahn
- Leibniz Institute of Surface Engineering (IOM), Department of Functional Surfaces, Permoserstrasse 15, 04318 Leipzig, Germany
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Evgeny Lugovoy
- Leibniz Institute of Surface Engineering (IOM), Department of Functional Surfaces, Permoserstrasse 15, 04318 Leipzig, Germany
- University of Leipzig, Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Linnéstrasse 3, 04318 Leipzig, Germany
| | - Bernd Abel
- Leibniz Institute of Surface Engineering (IOM), Department of Functional Surfaces, Permoserstrasse 15, 04318 Leipzig, Germany
- University of Leipzig, Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Linnéstrasse 3, 04318 Leipzig, Germany
| | - Bernd Winter
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22671 Hamburg, Germany
| | - Stephen E Bradforth
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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5
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Bhattacharyya D, Zhang Y, Elles CG, Bradforth SE. Electronic Structure of Liquid Methanol and Ethanol from Polarization-Dependent Two-Photon Absorption Spectroscopy. J Phys Chem A 2019; 123:5789-5804. [DOI: 10.1021/acs.jpca.9b04040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dhritiman Bhattacharyya
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Yuyuan Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Christopher G. Elles
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Stephen E. Bradforth
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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6
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Zho CC, Vlček V, Neuhauser D, Schwartz BJ. Thermal Equilibration Controls H-Bonding and the Vertical Detachment Energy of Water Cluster Anions. J Phys Chem Lett 2018; 9:5173-5178. [PMID: 30129761 DOI: 10.1021/acs.jpclett.8b02152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
One of the outstanding puzzles in the photoelectron spectroscopy of water anion clusters, which serve as precursors to the hydrated electron, is that the excess electron has multiple vertical detachment energies (VDEs), with different groups seeing different distributions of VDEs. We have studied the photoelectron spectroscopy of water cluster anions using simulation techniques designed to mimic the different ways that water cluster anions are produced experimentally. Our simulations take advantage of density functional theory-based Born-Oppenheimer molecular dynamics with an optimally tuned range-separated hybrid functional that is shown to give outstanding accuracy for calculating electron binding energies for this system. We find that our simulations are able to accurately reproduce the experimentally observed VDEs for cluster anions of different sizes, with different VDE distributions observed depending on how the water cluster anions are prepared. For cluster anion sizes up to 20 water molecules, we see that the excess electron always resides on the surface of the cluster and that the different discrete VDEs result from the discrete number of hydrogen bonds made to the electron by water molecules on the surface. Clusters that are less thermally equilibrated have surface waters that tend to make single H-bonds to the electron, resulting in lower VDEs, while clusters that are more thermally equilibrated have surface waters that prefer to make two H-bonds to the electron, resulting in higher VDEs.
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Affiliation(s)
- Chen-Chen Zho
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095-1569 , United States
| | - Vojtěch Vlček
- Department of Chemistry and Biochemistry , University of California, Santa Barbara , Santa Barbara , California 93106 , United States
| | - Daniel Neuhauser
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095-1569 , United States
| | - Benjamin J Schwartz
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095-1569 , United States
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7
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Hirshberg B, Gerber RB, Krylov AI. Autocorrelation of electronic wave-functions: a new approach for describing the evolution of electronic structure in the course of dynamics. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1464675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Barak Hirshberg
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry , Jerusalem, Israel
| | - R. Benny Gerber
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry , Jerusalem, Israel
- Department of Chemistry, University of California , Irvine, CA, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California , Los Angeles, CA, USA
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8
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Ambrosio F, Pasquarello A. Reactivity and energy level of a localized hole in liquid water. Phys Chem Chem Phys 2018; 20:30281-30289. [DOI: 10.1039/c8cp03682a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reaction and redox level of hole capture in liquid water from first principles.
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Affiliation(s)
- Francesco Ambrosio
- Chaire de Simulation à l’Echelle Atomique (CSEA)
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- CH-1015 Lausanne
- Switzerland
| | - Alfredo Pasquarello
- Chaire de Simulation à l’Echelle Atomique (CSEA)
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- CH-1015 Lausanne
- Switzerland
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9
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Floris SD, Talbot JJ, Wilkinson MJ, Herr JD, Steele RP. Quantum molecular motion in the mixed ion-radical complex, [(H 2O)(H 2S)] . Phys Chem Chem Phys 2016; 18:27450-27459. [PMID: 27711703 DOI: 10.1039/c6cp05299a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The cation dimer of water and hydrogen sulfide, [(H2O)(H2S)]+, serves as a fundamental model for the oxidation chemistry of H2S. The known oxidative metabolism of H2S by biological species in sulfur-rich environments has motivated the study of the inherent properties of this benchmark complex, with possible mechanistic implications for modern water oxidation chemistry. The low-energy isomer of this open-shell ion is a proton-transferred (PT) structure, H3O+SH˙. An alternative PT structure, H3S+OH˙, and a hemibonded (HB) isomer, [H2O·SH2]+, are also stable isomers, placing this complex intermediate to known (H2O)2+ (PT) and (H2S)2+ (HB) limiting regimes. This intermediate character suggested the possibility of unique molecular motion, even in the vibrational ground state. Path integral molecular dynamics and anharmonic vibrational spectroscopy simulations have been performed in this study, in order to understand the inherent quantum molecular motion of this complex. The resulting structural distributions were found to deviate significantly from both classical and harmonic analyses, including the observation of large-amplitude anharmonic motion of the central proton and nearly free rotation of the terminal hydrogens. The predicted vibrational spectra are particularly unique and suggest characteristic signatures of the strong electronic interactions and anharmonic vibrational mode couplings in this radical cation.
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Affiliation(s)
- S D Floris
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, UT, USA.
| | - J J Talbot
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, UT, USA.
| | - M J Wilkinson
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, UT, USA.
| | - J D Herr
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, UT, USA.
| | - R P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, UT, USA.
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10
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Herr JD, Steele RP. Ion–Radical Pair Separation in Larger Oxidized Water Clusters, (H2O)+n=6–21. J Phys Chem A 2016; 120:7225-39. [DOI: 10.1021/acs.jpca.6b07465] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jonathan D. Herr
- Department
of Chemistry and Henry Eyring Center for
Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Ryan P. Steele
- Department
of Chemistry and Henry Eyring Center for
Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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11
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Talbot JJ, Cheng X, Herr JD, Steele RP. Vibrational Signatures of Electronic Properties in Oxidized Water: Unraveling the Anomalous Spectrum of the Water Dimer Cation. J Am Chem Soc 2016; 138:11936-45. [DOI: 10.1021/jacs.6b07182] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Justin J. Talbot
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Xiaolu Cheng
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Jonathan D. Herr
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Ryan P. Steele
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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12
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Pan PR, Lu EP, Kuo JL, Tsai MK. The Spectroscopic Features of Ionized Water Medium: Theoretical Characterization and Implication Using (H 2O) n+, n=3-4, Cluster Model. J CHIN CHEM SOC-TAIP 2016. [DOI: 10.1002/jccs.201600030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Thompson LM, Harb H, Hratchian HP. Natural ionization orbitals for interpreting electron detachment processes. J Chem Phys 2016; 144:204117. [DOI: 10.1063/1.4951738] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Lee M. Thompson
- Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Hassan Harb
- Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Hrant P. Hratchian
- Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
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14
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Chalabala J, Slavíček P. Nonadiabatic dynamics of floppy hydrogen bonded complexes: the case of the ionized ammonia dimer. Phys Chem Chem Phys 2016; 18:20422-32. [DOI: 10.1039/c6cp02714h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Non-adiabatic dynamics of a floppy hydrogen bonded ammonia dimer was studied by ab initio molecular dynamics simulations.
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Affiliation(s)
- Jan Chalabala
- University of Chemistry and Technology
- Department of Physical Chemistry
- 16628 Prague 6
- Czech Republic
| | - Petr Slavíček
- University of Chemistry and Technology
- Department of Physical Chemistry
- 16628 Prague 6
- Czech Republic
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15
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Zadorozhnaya AA, Krylov AI. Ionization-Induced Structural Changes in Uracil Dimers and Their Spectroscopic Signatures. J Chem Theory Comput 2015; 6:705-17. [PMID: 26613301 DOI: 10.1021/ct900515a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The electronic structure of the three representative isomers of the ionized uracil dimers is characterized by high-level electronic structure calculations. Noncovalent interactions between the fragments lower the vertical ionization energies by 0.13-0.35 eV, the largest drop being observed for the stacked and the T-shaped isomers. The initial hole is delocalized in the stacked and the H-bonded isomers and is localized in the T-shaped one. The ionization induces significant structural relaxation and increases the binding energies. The stacked dimer cation relaxes to the symmetric structure bound by 22.7 kcal/mol. The T-shaped dimer cation has a binding energy of 25.1 kcal/mol. Thus, the relative order of the stacked and T-shaped isomers is reversed upon ionization. Finally, the H-bonded isomer, which relaxes to the proton-transferred structure, is bound by 37.0 kcal/mol. The electronic spectra of all three isomers characterized at the vertical and the relaxed geometries show different patterns, which may be exploited in spectroscopic probing of ionization-induced dynamics in these species.
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Affiliation(s)
- Anna A Zadorozhnaya
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482
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16
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Lin LC, Liang JM, Lu EP, Tsai MK. Response of the hydrogen bond network to the ionization of bulk water: ab initio molecular dynamic simulations using H2S(aq). Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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17
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Herr JD, Talbot J, Steele RP. Structural Progression in Clusters of Ionized Water, (H2O)n=1–5+. J Phys Chem A 2015; 119:752-66. [DOI: 10.1021/jp509698y] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Jonathan D. Herr
- Henry Eyring
Center for Theoretical
Chemistry, Thatcher Building for Biological and Biophysical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Justin Talbot
- Henry Eyring
Center for Theoretical
Chemistry, Thatcher Building for Biological and Biophysical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Ryan P. Steele
- Henry Eyring
Center for Theoretical
Chemistry, Thatcher Building for Biological and Biophysical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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18
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Lu EP, Pan PR, Li YC, Tsai MK, Kuo JL. Structural evolution and solvation of the OH radical in ionized water radical cations (H2O)n+, n = 5–8. Phys Chem Chem Phys 2014; 16:18888-95. [DOI: 10.1039/c4cp02293a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Structural evolution of ionized water radical cations (H2O)n+, n = 5–8, is studied by ab intio methods.
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Affiliation(s)
- En-Ping Lu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617, Taiwan
| | - Piin-Ruey Pan
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617, Taiwan
| | - Ying-Cheng Li
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617, Taiwan
| | - Ming-Kang Tsai
- Department of Chemistry
- National Taiwan Normal University
- Taipei 10677, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617, Taiwan
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19
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Khistyaev K, Golan A, Bravaya KB, Orms N, Krylov AI, Ahmed M. Proton Transfer in Nucleobases is Mediated by Water. J Phys Chem A 2013; 117:6789-97. [DOI: 10.1021/jp406029p] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kirill Khistyaev
- Department of Chemistry, University of Southern California, Los
Angeles, California 90089-0482, United States
| | - Amir Golan
- Chemical Sciences
Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ksenia B. Bravaya
- Department of Chemistry, University of Southern California, Los
Angeles, California 90089-0482, United States
| | - Natalie Orms
- Department of Chemistry, University of Southern California, Los
Angeles, California 90089-0482, United States
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los
Angeles, California 90089-0482, United States
| | - Musahid Ahmed
- Chemical Sciences
Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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20
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21
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Svoboda O, Hollas D, Ončák M, Slavíček P. Reaction selectivity in an ionized water dimer: nonadiabatic ab initio dynamics simulations. Phys Chem Chem Phys 2013; 15:11531-42. [DOI: 10.1039/c3cp51440d] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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22
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Bravaya KB, Epifanovsky E, Krylov AI. Four Bases Score a Run: Ab Initio Calculations Quantify a Cooperative Effect of H-Bonding and π-Stacking on the Ionization Energy of Adenine in the AATT Tetramer. J Phys Chem Lett 2012; 3:2726-2732. [PMID: 26295899 DOI: 10.1021/jz3011139] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Benchmark calculations of the lowest ionized state of the (A:T)2 (mixed adenine-thymine) cluster at the geometry taken from the DNA X-ray structure are presented. Vertical ionization energies (IEs) computed by the equation-of-motion coupled-cluster method with single and double substitutions are reported and analyzed. The shift in IE relative to the monomer (A) is -0.7 eV. The performance of the widely used B3LYP, ωB97X-D, and M06-2X functionals with respect to their ability to describe energetics and the character (localization versus delocalization) of the ionized states is also investigated. The shifts in IEs caused by H-bonding and stacking interactions are analyzed in terms of additive versus cooperative effects. It is found that the cooperative effect accounts for more than 20% of the shift in IE relative to the monomer. The cooperative effect and, consequently, the magnitude of the shift are well reproduced by the hybrid quantum mechanics/molecular mechanics scheme in which neutral thymine bases are represented by point charges.
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Affiliation(s)
- Ksenia B Bravaya
- †Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Evgeny Epifanovsky
- †Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
- ‡Department of Chemistry, University of California, Berkeley, California 94720, United States and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Anna I Krylov
- †Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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23
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Ghosh D, Roy A, Seidel R, Winter B, Bradforth S, Krylov AI. First-principle protocol for calculating ionization energies and redox potentials of solvated molecules and ions: theory and application to aqueous phenol and phenolate. J Phys Chem B 2012; 116:7269-80. [PMID: 22497288 PMCID: PMC3381078 DOI: 10.1021/jp301925k] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The effect of hydration on the lowest vertical ionization energy (VIE) of phenol and phenolate solvated in bulk water was characterized using the equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods (referred to as EOM/EFP) and determined experimentally by valence photoemission measurements using microjets and synchrotron radiation. The computed solvent-induced shifts in VIEs (ΔVIEs) are -0.66 and +5.72 eV for phenol and phenolate, respectively. Our best estimates of the absolute values of VIEs (7.9 and 7.7 eV for phenol and phenolate) agree reasonably well with the respective experimental values (7.8 ± 0.1 and 7.1 ± 0.1 eV). The EOM/EFP scheme was benchmarked against full EOM-IP-CCSD using microsolvated phenol and phenolate clusters. A protocol for calculating redox potentials with EOM/EFP was developed based on linear response approximation (LRA) of free energy determination. The oxidation potentials of phenol and phenolate calculated using LRA and EOM/EFP are 1.32 and 0.89 V, respectively; they agree well with experimental values.
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Affiliation(s)
- Debashree Ghosh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
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Marsalek O, Elles CG, Pieniazek PA, Pluhařová E, VandeVondele J, Bradforth SE, Jungwirth P. Chasing charge localization and chemical reactivity following photoionization in liquid water. J Chem Phys 2012; 135:224510. [PMID: 22168706 DOI: 10.1063/1.3664746] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The ultrafast dynamics of the cationic hole formed in bulk liquid water following ionization is investigated by ab initio molecular dynamics simulations and an experimentally accessible signature is suggested that might be tracked by femtosecond pump-probe spectroscopy. This is one of the fastest fundamental processes occurring in radiation-induced chemistry in aqueous systems and biological tissue. However, unlike the excess electron formed in the same process, the nature and time evolution of the cationic hole has been hitherto little studied. Simulations show that an initially partially delocalized cationic hole localizes within ~30 fs after which proton transfer to a neighboring water molecule proceeds practically immediately, leading to the formation of the OH radical and the hydronium cation in a reaction which can be formally written as H(2)O(+) + H(2)O → OH + H(3)O(+). The exact amount of initial spin delocalization is, however, somewhat method dependent, being realistically described by approximate density functional theory methods corrected for the self-interaction error. Localization, and then the evolving separation of spin and charge, changes the electronic structure of the radical center. This is manifested in the spectrum of electronic excitations which is calculated for the ensemble of ab initio molecular dynamics trajectories using a quantum mechanics/molecular mechanics (QM∕MM) formalism applying the equation of motion coupled-clusters method to the radical core. A clear spectroscopic signature is predicted by the theoretical model: as the hole transforms into a hydroxyl radical, a transient electronic absorption in the visible shifts to the blue, growing toward the near ultraviolet. Experimental evidence for this primary radiation-induced process is sought using femtosecond photoionization of liquid water excited with two photons at 11 eV. Transient absorption measurements carried out with ~40 fs time resolution and broadband spectral probing across the near-UV and visible are presented and direct comparisons with the theoretical simulations are made. Within the sensitivity and time resolution of the current measurement, a matching spectral signature is not detected. This result is used to place an upper limit on the absorption strength and/or lifetime of the localized H(2)O(+) ((aq)) species.
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Affiliation(s)
- Ondrej Marsalek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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Golan A, Ahmed M. Ionization of Water Clusters Mediated by Exciton Energy Transfer from Argon Clusters. J Phys Chem Lett 2012; 3:458-462. [PMID: 26286046 DOI: 10.1021/jz2016654] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The exciton energy deposited in an argon cluster (Arn, ⟨n = 20⟩) using VUV radiation is transferred to softly ionize doped water clusters ((H2O)n, n = 1-9), leading to the formation of nonfragmented clusters. Following the initial excitation, electronic energy is channeled to ionize the doped water cluster while evaporating the Ar shell, allowing identification of fragmented and complete water cluster ions. Examination of the photoionization efficiency curve shows that cluster evaporation from excitons located above 12.6 eV is not enough to cool the energized water cluster ion and leads to their dissociation to (H2O)n-2H(+) (protonated) clusters.
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Affiliation(s)
- Amir Golan
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Musahid Ahmed
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Svoboda O, Ončák M, Slavíček P. Simulations of light induced processes in water based on ab initio path integrals molecular dynamics. II. Photoionization. J Chem Phys 2011; 135:154302. [DOI: 10.1063/1.3649943] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Ghosh D, Isayev O, Slipchenko LV, Krylov AI. Effect of solvation on the vertical ionization energy of thymine: from microhydration to bulk. J Phys Chem A 2011; 115:6028-38. [PMID: 21500795 PMCID: PMC3116069 DOI: 10.1021/jp110438c] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The effect of hydration on the vertical ionization energy (VIE) of thymine was characterized using equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods. We considered several microsolvated clusters as well as thymine solvated in bulk water. The VIE in bulk water was computed by averaging over solvent-solute configurations obtained from equilibrium molecular dynamics trajectories at 300 K. The effect of microsolvation was analyzed and contrasted against the combined effect of the first solvation shell in bulk water. Microsolvation reduces the ionization energy (IE) by about 0.1 eV per water molecule, while the first solvation shell increases the IE by 0.1 eV. The subsequent solvation lowers the IE, and the bulk value of the solvent-induced shift of thymine's VIE is approximately -0.9 eV. The combined effect of the first solvation shell was explained in terms of specific solute-solvent interactions, which were investigated using model structures. The convergence of IE to the bulk value requires the hydration sphere of approximately 13.5 Å radius. The performance of the EOM-IP-CCSD/EFP scheme was benchmarked against full EOM-IP-CCSD using microhydrated structures. The errors were found to be less than 0.01-0.02 eV. The relative importance of the polarization and higher multipole moments in EFP model was also investigated.
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Affiliation(s)
- Debashree Ghosh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
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Liu HT, Müller JP, Beutler M, Ghotbi M, Noack F, Radloff W, Zhavoronkov N, Schulz CP, Hertel IV. Ultrafast photo-excitation dynamics in isolated, neutral water clusters. J Chem Phys 2011; 134:094305. [DOI: 10.1063/1.3556820] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- H. T. Liu
- Max Born Institute, Max-Born-St. 2a, 12489 Berlin-Adlershof, Germany
| | - J. P. Müller
- Max Born Institute, Max-Born-St. 2a, 12489 Berlin-Adlershof, Germany
| | - M. Beutler
- Max Born Institute, Max-Born-St. 2a, 12489 Berlin-Adlershof, Germany
| | - M. Ghotbi
- Max Born Institute, Max-Born-St. 2a, 12489 Berlin-Adlershof, Germany
| | - F. Noack
- Max Born Institute, Max-Born-St. 2a, 12489 Berlin-Adlershof, Germany
| | - W. Radloff
- Max Born Institute, Max-Born-St. 2a, 12489 Berlin-Adlershof, Germany
| | - N. Zhavoronkov
- Max Born Institute, Max-Born-St. 2a, 12489 Berlin-Adlershof, Germany
| | - C. P. Schulz
- Max Born Institute, Max-Born-St. 2a, 12489 Berlin-Adlershof, Germany
| | - I. V. Hertel
- Max Born Institute, Max-Born-St. 2a, 12489 Berlin-Adlershof, Germany
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Khistyaev K, Bravaya KB, Kamarchik E, Kostko O, Ahmed M, Krylov AI. The effect of microhydration on ionization energies of thymine. Faraday Discuss 2011; 150:313-30; discussion 391-418. [DOI: 10.1039/c0fd00002g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Livshits E, Granot RS, Baer R. A Density Functional Theory for Studying Ionization Processes in Water Clusters. J Phys Chem A 2010; 115:5735-44. [DOI: 10.1021/jp1057572] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Ester Livshits
- Fritz Haber Center for Molecular Dynamics, Chaim Weizmann Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Rebecca S. Granot
- Fritz Haber Center for Molecular Dynamics, Chaim Weizmann Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Roi Baer
- Fritz Haber Center for Molecular Dynamics, Chaim Weizmann Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Kamarchik E, Kostko O, Bowman JM, Ahmed M, Krylov AI. Spectroscopic signatures of proton transfer dynamics in the water dimer cation. J Chem Phys 2010; 132:194311. [DOI: 10.1063/1.3432198] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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32
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Zadorozhnaya AA, Krylov AI. Zooming into π-Stacked Manifolds of Nucleobases: Ionized States of Dimethylated Uracil Dimers. J Phys Chem A 2010; 114:2001-9. [DOI: 10.1021/jp910440d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Anna A. Zadorozhnaya
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482
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Bravaya KB, Kostko O, Ahmed M, Krylov AI. The effect of π-stacking, H-bonding, and electrostatic interactions on the ionization energies of nucleic acid bases: adenine–adenine, thymine–thymine and adenine–thymine dimers. Phys Chem Chem Phys 2010; 12:2292-307. [DOI: 10.1039/b919930f] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Periyasamy G, Levine R, Remacle F. Electronic wave packet motion in water dimer cation: A many electron description. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2009.08.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Cheng Q, Evangelista FA, Simmonett AC, Yamaguchi Y, Schaefer HF. Water Dimer Radical Cation: Structures, Vibrational Frequencies, and Energetics. J Phys Chem A 2009; 113:13779-89. [DOI: 10.1021/jp907715a] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Qianyi Cheng
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, 30602-2525
| | | | - Andrew C. Simmonett
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, 30602-2525
| | - Yukio Yamaguchi
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, 30602-2525
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, 30602-2525
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