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Hetmańczyk Ł, Goremychkin EA, Waliszewski J, Vener MV, Lipkowski P, Tolstoy PM, Filarowski A. Spectroscopic Identification of Hydrogen Bond Vibrations and Quasi-Isostructural Polymorphism in N-Salicylideneaniline. Molecules 2021; 26:molecules26165043. [PMID: 34443632 PMCID: PMC8401763 DOI: 10.3390/molecules26165043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022] Open
Abstract
The ortho-hydroxy aryl Schiff base 2-[(E)-(phenylimino)methyl]phenol and its deutero-derivative have been studied by the inelastic incoherent neutron scattering (IINS), infrared (IR) and Raman experimental methods, as well as by Density Functional Theory (DFT) and Density-Functional Perturbation Theory (DFPT) simulations. The assignments of vibrational modes within the 3500–50 cm−1 spectral region made it possible to state that the strong hydrogen bond in the studied compound can be classified as the so-called quasi-aromatic bond. The isotopic substitution supplemented by the results of DFT calculations allowed us to identify vibrational bands associated with all five major hydrogen bond vibrations. Quasi-isostructural polymorphism of 2-[(E)-(phenylimino)methyl]phenol (SA) and 2-[(E)-(phenyl-D5-imino)methyl]phenol (SA-C6D5) has been studied by powder X-ray diffraction in the 20–320 K temperature range.
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Affiliation(s)
- Łukasz Hetmańczyk
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387 Cracow, Poland;
| | - Eugene A. Goremychkin
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research 6 F. Joliot-Curie str., 141980 Dubna, Russia;
| | - Janusz Waliszewski
- Faculty of Physics, University of Bialystok, 1L Ciolkowskiego str., 15-245 Bialystok, Poland;
| | - Mikhail V. Vener
- Quantum Chemistry Department, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia;
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia
| | - Paweł Lipkowski
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańnskiego 27, 50-370 Wrocław, Poland;
| | - Peter M. Tolstoy
- Institute of Chemistry, St. Petersburg State University, Universitetskij pr. 26, 198504 Saint Petersburg, Russia
- Correspondence: (P.M.T.); (A.F.); Tel.: +48-71-375-7229 (A.F.)
| | - Aleksander Filarowski
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research 6 F. Joliot-Curie str., 141980 Dubna, Russia;
- Faculty of Chemistry, University of Wrocław 14 F. Joliot-Curie str., 50-383 Wrocław, Poland
- Correspondence: (P.M.T.); (A.F.); Tel.: +48-71-375-7229 (A.F.)
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Gao A, Wang M. Ultrafast Photoisomerization of N-(2-Methoxybenzylidene)aniline: Nonadiabatic Surface-Hopping Study. J Phys Chem A 2021; 125:7151-7160. [PMID: 34383503 DOI: 10.1021/acs.jpca.1c02718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated the ultrafast photoisomerization of N-(2-methoxybenzylidene)aniline in the gas phase excited into the second singlet (S2) state by nonadiabatic surface-hopping dynamics calculations. Two trans isomers (1E and 1E') were taken into consideration in our dynamics simulation. Three conical intersections (CIs) were characterized in the optimization. The CI between S2 and the first singlet (S1) states presents a nearly planar structure, while the other two CIs (CItwist-I and CItwist-II) between S1 and the ground (S0) states show nearly perpendicular geometries. After two trans isomers excited to the S2 state, the torsion of the C-N bond connected the phenyl group and the stretch of the central bridging bond make the molecule reach CIplanar, and the S2/S1 hopping occurs. During the S1-state dynamics, the molecule moves to a S1/S0 CI (CItwist-I or CItwist-II) by the rotation of the central bridging bond. The cis isomer is obtained through a barrierless pathway in the S0 state with the torsion of the three bridging bonds. There is a main channel and an alternative one for the photoisomerization process of both trans isomers. CItwist-I and CItwist-II act as S1/S0 decay funnels in the main isomerization channels of 1E and 1E' isomers, respectively, and the photochemical processes of 1E and 1E' lead to different cis isomers.
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Affiliation(s)
- Aihua Gao
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Meishan Wang
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
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Zhao L, Zheng H, Zhan K, Guo Y, Liu B, Xu G. Position of the Benzene Ring Substituent Regulates the Excited-State Deactivation Process of the Benzyluracil Systems. J Phys Chem A 2021; 125:165-174. [PMID: 33373221 DOI: 10.1021/acs.jpca.0c08980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A systematic theoretical study of the regulating effect of the substituent position on the photoinduced deactivation process of the benzyluracil systems has been performed based on the high-level static electronic structure calculations and on-the-fly full-dimensional excited-state dynamics simulations. Similarities and differences coexist for the two systems by comparative studies on the photoinduced deactivation process of the 5-benzyluracil (5-BU) and 6-benzyluracil (6-BU) systems. They both obey an S2 → S1 → S0 two-step decay pattern, and the decay coordinates of the S2 → S1 and S1 → S0 processes are mainly driven by the elongation of the bridging bond and the out-of-plane ring deformation motion, respectively. However, the puckering motion occurring at the C2 atom in the uracil fragment dominates the decay pathway of the 5-BU system. On the contrary, the puckering motion at the C5 atom in the benzene fragment mainly drives the decay coordinate of the 6-BU system. Therefore, the substituent position could play significant roles in the deactivation process of the benzyluracil systems. Moreover, the S1 → S0 decay process of the 6-BU system consists of five pathways, possessing a more complex deactivation picture than the 5-BU system. The fitted time scale of the puckering motion is compatible with the experimentally observed lifetimes. This work provides a fundamental understanding of the photophysical and photochemical properties of the benzyluracil systems and can give rational suggestions to further design or regulate the bionic molecular systems.
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Affiliation(s)
- Li Zhao
- School of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China
| | - Haixia Zheng
- School of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China
| | - Kaiyun Zhan
- School of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China
| | - Yahui Guo
- School of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China
| | - Bing Liu
- School of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China
| | - Guiyin Xu
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Zhao L, Zhou P, Liu X, Zheng H, Zhan K, Luo J, Liu B. Theoretical studies of the ultrafast deactivation mechanism of 8-oxo-guanine on the S 1 and S 2 electronic states in gas phase. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 244:118884. [PMID: 32898726 DOI: 10.1016/j.saa.2020.118884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/18/2020] [Accepted: 08/22/2020] [Indexed: 06/11/2023]
Abstract
The 8-oxo-deoxyguanosine is the most abundant specie of the DNA oxidative damage. Despite the deleterious effects such as gene mutation it may cause, the 8-oxodG was also reported to have beneficial effect such as repairing the nearby cyclobutane pyrimidine dimer (CPD) after photoexcitation. Due to its strong biological relevance, the photoinduced excited state dynamics behavior of 8-oxo-deoxyguanosine is of particular interest. In this work, a theoretical investigation by combination of complete active space self-consistent field (CASSCF) ab initio calculations and on-the-fly nonadiabatic dynamics simulations are implemented to provide intrinsic deactivation mechanism of its free base 8-oxoguanine after being excited to the S1 and S2 states. Two minimum energy conical intersections (MECIs) characterized by the C3-puckered motion with attractive chiral character are located, which contribute appreciably to the S1 state deactivation process. When the system is being excited to the S2 state directly, a S2 → S1 → S0 two-step decay pattern is proposed. A nearly planar S2/S1 intersection plays a significant role in the S2 → S1 decay process. The subsequent S1 state relaxation process is also dominated by the C3-puckered deformation motion. One decay time is estimated to be 704 fs, which compares well with the experimental observation of 0.9 ± 0.1 ps in solvents. Particular illustration is the fact that the MECIs configurations we located bear an exceptional resemblance with previous reported thymine, cytosine and guanine, suggesting that the current work could lend support for better understanding of the non-natural nucleobases and derivatives.
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Affiliation(s)
- Li Zhao
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, PR China.
| | - Panwang Zhou
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao 266235, PR China
| | - Xiaoxu Liu
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, PR China
| | - Haixia Zheng
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, PR China
| | - Kaiyun Zhan
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, PR China
| | - Jianhui Luo
- Research Institute of Petroleum Exploration & Development (RIPED), PetroChina, Beijing 100083, PR China
| | - Bing Liu
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, PR China.
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Inamori M, Ikabata Y, Yoshikawa T, Nakai H. Unveiling controlling factors of the S0/S1 minimum energy conical intersection (2): Application to penalty function method. J Chem Phys 2020; 152:144108. [DOI: 10.1063/1.5142592] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Mayu Inamori
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Yasuhiro Ikabata
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Takeshi Yoshikawa
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520, Japan
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Gao A, Wang M. Volume-conserving photoisomerization of a nonplanar GFP chromophore derivative: Nonadiabatic dynamics simulation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 214:86-94. [PMID: 30769155 DOI: 10.1016/j.saa.2019.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/17/2019] [Accepted: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Nonadiabatic dynamics of a nonplanar green fluorescent protein (GFP) chromophore derivative was examined theoretically by trajectory surface hopping approach at the CASSCF level based on Zhu-Nakamura theory. The geometry optimizations show that there are four ground-state minima and four conical intersections between the ground (S0) and first excited (S1) states. Four S1-state minima were found at a perpendicularly twisted conformation around the imidazolinone-bridged bond. Upon excitation to S1 state, the main decay pathways of four isomers involve different S0/S1 potential energy surface conical intersections. The dominant excited-state relaxation mechanism of this GFP chromophore derivative is the twists of two bridging bonds and the methyl group in the bridge combined with the pyramidalization character of the central carbon atom. Further twists of two bridging bonds and the methyl group occur sequentially in the S0 state. It is worth to mention that the special volume-conserving motion of this molecule is attributed to twists of two bridging bonds in the same direction during the whole photoisomerization processes. The theoretical investigation presented herein provides important insights into the volume-conserving photoisomerization mechanisms of a nonplanar GFP chromophore derivative. We believe that the present work can benefit the design of the photochromic molecule devices in confined media.
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Affiliation(s)
- Aihua Gao
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.
| | - Meishan Wang
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.
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Nakai H, Inamori M, Ikabata Y, Wang Q. Unveiling Controlling Factors of the S0/S1 Minimum Energy Conical Intersection: A Theoretical Study. J Phys Chem A 2018; 122:8905-8910. [DOI: 10.1021/acs.jpca.8b07864] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520, Japan
| | - Mayu Inamori
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Yasuhiro Ikabata
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Qi Wang
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
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Gao A, Wang M, Ding J. Ultrafasttrans-cisphotoisomerization of the neutral chromophore in green fluorescent proteins: Surface-hopping dynamics simulation. J Chem Phys 2018; 149:074304. [DOI: 10.1063/1.5043246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Aihua Gao
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Meishan Wang
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Junxia Ding
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Zhao L, Liu J, Zhou P. The photoinduced isomerization mechanism of the 2-(1-(methylimino)methyl)-6-chlorophenol (SMAC): Nonadiabatic surface hopping dynamics simulations. J Chem Phys 2018; 149:034309. [PMID: 30037240 DOI: 10.1063/1.5034379] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The photophysical properties of the Schiff base family are crucial for their applications such as molecular switches and molecular memories. However, it was found that the photophysical behavior is not uniform for all Schiff base molecules, which shows a significant substituent dependent property. In this article, we studied the photoisomerization mechanism of one Schiff base chlorosubstituted derivative 2-(1-(methylimino)methyl)-6-chlorophenol by employing geometrical optimization, energy profiles scanning, and on-the-fly dynamical simulations. Three types of minimum energy conical intersections were located on the S1/S0 crossing seam, with two characterized by twisting motion of the C=N bond and one featured with the excited state intramolecular proton transfer process and then twisting motion around the C=C bond [excited-state intramolecular proton transfer process (ESIPT)-then-twisting]. By a combination of the dynamics simulation results with the energy profiles scanned along with the ESIPT coordinate, it was found that the photophysical property of the targeted molecule is different from that of most Schiff base members, which prefer to decay by a twisting motion around the C=N bridge bond rather than the ESIPT-then-twisting channel. The minor ESIPT channel is probably governed by a tunneling mechanism. The proposed deactivation mechanism can provide a reasonable explanation for the observations in the experiment and would provide fundamental indications for further design of new and efficient photochromic products.
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Affiliation(s)
- Li Zhao
- School of Science, China University of Petroleum, Qingdao 266580, Shandong, China
| | - Jianyong Liu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Gao A, Li J, Wang D, Ma X, Wang M. Nonadiabatic dynamics simulation of photoisomerization mechanism of the second stablest isomer of N-salicilydenemethylfurylamine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 191:315-324. [PMID: 29055276 DOI: 10.1016/j.saa.2017.10.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/07/2017] [Accepted: 10/12/2017] [Indexed: 06/07/2023]
Abstract
The photoisomerization processes of the second stablest isomer in the aromatic Schiff base, N-salicilydenemethylfurylamine, in the gas phase have been studied by static electronic structure calculations and surface-hopping dynamics simulations based on the Zhu-Nakamura theory. Various stable structures are obtained in the optimization because of different orientations of methyl-furyl part with respect to the salicylaldimine part and different orientations of hydroxy group with respect to the benzene ring. Upon photoexcitation into the first excited state, bond isomerization in the salicylaldimine part is completely suppressed until the strong excited-state hydrogen bond is broken. The decay pathway involves two excited-state minima, one in cis-enol form and the other in cis-keto form. After the excited-state proton transfer, twists of bonds lead to a conical intersection between the ground and excited states. After internal conversion around a conical intersection, the molecule is stabilized in cis- or trans-keto form. If the reverse hydrogen transfer process occurs in the ground state, the molecule will finally end up in the cis-enol region. The cis-keto and trans-keto isomers are observed as photoproducts. According to our full-dimensional nonadiabatic dynamics simulations, we find the excited-state intramolecular proton transfer and torsions of three single bonds in the chain to be responsible for photoisomerization of the second stablest isomer of N-salicilydenemethylfurylamine.
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Affiliation(s)
- Aihua Gao
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.
| | - Jianpeng Li
- Technical Test Center, Shengli Oil-field, Sinopec, Dongying 257000, China
| | - Dehua Wang
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Xiaoguang Ma
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Meishan Wang
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.
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Yue L, Liu Y, Zhu C. Performance of TDDFT with and without spin-flip in trajectory surface hopping dynamics: cis–trans azobenzene photoisomerization. Phys Chem Chem Phys 2018; 20:24123-24139. [DOI: 10.1039/c8cp03851a] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum yields simulated by LR-TDDFT and SF-TDDFT methods for azobenzene photoisomerizations.
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Affiliation(s)
- Ling Yue
- Department of Applied Chemistry and Institute of Molecular Science
- National Chiao-Tung University
- Hsinchu 30010
- Taiwan
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter
| | - Yajun Liu
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Chaoyuan Zhu
- Department of Applied Chemistry and Institute of Molecular Science
- National Chiao-Tung University
- Hsinchu 30010
- Taiwan
- Center for Emergent Functional Matter Science
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