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Samayoa-Oviedo HY, Knorke H, Warneke J, Laskin J. Spontaneous ligand loss by soft landed [Ni(bpy) 3] 2+ ions on perfluorinated self-assembled monolayer surfaces. Chem Sci 2024; 15:10770-10783. [PMID: 39027285 PMCID: PMC11253159 DOI: 10.1039/d4sc02527j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/11/2024] [Indexed: 07/20/2024] Open
Abstract
Transition metal (TM) complexes are widely used in catalysis, photochemical energy conversion, and sensing. Understanding factors that affect ligand loss from TM complexes at interfaces is important both for generating catalytically-active undercoordinated TM complexes and for controlling the degradation pathways of photosensitizers and photoredox catalysts. Herein, we demonstrate that well-defined TM complexes prepared on surfaces using ion soft landing undergo substantial structural rearrangements resulting in ligand loss and formation of both stable and reactive undercoordinated species. We employ nickel bipyridine (Ni-bpy) cations as a model system and explore their structural reorganization on surfaces using a combination of experimental and computational approaches. The controlled preparation of surface layers by mass-selected deposition of [Ni(bpy)3]2+ cations provides insights into the chemical reactivity of these species on surfaces. Both surface characterization using mass spectrometry and electronic structure calculations using density functional theory (DFT) indicate that [Ni(bpy)3]2+ undergoes a substantial geometry distortion on surfaces in comparison with its gas-phase structure. This distortion reduces the ligand binding energy and facilitates the formation of the undercoordinated [Ni(bpy)2]2+. Additionally, charge reduction by the soft landed [Ni(bpy)3]2+ facilitates ligand loss. We observe that ligand loss is inhibited by co-depositing [Ni(bpy)3]2+ with a stable anion such as closo-dodecaborate dianion, [B12F12]2-. The strong electrostatic interaction between [Ni(bpy)3]2+ and [B12F12]2- diminishes the distortion of the cation due to interactions with the surface. This interaction stabilizes the soft landed cation by reducing the extent of charge reduction and its structural reorganization. Overall, this study shows the intricate interplay of charge state, ion surface interactions, and stabilization by counterions on the structure and reactivity of metal complexes on surfaces. The combined experimental and computational approach used in this study offers detailed insights into factors that affect the integrity and stability of active species relevant to energy production and catalysis.
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Affiliation(s)
- Hugo Y Samayoa-Oviedo
- Department of Chemistry, Purdue University West Lafayette IN 47907 USA +1-765-494-5434
| | - Harald Knorke
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig 04103 Leipzig Germany
| | - Jonas Warneke
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig 04103 Leipzig Germany
- Leibniz Institut für Oberflächenmodifizierung (IOM) Permoserstraße 15 04318 Leipzig Germany
| | - Julia Laskin
- Department of Chemistry, Purdue University West Lafayette IN 47907 USA +1-765-494-5434
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2
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Geue N, Bennett TS, Arama AAM, Ramakers LAI, Whitehead GFS, Timco GA, Armentrout PB, McInnes EJL, Burton NA, Winpenny REP, Barran PE. Disassembly Mechanisms and Energetics of Polymetallic Rings and Rotaxanes. J Am Chem Soc 2022; 144:22528-22539. [PMID: 36459680 PMCID: PMC9756338 DOI: 10.1021/jacs.2c07522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Indexed: 12/04/2022]
Abstract
Understanding the fundamental reactivity of polymetallic complexes is challenging due to the complexity of their structures with many possible bond breaking and forming processes. Here, we apply ion mobility mass spectrometry coupled with density functional theory to investigate the disassembly mechanisms and energetics of a family of heterometallic rings and rotaxanes with the general formula [NH2RR'][Cr7MF8(O2CtBu)16] with M = MnII, FeII, CoII, NiII, CuII, ZnII, CdII. Our results show that their stability can be tuned both by altering the d-metal composition in the macrocycle and by the end groups of the secondary ammonium cation [NH2RR']+. Ion mobility probes the conformational landscape of the disassembly process from intact complex to structurally distinct isobaric fragments, providing unique insights to how a given divalent metal tunes the structural dynamics.
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Affiliation(s)
- Niklas Geue
- Michael
Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University
of Manchester, 131 Princess Street, ManchesterM1 7DN, U.K.
| | - Tom S. Bennett
- Department
of Chemistry, The University of Manchester, Oxford Road, ManchesterM13 9PL, U.K.
| | | | - Lennart A. I. Ramakers
- Michael
Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University
of Manchester, 131 Princess Street, ManchesterM1 7DN, U.K.
| | - George F. S. Whitehead
- Department
of Chemistry, The University of Manchester, Oxford Road, ManchesterM13 9PL, U.K.
| | - Grigore A. Timco
- Department
of Chemistry, The University of Manchester, Oxford Road, ManchesterM13 9PL, U.K.
| | - P. B. Armentrout
- Department
of Chemistry, University of Utah, Salt Lake City, Utah84112, United States
| | - Eric J. L. McInnes
- Department
of Chemistry, The University of Manchester, Oxford Road, ManchesterM13 9PL, U.K.
| | - Neil A. Burton
- Department
of Chemistry, The University of Manchester, Oxford Road, ManchesterM13 9PL, U.K.
| | - Richard E. P. Winpenny
- Department
of Chemistry, The University of Manchester, Oxford Road, ManchesterM13 9PL, U.K.
| | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University
of Manchester, 131 Princess Street, ManchesterM1 7DN, U.K.
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3
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Dong X, Fan X, Wang C, Saikia BK, Wang R, Lu Y, Bai H, Wei X. A Novel Evaluation Method Developed for the Denitrogenation and Deoxygenation on Molecules in Coal during Catalytic Treatments. ChemistrySelect 2019. [DOI: 10.1002/slct.201903286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xueming Dong
- College of Chemical and Environmental EngineeringShandong University of Science and Technology, Qingdao Shandong 266590 China
- Department of ChemistryPurdue University, Brown Building 560 Oval Drive, West Lafayette Indiana 47907 United States
| | - Xing Fan
- College of Chemical and Environmental EngineeringShandong University of Science and Technology, Qingdao Shandong 266590 China
- State Key Laboratory of High-efficiency Coal Utilization and Green Chemical EngineeringNingxia University, Yinchuan Ningxia 750021 China
| | - Chu‐Fan Wang
- Key Laboratory of Coal Processing and Efficient UtilizationMinistry of EducationChina University of Mining & Technology, Xuzhou Jiangsu 221116 China
| | - Binoy K. Saikia
- Polymer Petroleum and Coal Chemistry GroupMaterials Science and Technology DivisionCSIR-North East Institute of Science & Technology Jorhat 785006 India
| | - Rui‐Yu Wang
- Key Laboratory of Coal Processing and Efficient UtilizationMinistry of EducationChina University of Mining & Technology, Xuzhou Jiangsu 221116 China
| | - Yao Lu
- Key Laboratory of Coal Processing and Efficient UtilizationMinistry of EducationChina University of Mining & Technology, Xuzhou Jiangsu 221116 China
| | - Hong‐Cun Bai
- State Key Laboratory of High-efficiency Coal Utilization and Green Chemical EngineeringNingxia University, Yinchuan Ningxia 750021 China
| | - Xian‐Yong Wei
- State Key Laboratory of High-efficiency Coal Utilization and Green Chemical EngineeringNingxia University, Yinchuan Ningxia 750021 China
- Key Laboratory of Coal Processing and Efficient UtilizationMinistry of EducationChina University of Mining & Technology, Xuzhou Jiangsu 221116 China
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4
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Wu RR, Rodgers MT. Tautomerization lowers the activation barriers for N-glycosidic bond cleavage of protonated uridine and 2'-deoxyuridine. Phys Chem Chem Phys 2016; 18:24451-9. [PMID: 27536972 DOI: 10.1039/c6cp03620a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The gas-phase conformations of protonated uridine, [Urd+H](+), and its 2'-deoxy form, protonated 2'-deoxyuridine, [dUrd+H](+), have been examined in detail previously by infrared multiple photon dissociation action spectroscopy techniques. Both 2,4-dihydroxy tautomers and O4 protonated conformers of [Urd+H](+) and [dUrd+H](+) were found to coexist in the experiments with the 2,4-dihydroxy tautomers dominating the population. In the present study, the kinetic energy dependence of the collision-induced dissociation behavior of [Urd+H](+) and [dUrd+H](+) are examined using a guided ion beam tandem mass spectrometer to probe the mechanisms and energetics for activated dissociation of these protonated nucleosides. The primary dissociation pathways observed involve N-glycosidic bond cleavage leading to competitive elimination of protonated or neutral uracil. The potential energy surfaces (PESs) for these N-glycosidic bond cleavage pathways are mapped out via electronic structure calculations for the mixture of 2,4-dihydroxy tautomers and O4 protonated conformers of [Urd+H](+) and [dUrd+H](+) populated in the experiments. The calculated activation energies (AEs) and heats of reaction (ΔHrxns) for N-glycosidic bond cleavage at both the B3LYP and MP2(full) levels of theory are compared to the measured values. The agreement between experiment and theory indicates that B3LYP provides better estimates of the energetics of the species along the PESs for N-glycosidic bond cleavage than MP2, and that the 2,4-dihydroxy tautomers, which are stabilized by strong hydrogen-bonding interactions, predominantly influence the observed threshold dissociation behavior of [Urd+H](+) and [dUrd+H](+).
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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5
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Yang B, Rodgers MT. Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m(5)dCyd: Implications for the Stability of DNA i-Motif Conformations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1394-1403. [PMID: 26002790 DOI: 10.1007/s13361-015-1144-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/10/2015] [Accepted: 03/17/2015] [Indexed: 06/04/2023]
Abstract
Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m(5)dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m(5)dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m(5)dCyd)H(+)(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.
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Affiliation(s)
- Bo Yang
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
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6
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Yang B, Moehlig AR, Frieler CE, Rodgers MT. Base-pairing energies of protonated nucleobase pairs and proton affinities of 1-methylated cytosines: model systems for the effects of the sugar moiety on the stability of DNA i-motif conformations. J Phys Chem B 2015; 119:1857-68. [PMID: 25565341 DOI: 10.1021/acs.jpcb.5b00035] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Expansion of (CCG)n·(CGG)n trinucleotide repeats leads to hypermethylation of cytosine residues and results in Fragile X syndrome, the most common cause of inherited intellectual disability in humans. The (CCG)n·(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of noncanonical protonated nucleobase pairs of cytosine (C(+)·C). Previously, we investigated the effects of 5-methylation of cytosine on the base-pairing energies (BPEs) using threshold collision-induced dissociation (TCID) techniques. In the present work, we extend our investigations to include protonated homo- and heteronucleobase pairs of cytosine, 1-methylcytosine, 5-methylcytosine, and 1,5-dimethylcytosine. The 1-methyl substituent prevents most tautomerization processes of cytosine and serves as a mimic for the sugar moiety of DNA nucleotides. In contrast to permethylation of cytosine at the 5-position, 1-methylation is found to exert very little influence on the BPE. All modifications to both nucleobases lead to a small increase in the BPEs, with 5-methylation producing a larger enhancement than either 1-methyl or 1,5-dimethylation. In contrast, modifications to a single nucleobase are found to produce a small decrease in the BPEs, again with 5-methylation producing a larger effect than 1-methylation. However, the BPEs of all of the protonated nucleobase pairs examined here significantly exceed those of canonical G·C and neutral C·C base pairs, and thus should still provide the driving force stabilizing DNA i-motif conformations even in the presence of such modifications. The proton affinities of the methylated cytosines are also obtained from the TCID experiments by competitive analyses of the primary dissociation pathways that occur in parallel for the protonated heteronucleobase pairs.
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Affiliation(s)
- Bo Yang
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
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7
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Majumdar S, Stauber JM, Palluccio TD, Cai X, Velian A, Rybak-Akimova EV, Temprado M, Captain B, Cummins CC, Hoff CD. Role of Axial Base Coordination in Isonitrile Binding and Chalcogen Atom Transfer to Vanadium(III) Complexes. Inorg Chem 2014; 53:11185-96. [DOI: 10.1021/ic5017005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Subhojit Majumdar
- Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables Florida 33021, United States
| | - Julia M. Stauber
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Taryn D. Palluccio
- Department of Chemistry, Tufts University, 62
Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Xiaochen Cai
- Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables Florida 33021, United States
| | - Alexandra Velian
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Elena V. Rybak-Akimova
- Department of Chemistry, Tufts University, 62
Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Manuel Temprado
- Department of Analytical Chemistry, Physical Chemistry and Chemical
Engineering, Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, Madrid, 28871, Spain
| | - Burjor Captain
- Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables Florida 33021, United States
| | - Christopher C. Cummins
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Carl D. Hoff
- Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables Florida 33021, United States
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8
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Yang B, Rodgers MT. Alkali metal cation binding affinities of cytosine in the gas phase: revisited. Phys Chem Chem Phys 2014; 16:16110-20. [DOI: 10.1039/c4cp01128g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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Nose H, Rodgers MT. Influence of the d orbital occupation on the structures and sequential binding energies of pyridine to the late first-row divalent transition metal cations: a DFT study. J Phys Chem A 2014; 118:8129-40. [PMID: 24786545 DOI: 10.1021/jp500488t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The ground-state structures and sequential binding energies of the late first-row divalent transition metal cations to pyridine (Pyr) are determined using density functional theory (DFT) methods. Five late first-row transition metal cations in their +2 oxidation states are examined including: Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+). Calculations at B3LYP, BHandHLYP, and M06 levels of theory using 6-31G* and 6-311+G(2d,2p) basis sets are employed to determine the structures and theoretical estimates for the sequential binding energies of the M(2+)(Pyr)x complexes, where x = 1-6, respectively. Structures of the Ca(2+)(Pyr)x complexes are compared to those for the M(2+)(Pyr)x complexes of Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+) to further assess the effects of the d-orbital occupation on the preferred binding geometries. The B3LYP, BHandHLYP, and M06 levels of theory yield very similar geometries for the analogous M(2+)(Pyr)x complexes. The overall trends in the sequential BDEs for all five metal cations at all three levels of theory examined are highly parallel, and are determined by a balance of the effects of the valence electronic configuration and hybridization of the metal cation, but are also influenced by repulsive ligand-ligand interactions. Present results for the M(2+)(Pyr)x complexes are compared to the analogous complexes of the late first-row monovalent transition metal cations, Co(+), Ni(+), Cu(+), and Zn(+) previously investigated to assess the effect of the charge/oxidation state on the structures and sequential binding energies. Trends in the sequential binding energies of the M(2+)(Pyr)x complexes are also compared to the analogous M(2+)(water)x, M(2+)(imidazole)x, M(2+)(2,2'-bipyridine)x, and M(2+)(1,10-phenanthroline)x complexes.
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Affiliation(s)
- Holliness Nose
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
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10
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Yang B, Wu RR, Rodgers MT. Base-pairing energies of proton-bound homodimers determined by guided ion beam tandem mass spectrometry: application to cytosine and 5-substituted cytosines. Anal Chem 2013; 85:11000-6. [PMID: 24117448 DOI: 10.1021/ac402542g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Base-pairing interactions in proton-bound dimers of cytosine (C(+)·C) are the major forces responsible for stabilization of DNA i-motif conformations. Permethylation of cytosine in extended (CCG)·(CGG)n trinucleotide repeats has been shown to cause fragile-X syndrome, the most widespread inherited cause of mental retardation in humans. Oligonucleotides containing 5-bromo- or 5-fluorocytosine can bind to proteins that selectively bind methylated DNA, suggesting that halogenated cytosine damage products can potentially mimic methylation signals. However, the influence of methylation or halogenation on the base-pairing energies (BPEs) of proton-bound dimers of cytosine and their impact on the stability of DNA i-motif conformations is presently unknown. To address this, proton-bound homodimers of cytosine and 5-methyl-, 5-fluoro-, 5-bromo-, and 5-iodocytosine are investigated in detail both experimentally and theoretically. The BPEs of proton-bound homodimers of cytosine and the modified cytosines are measured by threshold collision-induced dissociation (TCID) techniques. 5-Methylation of cytosine is found to increase the BPE and would therefore tend to stabilize DNA i-motif conformations. In contrast, 5-halogenation lowers the BPE. However, the BPEs of the proton-bound 5-halocytosine homodimers examined here still significantly exceed that of Watson-Crick G·C base pairs, such that DNA i-motif conformations should be preserved in the presence of these modifications. Excellent agreement between TCID measured and B3LYP calculated BPEs is found, suggesting that B3LYP calculations can be used to provide reliable energetic predictions for related systems.
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Affiliation(s)
- Bo Yang
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
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