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Rivera JJ, Liang JH, Shimamura GR, Shafaat HS, Kim JE. Raman and Quantum Yield Studies of Trp48- d5 in Azurin: Closed-Shell and Neutral Radical Species. J Phys Chem B 2019; 123:6430-6443. [PMID: 31313925 DOI: 10.1021/acs.jpcb.9b04655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isotopologues are valuable vibrational probes that shift features in a vibrational spectrum while preserving the electronic structure of the molecule. We report the vibrational and electronic spectra of perdeuterated tryptophan in solution (l-Trp-d5), as Trp48-d5 in azurin, and as the photogenerated neutral tryptophan radical, Trp48-d5•, in azurin. The UV resonance Raman bands of the perdeuterated closed-shell tryptophan in solution and in azurin are lower in frequency relative to the protiated counterpart. The observed decrease in frequencies of l-Trp-d5 bands relative to l-Trp-h5 enables the analysis of vibrational markers of other amino acids, e.g., phenylalanine, that overlap with some modes of l-Trp-h5. The Raman intensities vary between l-Trp-d5 and l-Trp-h5; these differences likely reflect modifications in normal mode composition upon perdeuteration. Analysis of the W3, W6, and W17 modes suggests that the W3 mode retains its utility as a conformational marker; however, the H-bond markers W6 and W17 appear to be less sensitive upon perdeuteration. The neutral tryptophan radical, Trp48-d5•, was generated in azurin with a slightly lower radical quantum yield than for Trp48-h5•. The visible resonance Raman spectrum of Trp48-d5• is different from that of Trp48-h5•, especially in terms of relative intensities, and all assignable peaks decreased in frequency upon perdeuteration. The absorption and emission spectra of the perdeuterated closed-shell and radical species exhibited hypsochromic shifts of less than 1 nm relative to the protiated species. The data presented here indicate that l-Trp-d5 is a valuable probe of vibrational structure, with minimal modification of photoreactivity and photophysics compared to l-Trp-h5.
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Affiliation(s)
- Joel J Rivera
- Department of Chemistry and Biochemistry , University of California at San Diego , La Jolla , California 92093-0021 , United States
| | - Justine H Liang
- Department of Chemistry and Biochemistry , University of California at San Diego , La Jolla , California 92093-0021 , United States
| | - Gregory R Shimamura
- Department of Chemistry and Biochemistry , University of California at San Diego , La Jolla , California 92093-0021 , United States
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry , University of California at San Diego , La Jolla , California 92093-0021 , United States
| | - Judy E Kim
- Department of Chemistry and Biochemistry , University of California at San Diego , La Jolla , California 92093-0021 , United States
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Li Y, Nam K. Dynamic, structural and thermodynamic basis of insulin-like growth factor 1 kinase allostery mediated by activation loop phosphorylation. Chem Sci 2017; 8:3453-3464. [PMID: 28507717 PMCID: PMC5418630 DOI: 10.1039/c7sc00055c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/15/2017] [Indexed: 11/30/2022] Open
Abstract
Despite the importance of kinases' catalytic activity regulation in cell signaling, detailed mechanisms underlying their activity regulation are poorly understood. Herein, using insulin-like growth factor 1 receptor kinase (IGF-1RK) as a model, the mechanisms of kinase regulation by its activation loop (A-loop) phosphorylation were investigated through molecular dynamics (MD) and alchemical free energy simulations. Analyses of the simulation results and free energy landscapes determined for the entire catalytic cycle of the kinase revealed that A-loop phosphorylation affects each step in the IGF-1RK catalytic cycle, including conformational change, substrate binding/product release and catalytic phosphoryl transfer. Specifically, the conformational equilibrium of the kinase is shifted by 13.2 kcal mol-1 to favor the active conformation after A-loop phosphorylation, which increases substrate binding affinity of the activated kinase. This free energy shift is achieved primarily via destabilization of the inactive conformation. The free energy of the catalytic reaction is also changed by 3.3 kcal mol-1 after the phosphorylation and in the end, facilitates product release. Analyses of MD simulations showed that A-loop phosphorylation produces these energetic effects by perturbing the side chain interactions around each A-loop tyrosine. These interaction changes are propagated to the remainder of the kinase to modify the orientations and dynamics of the αC-helix and A-loop, and together yield the observed free energy changes. Since many protein kinases share similar interactions identified in this work, the mechanisms of kinase allostery and catalysis unraveled here can be applicable to them.
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Affiliation(s)
- Yaozong Li
- Department of Chemistry , Umeå University , SE-901 87 Umeå , Sweden
| | - Kwangho Nam
- Department of Chemistry , Umeå University , SE-901 87 Umeå , Sweden
- Department of Chemistry and Biochemistry , University of Texas at Arlington , Arlington , TX 76019-0065 , USA . ; Tel: +1-817-272-1091
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Munshi MU, Berden G, Martens J, Oomens J. Gas-phase vibrational spectroscopy of triphenylamine: the effect of charge on structure and spectra. Phys Chem Chem Phys 2017. [DOI: 10.1039/c7cp02638b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The effect of ionization by oxidation and protonation on the structure and IR spectrum of isolated, gas-phase triphenylamine (TPA) has been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy in the fingerprint range from 600 cm−1 to 1800 cm−1 using an infrared free electron laser.
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Affiliation(s)
- Musleh Uddin Munshi
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Jonathan Martens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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Steill JD, May AL, Campagna SR, Oomens J, Compton RN. Structure and stability of phenoxide and fluorophenoxide anions investigated with infrared multiple-photon dissociation and detachment spectroscopy and tandem mass spectrometry. J Phys Chem A 2014; 118:8597-605. [PMID: 24802281 DOI: 10.1021/jp503103a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The gas-phase infrared multiple-photon dissociation and detachment (IRMPD) vibrational action spectra of the unsubstituted phenoxide anion and a series of fluorine- and trifluoromethyl-substituted phenoxide anions in the spectral region between 600 and 1800 cm(-1) are presented along with density functional theory (DFT) harmonic vibrational frequency calculations to establish the characteristic vibrations of the phenoxide functionality. The fluorophenoxide anions studied include the conjugate bases of o-, m-, and p-fluorophenol (C6H4FO(-)) as well as o-, m-, and p-α,α,α-trifluorocresol (CF3C6H4O(-)). The influence of the substituent on the characteristic vibrational frequencies is interpreted in terms of inductive and resonance shifts. In addition to the dissociation induced by infrared multiple-photon excitation, the electron detachment is also shown to play an important role in the decomposition of the unsubstituted phenoxide. It is demonstrated that the amount of electron detachment relative to dissociation is strongly mitigated by fluorination, and interpretations aided by DFT energy calculations suggest this is primarily due to the increased availability of low-energy dissociation pathways in the substituted phenoxides. Collision-induced dissociation (CID) mass spectrometry of the parent ions is used to estimate relative energies of the dissociation processes, and particular fragmentation motifs are elucidated. In particular, overall HF and CO losses provide facile decomposition pathways, yielding interesting fragment ions such as C6H(-) or C3H2FO(-) from the CF3C6H4O(-) parent anions.
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Affiliation(s)
- Jeffrey D Steill
- Department of Chemistry, University of Tennessee , Knoxville, Tennessee 37996, United States
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Peng Q, Li M, Hu C, Pavlik JW, Oliver AG, Alp EE, Hu MY, Zhao J, Sage JT, Scheidt WR. Probing heme vibrational anisotropy: an imidazole orientation effect? Inorg Chem 2013; 52:11361-9. [PMID: 24020589 DOI: 10.1021/ic401644g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complete iron vibrational spectrum of the five-coordinate high-spin complex [Fe(OEP)(2-MeHIm)], where OEP = octaethylporphyrinato and 2-MeHIm = 2-methylimidazole, has been obtained by oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS) data. Measurements have been made in three orthogonal directions, which provides quantitative information for all iron motion. These experimental data, buttressed by density functional theory (DFT) calculations, have been used to define the effects of the axial ligand orientation. Although the axial imidazole removes the degeneracy in the in-plane vibrations, the imidazole orientation does not appear to control the direction of the in-plane iron motion. This is in contrast to the effect of the imidazolate ligand, as defined by DFT calculations, which does have substantial effects on the direction of the in-plane iron motion. The axial NO ligand has been found to have the strongest orientational effect (Angew. Chem., Int. Ed., 2010, 49, 4400). Thus the strength of the directional properties are in the order NO > imidazolate > imidazole, consistent with the varying strength of the Fe-ligand bond.
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Affiliation(s)
- Qian Peng
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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Barabanschikov A, Demidov A, Kubo M, Champion PM, Sage JT, Zhao J, Sturhahn W, Alp EE. Spectroscopic identification of reactive porphyrin motions. J Chem Phys 2011; 135:015101. [PMID: 21744919 PMCID: PMC3144962 DOI: 10.1063/1.3598473] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Accepted: 05/18/2011] [Indexed: 11/14/2022] Open
Abstract
Nuclear resonance vibrational spectroscopy (NRVS) reveals the vibrational dynamics of a Mössbauer probe nucleus. Here, (57)Fe NRVS measurements yield the complete spectrum of Fe vibrations in halide complexes of iron porphyrins. Iron porphine serves as a useful symmetric model for the more complex spectrum of asymmetric heme molecules that contribute to numerous essential biological processes. Quantitative comparison with the vibrational density of states (VDOS) predicted for the Fe atom by density functional theory calculations unambiguously identifies the correct sextet ground state in each case. These experimentally authenticated calculations then provide detailed normal mode descriptions for each observed vibration. All Fe-ligand vibrations are clearly identified despite the high symmetry of the Fe environment. Low frequency molecular distortions and acoustic lattice modes also contribute to the experimental signal. Correlation matrices compare vibrations between different molecules and yield a detailed picture of how heme vibrations evolve in response to (a) halide binding and (b) asymmetric placement of porphyrin side chains. The side chains strongly influence the energetics of heme doming motions that control Fe reactivity, which are easily observed in the experimental signal.
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Affiliation(s)
- Alexander Barabanschikov
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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Schmidt PP. On the construction of hybrid potential energy functions for the treatment of local anharmonicity in molecular vibrations. Mol Phys 2010. [DOI: 10.1080/00268970701647969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Murdachaew G, Mundy CJ, Schenter GK. Improving the density functional theory description of water with self-consistent polarization. J Chem Phys 2010; 132:164102. [DOI: 10.1063/1.3385797] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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McDonald WJ, Einarsdóttir Ó. Solvent Effects on the Vibrational Frequencies of the Phenolate Anion, the para-Cresolate Anion, and Their Radicals. J Phys Chem A 2008; 112:11400-13. [DOI: 10.1021/jp800169w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- William J. McDonald
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064
| | - Ólöf Einarsdóttir
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064
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11
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Bender SL, Keough JM, Boesch SE, Wheeler RA, Barry BA. The Vibrational Spectrum of the Secondary Electron Acceptor, A1, in Photosystem I. J Phys Chem B 2008; 112:3844-52. [DOI: 10.1021/jp0775146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shana L. Bender
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - James M. Keough
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Scott E. Boesch
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Ralph A. Wheeler
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Bridgette A. Barry
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
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Range K, Ayala I, York D, Barry BA. Normal modes of redox-active tyrosine: conformation dependence and comparison to experiment. J Phys Chem B 2007; 110:10970-81. [PMID: 16771350 DOI: 10.1021/jp061503f] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Redox-active tyrosine residues play important roles in long-distance electron reactions in enzymes such as prostaglandin H synthase, ribonucleotide reductase, and photosystem II (PSII). Spectroscopic characterization of tyrosyl radicals in these systems provides a powerful experimental probe into the role of the enzyme in mediation of long-range electron transfer processes. Interpretation of such data, however, relies critically on first establishing a spectroscopic fingerprint of isotopically labeled tyrosinate and tyrosyl radicals in nonenzymatic environments. In this report, FT-IR results obtained from tyrosinate, tyrosyl radical (produced by ultraviolet photolysis of polycrystalline tyrosinate), and their isotopologues at 77 K are presented. Assignment of peaks and isotope shifts is aided by density-functional B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p) calculations of tyrosine and tyrosyl radical in several different charge and protonation states. In addition, characterization of the potential energy surfaces of tyrosinate and tyrosyl radical as a function of the backbone and ring torsion angles provides detailed insight into the sensitivity of the vibrational frequencies to conformational changes. These results provide a detailed spectroscopic interpretation, which will elucidate the structures of redox-active tyrosine residues in complex protein environments. Specific application of these data is made to enzymatic systems.
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Affiliation(s)
- Kevin Range
- Department of Chemistry, Lock Haven University of Pennsylvania, Lock Haven, Pennsylvania 17745, USA
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Waterland MR, Howell SL, Gordon KC. Using Internal Coordinates to Describe Photoinduced Geometry Changes in MLCT Excited States. J Phys Chem A 2007; 111:4604-11. [PMID: 17488100 DOI: 10.1021/jp070389d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A resonance Raman intensity analysis of the metal-to-ligand charge-transfer (MLCT) transition for the rhenium compound Re(2-(2'-pyridyl)quinoxaline)(CO)(3)Cl (RePQX) is presented. Photoinduced geometry changes are calculated, and the results are presented using the vibrational normal modes and the redundant internal coordinates. A density functional theory calculation is used to determine the ground-state nonresonant Raman spectrum and a transformation matrix that transforms the redundant internal coordinates into the normal modes. The normal modes nu(37) (rhenium coordination sphere distortion) and nu(75) (ligand skeletal stretch) show the largest photoinduced geometry change (Delta = 1.0 and 0.7, respectively). A single carbonyl mode is enhanced in the resonance Raman spectra. Time-dependent density functional theory is used to calculate excited-state geometry changes, which are subsequently used to determine the signs of the photoinduced normal mode displacements. Transforming to internal coordinates reveals that all the CO bond lengths are displaced in the excited state. The Re-C and C-C ligand bond lengths are also displaced in the excited state. The results are discussed in terms of a simple one-electron picture for the electronic transition. Many bond angles and torsional coordinates are also displaced by the metal-to-ligand charge transfer, and most of these are associated with the rhenium coordination sphere. It is demonstrated that using internal coordinates presents a clear picture of the geometry changes associated with photoinduced electron transfer in metal polypyridyl systems.
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Affiliation(s)
- Mark R Waterland
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand.
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Grafton AK. Vibalizer: A free, web-based tool for rapid, quantitative comparison and analysis of calculated vibrational modes. J Comput Chem 2007; 28:1290-305. [PMID: 17299728 DOI: 10.1002/jcc.20642] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This report describes the development and applications of a software package called Vibalizer, the first and only method that provides free, fast, interactive, and quantitative comparison and analysis of calculated vibrational modes. Using simple forms and menus in a web-based interface, Vibalizer permits the comparison of vibrational modes from different, but similar molecules and also performs rapid calculation and comparison of isotopically substituted molecules' normal modes. Comparing and matching complex vibrational modes can be completed in seconds with Vibalizer, whereas matching vibrational modes manually can take hours and gives only qualitative comparisons subject to human error and differing individual judgments. In addition to these core features, Vibalizer also provides several other useful features, including the ability to automatically determine first-approximation mode descriptions, to help users analyze the results of vibrational frequency calculations. Because the software can be dimensioned to handle almost arbitrarily large systems, Vibalizer may be of particular use when analyzing the vibrational modes of complex systems such as proteins and extended materials systems. Additionally, the ease of use of the Vibalizer interface and the straightforward interpretation of results may find favor with educators who incorporate molecular modeling into their classrooms. The Vibalizer interface is available for free use at http://www.compchem.org, and it is also available as a locally-installable package that will run on a Linux-based web server.
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Affiliation(s)
- Anthony K Grafton
- Division of Science, Lyon College, P.O. Box 2317, Batesville, Arkansas 72503, USA.
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Krause M, Popov A, Dunsch L. Vibrational Structure of Endohedral Fullerene Sc3N@C78 (D3h′): Evidence for a Strong Coupling between the Sc3N Cluster and C78 Cage. Chemphyschem 2006; 7:1734-40. [PMID: 16888747 DOI: 10.1002/cphc.200600139] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The vibrational structure of the endohedral cluster fullerene Sc(3)N@C(78) is studied by FTIR spectroscopy, Raman spectroscopy and DFT-based quantum chemical calculations. Remarkably good agreement between experimental and calculated spectra is achieved and a full assignment of the Sc(3)N-based vibrational modes is given. Significant differences in the vibrational structure of the endohedral cluster fullerene Sc(3)N@C(78) and the empty, charged C(78) (6-): 5 (D(3h)') are rationalized by the strong coupling between the Sc(3)N cluster and the fullerene cage. This coupling has its origin in a significant overlap of the Sc(3)N and C(78) molecular orbitals, and causes atomic-charge and bond-length redistributions compared to the neutral C(78) and the C(78) (6-) anion. An ionic model is not sufficient to describe the electronic, geometric and vibrational structure of the Sc(3)N@C(78) nitride cluster fullerene.
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Affiliation(s)
- Matthias Krause
- Group of Electrochemistry and Conducting Polymers, Leibniz-Institute for Solid State and Materials Research Dresden, 01171 Dresden, Germany.
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de Groot M, Buma WJ. A time-dependent density functional study of vibrationally resolved excitation, emission, and ionization spectra of the S1 state of phenol. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2005.12.095] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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O'Malley PJ. Electronic structure calculated anharmonic vibrational frequencies for phenol. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2005.07.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Howell SL, Matthewson BJ, Polson MIJ, Burrell AK, Gordon KC. Structural Changes upon Reduction of Dipyrido[2,3-a:3‘,2‘-c]phenazine Probed by Vibrational Spectroscopy, ab Initio Calculations, and Deuteration Studies. Inorg Chem 2004; 43:2876-87. [PMID: 15106975 DOI: 10.1021/ic030225l] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of bridging ligands, dipyrido[2,3-a:3',2'-c]phenazine (ppb), dipyrido[2,3-a:3',2'-c]-6,7-dichlorophenazine (ppbCl2), and dipyrido[2,3-a:3',2'-c]-6,7-dimethylphenazine (ppbMe2), and their binuclear copper(I) complexes have been synthesized, and their spectral properties were measured. The single-crystal structure of the complex, [(PPh3)2Cu(mu-ppbCl2)Cu(PPh3)2](BF4)2 in the monoclinic space group P21/c, 18.2590(1), 21.1833(3), 23.2960(3) A with Z = 4 is reported. The copper(I) complexes are deeply colored through MLCT transitions in the visible region. The vibrational spectra of the ligands have been modeled using ab initio hybrid density functional theory (DFT) methods (B3LYP/6-31G(d)) and compared to experimental FT-Raman and IR data. The DFT calculations are used to interpret the resonance Raman spectra, and thus the electronic spectra, of the complexes. The preferential enhancement of modes associated with the phenanthroline section of the ligands with blue excitation (lambda(exc) = 457.9 nm) over phenazine-based modes with redder excitation (lambda(exc) = 514.5 and 632.8 nm) suggests the 2 MLCT transitions terminated on different unoccupied MOs are present under the visible absorption envelope. The radical anion species of the ligands are prepared by the electrochemical reduction of the binuclear copper(I) complexes; no evidence of dechelation prevalent in other copper(I) complexes is observed. The resonance Raman spectra of the reduced complexes are dramatically different from those of the parent species. Across the series common bands are observed at about 1590 and 1570 cm(-1) which do not shift with reduction but are altered in intensity. The normal-mode analysis of the radical anion species suggests that these normal modes primarily involve bond length distortions that are unaffected by reduction.
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Affiliation(s)
- Sarah L Howell
- Department of Chemistry, University of Otago, Union Place, Dunedin, New Zealand
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Affiliation(s)
- Ralph A Wheeler
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Room 208, Norman, OK 73019, USA.
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York SS, Boesch SE, Wheeler RA, Frech R. Vibrational Assignments for High Molecular Weight Linear Polyethylenimine (LPEI) Based on Monomeric and Tetrameric Model Compounds. Macromolecules 2003. [DOI: 10.1021/ma030016k] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shawna S. York
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Scott E. Boesch
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Ralph A. Wheeler
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Roger Frech
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
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Zierkiewicz W, Michalska D, Czarnik-Matusewicz B, Rospenk M. Molecular Structure and Infrared Spectra of 4-Fluorophenol: A Combined Theoretical and Spectroscopic Study. J Phys Chem A 2003. [DOI: 10.1021/jp022564q] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Vaiana AC, Schulz A, Wolfrum J, Sauer M, Smith JC. Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching. J Comput Chem 2003; 24:632-9. [PMID: 12632478 DOI: 10.1002/jcc.10190] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Novel single-molecule fluorescence experimental techniques have prompted a growing need to develop refined computational models of dye-tagged biomolecules. As a necessary first step towards useful molecular simulations of fluorescence-labeled biomolecules, we have derived a force field for the commonly used dye, rhodamine 6G (R6G). A novel automated method is used that includes fitting the molecular mechanics potential to both vibrational frequencies and eigenvector projections derived from quantum chemical calculations. The method is benchmarked on a series of aromatic molecules then applied to derive new parameters for R6G. The force field derived reproduces well the crystal structure of R6G.
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Affiliation(s)
- Andrea C Vaiana
- IWR-Biocomputing, Universität Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany
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Wheeler RA, Dong H, Boesch SE. Quasiharmonic vibrations of water, water dimer, and liquid water from principal component analysis of quantum or QM/MM trajectories. Chemphyschem 2003; 4:382-4. [PMID: 12728554 DOI: 10.1002/cphc.200390066] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ralph A Wheeler
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019, USA.
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Almeida LCJ, Santos PS. The anomalous solvent effect in the vibrational spectrum of 2,3-diphenyl-cycloprop-2-enone: an experimental and theoretical investigation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2002; 58:3139-3148. [PMID: 12511098 DOI: 10.1016/s1386-1425(02)00103-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
2,3-Diphenyl-cycloprop-2-enone (DPC) was investigated aiming to understand the origins of the anomalous solvatochromism in its vibrational spectrum. Its Raman and IR spectra in several solvents were obtained revealing that the v(C=C) mode is much more sensitive to the solvent than the v(C=O) mode. Hartree-Fock and density functional theory calculations were undertaken for obtaining the structure and the vibrational spectra of DPC and 2,3-dimethylcycloprop-2-enone (DMC), revealing that both in terms of structure as well as of vibrational spectrum, DPC and DMC are very similar. Such results indicated that DMC could be used as a model system to simulate the solvent effect in DPC, what was done using three different methods: the first takes into account the dielectric effect via the self-consistent reaction field (SCRF); the second is the supermolecular approach that considers explicity the formation of solute-solvent clusters and the third is a combined approach, SCRF + supermolecule. The anomalous solvatochromism in the vibrational spectrum of DPC can be understood on basis of the significant participation of the v(C=O) mode in the one assigned to the v(C=C) vibration, as well as by the presence of a Fermi resonance involving the former. In addition, the v(C=O) mode involves a significant participation of the (C-C) mode (C(cyclopropene)-C(phenyl)) and the two interatomic distances, C=O and C-C, show opposite trends with increasing solvent polarity. Summing up, the anomalous solvatochromic effect of DPC can be understood by the complex composition of its v(C=O) mode that, in addition, is affected by the presence of a Fermi resonance.
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Affiliation(s)
- L C J Almeida
- Instituto de Química da Universidade de São Paulo, Sao Paulo, CEP, 05508-900, SP, Brazil
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Matthewson BJ, Flood A, Polson MIJ, Armstrong C, Phillips DL, Gordon KC. Vibrational Spectra of Dipyrido[3,2-a:2′,3′-c]phenazine and Its Radical Anion Analyzed by Ab Initio Calculations and Deuteration Studies. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2002. [DOI: 10.1246/bcsj.75.933] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Le HT, Flammang R, Gerbaux P, Bouchoux G, Nguyen MT. Ionized Phenol and Its Isomers in the Gas Phase. J Phys Chem A 2001. [DOI: 10.1021/jp012679e] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hung Thanh Le
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium, Laboratoire de Chimie Organique, Université de Mons-Hainaut, Avenue Maistriau 19, B-7000 Mons, Belgium, Laboratoire des Mécanismes Réactionnels, UMR CNRS 7651, Ecole Polytechnique, F-91128 Palaiseau cedex, France, and Group of Computational Chemistry, Faculty of Chemical Engineering, HoChiMinh City University of Technology, Vietnam
| | - Robert Flammang
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium, Laboratoire de Chimie Organique, Université de Mons-Hainaut, Avenue Maistriau 19, B-7000 Mons, Belgium, Laboratoire des Mécanismes Réactionnels, UMR CNRS 7651, Ecole Polytechnique, F-91128 Palaiseau cedex, France, and Group of Computational Chemistry, Faculty of Chemical Engineering, HoChiMinh City University of Technology, Vietnam
| | - Pascal Gerbaux
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium, Laboratoire de Chimie Organique, Université de Mons-Hainaut, Avenue Maistriau 19, B-7000 Mons, Belgium, Laboratoire des Mécanismes Réactionnels, UMR CNRS 7651, Ecole Polytechnique, F-91128 Palaiseau cedex, France, and Group of Computational Chemistry, Faculty of Chemical Engineering, HoChiMinh City University of Technology, Vietnam
| | - Guy Bouchoux
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium, Laboratoire de Chimie Organique, Université de Mons-Hainaut, Avenue Maistriau 19, B-7000 Mons, Belgium, Laboratoire des Mécanismes Réactionnels, UMR CNRS 7651, Ecole Polytechnique, F-91128 Palaiseau cedex, France, and Group of Computational Chemistry, Faculty of Chemical Engineering, HoChiMinh City University of Technology, Vietnam
| | - Minh Tho Nguyen
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium, Laboratoire de Chimie Organique, Université de Mons-Hainaut, Avenue Maistriau 19, B-7000 Mons, Belgium, Laboratoire des Mécanismes Réactionnels, UMR CNRS 7651, Ecole Polytechnique, F-91128 Palaiseau cedex, France, and Group of Computational Chemistry, Faculty of Chemical Engineering, HoChiMinh City University of Technology, Vietnam
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Michalska D, Zierkiewicz W, Bieńko DC, Wojciechowski W, Zeegers-Huyskens T. “Troublesome” Vibrations of Aromatic Molecules in Second-Order Möller−Plesset and Density Functional Theory Calculations: Infrared Spectra of Phenol and Phenol-OD Revisited. J Phys Chem A 2001. [DOI: 10.1021/jp0113376] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Danuta Michalska
- Institute of Inorganic Chemistry, Technical University of Wrocław, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland, and Department of Chemistry, University of Leuven, 200F Celestijnenlaan, B3001, Heverlee, Belgium
| | - Wiktor Zierkiewicz
- Institute of Inorganic Chemistry, Technical University of Wrocław, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland, and Department of Chemistry, University of Leuven, 200F Celestijnenlaan, B3001, Heverlee, Belgium
| | - Dariusz C. Bieńko
- Institute of Inorganic Chemistry, Technical University of Wrocław, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland, and Department of Chemistry, University of Leuven, 200F Celestijnenlaan, B3001, Heverlee, Belgium
| | - Walter Wojciechowski
- Institute of Inorganic Chemistry, Technical University of Wrocław, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland, and Department of Chemistry, University of Leuven, 200F Celestijnenlaan, B3001, Heverlee, Belgium
| | - Thérèse Zeegers-Huyskens
- Institute of Inorganic Chemistry, Technical University of Wrocław, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland, and Department of Chemistry, University of Leuven, 200F Celestijnenlaan, B3001, Heverlee, Belgium
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Matthäus C, Wheeler RA. Fragment mode analysis and its application to the vibrational normal modes of boron trichloride-ammonia and boron trichloride-pyridine complexes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2001; 57:521-534. [PMID: 11300564 DOI: 10.1016/s1386-1425(00)00400-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A method for expressing quantitatively the vibrational normal modes of a molecule in a basis set consisting of the normal vibrations (plus translations and rotations) of its constituent fragments is presented. The method is illustrated by describing the vibrational modes of BCl3-NH3 and BCl3-pyridine electron donor-acceptor complexes in terms of motions of BCl3 and either NH3 or pyridine. These complexes show examples of mixing between modes located on different fragments, mixing between modes of one fragment due to symmetry lowering, and the transformation of six fragment translations/rotations into vibrations of the complex. Although perturbation theory has been proposed to explain such examples of mode mixing, calculations imply that interactions between fragments of both complexes are too strong for perturbation theory to be generally applicable. In addition, the transformation of fragment rotations and/or translations into vibrations of the composite molecule will always occur and cannot be understood in detail by using perturbation theory. For the BCl3-pyridine complex, a band observed at 1107 cm(-1) is re-assigned as a combination of C-H in-plane bending and a ring-breathing mode of the pyridine fragment.
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Affiliation(s)
- C Matthäus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman 73019, USA
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Wheeler RA. Quinones and quinoidal radicals in photosynthesis. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1380-7323(01)80016-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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Pan D, Shoute LCT, Phillips DL. Time-Resolved Resonance Raman and Density Functional Study of the Radical Cation of Chlorpromazine. J Phys Chem A 2000. [DOI: 10.1021/jp992196z] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Duohai Pan
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong
| | - Lian C. T. Shoute
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong
| | - David Lee Phillips
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong
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Fukui K, Sumpter BG, Noid DW, Yang C, Tuzun RE. Large-Scale Normal Coordinate Analysis of Macromolecular Systems: Thermal Properties of Polymer Particles and Crystals†. J Phys Chem B 2000. [DOI: 10.1021/jp993149+] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Razeghifard MR, Kim S, Patzlaff JS, Hutchison RS, Krick T, Ayala I, Steenhuis JJ, Boesch SE, Wheeler RA, Barry BA. In Vivo, in Vitro, and Calculated Vibrational Spectra of Plastoquinone and the Plastosemiquinone Anion Radical. J Phys Chem B 1999. [DOI: 10.1021/jp991942x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Reza Razeghifard
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Sunyoung Kim
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Jason S. Patzlaff
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Ronald S. Hutchison
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Thomas Krick
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Idelisa Ayala
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Jacqueline J. Steenhuis
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Scott E. Boesch
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Ralph A. Wheeler
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Bridgette A. Barry
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
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Wise KE, Pate JB, Wheeler RA. Phenoxyl, (Methylthio)phenoxyl, and (Methylthio)cresyl Radical Models for the Structures, Vibrations, and Spin Properties of the Cysteine-Linked Tyrosyl Radical in Galactose Oxidase. J Phys Chem B 1999. [DOI: 10.1021/jp990580q] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kristopher E. Wise
- Department of Chemistry and Biochemistry, 620 Parrington Oval, Room 208, University of Oklahoma, Norman, Oklahoma 73019
| | - J. Brett Pate
- Department of Chemistry and Biochemistry, 620 Parrington Oval, Room 208, University of Oklahoma, Norman, Oklahoma 73019
| | - Ralph A. Wheeler
- Department of Chemistry and Biochemistry, 620 Parrington Oval, Room 208, University of Oklahoma, Norman, Oklahoma 73019
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