Tackling a Curious Case: Generation of Charge-Tagged Guanosine Radicals by Gas-Phase Electron Transfer and Their Characterization by UV-vis Photodissociation Action Spectroscopy and Theory

. 2021 Mar 03 ; 32 (3) : 772-785. [epub] 20210210

Status PubMed-not-MEDLINE Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid33567214

Grantová podpora
R01 GM110430 NIGMS NIH HHS - United States
R01 HD097408 NICHD NIH HHS - United States
T32 GM008268 NIGMS NIH HHS - United States

We report the generation of gas-phase riboguanosine radicals that were tagged at ribose with a fixed-charge 6-(trimethylammonium)hexane-1-aminocarbonyl group. The radical generation relied on electron transfer from fluoranthene anion to noncovalent dibenzocrown-ether dication complexes which formed nucleoside cation radicals upon one-electron reduction and crown-ether ligand loss. The cation radicals were characterized by collision-induced dissociation (CID), photodissociation (UVPD), and UV-vis action spectroscopy. Identification of charge-tagged guanosine radicals was challenging because of spontaneous dissociations by loss of a hydrogen atom and guanine that occurred upon storing the ions in the ion trap without further excitation. The loss of H proceeded from an exchangeable position on N-7 in guanine that was established by deuterium labeling and was the lowest energy dissociation of the guanosine radicals according to transition-state energy calculations. Rate constant measurements revealed an inverse isotope effect on the loss of either hydrogen or deuterium with rate constants kH = 0.25-0.26 s-1 and kD = 0.39-0.54 s-1. We used time-dependent density functional theory calculations, including thermal vibronic effects, to predict the absorption spectra of several protomeric radical isomers. The calculated spectra of low-energy N-7-H guanine-radical tautomers closely matched the action spectra. Transition-state-theory calculations of the rate constants for the loss of H-7 and guanine agreed with the experimental rate constants for a narrow range of ion effective temperatures. Our calculations suggest that the observed inverse isotope effect does not arise from the isotope-dependent differences in the transition-state energies. Instead, it may be caused by the dynamics of post-transition-state complexes preceding the product separation.

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Dougherty D; Younathan ES; Voll R; Abdulnur S; McGlynn SP Photoelectron Spectroscopy of Some Biological Molecules. J. Electron Spectr. Rel. Phenom 1978, 13, 370–393.

Xie H; Yang D; Heller A; Gao Z. Electrocatalytic Oxidation of Guanine, Guanosine, and Guanosine Monophosphate. Biophys. J 2007, 92, L70–L72. PubMed PMC

Seidel CAM; Schulz A; Sauer MHM Nucleobase-Specific Quenching of Fluorescent Dyes. 1. Nucleobase One-Electron Redox Potentials and Their Correlation with Static and Dynamic Quenching Efficiencies. J. Phys. Chem 1996, 100, 5541–5553.

Steenken S; Jovanovic SV How Easily Oxidizable Is DNA? One-Electron Reduction Potentials of Adenosine and Guanosine Radicals in Aqueous Solution. J. Am. Chem. Soc 1997, 119, 617–618.

Kanvah S; Joseph J; Schuster GB; Barnett RN; Cleveland CL; Landman U. Oxidation of DNA: Damage to Nucleobases. Acc. Chem. Res 2010, 43, 280–287. PubMed

Kino K; Hirao-Suzuki M; Morikawa M; Sakaga A; Miyazawa H. Generation, Repair and Replication of Guanine Oxidation Products. Genes Environ. 2017, 39, 21. PubMed PMC

Szyperska A; Rak J; Leszczynski J; Li X; Ko YJ; Wang H; Bowen KH Valence Anions of 9-Methylguanine-1-Methylcytosine Complexes. Computational and Photoelectron Spectroscopy Studies. J. Am. Chem. Soc 2009, 131, 2663–2669. PubMed

Hsing-Yin Chen H-Y; Kao C-L; Hsu SCN Proton Transfer in Guanine−Cytosine Radical Anion Embedded in B-Form DNA. J. Am. Chem. Soc 2009, 131, 15930–15938. PubMed

Liu Y; Korn JA; Dang A; Turecek F. Hydrogen-Rich Cation Radicals of DNA Dinucleotides. Generation and Structure Elucidation by UV-Vis Action Spectroscopy. J. Phys Chem. B 2018, 122, 9665–9680. PubMed

Coon JJ; Ueberheide B; Syka JEP; Dryhurst DD; Ausio J; Shabanowitz J; Hunt DF Protein Identification Using Sequential Ion/Ion Reactions and Tandem Mass Spectrometry. Proc. Natl. Acad. Sci. U. S. A 2005, 102, 9463–9468. PubMed PMC

Shaffer SA; Tureček F. Hydrogentrimethylammonium. A Marginally Stable Hypervalent Radical. J. Am. Chem. Soc 1994, 116, 8647–8653.

Frøsig L; Tureček F. Hypervalent Pyrrolidinium Radicals by Neutralization-Reionization Mass Spectrometry. Metastability and Radical Leaving Group Abilities. J. Am. Soc. Mass Spectrom 1998, 9, 242–254.

Dang A; Korn JA; Gladden J; Mozzone B; Tureček F. UV-Vis Photodissociation Action Spectroscopy on Thermo LTQ-XL ETD and Bruker amaZon Ion Trap Mass Spectrometers: A Practical Guide. J. Am. Soc. Mass Spectrom 2019, 30, 1558–1564. PubMed

Shaffer CJ; Andrikopoulos PC; Řezáč J; Rulíšek L; Tureček F. Efficient Covalent Bond Formation in Gas-Phase Peptide-Peptide Ion Complexes with the Photoleucine Stapler. J. Am. Soc. Mass Spectrom 2016, 27, 633–645. PubMed

Nguyen HTH; Andrikopoulos PC; Bím D; Rulíšek L; Dang A; Tureček F. Radical Reactions Affecting Polar Groups in Threonine Peptide Ions. J. Phys. Chem. B, 2017,121, 6557–6569. PubMed

Řezáč J; Fanfrlík J; Salahub D; Hobza P. Semi-Empirical Quantum Chemical PM6 Method Augmented by Dispersion and H Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes. J. Chem. Theory Comput 2009, 5, 1749–1760. PubMed

Berendsen HJ; Postma JV; van Gunsteren WF; DiNola ARHJ; Haak JR Molecular Dynamics with Coupling to an External Bath. J. Chem. Phys 1984, 81, 3684–3690.

Řezáč J. Cuby: An Integrative Framework for Computational Chemistry. J. Comput. Chem 2016, 37, 1230–1237. PubMed

Stewart JJP MOPAC 16. Stewart Computational Chemistry; Colorado Springs: CO, 2016.

Becke AD Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior. Phys. Rev. A 1988, 38, 3098–3100. PubMed

Robb MA; Cheeseman JR; Scalmani G; Barone V; Petersson GA; Nakatsuji H; Caricato M; Marenich AV; Bloino J; Janesko BG; Gomperts R; Mennucci B; Hratchian HP; Ortiz JV; Izmaylov AF; Sonnenberg JL; Williams-Young D; Ding F; Lipparini F; Egidi F; Goings J; Peng B; Petrone A; Henderson T; Ranasinghe D; Zakrzewski VG; Gao J; Rega N; Zheng G; Liang W; Hada M; Ehara M; Toyota K; Fukuda R; Hasegawa J; Ishida M; Nakajima T; Honda Y; Kitao O; Nakai H; Vreven T; Throssell K; Montgomery JA Jr.; Peralta JE; Ogliaro F; Bearpark MJ; Heyd JJ; Brothers EN; Kudin KN; Staroverov VN; Keith TA; Kobayashi R; Normand J; Raghavachari K; Rendell AP; Burant JC; Iyengar SS; Tomasi J; Cossi M; Millam JM; Klene M; Adamo C; Cammi R; Ochterski JW; Martin RL; Morokuma K; Farkas O; Foresman JB; Fox DJ Gaussian 16, Revision A03; Gaussian, Inc.: Wallingford, CT, 2016.

McClurg RB; Flagan RC; Goddard WA III.; The Hindered Rotor Density-of-States Interpolation Function. J. Chem. Phys 1997, 106, 6675–6680.

Zhao Y; Truhlar DG The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals. Theor. Chem. Acc 2008, 120, 215–241.

Furche F; Ahlrichs R. Adiabatic Time-Dependent Density Functional Methods for Excited State Properties. J. Chem. Phys 2002, 117, 7433–7447.

Huang SR; Tureček F. Cation Radicals of Hachimoji Nucleobases. Canonical Purine and Noncanonical Pyrimidine Forms Generated in the Gas Phase and Characterized by UV-Vis Photodissociation Action Spectroscopy. J. Phys. Chem. A 2020, 124, 7101–7112. PubMed

Huang SR; Dang A; Tureček F. Ground and Excited States of Gas-Phase DNA Nucleobase Cation-Radicals. A UV−Vis Photodisociation Action Spectroscopy and Computational Study of Adenine and 9-Methyladenine. J. Am. Soc. Mass Spectrom 2020. 31, 1271–1281. PubMed

Comeau DC; Bartlett RJ The Equation-of-Motion Coupled-Cluster Method. Applications to Open- and Closed-Shell Reference States. Chem. Phys. Lett 1993, 207, 414–423.

Wigner E. The Quantum Correction for Thermodynamic Equilibrium. Phys. Rev 1932, 40, 749–759.

Bonacic-Koutecky V; Mitric R. Theoretical Exploration of Ultrafast Dynamics in Atomic Clusters: Analysis and Control. Chem. Rev 2005, 105, 11–65. PubMed

Barbatti M; Ruckenbauer M; Plasser F; Pittner J; Granucci G; Persico M; Lischka H. Newton-X: A Surface-Hopping Program for Nonadiabatic Molecular Dynamics. Wiley Interdiscip. Rev. Comput. Mol. Sci 2014, 4, 26–33.

Korn JA; Urban J; Dang A; Nguyen HTH; Turecek F. UV-Vis Action Spectroscopy Reveals a Conformational Collapse in Hydrogen-Rich Dinucleotide Cation Radicals. J. Phys. Chem. Lett 2017, 8, 4100–4107. PubMed

Liu Y; Dang A; Urban J; Tureček F. Charge-Tagged DNA Radicals in the Gas Phase Characterized by UV-Vis Photodissociation Action Spectroscopy. Angew. Chem. Int. Ed. Engl 2020, 59, 7772–7777. PubMed

McClellan JE; Murphy III JP; Mulholland JJ; Yost RA Effects of Fragile Ions on Mass Resolution and on Isolation for Tandem Mass Spectrometry in the Quadrupole Ion Trap Mass Spectrometer. Anal. Chem 2002, 74, 402–412. PubMed

Swaney DL; McAlister GC; Wirtala M; Schwartz JC; Syka JEP; Coon JJ Supplemental Activation Method for Highly Efficient Electron Transfer Dissociation of Doubly Protonated Peptide Precursors. Anal. Chem 2007, 79, 477–485. PubMed PMC

Pepin R; Layton ED; Liu Y; Afonso C; Tureček F. Where Does the Electron Go? Stable and Metastable Peptide Cation Radicals Formed by Electron Transfer. J. Am. Soc. Mass Spectrom 2017. 28, 164–181. PubMed

Colominas C; Luque FJ; Orozco M. Tautomerism and Protonation of Guanine and Cytosine. Implications in the Formation of Hydrogen-Bonded Complexes. J. Am. Chem. Soc 1996, 118, 6811–6821.

Halder A; Bhattacharya S; Datta A; Bhattacharya D; Mitra A. The Role of N7 Protonation of Guanine in Determining the Structure, Stability and Function of RNA Base Pairs. Phys. Chem. Chem. Phys 2015, 17, 26249–26263. PubMed

Wu RR; Yang B; Berden G; Oomens J; Rodgers MT Gas-Phase Conformations and Energetics of Protonated 2-Deoxyguanosine and Guanosine: IRMPD Action Spectroscopy and Theoretical Studies. J. Phys. Chem. B 2014, 118, 14774–14784. PubMed

Karton A. Thermochemistry of Guanine Tautomers Re-​Examined by Means of High-​Level CCSD(T) Composite Ab Initio Methods. Austr. J. Chem 2019, 72, 607–613.

Hanus M; Ryjacek F; Kabelac M; Kubar T; Bogdan TV; Trygubenko SA; Hobza P. Correlated ab Initio Study of Nucleic Acid Bases and Their Tautomers in the Gas Phase, in a Microhydrated Environment and in Aqueous Solution. Guanine: Surprising Stabilization of Rare Tautomers in Aqueous Solution. J. Am. Chem. Soc 2003, 125, 7678–7688. PubMed

Sponer J; Hobza P. Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies. Coll. Czech. Chem. Commun 2003, 68, 2231–2282.

Goeringer DE; McLuckey SA Evolution of Ion Internal Energy during Collisional Excitation in the Paul Ion Trap: A Stochastic Approach. J. Chem. Phys 1996, 104, 2214–2221. 815

Gronert S. Estimation of Effective Ion Temperatures in a Quadrupole Ion Trap. J. Am. Soc. Mass Spectrom 1998, 9, 845–848.

Lovejoy ER; Wilson RR Kinetic Studies of Negative Ion Reactions in a Quadrupole Ion Trap: Absolute Rate Coefficients and Ion Energies. J. Phys. Chem. A 1998, 102, 2309–2315.

Donald WA; Khairallah GN; O’Hair RAJ The Effective Temperature of Ions Stored in a Linear Quadrupole Ion Trap Mass Spectrometer. J. Am. Soc. Mass Spectrom. 2013, 24, 811–815. PubMed

Parkin G. Temperature-Dependent Transitions Betweem Normal and Inverse Isotope Effects Pertaining to the Interaction of H-H and C-H Bonds with Transition Metal Centers. Acc. Chem. Res 2009, 42, 315–325. PubMed

Cheng TY; Bullock RM Isotope Effects on Hydride Transfer Reactions from Transition Metal Hydrides to Trityl Cation. An Inverse Isotope Effect for a Hydride Transfer. J. Am. Chem. Soc 1999, 121, 3150–3155.

Jones WD Isotope Effects in C-H Bond Activation Reactions by Transition Metals. Acc. Chem. Res 2003, 36, 140–146. PubMed

Petralia LS; Tsikritea A; Loreau J; Softley TP; Heazlewood BR Strong Inverse Kinetic Isotope Effect Observed in Ammonia Charge Exchange Reactions. Nature Commun. 2020, 11, 173. PubMed PMC

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