Jianbo Liu Department of Chemistry & Biochemistry Queens - PowerPoint PPT Presentation

Jianbo Liu Department of Chemistry & Biochemistry Queens College and the Graduate Center of the City University of New York 08/23/2018

Singlet O 2 and DNA damage https://nasa.tumblr.com/post/151016092994/why-sequencing-dna-in-space-is-a-big-deal Guanine is the exclusive DNA target for 1 O 2 • Mutation such as G-C  A-T transversion • DNA-protein cross-link Cell death • 2

Guanine oxidation mechanism and questions OH OH HO OH H HOOC H H O (1) Sheu, C.; Foote, C. S. J. Am. Chem. Soc. 1993, 115 , 10446- N N N -CO 2 N NH NH 2 O O O 10447; (2) Ye, Y.; Muller, J. G.; Luo, W.; Mayne, C. L.; Shallop, A. J.; N H 2 N N H 2 N N N N H 2 N N H Jones, R. A.; Burrows, C. J. J. Am. Chem. Soc. 2003, 125 , 13926- dR dR dR gem -diol 4-carboxydGh dGh 13927; (3) McCallum, J. E. B.; Kuniyoshi, C. Y.; Foote, C. S. J. Am. pH < 7 +H 2 O Chem. Soc. 2004, 126 , 16777-16782; (4) Cadet, J.; Ravanat, J.-L.; O O O O O OH OO Martinez, G. R.; Medeiros, M. H. G.; Mascio, P. D. Photochem. 7 major in H 1 5 N N N N 1 O 2 free dGuo +H 2 O pH > 7 N NH N HN HN N N 6 H Photobiol. 2006, 82 , 1219-1225;(5) Neeley, W. L.; Essigmann, J. M. HN OOH O O 8 -H 2 O acyl shift N N N N N N H 2 N N O H 2 N N H 2 N N H 2 N 2 3 H 2 N N O Chem. Res. Toxicol. 2006, 19 , 491-505; (6) Fleming, A. M.; Burrows, H O 4 N 9 dR dR dR H 2 N N dR dR endoperoxide 8-OOHdGuo OdGuo ox 5-OHOdGuo dSp C. J. Free Radic. Biol. Med. 2017, 107 , 35-52. dR dGuo major red. red. in DNA dR=2'-deoxyribose O O O OOH H H O H H O N N 1 O 2 N N -CO 2 NH HN HN N O O O O O N N N N H 2 N H 2 N N H 2 N N H 2 N N N dR dR dR dR dGh ox OdGuo dioxetane 5-OOHOdGuo Q1 Reaction intermediate NMR of photooxidation of a model compound at -78  C , C. Sheu and C. Foote, JACS , 1993, 115, 10446 Q2 Concerted OR stepwise O 2 addition R Grüber, A Monari, E. Dumont, JPC A, 2014, 118, 11612 Q3 Activation barrier and kinetics 3

A approach different than solution ‐ phase photooxidation Collisions of single biomolecule with 1 O 2 in the gas phase 1 O 2 mass spectrometry computation electronic structure products m/z and calculations s tructure by MS, MS 2 reaction PES and capture transient statistical properties intermediates intrinsic reactivity: direct dynamics energy dependence, simulation activation barriers, etc. 4

Guided ‐ Ion ‐ Beam Tandem Mass Spectrometer I k T    product B k / v rel I P l reac tan t cell cell 2. Ions are passed into a quadrupole for mass selection 1. Generation of biomolecular ions by ESI Hexapole Quadrupole Octopole ion guide 2nd quadrupole ESI source ion guide mass filter & Scattering cell mass filter & Detector ESI HV 3. Mass-selected ions are guided into an 4. Product ions are m/z octopole surrounded by a collision cell, and analyzed & counted scattered from 1 O 2 contained within 5 Y. Fang and J. Liu, JPC A. 2009, 113, 11250-11261

1. What we wanted to do first was to capture reaction intermediates k 1 k 2 k 10 k 8 k 4 k 3 k 9 k 14 k 11 k 7 k 12 k 13 k 15 k 5 k 6 6

Protonated Deprotonated [G + H] + [G ‐ H] ‐ 7

RRKM analysis and implications Estimate unimolecular k 0.2 eV using RRKM theory k 1 k 2 k 10 k 8 k 4 k 3 k 9 k 14 k 11 k 7 k 12 k 13 k 15 k 5 k 6 t =10 μ s (time of flight)  = 20 ns 8

Direct dynamics simulation of guanine ion ‐ beam scattering simulated at B3LYP/6-31G* Form a 5,8-endoperoxide rather than a 4,8-endoperoxide that was proposed for neutral guanosine 9

Reactions of 1 O 2 with [G + H] + (H 2 O) and [G ‐ H] ‐ (H 2 O) Capture of transient endoperoxides via water evaporation cooling Experimental assessment of the activation barrier associated with O 2 addition to guanine Wenchao Lu and J. Liu, Chem. Eur. J. , 2016, 22, 3127-3138 10

2. More about O 2 addition mechanism:  A model study using 9MG Guanine base Guanosine 1.5 a) b) - (H 2 O) + (H 2 O) [9MG - H] [9MG + H] 182 184 Cross Section (Å 2 ) product ion 1.0 product ion 196 198 ( x 1000) ( x 1000) 180 185 190 195 200 180 185 190 195 200 0.5 m/z m/z 0.0 [9MG + H] + (H 2 O) + 1 O 2 [9MG - H] - (H 2 O) + 1 O 2 [G + H] + (H 2 O) + 1 O 2 [G - H] - (H 2 O) + 1 O 2 Efficiency % 2 1 0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 CH 3 Collision Energy (eV) Collision Energy (eV) 9-Methylguanine (9MG) has similar hydration, ionization, pK a and reaction  H as guanosine Wenchao Lu, Huayu Teng, and J. Liu, PCCP , 2016, 18 , 15223-15234 11

pH ‐ dependent 1 O 2 addition [9MG + H] + and [G + H] + : a concerted cycloaddition to a 5,8-endoperoxide, different than neutral guanosine which leads to a 4,8-endoperoixde 12

Switches to stepwise addition upon deprotonation [9MG – H] ‐ + 1 O 2 : 1) Different than neutral guanosine in a stepwise addition 2) Different than [9MG + H] + in 4,8 ‐ OO ‐ [9MG – H] ‐ vs. 5,8 ‐ OO ‐ 9MG + H] + 13

3. From gas ‐ phase dynamics to solution ‐ phase kinetics and product distributions Fangwei Liu, Wenchao Lu, Vincent Yin, and J. Liu, J. Am. Soc. Mass. Spec. , 2016, 27, 59-72. 14

Kinetics of 9MG + 1 O 2 pH = 10 pH = 7 9MSp : ( gem ‐ 9Mdiol + 9MGh) : (9MOG + 9MGh ox ) 9MSp : ( gem ‐ 9Mdiol + 9MGh) : 9MGh ox 0.45 0.33 0.22 0.72 0.09 0.19 15

Solution ‐ phase PES & kinetics k 1 k 2 k 3 k 4 k 5 k 6 k 7 k 8 k -1 k -2 fast pH 3 pH 7 pH 10 SMD ‐ wB97XD/aug ‐ cc ‐ pVQZ//SMD ‐ wB97XD/6 ‐ 31+G(d,p)  Deprotonated guanine favors formation of Sp.  Oxidation of protonated guanine is blocked by early ‐ stage barriers.  Initial 1 O 2 addition is is ra rate te ‐ lim limitin iting. g. 16

Oxidation rate constant � d � [9MG – H] – � – � [9MG – H] – � [ 1 O 2 ] = k 1 d t product i ➖ [ 1 O 2 ] ave  t ln [9MG – H] ➖ Σ i ( reactant + product i ) = – k 1 t % = - = 4.9  10 7 M ‒ 1  s ‒ 1 K 1 Wenchao Lu, Yan Sun, Wenjing Zhou, and J Liu, JPC B, 2018, 122 , 40-53 17

Summary Guided by PES, kinetics & dynamics simulation Gas-phase scattering probed early-stage dynamics & intermediates that is missing in condensed phase study Solution-phase MS & spectroscopy measured late-stage kinetics & product distributions Gas phase Aqueous solution 1 O 2 addition Intermediates Efficiency End products k 1 none protonated concerted 5,8-endoperoxide 1.3% pH 3 — 9MSp, gem ‐ 9Mdiol, 1.2 × 10 6 M ‐ 1  s ‐ 1 neutral — pH 7 9MGh, 9MGh ox stepwise 4,8-endoperoxide 9MSp, gem ‐ 9Mdiol, 4.6 × 10 7 M ‐ 1  s ‐ 1 deprotonated 1.7% pH 10 9MGh, 9MGh ox , 9MOG

Acknowledgements Dr. Wenchao Lu Yan Sun Maida Tsai (collaborator, CUNY LGCC) Wenjing Zhou Bilal Karatash Research CHE-1464171 PSC Enhancement Funds Research Awards