Photoelectron Spectroscopy and Theoretical Investigations of Gaseous Doubly Deprotonated 2’-Deoxynucleoside 5’-Monophosphate Dianions

Yuan, Qinqin; Chomicz-Manka, Lidia; Makurat, Samanta; Cao, Wenjin; Rak, Janusz; Wang, Xue-Bin

doi:10.1021/acs.jpclett.1c02678

Photoelectron Spectroscopy and Theoretical Investigations of Gaseous Doubly Deprotonated 2’-Deoxynucleoside 5’-Monophosphate Dianions

Journal Article · 07 October 2021 · The Journal of Physical Chemistry Letters

DOI:https://doi.org/10.1021/acs.jpclett.1c02678· OSTI ID:1829810

Yuan, Qinqin ^[1]; Chomicz-Manka, Lidia ^[2]; Makurat, Samanta ^[2]; Cao, Wenjin ^[1]; Rak, Janusz ^[2]; ^[1]

BATTELLE (PACIFIC NW LAB)
University of Gdansk

This work reports a systematic photoelectron spectroscopy and theoretical investigation on the electronic and geometric structures of four doubly deprotonated 2’-deoxynucleoside 5’-monophosphate dianions, the smallest quintessential DNA building block. These dianions are intrinsically stable with their adiabatic/vertical detachment energies (ADE/VDE) ranging from 0.85/1.07 (A), 1.05/1.30 (G) to 1.20/1.50 (C) and 1.80/2.10 eV (T). The repulsive Coulomb barrier against electron detachment is 2.0 eV for purines and 2.5 eV for pyrimidines. Dianions are deprotonated at the phosphate group and the amino group of a nucleobase. The calculated ADE/VDE values, as well as the simulated spectrum, agree well with the experimental results. The ?-type HOMO orbital resides on the nucleobase moiety for each dianion. This spatial distribution of HOMO suggests that the most loosely bound electron is detached along the direction perpendicular to the nucleobase. When combined with the previous results this work makes complete the depiction of basic building blocks of DNA at the molecular level.

Research Organization:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1829810

Report Number(s):: PNNL-SA-165708

Journal Information:: The Journal of Physical Chemistry Letters, Vol. 12, Issue 39

Country of Publication:: United States

Language:: English

References (40)

LASER-INDUCED STRAND BREAK FORMATION IN DNA and POLYNUCLEOTIDES No authors listed Photochemistry and Photobiology https://doi.org/10.1111/j.1751-1097.1990.tb08453.x		December 1990
Photolysis of polycytidylic acid on 193 nm laser excitation No authors listed Journal of Photochemistry and Photobiology A: Chemistry https://doi.org/10.1016/1010-6030(93)85067-I		April 1993
Induction of Strand Breaks in Single-Stranded Polyribonucleotides and DNA by Photoionization: One Electron Oxidized Nucleobase Radicals as Precursors No authors listed Journal of the American Chemical Society https://doi.org/10.1021/ja961722m		January 1996
Charge Hopping in DNA No authors listed Journal of the American Chemical Society https://doi.org/10.1021/ja001496n		January 2001
Oxidative DNA damage through long-range electron transfer No authors listed Nature https://doi.org/10.1038/382731a0		August 1996
Conduction-band-edge ionization thresholds of DNA components in aqueous solution No authors listed Proceedings of the National Academy of Sciences https://doi.org/10.1073/pnas.95.10.5550		May 1998
Direct experimental observation of the low ionization potentials of guanine in free oligonucleotides by using photoelectron spectroscopy No authors listed Proceedings of the National Academy of Sciences https://doi.org/10.1073/pnas.0405157101		December 2004
Base-Specific Ionization of Deprotonated Nucleotides by Resonance Enhanced Two-Photon Detachment No authors listed The Journal of Physical Chemistry A https://doi.org/10.1021/jp4041315		May 2013
Base and Phosphate Electron Detachment Energies of Deoxyribonucleotide Anions No authors listed Journal of the American Chemical Society https://doi.org/10.1021/ja064621p		October 2006
Determination of the Electron-Detachment Energies of 2′-Deoxyguanosine 5′-Monophosphate Anion: Influence of the Conformation No authors listed The Journal of Physical Chemistry B https://doi.org/10.1021/jp806105h		January 2009
Infrared Multiple Photon Dissociation Action Spectroscopy of Deprotonated DNA Mononucleotides: Gas-Phase Conformations and Energetics No authors listed The Journal of Physical Chemistry A https://doi.org/10.1021/jp3077936		October 2012
Time-resolved photoelectron imaging of the isolated deprotonated nucleotides No authors listed Chem. Sci. https://doi.org/10.1039/C4SC01493F		January 2014
Mapping the Ultrafast Dynamics of Adenine onto Its Nucleotide and Oligonucleotides by Time-Resolved Photoelectron Imaging No authors listed The Journal of Physical Chemistry Letters https://doi.org/10.1021/jz500264c		February 2014
Gas-Phase Femtosecond Particle Spectroscopy: A Bottom-Up Approach to Nucleotide Dynamics No authors listed Annual Review of Physical Chemistry https://doi.org/10.1146/annurev-physchem-040215-112428		May 2016
Ultrafast Dynamics of the Isolated Adenosine-5′-triphosphate Dianion Probed by Time-Resolved Photoelectron Imaging No authors listed The Journal of Physical Chemistry A https://doi.org/10.1021/acs.jpca.1c01646		April 2021
Ionization Energies of the Nucleotides No authors listed The Journal of Physical Chemistry A https://doi.org/10.1021/jp805308p		October 2008
Photoelectron spectroscopy of the parent anions of the nucleotides, adenosine-5′-monophosphate and 2′deoxyadenosine-5′-monophosphate No authors listed The Journal of Chemical Physics https://doi.org/10.1063/1.2823001		January 2008
Barrier-free proton transfer in the valence anion of 2′-deoxyadenosine-5′-monophosphate. II. A computational study No authors listed The Journal of Chemical Physics https://doi.org/10.1063/1.2823002		January 2008
Fraying and electron autodetachment dynamics of trapped gas phase oligonucleotides No authors listed Journal of the American Society for Mass Spectrometry https://doi.org/10.1016/S1044-0305(03)00578-6		December 2003
193 nm photodissociation of larger multiply-charged biomolecules No authors listed International Journal of Mass Spectrometry and Ion Processes https://doi.org/10.1016/S0168-1176(96)04399-6		December 1996
Electron Photodetachment Dissociation of DNA Polyanions in a Quadrupole Ion Trap Mass Spectrometer No authors listed Analytical Chemistry https://doi.org/10.1021/ac060753p		September 2006
Photoelectron Spectroscopy of Isolated Multiply Negatively Charged Oligonucleotides No authors listed Journal of the American Chemical Society https://doi.org/10.1021/ja049736c		July 2004
Isomer-Selected Photoelectron Spectroscopy of Isolated DNA Oligonucleotides: Phosphate and Nucleobase Deprotonation at High Negative Charge States No authors listed Journal of the American Chemical Society https://doi.org/10.1021/ja300619j		April 2012
Spectroscopic and theoretical investigations of adenosine 5′-diphosphate and adenosine 5′-triphosphate dianions in the gas phase No authors listed Phys. Chem. Chem. Phys. https://doi.org/10.1039/C2CP43808A		January 2013
Structural characterization of nucleotide 5′-triphosphates by infrared ion spectroscopy and theoretical studies No authors listed Physical Chemistry Chemical Physics https://doi.org/10.1039/C8CP03314E		January 2018
Site-Specific Photo-oxidation of the Isolated Adenosine-5′-triphosphate Dianion Determined by Photoelectron Imaging No authors listed The Journal of Physical Chemistry Letters https://doi.org/10.1021/acs.jpclett.0c02089		September 2020
Photoexcitation of Adenosine 5′-Triphosphate Anions in Vacuo: Probing the Influence of Charge State on the UV Photophysics of Adenine No authors listed The Journal of Physical Chemistry B https://doi.org/10.1021/acs.jpcb.7b03435		May 2017
Cryogenic and temperature-dependent photoelectron spectroscopy of metal complexes No authors listed International Reviews in Physical Chemistry https://doi.org/10.1080/0144235X.2020.1719699		January 2020
cclib: A library for package-independent computational chemistry algorithms No authors listed Journal of Computational Chemistry https://doi.org/10.1002/jcc.20823		January 2008
Ionization Energies of Aqueous Nucleic Acids: Photoelectron Spectroscopy of Pyrimidine Nucleosides and ab Initio Calculations No authors listed Journal of the American Chemical Society https://doi.org/10.1021/ja8091246		May 2009
Ionization of Purine Tautomers in Nucleobases, Nucleosides, and Nucleotides: From the Gas Phase to the Aqueous Environment No authors listed The Journal of Physical Chemistry B https://doi.org/10.1021/jp110388v		February 2011
Photoelectron Spectroscopy of Multiply Charged Anions No authors listed Annual Review of Physical Chemistry https://doi.org/10.1146/annurev.physchem.59.032607.093724		May 2009
Probing Free Multiply Charged Anions Using Photodetachment Photoelectron Spectroscopy No authors listed The Journal of Physical Chemistry A https://doi.org/10.1021/jp9940093		March 2000
Photoelectron spectroscopy of hexachloroplatinate-nucleobase complexes: Nucleobase excited state decay observed via delayed electron emission No authors listed The Journal of Chemical Physics https://doi.org/10.1063/1.4935171		November 2015
Electron Detachment as a Probe of Intrinsic Nucleobase Dynamics in Dianion-Nucleobase Clusters: Photoelectron Spectroscopy of the Platinum II Cyanide Dianion Bound to Uracil, Thymine, Cytosine, and Adenine No authors listed The Journal of Physical Chemistry B https://doi.org/10.1021/acs.jpcb.5b07108		August 2015
A benchmark photoelectron spectroscopic and theoretical study of the electronic stability of [B ₁₂ H ₁₂ ] ²⁻ No authors listed The Journal of Chemical Physics https://doi.org/10.1063/1.5089510		April 2019
Electronic Structure and Stability of [B ₁₂ X ₁₂ ] ^2– (X = F–At): A Combined Photoelectron Spectroscopic and Theoretical Study No authors listed Journal of the American Chemical Society https://doi.org/10.1021/jacs.7b08598		October 2017
Properties of gaseous closo -[B ₆ X ₆ ] ²⁻ dianions (X = Cl, Br, I) No authors listed Physical Chemistry Chemical Physics https://doi.org/10.1039/D0CP02581J		January 2020
Gas-Phase Conformations of Deprotonated and Protonated Mononucleotides Determined by Ion Mobility and Theoretical Modeling No authors listed The Journal of Physical Chemistry B https://doi.org/10.1021/jp035894z		November 2003
Ionization potentials and donor properties of nucleic acid bases and related compounds No authors listed Chemical Physics Letters https://doi.org/10.1016/0009-2614(75)80190-4		July 1975

Similar Records

Guanosine Dianions Hydrated by One to Four Water Molecules

Journal Article · 2022 · Journal of Physical Chemistry Letters · OSTI ID:1867366

Makurat, Samanta; Yuan, Qinqin; Czub, Jacek; +4 more

Can an Excess Electron Localise on a Purine Moiety in the Adenine-thymine Watson-Crick Base Pair? A Computational Study

Journal Article · 2007 · International Journal of Quantum Chemistry, 107(12):2224-2232 · OSTI ID:1012313

Mazurkiewicz, Kamil; Haranczyk, Maciej; Gutowski, Maciej S; +1 more

Electron Detachment as a Probe of Intrinsic Nucleobase Dynamics in Dianion-Nucleobase Clusters: Photoelectron Spectroscopy of the Platinum II Cyanide Dianion Bound to Uracil, Thymine, Cytosine and Adenine

Journal Article · 2015 · Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry · OSTI ID:1243268

Sen, Ananya; Hou, Gao-Lei; Wang, Xue B.; +1 more

Photoelectron Spectroscopy and Theoretical Investigations of Gaseous Doubly Deprotonated 2’-Deoxynucleoside 5’-Monophosphate Dianions

Citation Formats

References (40)

Similar Records

Related Subjects