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Nichols CM, Wang ZC, Lineberger WC, Bierbaum VM. Gas-Phase Reactions of Deprotonated Nucleobases with H, N, and O Atoms. J Phys Chem Lett 2019; 10:4863-4867. [PMID: 31407903 DOI: 10.1021/acs.jpclett.9b01997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Complex organic molecules, the hallmark of terrestrial life, are increasingly detected in exotic environments throughout the universe. Our studies probe the ion chemistry of these biomolecules. We report gas-phase reaction rate constants for five deprotonated nucleobases (adenine, cytosine, guanine, thymine, and uracil) reacting with the atomic species H, N, and O. Hydrogen atoms react at moderate rates via associative electron detachment. Oxygen atom reactions occur more rapidly, generating complex product distributions; reaction pathways include associative electron detachment, substitution of the hydrogen atom by an oxygen atom, and generation of OCN-. Nitrogen atoms do not react with the nucleobase anions. The reaction thermodynamics were investigated computationally, and reported product channels are exothermic. Many of the proposed products have been observed in various astrochemical environments. These reactions provide insight into chemical processes that may occur at the boundaries between diffuse and dense interstellar clouds and in complex extraterrestrial ionospheres.
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Affiliation(s)
- Charles M Nichols
- Department of Chemistry and JILA, University of Colorado, Boulder, Colorado 80309, United States
| | - Zhe-Chen Wang
- Department of Chemistry and JILA, University of Colorado, Boulder, Colorado 80309, United States
| | - W Carl Lineberger
- Department of Chemistry and JILA, University of Colorado, Boulder, Colorado 80309, United States
| | - Veronica M Bierbaum
- Department of Chemistry and JILA, University of Colorado, Boulder, Colorado 80309, United States
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2
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Ilyina MG, Khamitov EM, Mustafin AG, Khursan SL. A theoretical quantitative estimation of acidity of uracil and its derivatives through the p
K
a
values. J CHIN CHEM SOC-TAIP 2018. [DOI: 10.1002/jccs.201800087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Margarita G. Ilyina
- Department of ChemistryBashkir State University Ufa Russia
- Laboratory of Quantum Chemistry and Molecular Dynamics of the Department of Chemistry and TechnologyInstitute of Petroleum Refining and Petrochemistry Ufa Russia
| | - Edward M. Khamitov
- Department of ChemistryBashkir State University Ufa Russia
- Laboratory of Quantum Chemistry and Molecular Dynamics of the Department of Chemistry and TechnologyInstitute of Petroleum Refining and Petrochemistry Ufa Russia
- Russian Academy of Sciences, Laboratory of Chemical PhysicsUfa Institute of Chemistry Ufa Russia
| | - Akhat G. Mustafin
- Department of ChemistryBashkir State University Ufa Russia
- Russian Academy of Sciences, Laboratory of Chemical PhysicsUfa Institute of Chemistry Ufa Russia
| | - Sergey L. Khursan
- Russian Academy of Sciences, Laboratory of Chemical PhysicsUfa Institute of Chemistry Ufa Russia
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3
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Lu W, Liu J. Deprotonated guanine·cytosine and 9-methylguanine·cytosine base pairs and their "non-statistical" kinetics: a combined guided-ion beam and computational study. Phys Chem Chem Phys 2018; 18:32222-32237. [PMID: 27849082 DOI: 10.1039/c6cp06670d] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a guided-ion beam mass spectrometric study on collision-induced dissociation (CID) of deprotonated guanine(G)·cytosine(C) base pairs and their 9-methylguanine (9MG) analogue with Xe, including measurements of product cross sections as a function of collision energy and determination of dissociation thresholds. DFT, RI-MP2 and DLPNO-CCSD(T) calculations and Rice-Ramsperger-Kassel-Marcus (RRKM) modeling were performed to elucidate structures and kinetics. The experiment and theoretical study have provided considerable insight into tautomerization, intra-base-pair proton transfer and dissociation of deprotonated G·C and 9MG·C. In contrast to the previously reported lowest-energy deprotonated base pair structure G·[C-H1]- that consists of H-bonded neutral guanine and N1-deprotonated cytosine, we found that proton transfer from guanine N1 to cytosine N3 within G·[C-H1]- (or 9MG·[C-H1]-) leads to another slightly more stable conformer denoted as G·[C-H1]-_PT1 (or 9MG·[C-H1]-_PT1). The conventional (non-proton-transferred) and the proton-transferred conformers are close in energy and interconvert quickly, but they can be distinguished by dissociation products. The conventional structure dissociates into deprotonated cytosine and neutral guanine, while the other dissociates into deprotonated guanine and neutral cytosine. The two dissociation asymptotes have similar threshold energies, but surprisingly the CID product mass spectra of deprotonated G·C and 9MG·C are both overwhelmingly dominated by deprotonated G or 9MG, with their branching ratios greater than RRKM predictions by one to two orders of magnitude. The proton-transferred structures of deprotonated base pairs and the "unexpected" non-statistical kinetics provide new leads for understanding purine-pyrimidine interactions, forming rare nucleobase tautomers, and base pair opening.
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Affiliation(s)
- Wenchao Lu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. and Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. and Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
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4
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Ilyina MG, Khamitov EM, Ivanov SP, Mustafin AG, Khursan SL. Theoretical Models for Quantitative Description of the Acid-Base Equilibria of the 5,6-Substituted Uracils. J Phys Chem A 2018; 122:341-349. [PMID: 29215882 DOI: 10.1021/acs.jpca.7b09330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The acidities of 18 5,6-substituted uracils have been numerically estimated as pKa values in terms of three theoretical models. The first scheme includes the calculation of the gas-phase acidity of uracil with the G3MP2B3 method and taking into account the solvent effect using the polarizable continuum approximation PCM(SMD)-TPSS/aug-cc-pVTZ. The second model is one step and implies calculation of the free Gibbs energies of the hydrate complex of uracil (and its anion) with 5 water molecules by the TPSS/aug-cc-pVTZ method. This model accounts for the solvent effect corresponding to both specific and nonspecific solvation. The third scheme required high time and computational resources and includes the strong features of the two previous schemes. Here, the theoretical estimation of pKa is performed by the CBS-QB3 composite method. As in the second approach, both specific (as pentahydrate) and nonspecific solvent effects are determined. We have analyzed the advantages and model restrictions of the considered schemes for the pKa calculations. All models have systematic errors, which have been corrected with the linear empirical regression relations. In the presented model, the absolute mean deviations of the pKa values of uracils dissociating via the N1-H bonds diminish to 0.25, 0.28, and 0.23 pKa units (respectively, for I, II, and III models), which corresponds to ∼0.3 kcal/mol on the energy scale. The applicability of our computational schemes to uracils dissociating via N3-H, O-H (orotic acids) and C-H bonds is discussed.
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Affiliation(s)
- Margarita G Ilyina
- Department of Physical Chemistry and Chemical Ecology, Bashkir State University Chemical Faculty , 32 Zaki Validi Street, Ufa 450074, Russia.,Laboratory of Quantum Chemistry and Molecular Dynamics of the Department of Chemistry and Technology, Institute of Petroleum Refining and Petrochemistry , 12 Initsiativnaya Street, Ufa 450065, Republic of Bashkortostan, Russia
| | - Edward M Khamitov
- Department of Physical Chemistry and Chemical Ecology, Bashkir State University Chemical Faculty , 32 Zaki Validi Street, Ufa 450074, Russia.,Ufa Institute of Chemistry, Russian Academy of Sciences, Laboratory of Chemical Physics , 69 Prospekt Oktyabrya, Ufa 450054, Russia.,Laboratory of Quantum Chemistry and Molecular Dynamics of the Department of Chemistry and Technology, Institute of Petroleum Refining and Petrochemistry , 12 Initsiativnaya Street, Ufa 450065, Republic of Bashkortostan, Russia
| | - Sergey P Ivanov
- Ufa Institute of Chemistry, Russian Academy of Sciences, Laboratory of Chemical Physics , 69 Prospekt Oktyabrya, Ufa 450054, Russia
| | - Akhat G Mustafin
- Department of Physical Chemistry and Chemical Ecology, Bashkir State University Chemical Faculty , 32 Zaki Validi Street, Ufa 450074, Russia.,Ufa Institute of Chemistry, Russian Academy of Sciences, Laboratory of Chemical Physics , 69 Prospekt Oktyabrya, Ufa 450054, Russia
| | - Sergey L Khursan
- Ufa Institute of Chemistry, Russian Academy of Sciences, Laboratory of Chemical Physics , 69 Prospekt Oktyabrya, Ufa 450054, Russia
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Ilyina MG, Khamitov EM, Mustafin AG, Khursan SL. Controlled stabilization of anionic forms of the uracil derivatives: A DFT study. J Mol Graph Model 2017; 79:65-71. [PMID: 29145035 DOI: 10.1016/j.jmgm.2017.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 11/29/2022]
Abstract
Relative stabilities of the N1/N3/О5/О6 anions of 42 substituted uracils in gas phase and aqueous solutions have been theoretically studied using approximation IEFPCM (SMD) - TPSS/aug-cc-pVTZ. The specific solvation of uracil and its anions has been simulated with the first hydrate shell made up with 5 water molecules. The nonspecific solvation has been accounted in terms of the SMD model. We have found a series of relative stability under conditions of both specific and nonspecific hydration. The series is ranked according to the increase of the relative stability of the N3 anion. In gas phase, the N1 anion is significantly more stable than its N3 counterpart: the ΔGgas values vary in the range from 19.54 (5OH6СН3U) to 83.14 (5NO26NH2U) kJ/mol that is caused by a more effective delocalization of the excess charge through the uracil framework in the N1 anion. The hydration pronouncedly diminishes ΔG to the range from -0.02 (5OH6СН3U) to 38.16 (5Br6NO2U) kJ/mol due to the fact that the polar solvent is prone to stabilize more polar anionic states of uracils. Therefore, less polar uracil anions are more stable. We have defined the main factor influencing the N1/N3/О5/О6 distribution of anions, viz. the presence of the substituents in 5 and 6 positions of the pyrimidine ring. Herewith, the most favorable mechanism of the influence of 5-substituents has been previously defined as resonant whereas, as we found in this work, the inductive mechanism is more pronounced in the case of 6-substituents.
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Affiliation(s)
- Margarita G Ilyina
- Bashkir State University, Department of Chemistry, Chair of Physical Chemistry and Chemical Ecology, 32 Zaki Validi Str., Ufa 450074, Russia; Institute of Petroleum Refining and Petrochemistry, Laboratory of Quantum Chemistry and Molecular Dynamics of the Department of Chemistry and Technology, 12 Initsiativnaya Str., Ufa 450065, Republic of Bashkortostan, Russia.
| | - Edward M Khamitov
- Bashkir State University, Department of Chemistry, Chair of Physical Chemistry and Chemical Ecology, 32 Zaki Validi Str., Ufa 450074, Russia; Ufa Institute of Chemistry, Russian Academy of Sciences, Laboratory of Chemical Physics, 69 Prospekt Oktyabrya, Ufa 450054, Russia; Institute of Petroleum Refining and Petrochemistry, Laboratory of Quantum Chemistry and Molecular Dynamics of the Department of Chemistry and Technology, 12 Initsiativnaya Str., Ufa 450065, Republic of Bashkortostan, Russia
| | - Akhat G Mustafin
- Bashkir State University, Department of Chemistry, Chair of Physical Chemistry and Chemical Ecology, 32 Zaki Validi Str., Ufa 450074, Russia; Ufa Institute of Chemistry, Russian Academy of Sciences, Laboratory of Chemical Physics, 69 Prospekt Oktyabrya, Ufa 450054, Russia
| | - S L Khursan
- Ufa Institute of Chemistry, Russian Academy of Sciences, Laboratory of Chemical Physics, 69 Prospekt Oktyabrya, Ufa 450054, Russia
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6
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Ilyina MG, Khamitov EM, Ivanov SP, Mustafin AG, Khursan SL. Anions of uracils: N1 or N3? That is the question. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2015.12.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Minaev BF, Shafranyosh MI, Svida YY, Sukhoviya MI, Shafranyosh II, Baryshnikov GV, Minaeva VA. Fragmentation of the adenine and guanine molecules induced by electron collisions. J Chem Phys 2015; 140:175101. [PMID: 24811665 DOI: 10.1063/1.4871881] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Secondary electron emission is the most important stage in the mechanism of radiation damage to DNA biopolymers induced by primary ionizing radiation. These secondary electrons ejected by the primary electron impacts can produce further ionizations, initiating an avalanche effect, leading to genome damage through the energy transfer from the primary objects to sensitive biomolecular targets, such as nitrogenous bases, saccharides, and other DNA and peptide components. In this work, the formation of positive and negative ions of purine bases of nucleic acids (adenine and guanine molecules) under the impact of slow electrons (from 0.1 till 200 eV) is studied by the crossed electron and molecular beams technique. The method used makes it possible to measure the molecular beam intensity and determine the total cross-sections for the formation of positive and negative ions of the studied molecules, their energy dependences, and absolute values. It is found that the maximum cross section for formation of the adenine and guanine positive ions is reached at about 90 eV energy of the electron beam and their absolute values are equal to 2.8 × 10(-15) and 3.2 × 10(-15) cm(2), respectively. The total cross section for formation of the negative ions is 6.1 × 10(-18) and 7.6 × 10(-18) cm(2) at the energy of 1.1 eV for adenine and guanine, respectively. The absolute cross-section values for the molecular ions are measured and the cross-sections of dissociative ionization are determined. Quantum chemical calculations are performed for the studied molecules, ions and fragments for interpretation of the crossed beams experiments.
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Affiliation(s)
- B F Minaev
- Bohdan Khmelnitsky National University, 18031 Cherkasy, Ukraine
| | | | - Yu Yu Svida
- Uzhgorod National University, 88000 Uzhgorod, Ukraine
| | - M I Sukhoviya
- Uzhgorod National University, 88000 Uzhgorod, Ukraine
| | | | - G V Baryshnikov
- Bohdan Khmelnitsky National University, 18031 Cherkasy, Ukraine
| | - V A Minaeva
- Bohdan Khmelnitsky National University, 18031 Cherkasy, Ukraine
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8
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Huang DL, Liu HT, Ning CG, Zhu GZ, Wang LS. Probing the vibrational spectroscopy of the deprotonated thymine radical by photodetachment and state-selective autodetachment photoelectron spectroscopy via dipole-bound states. Chem Sci 2015; 6:3129-3138. [PMID: 29142686 PMCID: PMC5657408 DOI: 10.1039/c5sc00704f] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 03/17/2015] [Indexed: 11/21/2022] Open
Abstract
Deprotonated thymine can exist in two different forms, depending on which of its two N sites is deprotonated: N1[T-H]- or N3[T-H]-. Here we report a photodetachment study of the N1[T-H]- isomer cooled in a cryogenic ion trap and the observation of an excited dipole-bound state. Eighteen vibrational levels of the dipole-bound state are observed, and its vibrational ground state is found to be 238 ± 5 cm-1 below the detachment threshold of N1[T-H]-. The electron affinity of the deprotonated thymine radical (N1[T-H]˙) is measured accurately to be 26 322 ± 5 cm-1 (3.2635 ± 0.0006 eV). By tuning the detachment laser to the sixteen vibrational levels of the dipole-bound state that are above the detachment threshold, highly non-Franck-Condon resonant-enhanced photoelectron spectra are obtained due to state- and mode-selective vibrational autodetachment. Much richer vibrational information is obtained for the deprotonated thymine radical from the photodetachment and resonant-enhanced photoelectron spectroscopy. Eleven fundamental vibrational frequencies in the low-frequency regime are obtained for the N1[T-H]˙ radical, including the two lowest-frequency internal rotational modes of the methyl group at 70 ± 8 cm-1 and 92 ± 5 cm-1.
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Affiliation(s)
- Dao-Ling Huang
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , USA .
| | - Hong-Tao Liu
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , USA . .,Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China
| | - Chuan-Gang Ning
- Department of Physics , State Key Laboratory of Low-Dimensional Quantum Physics , Tsinghua University , Beijing 100084 , China
| | - Guo-Zhu Zhu
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , USA .
| | - Lai-Sheng Wang
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , USA .
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9
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Liu HT, Ning CG, Huang DL, Wang LS. Vibrational Spectroscopy of the Dehydrogenated Uracil Radical by Autodetachment of Dipole-Bound Excited States of Cold Anions. Angew Chem Int Ed Engl 2014; 53:2464-8. [DOI: 10.1002/anie.201310323] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Indexed: 01/29/2023]
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10
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Liu HT, Ning CG, Huang DL, Wang LS. Vibrational Spectroscopy of the Dehydrogenated Uracil Radical by Autodetachment of Dipole-Bound Excited States of Cold Anions. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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Schinle F, Crider PE, Vonderach M, Weis P, Hampe O, Kappes MM. Spectroscopic and theoretical investigations of adenosine 5'-diphosphate and adenosine 5'-triphosphate dianions in the gas phase. Phys Chem Chem Phys 2013; 15:6640-50. [PMID: 23258289 DOI: 10.1039/c2cp43808a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Doubly deprotonated adenosine 5'-diphosphate ([ADP-2H](2-)) and adenosine 5'-triphosphate ([ATP-2H](2-)) dianions were investigated using infrared multiple photon dissociation (IR-MPD) and photoelectron spectroscopy. Vibrational spectra acquired in the X-H stretch region (X = C, N, O) and augmented by isotope-labelling were compared to density functional theory (DFT) calculations at the B3LYP/TZVPP level. This suggests that in [ATP-2H](2-) the two phosphate groups adjacent to the ribose ring are preferentially deprotonated. Photoelectron spectra recorded at 4.66 and 6.42 eV photon energies revealed adiabatic detachment energies of 1.35 eV for [ADP-2H](2-) and 3.35 eV for [ATP-2H](2-). Repulsive Coulomb barriers were estimated at ~2.2 eV for [ADP-2H](2-) and ~1.9 eV for [ATP-2H](2-). Time-dependent DFT calculations have been used to simulate the photoelectron spectra. Photodetachment occurs primarily from lone pair orbitals on oxygen atoms within the phosphate chain.
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Affiliation(s)
- Florian Schinle
- Institut für Physikalische Chemie, Karlsruhe Institute of Technology (KIT), 76128 Karlsruhe, Germany
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12
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Vonderach M, Ehrler OT, Matheis K, Weis P, Kappes MM. Isomer-selected photoelectron spectroscopy of isolated DNA oligonucleotides: phosphate and nucleobase deprotonation at high negative charge states. J Am Chem Soc 2012; 134:7830-41. [PMID: 22524691 DOI: 10.1021/ja300619j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Fractionation according to ion mobility and mass-to-charge ratio has been used to select individual isomers of deprotonated DNA oligonucleotide multianions for subsequent isomer-resolved photoelectron spectroscopy (PES) in the gas phase. Isomer-resolved PE spectra have been recorded for tetranucleotides, pentanucleotides, and hexanucleotides. These were studied primarily in their highest accessible negative charge states (3-, 4-, and 5-, respectively), as provided by electrospraying from room temperature solutions. In particular, the PE spectra obtained for pentanucleotide tetraanions show evidence for two coexisting classes of gas-phase isomeric structures. We suggest that these two classes comprise: (i) species with excess electrons localized exclusively at deprotonated phosphate backbone sites and (ii) species with at least one deprotonated base (in addition to several deprotonated phosphates). By permuting the sequence of bases in various [A(5-x)T(x)](4-) and [GT(4)](4-) pentanucleotides, we have established that the second type of isomer is most likely to occur if the deprotonated base is located at the first or last position in the sequence. We have used a combination of molecular mechanics and semiempirical calculations together with a simple electrostatic model to explore the photodetachment mechanism underlying our photoelectron spectra. Comparison of predicted to measured photoelectron spectra suggests that a significant fraction of the detected electrons originates from the DNA bases (both deprotonated and neutral).
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Affiliation(s)
- Matthias Vonderach
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
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13
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Chen ES, Chen EC. The role of spin in biological processes: O2, NO, nucleobases, nucleosides, nucleotides and Watson–Crick base pairs. MOLECULAR SIMULATION 2009. [DOI: 10.1080/08927020902865931] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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