1
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Brundridge NM, Fritz JM, Dickerhoff J, Yang D, McLuckey SA. Negative Electron Transfer Collision-Induced Dissociation of G-Quadruplexes: Uncovering the Guanine Radical Anion Loss Pathway. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:756-766. [PMID: 38456425 PMCID: PMC11022967 DOI: 10.1021/jasms.3c00443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
G-quadruplex (G4) DNA can form highly stable secondary structures in the presence of metal cations, and research has shown its potential as a transcriptional regulator for oncogenes in the human genome. In order to explore the interactions of DNA with metal cations using mass spectrometry, employing complementary fragmentation methods can enhance structural information. This study explores the use of ion-ion reactions for sequential negative electron transfer collision-induced dissociation (nET-CID) as a complement to traditional ion-trap CID (IT-CID). The resulting nET-CID data for G4 anions with and without metal cations show an increase in fragment ion type diversity and yield of structurally informative ions relative to IT-CID. The nET-CID yields greater sequence coverage by virtue of fragmentation at the 3'-side of thymine residues, which is lacking with IT-CID. Potassium adductions to backbone fragments in IT-CID and nET-CID spectra were nearly identical. Of note is a prominent fragment resulting from a loss of a 149 Da anion seen in nET-CID of large, G-rich sequences, proposed to be radical anion guanine loss. Neutral loss of neutral guanine (151 Da) and deprotonated nucleobase loss (150 Da) have been previously reported, but this is the first report of radical anion guanine loss (149 Da). Confirmation of the identity of the 149 Da anion results from the examination of the homonucleobase sequence 5'-GGGGGGGG-3'. Loss of a charged adenine radical anion at much lower relative abundance was also noted for the sequence 5'-AAAAAAAA-3'. DFT modeling indicates that the loss of a nucleobase as a radical anion from odd-electron nucleic acid anions is a thermodynamically favorable fragmentation pathway for G.
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Affiliation(s)
- Nicole M Brundridge
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jordan M Fritz
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jonathan Dickerhoff
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, 575 W. Stadium Avenue, West Lafayette, Indiana 47904, United States
| | - Danzhou Yang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, 575 W. Stadium Avenue, West Lafayette, Indiana 47904, United States
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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2
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Opoku E, Pawłowski F, Ortiz JV. A new generation of non-diagonal, renormalized self-energies for calculation of electron removal energies. J Chem Phys 2023; 159:124109. [PMID: 38127383 DOI: 10.1063/5.0168779] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/06/2023] [Indexed: 12/23/2023] Open
Abstract
A new generation of diagonal self-energies for the calculation of electron removal energies of molecules and molecular ions that has superseded its predecessors with respect to accuracy, efficiency, and interpretability is extended to include non-diagonal self-energies that permit Dyson orbitals to be expressed as linear combinations of canonical Hartree-Fock orbitals. In addition, an improved algorithm for renormalized methods eliminates the convergence difficulties encountered in the first studies of the new, diagonal self-energies. A dataset of outer-valence, vertical ionization energies with almost full-configuration-interaction quality serves as a standard of comparison in numerical tests. The new non-diagonal, renormalized methods are slightly more accurate than their diagonal counterparts, with mean absolute errors between 0.10 and 0.06 eV for outer-valence final states. This advantage is procured at the cost of an increase in the scaling of arithmetic bottlenecks that accompany the inclusion of non-diagonal self-energy terms. The new, non-diagonal, renormalized self-energies are also more accurate and efficient than their non-diagonal predecessors.
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Affiliation(s)
- Ernest Opoku
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, USA
| | - Filip Pawłowski
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, USA
| | - J V Ortiz
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, USA
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3
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Pandey AN, Taketsugu T, Singh RK. Theoretical investigation of copper clusters using the electron propagator theory. J CHEM SCI 2023. [DOI: 10.1007/s12039-023-02146-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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4
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Opoku E, Pawłowski F, Ortiz JV. Electron Propagator Theory of Vertical Electron Detachment Energies of Anions: Benchmarks and Applications to Nucleotides. J Phys Chem A 2023; 127:1085-1101. [PMID: 36656801 DOI: 10.1021/acs.jpca.2c08372] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A new generation of ab initio electron-propagator self-energy approximations that are free of adjustable parameters is tested on a benchmark set of 55 vertical electron detachment energies of closed-shell anions. Comparisons with older self-energy approximations indicate that several new methods that make the diagonal self-energy approximation in the canonical Hartree-Fock orbital basis provide superior accuracy and computational efficiency. These methods and their acronyms, mean absolute errors (in eV), and arithmetic bottlenecks expressed in terms of occupied (O) and virtual (V) orbitals are the opposite-spin, non-Dyson, diagonal second-order method (os-nD-D2, 0.2, OV2), the approximately renormalized quasiparticle third-order method (Q3+, 0.15, O2V3) and the approximately renormalized, non-Dyson, linear, third-order method (nD-L3+, 0.1, OV4). The Brueckner doubles with triple field operators (BD-T1) nondiagonal electron-propagator method provides such close agreement with coupled-cluster single, double, and perturbative triple replacement total energy differences that it may be used as an alternative means of obtaining standard data. The new methods with diagonal self-energy matrices are the foundation of a composite procedure for estimating basis-set effects. This model produces accurate predictions and clear interpretations based on Dyson orbitals for the photoelectron spectra of the nucleotides found in DNA.
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Affiliation(s)
- Ernest Opoku
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, United States
| | - Filip Pawłowski
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, United States
| | - J V Ortiz
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, United States
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5
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Makurat S, Yuan Q, Czub J, Chomicz-Mańka L, Cao W, Wang XB, Rak J. Guanosine Dianions Hydrated by One to Four Water Molecules. J Phys Chem Lett 2022; 13:3230-3236. [PMID: 35380844 PMCID: PMC9014458 DOI: 10.1021/acs.jpclett.2c00512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Intermolecular interactions such as those present in molecule···water complexes may profoundly influence the physicochemical properties of molecules. Here, we carried out an experimental-computational study on doubly deprotonated guanosine monophosphate···water clusters, [dGMP - 2H]2-·nH2O (n = 1-4), using a combination of negative anion photoelectron spectroscopy (NIPES) with molecular dynamics (MD) and quantum chemical (QM) calculations. Successive addition of water molecules to [dGMP - 2H]2- increases the experimental adiabatic detachment (ADE) and vertical detachment energy (VDE) by 0.5-0.1 eV, depending on the cluster size. In order to choose the representative conformations, we combined MD simulations with a clustering procedure to identify low energy geometries for which ADEs and VDEs were computed at the CAM-B3LYP/6-31++G(d,p) level. Our results demonstrate that the assumed approach leads to sound geometries and energetics of the studied microsolvates since the calculated ADEs and VDEs are in pretty good agreement with the experimental characteristics. The evolution of hydrogen bonding with cluster size indicates the possibility of the occurrence of proton transfer for clusters comprising a larger number of water molecules.
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Affiliation(s)
- Samanta Makurat
- Faculty
of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Qinqin Yuan
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
- Department
of Chemistry, Anhui University, Hefei, Anhui 230601, China
| | - Jacek Czub
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza
11/12, Gdańsk 80-233, Poland
- BioTechMed
Center, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk 80-233, Poland
| | - Lidia Chomicz-Mańka
- Faculty
of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Wenjin Cao
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Xue-Bin Wang
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Janusz Rak
- Faculty
of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
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6
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Chen CG, Nardi AN, Amadei A, D’Abramo M. Theoretical Modeling of Redox Potentials of Biomolecules. Molecules 2022; 27:molecules27031077. [PMID: 35164342 PMCID: PMC8838479 DOI: 10.3390/molecules27031077] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022] Open
Abstract
The estimation of the redox potentials of biologically relevant systems by means of theoretical-computational approaches still represents a challenge. In fact, the size of these systems typically does not allow a full quantum-mechanical treatment needed to describe electron loss/gain in such a complex environment, where the redox process takes place. Therefore, a number of different theoretical strategies have been developed so far to make the calculation of the redox free energy feasible with current computational resources. In this review, we provide a survey of such theoretical-computational approaches used in this context, highlighting their physical principles and discussing their advantages and limitations. Several examples of these approaches applied to the estimation of the redox potentials of both proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported.
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Affiliation(s)
- Cheng Giuseppe Chen
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
| | | | - Andrea Amadei
- Department of Chemical and Technological Sciences, Tor Vergata University, 00133 Rome, Italy;
| | - Marco D’Abramo
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
- Correspondence:
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7
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Yuan Q, Chomicz-Mańka L, Makurat S, Cao W, Rak J, Wang XB. Photoelectron Spectroscopy and Theoretical Investigations of Gaseous Doubly Deprotonated 2'-Deoxynucleoside 5'-Monophosphate Dianions. J Phys Chem Lett 2021; 12:9463-9469. [PMID: 34558897 DOI: 10.1021/acs.jpclett.1c02678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A better understanding of the mechanism of oxidative DNA damage requires obtaining a molecular level description of nucleotides in various charge states. Herein, we report a systematic photoelectron spectroscopy and theoretical investigation of 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) and 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 π-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.
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Affiliation(s)
- Qinqin Yuan
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Lidia Chomicz-Mańka
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Samanta Makurat
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Wenjin Cao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Janusz Rak
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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8
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Harb H, Hratchian HP. ΔSCF Dyson orbitals and pole strengths from natural ionization orbitals. J Chem Phys 2021; 154:084104. [DOI: 10.1063/5.0040454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Hassan Harb
- Department of Chemistry and Chemical Biology and Center for Chemical Computation and Theory, University of California, Merced, California 95343, USA
| | - Hrant P. Hratchian
- Department of Chemistry and Chemical Biology and Center for Chemical Computation and Theory, University of California, Merced, California 95343, USA
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9
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Ortiz JV. Dyson-orbital concepts for description of electrons in molecules. J Chem Phys 2020; 153:070902. [DOI: 10.1063/5.0016472] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- J. V. Ortiz
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, USA
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10
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Peng B, Kowalski K, Panyala A, Krishnamoorthy S. Green’s function coupled cluster simulation of the near-valence ionizations of DNA-fragments. J Chem Phys 2020; 152:011101. [DOI: 10.1063/1.5138658] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Bo Peng
- Advanced Computing, Mathematics, and Data Division, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
| | - Karol Kowalski
- William R. Wiley Environmental Molecular Sciences Laboratory, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
| | - Ajay Panyala
- High Performance Computing, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
| | - Sriram Krishnamoorthy
- High Performance Computing, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
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11
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Díaz-Tinoco M, Corzo HH, Ortiz JV. Electron Propagator Methods for Vertical Electron Detachment Energies of Anions: Benchmarks and Case Studies. J Chem Theory Comput 2018; 14:5881-5895. [DOI: 10.1021/acs.jctc.8b00736] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manuel Díaz-Tinoco
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, United States
| | - H. H. Corzo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, United States
| | - J. V. Ortiz
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, United States
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12
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Ravell E, Jalife S, Barroso J, Orozco-Ic M, Hernández-Juárez G, Ortiz-Chi F, Pan S, Cabellos JL, Merino G. Structure and Bonding in CE 5- (E=Al-Tl) Clusters: Planar Tetracoordinate Carbon versus Pentacoordinate Carbon. Chem Asian J 2018; 13:1467-1473. [PMID: 29575767 DOI: 10.1002/asia.201800261] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Indexed: 11/11/2022]
Abstract
The structure, bonding, and stability of clusters with the empirical formula CE5- (E=Al-Tl) have been analyzed by means of high-level computations. The results indicate that, whereas aluminum and gallium clusters have C2v structures with a planar tetracoordinate carbon (ptC), their heavier homologues prefer three-dimensional C4v forms with a pentacoordinate carbon center over the ptC one. The reason for such a preference is a delicate balance between the interaction energy of the fifth E atom with CE4 and the distortion energy. Moreover, bonding analysis shows that the ptC systems can be better described as CE4- , with 17-valence electrons interacting with E. The ptC core in these systems exhibits double aromatic (both σ and π) behavior, but the σ contribution is dominating.
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Affiliation(s)
- Estefanía Ravell
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados Unidad Mérida, km 6 Antigua carretera a Progreso. Apdo. Postal 73, Cordemex, 97310, Mérida, Yuc., Mexico
| | - Said Jalife
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados Unidad Mérida, km 6 Antigua carretera a Progreso. Apdo. Postal 73, Cordemex, 97310, Mérida, Yuc., Mexico
| | - Jorge Barroso
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados Unidad Mérida, km 6 Antigua carretera a Progreso. Apdo. Postal 73, Cordemex, 97310, Mérida, Yuc., Mexico
| | - Mesías Orozco-Ic
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados Unidad Mérida, km 6 Antigua carretera a Progreso. Apdo. Postal 73, Cordemex, 97310, Mérida, Yuc., Mexico
| | - Gerardo Hernández-Juárez
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados Unidad Mérida, km 6 Antigua carretera a Progreso. Apdo. Postal 73, Cordemex, 97310, Mérida, Yuc., Mexico
| | - Filiberto Ortiz-Chi
- CONACyT-Universidad Juárez Autónoma de Tabasco, Centro de Investigación de Ciencia y Tecnología, Aplicada de Tabasco, C. P., 86690, Cunduacán, Tab., Mexico
| | - Sudip Pan
- Institute of Advanced Synthesis, School of Chemistry, and Molecular Engineering, Jiangsu National Synergetic, Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, 211816, P.R. China
| | - José Luis Cabellos
- Departamento de Investigación en Polímeros y Materiales, Universidad de Sonora, Edif. 3G, Blvd. Luis Encinas y Rosales S/N, Centro, 83000, Hermosillo, Son., Mexico
| | - Gabriel Merino
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados Unidad Mérida, km 6 Antigua carretera a Progreso. Apdo. Postal 73, Cordemex, 97310, Mérida, Yuc., Mexico
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13
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Chakraborty R, Bose S, Ghosh D. Effect of solvation on the ionization of guanine nucleotide: A hybrid QM/EFP study. J Comput Chem 2017; 38:2528-2537. [PMID: 28856705 DOI: 10.1002/jcc.24913] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 11/11/2022]
Abstract
Ionization of nucleobases is affected by their biological environment, which includes both the effect of adjacent nucleotides as well as the presence of water around it. Guanine and its nucleotide have the lowest ionization potentials among the various DNA bases. Therefore, the threshold of ionization is dependent on that of guanine and its characterization is crucial to the prediction of interaction of light with DNA. We investigate the effect of solvation on the vertical ionization energies (VIEs) of guanine and its nucleotide. In this work, we have used hybrid quantum mechanics/molecular mechanics (QM/MM) approach with effective fragment potential as the MM method of choice and equation-of-motion coupled-cluster for ionization potential with singles and doubles (EOM-IP-CCSD) as the QM method. The performance of the hybrid scheme with respect to the full QM method shows an accuracy of ≤ 0.02-0.04 eV. The lowest few ionizations of the nucleotide are found to be from different parts of the moiety, that is, the nucleic acid base, phosphate, or sugar, and these ionization energies are very closely spaced giving rise to a very complicated spectrum. Furthermore, microsolvation has large effects on these ionizations and can lead to red or blue shift depending on the position of the water molecule. Even a single water molecule can change the order of ionized states in the nucleotide. The VIEs of the bulk solvated chromophores are predicted and compared to existing experimental spectra. The predominant role of polarization in the solvatochromic shift is noticed. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Rahul Chakraborty
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Samik Bose
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Debashree Ghosh
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700032, India
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14
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Eichler DR, Hamann HA, Harte KA, Papadantonakis GA. Hydration effects on the photoionization energy of 2′-deoxyguanosine 5′-phosphate and activation barriers for guanine methylation by carcinogenic methane diazonium ions. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.05.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Chakraborty R, Ghosh D. The effect of sequence on the ionization of guanine in DNA. Phys Chem Chem Phys 2016; 18:6526-33. [PMID: 26864778 DOI: 10.1039/c5cp07804k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The accurate estimation of the ionization energies and understanding the nature of the ionized states of the nucleic acid bases (NABs) are crucial to the understanding of the DNA damage mechanism. The vertical ionization energy (VIE) of guanine is the lowest among the NABs and the ionization energies are strongly affected by the environment, such as solvation and characteristics of nearby NABs. Therefore, we investigate the sequence dependence of the VIEs of guanine in B-DNA. We use the equation of motion coupled cluster method for the estimation of ionization potential with single and double excitations (EOM-IP-CCSD) and density functional theory with dispersion corrected ωB97x-D for the estimation of VIEs. A significant amount of non-additivity or cooperativity, directly proportional to charge delocalization, is noticed in the change in VIE due to the interaction with the nearby NABs. While the change in VIE due to base pairing originates predominantly from charge-dipole interactions, stacking between base pairs is a more complicated balance of dispersion and charge-dipole interactions as well as stabilization due to the delocalization of the positive charge. The long range interactions are however dominated by 1/r(3) distance dependence which shows the major role played by charge-dipole interactions. The extent of localization of positive holes on guanine is also estimated for various sequences.
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Affiliation(s)
- Rahul Chakraborty
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India.
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16
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Thompson LM, Harb H, Hratchian HP. Natural ionization orbitals for interpreting electron detachment processes. J Chem Phys 2016; 144:204117. [DOI: 10.1063/1.4951738] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Lee M. Thompson
- Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Hassan Harb
- Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Hrant P. Hratchian
- Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
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17
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Pluhařová E, Slavíček P, Jungwirth P. Modeling photoionization of aqueous DNA and its components. Acc Chem Res 2015; 48:1209-17. [PMID: 25738773 DOI: 10.1021/ar500366z] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Radiation damage to DNA is usually considered in terms of UVA and UVB radiation. These ultraviolet rays, which are part of the solar spectrum, can indeed cause chemical lesions in DNA, triggered by photoexcitation particularly in the UVB range. Damage can, however, be also caused by higher energy radiation, which can ionize directly the DNA or its immediate surroundings, leading to indirect damage. Thanks to absorption in the atmosphere, the intensity of such ionizing radiation is negligible in the solar spectrum at the surface of Earth. Nevertheless, such an ionizing scenario can become dangerously plausible for astronauts or flight personnel, as well as for persons present at nuclear power plant accidents. On the beneficial side, ionizing radiation is employed as means for destroying the DNA of cancer cells during radiation therapy. Quantitative information about ionization of DNA and its components is important not only for DNA radiation damage, but also for understanding redox properties of DNA in redox sensing or labeling, as well as charge migration along the double helix in nanoelectronics applications. Until recently, the vast majority of experimental and computational data on DNA ionization was pertinent to its components in the gas phase, which is far from its native aqueous environment. The situation has, however, changed for the better due to the advent of photoelectron spectroscopy in liquid microjets and its most recent application to photoionization of aqueous nucleosides, nucleotides, and larger DNA fragments. Here, we present a consistent and efficient computational methodology, which allows to accurately evaluate ionization energies and model photoelectron spectra of aqueous DNA and its individual components. After careful benchmarking, the method based on density functional theory and its time-dependent variant with properly chosen hybrid functionals and polarizable continuum solvent model provides ionization energies with accuracy of 0.2-0.3 eV, allowing for faithful modeling and interpretation of DNA photoionization. The key finding is that the aqueous medium is remarkably efficient in screening the interactions within DNA such that, unlike in the gas phase, ionization of a base, nucleoside, or nucleotide depends only very weakly on the particular DNA context. An exception is the electronic interaction between neighboring bases which can lead to sequence-specific effects, such as a partial delocalization of the cationic hole upon ionization enabled by presence of adjacent bases of the same type.
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Affiliation(s)
- Eva Pluhařová
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Petr Slavíček
- University of Chemistry and Technology, Department
of Physical Chemistry, Technická 5, 16628 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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18
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Sengupta C, Basu S. A spectroscopic study to decipher the mode of interaction of some common acridine derivatives with CT DNA within nanosecond and femtosecond time domains. RSC Adv 2015. [DOI: 10.1039/c5ra13035b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Our spectroscopic investigation with acridine derivatives presents the electronic control of their substituents on intercalation, solvation and PET with DNA.
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Affiliation(s)
- Chaitrali Sengupta
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700 064
- India
| | - Samita Basu
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700 064
- India
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19
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Abstract
Nucleic acids are diverse polymeric macromolecules that are essential for all life forms. These biomolecules possess a functional three-dimensional structure under aqueous physiological conditions. Mass spectrometry-based approaches have on the other hand opened the possibility to gain structural information on nucleic acids from gas-phase measurements. To correlate gas-phase structural probing results with solution structures, it is therefore important to grasp the extent to which nucleic acid structures are preserved, or altered, when transferred from the solution to a fully anhydrous environment. We will review here experimental and theoretical approaches available to characterize the structure of nucleic acids in the gas phase (with a focus on oligonucleotides and higher-order structures), and will summarize the structural features of nucleic acids that can be preserved in the gas phase on the experiment time scale.
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20
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Pérez-González A, Galano A, Ortiz JV. Vertical Ionization Energies of Free Radicals and Electron Detachment Energies of Their Anions: A Comparison of Direct and Indirect Methods Versus Experiment. J Phys Chem A 2014; 118:6125-31. [DOI: 10.1021/jp505276n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Adriana Pérez-González
- Departamento
de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, México DF 04510, México
| | - Annia Galano
- Departamento
de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina. Iztapalapa, C.P. 09340 México DF, México
| | - J. V. Ortiz
- Department
of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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21
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Tamayo-Mendoza T, Flores-Moreno R. Symbolic Algebra Development for Higher-Order Electron Propagator Formulation and Implementation. J Chem Theory Comput 2014; 10:2363-70. [DOI: 10.1021/ct500204v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Teresa Tamayo-Mendoza
- Departmento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, Guadalajara Jal., C.P. 44430, México
| | - Roberto Flores-Moreno
- Departmento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, Guadalajara Jal., C.P. 44430, México
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22
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Chatterley AS, West CW, Stavros VG, Verlet JRR. Time-resolved photoelectron imaging of the isolated deprotonated nucleotides. Chem Sci 2014. [DOI: 10.1039/c4sc01493f] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Time-resolved photoelectron spectroscopy of deprotonated nucleotides provides new insights into their relaxation dynamics.
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Affiliation(s)
- Adam S. Chatterley
- Department
- of Chemistry
- University of Durham
- Durham DH1 3LE, United Kingdom
- Department of Chemistry
| | | | - Vasilios G. Stavros
- Department of Chemistry
- University of Warwick
- Coventry CV4 7AL, United Kingdom
| | - Jan R. R. Verlet
- Department
- of Chemistry
- University of Durham
- Durham DH1 3LE, United Kingdom
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23
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Wang K, Hamill JM, Wang B, Guo C, Jiang S, Huang Z, Xu B. Structure determined charge transport in single DNA molecule break junctions. Chem Sci 2014. [DOI: 10.1039/c4sc00888j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Single DNA conductance measurements with increasing MgCl2concentrations unambiguously revealed two DNA (B and Z) conformations and the B–Z transition process.
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Affiliation(s)
- Kun Wang
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
| | - Joseph M. Hamill
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
| | - Bin Wang
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
| | - Cunlan Guo
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
| | - Sibo Jiang
- Department of Chemistry
- Georgia State University
- Atlanta, USA
| | - Zhen Huang
- Department of Chemistry
- Georgia State University
- Atlanta, USA
| | - Bingqian Xu
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
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24
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Chatterley AS, Johns AS, Stavros VG, Verlet JRR. Base-specific ionization of deprotonated nucleotides by resonance enhanced two-photon detachment. J Phys Chem A 2013; 117:5299-305. [PMID: 23642262 DOI: 10.1021/jp4041315] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The intrinsic ionization energy of a base in DNA plays a critical role in determining the energies at which damage mechanisms may emerge. Here, a two-photon resonance-enhanced ionization scheme is presented that utilizes the (1)ππ* transition, localized on the DNA base, to elucidate the base-specific ionization in a deprotonated nucleotide. In contrast to previous reports, the scheme is insensitive to competing ionization channels arising from the sugar-phosphate backbone. Using this approach, we demonstrate that for all bases except guanine, the lowest electron detachment energy corresponds to detachment from the sugar-phosphate backbone and allows us to determine the lowest adiabatic ionization energy for the other three bases for the first time in an isolated nucleotide.
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Affiliation(s)
- Adam S Chatterley
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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25
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Nei YW, Hallowita N, Steill JD, Oomens J, Rodgers MT. Infrared multiple photon dissociation action spectroscopy of deprotonated DNA mononucleotides: gas-phase conformations and energetics. J Phys Chem A 2013; 117:1319-35. [PMID: 23289585 DOI: 10.1021/jp3077936] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The gas phase structures of the deprotonated 2'-deoxymononucleotides including 2'-deoxyadenosine-5'-monophosphate (dA5'p), 2'-deoxycytidine-5'-monophosphate (dC5'p), 2'-deoxyguanosine-5'-monophosphate (dG5'p), and thymidine-5'-monophosphate (T5'p) are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical electronic structure calculations. The measured IRMPD action spectra of all four deprotonated DNA mononucleotides exhibit unique spectral features in the region extending from ~600 to 1800 cm(-1) such that they can be readily differentiated from one another. The measured IRMPD action spectra are compared to the linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformations of these species accessed in the experiments. On the basis of these comparisons and the computed energetic information, the most stable conformations of the deprotonated forms of dA5'p, dC5'p, and T5'p are conformers where the ribose moiety adopts a C3' endo conformation and the nucleobase is in an anti conformation. By contrast, the most stable conformations of the deprotonated form of dG5'p are conformers where the ribose adapts a C3' endo conformation and the nucleobase is in a syn conformation. In addition to the ground-state conformers, several stable low-energy excited conformers that differ slightly in the orientation of the phosphate ester moiety were also accessed in the experiments.
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Affiliation(s)
- Y-w Nei
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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26
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Weber JM, Marcum J, Nielsen SB. UV Photophysics of DNA and RNA Nucleotides In Vacuo: Dissociation Channels, Time Scales, and Electronic Spectra. PHOTOPHYSICS OF IONIC BIOCHROMOPHORES 2013. [DOI: 10.1007/978-3-642-40190-9_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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27
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Taucher M, Breuker K. Characterization of modified RNA by top-down mass spectrometry. Angew Chem Int Ed Engl 2012; 51:11289-92. [PMID: 23042528 PMCID: PMC3532624 DOI: 10.1002/anie.201206232] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Indexed: 11/11/2022]
Abstract
Characteristic mass differences between fragment ions from backbone cleavage of RNA by electron detachment (d, w) and fragment ions from collisionally activated dissociation (c, y) provide extensive sequence information. Structure analysis by this approach should be especially useful for the detailed characterization of synthetic or post-transcriptionally modified RNA.
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Affiliation(s)
- Monika Taucher
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI), Universität InnsbruckInnrain 80–82, 6020 Innsbruck (Austria)
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI), Universität InnsbruckInnrain 80–82, 6020 Innsbruck (Austria)
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28
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Taucher M, Breuker K. Characterization of Modified RNA by Top-Down Mass Spectrometry. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206232] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Ortiz JV. Electron propagator theory: an approach to prediction and interpretation in quantum chemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1116] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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30
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Romero J, Posada E, Flores-Moreno R, Reyes A. A generalized any particle propagator theory: Assessment of nuclear quantum effects on electron propagator calculations. J Chem Phys 2012; 137:074105. [DOI: 10.1063/1.4745076] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Pérez-González A, Galano A. Ionization Energies, Proton Affinities, and pKa Values of a Large Series of Edaravone Derivatives: Implication for Their Free Radical Scavenging Activity. J Phys Chem B 2011; 115:10375-84. [DOI: 10.1021/jp2047163] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Adriana Pérez-González
- Departamento de Química, División de Ciencias Básicas e Ingeniería. Universidad Autónoma Metropolitana-Iztapalapa, Av San Rafael Atlixco No.186, Col.Vicentina C. P. 09340, México D. F
| | - Annia Galano
- Departamento de Química, División de Ciencias Básicas e Ingeniería. Universidad Autónoma Metropolitana-Iztapalapa, Av San Rafael Atlixco No.186, Col.Vicentina C. P. 09340, México D. F
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32
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Mechanism and kinetics of the hydroxyl and hydroperoxyl radical scavenging activity of N-acetylcysteine amide. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0958-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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33
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Pluharrová E, Jungwirth P, Bradforth SE, Slavícek P. Ionization of purine tautomers in nucleobases, nucleosides, and nucleotides: from the gas phase to the aqueous environment. J Phys Chem B 2011; 115:1294-305. [PMID: 21247073 DOI: 10.1021/jp110388v] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We have simulated ionization of purine nucleic acid components in the gas phase and in a water environment. The vertical and adiabatic ionization processes were calculated at the PMP2/aug-cc-pVDZ level with the TDDFT method applied to obtain ionization from the deeper lying orbitals. The water environment was modeled via microsolvation approach and using a nonequilibrium polarizable continuum model. We have characterized a set of guanine tautomers and investigated nucleosides and nucleotides in different conformations. The results for guanine, i.e., the nucleic acid base with the lowest vertical ionization potential, were also compared to those for the other purine base, adenine. The main findings of our study are the following: (i) Guanine remains clearly the base with the lowest ionization energy even upon aqueous solvation. (ii) Water solvent has a strong effect on the ionization energetics of guanine and adenine and their derivatives; the vertical ionization potential (VIP) is lowered by about 1 eV for guanine while it is ∼1.5 eV higher in the nucleotides, overall resulting in similar VIPs for GMP(-), guanosine and guanine in water. (iii) Water efficiently screens the electrostatic interactions between nucleic acid components. Consequently, ionization in water always originates from the base unit of the nucleic acid and all the information about conformational state is lost in the ionization energetics. (iv) The energy splitting between ionization of the two least bound electrons increases upon solvation. (v) Tautomerism does not contribute to the width of the photoelectron spectra in water. (vi) The effect of specific short-range interactions with individual solvent molecules is negligible for purine bases, compared to the long-range dielectric effects of the aqueous medium.
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Affiliation(s)
- Eva Pluharrová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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34
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Zakrzewski VG, Dolgounitcheva O, Zakjevskii AV, Ortiz J. Ab initio Electron Propagator Calculations on Electron Detachment Energies of Fullerenes, Macrocyclic Molecules, and Nucleotide Fragments. ADVANCES IN QUANTUM CHEMISTRY 2011. [DOI: 10.1016/b978-0-12-386477-2.00009-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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35
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Cauët E, Valiev M, Weare JH. Vertical ionization potentials of nucleobases in a fully solvated DNA environment. J Phys Chem B 2010; 114:5886-94. [PMID: 20394358 DOI: 10.1021/jp9120723] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Vertical ionization potentials (IPs) of nucleobases embedded in a fully solvated DNA fragment (12-mer B-DNA fragment + 22 sodium counterions + 5760 water molecules equilibrated to 298 K) have been calculated using a combined quantum mechanical molecular mechanics (QM/MM) approach. Calculations of the vertical IP of the anion Cl(-) are reported that support the accuracy of the application of a QM/MM method to this problem. It is shown that the pi nucleotide HOMO origin for the emitted electron is localized on the base by the hydration structure surrounding the DNA in a way similar to that recently observed for pyrimidine nucleotides in aqueous solutions (Slavicek, P.; et al. J. Am. Chem. Soc. 2009, 131, 6460). In a first step, a high level of theory, CCSD(T)/aug-cc-pVDZ, was used to calculate the vertical IP of each of the four single bases isolated in the QM region while the remaining DNA fragment, counterions, and water solvent molecules were included in the MM region. The calculated vertical IPs show a large positive shift of 3.2-3.3 eV compared to the corresponding gas-phase values. This shift is similar for all four DNA bases. The origin of the large increase in vertical IPs of nucleobases is found to be the long-range electrostatic interactions with the solvation structure outside the DNA helix. Thermal fluctuations in the fluid can result in IP changes of roughly 1 eV on a picosecond time scale. IPs of pi-stacked and H-bonded clusters of DNA bases were also calculated using the same QM/MM model but with a lower level of theory, B3LYP/6-31G(d=0.2). An IP shift of 4.02 eV relative to the gas phase is found for a four-base-pair B-DNA duplex configuration. The primary goal of this work was to estimate the influence of long-range solvation interactions on the ionization properties of DNA bases rather than provide highly precise IP evaluations. The QM/MM model presented in this work provides an attractive method to treat the difficult problem of incorporating a detailed long-range structural model of physiological conditions into investigations of the electronic processes in DNA.
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Affiliation(s)
- Emilie Cauët
- Chemistry and Biochemistry Department, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
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36
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Affiliation(s)
- Joseph C. Genereux
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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37
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38
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Slavícek P, Winter B, Faubel M, Bradforth SE, Jungwirth P. Ionization energies of aqueous nucleic acids: photoelectron spectroscopy of pyrimidine nucleosides and ab initio calculations. J Am Chem Soc 2009; 131:6460-7. [PMID: 19374336 DOI: 10.1021/ja8091246] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vertical ionization energies of the nucleosides cytidine and deoxythymidine in water, the lowest ones amounting in both cases to 8.3 eV, are obtained from photoelectron spectroscopy measurements in aqueous microjets. Ab initio calculations employing a nonequilibrium polarizable continuum model quantitatively reproduce the experimental spectra and provide molecular interpretation of the individual peaks of the photoelectron spectrum, showing also that lowest ionization originates from the base. Comparison of calculated vertical ionization potentials of pyrimidine bases, nucleosides, and nucleotides in water and in the gas phase underlines the dramatic effect of bulk hydration on the electronic structure. In the gas phase, the presence of sugar and, in particular, of phosphate has a strong effect on the energetics of ionization of the base. Upon bulk hydration, the ionization potential of the base in contrast becomes rather insensitive to the presence of the sugar and phosphate, which indicates a remarkable screening ability of the aqueous solvent. Accurate aqueous-phase vertical ionization potentials provide a significant improvement to the corrected gas-phase values used in the literature and represent important information in assessing the threshold energies for photooxidation and oxidation free energies of solvent-exposed DNA components. Likewise, such energetic data should allow improved assessment of delocalization and charge-hopping mechanisms in DNA ionized by radiation.
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Affiliation(s)
- Petr Slavícek
- Department of Physical Chemistry, Institute of Chemical Technology, Technicka 5, Prague 6, Czech Republic
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39
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Rubio M, Roca-Sanjuán D, Serrano-Andrés L, Merchán M. Determination of the electron-detachment energies of 2'-deoxyguanosine 5'-monophosphate anion: influence of the conformation. J Phys Chem B 2009; 113:2451-7. [PMID: 19182942 DOI: 10.1021/jp806105h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The vertical electron-detachment energies (VDEs) of the singly charged 2'-deoxyguanosine 5'-monophosphate anion (dGMP-) are determined by using the multiconfigurational second-order perturbation CASPT2 method at the MP2 ground-state equilibrium geometry of relevant conformers. The origin of the unique low-energy band in the gas phase photoelectron spectrum of dGMP-, with maximum at around 5.05 eV, is unambiguously assigned to electron detachment from the highest occupied molecular orbital of pi-character belonging to guanine fragment of a syn conformation. The presence of a short H-bond linking the 2-amino and phosphate groups, the guanine moiety acting as proton donor, is precisely responsible for the pronounced decrease of the computed VDE with respect to that obtained in other conformations. As a whole, the present research supports the nucleobase as the site with the lowest ionization potential in negatively charged (deprotonated) nucleotides at the most stable conformations as well as for B-DNA-like type arrangements, in agreement with experimental evidence.
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Affiliation(s)
- Mercedes Rubio
- Instituto de Ciencia Molecular, Universitat de València, Apartado 22085, ES-46071 Valencia, Spain.
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40
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Kamerlin SCL, Haranczyk M, Warshel A. Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies. J Phys Chem B 2009; 113:1253-72. [PMID: 19055405 PMCID: PMC2679392 DOI: 10.1021/jp8071712] [Citation(s) in RCA: 253] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) approaches have been used to provide a general scheme for chemical reactions in proteins. However, such approaches still present a major challenge to computational chemists, not only because of the need for very large computer time in order to evaluate the QM energy but also because of the need for proper computational sampling. This review focuses on the sampling issue in QM/MM evaluations of electrostatic energies in proteins. We chose this example since electrostatic energies play a major role in controlling the function of proteins and are key to the structure-function correlation of biological molecules. Thus, the correct treatment of electrostatics is essential for the accurate simulation of biological systems. Although we will be presenting different types of QM/MM calculations of electrostatic energies (and related properties) here, our focus will be on pKa calculations. This reflects the fact that pKa's of ionizable groups in proteins provide one of the most direct benchmarks for the accuracy of electrostatic models of macromolecules. While pKa calculations by semimacroscopic models have given reasonable results in many cases, existing attempts to perform pKa calculations using QM/MM-FEP have led to discrepancies between calculated and experimental values. In this work, we accelerate our QM/MM calculations using an updated mean charge distribution and a classical reference potential. We examine both a surface residue (Asp3) of the bovine pancreatic trypsin inhibitor and a residue buried in a hydrophobic pocket (Lys102) of the T4-lysozyme mutant. We demonstrate that, by using this approach, we are able to reproduce the relevant side chain pKa's with an accuracy of 3 kcal/mol. This is well within the 7 kcal/mol energy difference observed in studies of enzymatic catalysis, and is thus sufficient accuracy to determine the main contributions to the catalytic energies of enzymes. We also provide an overall perspective of the potential of QM/MM calculations in general evaluations of electrostatic free energies, pointing out that our approach should provide a very powerful and accurate tool to predict the electrostatics of not only solution but also enzymatic reactions, as well as the solvation free energies of even larger systems, such as nucleic acid bases incorporated into DNA.
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Affiliation(s)
- Shina C. L. Kamerlin
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
| | - Maciej Haranczyk
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
- Computational Research Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mail Stop 50F-1650, Berkeley, CA 94720-8139, USA
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
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41
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Marcum JC, Halevi A, Weber JM. Photodamage to isolated mononucleotides—photodissociation spectra and fragment channels. Phys Chem Chem Phys 2009; 11:1740-51. [DOI: 10.1039/b819273a] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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42
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Abstract
The vertical ionization energies of the four nucleotides have been computed. Geometries have been chosen to mimic orientations as they appear in B-DNA. The negative charge on the phosphate was neutralized by protonation, and also by the inclusion of counterions. Calculations have been performed with electron propagator methods (P3), Møller-Plesset second-order perturbation theory, and density functional theory to determine the nature of the orbitals associated with the highest lying ionization energies. Calculations at the MP2/6-311G(d,p)//P3/6-311G(d,p) level of theory yield vertical ionization energies for 5'-dTMP 9.05 eV, for 5'-dCMP 8.40 eV, for 5'-dAMP 8.16 eV and for 5'-dGMP 7.96 eV. In all cases the highest occupied molecular orbital resides on the base moieties.
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Affiliation(s)
- David M Close
- Department of Physics, Box 70652, East Tennessee State University, Johnson City, Tennessee 37614, USA.
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43
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Haranczyk M, Gutowski M, Warshel A. Solvation free energies of molecules. The most stable anionic tautomers of uracil. Phys Chem Chem Phys 2008; 10:4442-8. [PMID: 18654684 PMCID: PMC2562795 DOI: 10.1039/b802300j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Anionic states of nucleic acid bases are suspected to play a role in the radiation damage processes of DNA. Our recent studies suggested that the excess electron attachment to the nucleic acid bases can stabilize some rare tautomers, i.e. imine-enamine tautomers and other tautomers with a proton being transferred from nitrogen sites to carbon sites (with respect to the canonical tautomer). So far, these new anionic tautomers have been characterized by the gas-phase electronic structure calculations and photoelectron spectroscopy experiments. In the current contribution we explore the effect of water solvation on the stability of the new anionic tautomers of uracil. The accurate free energies of solvation are calculated in a two step approach. The major contribution was calculated using the classical free-energy perturbation adiabatic-charging approach, where it is assumed that the solvated molecule has the charge distribution given by the polarizable continuum model. In the second step the free energy of solvation is refined by taking into account the real, average solvent charge distribution. This is done using our accelerated QM/MM simulations, where the QM energy of the solute is calculated in the mean potential averaged over many MD steps. We found that in water solution three of the recently identified anionic tautomers are 6.5-3.6 kcal mol(-1) more stable than the anion of the canonical tautomer.
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Affiliation(s)
- Maciej Haranczyk
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA.
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Haranczyk M, Holliday J, Willett P, Gutowski M. Structure and singly occupied molecular orbital analysis of anionic tautomers of guanine. J Comput Chem 2008; 29:1277-91. [PMID: 18161682 DOI: 10.1002/jcc.20886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Recently, we reported the discovery of adiabatically bound anions of guanine that might be involved in the processes of DNA damage by low-energy electrons and in charge transfer through DNA. These anions correspond to some tautomers that have been ignored thus far. They were identified using a hybrid quantum mechanical-combinatorial approach in which an energy-based screening was performed on the library of 499 tautomers with their relative energies calculated with quantum chemistry methods. In the current study, we analyze the adiabatically bound anions of guanine in two aspects: (1) the geometries and excess electron distributions are analyzed and compared with anions of the most stable neutrals to identify the sources of stability; (2) the chemical space of guanine tautomers is explored to verify if these new tautomers are contained in a particular subspace of the tautomeric space. The first task involves the development of novel approaches-the quantum chemical data like electron density, orbital, and information on its bonding/antibonding character are coded into holograms and analyzed using chemoinformatics techniques. The second task is completed using substructure analysis and clustering techniques performed on molecules represented by 2D fingerprints. The major conclusion is that the high stability of adiabatically bound anions originates from the bonding character of the pi orbital occupied by the excess electron. This compensates for the antibonding character that usually causes significant buckling of the ring. Also, the excess electron is more homogenously distributed over both rings than in the case of anions of the most stable neutral species. In terms of 2D substructure, the most stable anionic tautomers generally have additional hydrogen atoms at C8 and/or C2 and they do not have hydrogen atoms attached to C4, C5, and C6. They also form an "island of stability" in the tautomeric space of guanine.
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Affiliation(s)
- Maciej Haranczyk
- Department of Chemistry, University of Gdańsk, 80-952 Gdańsk, Poland
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Flores-Moreno R, Ortiz JV. Quasiparticle virtual orbitals in electron propagator calculations. J Chem Phys 2008; 128:164105. [DOI: 10.1063/1.2902288] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Radiation Effects On DNA: Theoretical Investigations Of Electron, Hole And Excitation Pathways To DNA Damage. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-1-4020-8184-2_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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Gabelica V, Rosu F, De Pauw E, Antoine R, Tabarin T, Broyer M, Dugourd P. Electron photodetachment dissociation of DNA anions with covalently or noncovalently bound chromophores. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1990-2000. [PMID: 17900923 DOI: 10.1016/j.jasms.2007.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Revised: 08/17/2007] [Accepted: 08/17/2007] [Indexed: 05/17/2023]
Abstract
Double stranded DNA multiply charged anions coupled to chromophores were subjected to UV-Vis photoactivation in a quadrupole ion trap mass spectrometer. The chromophores included noncovalently bound minor groove binders (activated in the near UV), noncovalently bound intercalators (activated with visible light), and covalently linked fluorophores and quenchers (activated at their maximum absorption wavelength). We found that the activation of only chromophores having long fluorescence lifetimes did result in efficient electron photodetachment from the DNA complexes. In the case of ethidium-dsDNA complex excited at 500 nm, photodetachment is a multiphoton process. The MS(3) fragmentation of radicals produced by photodetachment at lambda = 260 nm (DNA excitation) and by photodetachment at lambda > 300 nm (chromophore excitation) were compared. The radicals keep no memory of the way they were produced. A weakly bound noncovalent ligand (m-amsacrine) allowed probing experimentally that a fraction of the electronic internal energy was converted into vibrational internal energy. This fragmentation channel was used to demonstrate that excitation of the quencher DABSYL resulted in internal conversion, unlike the fluorophore 6-FAM. Altogether, photodetachment of the DNA complexes upon chromophore excitation can be interpreted by the following mechanism: (1) ligands with sufficiently long excited-state lifetime undergo resonant two-photon excitation to reach the level of the DNA excited states, then (2) the excited-state must be coupled to the DNA excited states for photodetachment to occur. Our experiments also pave the way towards photodissociation probes of biomolecule conformation in the gas-phase by Förster resonance energy transfer (FRET).
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Affiliation(s)
- Valérie Gabelica
- Mass Spectrometry Laboratory, Université de Liège, Institut de Chimie Liège, Belgium.
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Gabelica V, Rosu F, Tabarin T, Kinet C, Antoine R, Broyer M, De Pauw E, Dugourd P. Base-dependent electron photodetachment from negatively charged DNA strands upon 260-nm laser irradiation. J Am Chem Soc 2007; 129:4706-13. [PMID: 17378565 DOI: 10.1021/ja068440z] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA multiply charged anions stored in a quadrupole ion trap undergo one-photon electron ejection (oxidation) when subjected to laser irradiation at 260 nm (4.77 eV). Electron photodetachment is likely a fast process, given that photodetachment is able to compete with internal conversion or radiative relaxation to the ground state. The DNA [6-mer]3- ions studied here show a marked sequence dependence of electron photodetachment yield. Remarkably, the photodetachment yield (dG6 > dA6 > dC6 > dT6) is inversely correlated with the base ionization potentials (G < A < C < T). Sequences with guanine runs show increased photodetachment yield as the number of guanine increases, in line with the fact that positive holes are the most stable in guanine runs. This correlation between photodetachment yield and the stability of the base radical may be explained by tunneling of the electron through the repulsive Coulomb barrier. Theoretical calculations on dinucleotide monophosphates show that the HOMO and HOMO-1 orbitals are localized on the bases. The wavelength dependence of electron detachment yield was studied for dG63-. Maximum electron photodetachment is observed in the wavelength range corresponding to base absorption (260-270 nm). This demonstrates the feasibility of gas-phase UV spectroscopy on large DNA anions. The calculations and the wavelength dependence suggest that the electron photodetachment is initiated at the bases and not at the phosphates. This also indicates that, although direct photodetachment could also occur, autodetachment from excited states, presumably corresponding to base excitation, is the dominant process at 260 nm. Excited-state dynamics of large DNA strands still remains largely unexplored, and photo-oxidation studies on trapped DNA multiply charged anions can help in bridging the gap between gas-phase studies on isolated bases or base pairs and solution-phase studies on full DNA strands.
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Affiliation(s)
- Valérie Gabelica
- Laboratoire de Spectrométrie de Masse, Université de Liège, Institut de Chimie Bat B6c, B-4000 Liège, Belgium.
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