1
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Gałyńska M, Boguslawski K. Benchmarking Ionization Potentials from pCCD Tailored Coupled Cluster Models. J Chem Theory Comput 2024; 20:4182-4195. [PMID: 38752491 PMCID: PMC11137826 DOI: 10.1021/acs.jctc.4c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024]
Abstract
The ionization potential (IP) is an important parameter providing essential insights into the reactivity of chemical systems. IPs are also crucial for designing, optimizing, and understanding the functionality of modern technological devices. We recently showed that limiting the CC ansatz to the seniority-zero sector proves insufficient in predicting reliable and accurate ionization potentials within an IP equation-of-motion coupled-cluster formalism. Specifically, the absence of dynamical correlation in the seniority-zero pair coupled cluster doubles (pCCD) model led to unacceptably significant errors of approximately 1.5 eV. In this work, we aim to explore the impact of dynamical correlation and the choice of the molecular orbital basis (canonical vs localized) in CC-type methods targeting 230 ionized states in 70 molecules, comprising small organic molecules, medium-sized organic acceptors, and nucleobases. We focus on pCCD-based approaches as well as the conventional IP-EOM-CCD and IP-EOM-CCSD. Their performance is compared to the CCSD(T) or CCSDT equivalent and experimental reference data. Our statistical analysis reveals that all investigated frozen-pair coupled cluster methods exhibit similar performance, with differences in errors typically within chemical accuracy (1 kcal/mol or 0.05 eV). Notably, the effect of the molecular orbital basis, such as canonical Hartree-Fock or natural pCCD-optimized orbitals, on the IPs is marginal if dynamical correlation is accounted for. Our study suggests that triple excitations are crucial in achieving chemical accuracy in IPs when modeling electron detachment processes with pCCD-based methods.
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Affiliation(s)
- Marta Gałyńska
- Institute of Physics, Faculty of Physics,
Astronomy, and Informatics, Nicolaus Copernicus
University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics,
Astronomy, and Informatics, Nicolaus Copernicus
University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland
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2
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Molina FL, Broquier M, Soorkia S, Grégoire G, Pino GA. Selective Tautomer Production and Cryogenic Ion Spectroscopy of Radical Cations: The Uracil and Thymine Cases. J Phys Chem A 2024. [PMID: 38656804 DOI: 10.1021/acs.jpca.4c02199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The vibrational and electronic spectroscopy of the radical cations of two nucleobases (NB) (uracil and thymine) was studied by cryogenic ion photodissociation spectroscopy. The radical cations have been generated from the photodissociation of NB-Ag+ complexes. A charge transfer process from the NB to Ag+ governs the deactivation mechanism, leading to the formation of the radical cation without further tautomerization. Single- and double-resonance spectroscopy allows for structural assignments of both the silver complexes and the radical cations by comparison with DFT-based calculations. Interestingly, a tautomer-dependent fragmentation is observed in the thymine enol form that involves the loss of NCO, a fragment which was never reported before for this NB. This selective photodissociation of silver complexes containing aromatic chromophore greatly expands the current technique to produce isomer-selected radical cations in the gas phase providing benchmark experimental data to assess calculations of open-shell species.
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Affiliation(s)
- Franco L Molina
- Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba. Haya de la Torre y Medina Allende. Pabellón Argentina, Ciudad Universitaria, Córdoba X5000HUA, Argentina
- INFIQC: Instituto de Investigaciones en Físico-Química de Córdoba (CONICET-UNC). Haya de la Torre y Medina Allende. Pabellón Argentina, Ciudad Universitaria, Córdoba X5000HUA, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba. Haya de la Torre y Medina Allende. Pabellón Argentina, Ciudad Universitaria, Córdoba X5000HUA, Argentina
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, Orsay F-91405, France
| | - Michel Broquier
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, Orsay F-91405, France
| | - Satchin Soorkia
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, Orsay F-91405, France
| | - Gilles Grégoire
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, Orsay F-91405, France
| | - Gustavo A Pino
- Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba. Haya de la Torre y Medina Allende. Pabellón Argentina, Ciudad Universitaria, Córdoba X5000HUA, Argentina
- INFIQC: Instituto de Investigaciones en Físico-Química de Córdoba (CONICET-UNC). Haya de la Torre y Medina Allende. Pabellón Argentina, Ciudad Universitaria, Córdoba X5000HUA, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba. Haya de la Torre y Medina Allende. Pabellón Argentina, Ciudad Universitaria, Córdoba X5000HUA, Argentina
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3
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Tiek DM, Erdogdu B, Razaghi R, Jin L, Sadowski N, Alamillo-Ferrer C, Hogg JR, Haddad BR, Drewry DH, Wells CI, Pickett JE, Song X, Goenka A, Hu B, Goldlust SA, Zuercher WJ, Pertea M, Timp W, Cheng SY, Riggins RB. Temozolomide-induced guanine mutations create exploitable vulnerabilities of guanine-rich DNA and RNA regions in drug-resistant gliomas. SCIENCE ADVANCES 2022; 8:eabn3471. [PMID: 35731869 PMCID: PMC9216507 DOI: 10.1126/sciadv.abn3471] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/04/2022] [Indexed: 05/28/2023]
Abstract
Temozolomide (TMZ) is a chemotherapeutic agent that has been the first-line standard of care for the aggressive brain cancer glioblastoma (GBM) since 2005. Although initially beneficial, TMZ resistance is universal and second-line interventions are an unmet clinical need. Here, we took advantage of the known mechanism of action of TMZ to target guanines (G) and investigated G-rich G-quadruplex (G4) and splice site changes that occur upon TMZ resistance. We report that TMZ-resistant GBM has guanine mutations that disrupt the G-rich DNA G4s and splice sites that lead to deregulated alternative splicing. These alterations create vulnerabilities, which are selectively targeted by either the G4-stabilizing drug TMPyP4 or a novel splicing kinase inhibitor of cdc2-like kinase. Last, we show that the G4 and RNA binding protein EWSR1 aggregates in the cytoplasm in TMZ-resistant GBM cells and patient samples. Together, our findings provide insight into targetable vulnerabilities of TMZ-resistant GBM and present cytoplasmic EWSR1 as a putative biomarker.
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Affiliation(s)
- Deanna M. Tiek
- The Ken and Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute, and Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Beril Erdogdu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Roham Razaghi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Lu Jin
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Norah Sadowski
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Carla Alamillo-Ferrer
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J. Robert Hogg
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bassem R. Haddad
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Lineberger Comprehensive Cancer Center, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carrow I. Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Julie E. Pickett
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xiao Song
- The Ken and Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute, and Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Anshika Goenka
- The Ken and Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute, and Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Bo Hu
- The Ken and Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute, and Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Samuel A. Goldlust
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ 07601, USA
| | - William J. Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mihaela Pertea
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Shi-Yuan Cheng
- The Ken and Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute, and Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Rebecca B. Riggins
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
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4
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Molina F, Dezalay J, Soorkia S, Broquier M, Hochlaf M, Pino GA, Grégoire G. Cryogenic IR and UV spectroscopy of isomer-selected cytosine radical cation. Phys Chem Chem Phys 2022; 24:25182-25190. [DOI: 10.1039/d2cp03953b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
The UV photodissociation of cryogenic-cooled isomer-selected cytosine–silver complex leads to the production of cytosine radical cation without isomerization.
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Affiliation(s)
- Franco Molina
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
- INFIQC (CONICET-UNC), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
- Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Jordan Dezalay
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
| | - Satchin Soorkia
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
| | - Michel Broquier
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
| | - Majdi Hochlaf
- Université Gustave Eiffel, COSYS/IMSE, 5 Bd Descartes 77454, Champs sur Marne, France
| | - Gustavo Ariel Pino
- INFIQC (CONICET-UNC), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Gilles Grégoire
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
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5
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Savee J, Sztáray B, Hemberger P, Zádor J, Bodi A, Osborn DL. Unimolecular isomerisation of 1,5-hexadiyne observed by threshold photoelectron photoion coincidence spectroscopy. Faraday Discuss 2022; 238:645-664. [DOI: 10.1039/d2fd00028h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The unimolecular isomerisation of the prompt propargyl + propargyl "head-to-head" adduct, 1,5- hexadiyne, to fulvene and benzene by the 3,4-dimethylenecyclobut-1-ene (DMCB) intermediate (all C6H6) was studied in the high-pressure limit...
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6
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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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7
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Ionization of adenine in the presence of Na+ in the gas phase and water. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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8
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Stemer DM, Abendroth JM, Cheung KM, Ye M, El Hadri MS, Fullerton EE, Weiss PS. Differential Charging in Photoemission from Mercurated DNA Monolayers on Ferromagnetic Films. NANO LETTERS 2020; 20:1218-1225. [PMID: 31960675 PMCID: PMC7058983 DOI: 10.1021/acs.nanolett.9b04622] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Spin-dependent and enantioselective electron-molecule scattering occurs in photoelectron transmission through chiral molecular films. This spin selectivity leads to electron spin filtering by molecular helices, with increasing magnitude concomitant with increasing numbers of helical turns. Using ultraviolet photoelectron spectroscopy, we measured spin-selective surface charging accompanying photoemission from ferromagnetic substrates functionalized with monolayers of mercurated DNA hairpins that constitute only one helical turn. Mercury ions bind specifically at thymine-thymine mismatches within self-hybridized single-stranded DNA, enabling precise control over the number and position of Hg2+ along the helical axis. Differential charging of the organic layers, manifested as substrate-magnetization-dependent photoionization energies, was observed for DNA hairpins containing Hg2+; no differences were measured for hairpin monolayers in the absence of Hg2+. Inversion of the DNA helical secondary structure at increased metal loading led to complementary inversion in spin selectivity. We attribute these results to increased scattering probabilities from relativistic enhancement of spin-orbit interactions in mercurated DNA.
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Affiliation(s)
- Dominik M. Stemer
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Materials Science & Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - John M. Abendroth
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Kevin M. Cheung
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Matthew Ye
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Mohammed S. El Hadri
- Center for Memory and Recording Research, University of California, San Diego, La Jolla, California 92093, United States
| | - Eric E. Fullerton
- Center for Memory and Recording Research, University of California, San Diego, La Jolla, California 92093, United States
| | - Paul S. Weiss
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Materials Science & Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Corresponding author: (PSW)
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9
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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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10
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Jena NR. Electron and hole interactions with P, Z, and P:Z and the formation of mutagenic products by proton transfer reactions. Phys Chem Chem Phys 2020; 22:919-931. [DOI: 10.1039/c9cp05367k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Z would act as an electron acceptor and P would capture a hole in the unnatural DNA. The latter process would produce mutagenic products via a proton transfer reaction.
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Affiliation(s)
- N. R. Jena
- Discipline of Natural Sciences
- Indian Institute of Information Technology, Design, and Manufacturing
- Jabalpur-482005
- India
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11
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Majer K, Signorell R, Heringa MF, Goldmann M, Hemberger P, Bodi A. Valence Photoionization of Thymine: Ionization Energies, Vibrational Structure, and Fragmentation Pathways from the Slow to the Ultrafast. Chemistry 2019; 25:14192-14204. [PMID: 31469456 DOI: 10.1002/chem.201903282] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Indexed: 11/06/2022]
Abstract
The photoionization of thymine has been studied by using vacuum ultraviolet radiation and imaging photoelectron photoion coincidence spectroscopy after aerosol flash vaporization and bulk evaporation. The two evaporation techniques have been evaluated by comparison of the photoelectron spectra and breakdown diagrams. The adiabatic ionization energies for the first four electronic states were determined to be 8.922±0.008, 9.851±0.008, 10.30±0.02, and 10.82±0.01 eV. Vibrational features have been assigned for the first three electronic states with the help of Franck-Condon factor calculations based on density functional theory and wave function theory vibrational analysis within the harmonic approximation. The breakdown diagram of thymine, as supported by composite method ab initio calculations, suggests that the main fragment ions are formed in sequential HNCO-, CO-, and H-loss dissociation steps from the thymine parent ion, with the first step corresponding to a retro-Diels-Alder reaction. The dissociation rate constants were extracted from the photoion time-of-flight distributions and used together with the breakdown curves to construct a statistical model to determine 0 K appearance energies of 11.15±0.16 and 11.95±0.09 eV for the m/z 83 and 55 fragment ions, respectively. These results have allowed us to revise previously proposed fragmentation mechanisms and to propose a model for the final, nonstatistical H-loss step in the breakdown diagram, yielding the m/z 54 fragment ion at an appearance energy of 13.24 eV.
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Affiliation(s)
- Katharina Majer
- Paul Scherrer Institute, 5232, Villigen, Switzerland.,Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Ruth Signorell
- Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Maarten F Heringa
- Paul Scherrer Institute, 5232, Villigen, Switzerland.,Present address: Givaudan Schweiz AG, 8310, Kemptthal, Switzerland
| | - Maximilian Goldmann
- Gymnasium Lerbermatt, 3098, Köniz, Switzerland.,Hochschule Luzern - Technik & Architektur, 6048, Horw, Switzerland
| | | | - Andras Bodi
- Paul Scherrer Institute, 5232, Villigen, Switzerland
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12
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Peng B, Van Beeumen R, Williams-Young DB, Kowalski K, Yang C. Approximate Green's Function Coupled Cluster Method Employing Effective Dimension Reduction. J Chem Theory Comput 2019; 15:3185-3196. [PMID: 30951302 DOI: 10.1021/acs.jctc.9b00172] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Green's function coupled cluster (GFCC) method, originally proposed in the early 1990s, is a powerful many-body tool for computing and analyzing the electronic structure of molecular and periodic systems, especially when electrons of the system are strongly correlated. However, in order for the GFCC to become a method that may be routinely used in the electronic structure calculations, robust numerical techniques and approximations must be employed to reduce its extremely high computational overhead. In our recent studies, it has been demonstrated that the GFCC equations can be solved directly in the frequency domain using iterative linear solvers, which can be easily distributed in a massively parallel environment. In the present work, we demonstrate a successful application of model-order-reduction (MOR) techniques in the GFCC framework. Briefly speaking, for a frequency regime of interest that requires high-resolution descriptions of spectral function, instead of solving the GFCC linear equation of full dimension for every single frequency point of interest, an efficiently solvable linear system model of a reduced dimension may be built upon projecting the original GFCC linear system onto a subspace. From this reduced order model is obtained a reasonable approximation to the full dimensional GFCC linear equations in both interpolative and extrapolative spectral regions. Here, we show that the subspace can be properly constructed in an iterative manner from the auxiliary vectors of the GFCC linear equations at some selected frequencies within the spectral region of interest. During the iterations, the quality of the subspace, as well as the linear system model, can be systematically improved. The method is tested in this work in terms of the efficiency and accuracy of computing spectral functions for some typical molecular systems such as carbon monoxide, 1,3-butadiene, benzene, and adenine. To reach the same level of accuracy as that of the original GFCC method, the application of MOR in the GFCC method is able to significantly lower the original computational cost for the aforementioned molecules in designated frequency regimes. As a byproduct, the reduced order model obtained by this method is found to provide a high-quality initial guess, which improves the convergence rate for the existing iterative linear solver.
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Affiliation(s)
- Bo Peng
- William R. Wiley Environmental Molecular Sciences Laboratory, Battelle , Pacific Northwest National Laboratory , K8-91, P.O. Box 999, Richland , Washington 99352 , United States
| | - Roel Van Beeumen
- Computational Research Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - David B Williams-Young
- Computational Research Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Karol Kowalski
- William R. Wiley Environmental Molecular Sciences Laboratory, Battelle , Pacific Northwest National Laboratory , K8-91, P.O. Box 999, Richland , Washington 99352 , United States
| | - Chao Yang
- Computational Research Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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13
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Zhang Y, Xie P, Yang S, Han K. Ionization and Electron Attachment for Nucleobases in Water. J Phys Chem B 2019; 123:1237-1247. [DOI: 10.1021/acs.jpcb.8b09435] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yan Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao, Binhai Road 72, Qingdao 266237, China
| | - Peng Xie
- School of Chemistry & Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Songqiu Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
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14
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Karton A. Thermochemistry of Guanine Tautomers Re-Examined by Means of High-Level CCSD(T) Composite Ab Initio Methods. Aust J Chem 2019. [DOI: 10.1071/ch19276] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We obtained accurate gas-phase tautomerization energies for a set of 14 guanine tautomers by means of high-level thermochemical procedures approximating the CCSD(T) energy at the complete basis set (CBS) limit. For the five low-lying tautomers, we use the computationally demanding W1-F12 composite method for obtaining the tautomerization energies. The relative W1-F12 tautomerization enthalpies at 298K are: 0.00 (1), 2.37 (2), 2.63 (3), 4.03 (3′), and 14.31 (4) kJmol−1. Thus, as many as four tautomers are found within a small energy window of less than 1.0kcalmol−1 (1kcalmol−1=4.184kJmol−1). We use these highly accurate W1-F12 tautomerization energies to evaluate the performance of a wide range of lower-level composite ab initio procedures. The Gn composite procedures (G4, G4(MP2), G4(MP2)-6X, G3, G3B3, G3(MP2), and G3(MP2)B3) predict that the enol tautomer (3) is more stable than the keto tautomer (2) by amounts ranging from 0.36 (G4) to 1.28 (G3(MP2)) kJmol−1. We also find that an approximated CCSD(T)/CBS energy calculated as HF/jul-cc-pV{D,T}Z+CCSD/jul-cc-pVTZ+(T)/jul-cc-pVDZ results in a root-mean-square deviation (RMSD) of merely 0.11kJmol−1 relative to the W1-F12 reference values. We use this approximated CCSD(T)/CBS method to obtain the tautomerization energies of 14 guanine tautomers. The relative tautomerization enthalpies at 298K are: 0.00 (1), 2.20 (2), 2.51 (3), 4.06 (3′), 14.30 (4), 25.65 (5), 43.78 (4′), 53.50 (6′), 61.58 (6), 77.37 (7), 82.52 (8′), 86.02 (9), 100.70 (10), and 121.01 (8) kJmol−1. Using these tautomerization enthalpies, we evaluate the performance of standard and composite methods for the entire set of 14 guanine tautomers. The best-performing procedures emerge as (RMSDs are given in parentheses): G4(MP2)-6X (0.51), CCSD(T)+ΔMP2/CBS (0.52), and G4(MP2) (0.64kJmol−1). The worst performers are CCSD(T)/AVDZ (1.05), CBS-QB3 (1.24), and CBS-APNO (1.38kJmol−1).
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15
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Peng B, Kowalski K. Green's function coupled cluster formulations utilizing extended inner excitations. J Chem Phys 2018; 149:214102. [PMID: 30525725 DOI: 10.1063/1.5046529] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this paper, we analyze new approximations of the Green's function coupled cluster (GFCC) method where locations of poles are improved by extending the excitation level of inner auxiliary operators. These new GFCC approximations can be categorized as the GFCC-i(n, m) method, where the excitation level of the inner auxiliary operators (m) used to describe the ionization potential and electron affinity effects in the N - 1 and N + 1 particle spaces is higher than the excitation level (n) used to correlate the ground-state coupled cluster wave function for the N-electron system. Furthermore, we reveal the so-called "n + 1" rule in this category [or the GFCC-i(n, n + 1) method], which states that in order to maintain size-extensivity of the Green's function matrix elements, the excitation level of inner auxiliary operators X p (ω) and Y q (ω) cannot exceed n + 1. We also discuss the role of the moments of coupled cluster equations that in a natural way assures these properties. Our implementation in the present study is focused on the first approximation in this GFCC category, i.e., the GFCC-i(2,3) method. As our first practice, we use the GFCC-i(2,3) method to compute the spectral functions for the N2 and CO molecules in the inner and outer valence regimes. In comparison with the Green's function coupled cluster singles, doubles results, the computed spectral functions from the GFCC-i(2,3) method exhibit better agreement with the experimental results and other theoretical results, particularly in terms of providing higher resolution of satellite peaks and more accurate relative positions of these satellite peaks with respect to the main peak positions.
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Affiliation(s)
- Bo Peng
- William R. Wiley Environmental Molecular Sciences Laboratory, 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
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16
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Schulz CE, Dutta AK, Izsák R, Pantazis DA. Systematic High-Accuracy Prediction of Electron Affinities for Biological Quinones. J Comput Chem 2018; 39:2439-2451. [PMID: 30281169 DOI: 10.1002/jcc.25570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 11/07/2022]
Abstract
Quinones play vital roles as electron carriers in fundamental biological processes; therefore, the ability to accurately predict their electron affinities is crucial for understanding their properties and function. The increasing availability of cost-effective implementations of correlated wave function methods for both closed-shell and open-shell systems offers an alternative to density functional theory approaches that have traditionally dominated the field despite their shortcomings. Here, we define a benchmark set of quinones with experimentally available electron affinities and evaluate a range of electronic structure methods, setting a target accuracy of 0.1 eV. Among wave function methods, we test various implementations of coupled cluster (CC) theory, including local pair natural orbital (LPNO) approaches to canonical and parameterized CCSD, the domain-based DLPNO approximation, and the equations-of-motion approach for electron affinities, EA-EOM-CCSD. In addition, several variants of canonical, spin-component-scaled, orbital-optimized, and explicitly correlated (F12) Møller-Plesset perturbation theory are benchmarked. Achieving systematically the target level of accuracy is challenging and a composite scheme that combines canonical CCSD(T) with large basis set LPNO-based extrapolation of correlation energy proves to be the most accurate approach. Methods that offer comparable performance are the parameterized LPNO-pCCSD, the DLPNO-CCSD(T0 ), and the orbital optimized OO-SCS-MP2. Among DFT methods, viable practical alternatives are only the M06 and the double hybrids, but the latter should be employed with caution because of significant basis set sensitivity. A highly accurate yet cost-effective DLPNO-based coupled cluster approach is used to investigate the methoxy conformation effect on the electron affinities of ubiquinones found in photosynthetic bacterial reaction centers. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Christine E Schulz
- Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, 44780, Bochum, Germany
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Achintya Kumar Dutta
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Róbert Izsák
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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17
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Zhao HY, Lau KC, Garcia GA, Nahon L, Carniato S, Poisson L, Schwell M, Al-Mogren MM, Hochlaf M. Unveiling the complex vibronic structure of the canonical adenine cation. Phys Chem Chem Phys 2018; 20:20756-20765. [PMID: 29989120 DOI: 10.1039/c8cp02930j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adenine, a DNA base, exists as several tautomers and isomers that are closely lying in energy and that may form a mixture upon vaporization of solid adenine. Indeed, it is challenging to bring adenine into the gas phase, especially as a unique tautomer. The experimental conditions were tuned to prepare a jet-cooled canonical adenine (9H-adenine). This isolated DNA base was ionized by single VUV photons from a synchrotron beamline and the corresponding slow photoelectron spectrum was compared to ab initio computations of the neutral and ionic species. We report the vibronic structure of the X+ 2A'' (D0), A+ 2A' (D1) and B+ 2A'' (D2) electronic states of the 9H adenine cation, from the adiabatic ionization energy (AIE) up to AIE + 1.8 eV. Accurate AIEs are derived for the 9H-adenine (X[combining tilde] 1A') + hν → 9H-adenine+ (X+ 2A'', A+ 2A', B+ 2A'') + e- transitions. Close to the AIE, we fully assign the rich vibronic structure solely to the 9H-adenine (X 1A') + hν → 9H-adenine+ (X+ 2A'') transition. Importantly, we show that the lowest cationic electronic states of canonical adenine are coupled vibronically. The present findings are important for understanding the effects of ionizing radiation and the charge distribution on this elementary building block of life, at ultrafast, short, and long timescales.
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Affiliation(s)
- Hong Yan Zhao
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong
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18
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Peng B, Kowalski K. Green's Function Coupled-Cluster Approach: Simulating Photoelectron Spectra for Realistic Molecular Systems. J Chem Theory Comput 2018; 14:4335-4352. [PMID: 29957945 DOI: 10.1021/acs.jctc.8b00313] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper, we present an efficient implementation for the analytical energy-dependent Green's function coupled-cluster with singles and doubles (GFCCSD) approach with our first practice being computing spectral functions of realistic molecular systems. Because of its algebraic structure, the presented method is highly scalable and is capable of computing spectral function for a given molecular system in any energy region. Several typical examples have been given to demonstrate its capability of computing spectral functions not only in the valence band but also in the core-level energy region. Satellite peaks have been observed in the inner valence band and core-level energy region where a many-body effect becomes significant and the single particle picture of ionization often breaks down. The accuracy test has been carried out by extensively comparing the computed spectral functions by our GFCCSD method with experimental photoelectron spectra as well as the theoretical ionization potentials obtained from other methods. It turns out the GFCCSD method is able to provide a qualitative or semiquantitative level of description of ionization processes in both the core and valence regimes. To significantly improve the GFCCSD results for the main ionic states, a larger basis set can usually be employed, whereas the improvement of the GFCCSD results for the satellite states needs higher-order many-body terms to be included in the GFCC implementation.
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Affiliation(s)
- Bo Peng
- William R. Wiley Environmental Molecular Sciences Laboratory, Battelle, Pacific Northwest National Laboratory , K8-91, P.O. Box 999, Richland , Washington 99352 , United States
| | - Karol Kowalski
- William R. Wiley Environmental Molecular Sciences Laboratory, Battelle, Pacific Northwest National Laboratory , K8-91, P.O. Box 999, Richland , Washington 99352 , United States
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19
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Heil A, Marian CM. DFT/MRCI Hamiltonian for odd and even numbers of electrons. J Chem Phys 2017; 147:194104. [DOI: 10.1063/1.5003246] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Adrian Heil
- Institute of Theoretical and Computational Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Christel M. Marian
- Institute of Theoretical and Computational Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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20
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Kumar D, Dutta AK, Manohar PU. Resolution of the Identity and Cholesky Representation of EOM-MP2 Approximation: Implementation, Accuracy and Efficiency. J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1378-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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21
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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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22
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Bose S, Ghosh D. An interaction energy driven biased sampling technique: A faster route to ionization spectra in condensed phase. J Comput Chem 2017; 38:2248-2257. [DOI: 10.1002/jcc.24875] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/06/2017] [Accepted: 06/19/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Samik Bose
- Physical and Materials Chemistry Division; CSIR-National Chemical Laboratory; Pune 411008 India
| | - Debashree Ghosh
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; Kolkata 700032 India
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23
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Trofimov AB, Holland DMP, Powis I, Menzies RC, Potts AW, Karlsson L, Gromov EV, Badsyuk IL, Schirmer J. Ionization of pyridine: Interplay of orbital relaxation and electron correlation. J Chem Phys 2017; 146:244307. [DOI: 10.1063/1.4986405] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- A. B. Trofimov
- Laboratory of Quantum Chemistry, Irkutsk State University, Karl Marx St. 1, 664003 Irkutsk, Russia
- Favorsky’s Institute of Chemistry, SB RAS, Favorsky St. 1, 664033 Irkutsk, Russia
| | - D. M. P. Holland
- Daresbury Laboratory, Daresbury, Warrington, Cheshire WA4 4AD, United Kingdom
| | - I. Powis
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - R. C. Menzies
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - A. W. Potts
- Department of Physics, King’s College, Strand, London WC2R 2LS, United Kingdom
| | - L. Karlsson
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - E. V. Gromov
- Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
| | - I. L. Badsyuk
- Favorsky’s Institute of Chemistry, SB RAS, Favorsky St. 1, 664033 Irkutsk, Russia
| | - J. Schirmer
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
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24
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Krylov AI. The Quantum Chemistry of Open-Shell Species. REVIEWS IN COMPUTATIONAL CHEMISTRY 2017. [DOI: 10.1002/9781119356059.ch4] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Anna I. Krylov
- Department of Chemistry; University of Southern California; Los Angeles CA United States
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25
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Rubešová M, Jurásková V, Slavíček P. Efficient modeling of liquid phase photoemission spectra and reorganization energies: Difficult case of multiply charged anions. J Comput Chem 2017; 38:427-437. [DOI: 10.1002/jcc.24696] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/25/2016] [Accepted: 11/23/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Martina Rubešová
- Department of Physical Chemistry; University of Chemistry and Technology; Technická 5 Prague 16628 Czech Republic
| | - Veronika Jurásková
- Department of Physical Chemistry; University of Chemistry and Technology; Technická 5 Prague 16628 Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry; University of Chemistry and Technology; Technická 5 Prague 16628 Czech Republic
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26
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Chen Z, Lau KC, Garcia GA, Nahon L, Božanić DK, Poisson L, Al-Mogren MM, Schwell M, Francisco JS, Bellili A, Hochlaf M. Identifying Cytosine-Specific Isomers via High-Accuracy Single Photon Ionization. J Am Chem Soc 2016; 138:16596-16599. [DOI: 10.1021/jacs.6b10413] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Ziyong Chen
- Department
of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Kai-Chung Lau
- Department
of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Gustavo A. Garcia
- Synchrotron SOLEIL, L’orme des
Merisiers, Saint-Aubin
- BP 48, 91192 Gif-sur-Yvette Cedex, France
| | - Laurent Nahon
- Synchrotron SOLEIL, L’orme des
Merisiers, Saint-Aubin
- BP 48, 91192 Gif-sur-Yvette Cedex, France
| | - Dušan K. Božanić
- Synchrotron SOLEIL, L’orme des
Merisiers, Saint-Aubin
- BP 48, 91192 Gif-sur-Yvette Cedex, France
| | - Lionel Poisson
- LIDYL,
CEA, CNRS, Université Paris-Saclay, CEA Saclay, F-91191 Gif-sur-Yvette, France
| | - Muneerah Mogren Al-Mogren
- Chemistry
Department, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Martin Schwell
- Laboratoire
Interuniversitaire des Systèmes Atmosphériques (LISA),
UMR 7583 CNRS, Universités Paris-Est Créteil et Paris Diderot, 61 Avenue du Général de Gaulle, 94010 Créteil, France
| | - Joseph S. Francisco
- Department
of Chemistry, University of Nebraska-Lincoln. 433 Hamilton Hall, Lincoln, Nebraska 68588-0304, United States
| | - Ayad Bellili
- Laboratoire
Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est. 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - Majdi Hochlaf
- Laboratoire
Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est. 5 bd Descartes, 77454 Marne-la-Vallée, France
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27
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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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28
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Raeber AE, Wong BM. The Importance of Short- and Long-Range Exchange on Various Excited State Properties of DNA Monomers, Stacked Complexes, and Watson-Crick Pairs. J Chem Theory Comput 2016; 11:2199-209. [PMID: 26574420 DOI: 10.1021/acs.jctc.5b00105] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a detailed analysis of several time-dependent DFT (TD-DFT) methods, including conventional hybrid functionals and two types of nonempirically tuned range-separated functionals, for predicting a diverse set of electronic excitations in DNA nucleobase monomers and dimers. This large and extensive set of excitations comprises a total of 50 different transitions (for each tested DFT functional) that includes several n → π and π → π* valence excitations, long-range charge-transfer excitations, and extended Rydberg transitions (complete with benchmark calculations from high-level EOM-CCSD(T) methods). The presence of localized valence excitations as well as extreme long-range charge-transfer excitations in these systems poses a serious challenge for TD-DFT methods that allows us to assess the importance of both short- and long-range exchange contributions for simultaneously predicting all of these various transitions. In particular, we find that functionals that do not have both short- and full long-range exchange components are unable to predict the different types of nucleobase excitations with the same accuracy. Most importantly, the current study highlights the importance of both short-range exchange and a nonempirically tuned contribution of long-range exchange for accurately predicting the diverse excitations in these challenging nucleobase systems.
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Affiliation(s)
- Alexandra E Raeber
- Department of Chemical & Environmental Engineering and Materials Science & Engineering Program, University of California, Riverside , Riverside, California 92521, United States
| | - Bryan M Wong
- Department of Chemical & Environmental Engineering and Materials Science & Engineering Program, University of California, Riverside , Riverside, California 92521, United States
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29
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Nguyen NL, Borghi G, Ferretti A, Marzari N. First-Principles Photoemission Spectroscopy of DNA and RNA Nucleobases from Koopmans-Compliant Functionals. J Chem Theory Comput 2016; 12:3948-58. [DOI: 10.1021/acs.jctc.6b00145] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ngoc Linh Nguyen
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Giovanni Borghi
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Centro
S3, CNR−Istituto Nanoscienze, 41125 Modena, Italy
| | | | - Nicola Marzari
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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30
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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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31
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Kostko O, Bandyopadhyay B, Ahmed M. Vacuum Ultraviolet Photoionization of Complex Chemical Systems. Annu Rev Phys Chem 2016; 67:19-40. [DOI: 10.1146/annurev-physchem-040215-112553] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Oleg Kostko
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
| | - Biswajit Bandyopadhyay
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
| | - Musahid Ahmed
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
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32
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King SB, Stephansen AB, Yokoi Y, Yandell MA, Kunin A, Takayanagi T, Neumark DM. Electron accommodation dynamics in the DNA base thymine. J Chem Phys 2016; 143:024312. [PMID: 26178110 DOI: 10.1063/1.4923343] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The dynamics of electron attachment to the DNA base thymine are investigated using femtosecond time-resolved photoelectron imaging of the gas phase iodide-thymine (I(-)T) complex. An ultraviolet pump pulse ejects an electron from the iodide and prepares an iodine-thymine temporary negative ion that is photodetached with a near-IR probe pulse. The resulting photoelectrons are analyzed with velocity-map imaging. At excitation energies ranging from -120 meV to +90 meV with respect to the vertical detachment energy (VDE) of 4.05 eV for I(-)T, both the dipole-bound and valence-bound negative ions of thymine are observed. A slightly longer rise time for the valence-bound state than the dipole-bound state suggests that some of the dipole-bound anions convert to valence-bound species. No evidence is seen for a dipole-bound anion of thymine at higher excitation energies, in the range of 0.6 eV above the I(-)T VDE, which suggests that if the dipole-bound anion acts as a "doorway" to the valence-bound anion, it only does so at excitation energies near the VDE of the complex.
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Affiliation(s)
- Sarah B King
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Anne B Stephansen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 København Ø, Denmark
| | - Yuki Yokoi
- Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Margaret A Yandell
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Alice Kunin
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Toshiyuki Takayanagi
- Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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33
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Bhaskaran-Nair K, Kowalski K, Shelton WA. Coupled cluster Green function: Model involving single and double excitations. J Chem Phys 2016; 144:144101. [DOI: 10.1063/1.4944960] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kiran Bhaskaran-Nair
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, USA
- Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803, 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
| | - William A. Shelton
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, USA
- Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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34
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Markush P, Bolognesi P, Cartoni A, Rousseau P, Maclot S, Delaunay R, Domaracka A, Kocisek J, Castrovilli MC, Huber BA, Avaldi L. The role of the environment in the ion induced fragmentation of uracil. Phys Chem Chem Phys 2016; 18:16721-9. [DOI: 10.1039/c6cp01940d] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fragmentation of uracil molecules and pure and nano-hydrated uracil clusters by 12C4+ ion impact is investigated.
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Affiliation(s)
| | | | - Antonella Cartoni
- CNR-ISM
- Monterotondo Scalo
- Italy
- Dipartimento di Chimica
- Sapienza Università di Roma
| | - Patrick Rousseau
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
| | - Sylvain Maclot
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
| | - Rudy Delaunay
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
| | - Alicja Domaracka
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
| | - Jaroslav Kocisek
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
- J. Heyrovský Institute of Physical Chemistry
| | | | - Bernd A. Huber
- Normandie Université
- CIMAP (UMR6252 CEA/CNRS/ENSICAEN/UNICAEN)
- 14070 Caen Cedex 5
- France
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35
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Mantela M, Morphis A, Tassi M, Simserides C. Lowest ionisation and excitation energies of biologically important heterocyclic planar molecules. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1113313] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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36
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A State-Specific PCM–DFT method to include dynamic solvent effects in the calculation of ionization energies: Application to DNA bases. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.05.045] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Fulfer KD, Hardy D, Aguilar AA, Poliakoff ED. High-resolution photoelectron spectra of the pyrimidine-type nucleobases. J Chem Phys 2015; 142:224310. [DOI: 10.1063/1.4922310] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- K. D. Fulfer
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - D. Hardy
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - A. A. Aguilar
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - E. D. Poliakoff
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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38
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Dutta AK, Vaval N, Pal S. EOMIP-CCSD(2)*: An Efficient Method for the Calculation of Ionization Potentials. J Chem Theory Comput 2015; 11:2461-72. [DOI: 10.1021/ct500927h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Achintya Kumar Dutta
- Physical Chemistry Division, CSIR−National Chemical Laboratory, Pune-411008, India
| | - Nayana Vaval
- Physical Chemistry Division, CSIR−National Chemical Laboratory, Pune-411008, India
| | - Sourav Pal
- Physical Chemistry Division, CSIR−National Chemical Laboratory, Pune-411008, India
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39
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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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40
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Hochlaf M, Pan Y, Lau KC, Majdi Y, Poisson L, Garcia GA, Nahon L, Al Mogren MM, Schwell M. Vibrationally resolved photoelectron spectroscopy of electronic excited states of DNA bases: application to the ã state of thymine cation. J Phys Chem A 2015; 119:1146-53. [PMID: 25611856 DOI: 10.1021/acs.jpca.5b00466] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For fully understanding the light-molecule interaction dynamics at short time scales, recent theoretical and experimental studies proved the importance of accurate characterizations not only of the ground (D0) but also of the electronic excited states (e.g., D1) of molecules. While ground state investigations are currently straightforward, those of electronic excited states are not. Here, we characterized the à electronic state of ionic thymine (T(+)) DNA base using explicitly correlated coupled cluster ab initio methods and state-of-the-art synchrotron-based electron/ion coincidence techniques. The experimental spectrum is composed of rich and long vibrational progressions corresponding to the population of the low frequency modes of T(+)(Ã). This work challenges previous numerous works carried out on DNA bases using common synchrotron and VUV-based photoelectron spectroscopies. We provide hence a powerful theoretical and experimental framework to study the electronic structure of ionized DNA bases that could be generalized to other medium-sized biologically relevant systems.
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Affiliation(s)
- Majdi Hochlaf
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
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41
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Dutta AK, Vaval N, Pal S. A new scheme for perturbative triples correction to (0,1) sector of Fock space multi-reference coupled cluster method: Theory, implementation, and examples. J Chem Phys 2015; 142:044113. [DOI: 10.1063/1.4906233] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Achintya Kumar Dutta
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Nayana Vaval
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Sourav Pal
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
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42
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Majdi Y, Hochlaf M, Pan Y, Lau KC, Poisson L, Garcia GA, Nahon L, Al-Mogren MM, Schwell M. Theoretical and Experimental Photoelectron Spectroscopy Characterization of the Ground State of Thymine Cation. J Phys Chem A 2015; 119:5951-8. [DOI: 10.1021/jp510716c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Youssef Majdi
- Laboratoire de Spectroscopie Atomique,
Moléculaire et Applications (LSAMA), Université de Tunis El Manar, Tunis, Tunisia
| | - Majdi Hochlaf
- Laboratoire
Modélisation et Simulation
Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est, 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - Yi Pan
- Department of Biology and
Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Kai-Chung Lau
- Department of Biology and
Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Lionel Poisson
- Laboratoire Francis
Perrin, CNRS URA 2453, CEA, IRAMIS, Laboratoire
Interactions
Dynamique et Lasers, Bât 522, F-91191 Gif/Yvette, France
| | - Gustavo A. Garcia
- Synchrotron SOLEIL, L’orme des Merisiers, Saint-Aubin, BP 48 91192 Gif-sur-Yvette Cedex France
| | - Laurent Nahon
- Synchrotron SOLEIL, L’orme des Merisiers, Saint-Aubin, BP 48 91192 Gif-sur-Yvette Cedex France
| | - Muneerah Mogren Al-Mogren
- Chemistry Department, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Martin Schwell
- Laboratoire Interuniversitaire
des Systèmes
Atmosphériques (LISA), UMR 7583 CNRS, Universités Paris-Est Créteil et Paris Diderot, Institut Pierre et Simon Laplace, 61 Avenue du
Général de Gaulle, 94010 Créteil, France
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43
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Grimme S, Bauer CA. Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases Uracil, Thymine, Cytosine, and Guanine. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:125-140. [PMID: 26307693 DOI: 10.1255/ejms.1313] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich- Wilhelms-Universität Bonn, Beringstr. 4, D-53115, Bonn, Germany. - bonn.de
| | - Christopher Alexander Bauer
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, D-53115, Bonn, Germany.
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44
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Poully JC, Miles J, De Camillis S, Cassimi A, Greenwood JB. Proton irradiation of DNA nucleosides in the gas phase. Phys Chem Chem Phys 2015; 17:7172-80. [DOI: 10.1039/c4cp05303f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Charge localization within nucleosides after proton irradiation is strongly influenced by the ionization energy of the base.
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Affiliation(s)
| | - Jordan Miles
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Northern Ireland
- UK
| | - Simone De Camillis
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Northern Ireland
- UK
| | - Amine Cassimi
- CIMAP (UMR 6252 CEA, Université de Caen, ENSICAEN, CNRS)
- 14070 CAEN Cedex 5
- France
| | - Jason B. Greenwood
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Northern Ireland
- UK
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45
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Camillis SD, Miles J, Alexander G, Ghafur O, Williams ID, Townsend D, Greenwood JB. Ultrafast non-radiative decay of gas-phase nucleosides. Phys Chem Chem Phys 2015; 17:23643-50. [DOI: 10.1039/c5cp03806e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
De-excitation of DNA nucleosides on picosecond timescales was measured and found to be twice as fast as the equivalent nucleobases.
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Affiliation(s)
- Simone De Camillis
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Jordan Miles
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Grace Alexander
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Omair Ghafur
- Institute of Photonics and Quantum Sciences
- Heriot-Watt University
- Edinburgh EH14 4AS
- UK
| | - Ian D. Williams
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Dave Townsend
- Institute of Photonics and Quantum Sciences
- Heriot-Watt University
- Edinburgh EH14 4AS
- UK
- Institute of Chemical Sciences
| | - Jason B. Greenwood
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
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46
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Dawley MM, Tanzer K, Cantrell WA, Plattner P, Brinkmann NR, Scheier P, Denifl S, Ptasińska S. Electron ionization of the nucleobases adenine and hypoxanthine near the threshold: a combined experimental and theoretical study. Phys Chem Chem Phys 2014; 16:25039-53. [DOI: 10.1039/c4cp03452j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Electronic transport through oligopeptide chains: An artificial prototype of a molecular diode. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.07.062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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48
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Das T, Ghosh D. Ionization-Induced Tautomerization in Cytosine and Effect of Solvation. J Phys Chem A 2014; 118:5323-32. [DOI: 10.1021/jp503947d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tamal Das
- 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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49
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Schwell M, Hochlaf M. Photoionization Spectroscopy of Nucleobases and Analogues in the Gas Phase Using Synchrotron Radiation as Excitation Light Source. Top Curr Chem (Cham) 2014; 355:155-208. [DOI: 10.1007/128_2014_550] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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50
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Modrzejewski M, Rajchel Ł, Chalasinski G, Szczesniak MM. Density-Dependent Onset of the Long-Range Exchange: A Key to Donor–Acceptor Properties. J Phys Chem A 2013; 117:11580-6. [DOI: 10.1021/jp4088404] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marcin Modrzejewski
- Faculty
of Chemistry, University of Warsaw, 02-093 Warsaw, Pasteura 1, Poland
| | - Łukasz Rajchel
- Faculty
of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45117 Essen, Germany
- Interdisciplinary
Centre for Mathematical and Computational Modelling, University of Warsaw, Prosta 69, 00-838 Warsaw, Poland
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