1
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Zhou Q, Guo W, Hu Z, Yan S, Jie J, Su H. Can methylated purine bases act as photoionization hotspots? Photochem Photobiol 2024; 100:368-379. [PMID: 37792888 DOI: 10.1111/php.13862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 10/06/2023]
Abstract
The direct photoionization of DNA canonical bases under ultraviolet radiation is difficult due to the high ionization potentials. According to previous quantum chemical calculations, methylation can have great influence on the ionization potential. Are methylated nucleobases prone to photoionization and cause DNA damage? As an important epigenetic modification in transcription, expression, and regulation of genes, it is of great biological significance to explore the effect of methylation on base photoionization from the experimental perspective. Herein, we study the photoionization behavior of methylated purines 6 mA and 6mG at 266 nm using a nanosecond transient UV-Vis spectroscopy. The hydrated electron and methylated base radicals are observed, indicating the occurrence of photoionization for both 6mG and 6 mA. We measured one-photon ionization yields to be (5.0 ± 0.2) × 10-3 and (1.4 ± 0.2) × 10-3 for 6mG and 6 mA, respectively. These are higher than those of (dA)20 and (dA20 )·(dT20 ) previously reported, indicating that methylation significantly promotes base photoionization with a stronger effect than base stacking, consistent with calculations in literature. Given that the hydrated electrons and methylated base radicals from photoionization can trigger a cascade of deleterious reactions, the methylated purine bases may act as hotspots of DNA photoionization damage of living organisms.
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Affiliation(s)
- Qian Zhou
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Wenwen Guo
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Zheng Hu
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Shuyi Yan
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing, China
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2
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Mohammad H, Anantram MP. Charge transport through DNA with energy-dependent decoherence. Phys Rev E 2023; 108:044403. [PMID: 37978586 DOI: 10.1103/physreve.108.044403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/08/2023] [Indexed: 11/19/2023]
Abstract
Modeling charge transport in DNA is essential to understand and control the electrical properties and develop DNA-based nanoelectronics. DNA is a fluctuating molecule that exists in a solvent environment, which makes the electron susceptible to decoherence. While knowledge of the Hamiltonian responsible for decoherence will provide a microscopic description, the interactions are complex and methods to calculate decoherence are unclear. One prominent phenomenological model to include decoherence is through fictitious probes that depend on spatially variant scattering rates. However, the built-in energy independence of the decoherence (E-indep) model overestimates the transmission in the bandgap and washes out distinct features inside the valence or conduction bands. In this study, we introduce a related model where the decoherence rate is energy-dependent (E-dep). This decoherence rate is maximum at energy levels and decays away from these energies. Our results show that the E-dep model allows for exponential transmission decay with the DNA length and maintains features within the bands' transmission spectra. We further demonstrate that we can obtain DNA conductance values within the experimental range. Our model can help study and design nanoelectronics devices that utilize weakly coupled molecular structures such as DNA.
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Affiliation(s)
- Hashem Mohammad
- Department of Electrical Engineering, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98195, USA
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3
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Asmussen JD, Abid AR, Sundaralingam A, Bastian B, Sishodia K, De S, Ben Ltaief L, Krishnan S, Pedersen HB, Mudrich M. Secondary ionization of pyrimidine nucleobases and their microhydrated derivatives in helium nanodroplets. Phys Chem Chem Phys 2023; 25:24819-24828. [PMID: 37671772 DOI: 10.1039/d3cp02879h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Radiation damage in biological systems by ionizing radiation is predominantly caused by secondary processes such as charge and energy transfer leading to the breaking of bonds in DNA. Here, we study the fragmentation of cytosine (Cyt) and thymine (Thy) molecules, clusters and microhydrated derivatives induced by direct and indirect ionization initiated by extreme-ultraviolet (XUV) irradiation. Photofragmentation mass spectra and photoelectron spectra of free Cyt and Thy molecules are compared with mass and electron spectra of Cyt/Thy clusters and microhydrated Cyt/Thy molecules formed by aggregation in superfluid helium (He) nanodroplets. Penning ionization after resonant excitation of the He droplets is generally found to cause less fragmentation compared to direct photoionization and charge-transfer ionization after photoionization of the He droplets. When Cyt/Thy molecules and oligomers are complexed with water molecules, their fragmentation is efficiently suppressed. However, a similar suppression of fragmentation is observed when homogeneous Cyt/Thy clusters are formed in He nanodroplets, indicating a general trend. Penning ionization electron spectra (PIES) of Cyt/Thy are broad and nearly featureless but PIES of their microhydrated derivatives point at a sequential ionization process ending in unfragmented microsolvated Cyt/Thy cations.
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Affiliation(s)
- Jakob D Asmussen
- Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark.
| | - Abdul R Abid
- Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark.
| | | | - Björn Bastian
- Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark.
| | - Keshav Sishodia
- Quantum Center of Excellence for Diamond and Emergent Materials and Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
| | - Subhendu De
- Quantum Center of Excellence for Diamond and Emergent Materials and Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
| | - Ltaief Ben Ltaief
- Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark.
| | - Sivarama Krishnan
- Quantum Center of Excellence for Diamond and Emergent Materials and Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
| | - Henrik B Pedersen
- Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark.
| | - Marcel Mudrich
- Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark.
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4
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Lucia-Tamudo J, Díaz-Tendero S, Nogueira JJ. Intramolecular and intermolecular hole delocalization rules the reducer character of isolated nucleobases and homogeneous single-stranded DNA. Phys Chem Chem Phys 2023; 25:14578-14589. [PMID: 37191244 DOI: 10.1039/d3cp00884c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The use of DNA strands as nanowires or electrochemical biosensors requires a deep understanding of charge transfer processes along the strand, as well as of the redox properties. These properties are computationally assessed in detail throughout this study. By applying molecular dynamics and hybrid QM/continuum and QM/QM/continuum schemes, the vertical ionization energies, adiabatic ionization energies, vertical attachment energies, one-electron oxidation potentials, and delocalization of the hole generated upon oxidation have been determined for nucleobases in their free form and as part of a pure single-stranded DNA. We show that the reducer ability of the isolated nucleobases is explained by the intramolecular delocalization of the positively charged hole, while the enhancement of the reducer character when going from aqueous solution to the strand correlates very well with the intermolecular hole delocalization. Our simulations suggest that the redox properties of DNA strands can be tuned by playing with the balance between intramolecular and intermolecular charge delocalization.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Sergio Díaz-Tendero
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan J Nogueira
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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5
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Rooman M, Pucci F. Estimating the Vertical Ionization Potential of Single-Stranded DNA Molecules. J Chem Inf Model 2023; 63:1766-1775. [PMID: 36877828 DOI: 10.1021/acs.jcim.2c01525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The electronic properties of DNA molecules, defined by the sequence-dependent ionization potentials of nucleobases, enable long-range charge transport along the DNA stacks. This has been linked to a range of key physiological processes in the cells and to the triggering of nucleobase substitutions, some of which may cause diseases. To gain molecular-level understanding of the sequence dependence of these phenomena, we estimated the vertical ionization potential (vIP) of all possible nucleobase stacks in B-conformation, containing one to four Gua, Ade, Thy, Cyt, or methylated Cyt. To do this, we used quantum chemistry calculations and more precisely the second-order Møller-Plesset perturbation theory (MP2) and three double-hybrid density functional theory methods, combined with several basis sets for describing atomic orbitals. The calculated vIP of single nucleobases were compared to experimental data and those of nucleobase pairs, triplets, and quadruplets, to observed mutability frequencies in the human genome, reported to be correlated with vIP values. This comparison selected MP2 with the 6-31G* basis set as the best of the tested calculation levels. These results were exploited to set up a recursive model, called vIPer, which estimates the vIP of all possible single-stranded DNA sequences of any length based on the calculated vIPs of overlapping quadruplets. vIPer's vIP values correlate well with oxidation potentials measured by cyclic voltammetry and activities obtained through photoinduced DNA cleavage experiments, further validating our approach. vIPer is freely available on the github.com/3BioCompBio/vIPer repository.
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Affiliation(s)
- Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
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6
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Heindel JP, Hao H, LaCour RA, Head-Gordon T. Spontaneous Formation of Hydrogen Peroxide in Water Microdroplets. J Phys Chem Lett 2022; 13:10035-10041. [PMID: 36264238 DOI: 10.1021/acs.jpclett.2c01721] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
There is accumulating evidence that many chemical reactions are accelerated by several orders of magnitude in micrometer-sized aqueous or organic liquid droplets compared to their corresponding bulk liquid phase. However, the molecular origin of the enhanced rates remains unclear as in the case of spontaneous appearance of 1 μM hydrogen peroxide in water microdroplets. In this Letter, we consider the range of ionization energies and whether interfacial electric fields of a microdroplet can feasibly overcome the high energy step from hydroxide ions (OH-) to hydroxyl radicals (OH•) in a primary H2O2 mechanism. We find that the vertical ionization energies (VIEs) of partially solvated OH- ions are greatly lowered relative to the average VIE in the bulk liquid, unlike the case of the Cl- anion which shows no reduction in the VIEs regardless of solvation environment. Overall reduced hydrogen-bonding and undercoordination of OH- are structural features that are more readily present at the air-water interface, where the energy scale for ionization can be matched by statistically probable electric field values.
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Affiliation(s)
- Joseph P Heindel
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Hongxia Hao
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California94720, United States
| | - R Allen LaCour
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
- Departments of Bioengineering and Chemical and Biomolecular EngineeringUniversity of California, Berkeley, California94720, United States
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7
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Valverde D, Mai S, Canuto S, Borin AC, González L. Ultrafast Intersystem Crossing Dynamics of 6-Selenoguanine in Water. JACS AU 2022; 2:1699-1711. [PMID: 35911449 PMCID: PMC9327080 DOI: 10.1021/jacsau.2c00250] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Rationalizing the photochemistry of nucleobases where an oxygen is replaced by a heavier atom is essential for applications that exploit near-unity triplet quantum yields. Herein, we report on the ultrafast excited-state deactivation mechanism of 6-selenoguanine (6SeGua) in water by combining nonadiabatic trajectory surface-hopping dynamics with an electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) scheme. We find that the predominant relaxation mechanism after irradiation starts on the bright singlet S2 state that converts internally to the dark S1 state, from which the population is transferred to the triplet T2 state via intersystem crossing and finally to the lowest T1 state. This S2 → S1 → T2 → T1 deactivation pathway is similar to that observed for the lighter 6-thioguanine (6tGua) analogue, but counterintuitively, the T1 lifetime of the heavier 6SeGua is shorter than that of 6tGua. This fact is explained by the smaller activation barrier to reach the T1/S0 crossing point and the larger spin-orbit couplings of 6SeGua compared to 6tGua. From the dynamical simulations, we also calculate transient absorption spectra (TAS), which provide two time constants (τ1 = 131 fs and τ2 = 191 fs) that are in excellent agreement with the experimentally reported value (τexp = 130 ± 50 fs) (Farrel et al. J. Am. Chem. Soc. 2018, 140, 11214). Intersystem crossing itself is calculated to occur with a time scale of 452 ± 38 fs, highlighting that the TAS is the result of a complex average of signals coming from different nonradiative processes and not intersystem crossing alone.
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Affiliation(s)
- Danillo Valverde
- Department
of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo, São Paulo CEP 05508-000, Brazil
- Institute
of Physics, University of São Paulo, Rua do Matão 1371, São Paulo, São Paulo CEP 05508-090, Brazil
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Sylvio Canuto
- Institute
of Physics, University of São Paulo, Rua do Matão 1371, São Paulo, São Paulo CEP 05508-090, Brazil
| | - Antonio Carlos Borin
- Department
of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo, São Paulo CEP 05508-000, Brazil
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
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8
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Huang SR, Tureček F. Noncanonical Isomers of Nucleoside Cation Radicals: An Ab Initio Study of the Dark Matter of DNA Ionization. J Phys Chem A 2022; 126:2480-2497. [PMID: 35439003 DOI: 10.1021/acs.jpca.2c00894] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cation radicals of DNA nucleosides, 2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and 2'-deoxythymidine, can exist in standard canonical forms or as noncanonical isomers in which the charge is introduced by protonation of the nucleobase, whereas the radical predominantly resides in the deoxyribose moiety. Density functional theory as well as correlated ab initio calculations with coupled clusters (CCSD(T)) that were extrapolated to the complete basis set limit showed that noncanonical nucleoside ion isomers were thermodynamically more stable than their canonical forms in both the gas phase and as water-solvated ions. This indicated the possibility of exothermic conversion of canonical to noncanonical forms. The noncanonical isomers were calculated to have very low adiabatic ion-electron recombination energies (REad) for the lowest-energy isomers 2'-deoxy-(N-3H)adenos-1'-yl (4.74 eV), 2'-deoxy-(N-7H)guanos-1'-yl (4.66 eV), 2'-deoxy-(N-3H)cytid-1'-yl (5.12 eV), and 2'-deoxy-5-methylene-(O-2H)uridine (5.24 eV). These were substantially lower than the REad value calculated for the canonical 2'-deoxyadenosine, 2'-deoxy guanosine, 2'-deoxy cytidine, and 2'-deoxy thymidine cation radicals, which were 7.82, 7.46, 8.14, and 8.20 eV, respectively, for the lowest-energy ion conformers of each type. Charge and spin distributions in noncovalent cation-radical dA⊂dT and dG⊂dC nucleoside pairs and dAT, dCT, dTC, and dGC dinucleotides were analyzed to elucidate the electronic structure of the cation radicals. Born-Oppenheimer molecular dynamics trajectory calculations of the dinucleotides and nucleoside pairs indicated rapid exothermic proton transfer from noncanonical T+· to A in both dAT+· and dA⊂dT+·, leading to charge and radical separation. Noncanonical T+· in dCT+· and dTC+· initiated rapid proton transfer to cytosine, whereas the canonical dCT+· dinucleotide ion retained the cation radical structure without isomerization. No spontaneous proton transfer was found in dGC+· and dG⊂dC+· containing canonical neutral and noncanonical ionized deoxycytidine.
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Affiliation(s)
- Shu R Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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9
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Chen CG, Nardi AN, Amadei A, D’Abramo M. Theoretical Modeling of Redox Potentials of Biomolecules. Molecules 2022; 27:1077. [PMID: 35164342 PMCID: PMC8838479 DOI: 10.3390/molecules27031077] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [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.)
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10
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Intermolecular interactions in microhydrated ribonucleoside and deoxyribonucleoside: A computational study. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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11
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Semmeq A, Badawi M, Dziurla MA, Ouaskit S, Monari A. Nucleic Acids under Stress: Understanding and Simulating Nucleobase Fragmentation Pathways. Chempluschem 2021; 86:1426-1435. [PMID: 34637193 DOI: 10.1002/cplu.202100323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/24/2021] [Indexed: 11/10/2022]
Abstract
The effects of radiations on nucleic acids and their constituents is widely studied across several research fields using different experimental and theoretical protocols. While a large number of studies were performed in this context, many fundamental physical and chemical effects are still being investigated, particularly involving the effect of the biological environment. As an example, the interpretation of experimental nucleic acid bases mass spectra, and hence inferring their reactivity in complex environment still poses great challenge. This Minireview summarizes recent theoretical advancements aiming to predict and interpret the reactivity of nucleic acid bases. We focus not only on the understanding of the inherent fragmentation pathways of isolated nucleobases but also on the modeling of a realistic nano-environments highlighting the importance of molecular dynamics simulations and the non-innocent role of the environment and also the possibility to open novel fragmentation pathways.
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Affiliation(s)
| | - Michael Badawi
- Université de Lorraine and CNRS, UMR 7019 LPCT, 54000, Nancy, France
| | | | - Said Ouaskit
- Laboratoire de Physique de la Matière Condensée, Faculté de Sciences Ben M'sick, University Hassan II of Casablanca, Morocco
| | - Antonio Monari
- Université de Lorraine and CNRS, UMR 7019 LPCT, 54000, Nancy, France
- Université de Paris and CNRS, ITODYS, 75006, Paris, France
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12
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Weng G, Vlček V. Efficient treatment of molecular excitations in the liquid phase environment via stochastic many-body theory. J Chem Phys 2021; 155:054104. [PMID: 34364336 DOI: 10.1063/5.0058410] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Accurate predictions of charge excitation energies of molecules in the disordered condensed phase are central to the chemical reactivity, stability, and optoelectronic properties of molecules and critically depend on the specific environment. Herein, we develop a stochastic GW method for calculating these charge excitation energies. The approach employs maximally localized electronic states to define the electronic subspace of a molecule and the rest of the system, both of which are randomly sampled. We test the method on three solute-solvent systems: phenol, thymine, and phenylalanine in water. The results are in excellent agreement with the previous high-level calculations and available experimental data. The stochastic calculations for supercells containing up to 1000 electrons representing the solvated systems are inexpensive and require ≤1000 central processing unit hrs. We find that the coupling with the environment accounts for ∼40% of the total correlation energy. The solvent-to-solute feedback mechanism incorporated in the molecular correlation term causes up to 0.6 eV destabilization of the quasiparticle energy. Simulated photo-emission spectra exhibit red shifts, state-degeneracy lifting, and lifetime shortening. Our method provides an efficient approach for an accurate study of excitations of large molecules in realistic condensed phase environments.
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Affiliation(s)
- Guorong Weng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, USA
| | - VojtĚch Vlček
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, USA
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13
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Paul SK, Herbert JM. Probing Interfacial Effects on Ionization Energies: The Surprising Banality of Anion-Water Hydrogen Bonding at the Air/Water Interface. J Am Chem Soc 2021; 143:10189-10202. [PMID: 34184532 DOI: 10.1021/jacs.1c03131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Liquid microjet photoelectron spectroscopy is an increasingly common technique to measure vertical ionization energies (VIEs) of aqueous solutes, but the interpretation of these experiments is subject to questions regarding sensitivity to bulk versus interfacial solvation environments. We have computed aqueous-phase VIEs for a set of inorganic anions, using a combination of molecular dynamics simulations and electronic structure calculations, with results that are in excellent agreement with experiment regardless of whether the simulation data are restricted to ions at the air/water interface or to those in bulk aqueous solution. Although the computed VIEs are sensitive to ion-water hydrogen bonding, we find that the short-range solvation structure is sufficiently similar in both environments that it proves impossible to discriminate between the two on the basis of the VIE, a conclusion that has important implications for the interpretation of liquid-phase photoelectron spectroscopy. More generally, analysis of the simulation data suggests that the surface activity of soft anions is largely a second or third solvation shell effect, arising from disruption of water-water hydrogen bonds and not from significant changes in first-shell anion-water hydrogen bonding.
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Affiliation(s)
- Suranjan K Paul
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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14
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Kostal V, Brezina K, Marsalek O, Jungwirth P. Benzene Radical Anion Microsolvated in Ammonia Clusters: Modeling the Transition from an Unbound Resonance to a Bound Species. J Phys Chem A 2021; 125:5811-5818. [PMID: 34165987 DOI: 10.1021/acs.jpca.1c04594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The benzene radical anion, well-known in organic chemistry as the first intermediate in the Birch reduction of benzene in liquid ammonia, exhibits intriguing properties from the point of view of quantum chemistry. Notably, it has the character of a metastable shape resonance in the gas phase, while measurements in solution find it to be experimentally detectable and stable. In this light, our previous calculations performed in bulk liquid ammonia explicitly reveal that solvation leads to stabilization. Here, we focus on the transition of the benzene radical anion from an unstable gas-phase ion to a fully solvated bound species by explicit ionization calculations of the radical anion solvated in molecular clusters of increasing size. The computational cost of the largest systems is mitigated by combining density functional theory with auxiliary methods including effective fragment potentials or approximating the bulk by polarizable continuum models. Using this methodology, we obtain the cluster size dependence of the vertical binding energy of the benzene radical anion converging to the value of -2.3 eV at a modest computational cost.
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Affiliation(s)
- Vojtech Kostal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Krystof Brezina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.,Charles University, Faculty of Mathematics and Physics, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Ondrej Marsalek
- Charles University, Faculty of Mathematics and Physics, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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15
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Veclani D, Tolazzi M, Cerón-Carrasco JP, Melchior A. Intercalation Ability of Novel Monofunctional Platinum Anticancer Drugs: A Key Step in Their Biological Action. J Chem Inf Model 2021; 61:4391-4399. [PMID: 34156233 PMCID: PMC8479807 DOI: 10.1021/acs.jcim.1c00430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Phenanthriplatin
(PtPPH) is a monovalent platinum(II)-based complex
with a large cytotoxicity against cancer cells. Although the aqua-activated
drug has been assumed to be the precursor for DNA damage, it is still
under debate whether the way in which that metallodrug attacks to
DNA is dominated by a direct binding to a guanine base or rather by
an intercalated intermediate product. Aiming to capture the mechanism
of action of PtPPH, the present contribution used theoretical tools
to systematically assess the sequence of all possible mechanisms on
drug activation and reactivity, for example, hydrolysis, intercalation,
and covalent damage to DNA. Ab initio quantum mechanical
(QM) methods, hybrid QM/QM′ schemes, and independent gradient
model approaches are implemented in an unbiased protocol. The performed
simulations show that the cascade of reactions is articulated in three
well-defined stages: (i) an early and fast intercalation of the complex
between the DNA bases, (ii) a subsequent hydrolysis reaction that
leads to the aqua-activated form, and (iii) a final formation of the
covalent bond between PtPPH and DNA at a guanine site. The permanent
damage to DNA is consequently driven by that latter bond to DNA but
with a simultaneous π–π intercalation of the phenanthridine
into nucleobases. The impact of the DNA sequence and the lateral backbone
was also discussed to provide a more complete picture of the forces
that anchor the drug into the double helix.
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Affiliation(s)
- Daniele Veclani
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA), Laboratori di Chimica, Università di Udine, via delle Scienze 99, 33100 Udine, Italy
| | - Marilena Tolazzi
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA), Laboratori di Chimica, Università di Udine, via delle Scienze 99, 33100 Udine, Italy
| | - José P Cerón-Carrasco
- Reconocimiento y Encapsulación Molecular, Universidad Católica San Antonio de Murcia (UCAM). Campus de los Jerónimos, 30107 Murcia, Spain
| | - Andrea Melchior
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA), Laboratori di Chimica, Università di Udine, via delle Scienze 99, 33100 Udine, Italy
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16
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Diamantis P, Tavernelli I, Rothlisberger U. Redox Properties of Native and Damaged DNA from Mixed Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations. J Chem Theory Comput 2020; 16:6690-6701. [PMID: 32926773 DOI: 10.1021/acs.jctc.0c00568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The redox properties of two large DNA fragments composed of 39 base pairs, differing only by an 8-oxoguanine (8oxoG) defect replacing a guanine (G), were investigated in physiological conditions using mixed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations. The quantum region of the native fragment comprised 3 G-C base pairs, while one G was replaced by an 8oxoG in the defect fragment. The calculated values for the redox free energy are 6.55 ± 0.28 eV and 5.62 ± 0.30 eV for the native and the 8oxoG-containing fragment, respectively. The respective estimates for the reorganization free energy are 1.25 ± 0.18 eV and 1.00 ± 0.18 eV. Both reactions follow the Marcus theory for electron transfer. The large difference in redox potential between the two fragments shows that replacement of a G by an 8oxoG renders the DNA more easily oxidizable. This finding is in agreement with the suggestion that DNA fragments containing an 8oxoG defect can act as sinks of oxidative damage that protect the rest of the genome from assault. In addition, the difference in redox potential between the native and the defect DNA fragment indicates that a charge transfer-based mechanism for the recognition of DNA defects might be feasible, in line with recent suggestions based on experimental observations.
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Affiliation(s)
- Polydefkis Diamantis
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
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17
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A computational investigation of cytosine and 5-methyl cytosine reactivity by means of ionization potentials and one specific methylation pathway. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Semmeq A, Badawi M, Hasnaoui A, Ouaskit S, Monari A. DNA Nucleobase under Ionizing Radiation: Unexpected Proton Transfer by Thymine Cation in Water Nanodroplets. Chemistry 2020; 26:11340-11344. [PMID: 32511805 DOI: 10.1002/chem.202002025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/04/2020] [Indexed: 11/07/2022]
Abstract
The effect of ionizing radiation on DNA constituents is a widely studied fundamental process using experimental and computational techniques. In particular, radiation effects on nucleobases are usually tackled by mass spectrometry in which the nucleobase is embedded in a water nanodroplet. Here, we present a multiscale theoretical study revealing the effects and the dynamics of water droplets towards neutral and ionized thymine. In particular, by using both hybrid quantum mechanics/molecular mechanics and full ab initio molecular dynamics, we reveal an unexpected proton transfer from thymine cation to a nearby water molecule. This leads to the formation of a neutral radical thymine and a Zundel structure, while the hydrated proton localizes at the interface between the deprotonated thymine and the water droplet. This observation opens entirely novel perspectives concerning the reactivity and further fragmentation of ionized nucleobases.
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Affiliation(s)
- Abderrahmane Semmeq
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France.,Laboratoire de Physique de la Matière Condensée LPMC Faculté des, Sciences Ben M'sik, University Hassan II of Casablanca, BP 7955 Av. Driss El Harti, Sidi Othmane, 20000, Casablanca, Morocco
| | - Michael Badawi
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | - Abdellatif Hasnaoui
- LS3M, Faculté Polydisicplinaire-Khouribga, University Sultan Moulay Slimane of Beni Mellal, B.P 145, 25000, Khouribga, Morocco
| | - Said Ouaskit
- Laboratoire de Physique de la Matière Condensée LPMC Faculté des, Sciences Ben M'sik, University Hassan II of Casablanca, BP 7955 Av. Driss El Harti, Sidi Othmane, 20000, Casablanca, Morocco
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
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19
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Behmand B, Balanikas E, Martinez-Fernandez L, Improta R, Banyasz A, Baldacchino G, Markovitsi D. Potassium Ions Enhance Guanine Radical Generation upon Absorption of Low-Energy Photons by G-Quadruplexes and Modify Their Reactivity. J Phys Chem Lett 2020; 11:1305-1309. [PMID: 31967478 DOI: 10.1021/acs.jpclett.9b03667] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
G-Quadruplexes are formed by guanine rich DNA/RNA sequences in the presence of metal ions, which occupy the central cavity of these four-stranded structures. We show that these metal ions have a significant effect on the photogeneration and the reactivity of guanine radicals. Transient absorption experiments on G-quadruplexes formed by association of four TGGGGT strands in the presence of K+ reveal that the quantum yield of one-photon ionization at 266 nm (8.1 × 10-3) is twice as high as that determined in the presence of Na+. Replacement of Na+ with K+ also suppresses one reaction path involving deprotonated radicals, (G-H2)• → (G-H1)• tautomerization. Such behavior shows that the underlying mechanisms are governed by dynamical processes, controlled by the mobility of metal ions, which is higher for Na+ than for K+. These findings may contribute to our understanding of the ultraviolet-induced DNA damage and optimize optoelectronic devices based on four-stranded structures, beyond DNA.
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Affiliation(s)
- Behnaz Behmand
- Université Paris-Saclay , CEA, CNRS, LIDYL , F-91191 Gif-sur-Yvette , France
| | - Evangelos Balanikas
- Université Paris-Saclay , CEA, CNRS, LIDYL , F-91191 Gif-sur-Yvette , France
| | - Lara Martinez-Fernandez
- Departamento de Quı́mica, Facultad de Ciencias , Universidad Autónoma de Madrid , 28049 Cantoblanco , Spain
- IADCHEM, Institute for Advanced Research in Chemistry , Universidad Autónoma de Madrid , 28049 Cantoblanco , Spain
| | - Roberto Improta
- Istituto Biostrutture e Bioimmagini-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16 , I-80134 Napoli , Italy
| | - Akos Banyasz
- Univ Lyon, ENS de Lyon, CNRS UMR 5182 , Université Claude Bernard Lyon 1, Laboratoire de Chimie , F-69342 Lyon , France
| | - Gérard Baldacchino
- Université Paris-Saclay , CEA, CNRS, LIDYL , F-91191 Gif-sur-Yvette , France
| | - Dimitra Markovitsi
- Université Paris-Saclay , CEA, CNRS, LIDYL , F-91191 Gif-sur-Yvette , France
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20
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Karwowski BT. Clustered DNA Damage: Electronic Properties and Their Influence on Charge Transfer. 7,8-Dihydro-8-Oxo-2'-Deoxyguaosine Versus 5',8-Cyclo-2'-Deoxyadenosines: A Theoretical Approach. Cells 2020; 9:cells9020424. [PMID: 32059490 PMCID: PMC7072346 DOI: 10.3390/cells9020424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/02/2020] [Accepted: 02/11/2020] [Indexed: 11/18/2022] Open
Abstract
Approximately 3 × 1017 DNA damage events take place per hour in the human body. Within clustered DNA lesions, they pose a serious problem for repair proteins, especially for iron–sulfur glycosylases (MutyH), which can recognize them by the electron-transfer process. It has been found that the presence of both 5′,8-cyclo-2′-deoxyadenosine (cdA) diastereomers in the ds-DNA structure, as part of a clustered lesion, can influence vertical radical cation distribution within the proximal part of the double helix, i.e., d[~oxoGcAoxoG~] (7,8-dihydro-8-oxo-2′-deoxyguaosine - oxodG). Here, the influence of cdA, “the simplest tandem lesion”, on the charge transfer through ds-DNA was taken into theoretical consideration at the M062x/6-31+G** level of theory in the aqueous phase. It was shown that the presence of (5′S)- or (5′R)-cdA leads to a slowdown in the hole transfer by one order of magnitude between the neighboring dG→oxodG in comparison to “native” ds-DNA. Therefore, it can be concluded that such clustered lesions can lead to defective damage recognition with a subsequent slowing down of the DNA repair process, giving rise to an increase in mutations. As a result, the unrepaired, oxodG: dA base pair prior to genetic information replication can finally result in GC → TA or AT→CG transversion. This type of mutation is commonly observed in human cancer cells. Moreover, because local multiple damage sites (LMSD) are effectively produced as a result of ionization factors, the presented data in this article might be useful in developing a new scheme of radiotherapy treatment against the background of DNA repair efficiency.
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Affiliation(s)
- Boleslaw T Karwowski
- DNA Damage Laboratory of Food Science Department, Faculty of Pharmacy, Medical University of Lodz, ul. Muszynskiego 1, 90-151 Lodz, Poland
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21
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Pucci F, Rooman M. Relation between DNA ionization potentials, single base substitutions and pathogenic variants. BMC Genomics 2019; 20:551. [PMID: 31307386 PMCID: PMC6631442 DOI: 10.1186/s12864-019-5867-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background It is nowadays clear that single base substitutions that occur in the human genome, of which some lead to pathogenic conditions, are non-random and influenced by their flanking nucleobase sequences. However, despite recent progress, the understanding of these "non-local" effects is still far from being achieved. Results To advance this problem, we analyzed the relationship between the base mutability in specific gene regions and the electron hole transport along the DNA base stacks, as it is one of the mechanisms that have been suggested to contribute to these effects. More precisely, we studied the connection between the normalized frequency of single base substitutions and the vertical ionization potential of the base and its flanking sequence, estimated using MP2/6-31G* ab initio quantum chemistry calculations. We found a statistically significant overall anticorrelation between these two quantities: the lower the vIP value, the more probable the substitution. Moreover, the slope of the regression lines varies. It is larger for introns than for exons and untranslated regions, and for synonymous than for missense substitutions. Interestingly, the correlation appears to be more pronounced when considering the flanking sequence of the substituted base in the 3’ rather than in the 5’ direction, which corresponds to the preferred direction of charge migration. A weaker but still statistically significant correlation is found between the ionization potentials and the pathogenicity of the base substitutions. Moreover, pathogenicity is also preferentially associated with larger changes in ionization potentials upon base substitution. Conclusions With this analysis we gained new insights into the complex biophysical mechanisms that are at the basis of mutagenesis and pathogenicity, and supported the role of electron-hole transport in these matters. Electronic supplementary material The online version of this article (10.1186/s12864-019-5867-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Roosevelt Ave. 50, Bruxelles, 1050, Belgium.,John von Neumann Institute for Computing, Jülich Supercomputer Centre, Forschungszentrum Jülich, Jülich, 52428, Germany
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Roosevelt Ave. 50, Bruxelles, 1050, Belgium.
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22
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i-Motif DNA structures upon electric field exposure: completing the map of induced genetic errors. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2423-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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23
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Muchová E, Slavíček P. Beyond Koopmans' theorem: electron binding energies in disordered materials. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:043001. [PMID: 30524069 DOI: 10.1088/1361-648x/aaf130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The topical review focuses on calculating ionization energies (IE), or electronic polarons in quasi-particle terminology, in large disordered systems, e.g. for a solute dissolved in a molecular solvent. The simplest estimate of the ionization energy is provided by one-electron energies in the Hartree-Fock theory, but the calculated quantities are not accurate. Density functional theory as many-body theory provides a principal opportunity for calculating one-electron energies including correlation and relaxation effects, i.e. the true energies of electronic polarons. We argue that such a principal possibility materializes within the concept of optimally tuned range-separated hybrid functionals (OT-RSH). We describe various schemes for optimal tuning. Importantly, the OT-RSH scheme is investigated for systems capped with dielectric continuum, providing a consistent picture on the QM/dielectric boundary. Finally, some limitations and open issues of the OT-RSH approach are addressed.
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Affiliation(s)
- Eva Muchová
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic
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24
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Segarra-Martí J, Tran T, Bearpark MJ. Ultrafast and radiationless electronic excited state decay of uracil and thymine cations: computing the effects of dynamic electron correlation. Phys Chem Chem Phys 2019; 21:14322-14330. [PMID: 30698175 DOI: 10.1039/c8cp07189f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this article we characterise the radiationless decay of the first few electronic excited states of the cations of DNA/RNA nucleobases uracil and thymine, including the effects of dynamic electron correlation on energies and geometries (optimised with XMS-CASPT2). In both systems, we find that one state of 2n and another two of 2π+ character can be populated following photoionisation, and their different minima and interstate crossings are located. We find strong similarities between uracil and thymine cations: with accessible conical intersections suggesting that depopulation of their electronic excited states takes place on ultrafast timescales in both systems, suggesting that they are photostable in agreement with previous theoretical (uracil+) evidence. We find that dynamic electron correlation separates the energy levels of the "3-state" conical intersection (D2/D1/D0)CI previously located with CASSCF for uracil+, which will therefore have a different geometry and higher energy. Simulating the electronic and vibrational absorptions allows us to characterise spectral fingerprints that could be used to monitor these cation photo-processes experimentally.
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Affiliation(s)
- Javier Segarra-Martí
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ, London, UK.
| | - Thierry Tran
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ, London, UK.
| | - Michael J Bearpark
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ, London, UK.
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25
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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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26
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Li Y, Artés JM, Demir B, Gokce S, Mohammad HM, Alangari M, Anantram MP, Oren EE, Hihath J. Detection and identification of genetic material via single-molecule conductance. NATURE NANOTECHNOLOGY 2018; 13:1167-1173. [PMID: 30397286 DOI: 10.1038/s41565-018-0285-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 09/20/2018] [Indexed: 05/05/2023]
Abstract
The ongoing discoveries of RNA modalities (for example, non-coding, micro and enhancer) have resulted in an increased desire for detecting, sequencing and identifying RNA segments for applications in food safety, water and environmental protection, plant and animal pathology, clinical diagnosis and research, and bio-security. Here, we demonstrate that single-molecule conductance techniques can be used to extract biologically relevant information from short RNA oligonucleotides, that these measurements are sensitive to attomolar target concentrations, that they are capable of being multiplexed, and that they can detect targets of interest in the presence of other, possibly interfering, RNA sequences. We also demonstrate that the charge transport properties of RNA:DNA hybrids are sensitive to single-nucleotide polymorphisms, thus enabling differentiation between specific serotypes of Escherichia coli. Using a combination of spectroscopic and computational approaches, we determine that the conductance sensitivity primarily arises from the effects that the mutations have on the conformational structure of the molecules, rather than from the direct chemical substitutions. We believe that this approach can be further developed to make an electrically based sensor for diagnostic purposes.
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Affiliation(s)
- Yuanhui Li
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA, USA
| | - Juan M Artés
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA, USA
- Biophysics and Photosynthesis, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Chemistry Department, University of Massachusetts Lowell, Lowell, MA, USA
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - Sumeyye Gokce
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - Hashem M Mohammad
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA
| | - Mashari Alangari
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA, USA
| | - M P Anantram
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA.
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey.
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey.
| | - Joshua Hihath
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA, USA.
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27
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Olivieri G, Goel A, Kleibert A, Cvetko D, Brown MA. Quantitative ionization energies and work functions of aqueous solutions. Phys Chem Chem Phys 2018; 18:29506-29515. [PMID: 27747349 DOI: 10.1039/c6cp05682b] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Despite the ubiquitous nature of aqueous solutions across the chemical, biological and environmental sciences our experimental understanding of their electronic structure is rudimentary-qualitative at best. One of the most basic and seemingly straightforward properties of aqueous solutions-ionization energies-are (qualitatively) tabulated at the water-air interface for a mere handful of solutes, and the manner in which these results are obtained assume the aqueous solutions behave like a gas in the photoelectron experiment (where the vacuum levels of the aqueous solution and of the photoelectron analyzer are equilibrated). Here we report the experimental measure of a sizeable offset (ca. 0.6 eV) between the vacuum levels of an aqueous solution (0.05 M NaCl) and that of our photoelectron analyzer, indicating a breakdown of the gas-like vacuum level alignment assumption for the aqueous solution. By quantifying the vacuum level offset as a function of solution chemical composition our measurements enable, for the first time, quantitative determination of ionization energies in liquid solutions. These results reveal that the ionization energy of liquid water is not independent of the chemical composition of the solution as is usually inferred in the literature, a finding that has important ramifications as measured ionization energies are frequently used to validate theoretical models that posses the ability to provide microscopic insight not directly available by experiment. Finally, we derive the work function, or the electrochemical potential of the aqueous solution and show that it too varies with the chemical composition of the solution.
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Affiliation(s)
- Giorgia Olivieri
- Laboratory for Surface Science and Technology, Department of Materials, ETH Zürich, Switzerland.
| | - Alok Goel
- Laboratory for Surface Science and Technology, Department of Materials, ETH Zürich, Switzerland.
| | - Armin Kleibert
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Dean Cvetko
- Faculty for Mathematics and Physics, University of Ljubljana and Jožef Stefan Institute, Ljubljana, Slovenia
| | - Matthew A Brown
- Laboratory for Surface Science and Technology, Department of Materials, ETH Zürich, Switzerland.
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28
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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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29
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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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30
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Cerón-Carrasco JP, Jacquemin D. Exposing the G-quadruplex to electric fields: the role played by telomeres in the propagation of DNA errors. Phys Chem Chem Phys 2017; 19:9358-9365. [DOI: 10.1039/c7cp01034f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We use quantum calculations to assess the impact of external electric fields on the stability of G-quadruplex, a key structure in telomere functionality.
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Affiliation(s)
- José Pedro Cerón-Carrasco
- Bioinformatics and High Performance Computing Research Group (BIO-HPC)
- Universidad Católica San Antonio de Murcia (UCAM)
- Murcia
- Spain
| | - Denis Jacquemin
- CEISAM
- UMR CNRS 6230
- BP 92208
- Université de Nantes
- 44322 Nantes Cedex 3
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31
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Shirmovsky SE. Quantum dynamics of a hole migration through DNA: A single strand DNA model. Biophys Chem 2016; 217:42-57. [PMID: 27497061 DOI: 10.1016/j.bpc.2016.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/05/2016] [Accepted: 07/17/2016] [Indexed: 11/24/2022]
Abstract
A model predicting the behavior of a hole acting on the DNA strand was investigated. The hole-DNA interaction on the basis of a quantum-classical, non-linear DNA single strand model was described. The fact that a DNA molecule is formed by a furanose ring as its sugar, phosphate group and bases was taken into consideration. Based on the model, results were obtained for the probability of a hole location on the DNA base sequences, such as GTTGGG, GATGTGGG, GTTGTTGGG as well as on the sugar-phosphate groups mated with them.
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Affiliation(s)
- S Eh Shirmovsky
- Far Eastern Federal University, 8 Sukhanov St., Vladivostok 690950, Russia.
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32
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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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33
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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: 62] [Impact Index Per Article: 6.9] [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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34
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Bull JN, Lee JWL, Vallance C. Absolute electron total ionization cross-sections: molecular analogues of DNA and RNA nucleobase and sugar constituents. Phys Chem Chem Phys 2015; 16:10743-52. [PMID: 24756123 DOI: 10.1039/c4cp00490f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Accurate ionization cross-sections for DNA and RNA constituents in the condensed or aqueous phase are important parameters for models simulating radiation damage to genetic material in living cells. In this work, absolute gas-phase electron total ionization cross-sections (TICSs) have been measured for a series of six aromatic and eight non-aromatic cyclic species that can be considered as prototype functional group analogues for the nucleobases and sugar backbone constituents of DNA and RNA. TICSs for water, hexane, and ethylacetamide (a peptide bond analogue) are also reported. The experimental apparatus utilizes a cylindrical ion collector that surrounds the ionization region, providing essentially unit detection efficiency. Two theoretical models, the polarizability-correlation method and binary-encounter Bethe theory, are able to reproduce the measured maximum TICS well for all species studied. An empirical energy-dependent correction is found to yield improvement in the agreement between experimental energy-dependent cross sections and the predictions of the BEB model. Having characterised and optimised the performance of both models, they are then used to predict TICSs for gas-phase DNA and RNA nucleobases and sugars. Direct experimental determinations of TICSs for these species are difficult because of their low volatility, which makes it difficult to prepare suitable gas-phase samples for measurement.
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Affiliation(s)
- James N Bull
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
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35
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Computational modeling of photoexcitation in DNA single and double strands. Top Curr Chem (Cham) 2015; 356:89-122. [PMID: 24647841 DOI: 10.1007/128_2014_533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.
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36
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Cerón-Carrasco JP, Requena A, Zúñiga J, Jacquemin D. Mutagenic effects induced by the attack of NO2 radical to the guanine-cytosine base pair. Front Chem 2015; 3:13. [PMID: 25798437 PMCID: PMC4351615 DOI: 10.3389/fchem.2015.00013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/16/2015] [Indexed: 12/04/2022] Open
Abstract
We investigate the attack of the nitrogen dioxide radical (NO•2) to the guanine—cytosine (GC) base pair and the subsequent tautomeric reactions able to induce mutations, by means of density functional theory (DFT) calculations. The conducted simulations allow us to identify the most reactive sites of the GC base pair. Indeed, the computed relative energies demonstrate that the addition of the NO•2 radical to the C8 position of the guanine base forms to the most stable adduct. Although the initial adducts might evolve to non-canonical structures via inter-base hydrogen bonds rearrangements, the probability for the proton exchange to occur lies in the same range as that observed for undamaged DNA. As a result, tautomeric errors in NO2-attacked DNA arises at the same rate as in canonical DNA, with no macroscopic impact on the overall stability of DNA. The potential mutagenic effects of the GC–NO•2 radical adducts likely involve side reactions, e.g., the GC deprotonation to the solvent, rather than proton exchange between guanine and cytosine basis.
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Affiliation(s)
| | - Alberto Requena
- Departamento de Química Física, Universidad de Murcia Murcia, Spain
| | - José Zúñiga
- Departamento de Química Física, Universidad de Murcia Murcia, Spain
| | - Denis Jacquemin
- Chimie et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR Centre National de la Recherche Scientifique, Université de Nantes Nantes, France ; Institut Universitaire de France Paris, France
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37
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Schroeder CA, Pluhařová E, Seidel R, Schroeder WP, Faubel M, Slavíček P, Winter B, Jungwirth P, Bradforth SE. Oxidation half-reaction of aqueous nucleosides and nucleotides via photoelectron spectroscopy augmented by ab initio calculations. J Am Chem Soc 2014; 137:201-9. [PMID: 25551179 DOI: 10.1021/ja508149e] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Oxidative damage to DNA and hole transport between nucleobases in oxidized DNA are important processes in lesion formation for which surprisingly poor thermodynamic data exist, the relative ease of oxidizing the four nucleobases being one such example. Theoretical simulations of radiation damage and charge transport in DNA depend on accurate values for vertical ionization energies (VIEs), reorganization energies, and standard reduction potentials. Liquid-jet photoelectron spectroscopy can be used to directly study the oxidation half-reaction. The VIEs of nucleic acid building blocks are measured in their native buffered aqueous environment. The experimental investigation of purine and pyrimidine nucleotides, nucleosides, pentose sugars, and inorganic phosphate demonstrates that photoelectron spectra of nucleotides arise as a spectral sum over their individual chemical components; that is, the electronic interactions between each component are effectively screened from one another by water. Electronic structure theory affords the assignment of the lowest energy photoelectron band in all investigated nucleosides and nucleotides to a single ionizing transition centered solely on the nucleobase. Thus, combining the measured VIEs with theoretically determined reorganization energies allows for the spectroscopic determination of the one-electron redox potentials that have been difficult to establish via electrochemistry.
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Affiliation(s)
- Christi A Schroeder
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
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38
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Bogatko S, Cauët E, Geerlings P, De Proft F. On the coupling of solvent characteristics to the electronic structure of solute molecules. Phys Chem Chem Phys 2014; 16:3807-14. [PMID: 24435016 DOI: 10.1039/c3cp54944e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present the results of a theoretical investigation focusing on the solvent structure surrounding the -1, 0 and +1 charged species of F, Cl, Br and I halogen atoms and F2, Cl2, Br2 and I2 di-halogen molecules in a methanol solvent and its influence on the electronic structure of the solute molecules. Our results show a large stabilizing effect arising from the solute-solvent interactions. Well-formed first solvation shells are observed for all species, the structure of which is strongly influenced by the charge of the solute species. Detailed analysis reveals that coordination number, CN, solvent orientation, θ, and solute-solvent distance, d, are important structural characteristics which are coupled to changes in the electronic structure of the solute. We propose that the fundamental chemistry of any solute species is generally regulated by these solvent degrees of freedom.
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Affiliation(s)
- Stuart Bogatko
- Eenheid Algemene Chemie, Vrije Universiteit Brussel (VUB), Faculteit Wetenschappen, Pleinlaan 2, 1050 Brussels, Belgium.
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39
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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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40
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Farrokhpour H, Ghandehari M. Photoelectron Spectra of Some Important Biological Molecules: Symmetry-Adapted-Cluster Configuration Interaction Study. J Phys Chem B 2013; 117:6027-41. [DOI: 10.1021/jp311213c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Hossein Farrokhpour
- Chemistry Department, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Maryam Ghandehari
- Chemistry Department, Isfahan University of Technology, Isfahan, 84156-83111, Iran
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41
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Rooman M, Wintjens R. Sequence and conformation effects on ionization potential and charge distribution of homo-nucleobase stacks using M06-2X hybrid density functional theory calculations. J Biomol Struct Dyn 2013; 32:532-45. [PMID: 23582046 PMCID: PMC3919198 DOI: 10.1080/07391102.2013.783508] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
DNA is subject to oxidative damage due to radiation or by-products of cellular metabolism, thereby creating electron holes that migrate along the DNA stacks. A systematic computational analysis of the dependence of the electronic properties of nucleobase stacks on sequence and conformation was performed here, on the basis of single- and double-stranded homo-nucleobase stacks of 1-10 bases or 1-8 base pairs in standard A-, B-, and Z-conformation. First, several levels of theory were tested for calculating the vertical ionization potentials of individual nucleobases; the M06-2X/6-31G* hybrid density functional theory method was selected by comparison with experimental data. Next, the vertical ionization potential, and the Mulliken charge and spin density distributions were calculated and considered on all nucleobase stacks. We found that (1) the ionization potential decreases with the number of bases, the lowest being reached by Gua≡Cyt tracts; (2) the association of two single strands into a double-stranded tract lowers the ionization potential significantly (3) differences in ionization potential due to sequence variation are roughly three times larger than those due to conformational modifications. The charge and spin density distributions were found (1) to be located toward the 5'-end for single-stranded Gua-stacks and toward the 3'-end for Cyt-stacks and basically delocalized over all bases for Ade- and Thy-stacks; (2) the association into double-stranded tracts empties the Cyt- and Thy-strands of most of the charge and all the spin density and concentrates them on the Gua- and Ade-strands. The possible biological implications of these results for transcription are discussed.
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Affiliation(s)
- Marianne Rooman
- a BioModeling, BioInformatics and BioProcesses Department , CP 165/61 Université Libre de Bruxelles , 50 Roosevelt ave, 1050 Brussels , Belgium
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42
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Cerón-Carrasco JP, Jacquemin D. Electric-field induced mutation of DNA: a theoretical investigation of the GC base pair. Phys Chem Chem Phys 2013; 15:4548-53. [DOI: 10.1039/c2cp44066k] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Cauët E, Carette T, Lauzin C, Li JG, Loreau J, Delsaut M, Nazé C, Verdebout S, Vranckx S, Godefroid M, Liévin J, Vaeck N. From atoms to biomolecules: a fruitful perspective. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1254-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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44
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Kumar SVK, Pota T, Peri D, Dongre AD, Rao BJ. Low energy electron induced damage to plasmid DNA pQE30. J Chem Phys 2012; 137:045101. [DOI: 10.1063/1.4737182] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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45
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Siriwong K, Voityuk AA. Electron transfer in DNA. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1102] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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46
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Lu Y, Lan Z, Thiel W. Monomeric adenine decay dynamics influenced by the DNA environment. J Comput Chem 2012; 33:1225-35. [DOI: 10.1002/jcc.22952] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 01/09/2012] [Accepted: 01/16/2012] [Indexed: 01/25/2023]
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47
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Cerón-Carrasco JP, Requena A, Jacquemin D. Impact of DFT functionals on the predicted magnesium–DNA interaction: an ONIOM study. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1188-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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48
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Morozov D, Khrenova M, Andrijchenko N, Grigorenko B, Nemukhin A. Minimum energy reaction profiles for the hydrolysis reaction of the cyclic guanosine monophosphate in water: Comparison of the results of two QM/MM approaches. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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49
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Cerón-Carrasco JP, Jacquemin D. Interplay between hydroxyl radical attack and H-bond stability in guanine–cytosine. RSC Adv 2012. [DOI: 10.1039/c2ra22389a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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50
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