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Folorunso AS, Mauger F, Hamer KA, Jayasinghe DD, Wahyutama IS, Ragains JR, Jones RR, DiMauro LF, Gaarde MB, Schafer KJ, Lopata K. Attochemistry Regulation of Charge Migration. J Phys Chem A 2023; 127:1894-1900. [PMID: 36791088 PMCID: PMC9986869 DOI: 10.1021/acs.jpca.3c00568] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Charge migration (CM) is a coherent attosecond process that involves the movement of localized holes across a molecule. To determine the relationship between a molecule's structure and the CM dynamics it exhibits, we perform systematic studies of para-functionalized bromobenzene molecules (X-C6H4-R) using real-time time-dependent density functional theory. We initiate valence-electron dynamics by emulating rapid strong-field ionization leading to a localized hole on the bromine atom. The resulting CM, which takes on the order of 1 fs, occurs via an X localized → C6H4 delocalized → R localized mechanism. Interestingly, the hole contrast on the acceptor functional group increases with increasing electron-donating strength. This trend is well-described by the Hammett σ value of the group, which is a commonly used metric for quantifying the effect of functionalization on the chemical reactivity of benzene derivatives. These results suggest that simple attochemistry principles and a density-based picture can be used to predict and understand CM.
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Affiliation(s)
| | | | | | | | | | | | - Robert R Jones
- Department of Physics, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Louis F DiMauro
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, United States
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2
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Liu Y, Ren X, He L. First-principles study of benzo[a]pyrene-7,8-dione and DNA adducts. J Chem Phys 2021; 154:175102. [PMID: 34241046 DOI: 10.1063/5.0046360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widely distributed in environments, and some of them are causative agents of human cancer. Previous studies concluded that benzo[a]pyrene-7,8-dione (BPQ), which is one kind of carcinogenic PAH metabolites, forms covalently bonded adducts with DNA, and the major adduct formed is a deoxyguanosine adduct. In this work, we investigate the interactions between BPQ and DNA molecules via first-principles calculations. We identify six possible DNA adducts with BPQ. In addition to the four adducts forming covalent bonds, there are two adducts bound purely by van der Waals (vdW) interactions. Remarkably, the two vdW-bound adducts have comparable, if not larger, binding energies as the covalent adducts. The results may help us gain more understanding of the interactions between PAH metabolites and DNA.
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Affiliation(s)
- Yue Liu
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Xinguo Ren
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Lixin He
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, China
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3
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Mantela M, Morphis A, Lambropoulos K, Simserides C, Di Felice R. Effects of Structural Dynamics on Charge Carrier Transfer in B-DNA: A Combined MD and RT-TDDFT Study. J Phys Chem B 2021; 125:3986-4003. [PMID: 33857373 DOI: 10.1021/acs.jpcb.0c11489] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hole transfer along the axis of duplex DNA has been the focus of physical chemistry research for decades, with implications in diverse fields, from nanotechnology to cell oxidative damage. Computational approaches are particularly amenable for this problem, to complement experimental data for interpretation of transfer mechanisms. To be predictive, computational results need to account for the inherent mobility of biological molecules during the time frame of experimental measurements. Here, we address the structural variability of B-DNA and its effects on hole transfer in a combined molecular dynamics (MD) and real-time time-dependent density functional theory (RT-TDDFT) study. Our results show that quantities that characterize the charge transfer process, such as the time-dependent dipole moment and hole population at a specific site, are sensitive to structural changes that occur on the nanosecond time scale. We extend the range of physical properties for which such a correlation has been observed, further establishing the fact that quantitative computational data on charge transfer properties should include statistical averages. Furthermore, we use the RT-TDDFT results to assess an efficient tight-binding method suitable for high-throughput predictions. We demonstrate that charge transfer, although affected by structural variability, on average, remains strong in AA and GG dimers.
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Affiliation(s)
- Marilena Mantela
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - Andreas Morphis
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - Konstantinos Lambropoulos
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - Constantinos Simserides
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
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4
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Aierken Y, Agrawal A, Sun M, Melander M, Crumlin EJ, Helms BA, Prendergast D. Revealing Charge-Transfer Dynamics at Electrified Sulfur Cathodes Using Constrained Density Functional Theory. J Phys Chem Lett 2021; 12:739-744. [PMID: 33405937 DOI: 10.1021/acs.jpclett.0c03334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
To understand and control the behavior of electrochemical systems, including batteries and electrocatalysts, we seek molecular-level details of the charge transfer mechanisms at electrified interfaces. Recognizing some key limitations of standard equilibrium electronic structure methods to model materials and their interfaces, we propose applying charge constraints to effectively separate electronic and nuclear degrees of freedom, which are especially beneficial to the study of conversion electrodes, where electronic charge carriers are converted to much slower polarons within a material that is nonmetallic. We demonstrate the need for such an approach within the context of sulfur cathodes and the arrival of Li ions during discharge of a Li-S cell. The requirement that electronic degrees of freedom are arrested is justified by comparison with real-time evolution of the electronic structure. Long-lived metastable configurations provide plenty of time for nuclear dynamics and relaxation in response to the electrification of the interface, a process that would be completely missed without applying charge constraints. This approach will be vital to the study of dynamics at electrified interfaces which may be created deliberately, adding charge to the electrode, or spontaneously, due to finite temperature dynamics in the electrolyte.
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Affiliation(s)
- Yierpan Aierken
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Ankit Agrawal
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Meiling Sun
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Marko Melander
- Nanoscience Center, Department of Chemistry, University of Jyväskylä, P.O. Box 35 (YN), Jyväskylä FI-40014, Finland
| | - Ethan J Crumlin
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Brett A Helms
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - David Prendergast
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
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Aggarwal A, Vinayak V, Bag S, Bhattacharyya C, Waghmare UV, Maiti PK. Predicting the DNA Conductance Using a Deep Feedforward Neural Network Model. J Chem Inf Model 2020; 61:106-114. [PMID: 33320660 DOI: 10.1021/acs.jcim.0c01072] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics and biological research. The charge migration rate is controlled by the electronic couplings between the two nucleobases of DNA/RNA. These electronic couplings strongly depend on the intermolecular geometry and orientation. Estimating these electronic couplings for all the possible relative geometries of molecules using the computationally demanding first-principles calculations requires a lot of time and computational resources. In this article, we present a machine learning (ML)-based model to calculate the electronic coupling between any two bases of dsDNA/dsRNA and bypass the computationally expensive first-principles calculations. Using the Coulomb matrix representation which encodes the atomic identities and coordinates of the DNA base pairs to prepare the input dataset, we train a feedforward neural network model. Our neural network (NN) model can predict the electronic couplings between dsDNA base pairs with any structural orientation with a mean absolute error (MAE) of less than 0.014 eV. We further use the NN-predicted electronic coupling values to compute the dsDNA/dsRNA conductance.
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Affiliation(s)
- Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Vinayak Vinayak
- Undergraduate Program, Indian Institute of Science, Bangalore 560012, India
| | - Saientan Bag
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Chiranjib Bhattacharyya
- Department of Computer Science and Automation, Indian Institute of Science, Bangalore 560012, India
| | - Umesh V Waghmare
- Theoretical Sciences Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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Liu Y, Ren X, He L. A DFT study of energetic and structural properties of a full turn of A-form DNA under relaxed and stretching conditions. J Chem Phys 2019; 151:215102. [DOI: 10.1063/1.5129716] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Yue Liu
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Xinguo Ren
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Lixin He
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
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7
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Tight-Binding Modeling of Nucleic Acid Sequences: Interplay between Various Types of Order or Disorder and Charge Transport. Symmetry (Basel) 2019. [DOI: 10.3390/sym11080968] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
This review is devoted to tight-binding (TB) modeling of nucleic acid sequences like DNA and RNA. It addresses how various types of order (periodic, quasiperiodic, fractal) or disorder (diagonal, non-diagonal, random, methylation et cetera) affect charge transport. We include an introduction to TB and a discussion of its various submodels [wire, ladder, extended ladder, fishbone (wire), fishbone ladder] and of the process of renormalization. We proceed to a discussion of aperiodicity, quasicrystals and the mathematics of aperiodic substitutional sequences: primitive substitutions, Perron–Frobenius eigenvalue, induced substitutions, and Pisot property. We discuss the energy structure of nucleic acid wires, the coupling to the leads, the transmission coefficients and the current–voltage curves. We also summarize efforts aiming to examine the potentiality to utilize the charge transport characteristics of nucleic acids as a tool to probe several diseases or disorders.
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Mantela M, Lambropoulos K, Theodorakou M, Simserides C. Quasi-Periodic and Fractal Polymers: Energy Structure and Carrier Transfer. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E2177. [PMID: 31284609 PMCID: PMC6651379 DOI: 10.3390/ma12132177] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 12/23/2022]
Abstract
We study the energy structure and the coherent transfer of an extra electron or hole along aperiodic polymers made of N monomers, with fixed boundaries, using B-DNA as our prototype system. We use a Tight-Binding wire model, where a site is a monomer (e.g., in DNA, a base pair). We consider quasi-periodic (Fibonacci, Thue-Morse, Double-Period, Rudin-Shapiro) and fractal (Cantor Set, Asymmetric Cantor Set) polymers made of the same monomer (I polymers) or made of different monomers (D polymers). For all types of such polymers, we calculate the highest occupied molecular orbital (HOMO) eigenspectrum and the lowest unoccupied molecular orbital (LUMO) eigenspectrum, the HOMO-LUMO gap and the density of states. We examine the mean over time probability to find the carrier at each monomer, the frequency content of carrier transfer (Fourier spectra, weighted mean frequency of each monomer, total weighted mean frequency of the polymer), and the pure mean transfer rate k. Our results reveal that there is a correspondence between the degree of structural complexity and the transfer properties. I polymers are more favorable for charge transfer than D polymers. We compare k ( N ) of quasi-periodic and fractal sequences with that of periodic sequences (including homopolymers) as well as with randomly shuffled sequences. Finally, we discuss aspects of experimental results on charge transfer rates in DNA with respect to our coherent pure mean transfer rates.
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Affiliation(s)
- Marilena Mantela
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos, GR-15784 Athens, Greece
| | - Konstantinos Lambropoulos
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos, GR-15784 Athens, Greece
| | - Marina Theodorakou
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos, GR-15784 Athens, Greece
| | - Constantinos Simserides
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos, GR-15784 Athens, Greece.
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Lambropoulos K, Simserides C. Periodic, quasiperiodic, fractal, Kolakoski, and random binary polymers: Energy structure and carrier transport. Phys Rev E 2019; 99:032415. [PMID: 30999536 DOI: 10.1103/physreve.99.032415] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 05/26/2023]
Abstract
We study periodic, quasiperiodic (Thue-Morse, Fibonacci, period doubling, Rudin-Shapiro), fractal (Cantor, generalized Cantor), Kolakoski, and random binary sequences using a tight-binding wire model, where a site is a monomer (e.g., in DNA, a base pair). We use B-DNA as our prototype system. All sequences have purines, guanine (G) or adenine (A), on the same strand, i.e., our prototype binary alphabet is {G,A}. Our aim is to examine the influence of sequence intricacy and magnitude of parameters on energy structure, localization, and charge transport. We study quantities such as autocorrelation function, eigenspectra, density of states, Lyapunov exponents, transmission coefficients, and current-voltage curves. We show that the degree of sequence intricacy and the presence of correlations decisively affect the aforementioned physical properties. Periodic segments have enhanced transport properties. Specifically, in homogeneous sequences transport efficiency is maximum. There are several deterministic aperiodic sequences that can support significant currents, depending on the Fermi level of the leads. Random sequences is the less efficient category.
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Affiliation(s)
- K Lambropoulos
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, 15784 Zografos, Athens, Greece
| | - C Simserides
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, 15784 Zografos, Athens, Greece
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Sarap CS, Partovi-Azar P, Fyta M. Optoelectronic Properties of Diamondoid-DNA Complexes. ACS APPLIED BIO MATERIALS 2018. [DOI: 10.1021/acsabm.8b00011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Chandra Shekar Sarap
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Pouya Partovi-Azar
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Maria Fyta
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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