1
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Zhao G, Jia R, Shi W, Zhuang H, Xin X, Ma F, Li Y. Substituent effects on the ESIPT process and the potential applications in materials transport field of 2'-aminochalcone derivatives. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124560. [PMID: 38843615 DOI: 10.1016/j.saa.2024.124560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/28/2024] [Accepted: 05/28/2024] [Indexed: 06/17/2024]
Abstract
This work investigates the different charge transfer characteristics and excited state intramolecular proton transfer process (ESIPT) of 2'-aminochalcones derivatives carrying different electron-withdrawing groups. Four new molecules are designed in the experiment and named as 2c, 3c, 4c and 5c, respectively. (Dyes and Pigments, 2022, 202.) Based on these four molecules, the effect of substituents on the ESIPT process and the charge transfer process are discussed in detail in our work. According to the study of the related parameters at the hydrogen bond site, infrared vibration spectrum, interaction region indicator isosurface (IRI) and scatter plots, it is concluded that the hydrogen bond interaction is enhanced under photoexcitation, and the descending order of the excited state hydrogen bond strength is 3c > 5c > 4c > 2c. The hydrogen bond energy is calculated by atoms in moleculs (AIM) topological analysis and core-valence bifurcation (CVB) index. The potential energy curve reveals the ESIPT mechanism. Frontier molecular orbital and electron-hole analyses explain the reasons for the changes in the ESIPT process at the electronic level. In addition, the ionization potentials (IPa and IPv), affinity energies (EAa and EAv) and reorganization energies are calculated to evaluate the potential application value of organic molecules in material transport field.
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Affiliation(s)
- Guijie Zhao
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Rulin Jia
- School of Forensic Science and Technology, Criminal Investigation Police University of China, Liaoning, Shenyang 110035, PR China
| | - Wei Shi
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Hongbin Zhuang
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Xin Xin
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Fengcai Ma
- School of Physics, Liaoning University, Shenyang 110036, PR China.
| | - Yongqing Li
- School of Physics, Liaoning University, Shenyang 110036, PR China.
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2
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Wang K, Deng P, Lin H, Sun W, Shen J. DNA-Based Conductors: From Materials Design to Ultra-Scaled Electronics. SMALL METHODS 2024:e2400694. [PMID: 39049716 DOI: 10.1002/smtd.202400694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 06/04/2024] [Indexed: 07/27/2024]
Abstract
Photolithography has been the foundational fabrication paradigm in current high-performance electronics. However, due to the limitation in fabrication resolution, scaling beyond a 20-nm critical dimension for metal conductors presents a significant challenge for photolithography. Structural DNA nanotechnology emerges as a promising alternative to photolithography, allowing for the site-specific assembly of nano-materials at single-molecule resolution. Substantial progresses have been achieved in the ultra-scaled DNA-based conductors, exhibiting novel transport characteristics and small critical dimensions. This review highlights the structure-transport property relationship for various DNA-based conductors and their potential applications in quantum /semiconductor electronics, going beyond the conventional scope focusing mainly on the shape diversity of DNA-templated metals. Different material synthesis methods and their morphological impacts on the conductivities are discussed in detail, with particular emphasis on the conducting mechanisms, such as insulating, metallic conducting, quantum tunneling, and superconducting. Furthermore, the ionic gating effect of self-assembled DNA structures in electrolyte solutions is examined. This review also suggests potential solutions to address current challenges in DNA-based conductors, encouraging multi-disciplinary collaborations for the future development of this exciting area.
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Affiliation(s)
- Kexin Wang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, Peking University, Beijing, 100871, China
| | - Pu Deng
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, Peking University, Beijing, 100871, China
| | - Huili Lin
- School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Wei Sun
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, Peking University, Beijing, 100871, China
- Zhangjiang Laboratory, Shanghai, 201210, China
| | - Jie Shen
- School of Materials Science and Engineering, Peking University, Beijing, 100871, China
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3
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Aminiranjbar Z, Gultakti CA, Alangari MN, Wang Y, Demir B, Koker Z, Das AK, Anantram MP, Oren EE, Hihath J. Identifying SARS-CoV-2 Variants Using Single-Molecule Conductance Measurements. ACS Sens 2024; 9:2888-2896. [PMID: 38773960 DOI: 10.1021/acssensors.3c02734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
The global COVID-19 pandemic has highlighted the need for rapid, reliable, and efficient detection of biological agents and the necessity of tracking changes in genetic material as new SARS-CoV-2 variants emerge. Here, we demonstrate that RNA-based, single-molecule conductance experiments can be used to identify specific variants of SARS-CoV-2. To this end, we (i) select target sequences of interest for specific variants, (ii) utilize single-molecule break junction measurements to obtain conductance histograms for each sequence and its potential mutations, and (iii) employ the XGBoost machine learning classifier to rapidly identify the presence of target molecules in solution with a limited number of conductance traces. This approach allows high-specificity and high-sensitivity detection of RNA target sequences less than 20 base pairs in length by utilizing a complementary DNA probe capable of binding to the specific target. We use this approach to directly detect SARS-CoV-2 variants of concerns B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron) and further demonstrate that the specific sequence conductance is sensitive to nucleotide mismatches, thus broadening the identification capabilities of the system. Thus, our experimental methodology detects specific SARS-CoV-2 variants, as well as recognizes the emergence of new variants as they arise.
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Affiliation(s)
- Zahra Aminiranjbar
- Department of Electrical and Computer Engineering, University of California Davis, Davis, California 95616, United States
| | - Caglanaz Akin Gultakti
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Mashari Nasser Alangari
- Department of Electrical and Computer Engineering, University of California Davis, Davis, California 95616, United States
- Department of Electrical Engineering, University of Hail, Hail 2240, Saudi Arabia
| | - Yiren Wang
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Zeynep Koker
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Arindam K Das
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98115, United States
- Department of Computer Science and Electrical Engineering, Eastern Washington University, Cheney, Washington 99004,United States
| | - M P Anantram
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Joshua Hihath
- Department of Electrical and Computer Engineering, University of California Davis, Davis, California 95616, United States
- Center for Bioelectronics and Biosensors, School of Electrical, Computer, and Energy Engineering, Arizona State University, Phoenix, Arizona 85287, United States
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4
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Polycarpou G, Skourtis SS. Intra-strand phosphate-mediated pathways in microsolvated double-stranded DNA. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:375301. [PMID: 38848732 DOI: 10.1088/1361-648x/ad559d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/07/2024] [Indexed: 06/09/2024]
Abstract
We argue that dry DNA charge transport in molecular junctions, over distances of tens of nanometers, can take place via independent intra-strand pathways involving the phosphate groups. Such pathways explain recent single-molecule experiments that compare currents in intact and nicked 100 base-pair double-stranded DNA. We explore the conditions that favor independent intra-strand transport channels with the participation of the phosphate groups, as opposed to purely base-mediated transport involving the pi-stacked bases and inter-strand transitions. Our computations demonstrate how long-distance transport pathways in DNA are tuned by the degree of solvation, which affects the level of dynamic disorder in the pi-stacking, and the energies of phosphate-group molecular orbitals.
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Qiao T, Shi W, Zhuang H, Zhao G, Xin X, Li Y. Effects of substitution and conjugation on photophysical properties of ESIPT-based fluorophores with the core of 4-aminophthalimide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 309:123802. [PMID: 38184881 DOI: 10.1016/j.saa.2023.123802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
4-Aminophthalimide is a highly fluorescent signaling unit with excellent photophysical properties and wide application foregrounds. Based on this, a range of theoretical investigations are conducted on the fluorescent probe (E)-5-((2-hydroxybenzylidene) amino) isoindoline-1, 3-dione (HID) with the core of 4-aminophthalimide using density functional theory (DFT) and time-containing density functional theory (TD-DFT) methods in this paper. The optimized configurations, vertical excitation and emission energies, electronic characteristics and excited-state intramolecular proton transfer (ESIPT) behaviors of the probe HID are discussed in detail. Furthermore, to enhance the luminescent properties of HID, five novel compounds have been designed based on the structure of HID by introducing amino, methoxy and naphthalene groups (-NH2, -OMe and C10H8). Our work thoroughly explores how the property and position of substituents and conjugation affect photophysical characteristics and ESIPT processes. We find that the ESIPT dynamics can be modulated by the substitution and conjugation effects. Specifically, the introduction of amino and methoxy groups at the ortho-position and the introduction of the naphthalene group promote the ESIPT behavior of HID1, whereas the introduction of amino and methoxy groups at the meta-position exhibits the contrary impact. Therefore, we boldly infer that the introduction of electron-donating groups in the ortho-position and the introduction of the conjugated group make the ESIPT process more effortless to occur, whereas the introduction of substituents with opposing natures in the meta-position makes the ESIPT process more difficult to occur. In addition, the ionization potentials (IP), electron affinities (EA) and reorganization energies (λh and λe) of molecules are calculated to assess their potential as luminescent materials. Our work not only reveals the luminescence and ESIPT mechanism of the probe HID1, but also proposes to modulate the ESIPT process through the substitution and conjugation effects. In particular, the designed molecules have better photoelectric properties as a result of their red-shifted absorption and fluorescence spectra, smaller energy gaps, larger transferred charges and greater charge transferred distances, which offers some valuable ideas for the experimental development of more efficient organic luminescent materials with ESIPT properties.
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Affiliation(s)
- Tiantian Qiao
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Wei Shi
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Hongbin Zhuang
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Guijie Zhao
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Xin Xin
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Yongqing Li
- School of Physics, Liaoning University, Shenyang 110036, PR China.
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6
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Siebert R, Ammerpohl O, Rossini M, Herb D, Rau S, Plenio MB, Jelezko F, Ankerhold J. A quantum physics layer of epigenetics: a hypothesis deduced from charge transfer and chirality-induced spin selectivity of DNA. Clin Epigenetics 2023; 15:145. [PMID: 37684676 PMCID: PMC10492394 DOI: 10.1186/s13148-023-01560-3] [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: 06/09/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Epigenetic mechanisms are informational cellular processes instructing normal and diseased phenotypes. They are associated with DNA but without altering the DNA sequence. Whereas chemical processes like DNA methylation or histone modifications are well-accepted epigenetic mechanisms, we herein propose the existence of an additional quantum physics layer of epigenetics. RESULTS We base our hypothesis on theoretical and experimental studies showing quantum phenomena to be active in double-stranded DNA, even under ambient conditions. These phenomena include coherent charge transfer along overlapping pi-orbitals of DNA bases and chirality-induced spin selectivity. Charge transfer via quantum tunneling mediated by overlapping orbitals results in charge delocalization along several neighboring bases, which can even be extended by classical (non-quantum) electron hopping. Such charge transfer is interrupted by flipping base(s) out of the double-strand e.g., by DNA modifying enzymes. Charge delocalization can directly alter DNA recognition by proteins or indirectly by DNA structural changes e.g., kinking. Regarding sequence dependency, charge localization, shown to favor guanines, could influence or even direct epigenetic changes, e.g., modification of cytosines in CpG dinucleotides. Chirality-induced spin selectivity filters electrons for their spin along DNA and, thus, is not only an indicator for quantum coherence but can potentially affect DNA binding properties. CONCLUSIONS Quantum effects in DNA are prone to triggering and manipulation by external means. By the hypothesis put forward here, we would like to foster research on "Quantum Epigenetics" at the interface of medicine, biology, biochemistry, and physics to investigate the potential epigenetic impact of quantum physical principles on (human) life.
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Affiliation(s)
- Reiner Siebert
- Institute of Human Genetics, Ulm University & Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
- Center for Integrated Quantum Science and Technology (IQST) Ulm-Stuttgart, Ulm, Germany.
| | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University & Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Mirko Rossini
- Center for Integrated Quantum Science and Technology (IQST) Ulm-Stuttgart, Ulm, Germany
- Institute for Complex Quantum Systems, Ulm University, 89069, Ulm, Germany
| | - Dennis Herb
- Institute for Complex Quantum Systems, Ulm University, 89069, Ulm, Germany
| | - Sven Rau
- Institute of Inorganic Chemistry I, Ulm University, 89081, Ulm, Germany
| | - Martin B Plenio
- Center for Integrated Quantum Science and Technology (IQST) Ulm-Stuttgart, Ulm, Germany
- Institute of Theoretical Physics, Ulm University, 89081, Ulm, Germany
| | - Fedor Jelezko
- Center for Integrated Quantum Science and Technology (IQST) Ulm-Stuttgart, Ulm, Germany
- Institute for Quantum Optics, Ulm University, 89081, Ulm, Germany
| | - Joachim Ankerhold
- Center for Integrated Quantum Science and Technology (IQST) Ulm-Stuttgart, Ulm, Germany
- Institute for Complex Quantum Systems, Ulm University, 89069, Ulm, Germany
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7
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Wang Y, Demir B, Mohammad H, Oren EE, Anantram MP. Computational study of the role of counterions and solvent dielectric in determining the conductance of B-DNA. Phys Rev E 2023; 107:044404. [PMID: 37198817 DOI: 10.1103/physreve.107.044404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 04/01/2023] [Indexed: 05/19/2023]
Abstract
DNA naturally exists in a solvent environment, comprising water and salt molecules such as sodium, potassium, magnesium, etc. Along with the sequence, the solvent conditions become a vital factor determining DNA structure and thus its conductance. Over the last two decades, researchers have measured DNA conductivity both in hydrated and almost dry (dehydrated) conditions. However, due to experimental limitations (the precise control of the environment), it is very difficult to analyze the conductance results in terms of individual contributions of the environment. Therefore, modeling studies can help us to gain a valuable understanding of various factors playing a role in charge transport phenomena. DNA naturally has negative charges located at the phosphate groups in the backbone, which provides both the connections between the base pairs and the structural support for the double helix. Positively charged ions such as the sodium ion (Na^{+}), one of the most commonly used counterions, balance the negative charges at the backbone. This modeling study investigates the role of counterions both with and without the solvent (water) environment in charge transport through double-stranded DNA. Our computational experiments show that in dry DNA, the presence of counterions affects electron transmission at the lowest unoccupied molecular orbital energies. However, in solution, the counterions have a negligible role in transmission. Using the polarizable continuum model calculations, we demonstrate that the transmission is significantly higher at both the highest occupied and lowest unoccupied molecular orbital energies in a water environment as opposed to in a dry one. Moreover, calculations also show that the energy levels of neighboring bases are more closely aligned to ease electron flow in the solution.
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Affiliation(s)
- Yiren Wang
- Deparment of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98105, USA
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06510, Turkey
| | - Hashem Mohammad
- Department of Electrical Engineering, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06510, Turkey
| | - M P Anantram
- Deparment of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98105, USA
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8
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Substituent effects on photophysical properties of ESIPT-based fluorophores bearing the 4-diethylaminosalicylaldehyde core. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Aggarwal A, Naskar S, Maiti PK. Molecular Rectifiers with a Very High Rectification Ratio Enabled by Oxidative Damage in Double-Stranded DNA. J Phys Chem B 2022; 126:4636-4646. [PMID: 35729785 DOI: 10.1021/acs.jpcb.2c01371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we report a novel strategy to construct highly efficient molecular diodes using oxidatively damaged DNA molecules. Being exposed to several endogenous and exogenous events, DNA suffers from constant oxidative damage, leading to the oxidation of guanine to 8-oxoguanine (8oxoG). Here, we study the charge migration properties of native and oxidatively damaged DNA using a multiscale multiconfigurational methodology comprising molecular dynamics, density functional theory, and kinetic Monte Carlo simulations. We perform a comprehensive study to understand the effect of different concentrations and locations of 8oxoG in a dsDNA sequence on its charge-transport properties and find tunable rectifier properties having potential applications in molecular electronics such as molecular switches and molecular rectifiers. We also discover the negative differential resistance properties of the fully oxidized Drew-Dickerson sequence. The presence of 8oxoG guanine leads to the trapping of charge, thus operating as a charge sink, which reveals how oxidized guanine saves the rest of the genome from further oxidative damage.
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Affiliation(s)
- Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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10
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Sosorev AY. Modeling of Electron Hole Transport within a Small Ribosomal Subunit. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022020224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract—
Synchronized operation of various parts of the ribosome during protein synthesis implies the presence of a coordinating pathway, however, this is still unknown. We have recently suggested that such a pathway can be based on charge transport along the transfer and ribosomal RNA molecules and localization of the charges in functionally important areas of the ribosome. In the current study, using density functional theory calculations, we show that charge carriers (electron holes) can efficiently migrate within the central element of the small ribosomal subunit—the h44 helix. Monte-Carlo modeling revealed that electron holes tend to localize in the functionally important areas of the h44 helix, near the decoding center and intersubunit bridges. On the basis of the results obtained, we suggest that charge transport and localization within the h44 helix could coordinate intersubunit ratcheting with other processes occurring during protein synthesis.
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11
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Gupta N, Wilkinson EA, Karuppannan SK, Bailey L, Vilan A, Zhang Z, Qi DC, Tadich A, Tuite EM, Pike AR, Tucker JHR, Nijhuis CA. Role of Order in the Mechanism of Charge Transport across Single-Stranded and Double-Stranded DNA Monolayers in Tunnel Junctions. J Am Chem Soc 2021; 143:20309-20319. [PMID: 34826219 PMCID: PMC8662729 DOI: 10.1021/jacs.1c09549] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Indexed: 11/29/2022]
Abstract
Deoxyribonucleic acid (DNA) has been hypothesized to act as a molecular wire due to the presence of an extended π-stack between base pairs, but the factors that are detrimental in the mechanism of charge transport (CT) across tunnel junctions with DNA are still unclear. Here we systematically investigate CT across dense DNA monolayers in large-area biomolecular tunnel junctions to determine when intrachain or interchain CT dominates and under which conditions the mechanism of CT becomes thermally activated. In our junctions, double-stranded DNA (dsDNA) is 30-fold more conductive than single-stranded DNA (ssDNA). The main reason for this large change in conductivity is that dsDNA forms ordered monolayers where intrachain tunneling dominates, resulting in high CT rates. By varying the temperature T and the length of the DNA fragments in the junctions, which determines the tunneling distance, we reveal a complex interplay between T, the length of DNA, and structural order on the mechanism of charge transport. Both the increase in the tunneling distance and the decrease in structural order result in a change in the mechanism of CT from coherent tunneling to incoherent tunneling (hopping). Our results highlight the importance of the interplay between structural order, tunneling distance, and temperature on the CT mechanism across DNA in molecular junctions.
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Affiliation(s)
- Nipun
Kumar Gupta
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- Centre
for Advanced 2D Materials, National University
of Singapore, 6 Science Drive 2, Singapore 117546, Singapore
| | - Edward A. Wilkinson
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, United Kingdom
| | - Senthil Kumar Karuppannan
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Lily Bailey
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, United Kingdom
| | - Ayelet Vilan
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 76100, Israel
| | - Ziyu Zhang
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Dong-Chen Qi
- Centre
for Materials Science, School of Chemistry and Physics, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Anton Tadich
- Australian
Synchrotron Clayton, 800 Blackburn Rd, Clayton, Victoria 3168, Australia
| | - Eimer M. Tuite
- Chemistry-School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - Andrew R. Pike
- Chemistry-School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - James H. R. Tucker
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, United Kingdom
| | - Christian A. Nijhuis
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- Centre
for Advanced 2D Materials, National University
of Singapore, 6 Science Drive 2, Singapore 117546, Singapore
- Department
of Molecules & Materials, MESA+ Institute for Nanotechnology,
Faculty of Science and Technology, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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12
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Yoon J, Hou Y, Knoepfel AM, Yang D, Ye T, Zheng L, Yennawar N, Sanghadasa M, Priya S, Wang K. Bio-inspired strategies for next-generation perovskite solar mobile power sources. Chem Soc Rev 2021; 50:12915-12984. [PMID: 34622260 DOI: 10.1039/d0cs01493a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Smart electronic devices are becoming ubiquitous due to many appealing attributes including portability, long operational time, rechargeability and compatibility with the user-desired form factor. Integration of mobile power sources (MPS) based on photovoltaic technologies with smart electronics will continue to drive improved sustainability and independence. With high efficiency, low cost, flexibility and lightweight features, halide perovskite photovoltaics have become promising candidates for MPS. Realization of these photovoltaic MPS (PV-MPS) with unconventionally extraordinary attributes requires new 'out-of-box' designs. Natural materials have provided promising designing solutions to engineer properties under a broad range of boundary conditions, ranging from molecules, proteins, cells, tissues, apparatus to systems in animals, plants, and humans optimized through billions of years of evolution. Applying bio-inspired strategies in PV-MPS could be biomolecular modification on crystallization at the atomic/meso-scale, bio-structural duplication at the device/system level and bio-mimicking at the functional level to render efficient charge delivery, energy transport/utilization, as well as stronger resistance against environmental stimuli (e.g., self-healing and self-cleaning). In this review, we discuss the bio-inspired/-mimetic structures, experimental models, and working principles, with the goal of revealing physics and bio-microstructures relevant for PV-MPS. Here the emphasis is on identifying the strategies and material designs towards improvement of the performance of emerging halide perovskite PVs and strategizing their bridge to future MPS.
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Affiliation(s)
- Jungjin Yoon
- Department of Materials Science & Engineering, Pennsylvania State University, University Park, 16802, PA, USA.
| | - Yuchen Hou
- Department of Materials Science & Engineering, Pennsylvania State University, University Park, 16802, PA, USA.
| | - Abbey Marie Knoepfel
- Department of Materials Science & Engineering, Pennsylvania State University, University Park, 16802, PA, USA.
| | - Dong Yang
- Department of Materials Science & Engineering, Pennsylvania State University, University Park, 16802, PA, USA.
| | - Tao Ye
- Department of Materials Science & Engineering, Pennsylvania State University, University Park, 16802, PA, USA.
| | - Luyao Zheng
- Department of Materials Science & Engineering, Pennsylvania State University, University Park, 16802, PA, USA.
| | - Neela Yennawar
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, 16802, PA, USA
| | - Mohan Sanghadasa
- U.S. Army Combat Capabilities Development Command Aviation & Missile Center, Redstone Arsenal, Alabama, 35898, USA
| | - Shashank Priya
- Department of Materials Science & Engineering, Pennsylvania State University, University Park, 16802, PA, USA.
| | - Kai Wang
- Department of Materials Science & Engineering, Pennsylvania State University, University Park, 16802, PA, USA.
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13
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Walking around Ribosomal Small Subunit: A Possible "Tourist Map" for Electron Holes. Molecules 2021; 26:molecules26185479. [PMID: 34576950 PMCID: PMC8467113 DOI: 10.3390/molecules26185479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/27/2021] [Accepted: 09/02/2021] [Indexed: 11/17/2022] Open
Abstract
Despite several decades of research, the physics underlying translation-protein synthesis at the ribosome-remains poorly studied. For instance, the mechanism coordinating various events occurring in distant parts of the ribosome is unknown. Very recently, we suggested that this allosteric mechanism could be based on the transport of electric charges (electron holes) along RNA molecules and localization of these charges in the functionally important areas; this assumption was justified using tRNA as an example. In this study, we turn to the ribosome and show computationally that holes can also efficiently migrate within the whole ribosomal small subunit (SSU). The potential sites of charge localization in SSU are revealed, and it is shown that most of them are located in the functionally important areas of the ribosome-intersubunit bridges, Fe4S4 cluster, and the pivot linking the SSU head to its body. As a result, we suppose that hole localization within the SSU can affect intersubunit rotation (ratcheting) and SSU head swiveling, in agreement with the scenario of electronic coordination of ribosome operation. We anticipate that our findings will improve the understanding of the translation process and advance molecular biology and medicine.
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14
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Valdiviezo J, Clever C, Beall E, Pearse A, Bae Y, Zhang P, Achim C, Beratan DN, Waldeck DH. Delocalization-Assisted Transport through Nucleic Acids in Molecular Junctions. Biochemistry 2021; 60:1368-1378. [PMID: 33870693 DOI: 10.1021/acs.biochem.1c00072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The flow of charge through molecules is central to the function of supramolecular machines, and charge transport in nucleic acids is implicated in molecular signaling and DNA repair. We examine the transport of electrons through nucleic acids to understand the interplay of resonant and nonresonant charge carrier transport mechanisms. This study reports STM break junction measurements of peptide nucleic acids (PNAs) with a G-block structure and contrasts the findings with previous results for DNA duplexes. The conductance of G-block PNA duplexes is much higher than that of the corresponding DNA duplexes of the same sequence; however, they do not display the strong even-odd dependence conductance oscillations found in G-block DNA. Theoretical analysis finds that the conductance oscillation magnitude in PNA is suppressed because of the increased level of electronic coupling interaction between G-blocks in PNA and the stronger PNA-electrode interaction compared to that in DNA duplexes. The strong interactions in the G-block PNA duplexes produce molecular conductances as high as 3% G0, where G0 is the quantum of conductance, for 5 nm duplexes.
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Affiliation(s)
- Jesús Valdiviezo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Caleb Clever
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Edward Beall
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Pearse
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yookyung Bae
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Catalina Achim
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| | - David H Waldeck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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15
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Derr JB, Rybicka-Jasińska K, Espinoza EM, Morales M, Billones MK, Clark JA, Vullev VI. On the Search of a Silver Bullet for the Preparation of Bioinspired Molecular Electrets with Propensity to Transfer Holes at High Potentials. Biomolecules 2021; 11:429. [PMID: 33804209 PMCID: PMC8001849 DOI: 10.3390/biom11030429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/01/2021] [Accepted: 03/07/2021] [Indexed: 01/24/2023] Open
Abstract
Biological structure-function relationships offer incomparable paradigms for charge-transfer (CT) science and its implementation in solar-energy engineering, organic electronics, and photonics. Electrets are systems with co-directionally oriented electric dopes with immense importance for CT science, and bioinspired molecular electrets are polyamides of anthranilic-acid derivatives with designs originating from natural biomolecular motifs. This publication focuses on the synthesis of molecular electrets with ether substituents. As important as ether electret residues are for transferring holes under relatively high potentials, the synthesis of their precursors presents formidable challenges. Each residue in the molecular electrets is introduced as its 2-nitrobenzoic acid (NBA) derivative. Hence, robust and scalable synthesis of ether derivatives of NBA is essential for making such hole-transfer molecular electrets. Purdie-Irvine alkylation, using silver oxide, produces with 90% yield the esters of the NBA building block for iso-butyl ether electrets. It warrants additional ester hydrolysis for obtaining the desired NBA precursor. Conversely, Williamson etherification selectively produces the same free-acid ether derivative in one-pot reaction, but a 40% yield. The high yields of Purdie-Irvine alkylation and the selectivity of the Williamson etherification provide important guidelines for synthesizing building blocks for bioinspired molecular electrets and a wide range of other complex ether conjugates.
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Affiliation(s)
- James Bennett Derr
- Department of Biochemistry, University of California, Riverside, CA 92521, USA;
| | | | - Eli Misael Espinoza
- Department of Chemistry, University of California, Riverside, CA 92521, USA; (E.M.E.); (M.M.)
| | - Maryann Morales
- Department of Chemistry, University of California, Riverside, CA 92521, USA; (E.M.E.); (M.M.)
| | | | - John Anthony Clark
- Department of Bioengineering, University of California, Riverside, CA 92521, USA; (K.R.-J.); (J.A.C.)
| | - Valentine Ivanov Vullev
- Department of Biochemistry, University of California, Riverside, CA 92521, USA;
- Department of Bioengineering, University of California, Riverside, CA 92521, USA; (K.R.-J.); (J.A.C.)
- Department of Chemistry, University of California, Riverside, CA 92521, USA; (E.M.E.); (M.M.)
- Department of Materials Science and Engineering Program, University of California, Riverside, CA 92521, USA
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16
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Sosorev A, Kharlanov O. Organic nanoelectronics inside us: charge transport and localization in RNA could orchestrate ribosome operation. Phys Chem Chem Phys 2021; 23:7037-7047. [PMID: 33448272 DOI: 10.1039/d0cp04970k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Translation - protein synthesis at the ribonucleic acid (RNA) based molecular machine, the ribosome, - proceeds in a similar manner in all life forms. However, despite several decades of research, the physics underlying this process remains enigmatic. Specifically, during translation, a ribosome undergoes large-scale conformational changes of its distant parts, and these motions are coordinated by an unknown mechanism. In this study, we suggest that such a mechanism could be related to charge (electron hole) transport along and between the RNA molecules, localization of these charges at certain sites and successive relaxation of the molecular geometry. Thus, we suppose that RNA-based molecular machines, e.g., the ribosome, could be electronically controlled, having "wires", "actuators", "a battery", and other "circuitry". Taking transfer RNA as an example, we justify the reasonability of our suggestion using ab initio and atomistic simulations. Specifically, very large hole transfer integrals between the nucleotides (up to above 100 meV) are observed so that the hole can migrate over nearly the whole tRNA molecule. Hole localization at several guanines located at functionally important sites (G27, G10, G34 and G63) is predicted, which is shown to induce geometry changes in these sites, their neighborhoods and even rather distant moieties. If our hypothesis is right, we anticipate that our findings will qualitatively advance the understanding of the key biological processes and could inspire novel approaches in medicine.
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Affiliation(s)
- Andrey Sosorev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Ulitsa Miklukho-Maklaya, 16/10, Moscow, GSP-7, 117997, Russia.
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17
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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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18
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Derr JB, Tamayo J, Clark JA, Morales M, Mayther MF, Espinoza EM, Rybicka-Jasińska K, Vullev VI. Multifaceted aspects of charge transfer. Phys Chem Chem Phys 2020; 22:21583-21629. [PMID: 32785306 PMCID: PMC7544685 DOI: 10.1039/d0cp01556c] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Charge transfer and charge transport are by far among the most important processes for sustaining life on Earth and for making our modern ways of living possible. Involving multiple electron-transfer steps, photosynthesis and cellular respiration have been principally responsible for managing the energy flow in the biosphere of our planet since the Great Oxygen Event. It is impossible to imagine living organisms without charge transport mediated by ion channels, or electron and proton transfer mediated by redox enzymes. Concurrently, transfer and transport of electrons and holes drive the functionalities of electronic and photonic devices that are intricate for our lives. While fueling advances in engineering, charge-transfer science has established itself as an important independent field, originating from physical chemistry and chemical physics, focusing on paradigms from biology, and gaining momentum from solar-energy research. Here, we review the fundamental concepts of charge transfer, and outline its core role in a broad range of unrelated fields, such as medicine, environmental science, catalysis, electronics and photonics. The ubiquitous nature of dipoles, for example, sets demands on deepening the understanding of how localized electric fields affect charge transfer. Charge-transfer electrets, thus, prove important for advancing the field and for interfacing fundamental science with engineering. Synergy between the vastly different aspects of charge-transfer science sets the stage for the broad global impacts that the advances in this field have.
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Affiliation(s)
- James B Derr
- Department of Biochemistry, University of California, Riverside, CA 92521, USA.
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19
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Molecular electrets – Why do dipoles matter for charge transfer and excited-state dynamics? J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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20
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Aggarwal A, Bag S, Venkatramani R, Jain M, Maiti PK. Multiscale modelling reveals higher charge transport efficiencies of DNA relative to RNA independent of mechanism. NANOSCALE 2020; 12:18750-18760. [PMID: 32970051 DOI: 10.1039/d0nr02382e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, we compare the charge transport properties of multiple double-stranded (ds)RNA sequences with corresponding dsDNA sequences. Recent studies have presented a contradictory picture of relative charge transport efficiencies in A-form DNA : RNA hybrids and dsDNA. Using a multiscale modelling framework, we compute conductance of dsDNA and dsRNA using Landauer formalism in the coherent limit and Marcus-Hush theory in the incoherent limit. We find that dsDNA conducts better than dsRNA in both the charge transport regimes. Our analysis shows that the structural differences in the twist angle and slide of dsDNA and dsRNA are the main reasons behind the higher conductance of dsDNA in the incoherent hopping regime. In the coherent limit however, for the same base pair length, the conductance of dsRNA is higher than that of dsDNA for the morphologies where dsRNA has a smaller end-to-end length relative to that of dsDNA.
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Affiliation(s)
- Abhishek Aggarwal
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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21
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Roy S, Xie O, Dorval Courchesne N. Challenges in engineering conductive protein fibres: Disentangling the knowledge. CAN J CHEM ENG 2020. [DOI: 10.1002/cjce.23836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sophia Roy
- Department of Chemical Engineering McGill University Montréal Québec Canada
| | - Oliver Xie
- Department of Chemical Engineering McGill University Montréal Québec Canada
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22
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Jiang H, Zimmerman PM. Charge transfer via spin flip configuration interaction: Benchmarks and application to singlet fission. J Chem Phys 2020; 153:064109. [DOI: 10.1063/5.0018267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Hanjie Jiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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23
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Daraghma SMA, Talebi S, Periasamy V. Understanding the electronic properties of single- and double-stranded DNA. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2020; 43:40. [PMID: 32557121 DOI: 10.1140/epje/i2020-11965-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
Understanding the charge transfer mechanism through deoxyribonucleic acid (DNA) molecules remains a challenge for numerous theoretical and experimental studies in order to be utilized in nanoelectronic devices. Various methods have attempted to investigate the conductivity of double-stranded (ds-) and single-stranded DNA (ssDNA) molecules. However, different electronic behaviors of these molecules are not clearly understood due to the complexity and lack of accuracy of the methods applied in these studies. In this work however, we demonstrated an electronic method to study the electrical behavior of synthetic ssDNA or dsDNA integrated within printed circuit board (PCB)-based metal (gold)-semiconductor (DNA) Schottky junctions. The results obtained in this work are in agreement with other studies reporting dsDNA as having higher conductivity than ssDNA as observed by us in the range of 4-6μA for the former and 2-3μA for the latter at an applied bias of 3V. Selected solid-state parameters such as turn-on voltage, series resistance, shunt resistance, ideality factor, and saturation current were also calculated for the specifically designed ss- and dsDNA sequences using the thermionic emission model. The results also showed that the highest conductance was observed for dsDNA with guanine and cytosine base pairs, while the lowest conductance was for ssDNA with adenine and thymine bases. We believe the results of this preliminary work involving the gold-DNA Schottky junction may allow the interrogation of DNA charge transfer mechanisms and contribute to better understanding its elusive electronic properties.
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Affiliation(s)
- Souhad M A Daraghma
- Low Dimensional Materials Research Centre (LDMRC), Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sara Talebi
- Low Dimensional Materials Research Centre (LDMRC), Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Vengadesh Periasamy
- Low Dimensional Materials Research Centre (LDMRC), Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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24
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Futera Z, Jiang X, Blumberger J. Ergodicity Breaking in Thermal Biological Electron Transfer? Cytochrome C Revisited II. J Phys Chem B 2020; 124:3336-3342. [PMID: 32223243 DOI: 10.1021/acs.jpcb.0c01414] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It was recently suggested that cytochrome c operates in an ergodicity-breaking regime characterized by unusually large energy gap thermal fluctuations and associated reorganization free energies for heme oxidation of up to 3.0 eV. The large fluctuations were reported to lower activation free energy for oxidation of the heme cofactor by almost a factor of 2 compared to the case where ergodicity is maintained. Our group has recently investigated this claim computationally at several levels of theory and found no evidence for such large energy gap fluctuations. Here we address the points of our earlier work that have raised criticism and we also extend our previous investigation by considering a simple linear polarizability model for cytochrome c oxidation. We find very consistent results among all our computational approaches, ranging from classical molecular dynamics, to the linear polarizability model to QM(PMM)/MM to full QM(DFT)/MM electrostatic emdedding. None of them support the notion of very large energy gap fluctuations or ergodicity breaking. The deviation between our simulations and the ones reported in [ J. Phys. Chem. B 2017, 121, 4958] is traced back to rather large electric fields at the Fe site of the heme c cofactor in that study, not seen in our simulations, neither with the AMBER nor with the CHARMM force field. While ergodicity breaking effects may well occur in other biological ET, our numerical evidence suggests that this is not the case for cytochrome c.
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Affiliation(s)
- Zdenek Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Xiuyun Jiang
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, U.K
| | - Jochen Blumberger
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, U.K
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25
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Skonieczny K, Espinoza EM, Derr JB, Morales M, Clinton JM, Xia B, Vullev VI. Biomimetic and bioinspired molecular electrets. How to make them and why does the established peptide chemistry not always work? PURE APPL CHEM 2020. [DOI: 10.1515/pac-2019-0111] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract“Biomimetic” and “bioinspired” define different aspects of the impacts that biology exerts on science and engineering. Biomimicking improves the understanding of how living systems work, and builds tools for bioinspired endeavors. Biological inspiration takes ideas from biology and implements them in unorthodox manners, exceeding what nature offers. Molecular electrets, i.e. systems with ordered electric dipoles, are key for advancing charge-transfer (CT) science and engineering. Protein helices and their biomimetic analogues, based on synthetic polypeptides, are the best-known molecular electrets. The inability of native polypeptide backbones to efficiently mediate long-range CT, however, limits their utility. Bioinspired molecular electrets based on anthranilamides can overcome the limitations of their biological and biomimetic counterparts. Polypeptide helices are easy to synthesize using established automated protocols. These protocols, however, fail to produce even short anthranilamide oligomers. For making anthranilamides, the residues are introduced as their nitrobenzoic-acid derivatives, and the oligomers are built from their C- to their N-termini via amide-coupling and nitro-reduction steps. The stringent requirements for these reduction and coupling steps pose non-trivial challenges, such as high selectivity, quantitative yields, and fast completion under mild conditions. Addressing these challenges will provide access to bioinspired molecular electrets essential for organic electronics and energy conversion.
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Affiliation(s)
- Kamil Skonieczny
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44-52, 01-224 Warsaw, Poland
| | - Eli M. Espinoza
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - James B. Derr
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Maryann Morales
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Jillian M. Clinton
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
| | - Bing Xia
- GlaxoSmithKline, 200 Cambridgepark Dr., Cambridge, MA 02140, USA
| | - Valentine I. Vullev
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
- Department of Chemistry, University of California, Riverside, CA 92521, USA
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
- Materials Science and Engineering Program, University of California, Riverside, CA 92521, USA
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26
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Bag S, Maiti PK. Tuning molecular fluctuation to boost the conductance in DNA based molecular wires. Phys Chem Chem Phys 2019; 21:23514-23520. [PMID: 31617554 DOI: 10.1039/c9cp03589c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Inherent molecular fluctuations are known to have a significant influence on the charge transport properties of biomolecules like DNA, PNA and proteins. In this work, we show ways to control these fluctuations and further demonstrate their use to enhance the conductance of two widely studied molecular wires, namely dsDNA (DNA) and G4 Quadruplex (G4-Quad). We quantify the molecular fluctuation in terms of the root mean square deviation (RMSD) of the molecule. In the case of DNA, we use temperature to control the fluctuations, while in the case of G4-Quad the fluctuations are tuned by the ions inside the pore. The electronic coupling between the bases of dsDNA and G4-Quad, which measures the conductance of these molecular wires, shows a non-monotonic behaviour with the increase in fluctuation. We find values of fluctuation which give rise to maximum electronic coupling and hence high conductivity for both the cases. In the case of DNA, these optimal fluctuations (∼2.5 Å) are achieved at a temperature of 210 K, which gives rise to an electronic coupling of 0.135 eV between the DNA bases. The optimal fluctuations in G4-Quad are achieved (∼7 Å) in a 4 base pair long system with 2 Na+ ions inside the pore, giving rise to an electronic coupling of 0.09 eV.
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Affiliation(s)
- Saientan Bag
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, Karnataka, India.
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27
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Kogikoski S, Paschoalino WJ, Cantelli L, Silva W, Kubota LT. Electrochemical sensing based on DNA nanotechnology. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.06.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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28
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Jiang X, Futera Z, Blumberger J. Ergodicity-Breaking in Thermal Biological Electron Transfer? Cytochrome C Revisited. J Phys Chem B 2019; 123:7588-7598. [PMID: 31405279 DOI: 10.1021/acs.jpcb.9b05253] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
It was recently suggested that certain redox proteins operate in an ergodicity-breaking regime to facilitate biological electron transfer (ET). A signature for this is a large variance reorganization free energy (several electronvolts) but a significantly smaller Stokes reorganization free energy due to incomplete protein relaxation on the time scale of the ET event. Here we investigate whether this picture holds for oxidation of cytochrome c in aqueous solution, at various levels of theory including classical molecular dynamics with two additive and one electronically polarizable force field, and QM/MM calculations with the QM region treated by full electrostatic DFT embedding and by the perturbed matrix method. Sampling the protein and energy gap dynamics over more than 250 ns, we find no evidence for ergodicity-breaking effects. In particular, the inclusion of electronic polarizability of the heme group at QM/MM levels did not induce nonergodic effects, contrary to previous reports by Matyushov et al. The well-known problem of overestimation of reorganization free energies with additive force fields is cured when the protein and solvent are treated as electronically polarizable. Ergodicity-breaking effects may occur in other redox proteins, and our results suggest that long simulations, ideally on the ET time scale, with electronically polarizable force fields are required to obtain strong numerical evidence for them.
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Affiliation(s)
- Xiuyun Jiang
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
| | - Zdenek Futera
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
| | - Jochen Blumberger
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
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29
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Ru X, Zhang P, Beratan DN. Assessing Possible Mechanisms of Micrometer-Scale Electron Transfer in Heme-Free Geobacter sulfurreducens Pili. J Phys Chem B 2019; 123:5035-5047. [PMID: 31095388 DOI: 10.1021/acs.jpcb.9b01086] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The electrically conductive pili of Geobacter sulfurreducens are of both fundamental and practical interest. They facilitate extracellular and interspecies electron transfer (ET) and also provide an electrical interface between living and nonliving systems. We examine the possible mechanisms of G. sulfurreducens electron transfer in regimes ranging from incoherent to coherent transport. For plausible ET parameters, electron transfer in G. sulfurreducens bacterial nanowires mediated only by the protein is predicted to be dominated by incoherent hopping between phenylalanine (Phe) and tyrosine (Tyr) residues that are 3 to 4 Å apart, where Phe residues in the hopping pathways may create delocalized "islands." This mechanism could be accessible in the presence of strong oxidants that are capable of oxidizing Phe and Tyr residues. We also examine the physical requirements needed to sustain biological respiration via nanowires. We find that the hopping regimes with ET rates on the order of 108 s-1 between Phe islands and Tyr residues, and conductivities on the order of mS/cm, can support ET fluxes that are compatible with cellular respiration rates, although sustaining this delocalization in the heterogeneous protein environment may be challenging. Computed values of fully coherent electron fluxes through the pili are orders of magnitude too low to support microbial respiration. We suggest experimental probes of the transport mechanism based on mutant studies to examine the roles of aromatic amino acids and yet to be identified redox cofactors.
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Affiliation(s)
- Xuyan Ru
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Peng Zhang
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - David N Beratan
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States.,Department of Biochemistry , Duke University , Durham , North Carolina 27710 , United States.,Department of Physics , Duke University , Durham , North Carolina 27708 , United States
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Lin K, Burke A, King NB, Kahanda D, Mazaheripour A, Bartlett A, Dibble DJ, McWilliams MA, Taylor DW, Jocson J, Minary‐Jolandan M, Gorodetsky AA, Slinker JD. Enhancement of the Electrical Properties of DNA Molecular Wires through Incorporation of Perylenediimide DNA Base Surrogates. Chempluschem 2019; 84:416-419. [DOI: 10.1002/cplu.201800661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/27/2019] [Indexed: 01/30/2023]
Affiliation(s)
- Kuo‐Yao Lin
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Anthony Burke
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Nolan B. King
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Dimithree Kahanda
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Amir Mazaheripour
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Andrew Bartlett
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - David J. Dibble
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Marc A. McWilliams
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - David W. Taylor
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Jonah‐Micah Jocson
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Majid Minary‐Jolandan
- Department of Mechanical Engineering The University of Texas at Dallas 800 W. Campbell Road, EC 38 Richardson TX 75080-3020 USA
| | - Alon A. Gorodetsky
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Jason D. Slinker
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
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Woźniak AP, Leś A, Adamowicz L. Theoretical modeling of DNA electron hole transport through polypyrimidine sequences: a QM/MM study. J Mol Model 2019; 25:97. [PMID: 30874898 DOI: 10.1007/s00894-019-3976-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 02/20/2019] [Indexed: 11/25/2022]
Abstract
The phenomenon of DNA hole transport (HT) has attracted of scientists for several decades, mainly due to its potential application in molecular electronics. As electron holes mostly localize on purine bases in DNA, the majority of scientific effort has been invested into chemically modifying the structures of adenine and guanine in order to increase their HT-mediating properties. In this work we examine an alternative, never yet explored, way of affecting the HT efficiency by forcing electron holes to localize on pyrimidine bases and move between them. Using an enhanced and revised version of our previously developed QM/MM model, we perform simulations of HT through polyadenine, polycytosine, polyguanine, and polythymine stacks according to a multistep hopping mechanism. From these simulations, kinetic parameters for HT are obtained. The results indicate a particularly high efficiency of cytosine→cytosine hopping, which is about ten times higher than the G → G hopping. We also discuss possible improvement of cytosine HT by modifying the oxidoreductive properties of complementary guanine residues.
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Affiliation(s)
| | - Andrzej Leś
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
- Pharmaceutical Research Institute, Rydygiera 8, 01-793, Warsaw, Poland
| | - Ludwik Adamowicz
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, AZ, 85721, USA.
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Toruń, Poland.
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32
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Abstract
Achieving high-yielding photoinduced charge separation through the π-stacked bases of DNA is a critical requirement for realizing numerous DNA-based technologies. In the current work, we combine two strategies for achieving high-yield charge separation. First, a chromophore with a high driving force for charge injection, naphthalenediimide (NDI), is used because it generates hot carriers that enhance charge-transfer rates. Second, a diblock DNA sequence is used with two or three adenines followed by a series of guanines to implement an energy landscape that accelerates charge separation while retarding charge recombination. The photoinduced dynamics of these NDI diblock oligomers with and without a terminal hole acceptor are probed by femtosecond transient absorption spectroscopy. The measured rate constants for various charge separation and recombination processes are interpreted within the context of a full kinetic model of these systems. We find that the A2 and A3 oligomers achieve similar charge separation yields (as high as 20-25%) for a given length, yet the critical recombination process that determines these yields occurs at different distances from the NDI chromophore and on different time scales. This type of analysis could be used to predict charge separation efficiencies in candidate DNA structures.
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Abstract
The corpus of electron transfer (ET) theory provides considerable power to describe the kinetics and dynamics of electron flow at the nanoscale. How is it, then, that nucleic acid (NA) ET continues to surprise, while protein-mediated ET is relatively free of mechanistic bombshells? I suggest that this difference originates in the distinct electronic energy landscapes for the two classes of reactions. In proteins, the donor/acceptor-to-bridge energy gap is typically several-fold larger than in NAs. NA ET can access tunneling, hopping, and resonant transport among the bases, and fluctuations can enable switching among mechanisms; protein ET is restricted to tunneling among redox active cofactors and, under strongly oxidizing conditions, a few privileged amino acid side chains. This review aims to provide conceptual unity to DNA and protein ET reaction mechanisms. The establishment of a unified mechanistic framework enabled the successful design of NA experiments that switch electronic coherence effects on and off for ET processes on a length scale of multiple nanometers and promises to provide inroads to directing and detecting charge flow in soft-wet matter.
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Affiliation(s)
- David N Beratan
- Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina 27708, USA; .,Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
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34
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Cadet J, Wagner JR, Angelov D. Biphotonic Ionization of DNA: From Model Studies to Cell. Photochem Photobiol 2018; 95:59-72. [PMID: 30380156 DOI: 10.1111/php.13042] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/16/2018] [Indexed: 12/13/2022]
Abstract
Oxidation reactions triggered by low-intensity UV photons represent a minor contribution with respect to the overwhelming pyrimidine base dimerization in both isolated and cellular DNA. The situation is totally different when DNA is exposed to high-intensity UVC radiation under conditions where biphotonic ionization of the four main purine and pyrimidine bases becomes predominant at the expense of singlet excitation processes. The present review article provides a critical survey of the main chemical reactions of the base radical cations thus generated by one-electron oxidation of nucleic acids in model systems and cells. These include oxidation of the bases with the predominant formation of 8-oxo-7,8-dihydroguanine as the result of preferential hole transfer to guanine bases that act as sinks in isolated and cellular DNA. In addition to hydration, other nucleophilic addition reactions involving the guanine radical cation give rise to intra- and interstrand cross-links together with DNA-protein cross-links. Information is provided on the utilization of high-intensity UV laser pulses as molecular biology tools for studying DNA conformational features, nucleic acid-protein interactions and nucleic acid reactivity through DNA-protein cross-links and DNA footprinting experiments.
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Affiliation(s)
- Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Dimitar Angelov
- Laboratoire de Biologie et Modélisation de la Cellule LBMC, CNRS-UMR 5239, Université de Lyon, École Normale Supérieure de Lyon, Lyon, France
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35
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Teo RD, Terai K, Migliore A, Beratan DN. Electron transfer characteristics of 2'-deoxy-2'-fluoro-arabinonucleic acid, a nucleic acid with enhanced chemical stability. Phys Chem Chem Phys 2018; 20:26063-26067. [PMID: 30191207 PMCID: PMC6202212 DOI: 10.1039/c8cp04816a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The non-biological nucleic acid 2'-deoxy-2'-fluoro-arabinonucleic acid (2'F-ANA) may be of use because of its higher chemical stability than DNA in terms of resistance to hydrolysis and nuclease degradation. In order to investigate the charge transfer characteristics of 2'F-ANA, of relevance to applications in nucleic acid-based biosensors and chip technologies, we compare the electronic couplings for hole transfer between stacked nucleobase pairs in DNA and 2'F-ANA by carrying out density functional theory (DFT) calculations on geometries taken from molecular dynamics simulations. We find similar averages and distribution widths of the base-pair couplings in the two systems. On the basis of this result, 2'F-ANA is expected to have charge transfer properties similar to those of DNA, while offering the advantage of enhanced chemical stability. As such, 2'F-ANA may serve as a possible alternative to DNA for use in a broad range of nanobiotechnological applications. Furthermore, we show that the (experimentally observed) enhanced chemical stability resulting from the backbone modifications does not cause reduced fluctuations of the base-pair electronic couplings around the values found for "ideal" B-DNA (with standard step parameter values). Our study also supports the use of a DFT implementation, with the M11 functional, of the wave function overlap method to compute effective electronic couplings in nucleic acid systems.
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Affiliation(s)
- Ruijie D Teo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
| | - Kiriko Terai
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA. and Department of Natural Science, College of Liberal Arts, International Christian University, Osawa, Mitaka-shi, Tokyo 181-8585, Japan
| | - Agostino Migliore
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA. and Department of Physics, Duke University, Durham, North Carolina 27708, USA and Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
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36
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Karwowski BT. The AT Interstrand Cross-Link: Structure, Electronic Properties, and Influence on Charge Transfer in dsDNA. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 13:665-685. [PMID: 30500729 PMCID: PMC6258832 DOI: 10.1016/j.omtn.2018.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 10/22/2018] [Accepted: 10/22/2018] [Indexed: 12/01/2022]
Abstract
The interaction of chemical and physical agents with genetic material can lead to almost 80 different DNA damage formations. The targeted intentional DNA damage by radiotherapy or chemotherapy is a front-line anticancer therapy. An interstrand cross-link can result from ionization radiation or specific chemical agents, such as trans-/cisplatin activity. Here, the influence of the adenine and thymidine (AT) interstrand linkage, the covalent bond between the adenine N6 and thymidine C5 methylene group, on the isolated base pair as well as double-stranded DNA (dsDNA) was taken into quantum mechanical/molecular mechanical (QM/MM) consideration at the m062x/6-31+G*:UFF level of theory in the aqueous phase. All the results presented in this article, for the first time, show that an AT-interstrand cross-link (ICL) changes the positive and negative charge migration process due to a higher activation energy forced by the cross-link’s presence. However, the final radical cation destination in cross-linked DNA is left in the same place as in a native double-stranded-deoxyoligonucleotide. Additionally, the direction of the radical anion transfer was found to be opposite to that of native dsDNA. Therefore, it can be postulated that the appearance of the AT-ICL does not disturb the hole migration in the double helix, with subsequent effective changes in the electron migration process.
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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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37
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Derr JB, Tamayo J, Espinoza EM, Clark JA, Vullev VI. Dipole-induced effects on charge transfer and charge transport. Why do molecular electrets matter? CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0389] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Charge transfer (CT) and charge transport (CTr) are at the core of life-sustaining biological processes and of processes that govern the performance of electronic and energy-conversion devices. Electric fields are invaluable for guiding charge movement. Therefore, as electrostatic analogues of magnets, electrets have unexplored potential for generating local electric fields for accelerating desired CT processes and suppressing undesired ones. The notion about dipole-generated local fields affecting CT has evolved since the middle of the 20th century. In the 1990s, the first reports demonstrating the dipole effects on the kinetics of long-range electron transfer appeared. Concurrently, the development of molecular-level designs of electric junctions has led the exploration of dipole effects on CTr. Biomimetic molecular electrets such as polypeptide helices are often the dipole sources in CT systems. Conversely, surface-charge electrets and self-assembled monolayers of small polar conjugates are the preferred sources for modifying interfacial electric fields for controlling CTr. The multifaceted complexity of such effects on CT and CTr testifies for the challenges and the wealth of this field that still remains largely unexplored. This review outlines the basic concepts about dipole effects on CT and CTr, discusses their evolution, and provides accounts for their future developments and impacts.
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Affiliation(s)
- James B. Derr
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Jesse Tamayo
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Eli M. Espinoza
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - John A. Clark
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
| | - Valentine I. Vullev
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
- Department of Chemistry, University of California, Riverside, CA 92521, USA
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
- Materials Science and Engineering Program, University of California, Riverside, CA 92521, USA
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38
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Flamme M, Clarke E, Gasser G, Hollenstein M. Applications of Ruthenium Complexes Covalently Linked to Nucleic Acid Derivatives. Molecules 2018; 23:E1515. [PMID: 29932443 PMCID: PMC6099586 DOI: 10.3390/molecules23071515] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 11/16/2022] Open
Abstract
Oligonucleotides are biopolymers that can be easily modified at various locations. Thereby, the attachment of metal complexes to nucleic acid derivatives has emerged as a common pathway to improve the understanding of biological processes or to steer oligonucleotides towards novel applications such as electron transfer or the construction of nanomaterials. Among the different metal complexes coupled to oligonucleotides, ruthenium complexes, have been extensively studied due to their remarkable properties. The resulting DNA-ruthenium bioconjugates have already demonstrated their potency in numerous applications. Consequently, this review focuses on the recent synthetic methods developed for the preparation of ruthenium complexes covalently linked to oligonucleotides. In addition, the usefulness of such conjugates will be highlighted and their applications from nanotechnologies to therapeutic purposes will be discussed.
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Affiliation(s)
- Marie Flamme
- Laboratory for Inorganic Chemical Biology, Chimie ParisTech, PSL University, F-75005 Paris, France.
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institute Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
| | - Emma Clarke
- Laboratory for Inorganic Chemical Biology, Chimie ParisTech, PSL University, F-75005 Paris, France.
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institute Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
| | - Gilles Gasser
- Laboratory for Inorganic Chemical Biology, Chimie ParisTech, PSL University, F-75005 Paris, France.
| | - Marcel Hollenstein
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institute Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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39
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Larsen-Clinton JM, Espinoza EM, F Mayther M, Clark J, Tao C, Bao D, Larino CM, Wurch M, Lara S, Vullev VI. Fluorinated aminoanthranilamides: non-native amino acids for bringing proteomic approaches to charge-transfer systems. Phys Chem Chem Phys 2018; 19:7871-7876. [PMID: 28262882 DOI: 10.1039/c7cp00432j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The ability to control charge transfer at molecular and nanometer scales represents the ultimate level of electronic mastery, and its impacts cannot be overstated. As electrostatic analogues of magnets, electrets possess ordered electric dipoles that present key paradigms for directing transduction of electrons and holes. Herein we describe the design and development of fluorinated aminoanthranilamides, derivatives of non-native aromatic beta-amino acids, as building blocks for hole-transfer molecular electrets. A highly regio-selective nucleophilic aromatic substitution of difluorinated nitrobenzoic acid provides the underpinnings for an array of unprecedented anthranilamide structures. Spin density distribution and electrochemical analyses reveal that fluorine induces about 200 mV positive shifts in reduction potentials without compromising the stability of the oxidized residues, making them invaluable building blocks for hole-transfer systems. These findings open unexplored routes to novel amino-acid structures, setting a foundation for bringing principles of proteomics to designs of charge-transfer systems.
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Affiliation(s)
| | - Eli M Espinoza
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | | | - John Clark
- Department of Bioengineering, University of California, Riverside, CA 92521, USA.
| | - Christina Tao
- Department of Bioengineering, University of California, Riverside, CA 92521, USA.
| | - Duoduo Bao
- Department of Bioengineering, University of California, Riverside, CA 92521, USA.
| | - Christa M Larino
- Department of Bioengineering, University of California, Riverside, CA 92521, USA.
| | - Michelle Wurch
- Department of Bioengineering, University of California, Riverside, CA 92521, USA. and Materials Science and Engineering Program, University of California, Riverside, CA 92521, USA
| | - Stephanie Lara
- Department of Bioengineering, University of California, Riverside, CA 92521, USA.
| | - Valentine I Vullev
- Department of Bioengineering, University of California, Riverside, CA 92521, USA. and Department of Chemistry, University of California, Riverside, CA 92521, USA and Materials Science and Engineering Program, University of California, Riverside, CA 92521, USA and Department of Biochemistry, University of California, Riverside, CA 92521, USA
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40
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Aggarwal A, Bag S, Maiti PK. Remarkable similarity of force induced dsRNA conformational changes to stretched dsDNA and their detection using electrical measurements. Phys Chem Chem Phys 2018; 20:28920-28928. [DOI: 10.1039/c8cp03574a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We show the emergence of S-RNA under stretching in analogy to S-DNA and propose a method for its detection using electrical measurement.
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41
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Hrdlicka PJ, Karmakar S. 25 years and still going strong: 2'-O-(pyren-1-yl)methylribonucleotides - versatile building blocks for applications in molecular biology, diagnostics and materials science. Org Biomol Chem 2017; 15:9760-9774. [PMID: 29135014 PMCID: PMC5711458 DOI: 10.1039/c7ob02152f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oligonucleotides (ONs) modified with 2'-O-(pyren-1-yl)methylribonucleotides have been explored for a range of applications in molecular biology, nucleic acid diagnostics, and materials science for more than 25 years. The first part of this review provides an overview of synthetic strategies toward 2'-O-(pyren-1-yl)methylribonucleotides and is followed by a summary of biophysical properties of nucleic acid duplexes modified with these building blocks. Insights from structural studies are then presented to rationalize the reported properties. In the second part, applications of ONs modified with 2'-O-(pyren-1-yl)methyl-RNA monomers are reviewed, which include detection of RNA targets, discrimination of single nucleotide polymorphisms, formation of self-assembled pyrene arrays on nucleic acid scaffolds, the study of charge transfer phenomena in nucleic acid duplexes, and sequence-unrestricted recognition of double-stranded DNA. The predictable binding mode of the pyrene moiety, coupled with the microenvironment-dependent properties and synthetic feasibility, render 2'-O-(pyren-1-yl)methyl-RNA monomers as a promising class of pyrene-functionalized nucleotide building blocks for new applications in molecular biology, nucleic acid diagnostics, and materials science.
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42
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Chaudhuri S, Hedström S, Méndez-Hernández DD, Hendrickson HP, Jung KA, Ho J, Batista VS. Electron Transfer Assisted by Vibronic Coupling from Multiple Modes. J Chem Theory Comput 2017; 13:6000-6009. [DOI: 10.1021/acs.jctc.7b00513] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Subhajyoti Chaudhuri
- Yale
Energy Sciences Institute and Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Svante Hedström
- Yale
Energy Sciences Institute and Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
- Department
of Physics, Stockholm University, Albanova University Center, 10691 Stockholm, Sweden
| | - Dalvin D. Méndez-Hernández
- Yale
Energy Sciences Institute and Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
- Departamento
de Química, Universidad de Puerto Rico en Cayey, Cayey, Puerto Rico 00736, United States
| | - Heidi P. Hendrickson
- Yale
Energy Sciences Institute and Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Kenneth A. Jung
- Yale
Energy Sciences Institute and Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Junming Ho
- Yale
Energy Sciences Institute and Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
- School
of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Victor S. Batista
- Yale
Energy Sciences Institute and Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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43
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Espinoza EM, Larsen-Clinton JM, Krzeszewski M, Darabedian N, Gryko DT, Vullev VI. Bioinspired approach toward molecular electrets: synthetic proteome for materials. PURE APPL CHEM 2017. [DOI: 10.1515/pac-2017-0309] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractMolecular-level control of charge transfer (CT) is essential for both, organic electronics and solar-energy conversion, as well as for a wide range of biological processes. This article provides an overview of the utility of local electric fields originating from molecular dipoles for directing CT processes. Systems with ordered dipoles, i.e. molecular electrets, are the centerpiece of the discussion. The conceptual evolution from biomimicry to biomimesis, and then to biological inspiration, paves the roads leading from testing the understanding of how natural living systems function to implementing these lessons into optimal paradigms for specific applications. This progression of the evolving structure-function relationships allows for the development of bioinspired electrets composed of non-native aromatic amino acids. A set of such non-native residues that are electron-rich can be viewed as a synthetic proteome for hole-transfer electrets. Detailed considerations of the electronic structure of an individual residue prove of key importance for designating the points for optimal injection of holes (i.e. extraction of electrons) in electret oligomers. This multifaceted bioinspired approach for the design of CT molecular systems provides unexplored paradigms for electronic and energy science and engineering.
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Affiliation(s)
- Eli M. Espinoza
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | | | - Maciej Krzeszewski
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44-52, 01-224 Warsaw, Poland
| | - Narek Darabedian
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
| | - Daniel T. Gryko
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44-52, 01-224 Warsaw, Poland
| | - Valentine I. Vullev
- Department of Chemistry, University of California, Riverside, CA 92521, USA
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
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44
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Prasad S, Mandal I, Singh S, Paul A, Mandal B, Venkatramani R, Swaminathan R. Near UV-Visible electronic absorption originating from charged amino acids in a monomeric protein. Chem Sci 2017; 8:5416-5433. [PMID: 28970921 PMCID: PMC5609530 DOI: 10.1039/c7sc00880e] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/18/2017] [Indexed: 11/21/2022] Open
Abstract
Electronic absorption spectra of proteins are primarily characterized over the ultraviolet region (185-320 nm) of the electromagnetic spectrum. While recent studies on peptide aggregates have revealed absorption beyond 350 nm, monomeric proteins lacking aromatic amino acids, disulphide bonds, and active site prosthetic groups are expected to remain optically silent beyond 250 nm. Here, in a joint theoretical and experimental investigation, we report the distinctive UV-Vis absorption spectrum between 250 nm [ε = 7338 M-1 cm-1] and 800 nm [ε = 501 M-1 cm-1] in a synthetic 67 residue protein (α3C), in monomeric form, devoid of aromatic amino acids. Systematic control studies with high concentration non-aromatic amino acid solutions revealed significant absorption beyond 250 nm for charged amino acids which constitute over 50% of the sequence composition in α3C. Classical atomistic molecular dynamics (MD) simulations of α3C reveal dynamic interactions between multiple charged sidechains of Lys and Glu residues present in α3C. Time-dependent density functional theory calculations on charged amino acid residues sampled from the MD trajectories of α3C reveal that the distinctive absorption features of α3C may arise from two different types of charge transfer (CT) transitions involving spatially proximal Lys/Glu amino acids. Specifically, we show that the charged amino (NH3+)/carboxylate (COO-) groups of Lys/Glu sidechains act as electronic charge acceptors/donors for photoinduced electron transfer either from/to the polypeptide backbone or to each other. Further, the sensitivity of the CT spectra to close/far/intermediate range of encounters between sidechains of Lys/Glu owing to the three dimensional protein fold can create the long tail in the α3C absorption profile between 300 and 800 nm. Finally, we experimentally demonstrate the sensitivity of α3C absorption spectrum to temperature and pH-induced changes in protein structure. Taken together, our investigation significantly expands the pool of spectroscopically active biomolecular chromophores and adds an optical 250-800 nm spectral window, which we term ProCharTS (Protein Charge Transfer Spectra), for label free probes of biomolecular structure and dynamics.
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Affiliation(s)
- Saumya Prasad
- Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati 781039 , Assam , India .
| | - Imon Mandal
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba , Mumbai 400005 , India .
| | - Shubham Singh
- Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati 781039 , Assam , India .
| | - Ashim Paul
- Department of Chemistry , Indian Institute of Technology Guwahati , Guwahati 781039 , Assam , India
| | - Bhubaneswar Mandal
- Department of Chemistry , Indian Institute of Technology Guwahati , Guwahati 781039 , Assam , India
| | - Ravindra Venkatramani
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba , Mumbai 400005 , India .
| | - Rajaram Swaminathan
- Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati 781039 , Assam , India .
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45
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Jiménez-Monroy KL, Renaud N, Drijkoningen J, Cortens D, Schouteden K, van Haesendonck C, Guedens WJ, Manca JV, Siebbeles LDA, Grozema FC, Wagner PH. High Electronic Conductance through Double-Helix DNA Molecules with Fullerene Anchoring Groups. J Phys Chem A 2017; 121:1182-1188. [PMID: 28094940 PMCID: PMC5330649 DOI: 10.1021/acs.jpca.7b00348] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
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Determining
the mechanism of charge transport through native DNA
remains a challenge as different factors such as measuring conditions,
molecule conformations, and choice of technique can significantly
affect the final results. In this contribution, we have used a new
approach to measure current flowing through isolated double-stranded
DNA molecules, using fullerene groups to anchor the DNA to a gold
substrate. Measurements were performed at room temperature in an inert
environment using a conductive AFM technique. It is shown that the
π-stacked B-DNA structure is conserved on depositing the DNA.
As a result, currents in the nanoampere range were obtained for voltages
ranging between ±1 V. These experimental results are supported
by a theoretical model that suggests that a multistep hopping mechanism
between delocalized domains is responsible for the long-range current
flow through this specific type of DNA.
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Affiliation(s)
- Kathia L Jiménez-Monroy
- IMO-IMOMEC, Hasselt University , Campus Diepenbeek, Wetenschapspark 1, 3590 Diepenbeek, Belgium
| | - Nicolas Renaud
- Department of Chemical Engineering, Delft University of Technology , Julianalaan 136, 2628 BL Delft, The Netherlands
| | - Jeroen Drijkoningen
- IMO-IMOMEC, Hasselt University , Campus Diepenbeek, Wetenschapspark 1, 3590 Diepenbeek, Belgium.,IMO & X-LaB, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - David Cortens
- IMO-IMOMEC, Hasselt University , Campus Diepenbeek, Wetenschapspark 1, 3590 Diepenbeek, Belgium
| | | | | | - Wanda J Guedens
- IMO-IMOMEC, Hasselt University , Campus Diepenbeek, Wetenschapspark 1, 3590 Diepenbeek, Belgium
| | - Jean V Manca
- IMO-IMOMEC, Hasselt University , Campus Diepenbeek, Wetenschapspark 1, 3590 Diepenbeek, Belgium.,IMO & X-LaB, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Laurens D A Siebbeles
- Department of Chemical Engineering, Delft University of Technology , Julianalaan 136, 2628 BL Delft, The Netherlands
| | - Ferdinand C Grozema
- Department of Chemical Engineering, Delft University of Technology , Julianalaan 136, 2628 BL Delft, The Netherlands
| | - Patrick H Wagner
- IMO-IMOMEC, Hasselt University , Campus Diepenbeek, Wetenschapspark 1, 3590 Diepenbeek, Belgium
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46
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Bag S, Mogurampelly S, Goddard WA, Maiti PK. Dramatic changes in DNA conductance with stretching: structural polymorphism at a critical extension. NANOSCALE 2016; 8:16044-16052. [PMID: 27545499 DOI: 10.1039/c6nr03418g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5%) stretching length, we carried out multiscale modeling to predict the conductance of dsDNA as it is mechanically stretched to promote various structural polymorphisms. We calculate the current along the stretched DNA using a combination of molecular dynamics simulations, non-equilibrium pulling simulations, quantum mechanics calculations, and kinetic Monte Carlo simulations. For 5'end1-5'end2 attachments we find an abrupt jump in the current within a very short stretching length (6 Å or 17%) leading to a melted DNA state. In contrast, for 3'end1-3'end2 pulling it takes almost 32 Å (84%) of stretching to cause a similar jump in the current. Thus, we demonstrate that charge transport in DNA can occur over stretching lengths of several nanometers. We find that this unexpected behaviour in the B to S conformational DNA transition arises from highly inclined base pair geometries that result from this pulling protocol. We found that the dramatically different conductance behaviors for two different pulling protocols arise from how the hydrogen bonds of DNA base pairs break.
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Affiliation(s)
- Saientan Bag
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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47
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Abstract
Many biochemical processes, such as charge hopping or protein folding, can be described by an average timescale to reach a final state, starting from an initial state. Here, we provide a pedagogical treatment of the mean first-passage time (MFPT) of a physical process, which depends on the number of intervening states between the initial state and the target state. Our aim in this tutorial review is to provide a clear development of the mean first-passage time formalism and to show some of its practical utility. The MFPT treatment can provide a useful link between microscopic rates and the average timescales often probed by experiment.
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Affiliation(s)
| | | | - David N Beratan
- Department of Biochemistry, Duke University, Durham, NC 27710 (USA).,Department of Chemistry, Duke University, Durham, NC 27708 (USA).,Department of Physics, Duke University, Durham, NC 27708 (USA)
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48
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Liu C, Xiang L, Zhang Y, Zhang P, Beratan DN, Li Y, Tao N. Engineering nanometre-scale coherence in soft matter. Nat Chem 2016; 8:941-5. [DOI: 10.1038/nchem.2545] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 05/06/2016] [Indexed: 01/19/2023]
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49
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Liu C, Beratan DN, Zhang P. Coarse-Grained Theory of Biological Charge Transfer with Spatially and Temporally Correlated Noise. J Phys Chem B 2016; 120:3624-33. [DOI: 10.1021/acs.jpcb.6b01018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chaoren Liu
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N. Beratan
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Departments
of Biochemistry and Physics, Duke University, Durham, North Carolina 27708, United States
| | - Peng Zhang
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
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50
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Abstract
Oligoamides composed of anthranilic acid derivatives present a promising choice for mediating long-range charge transfer and controlling its directionality. Hole hopping, modulated by the anthranilamide (Aa) permanent dipoles, provides a plausible means for such rectified long-range charge transduction. All aliphatic and most aromatic amides, however, decompose upon oxidation, rendering them unacceptable for hole-hopping pathways. We, therefore, employ electrochemical and computational analysis to examine how to suppress oxidative degradation and stabilize the radical cations of N-acylated Aa derivatives. Our findings reveal two requirements for attaining long-lived radical cations of these aromatic amides: (1) keeping the reduction potentials for oxidizing the Aa residues under about 1.4 V vs SCE and (2) adding an electron-donating group para to the N-terminal amide of the aromatic ring, which prevents the electron spin density of the radical cation from extending over the C-terminal amide. These findings provide essential information for the design of hole-transfer amides.
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Affiliation(s)
- Eli M Espinoza
- Department of Chemistry, University of California , Riverside, California 92521, United States
| | - Jillian M Larsen
- Department of Bioengineering, University of California , Riverside, California 92521, United States
| | - Valentine I Vullev
- Department of Chemistry, University of California , Riverside, California 92521, United States
- Department of Bioengineering, University of California , Riverside, California 92521, United States
- Department of Biochemistry, University of California , Riverside, California 92521, United States
- Materials Science and Engineering Program, University of California , Riverside, California 92521, United States
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