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Kang M, Nuomin H, Chowdhury SN, Yuly JL, Sun K, Whitlow J, Valdiviezo J, Zhang Z, Zhang P, Beratan DN, Brown KR. Seeking a quantum advantage with trapped-ion quantum simulations of condensed-phase chemical dynamics. Nat Rev Chem 2024:10.1038/s41570-024-00595-1. [PMID: 38641733 DOI: 10.1038/s41570-024-00595-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2024] [Indexed: 04/21/2024]
Abstract
Simulating the quantum dynamics of molecules in the condensed phase represents a longstanding challenge in chemistry. Trapped-ion quantum systems may serve as a platform for the analog-quantum simulation of chemical dynamics that is beyond the reach of current classical-digital simulation. To identify a 'quantum advantage' for these simulations, performance analysis of both analog-quantum simulation on noisy hardware and classical-digital algorithms is needed. In this Review, we make a comparison between a noisy analog trapped-ion simulator and a few choice classical-digital methods on simulating the dynamics of a model molecular Hamiltonian with linear vibronic coupling. We describe several simple Hamiltonians that are commonly used to model molecular systems, which can be simulated with existing or emerging trapped-ion hardware. These Hamiltonians may serve as stepping stones towards the use of trapped-ion simulators for systems beyond the reach of classical-digital methods. Finally, we identify dynamical regimes in which classical-digital simulations seem to have the weakest performance with respect to analog-quantum simulations. These regimes may provide the lowest hanging fruit to make the most of potential quantum advantages.
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Affiliation(s)
- Mingyu Kang
- Duke Quantum Center, Duke University, Durham, NC, USA.
- Department of Physics, Duke University, Durham, NC, USA.
| | - Hanggai Nuomin
- Department of Chemistry, Duke University, Durham, NC, USA
| | | | - Jonathon L Yuly
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Ke Sun
- Duke Quantum Center, Duke University, Durham, NC, USA
- Department of Physics, Duke University, Durham, NC, USA
| | - Jacob Whitlow
- Duke Quantum Center, Duke University, Durham, NC, USA
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, USA
| | - Jesús Valdiviezo
- Kenneth S. Pitzer Theory Center, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Departamento de Ciencias, Sección Química, Pontificia Universidad Católica del Perú, Lima, Peru
| | - Zhendian Zhang
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, NC, USA
| | - David N Beratan
- Department of Physics, Duke University, Durham, NC, USA.
- Department of Chemistry, Duke University, Durham, NC, USA.
- Department of Biochemistry, Duke University, Durham, NC, USA.
| | - Kenneth R Brown
- Duke Quantum Center, Duke University, Durham, NC, USA.
- Department of Physics, Duke University, Durham, NC, USA.
- Department of Chemistry, Duke University, Durham, NC, USA.
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, USA.
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2
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Mendis KC, Li X, Valdiviezo J, Banziger SD, Zhang P, Ren T, Beratan DN, Rubtsov IV. Electron transfer rate modulation with mid-IR in butadiyne-bridged donor-bridge-acceptor compounds. Phys Chem Chem Phys 2024; 26:1819-1828. [PMID: 38168814 DOI: 10.1039/d3cp03175f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Controlling electron transfer (ET) processes in donor-bridge-acceptor (DBA) compounds by mid-IR excitation can enhance our understanding of the ET dynamics and may find practical applications in molecular sensing and molecular-scale electronics. Alkyne moieties are attractive to serve as ET bridges, as they offer the possibility of fast ET and present convenient vibrational modes to perturb the ET dynamics. Yet, these bridges introduce complexity because of the strong torsion angle dependence of the ET rates and transition dipoles among electronic states and a shallow torsion barrier. In this study, we implemented ultrafast 3-pulse laser spectroscopy to investigate how the ET from the dimethyl aniline (D) electron donor to the N-isopropyl-1,8-napthalimide (NAP) electron acceptor can be altered by exciting the CC stretching mode (νCC) of the butadiyne bridge linking the donor and acceptor. The electron transfer was initiated by electronically exciting the acceptor moiety at 400 nm, followed by vibrational excitation of the alkyne, νCC, and detecting the changes in the absorption spectrum in the visible spectral region. The experiments were performed at different delay times t1 and t2, which are the delays between UV-mid-IR and mid-IR-Vis pulses, respectively. Two sets of torsion-angle conformers were identified, one featuring a very fast mean ET time of 0.63 ps (group A) and another featuring a slower mean ET time of 4.3 ps (group B), in the absence of the mid-IR excitation. TD-DFT calculations were performed to determine key torsion angle dependent molecular parameters, including the electronic and vibrational transition dipoles, transition frequencies, and electronic couplings. To describe the 3-pulse data, we developed a kinetic model that includes a locally excited, acceptor-based S2 state, a charge separated S1 state, and their vibrationally excited counterparts, with either excited νCC (denoted as S1Atr, S1Btr, S2Atr, and S2Btr, where tr stands for the excited triplet bond, νCC) or excited daughter modes of the νCC relaxation (S1Ah, S1Bh, S2Ah, and S2Bh, where h stands for vibrationally hot species). The kinetic model was solved analytically, and the species-associated spectra (SAS) were determined numerically using a matrix approach, treating first the experiments with longer t1 delays and then using the already determined SAS for modeling the experiments with shorter t1 delays. Strong vibronic coupling of νCC and of vibrationally hot states makes the analysis complicated. Nevertheless, the SAS were identified and the ET rates of the vibrationally excited species, S2Atr, S2Btr and S2Bh, were determined. The results show that the ET rate for the S2A species is ca. 1.2-fold slower when the νCC mode is excited. The ET rate for species S2B is slower by ca. 1.3-fold if the compound is vibrationally hot and is essentially unchanged when the νCC mode is excited. The SAS determined for the tr and h species resemble the SAS for their respective precursor species in the 2-pulse transient absorption experiments, which validates the procedure used and the results.
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Affiliation(s)
- Kasun C Mendis
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA.
| | - Xiao Li
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA.
| | - Jesús Valdiviezo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Susannah D Banziger
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Tong Ren
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
- Department of Physics, Duke University, Durham, North Carolina 27708, USA
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
| | - Igor V Rubtsov
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA.
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Dunlap-Shohl WA, Tabassum N, Zhang P, Shiby E, Beratan DN, Waldeck DH. Electron-donating functional groups strengthen ligand-induced chiral imprinting on CsPbBr 3 quantum dots. Sci Rep 2024; 14:336. [PMID: 38172244 PMCID: PMC10764765 DOI: 10.1038/s41598-023-50595-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
Chiral perovskite nanoparticles and films are promising for integration in emerging spintronic and optoelectronic technologies, yet few design rules exist to guide the development of chiral material properties. The chemical space of potential building blocks for these nanostructures is vast, and the mechanisms through which organic ligands can impart chirality to the inorganic perovskite lattice are not well understood. In this work, we investigate how the properties of chiral ammonium ligands, the most common organic ligand type used with perovskites, affect the circular dichroism of strongly quantum confined CsPbBr3 nanocrystals. We show that aromatic ammonium ligands with stronger electron-donating groups lead to higher-intensity circular dichroism associated with the lowest-energy excitonic transition of the perovskite nanocrystal. We argue that this behavior is best explained by a modulation of the exciton wavefunction overlap between the nanocrystal and the organic ligand, as the functional groups on the ligand can shift electron density toward the organic species-perovskite lattice interface to increase the imprinting.
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Affiliation(s)
| | - Nazifa Tabassum
- Department of Chemistry, University of Pittsburgh, Pittsburgh, 15213, USA
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, 27708, USA
| | - Elizabeth Shiby
- Department of Chemistry, University of Pittsburgh, Pittsburgh, 15213, USA
| | - David N Beratan
- Department of Physics, Duke University, Durham, 27705, USA
- Department of Biochemistry, Duke University, Durham, 27710, USA
| | - David H Waldeck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, 15213, USA.
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4
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Sun K, Fang C, Kang M, Zhang Z, Zhang P, Beratan DN, Brown KR, Kim J. Quantum Simulation of Polarized Light-Induced Electron Transfer with a Trapped-Ion Qutrit System. J Phys Chem Lett 2023:6071-6077. [PMID: 37358521 DOI: 10.1021/acs.jpclett.3c01166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
Electron transfer within and between molecules is crucial in chemistry, biochemistry, and energy science. This study describes a quantum simulation method that explores the influence of light polarization on electron transfer between two molecules. By implementing precise and coherent control among the quantum states of trapped atomic ions, we can induce quantum dynamics that mimic the electron-transfer dynamics in molecules. We use three-level systems (qutrits), rather than traditional two-level systems (qubits), to enhance the simulation efficiency and realize high-fidelity simulations of electron-transfer dynamics. We treat the quantum interference between the electron coupling pathways from a donor with two degenerate excited states to an acceptor and analyze the transfer efficiency. We also examine the potential error sources that enter the quantum simulations. The trapped-ion systems have favorable scalings with system size compared to those of classical computers, promising access to richer electron-transfer simulations.
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Affiliation(s)
- Ke Sun
- Duke Quantum Center, Duke University, Durham, North Carolina 27701, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Chao Fang
- Duke Quantum Center, Duke University, Durham, North Carolina 27701, United States
- Department of Electrical and Computer Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Mingyu Kang
- Duke Quantum Center, Duke University, Durham, North Carolina 27701, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Zhendian Zhang
- 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
- Duke Quantum Center, Duke University, Durham, North Carolina 27701, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| | - Kenneth R Brown
- Duke Quantum Center, Duke University, Durham, North Carolina 27701, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
- Department of Electrical and Computer Engineering, Duke University, Durham, North Carolina 27708, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Jungsang Kim
- Duke Quantum Center, Duke University, Durham, North Carolina 27701, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
- Department of Electrical and Computer Engineering, Duke University, Durham, North Carolina 27708, United States
- IonQ, Inc., College Park, Maryland 20740, United States
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5
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Terai K, Yuly JL, Zhang P, Beratan DN. Correlated particle transport enables biological free energy transduction. Biophys J 2023; 122:1762-1771. [PMID: 37056051 DOI: 10.1016/j.bpj.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/17/2023] [Accepted: 04/07/2023] [Indexed: 04/15/2023] Open
Abstract
Studies of biological transport frequently neglect the explicit statistical correlations among particle site occupancies (i.e., use a mean-field approximation). Neglecting correlations sometimes captures biological function, even for out-of-equilibrium and interacting systems. We show that neglecting correlations fails to describe free energy transduction, mistakenly predicting an abundance of slippage and energy dissipation, even for networks that are near reversible and lack interactions among particle sites. Interestingly, linear charge transport chains are well described without including correlations, even for networks that are driven and include site-site interactions typical of biological electron transfer chains. We examine three specific bioenergetic networks: a linear electron transfer chain (as found in bacterial nanowires), a near reversible electron bifurcation network (as in complex III of respiration and other recently discovered structures), and a redox-coupled proton pump (as in complex IV of respiration).
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Affiliation(s)
- Kiriko Terai
- Department of Chemistry, Duke University, Durham, NC, 27708
| | - Jonathon L Yuly
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, NC, 27708
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, NC, 27708; Department of Physics, Duke University, Durham, NC, 27708; Department of Biochemistry, Duke University, Durham, NC, 27710.
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6
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Rousseau BJG, Migliore A, Stanley RJ, Beratan DN. Adenine Fine-Tunes DNA Photolyase's Repair Mechanism. J Phys Chem B 2023; 127:2941-2954. [PMID: 36947863 DOI: 10.1021/acs.jpcb.3c00566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
The comparative study of DNA repair by mesophilic and extremophilic photolyases helps us understand the evolution of these enzymes and their role in preserving life on our changing planet. The mechanism of repair of cyclobutane pyrimidine dimer lesions in DNA by electron transfer from the flavin adenine dinucleotide cofactor is the subject of intense interest. The role of adenine in mediating this process remains unresolved. Using microsecond molecular dynamics simulations, we find that adenine mediates the electron transfer in both mesophile and extremophile DNA photolyases through a similar mechanism. In fact, in all photolyases studied, the molecular conformations with the largest electronic couplings between the enzyme cofactor and DNA show the presence of adenine in 10-20% of the strongest-coupling tunneling pathways between the atoms of the electron donor and acceptor. Our theoretical analysis finds that adenine serves the critical role of fine-tuning rather than maximizing the donor-acceptor coupling within the range appropriate for the repair function.
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Affiliation(s)
- Benjamin J G Rousseau
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Agostino Migliore
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Robert J Stanley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, 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
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7
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Chowdhury SN, Zhang P, Beratan DN. Interference between Molecular and Photon Field-Mediated Electron Transfer Coupling Pathways in Cavities. J Phys Chem Lett 2022; 13:9822-9828. [PMID: 36240481 DOI: 10.1021/acs.jpclett.2c02496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Cavity polaritonics creates novel opportunities to direct chemical reactions. Electron transfer (ET) reactions are among the simplest reactions, and they underpin energy conversion. New strategies to manipulate and direct electron flow at the nanoscale are of particular interest in biochemistry, energy science, bioinspired materials science, and chemistry. We show that optical cavities can modulate electron transfer pathway interferences and ET rates in donor-bridge-acceptor (DBA) systems. We derive the rate for DBA electron transfer when the molecules are coupled to cavity modes, emphasizing novel cavity-induced pathway interferences with the molecular electronic coupling pathways, as these interferences allow a new kind of ET rate tuning. The interference between the cavity-induced coupling pathways and the intrinsic molecular coupling pathway is dependent on the cavity properties. Thus, manipulating the interference between the cavity-induced DA coupling and the bridge-mediated coupling offers an approach to direct and manipulate charge flow at the nanoscale.
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Affiliation(s)
- Sutirtha N Chowdhury
- Department of Chemistry, Duke University, Durham, North Carolina27708, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina27708, United States
| | - David N Beratan
- Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina27708, United States
- Department of Biochemistry, Duke University, Durham, North Carolina27710, United States
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8
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Peterson EJ, Rawson J, Beratan DN, Zhang P, Therien MJ. Regulating Singlet-Triplet Energy Gaps through Substituent-Driven Modulation of the Exchange and Coulomb Interactions. J Am Chem Soc 2022; 144:15457-15461. [PMID: 35993849 DOI: 10.1021/jacs.2c06713] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Control of the singlet-triplet energy gap (ΔEST) is central to realizing productive energy conversion reactions, photochemical reaction trajectories, and emergent applications that exploit molecular spin physics. Despite this, no systematic methods have been defined to tune ΔEST in simple molecular frameworks, let alone by an approach that also holds chromophore size and electronic structural parameters (such as the HOMO-LUMO gap) constant. Using a combination of molecular design, photophysical and potentiometric experiments, and quantum chemical analyses, we show that the degree of electron-electron repulsion in excited singlet and triplet states may be finely controlled through the substitution pattern of a simple porphyrin absorber, enabling regulation of relative electronically excited singlet and triplet state energies by the designed restriction of the electron-electron Coulomb (J) and exchange (K) interaction magnitudes. This approach modulates the ΔEST magnitude by controlling the densities of state in the occupied and virtual molecular orbital manifolds, natural transition orbital polarization, and the relative contributions of one electron transitions involving select natural transition orbital pairs. This road map, which regulates electron density overlaps in the occupied and virtual states that define the singlet and triplet wave functions of these chromophores, enables new approaches to preserve excitation energy despite intersystem crossing.
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Affiliation(s)
- Erin J Peterson
- Department of Chemistry, French Family Science Center, Duke University, 124 Science Drive, Durham, North Carolina 27708-0346, United States
| | - Jeff Rawson
- Department of Chemistry, French Family Science Center, Duke University, 124 Science Drive, Durham, North Carolina 27708-0346, United States
| | - David N Beratan
- Department of Chemistry, French Family Science Center, Duke University, 124 Science Drive, Durham, North Carolina 27708-0346, United States
| | - Peng Zhang
- Department of Chemistry, French Family Science Center, Duke University, 124 Science Drive, Durham, North Carolina 27708-0346, United States
| | - Michael J Therien
- Department of Chemistry, French Family Science Center, Duke University, 124 Science Drive, Durham, North Carolina 27708-0346, United States
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9
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Parker KA, Schultz JD, Singh N, Wasielewski MR, Beratan DN. Mapping Simulated Two-Dimensional Spectra to Molecular Models Using Machine Learning. J Phys Chem Lett 2022; 13:7454-7461. [PMID: 35930790 DOI: 10.1021/acs.jpclett.2c01913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Two-dimensional (2D) spectroscopy encodes molecular properties and dynamics into expansive spectral data sets. Translating these data into meaningful chemical insights is challenging because of the many ways chemical properties can influence the spectra. To address the task of extracting chemical information from 2D spectroscopy, we study the capacity of simple feedforward neural networks (NNs) to map simulated 2D electronic spectra to underlying physical Hamiltonians. We examined hundreds of simulated 2D spectra corresponding to monomers and dimers with varied Franck-Condon active vibrations and monomer-monomer electronic couplings. We find the NNs are able to correctly characterize most Hamiltonian parameters in this study with an accuracy above 90%. Our results demonstrate that NNs can aid in interpreting 2D spectra, leading from spectroscopic features to underlying effective Hamiltonians.
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Affiliation(s)
- Kelsey A Parker
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Jonathan D Schultz
- Department of Chemistry and Institute for Sustainability and Energy, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Niven Singh
- Program in Computational Biology and Bioinformatics, Center for Genomics and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Michael R Wasielewski
- Department of Chemistry and Institute for Sustainability and Energy, Northwestern University, Evanston, Illinois 60208-3113, 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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10
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Shen W, Teo RD, Beratan DN, Warren JJ. Cofactor Dynamics Couples the Protein Surface to the Heme in Cytochrome c, Facilitating Electron Transfer. J Phys Chem B 2022; 126:3522-3529. [PMID: 35507916 PMCID: PMC9867876 DOI: 10.1021/acs.jpcb.2c01632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Electron transport through biomolecules and in biological transport networks is of great importance to bioenergetics and biocatalysis. More generally, it is of crucial importance to understand how the pathways that connect buried metallocofactors to other cofactors, and to protein surfaces, affect the biological chemistry of metalloproteins. In terms of electron transfer (ET), the strongest coupling pathways usually comprise covalent and hydrogen bonded networks, with a limited number of through-space contacts. Herein, we set out to determine the relative roles of hydrogen bonds involved in ET via an established heme-to-surface tunneling pathway in cytochrome (cyt) c (i.e., heme-W59-D60-E61-N62). A series of cyt c variants were produced where a ruthenium tris(diimine) photooxidant was placed at position 62 via covalent modification of the N62C residue. Surprisingly, variants where the H-bonding residues W59 and D60 were replaced (i.e., W59F and D60A) showed no change in ET rate from the ferrous heme to Ru(III). In contrast, changing the composition of an alternative tunneling pathway (i.e., heme-M64-N63-C62) with the M64L substitution shows a factor of 2 decrease in the rate of heme-to-Ru ET. This pathway involves a through-space tunneling step between the heme and M64 residue, and such steps are usually disfavored. To rationalize why the heme-M64-N63-C62 is preferred, molecular dynamics (MD) simulations and Pathways analysis were employed. These simulations show that the change in heme-Ru ET rates is attributed to different conformations with compressed donor-acceptor distances, by ∼2 Å in pathway distance, in the M64-containing protein as compared to the M64L protein. The change in distance is correlated with changes in the electronic coupling that are in accord with the experimentally observed heme-Ru ET rates. Remarkably, the M64L variation at the core of the protein translates to changes in cofactor dynamics at the protein surface. The surface changes identified by MD simulations include dynamic anion-π and dipole-dipole interactions. These interactions influence the strength of tunneling pathways and ET rates by facilitating decreases in through-space tunneling distances in key coupling pathways.
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Affiliation(s)
- William Shen
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby CA V5A 1S6, Canada
| | - Ruijie D. Teo
- 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 Physics, Duke University, Durham, North Carolina 27708, United States., Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| | - Jeffrey J. Warren
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby CA V5A 1S6, Canada,Corresponding Author
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11
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Aiello CD, Abendroth JM, Abbas M, Afanasev A, Agarwal S, Banerjee AS, Beratan DN, Belling JN, Berche B, Botana A, Caram JR, Celardo GL, Cuniberti G, Garcia-Etxarri A, Dianat A, Diez-Perez I, Guo Y, Gutierrez R, Herrmann C, Hihath J, Kale S, Kurian P, Lai YC, Liu T, Lopez A, Medina E, Mujica V, Naaman R, Noormandipour M, Palma JL, Paltiel Y, Petuskey W, Ribeiro-Silva JC, Saenz JJ, Santos EJG, Solyanik-Gorgone M, Sorger VJ, Stemer DM, Ugalde JM, Valdes-Curiel A, Varela S, Waldeck DH, Wasielewski MR, Weiss PS, Zacharias H, Wang QH. A Chirality-Based Quantum Leap. ACS Nano 2022; 16:4989-5035. [PMID: 35318848 PMCID: PMC9278663 DOI: 10.1021/acsnano.1c01347] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
There is increasing interest in the study of chiral degrees of freedom occurring in matter and in electromagnetic fields. Opportunities in quantum sciences will likely exploit two main areas that are the focus of this Review: (1) recent observations of the chiral-induced spin selectivity (CISS) effect in chiral molecules and engineered nanomaterials and (2) rapidly evolving nanophotonic strategies designed to amplify chiral light-matter interactions. On the one hand, the CISS effect underpins the observation that charge transport through nanoscopic chiral structures favors a particular electronic spin orientation, resulting in large room-temperature spin polarizations. Observations of the CISS effect suggest opportunities for spin control and for the design and fabrication of room-temperature quantum devices from the bottom up, with atomic-scale precision and molecular modularity. On the other hand, chiral-optical effects that depend on both spin- and orbital-angular momentum of photons could offer key advantages in all-optical and quantum information technologies. In particular, amplification of these chiral light-matter interactions using rationally designed plasmonic and dielectric nanomaterials provide approaches to manipulate light intensity, polarization, and phase in confined nanoscale geometries. Any technology that relies on optimal charge transport, or optical control and readout, including quantum devices for logic, sensing, and storage, may benefit from chiral quantum properties. These properties can be theoretically and experimentally investigated from a quantum information perspective, which has not yet been fully developed. There are uncharted implications for the quantum sciences once chiral couplings can be engineered to control the storage, transduction, and manipulation of quantum information. This forward-looking Review provides a survey of the experimental and theoretical fundamentals of chiral-influenced quantum effects and presents a vision for their possible future roles in enabling room-temperature quantum technologies.
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Affiliation(s)
- Clarice D. Aiello
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - John M. Abendroth
- Laboratory
for Solid State Physics, ETH Zürich, Zürich 8093, Switzerland
| | - Muneer Abbas
- Department
of Microbiology, Howard University, Washington, D.C. 20059, United States
| | - Andrei Afanasev
- Department
of Physics, George Washington University, Washington, D.C. 20052, United States
| | - Shivang Agarwal
- Department
of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Amartya S. Banerjee
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Materials Science and Engineering, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - David N. Beratan
- Departments
of Chemistry, Biochemistry, and Physics, Duke University, Durham, North Carolina 27708, United States
| | - Jason N. Belling
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Bertrand Berche
- Laboratoire
de Physique et Chimie Théoriques, UMR Université de Lorraine-CNRS, 7019 54506 Vandœuvre les
Nancy, France
| | - Antia Botana
- Department
of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Justin R. Caram
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Giuseppe Luca Celardo
- Institute
of Physics, Benemerita Universidad Autonoma
de Puebla, Apartado Postal J-48, 72570, Mexico
- Department
of Physics and Astronomy, University of
Florence, 50019 Sesto Fiorentino, Italy
| | - Gianaurelio Cuniberti
- Institute
for Materials Science and Max Bergmann Center of Biomaterials, Dresden University of Technology, 01062 Dresden, Germany
| | - Aitzol Garcia-Etxarri
- Donostia
International Physics Center, Paseo Manuel de Lardizabal 4, 20018 Donostia, San Sebastian, Spain
- IKERBASQUE,
Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
| | - Arezoo Dianat
- Institute
for Materials Science and Max Bergmann Center of Biomaterials, Dresden University of Technology, 01062 Dresden, Germany
| | - Ismael Diez-Perez
- Department
of Chemistry, Faculty of Natural and Mathematical Sciences, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Yuqi Guo
- School
for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Rafael Gutierrez
- Institute
for Materials Science and Max Bergmann Center of Biomaterials, Dresden University of Technology, 01062 Dresden, Germany
| | - Carmen Herrmann
- Department
of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Joshua Hihath
- Department
of Electrical and Computer Engineering, University of California, Davis, Davis, California 95616, United States
| | - Suneet Kale
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Philip Kurian
- Quantum
Biology Laboratory, Graduate School, Howard
University, Washington, D.C. 20059, United States
| | - Ying-Cheng Lai
- School
of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Tianhan Liu
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Alexander Lopez
- Escuela
Superior Politécnica del Litoral, ESPOL, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, PO Box 09-01-5863, Guayaquil 090902, Ecuador
| | - Ernesto Medina
- Departamento
de Física, Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito, Av. Diego de Robles
y Vía Interoceánica, Quito 170901, Ecuador
| | - Vladimiro Mujica
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Kimika
Fakultatea, Euskal Herriko Unibertsitatea, 20080 Donostia, Euskadi, Spain
| | - Ron Naaman
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 76100, Israel
| | - Mohammadreza Noormandipour
- Department
of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
- TCM Group,
Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Julio L. Palma
- Department
of Chemistry, Pennsylvania State University, Lemont Furnace, Pennsylvania 15456, United States
| | - Yossi Paltiel
- Applied
Physics Department and the Center for Nano-Science and Nano-Technology, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - William Petuskey
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - João Carlos Ribeiro-Silva
- Laboratory
of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo Medical School, 05508-900 São
Paulo, Brazil
| | - Juan José Saenz
- Donostia
International Physics Center, Paseo Manuel de Lardizabal 4, 20018 Donostia, San Sebastian, Spain
- IKERBASQUE,
Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
| | - Elton J. G. Santos
- Institute
for Condensed Matter Physics and Complex Systems, School of Physics
and Astronomy, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
- Higgs Centre
for Theoretical Physics, The University
of Edinburgh, Edinburgh, EH9 3FD, United Kingdom
| | - Maria Solyanik-Gorgone
- Department
of Electrical and Computer Engineering, George Washington University, Washington, D.C. 20052, United States
| | - Volker J. Sorger
- Department
of Electrical and Computer Engineering, George Washington University, Washington, D.C. 20052, United States
| | - Dominik M. Stemer
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Materials Science and Engineering, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jesus M. Ugalde
- Kimika
Fakultatea, Euskal Herriko Unibertsitatea, 20080 Donostia, Euskadi, Spain
| | - Ana Valdes-Curiel
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Solmar Varela
- School
of Chemical Sciences and Engineering, Yachay
Tech University, 100119 Urcuquí, Ecuador
| | - David H. Waldeck
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael R. Wasielewski
- Department
of Chemistry, Center for Molecular Quantum Transduction, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Paul S. Weiss
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Materials Science and Engineering, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California, 90095, United States
| | - Helmut Zacharias
- Center
for Soft Nanoscience, University of Münster, 48149 Münster, Germany
| | - Qing Hua Wang
- School
for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, United States
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12
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Roy P, Kundu S, Valdiviezo J, Bullard G, Fletcher JT, Liu R, Yang SJ, Zhang P, Beratan DN, Therien MJ, Makri N, Fleming GR. Synthetic Control of Exciton Dynamics in Bioinspired Cofacial Porphyrin Dimers. J Am Chem Soc 2022; 144:6298-6310. [PMID: 35353523 PMCID: PMC9011348 DOI: 10.1021/jacs.1c12889] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Indexed: 11/29/2022]
Abstract
Understanding how the complex interplay among excitonic interactions, vibronic couplings, and reorganization energy determines coherence-enabled transport mechanisms is a grand challenge with both foundational implications and potential payoffs for energy science. We use a combined experimental and theoretical approach to show how a modest change in structure may be used to modify the exciton delocalization, tune electronic and vibrational coherences, and alter the mechanism of exciton transfer in covalently linked cofacial Zn-porphyrin dimers (meso-beta linked ABm-β and meso-meso linked AAm-m). While both ABm-β and AAm-m feature zinc porphyrins linked by a 1,2-phenylene bridge, differences in the interporphyrin connectivity set the lateral shift between macrocycles, reducing electronic coupling in ABm-β and resulting in a localized exciton. Pump-probe experiments show that the exciton dynamics is faster by almost an order of magnitude in the strongly coupled AAm-m dimer, and two-dimensional electronic spectroscopy (2DES) identifies a vibronic coherence that is absent in ABm-β. Theoretical studies indicate how the interchromophore interactions in these structures, and their system-bath couplings, influence excitonic delocalization and vibronic coherence-enabled rapid exciton transport dynamics. Real-time path integral calculations reproduce the exciton transfer kinetics observed experimentally and find that the linking-modulated exciton delocalization strongly enhances the contribution of vibronic coherences to the exciton transfer mechanism, and that this coherence accelerates the exciton transfer dynamics. These benchmark molecular design, 2DES, and theoretical studies provide a foundation for directed explorations of nonclassical effects on exciton dynamics in multiporphyrin assemblies.
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Affiliation(s)
- Partha
Pratim Roy
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli
Energy Nanoscience Institute at Berkeley, Berkeley, California 94720, United States
| | - Sohang Kundu
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Jesús Valdiviezo
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department
of Electrical and Computer Engineering, Duke University, Durham, North Carolina 27708, United States
| | - George Bullard
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - James T. Fletcher
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rui Liu
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Shiun-Jr Yang
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, 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 Physics, Duke University, Durham, North Carolina 27708, United States
- Department
of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| | - Michael J. Therien
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Nancy Makri
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Department
of Physics, University of Illinois, Urbana, Illinois 61801, United States
- Illinois
Quantum Information Science & Technology Center, University of Illinois, Urbana, Illinois 61801, United States
| | - Graham R. Fleming
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli
Energy Nanoscience Institute at Berkeley, Berkeley, California 94720, United States
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13
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Wiebelhaus N, Singh N, Zhang P, Craig SL, Beratan DN, Fitzgerald MC. Discovery of the Xenon-Protein Interactome Using Large-Scale Measurements of Protein Folding and Stability. J Am Chem Soc 2022; 144:3925-3938. [PMID: 35213151 PMCID: PMC10166008 DOI: 10.1021/jacs.1c11900] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The intermolecular interactions of noble gases in biological systems are associated with numerous biochemical responses, including apoptosis, inflammation, anesthesia, analgesia, and neuroprotection. The molecular modes of action underlying these responses are largely unknown. This is in large part due to the limited experimental techniques to study protein-gas interactions. The few techniques that are amenable to such studies are relatively low-throughput and require large amounts of purified proteins. Thus, they do not enable the large-scale analyses that are useful for protein target discovery. Here, we report the application of stability of proteins from rates of oxidation (SPROX) and limited proteolysis (LiP) methodologies to detect protein-xenon interactions on the proteomic scale using protein folding stability measurements. Over 5000 methionine-containing peptides and over 5000 semi-tryptic peptides, mapping to ∼1500 and ∼950 proteins, respectively, in the yeast proteome, were assayed for Xe-interacting activity using the SPROX and LiP techniques. The SPROX and LiP analyses identified 31 and 60 Xe-interacting proteins, respectively, none of which were previously known to bind Xe. A bioinformatics analysis of the proteomic results revealed that these Xe-interacting proteins were enriched in those involved in ATP-driven processes. A fraction of the protein targets that were identified are tied to previously established modes of action related to xenon's anesthetic and organoprotective properties. These results enrich our knowledge and understanding of biologically relevant xenon interactions. The sample preparation protocols and analytical methodologies developed here for xenon are also generally applicable to the discovery of a wide range of other protein-gas interactions in complex biological mixtures, such as cell lysates.
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Affiliation(s)
- Nancy Wiebelhaus
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Niven Singh
- Program in Computational Biology and Bioinformatics, Center for Genomics and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Stephen L. Craig
- 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
- Program in Computational Biology and Bioinformatics, Center for Genomics and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Michael C. Fitzgerald
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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14
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Roy S, Zheng L, Silberbush O, Engel M, Atsmon-Raz Y, Miller Y, Migliore A, Beratan DN, Ashkenasy N. Mechanism of Side Chain-Controlled Proton Conductivity in Bioinspired Peptidic Nanostructures. J Phys Chem B 2021; 125:12741-12752. [PMID: 34780197 DOI: 10.1021/acs.jpcb.1c08857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bioinspired peptide assemblies are promising candidates for use as proton-conducting materials in electrochemical devices and other advanced technologies. Progress toward applications requires establishing foundational structure-function relationships for transport in these materials. This experimental-theoretical study sheds light on how the molecular structure and proton conduction are linked in three synthetic cyclic peptide nanotube assemblies that comprise the three canonical basic amino acids (lysine, arginine, and histidine). Experiments find an order of magnitude higher proton conductivity for lysine-containing peptide assemblies compared to histidine and arginine containing assemblies. The simulations indicate that, upon peptide assembly, the basic amino acid side chains are close enough to enable direct proton transfer. The proton transfer kinetics is determined in the simulations to be governed by the structure and flexibility of the side chains. Together, experiments and theory indicate that the proton mobility is the main determinant of proton conductivity, critical for the performance of peptide-based devices.
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Affiliation(s)
- Subhasish Roy
- Department of Materials Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
| | - Lianjun Zheng
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Ohad Silberbush
- Department of Materials Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
| | - Maor Engel
- Department of Materials Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
| | - Yoav Atsmon-Raz
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel.,Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
| | - Agostino Migliore
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Chemical Sciences, University of Padova, Via Marzolo, 1, Padova 35131, Italy
| | - 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
| | - Nurit Ashkenasy
- Department of Materials Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel.,Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
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15
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Nayak A, Park J, De Mey K, Hu X, Beratan DN, Clays K, Therien MJ. Excited-State Dynamics and Nonlinear Optical Properties of Hyperpolarizable Chromophores Based on Conjugated Bis(terpyridyl)Ru(II) and Palladium and Platinum Porphyrinic Components: Impact of Heavy Metals upon Supermolecular Electro-Optic Properties. Inorg Chem 2021; 60:15404-15412. [PMID: 34585577 DOI: 10.1021/acs.inorgchem.1c02041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new series of strongly coupled oscillators based upon (porphinato)Pd, (porphinato)Pt, and bis(terpyridyl)ruthenium(II) building blocks is described. These RuPPd, RuPPt, RuPPdRu, and RuPPtRu chromophores feature bis(terpyridyl)Ru(II) moieties connected to the (porphinato)metal unit via an ethyne linker that bridges the 4'-terpyridyl and porphyrin macrocycle meso-carbon positions. Pump-probe transient optical data demonstrate sub-picosecond excited singlet-to-triplet-state relaxation. The relaxed lowest-energy triplet (T1) excited states of these chromophores feature absorption manifolds that span the 800-1200 nm spectral region, microsecond triplet-state lifetimes, and large absorptive extinction coefficients [ε(T1 → Tn) > 4 × 104 M-1 cm-1]. Dynamic hyperpolarizability (βλ) values were determined from hyper-Rayleigh light scattering (HRS) measurements carried out at several incident irradiation wavelengths over the 800-1500 nm spectral region. Relative to benchmark RuPZn and RuPZnRu chromophores which showed large βHRS values over the 1200-1600 nm range, RuPPd, RuPPt, RuPPdRu, and RuPPtRu displayed large βHRS values over the 850-1200 nm region. Generalized Thomas-Kuhn sum (TKS) rules and experimental hyperpolarizability values were utilized to determine excited state-to-excited state transition dipole terms from experimental electronic absorption data and thus assessed frequency-dependent βλ values, including two- and three-level contributions for both βzzz and βxzx tensor components to the RuPPd, RuPPt, RuPPdRu, and RuPPtRu hyperpolarizability spectra. These analyses qualitatively rationalize how the βzzz and βxzx tensor elements influence the observed irradiation wavelength-dependent hyperpolarizability magnitudes. The TKS analysis suggests that supermolecules related to RuPPd, RuPPt, RuPPdRu, and RuPPtRu will likely feature intricate dependences of experimentally determined βHRS values as a function of irradiation wavelength that derive from substantial singlet-triplet mixing, and complex interactions among multiple different β tensor components that modulate the long wavelength regime of the nonlinear optical response.
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Affiliation(s)
- Animesh Nayak
- Department of Chemistry, Duke University, French Family Science Center, 124 Science Drive, Durham, North Carolina 27708-0346, United States.,Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Jaehong Park
- Department of Chemistry, Duke University, French Family Science Center, 124 Science Drive, Durham, North Carolina 27708-0346, United States.,Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Kurt De Mey
- Department of Chemistry, University of Leuven, B-3001 Leuven, Belgium
| | - Xiangqian Hu
- Department of Chemistry, Duke University, French Family Science Center, 124 Science Drive, Durham, North Carolina 27708-0346, United States
| | - David N Beratan
- Department of Chemistry, Duke University, French Family Science Center, 124 Science Drive, Durham, North Carolina 27708-0346, United States.,Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States.,Department of Physics, Duke University, Durham, North Carolina 27708-0346, United States
| | - Koen Clays
- Department of Chemistry, University of Leuven, B-3001 Leuven, Belgium
| | - Michael J Therien
- Department of Chemistry, Duke University, French Family Science Center, 124 Science Drive, Durham, North Carolina 27708-0346, United States
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16
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Abstract
Ratcheted multi-step hopping electron transfer systems can plausibly produce directional charge transport over very large distances without requiring a source-drain voltage bias. We examine molecular strategies to realize ratcheted charge transport based on multi-step charge hopping, and we illustrate two ratcheting mechanisms with examples based on DNA structures. The charge transport times and currents that may be generated in these assemblies are also estimated using kinetic simulations. The first ratcheting mechanism described for nanoscale systems requires local electric fields on the 109 V/m scale to realize nearly 100% population transport. The second ratcheting mechanism for even larger systems, based on electrochemical gating, is estimated to generate currents as large as 0.1 pA for DNA structures that are a few μm in length with a gate voltage of about 5 V, a magnitude comparable to currents measured in DNA wires at the nanoscale when a source-drain voltage bias of similar magnitude is applied, suggesting an approach to considerably extend the distance range over which DNA charge transport devices may operate.
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Affiliation(s)
- Jesús Valdiviezo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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17
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Ru X, Crane BR, Zhang P, Beratan DN. Why Do Most Aromatics Fail to Support Hole Hopping in the Cytochrome c Peroxidase-Cytochrome c Complex? J Phys Chem B 2021; 125:7763-7773. [PMID: 34235935 DOI: 10.1021/acs.jpcb.1c05064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electron transport through aromatic species (especially tryptophan and tyrosine) plays a central role in water splitting, redox signaling, oxidative damage protection, and bioenergetics. The cytochrome c peroxidase (CcP)-cytochrome c (Cc) complex (CcP:Cc) is used widely to study interprotein electron transfer (ET) mechanisms. Tryptophan 191 (Trp191) of CcP supports hole hopping charge recombination in the CcP:Cc complex. Experimental studies find that when Trp191 is substituted by tyrosine, phenylalanine, or redox-active aniline derivatives bound in the W191G cavity, enzymatic activity and charge recombination rates both decrease. Theoretical analysis of these CcP:Cc complexes finds that the ET kinetics depend strongly on the chemistry of the modified Trp site. The computed electronic couplings in the W191F and W191G species are orders of magnitude smaller than in the native protein, due largely to the absence of a hopping intermediate and the large tunneling distance. Small molecules bound in the W191G cavity are weakly coupled electronically to the Cc heme, and the structural disorder of the guest molecule in the binding pocket may contribute further to the lack of enzymatic activity. The couplings in W191Y are not substantially weakened compared to the native species, but the redox potential difference for tyrosine vs tryptophan oxidation accounts for the slower rate in the Tyr mutant. Thus, theoretical analysis explains why only the native Trp supports rapid hole hopping in the CcP:Cc complex. Favorable free energies and electronic couplings are essential for establishing an efficient hole hopping relay in this protein-protein complex.
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Affiliation(s)
- Xuyan Ru
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, 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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18
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Yuly JL, Zhang P, Ru X, Terai K, Singh N, Beratan DN. Efficient and reversible electron bifurcation with either normal or inverted potentials at the bifurcating cofactor. Chem 2021. [DOI: 10.1016/j.chempr.2021.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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19
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Pastore AJ, Teo RD, Montoya A, Burg MJ, Twahir UT, Bruner SD, Beratan DN, Angerhofer A. Oxalate decarboxylase uses electron hole hopping for catalysis. J Biol Chem 2021; 297:100857. [PMID: 34097877 PMCID: PMC8254039 DOI: 10.1016/j.jbc.2021.100857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 01/16/2023] Open
Abstract
The hexameric low-pH stress response enzyme oxalate decarboxylase catalyzes the decarboxylation of the oxalate mono-anion in the soil bacterium Bacillus subtilis. A single protein subunit contains two Mn-binding cupin domains, and catalysis depends on Mn(III) at the N-terminal site. The present study suggests a mechanistic function for the C-terminal Mn as an electron hole donor for the N-terminal Mn. The resulting spatial separation of the radical intermediates directs the chemistry toward decarboxylation of the substrate. A π-stacked tryptophan pair (W96/W274) links two neighboring protein subunits together, thus reducing the Mn-to-Mn distance from 25.9 Å (intrasubunit) to 21.5 Å (intersubunit). Here, we used theoretical analysis of electron hole-hopping paths through redox-active sites in the enzyme combined with site-directed mutagenesis and X-ray crystallography to demonstrate that this tryptophan pair supports effective electron hole hopping between the C-terminal Mn of one subunit and the N-terminal Mn of the other subunit through two short hops of ∼8.5 Å. Replacement of W96, W274, or both with phenylalanine led to a large reduction in catalytic efficiency, whereas replacement with tyrosine led to recovery of most of this activity. W96F and W96Y mutants share the wildtype tertiary structure. Two additional hole-hopping networks were identified leading from the Mn ions to the protein surface, potentially protecting the enzyme from high Mn oxidation states during turnover. Our findings strongly suggest that multistep hole-hopping transport between the two Mn ions is required for enzymatic function, adding to the growing examples of proteins that employ aromatic residues as hopping stations.
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Affiliation(s)
- Anthony J Pastore
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Ruijie D Teo
- Department of Chemistry, Duke University, Durham, North Carolina, USA
| | - Alvaro Montoya
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Matthew J Burg
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Umar T Twahir
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina, USA.
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20
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Sang Y, Mishra S, Tassinari F, Karuppannan SK, Carmieli R, Teo RD, Migliore A, Beratan DN, Gray HB, Pecht I, Fransson J, Waldeck DH, Naaman R. Temperature Dependence of Charge and Spin Transfer in Azurin. J Phys Chem C Nanomater Interfaces 2021; 125:9875-9883. [PMID: 34055128 PMCID: PMC8154855 DOI: 10.1021/acs.jpcc.1c01218] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/23/2021] [Indexed: 05/05/2023]
Abstract
The steady-state charge and spin transfer yields were measured for three different Ru-modified azurin derivatives in protein films on silver electrodes. While the charge-transfer yields exhibit weak temperature dependences, consistent with operation of a near activation-less mechanism, the spin selectivity of the electron transfer improves as temperature increases. This enhancement of spin selectivity with temperature is explained by a vibrationally induced spin exchange interaction between the Cu(II) and its chiral ligands. These results indicate that distinct mechanisms control charge and spin transfer within proteins. As with electron charge transfer, proteins deliver polarized electron spins with a yield that depends on the protein's structure. This finding suggests a new role for protein structure in biochemical redox processes.
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Affiliation(s)
- Yutao Sang
- Department
of Chemical and Biological Physics, Weizmann
Institute, Rehovot 76100, Israel
| | - Suryakant Mishra
- Department
of Chemical and Biological Physics, Weizmann
Institute, Rehovot 76100, Israel
| | - Francesco Tassinari
- Department
of Chemical and Biological Physics, Weizmann
Institute, Rehovot 76100, Israel
| | | | - Raanan Carmieli
- Department
of Chemical Research Support, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Ruijie D. Teo
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Agostino Migliore
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, Padova 35122, Italy
| | - David N. Beratan
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Harry B. Gray
- Beckman
Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Israel Pecht
- Department
of Immunology, Weizmann Institute, Rehovot 76100, Israel
| | - Jonas Fransson
- Department
of Physics and Astronomy, Uppsala University, Uppsala 752 36, Sweden
| | - David H. Waldeck
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ron Naaman
- Department
of Chemical and Biological Physics, Weizmann
Institute, Rehovot 76100, Israel
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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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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22
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Bancroft L, Zhang J, Harvey SM, Krzyaniak MD, Zhang P, Schaller RD, Beratan DN, Young RM, Wasielewski MR. Charge Transfer and Spin Dynamics in a Zinc Porphyrin Donor Covalently Linked to One or Two Naphthalenediimide Acceptors. J Phys Chem A 2021; 125:825-834. [PMID: 33449684 DOI: 10.1021/acs.jpca.0c10471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Quantum coherence effects on charge transfer and spin dynamics in a system having two degenerate electron acceptors are studied using a zinc 5,10,15-tri(n-pentyl)-20-phenylporphyrin (ZnP) electron donor covalently linked to either one or two naphthalene-1,8:4,5-bis(dicarboximide) (NDI) electron acceptors using an anthracene (An) spacer, ZnP-An-NDI (1) and ZnP-An-NDI2 (2), respectively. Following photoexcitation of 1 and 2 in toluene at 295 K, femtosecond transient absorption spectroscopy shows that the electron transfer (ET) rate constant for 2 is about three times larger than that of 1, which can be accounted for by the statistical nature of incoherent ET as well as the electron couplings for the charge separation reactions. In contrast, the rate constant for charge recombination (CR) of 1 is about 25% faster than that of 2. Using femtosecond transient infrared spectroscopy and theoretical analysis, we find that the electron on NDI2•- in 2 localizes onto one of the two NDIs prior to CR, thus precluding electronically coherent CR from NDI2•-. Conversely, CR in both 1 and 2 is spin coherent as indicated by the observation of a resonance in the 3*ZnP yield following CR as a function of applied magnetic field, giving spin-spin exchange interaction energies of 2J = 210 and 236 mT, respectively, where the line width of the resonance for 2 is greater than 1. These data show that while CR is a spin-coherent process, incoherent hopping of the electron between the two NDIs in 2, consistent with the lack of delocalization noted above, results in greater spin decoherence in 2 relative to 1.
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Affiliation(s)
- Laura Bancroft
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Jinyuan Zhang
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Samantha M Harvey
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Matthew D Krzyaniak
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Richard D Schaller
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States.,Center for Nanoscale Materials, Argonne National Laboratory, Lemont, Illinois 60439, 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
| | - Ryan M Young
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R Wasielewski
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
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23
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Teo RD, Du X, Vera HLT, Migliore A, Beratan DN. Correlation between Charge Transport and Base Excision Repair in the MutY-DNA Glycosylase. J Phys Chem B 2021; 125:17-23. [PMID: 33371674 DOI: 10.1021/acs.jpcb.0c08598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Experimental evidence suggests that DNA-mediated redox signaling between high-potential [Fe4S4] proteins is relevant to DNA replication and repair processes, and protein-mediated charge transfer (CT) between [Fe4S4] clusters and nucleic acids is a fundamental process of the signaling and repair mechanisms. We analyzed the dominant CT pathways in the base excision repair glycosylase MutY using molecular dynamics simulations and hole hopping pathway analysis. We find that the adenine nucleobase of the mismatched A·oxoG DNA base pair facilitates [Fe4S4]-DNA CT prior to adenine excision by MutY. We also find that the R153L mutation in MutY (linked to colorectal adenomatous polyposis) influences the dominant [Fe4S4]-DNA CT pathways and appreciably decreases their effective CT rates.
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Affiliation(s)
- Ruijie D Teo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Xiaochen Du
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Computer Science, Duke University, Durham, North Carolina 27708, United States
| | - Héctor Luis Torres Vera
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Agostino Migliore
- 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 Physics, Duke University, Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
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24
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Abstract
The development of light-harvesting devices based on molecular materials depends critically on the ability to focus the electronic oscillator strength of molecules into the UV-vis spectral window. Typical molecular chromophores have only about 1% of their total electronic oscillator strength in this spectral region and thus perform at a small fraction of their possible effectiveness. This theoretical study finds that the electronic oscillator strength of polyenes in the UV-vis region may be enhanced by 1 order of magnitude using electrostatic fields, motivating specific experimental studies of oscillator strength focusing. We find scaling relationships between the polyene length, the intensity of the applied field, and the field-induced increase in oscillator strength that are useful for the implementation of light-harvesting strategies based on polyenes.
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Affiliation(s)
- Lianjun Zheng
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Agostino Migliore
- 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 Physics, Duke University, Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
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25
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Xiang L, Zhang P, Liu C, He X, Li HB, Li Y, Wang Z, Hihath J, Kim SH, Beratan DN, Tao N. Conductance and configuration of molecular gold-water-gold junctions under electric fields. Matter 2020; 3:166-179. [PMID: 33103114 PMCID: PMC7584381 DOI: 10.1016/j.matt.2020.03.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Water molecules can mediate charge transfer in biological and chemical reactions by forming electronic coupling pathways. Understanding the mechanism requires a molecular-level electrical characterization of water. Here, we describe the measurement of single water molecular conductance at room temperature, characterize the structure of water molecules using infrared spectroscopy, and perform theoretical studies to assist in the interpretation of the experimental data. The study reveals two distinct states of water, corresponding to a parallel and perpendicular orientation of the molecules. Water molecules switch from parallel to perpendicular orientations on applying an electric field, producing switching from high to low conductance states, thus enabling the determination of single water molecular dipole moments. The work further shows that water-water interactions affect the atomic scale configuration and conductance of water molecules. These findings demonstrate the importance of the discrete nature of water molecules in electron transfer and set limits on water-mediated electron transfer rates.
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Affiliation(s)
- Limin Xiang
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Lead contact
| | - Peng Zhang
- Departments of Chemistry and Physics, Duke University, Durham, North Carolina 27708, USA
| | - Chaoren Liu
- Departments of Chemistry and Physics, Duke University, Durham, North Carolina 27708, USA
| | - Xin He
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Haipeng B. Li
- Department of Electrical and Computing Engineering, University of California, Davis, Davis, California 95616, USA
| | - Yueqi Li
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Zixiao Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Joshua Hihath
- Department of Electrical and Computing Engineering, University of California, Davis, Davis, California 95616, USA
| | - Seong H. Kim
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - David N. Beratan
- Departments of Chemistry and Physics, Duke University, Durham, North Carolina 27708, USA
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
| | - Nongjian Tao
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
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26
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Tong J, Zhang P, Zhang L, Zhang D, Beratan DN, Song H, Wang Y, Li T. A Robust Bioderived Wavelength-Specific Photosensor Based on BLUF Proteins. Sens Actuators B Chem 2020; 310:127838. [PMID: 32296265 PMCID: PMC7157799 DOI: 10.1016/j.snb.2020.127838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Photosensitive proteins are naturally evolved photosensors that often respond to light signals of specific wavelengths. However, their poor stability under ambient conditions hinders their applications in non-biological settings. In this proof-of-principle study, we grafted the blue light using flavin (BLUF) protein reconstructed with flavin adenine dinucleotide (FAD) or roseoflavin (RoF) onto pristine graphene, and achieved selective sensitivity at 450 nm or 500 nm, respectively. We improved the thermal and operational stability substantially via structure-guided cross-linking, achieving 6-month stability under ambient condition and normal operation at temperatures up to 200 °C. Furthermore, the device exhibited rare negative photoconductivity behavior. The origins of this negative photoconductivity behavior were elucidated via a combination of experimental and theoretical analysis. In the photoelectric conversion studies, holes from photoexcited flavin migrated to graphene and recombined with electrons. The device allows facile modulation and detection of charge transfer, and provides a versatile platform for future studies of photoinduced charge transfer in biosensors as well as the development of stable wavelength-selective biophotosensors.
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Affiliation(s)
- Jing Tong
- Science and Technology on Microsytem Laboratory, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Lei Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- National engineering research center for protein drugs (NERCPD), Beijing 102206, China
| | - Dongwei Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- National engineering research center for protein drugs (NERCPD), Beijing 102206, China
| | - 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 Medical Center, Durham, North Carolina 27710, United States
| | - Haifeng Song
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- National engineering research center for protein drugs (NERCPD), Beijing 102206, China
| | - Yi Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- National engineering research center for protein drugs (NERCPD), Beijing 102206, China
| | - Tie Li
- Science and Technology on Microsytem Laboratory, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
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27
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Beratan DN. Autobiography of David N. Beratan. J Phys Chem B 2020; 124:3441-3446. [DOI: 10.1021/acs.jpcb.0c02604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Jin Y, Ru X, Su NQ, Mei Y, Beratan DN, Zhang P, Yang W. Revisiting the Hole Size in Double Helical DNA with Localized Orbital Scaling Corrections. J Phys Chem B 2020; 124:3428-3435. [PMID: 32272019 DOI: 10.1021/acs.jpcb.0c03112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The extent of electronic wave function delocalization for the charge carrier (electron or hole) in double helical DNA plays an important role in determining the DNA charge transfer mechanism and kinetics. The size of the charge carrier's wave function delocalization is regulated by the solvation induced localization and the quantum delocalization among the π stacked base pairs at any instant of time. Using a newly developed localized orbital scaling correction (LOSC) density functional theory method, we accurately characterized the quantum delocalization of the hole wave function in double helical B-DNA. This approach can be used to diagnose the extent of delocalization in fluctuating DNA structures. Our studies indicate that the hole state tends to delocalize among 4 guanine-cytosine (GC) base pairs and among 3 adenine-thymine (AT) base pairs when these adjacent bases fluctuate into degeneracy. The relatively small delocalization in AT base pairs is caused by the weaker π-π interaction. This extent of delocalization has significant implications for assessing the role of coherent, incoherent, or flickering coherent carrier transport in DNA.
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Affiliation(s)
- Ye Jin
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Xuyan Ru
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Neil Qiang Su
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Yuncai Mei
- 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 27705, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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29
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Teo RD, Migliore A, Beratan DN. Mutation effects on charge transport through the p58c iron-sulfur protein. Chem Sci 2020; 11:7076-7085. [PMID: 33250976 PMCID: PMC7690218 DOI: 10.1039/d0sc02245d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/16/2020] [Indexed: 12/25/2022] Open
Abstract
Growing experimental evidence indicates that iron–sulfur proteins play key roles in DNA repair and replication. In particular, charge transport between [Fe4S4] clusters, mediated by proteins and DNA, may convey signals to coordinate enzyme action. Human primase is a well studied [Fe4S4] protein, and its p58c domain (which contains an [Fe4S4] cluster) plays a role in the initiation of DNA replication. The Y345C mutation in p58c is linked to gastric tumors and may influence the protein-mediated charge transport. The complexity of protein–DNA systems, and the intricate electronic structure of [Fe4S4] clusters, have impeded progress into understanding functional charge transport in these systems. In this study, we built force fields to describe the high potential [Fe4S4] cluster in both oxidation states. The parameterization is compatible with AMBER force fields and enabled well-balanced molecular dynamics simulations of the p58c–RNA/DNA complex relevant to the initiation of DNA replication. Using the molecular mechanics Poisson–Boltzmann and surface area solvation method on the molecular dynamics trajectories, we find that the p58c mutation induces a modest change in the p58c–duplex binding free energy in agreement with recent experiments. Through kinetic modeling and analysis, we identify key features of the main charge transport pathways in p58c. In particular, we find that the Y345C mutation partially changes the composition and frequency of the most efficient (and potentially relevant to the biological function) charge transport pathways between the [Fe4S4] cluster and the duplex. Moreover, our approach sets the stage for a deeper understanding of functional charge transfer in [Fe4S4] protein–DNA complexes. Functional electron transfer between the [Fe4S4] cluster and the nucleic acid is impacted by a Y345C mutation in the p58c subunit of human primase.![]()
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Affiliation(s)
- Ruijie D Teo
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA . ;
| | - 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 . ; .,Department of Physics , Duke University , Durham , North Carolina 27708 , USA.,Department of Biochemistry , Duke University , Durham , North Carolina 27710 , USA
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30
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Li X, Valdiviezo J, Banziger SD, Zhang P, Ren T, Beratan DN, Rubtsov IV. Symmetry controlled photo-selection and charge separation in butadiyne-bridged donor–bridge–acceptor compounds. Phys Chem Chem Phys 2020; 22:9664-9676. [DOI: 10.1039/d0cp01235a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron transfer (ET) in donor–bridge–acceptor (DBA) compounds featuring alkyne bridges depends strongly on the torsion angle between the donor and acceptor.
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Affiliation(s)
- Xiao Li
- Department of Chemistry
- Tulane University
- New Orleans
- USA
| | | | | | - Peng Zhang
- Department of Chemistry
- Duke University
- Durham
- USA
| | - Tong Ren
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - David N. Beratan
- Department of Chemistry
- Duke University
- Durham
- USA
- Department of Physics, Duke University
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31
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Kang YK, Zhang P, Rubtsov IV, Zheng J, Bullard G, Beratan DN, Therien MJ. Orientational Dependence of Cofacial Porphyrin-Quinone Electronic Interactions within the Strong Coupling Regime. J Phys Chem B 2019; 123:10456-10462. [PMID: 31710233 DOI: 10.1021/acs.jpcb.9b07627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We examine the relative magnitudes of electronic coupling HDA in two face-to-face rigid and diastereomeric (porphinato)zinc(II)-quinone (PZn-Q) assemblies, 1β-ZnA and 1β-ZnB, in which the six quinonyl carbon atoms lie in virtually identical arrangements relative to the PZn plane at sub-van der Waals donor-acceptor (D-A) interplanar separations. Steady-state and time-resolved transient optical data and computational studies show that minor differences in relative D-A cofacial orientation give rise to disparate HDA magnitudes for both photoinduced charge separation (CS) and thermal charge recombination (CR). Time-dependent density functional theory (TDDFT) computations illuminate the nature of direct charge transfer states and the electronic structural factors that give rise to these differential HDAs. These data show more extensive mixing of locally excited (LE) and CS states in 1β-ZnA relative to 1β-ZnB and that these HDA differences track the magnitudes of electronic coupling matrix elements determined from steady-state electronic spectral data and thermal CR rate constants measured via pump-probe spectroscopy. Collectively, this work shows that electron transfer dynamics may be manipulated in cofacial D-A systems, even at sub-van der Waals contact, provided that conformational rigidity precludes structural fluctuations that modulate D-A interactions on the charge transfer time scale.
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Affiliation(s)
- Youn K Kang
- Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104-6323 , United States.,Department of Chemistry , Sangmyung University , Seoul 03016 , Korea
| | - Peng Zhang
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Igor V Rubtsov
- Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Jieru Zheng
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - George Bullard
- 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
| | - Michael J Therien
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
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32
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Banziger SD, Li X, Valdiviezo J, Zeller M, Zhang P, Beratan DN, Rubtsov IV, Ren T. Unsymmetrical Bis-Alkynyl Complexes Based on Co(III)(cyclam): Synthesis, Ultrafast Charge Separation, and Analysis. Inorg Chem 2019; 58:15487-15497. [DOI: 10.1021/acs.inorgchem.9b02557] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Susannah D. Banziger
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xiao Li
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Jesús Valdiviezo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Matthias Zeller
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, 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 Physics, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| | - Igor V. Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Tong Ren
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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33
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Ashfold M, Bender J, Beratan DN, Bradforth S, Cina J, Datta A, Dawlaty J, Dill R, Dodin A, Duchi M, Estergreen L, Fleming G, Frankcombe T, Gate G, Gessner O, Ginsberg N, Grieco C, Haggmark M, Hammes-Schiffer S, Huxter V, Kellogg M, Korovina N, Lee Y, Mahl J, Morenz K, Ogilvie J, Oliver TAA, Penfold T, Persson P, Schwartz B, Son M, Stavros V, Steen C, Thompson M, Wasielewski M, Weiss E, Woolley J. Photo-induced electron transfer: general discussion. Faraday Discuss 2019; 216:434-459. [PMID: 31259976 DOI: 10.1039/c9fd90029b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Teo RD, Rousseau BJ, Smithwick ER, Di Felice R, Beratan DN, Migliore A. Charge Transfer between [4Fe4S] Proteins and DNA Is Unidirectional: Implications for Biomolecular Signaling. Chem 2019; 5:1682-1684. [DOI: 10.1016/j.chempr.2019.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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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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Teo RD, Smithwick ER, Migliore A, Beratan DN. A single AT-GC exchange can modulate charge transfer-induced p53-DNA dissociation. Chem Commun (Camb) 2019; 55:206-209. [PMID: 30520908 DOI: 10.1039/c8cc09048c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Using molecular dynamics simulations and electronic structure theory, we shed light on the charge dynamics that causes the differential interaction of tumor suppressor protein p53 with the p21 and Gadd45 genes in response to oxidative stress. We show that the sequence dependence of this selectivity results from competing charge transfer to the protein and through the DNA, with implications on the use of genome editing tools to influence the p53 regulatory function.
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Affiliation(s)
- Ruijie D Teo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
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Abstract
Electron bifurcation moves electrons from a two-electron donor to reduce two spatially separated one-electron acceptors.
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Affiliation(s)
| | | | - Peng Zhang
- Department of Chemistry
- Duke University
- Durham
- USA
| | - David N. Beratan
- Department of Physics
- Duke University
- Durham
- USA
- Department of Chemistry
| | - John W. Peters
- Institute of Biological Chemistry
- Washington State University
- Pullman
- USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
The optical and electronic properties of semiconductor quantum dots (QDs) make them attractive candidates for applications in photovoltaics, spintronics, photocatalysis, and optoelectronics. Understanding how to control the flow of charge in QD assemblies is essential for realizing novel applications. This Account explores some unique characteristics of charge transport in QD dyads, triads, and their assemblies. The emerging features of these assemblies that provide new opportunities to manipulate charge flow at the nanoscale are (1) cascading energy landscapes and band offsets to inhibit charge recombination, (2) electrostatic fields that direct charge flow through QD-QD and QD-conjugated polymer junctions, and (3) QD chirality and chiral imprinting that promotes vectorial electron and spin selective transport. Charge flow kinetics is determined by a combination of familiar electron transfer parameters (reaction free energy, reorganization energy, and electronic coupling), donor and acceptor electronic densities of states, and internal electric fields. Electron transfer and electronic structure theory, combined with kinetic modeling, place the measured kinetics of QD electron transfer donor-acceptor assemblies into a unified conceptual context. The experimental transfer rates measured in these systems depend upon structure and the internal electric fields that are present in the assemblies. A negatively charged donor and positively charged acceptor, for example, facilitates (inhibits) electron (hole) transfer, while an electric field of opposite orientation (reversal of charges) inhibits (promotes) electron (hole) transfer. These and other emerging rules that govern charge flow in NP assemblies provide a strategy to design the directionality and yield of interfacial charge transport. Chirality at the nanoscale can induce spin selective charge transport, providing new ways to direct charge (and spin) flow in QD assemblies. Magnetoresistance and magnetic conductive probe atomic force microscopy experiments show spin selective electron transport for chirally imprinted QD assemblies. Photoinduced electron transfer from achiral donor-QDs to chiral acceptor-QDs depends on the electron spin and chiroptical properties of the acceptor-QDs. These assemblies show transport characteristics that correlate with features of the QDs' circular dichroism spectra, presenting intriguing challenges to theory, and indicating that spectroscopic signatures may assist in the design and diagnosis of functional molecular assemblies. Theoretical and experimental studies of charge transport in well-defined QD assemblies are establishing design principles for vectorial charge transport and are also refining questions surrounding the mechanism and control of these processes. These intensified efforts are forging links between fundamental discoveries regarding mechanism and practical applications for these novel assembled nanostructures.
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Affiliation(s)
- Brian P. Bloom
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ruibin Liu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Supriya Ghosh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ron Naaman
- Department of Chemical and Biological Physics, Weizmann Institute, Rehovot 76100, Israel
| | - 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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Affiliation(s)
- Spiros S Skourtis
- Department of Physics, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus.
| | - David N Beratan
- Departments of Chemistry and Physics, Duke University, Durham, NC 27708, USA; Department of Biochemistry, Duke University, Durham, NC 27710, USA.
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Abstract
Nitrogenase is a complicated two-component enzyme system that uses ATP binding and hydrolysis energy to achieve one of the most difficult chemical reactions in nature, the reduction of N2 to NH3. One component of the Mo-based nitrogenase system, Fe protein, delivers electrons one at a time to the second component, the catalytic MoFe protein. This process occurs through a series of synchronized events collectively called the "Fe protein cycle". Elucidating details of the events associated with this cycle has constituted an important challenge in understanding the nitrogenase mechanism. Electron delivery is a multistep process involving three metal clusters with intra- and interprotein events. It is proposed that the first electron transfer event is a gated intraprotein transfer of one electron from the MoFe protein P-cluster to the FeMo cofactor. Measurement of the effect of osmotic pressure on the rate of this electron transfer process revealed that it is gated by protein conformational changes. This first electron transfer is activated by binding of the Fe protein containing two bound ATP molecules. The mechanism of how this protein-protein association triggers electron transfer remains unknown. The second electron transfer event is proposed to be a rapid interprotein "backfill" with transfer of one electron from the reduced Fe protein 4Fe-4S cluster to the oxidized P-cluster. In this way, electron delivery can be viewed as a case of "deficit spending". Such a deficit-spending electron transfer process can be envisioned as a way to achieve one-direction electron flow, limiting the potential for back electron flow. Hydrolysis of two ATP molecules associated with the Fe protein occurs after the electron transfer and therefore is not used to directly drive the electron transfer. Rather, ATP hydrolysis is proposed to contribute to relaxation of the "activated" conformational state associated with the ATP form of the complex, with the free energy from ATP hydrolysis being used to pay back energy associated with component protein association and electron transfer. Release of inorganic phosphate (Pi) and protein-protein dissociation follow electron transfer and ATP hydrolysis. The rate-limiting step for the Fe protein cycle is not dissociation of the two proteins, as previously believed, but rather is release of Pi after ATP hydrolysis, which is then followed by rapid protein-protein complex dissociation. Nitrogenase is composed of two catalytic halves that do not function independently but rather exhibit anticooperative nuclear motion in which electron transfer in one-half of the complex partially inhibits electron transfer and ATP hydrolysis in the other half. Calculations indicated the existence of anticooperative interactions across the entire nitrogenase complex, suggesting a mechanism for the control of events on opposite ends of this large complex. The mechanistic necessity for this anticooperative process remains unknown. This Account presents a working model for how all of these processes work together in the nitrogenase "machine" to transduce the energy from ATP binding and hydrolysis to drive N2 reduction.
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Affiliation(s)
- Lance C. Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - John W. Peters
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Simone Raugei
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - David N. Beratan
- Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| | - Edwin Antony
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201, United States
| | - Dennis R. Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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Seefeldt LC, Peters JW, Beratan DN, Bothner B, Minteer SD, Raugei S, Hoffman BM. Control of electron transfer in nitrogenase. Curr Opin Chem Biol 2018; 47:54-59. [PMID: 30205289 DOI: 10.1016/j.cbpa.2018.08.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/06/2018] [Accepted: 08/21/2018] [Indexed: 11/30/2022]
Abstract
The bacterial enzyme nitrogenase achieves the reduction of dinitrogen (N2) to ammonia (NH3) utilizing electrons, protons, and energy from the hydrolysis of ATP. Building on earlier foundational knowledge, recent studies provide molecular-level details on how the energy of ATP hydrolysis is utilized, the sequencing of multiple electron transfer events, and the nature of energy transduction across this large protein complex. Here, we review the state of knowledge about energy transduction in nitrogenase.
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Affiliation(s)
- Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, USA.
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, 287 Clark Hall, Pullman, WA 99164, USA
| | - David N Beratan
- Departments of Chemistry, Physics, and Biochemistry, Duke University, Durham, NC 27708 and 27710, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Shelley D Minteer
- Departments of Chemistry and Materials Science & Engineering, University of Utah, 315 S 1400 E, Salt Lake City, UT 84112, USA
| | - Simone Raugei
- Physical and Computational Sciences, Pacific Northwestern National Laboratory, 602 Battelle Blvd, Richland, WA 99352, USA
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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Peters JW, Beratan DN, Bothner B, Dyer RB, Harwood CS, Heiden ZM, Hille R, Jones AK, King PW, Lu Y, Lubner CE, Minteer SD, Mulder DW, Raugei S, Schut GJ, Seefeldt LC, Tokmina-Lukaszewska M, Zadvornyy OA, Zhang P, Adams MW. A new era for electron bifurcation. Curr Opin Chem Biol 2018; 47:32-38. [PMID: 30077080 DOI: 10.1016/j.cbpa.2018.07.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/16/2018] [Accepted: 07/18/2018] [Indexed: 11/17/2022]
Abstract
Electron bifurcation, or the coupling of exergonic and endergonic oxidation-reduction reactions, was discovered by Peter Mitchell and provides an elegant mechanism to rationalize and understand the logic that underpins the Q cycle of the respiratory chain. Thought to be a unique reaction of respiratory complex III for nearly 40 years, about a decade ago Wolfgang Buckel and Rudolf Thauer discovered that flavin-based electron bifurcation is also an important component of anaerobic microbial metabolism. Their discovery spawned a surge of research activity, providing a basis to understand flavin-based bifurcation, forging fundamental parallels with Mitchell's Q cycle and leading to the proposal of metal-based bifurcating enzymes. New insights into the mechanism of electron bifurcation provide a foundation to establish the unifying principles and essential elements of this fascinating biochemical phenomenon.
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Affiliation(s)
- John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman WA 99163, United States; Pacific Northwest National Laboratory, Richland, WA 99352, United States.
| | - David N Beratan
- Department of Chemistry and Department of Physics, Duke University, Durham, NC 27708, United States; Department of Biochemistry, Duke University, Durham, NC 27710, United States
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States
| | - Caroline S Harwood
- Department of Microbiology, University of Washington, Seattle, WA 98195, United States
| | - Zachariah M Heiden
- Department of Chemistry, Washington State University, Pullman WA 99163, United States
| | - Russ Hille
- Biochemistry Department, University of California at Riverside, Riverside, CA 92521, United States
| | - Anne K Jones
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Paul W King
- National Renewable Energy Laboratory, Golden, CO 8040, United States
| | - Yi Lu
- Pacific Northwest National Laboratory, Richland, WA 99352, United States; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Carolyn E Lubner
- National Renewable Energy Laboratory, Golden, CO 8040, United States
| | - Shelley D Minteer
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, United States
| | - David W Mulder
- National Renewable Energy Laboratory, Golden, CO 8040, United States
| | - Simone Raugei
- Institute of Biological Chemistry, Washington State University, Pullman WA 99163, United States; Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Gerrit J Schut
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, United States
| | - Lance C Seefeldt
- Pacific Northwest National Laboratory, Richland, WA 99352, United States; Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, United States
| | | | - Oleg A Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman WA 99163, United States
| | - Peng Zhang
- Department of Biochemistry, Duke University, Durham, NC 27710, United States
| | - Michael Ww Adams
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, United States
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Ma Z, Antoniou P, Zhang P, Skourtis SS, Beratan DN. A Nonequilibrium Molecular Dynamics Study of Infrared Perturbed Electron Transfer. J Chem Theory Comput 2018; 14:4818-4832. [DOI: 10.1021/acs.jctc.8b00001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zheng Ma
- 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 Physics, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
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Ma Z, Lin Z, Lawrence CM, Rubtsov IV, Antoniou P, Skourtis SS, Zhang P, Beratan DN. How can infra-red excitation both accelerate and slow charge transfer in the same molecule? Chem Sci 2018; 9:6395-6405. [PMID: 30310568 PMCID: PMC6115705 DOI: 10.1039/c8sc00092a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/26/2018] [Indexed: 11/21/2022] Open
Abstract
A UV-IR-Vis 3-pulse study of infra-red induced changes to electron transfer (ET) rates in a donor-bridge-acceptor species finds that charge-separation rates are slowed, while charge-recombination rates are accelerated as a result of IR excitation during the reaction. We explore the underpinning mechanisms for this behavior, studying IR-induced changes to the donor-acceptor coupling, to the validity of the Condon approximation, and to the reaction coordinate distribution. We find that the dominant IR-induced rate effects in the species studied arise from changes to the density of states in the Marcus curve crossing region. That is, IR perturbation changes the probability of accessing the activated complex for the ET reactions. IR excitation diminishes the population of the activated complex for forward (activationless) ET, thus slowing the rate. However, IR excitation increases the population of the activated complex for (highly activated) charge recombination ET, thus accelerating the charge recombination rate.
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Affiliation(s)
- Zheng Ma
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA
| | - Zhiwei Lin
- Department of Chemistry , Tulane University , New Orleans , Louisiana 70118 , USA
| | - Candace M Lawrence
- Department of Chemistry , Xavier University of Louisiana , New Orleans , Louisiana 70125 , USA
| | - Igor V Rubtsov
- Department of Chemistry , Tulane University , New Orleans , Louisiana 70118 , USA
| | | | - Spiros S Skourtis
- Department of Physics , University of Cyprus , Nicosia 1678 , Cyprus
| | - Peng Zhang
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA
| | - David N Beratan
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA.,Department of Physics , Duke University , Durham , North Carolina 27708 , USA.,Department of Biochemistry , Duke University , Durham , North Carolina 27710 , USA
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47
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Sha R, Xiang L, Liu C, Balaeff A, Zhang Y, Zhang P, Li Y, Beratan DN, Tao N, Seeman NC. Charge splitters and charge transport junctions based on guanine quadruplexes. Nat Nanotechnol 2018; 13:316-321. [PMID: 29483600 DOI: 10.1038/s41565-018-0070-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/18/2018] [Indexed: 06/08/2023]
Abstract
Self-assembling circuit elements, such as current splitters or combiners at the molecular scale, require the design of building blocks with three or more terminals. A promising material for such building blocks is DNA, wherein multiple strands can self-assemble into multi-ended junctions, and nucleobase stacks can transport charge over long distances. However, nucleobase stacking is often disrupted at junction points, hindering electric charge transport between the two terminals of the junction. Here, we show that a guanine-quadruplex (G4) motif can be used as a connector element for a multi-ended DNA junction. By attaching specific terminal groups to the motif, we demonstrate that charges can enter the structure from one terminal at one end of a three-way G4 motif, and can exit from one of two terminals at the other end with minimal carrier transport attenuation. Moreover, we study four-way G4 junction structures by performing theoretical calculations to assist in the design and optimization of these connectors.
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Affiliation(s)
- Ruojie Sha
- Department of Chemistry, New York University, New York, NY, USA
| | - Limin Xiang
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Chaoren Liu
- Departments of Chemistry, Duke University, Durham, NC, USA
| | - Alexander Balaeff
- Departments of Chemistry, Duke University, Durham, NC, USA
- Nanoscience Technology Center & Department of Physics, University of Central Florida, Orlando, FL, USA
| | - Yuqi Zhang
- Departments of Chemistry, Duke University, Durham, NC, USA
| | - Peng Zhang
- Departments of Chemistry, Duke University, Durham, NC, USA
| | - Yueqi Li
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - David N Beratan
- Departments of Chemistry, Duke University, Durham, NC, USA.
- Department of Biochemistry, Duke University, Durham, NC, USA.
- Department of Physics, Duke University, Durham, NC, USA.
| | - Nongjian Tao
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, USA.
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Rousseau BJG, Shafei S, Migliore A, Stanley RJ, Beratan DN. Determinants of Photolyase's DNA Repair Mechanism in Mesophiles and Extremophiles. J Am Chem Soc 2018; 140:2853-2861. [PMID: 29401372 DOI: 10.1021/jacs.7b11926] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Light-driven DNA repair by extremophilic photolyases is of tremendous importance for understanding the early development of life on Earth. The mechanism for flavin adenine dinucleotide repair of DNA lesions is the subject of debate and has been studied mainly in mesophilic species. In particular, the role of adenine in the repair process is poorly understood. Using molecular docking, molecular dynamics simulations, electronic structure calculations, and electron tunneling pathways analysis, we examined adenine's role in DNA repair in four photolyases that thrive at different temperatures. Our results indicate that the contribution of adenine to the electronic coupling between the flavin and the cyclobutane pyrimidine dimer lesion to be repaired is significant in three (one mesophilic and two extremophilic) of the four enzymes studied. Our analysis suggests that thermophilic and hyperthermophilic photolyases have evolved structurally to preserve the functional position (and thus the catalytic function) of adenine at their high temperatures of operation. Water molecules can compete with adenine in establishing the strongest coupling pathway for the electron transfer repair process, but the adenine contribution remains substantial. The present study also reconciles prior seemingly contradictory conclusions on the role of adenine in mesophile electron transfer repair reactions, showing how adenine-mediated superexchange is conformationally gated.
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Affiliation(s)
| | | | | | - Robert J Stanley
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - David N Beratan
- Department of Biochemistry, Duke University , Durham, North Carolina 27710, United States
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Peters JW, Beratan DN, Schut GJ, Adams MWW. On the nature of organic and inorganic centers that bifurcate electrons, coupling exergonic and endergonic oxidation–reduction reactions. Chem Commun (Camb) 2018; 54:4091-4099. [DOI: 10.1039/c8cc01530a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bifurcating electrons to couple endergonic and exergonic electron-transfer reactions has been shown to have a key role in energy conserving redox enzymes.
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Affiliation(s)
- John W. Peters
- Institute of Biological Chemistry, Washington State University
- Pullman
- USA
| | - David N. Beratan
- Department of Chemistry and Department of Physics, Duke University
- Durham
- USA
- Department of Biochemistry, Duke University
- Durham
| | - Gerrit J. Schut
- Department of Biochemistry and Molecular Biology, University of Georgia
- Athens
- USA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia
- Athens
- USA
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Zhang P, Yuly JL, Lubner CE, Mulder DW, King PW, Peters JW, Beratan DN. Electron Bifurcation: Thermodynamics and Kinetics of Two-Electron Brokering in Biological Redox Chemistry. Acc Chem Res 2017; 50:2410-2417. [PMID: 28876046 DOI: 10.1021/acs.accounts.7b00327] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
How can proteins drive two electrons from a redox active donor onto two acceptors at very different potentials and distances? And how can this transaction be conducted without dissipating very much energy or violating the laws of thermodynamics? Nature appears to have addressed these challenges by coupling thermodynamically uphill and downhill electron transfer reactions, using two-electron donor cofactors that have very different potentials for the removal of the first and second electron. Although electron bifurcation is carried out with near perfection from the standpoint of energy conservation and electron delivery yields, it is a biological energy transduction paradigm that has only come into focus recently. This Account provides an exegesis of the biophysical principles that underpin electron bifurcation. Remarkably, bifurcating electron transfer (ET) proteins typically send one electron uphill and one electron downhill by similar energies, such that the overall reaction is spontaneous, but not profligate. Electron bifurcation in the NADH-dependent reduced ferredoxin: NADP+ oxidoreductase I (Nfn) is explored in detail here. Recent experimental progress in understanding the structure and function of Nfn allows us to dissect its workings in the framework of modern ET theory. The first electron that leaves the two-electron donor flavin (L-FAD) executes a positive free energy "uphill" reaction, and the departure of this electron switches on a second thermodynamically spontaneous ET reaction from the flavin along a second pathway that moves electrons in the opposite direction and at a very different potential. The singly reduced ET products formed from the bifurcating flavin are more than two nanometers distant from each other. In Nfn, the second electron to leave the flavin is much more reducing than the first: the potentials are said to be "crossed." The eventually reduced cofactors, NADH and ferredoxin in the case of Nfn, perform crucial downstream redox processes of their own. We dissect the thermodynamics and kinetics of electron bifurcation in Nfn and find that the key features of electron bifurcation are (1) spatially separated transfer pathways that diverge from a two-electron donor, (2) one thermodynamically uphill and one downhill redox pathway, with a large negative shift in the donor's reduction potential after departure of the first electron, and (3) electron tunneling and activation factors that enable bifurcation, producing a 1:1 partitioning of electrons onto the two pathways. Electron bifurcation is found in the CO2 reducing pathways of methanogenic archaea, in the hydrogen pathways of hydrogenases, in the nitrogen fixing pathway of Fix, and in the mitochondrial charge transfer chain of complex III, cytochrome bc1. While crossed potentials may offer the biological advantage of producing tightly regulated high energy reactive species, neither kinetic nor thermodynamic considerations mandate crossed potentials to generate successful electron bifurcation. Taken together, the theoretical framework established here, focusing on the underpinning electron tunneling barriers and activation free energies, explains the logic of electron bifurcation that enables energy conversion and conservation in Nfn, points toward bioinspired schemes to execute multielectron redox chemistry, and establishes a roadmap for examining novel electron bifurcation networks in nature.
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Affiliation(s)
| | | | - Carolyn E. Lubner
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - David W. Mulder
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Paul W. King
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - John W. Peters
- Institute
of Biological Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - David N. Beratan
- Department
of Biochemistry, Duke University, Durham, North Carolina 27710, United States
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