1
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Pann J, Viertl W, Roithmeyer H, Pehn R, Hofer TS, Brüggeller P. Insights into Proton Coupled Electron Transfer in the Field of Artificial Photosynthesis. Isr J Chem 2022. [DOI: 10.1002/ijch.202100035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Johann Pann
- Institute of General Inorganic and Theoretical Chemistry Centrum for Chemistry and Biomedicine University of Innsbruck Innrain 80-82 A-6020 Innsbruck Austria
| | - Wolfgang Viertl
- Institute of General Inorganic and Theoretical Chemistry Centrum for Chemistry and Biomedicine University of Innsbruck Innrain 80-82 A-6020 Innsbruck Austria
| | - Helena Roithmeyer
- Institute of General Inorganic and Theoretical Chemistry Centrum for Chemistry and Biomedicine University of Innsbruck Innrain 80-82 A-6020 Innsbruck Austria
| | - Richard Pehn
- Institute of General Inorganic and Theoretical Chemistry Centrum for Chemistry and Biomedicine University of Innsbruck Innrain 80-82 A-6020 Innsbruck Austria
| | - Thomas S. Hofer
- Institute of General Inorganic and Theoretical Chemistry Centrum for Chemistry and Biomedicine University of Innsbruck Innrain 80-82 A-6020 Innsbruck Austria
| | - Peter Brüggeller
- Institute of General Inorganic and Theoretical Chemistry Centrum for Chemistry and Biomedicine University of Innsbruck Innrain 80-82 A-6020 Innsbruck Austria
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2
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Role of intramolecular hydrogen bonds in promoting electron flow through amino acid and oligopeptide conjugates. Proc Natl Acad Sci U S A 2021; 118:2026462118. [PMID: 33707214 DOI: 10.1073/pnas.2026462118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Elucidating the factors that control charge transfer rates in relatively flexible conjugates is of importance for understanding energy flows in biology as well as assisting the design and construction of electronic devices. Here, we report ultrafast electron transfer (ET) and hole transfer (HT) between a corrole (Cor) donor linked to a perylene-diimide (PDI) acceptor by a tetrameric alanine (Ala)4 Selective photoexcitation of the donor and acceptor triggers subpicosecond and picosecond ET and HT. Replacement of the (Ala)4 linker with either a single alanine or phenylalanine does not substantially affect the ET and HT kinetics. We infer that electronic coupling in these reactions is not mediated by tetrapeptide backbone nor by direct donor-acceptor interactions. Employing a combination of NMR, circular dichroism, and computational studies, we show that intramolecular hydrogen bonding brings the donor and the acceptor into proximity in a "scorpion-shaped" molecular architecture, thereby accounting for the unusually high ET and HT rates. Photoinduced charge transfer relies on a (Cor)NH…O=C-NH…O=C(PDI) electronic-coupling pathway involving two pivotal hydrogen bonds and a central amide group as a mediator. Our work provides guidelines for construction of effective donor-acceptor assemblies linked by long flexible bridges as well as insights into structural motifs for mediating ET and HT in proteins.
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3
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Osella S. Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead? NANOMATERIALS 2021; 11:nano11020299. [PMID: 33498961 PMCID: PMC7911014 DOI: 10.3390/nano11020299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022]
Abstract
A tremendous effort is currently devoted to the generation of novel hybrid materials with enhanced electronic properties for the creation of artificial photosynthetic systems. This compelling and challenging problem is well-defined from an experimental point of view, as the design of such materials relies on combining organic materials or metals with biological systems like light harvesting and redox-active proteins. Such hybrid systems can be used, e.g., as bio-sensors, bio-fuel cells, biohybrid photoelectrochemical cells, and nanostructured photoelectronic devices. Despite these efforts, the main bottleneck is the formation of efficient interfaces between the biological and the organic/metal counterparts for efficient electron transfer (ET). It is within this aspect that computation can make the difference and improve the current understanding of the mechanisms underneath the interface formation and the charge transfer efficiency. Yet, the systems considered (i.e., light harvesting protein, self-assembly monolayer and surface assembly) are more and more complex, reaching (and often passing) the limit of current computation power. In this review, recent developments in computational methods for studying complex interfaces for artificial photosynthesis will be provided and selected cases discussed, to assess the inherent ability of computation to leave a mark in this field of research.
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Affiliation(s)
- Silvio Osella
- Chemical and Biological Systems Simulation Lab, Center of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
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4
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Wörner S, Leier J, Michenfelder NC, Unterreiner A, Wagenknecht H. Directed Electron Transfer in Flavin Peptides with Oligoproline-Type Helical Conformation as Models for Flavin-Functional Proteins. ChemistryOpen 2020; 9:1264-1269. [PMID: 33318882 PMCID: PMC7729625 DOI: 10.1002/open.202000199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/23/2020] [Indexed: 11/26/2022] Open
Abstract
To mimic the charge separation in functional proteins we studied flavin-modified peptides as models. They were synthesized as oligoprolines that typically form a polyproline type-II helix, because this secondary structure supports the electron transfer properties. We placed the flavin as photoexcitable chromophore and electron acceptor at the N-terminus. Tryptophans were placed as electron donors to direct the electron transfer over 0-3 intervening prolines. Spectroscopic studies revealed competitive photophysical pathways. The reference peptide without tryptophan shows dominant non-specific ET dynamics, leading to an ion pair formation, whereas peptides with tryptophans have weak non-specific ET and intensified directed electron transfer. By different excitation wavelengths, we can conclude that the corresponding ion pair state of flavin within the peptide environment has to be energetically located between the S1 and S4 states, whereas the directed electron transfer to tryptophan occurs directly from the S1 state. These photochemical results have fundamental significance for proteins with flavin as redoxactive cofactor.
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Affiliation(s)
- Samantha Wörner
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Julia Leier
- Institute of Physical ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 276131KarlsruheGermany
| | - Nadine C. Michenfelder
- Institute of Physical ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 276131KarlsruheGermany
| | - Andreas‐Neil Unterreiner
- Institute of Physical ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 276131KarlsruheGermany
| | - Hans‐Achim Wagenknecht
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
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5
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Abstract
A recently proposed oxidative damage protection mechanism in proteins relies on hole hopping escape routes formed by redox-active amino acids. We present a computational tool to identify the dominant charge hopping pathways through these residues based on the mean residence times of the transferring charge along these hopping pathways. The residence times are estimated by combining a kinetic model with well-known rate expressions for the charge-transfer steps in the pathways. We identify the most rapid hole hopping escape routes in cytochrome P450 monooxygenase, cytochrome c peroxidase, and benzylsuccinate synthase (BSS). This theoretical analysis supports the existence of hole hopping chains as a mechanism capable of providing hole escape from protein catalytic sites on biologically relevant timescales. Furthermore, we find that pathways involving the [4Fe4S] cluster as the terminal hole acceptor in BSS are accessible on the millisecond timescale, suggesting a potential protective role of redox-active cofactors for preventing protein oxidative damage.
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6
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Sato M, Kumada A, Hidaka K. Multiscale modeling of charge transfer in polymers with flexible backbones. Phys Chem Chem Phys 2019; 21:1812-1819. [DOI: 10.1039/c8cp05558k] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In order to evaluate carrier transfer properties in polymers with flexible backbones, we have proposed a simplified multi-scale modeling approach combining molecular dynamics simulations, first-principles calculations and kinetic Monte Carlo simulations.
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Affiliation(s)
- Masahiro Sato
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-0032
- Japan
| | - Akiko Kumada
- Department of Electrical Engineering and Information Systems
- The University of Tokyo
- Tokyo 113-8656
- Japan
| | - Kunihiko Hidaka
- Department of Electrical Engineering and Information Systems
- The University of Tokyo
- Tokyo 113-8656
- Japan
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7
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Khosa M, Ullah A. Mechanistic insight into protein supported biosorption complemented by kinetic and thermodynamics perspectives. Adv Colloid Interface Sci 2018; 261:28-40. [PMID: 30301519 DOI: 10.1016/j.cis.2018.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 09/17/2018] [Accepted: 09/25/2018] [Indexed: 10/28/2022]
Abstract
In this review, we discussed the micro-level aspects of protein supported biosorption. The mechanism, surface chemistry in terms of energy interactions and electron transfer process (ETP) of peptide systems within protein are three important areas that provide mechanistic insight into protein supported biosorption. The functional groups in proteinous material like hydroxyl (-OH), carbonyl (>C=O), carboxyl (-COOH) and sulfhydryl (-SH) play a significant role in the biosorption of variety of pollutants such as metal ions, metalloids, and organic matters in wastewaters. The mechanistic aspects of biosorption are crucial not only for the separation process but also they contribute towards stoichiometric considerations and mathematical modelling process. The surface chemistry of applied biosorbents relies on interfacial components whose interaction energies are estimated with help of classical Derjaguin, Landau, Verwey, and Overbeek (DLVO) theory mathematically. Proteins are the fundamental molecules of many biomaterial used for the biosorption of contaminents and peptide bond is considered as the backbone of proteins. The charge variations on peptide bonding is the result of ETP whose discussion was made part of this review for understaning number of biological and technological processes of vital interests. In addition, this review was complemented by exhaustive overview of kinetic and thermodynamics perspectives of biosorption process.
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8
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López-Estrada O, Laguna HG, Barrueta-Flores C, Amador-Bedolla C. Reassessment of the Four-Point Approach to the Electron-Transfer Marcus-Hush Theory. ACS OMEGA 2018; 3:2130-2140. [PMID: 31458519 PMCID: PMC6641260 DOI: 10.1021/acsomega.7b01425] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/08/2018] [Indexed: 05/25/2023]
Abstract
The Marcus-Hush theory has been successfully applied to describe and predict the activation barriers and hence the electron-transfer (ET) rates in several physicochemical and biological systems. This theory assumes that in the ET reaction, the geometry of the free Gibbs energy landscape is parabolic, with equal curvature near the local minimum for both reactants and products. In spite of its achievements, more realistic models have included the assumption of the two parabolas having not the same curvature. This situation is analyzed by the Nelsen's four-point method. As a benchmark to compare the Marcus-Hush approximation to a precise calculation of the excitation energy, we studied the non-ET process of the electronic excitation of the aluminum dimer that has two local minima (3∑g - and 3∏u electronic states) and allows to obtain analytically the Marcus-Hush nonsymmetric parameters. We appraise the ability of the Marcus-Hush formula to approximate the analytical results by using several averages of the two reorganization energies associated with the forward and backward transitions and analyze the error. It is observed that the geometric average minimizes the relative error and that the analytical case is recovered. The main results of this paper are obtained by the application of the Nelsen's four-point method to compute the reorganization energies of a large set of potential π-conjugated molecules proposed for organic photovoltaic devices using the above-mentioned averages for the Marcus-Hush formula. The activation energies obtained with the geometric average are significantly larger for some donor-acceptor pairs in comparison with the previously employed arithmetic average, their differences being suitable for experimental testing.
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9
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Puiu M, Bala C. Peptide-based biosensors: From self-assembled interfaces to molecular probes in electrochemical assays. Bioelectrochemistry 2017; 120:66-75. [PMID: 29182910 DOI: 10.1016/j.bioelechem.2017.11.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 11/21/2017] [Accepted: 11/21/2017] [Indexed: 02/06/2023]
Abstract
Redox-tagged peptides have emerged as functional materials with multiple applications in the area of sensing and biosensing applications due to their high stability, excellent redox properties and versatility of biomolecular interactions. They allow direct observation of molecular interactions in a wide range of affinity and enzymatic assays and act as electron mediators. Short helical peptides possess the ability to self-assemble in specific configurations with the possibility to develop in highly-ordered, stable 1D, 2D and 3D architectures in a hierarchical controlled manner. We provide here a brief overview of the electrochemical techniques available to study the electron transfer in peptide films with particular interest in developing biosensors with immobilized peptide motifs, for biological and clinical applications.
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Affiliation(s)
- Mihaela Puiu
- R&D Center LaborQ, University of Bucharest, 4-12 Regina Elisabeta Blvd., 030018 Bucharest, Romania
| | - Camelia Bala
- R&D Center LaborQ, University of Bucharest, 4-12 Regina Elisabeta Blvd., 030018 Bucharest, Romania; Department of Analytical Chemistry, University of Bucharest, 4-12 Regina Elisabeta Blvd., 030018 Bucharest, Romania.
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10
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Martin DR, Matyushov DV. Electron-transfer chain in respiratory complex I. Sci Rep 2017; 7:5495. [PMID: 28710385 PMCID: PMC5511282 DOI: 10.1038/s41598-017-05779-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/01/2017] [Indexed: 12/23/2022] Open
Abstract
Complex I is a part of the respiration energy chain converting the redox energy into the cross-membrane proton gradient. The electron-transfer chain of iron-sulfur cofactors within the water-soluble peripheral part of the complex is responsible for the delivery of electrons to the proton pumping subunit. The protein is porous to water penetration and the hydration level of the cofactors changes when the electron is transferred along the chain. High reaction barriers and trapping of the electrons at the iron-sulfur cofactors are prevented by the combination of intense electrostatic noise produced by the protein-water interface with the high density of quantum states in the iron-sulfur clusters caused by spin interactions between paramagnetic iron atoms. The combination of these factors substantially lowers the activation barrier for electron transfer compared to the prediction of the Marcus theory, bringing the rate to the experimentally established range. The unique role of iron-sulfur clusters as electron-transfer cofactors is in merging protein-water fluctuations with quantum-state multiplicity to allow low activation barriers and robust operation. Water plays a vital role in electron transport energetics by electrowetting the cofactors in the chain upon arrival of the electron. A general property of a protein is to violate the fluctuation-dissipation relation through nonergodic sampling of its landscape. High functional efficiency of redox enzymes is a direct consequence of nonergodicity.
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Affiliation(s)
- Daniel R Martin
- Department of Physics and School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, AZ, 85287-1504, USA
| | - Dmitry V Matyushov
- Department of Physics and School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, AZ, 85287-1504, USA.
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11
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Oberhofer H, Reuter K, Blumberger J. Charge Transport in Molecular Materials: An Assessment of Computational Methods. Chem Rev 2017. [PMID: 28644623 DOI: 10.1021/acs.chemrev.7b00086] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The booming field of molecular electronics has fostered a surge of computational research on electronic properties of organic molecular solids. In particular, with respect to a microscopic understanding of transport and loss mechanisms, theoretical studies assume an ever-increasing role. Owing to the tremendous diversity of organic molecular materials, a great number of computational methods have been put forward to suit every possible charge transport regime, material, and need for accuracy. With this review article we aim at providing a compendium of the available methods, their theoretical foundations, and their ranges of validity. We illustrate these through applications found in the literature. The focus is on methods available for organic molecular crystals, but mention is made wherever techniques are suitable for use in other related materials such as disordered or polymeric systems.
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Affiliation(s)
- Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom.,Institute for Advanced Study, Technische Universität München , Lichtenbergstrasse 2 a, D-85748 Garching, Germany
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12
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Abstract
Extensive simulations of cytochrome c in solution are performed to address the apparent contradiction between large reorganization energies of protein electron transfer typically reported by atomistic simulations and much smaller values produced by protein electrochemistry. The two sets of data are reconciled by deriving the activation barrier for electrochemical reaction in terms of an effective reorganization energy composed of half the Stokes shift (characterizing the medium polarization in response to electron transfer) and the variance reorganization energy (characterizing the breadth of electrostatic fluctuations). This effective reorganization energy is much smaller than each of the two components contributing to it and is fully consistent with electrochemical measurements. Calculations in the range of temperatures between 280 and 360 K combine long, classical molecular dynamics simulations with quantum calculations of the protein active site. The results agree with the Arrhenius plots for the reaction rates and with cyclic voltammetry of cytochrome c immobilized on self-assembled monolayers. Small effective reorganization energy, and the resulting small activation barrier, is a general phenomenology of protein electron transfer allowing fast electron transport within biological energy chains.
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Affiliation(s)
- Salman S Seyedi
- Department of Physics, Arizona State University , P.O. Box 871504, Tempe, Arizona 85287-1504, United States
| | - Morteza M Waskasi
- School of Molecular Sciences, Arizona State University , P.O. Box 871604, Tempe, Arizona 85287-1604, United States
| | - Dmitry V Matyushov
- Department of Physics, Arizona State University , P.O. Box 871504, Tempe, Arizona 85287-1504, United States.,School of Molecular Sciences, Arizona State University , P.O. Box 871604, Tempe, Arizona 85287-1604, United States
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13
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Gillet N, Berstis L, Wu X, Gajdos F, Heck A, de la Lande A, Blumberger J, Elstner M. Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level. J Chem Theory Comput 2016; 12:4793-4805. [DOI: 10.1021/acs.jctc.6b00564] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Natacha Gillet
- Institute
of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Laura Berstis
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Xiaojing Wu
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, Université Paris Saclay, Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Fruzsina Gajdos
- Department
of Physics and Astronomy, University College London, Gower Street, London WCIE 6BT, United Kingdom
| | - Alexander Heck
- Institute
of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Aurélien de la Lande
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, Université Paris Saclay, Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Jochen Blumberger
- Department
of Physics and Astronomy, University College London, Gower Street, London WCIE 6BT, United Kingdom
| | - Marcus Elstner
- Institute
of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
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14
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Joy S, Sureshbabu VV, Periyasamy G. Computational Studies on Structural, Excitation, and Charge-Transfer Properties of Ureidopeptidomimetics. J Phys Chem B 2016; 120:6469-78. [PMID: 27314639 DOI: 10.1021/acs.jpcb.6b02210] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptides with ureido group enclosing backbones are considered peptidomimetics and are known for their higher stabilities, biocompatibilities, antibiotic, inhibitor, and charge-transduction activities. These peptidomimetics have some unique applications, which are quite different from those of natural peptides. Hence, it is imperative to appreciate their properties at a microscopic level. In this regard, this work outlines, in detail, the charge transfer (CT) properties, hole-migration dynamics, and electronic structures of various experimentally comprehended ureidopeptidomimetic models using density functional theory (DFT). Time-dependent DFT and complete active space self-consistent field computations on basic models provide the necessary evidence for the viability of CT from the end enfolding the ureido group to the other end with a carboxylate entity. This donor-to-acceptor CT has been reflected in excitation studies, in which the higher intensity band corresponds to CT from the π orbital of the ureido group to the π* orbital of the carboxylate entity. Further, hole-migration studies have shown that charge can evolve from the ureido end, whereas the hole generated at the carboxylate end does not migrate. However, hole migration has been reported to occur from both ends (amino and carboxylate ends) in glycine oligopeptides, and our studies show that the ability to transfer and migrate charge can be tuned by modifying the donor and acceptor functional groups in both the neutral and cationic charge states. We have analyzed the possibility of hole migration following ionization using DFT-based wave-packet propagation and found its occurrence on a ∼2-5 fs time scale, which reflects the charge-transduction ability of peptidomimetics.
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Affiliation(s)
- Sherin Joy
- Department of Chemistry, Central College Campus, Bangalore University , Bangalore 560 001, Karnataka, India
| | - Vommina V Sureshbabu
- Department of Chemistry, Central College Campus, Bangalore University , Bangalore 560 001, Karnataka, India
| | - Ganga Periyasamy
- Department of Chemistry, Central College Campus, Bangalore University , Bangalore 560 001, Karnataka, India
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15
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Yamamoto T, Dai J, Jacobsen NE, Ammam M, Hall GB, Mozziconacci O, Schöneich C, Wilson GS, Glass RS. Neighboring π-Amide Participation in Thioether Oxidation: Conformational Control. Org Lett 2016; 18:3522-5. [DOI: 10.1021/acs.orglett.6b01309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takuhei Yamamoto
- Department
of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Jixun Dai
- Department
of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Neil E. Jacobsen
- Department
of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Malika Ammam
- Department
of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Gabriel B. Hall
- Department
of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Olivier Mozziconacci
- Department
of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Christian Schöneich
- Department
of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, United States
| | - George S. Wilson
- Department
of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Richard S. Glass
- Department
of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
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16
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Donoli A, Marcuzzo V, Moretto A, Crisma M, Toniolo C, Cardena R, Bisello A, Santi S. New bis-ferrocenyl end-capped peptides: synthesis and charge transfer properties. Biopolymers 2016; 100:14-24. [PMID: 23335164 DOI: 10.1002/bip.22197] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 09/26/2012] [Accepted: 10/30/2012] [Indexed: 01/19/2023]
Abstract
In this article, the successful preparation of a new series of 3(10) -helical peptides of different length containing two terminal ferrocenyl (Fc) units and based on the strongly foldameric α-aminoisobutyric (Aib) acid is reported. The synthesis of the Fc-CO-(Aib)(n) -NH-Fc (n = 1-5) homo-peptides was performed by solution methods. Moderate to good yields (26-85%) were obtained in each of the difficult coupling steps of Fc-COOH and the corresponding H-(Aib)(n)-NH-Fc compounds by C-activation with the 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide/7-aza-1-hydroxy-1,2,3-benzotriazole method. Information on the C=O···H-N intramolecularly hydrogen-bonded networks was initially obtained from FT-IR absorption measurements. The N-H stretching (amide A) region allowed us to distinguish which amide protons are involved in intramolecular hydrogen bonds and indicates the formation of an incipient 3(10) -helix structure for peptides containing at least two Aib residues. This conclusion was confirmed by (1)H NMR titrations of the N-H groups of the peptides in CDCl(3) with dimethylsulfoxide and by crystallographic analysis of the N(α) -acylated Fc-CO-(Aib)(5)-NH-Fc pentapeptide amide. The two redox-active Fc groups covalently bound to the termini of the foldameric peptide architectures were used as electrochemical probes. The end-to-end effects of electron holes generated by single and double oxidations were analyzed by means of electrochemical and spectroelectrochemical techniques. The results of these studies indicate that charge transfer across the peptide main chain does occur in the five peptides. In particular, in the pentapeptide 5, charge is transferred through an intramolecular Fe···Fe separation of 14 Å.
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Affiliation(s)
- Alessandro Donoli
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
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17
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Shah A, Adhikari B, Martic S, Munir A, Shahzad S, Ahmad K, Kraatz HB. Electron transfer in peptides. Chem Soc Rev 2015; 44:1015-27. [PMID: 25619931 DOI: 10.1039/c4cs00297k] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In this review, we discuss the factors that influence electron transfer in peptides. We summarize experimental results from solution and surface studies and highlight the ongoing debate on the mechanistic aspects of this fundamental reaction. Here, we provide a balanced approach that remains unbiased and does not favor one mechanistic view over another. Support for a putative hopping mechanism in which an electron transfers in a stepwise manner is contrasted with experimental results that support electron tunneling or even some form of ballistic transfer or a pathway transfer for an electron between donor and acceptor sites. In some cases, experimental evidence suggests that a change in the electron transfer mechanism occurs as a result of donor-acceptor separation. However, this common understanding of the switch between tunneling and hopping as a function of chain length is not sufficient for explaining electron transfer in peptides. Apart from chain length, several other factors such as the extent of the secondary structure, backbone conformation, dipole orientation, the presence of special amino acids, hydrogen bonding, and the dynamic properties of a peptide also influence the rate and mode of electron transfer in peptides. Electron transfer plays a key role in physical, chemical and biological systems, so its control is a fundamental task in bioelectrochemical systems, the design of peptide based sensors and molecular junctions. Therefore, this topic is at the heart of a number of biological and technological processes and thus remains of vital interest.
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Affiliation(s)
- Afzal Shah
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, M1C 1A4, Canada.
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18
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Kubas A, Gajdos F, Heck A, Oberhofer H, Elstner M, Blumberger J. Electronic couplings for molecular charge transfer: benchmarking CDFT, FODFT and FODFTB against high-level ab initio calculations. II. Phys Chem Chem Phys 2015; 17:14342-54. [PMID: 25573447 DOI: 10.1039/c4cp04749d] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A new database (HAB7-) of electronic coupling matrix elements (Hab) for electron transfer in seven medium-sized negatively charged π-conjugated organic dimers is introduced. Reference data are obtained with spin-component scaled approximate coupled cluster method (SCS-CC2) and large basis sets. Assessed DFT-based approaches include constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), self-consistent charge density functional tight-binding (FODFTB) and the recently described analytic overlap method (AOM). This complements the previously reported HAB11 database where only cationic dimers were considered. The CDFT method in combination with a functional based on PBE and including 50% of exact exchange (HFX) was found to provide best estimates, with a mean relative unsigned error (MRUE) of 8.2%. CDFT couplings systematically increase with decreasing fraction of HFX as a consequence of increasing delocalisation of the SOMO orbital. The FODFT method is found to be very robust underestimating electronic couplings by 28%. The FODFTB and AOM methods, although orders of magnitude more efficient in terms of computational effort than the DFT approaches, perform well with reasonably small errors of 54% and 29%, respectively, translating in errors in the non-adiabatic electron transfer rate of a factor of 2.4 and 1.7, respectively. We discuss carefully various sources of errors and the scope and limitations of all assessed methods taking into account the results obtained for both HAB7- and HAB11 databases.
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Affiliation(s)
- Adam Kubas
- University College London, Department of Physics and Astronomy, Gower Street, London WC1E 6BT, UK.
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19
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de la Lande A, Gillet N, Chen S, Salahub DR. Progress and challenges in simulating and understanding electron transfer in proteins. Arch Biochem Biophys 2015; 582:28-41. [PMID: 26116376 DOI: 10.1016/j.abb.2015.06.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 06/15/2015] [Accepted: 06/22/2015] [Indexed: 11/19/2022]
Abstract
This Review presents an overview of the most common numerical simulation approaches for the investigation of electron transfer (ET) in proteins. We try to highlight the merits of the different approaches but also the current limitations and challenges. The article is organized into three sections. Section 2 deals with direct simulation algorithms of charge migration in proteins. Section 3 summarizes the methods for testing the applicability of the Marcus theory for ET in proteins and for evaluating key thermodynamic quantities entering the reaction rates (reorganization energies and driving force). Recent studies interrogating the validity of the theory due to the presence of non-ergodic effects or of non-linear responses are also described. Section 4 focuses on the tunneling aspects of electron transfer. How can the electronic coupling between charge transfer states be evaluated by quantum chemistry approaches and rationalized? What interesting physics regarding the impact of protein dynamics on tunneling can be addressed? We will illustrate the different sections with examples taken from the literature to show what types of system are currently manageable with current methodologies. We also take care to recall what has been learned on the biophysics of ET within proteins thanks to the advent of atomistic simulations.
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Affiliation(s)
- Aurélien de la Lande
- Laboratoire de Chimie Physique, UMR 8000, CNRS, Université Paris Sud. 15, av. Jean Perrin, 91405 Orsay, France.
| | - Natacha Gillet
- Laboratoire de Chimie Physique, UMR 8000, CNRS, Université Paris Sud. 15, av. Jean Perrin, 91405 Orsay, France
| | - Shufeng Chen
- Laboratoire de Chimie Physique, UMR 8000, CNRS, Université Paris Sud. 15, av. Jean Perrin, 91405 Orsay, France
| | - Dennis R Salahub
- Department of Chemistry, CMS - Centre for Molecular Simulation and IQST - Institute for Quantum Science and Technology, University of Calgary, 2500 University Drive N.W., Calgary, Alberta T2N 1N4, Canada.
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20
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Monney NPA, Bally T, Giese B. Electronic Structure of Hole-Conducting States in Polyprolines. J Phys Chem B 2015; 119:6584-90. [DOI: 10.1021/acs.jpcb.5b02580] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Thomas Bally
- University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Bernd Giese
- University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
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21
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Plehn T, Megow J, May V. Concerted charge and energy transfer processes in a highly flexible fullerene-dye system: a mixed quantum-classical study. Phys Chem Chem Phys 2015; 16:12949-58. [PMID: 24852441 DOI: 10.1039/c4cp01081g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Photoinduced excitation energy transfer and accompanying charge separation are elucidated for a supramolecular system of a single fullerene covalently linked to six pyropheophorbide-a dye molecules. Molecular dynamics simulations are performed to gain an atomistic picture of the architecture and the surrounding solvent. Excitation energy transfer among the dye molecules and electron transfer from the excited dyes to the fullerene are described by a mixed quantum-classical version of the Förster rate and the semiclassical Marcus rate, respectively. The mean characteristic time of energy redistribution lies in the range of 10 ps, while electron transfer proceeds within 150 ps. In between, on a 20 to 50 ps time-scale, conformational changes take place in the system. This temporal hierarchy of processes guarantees efficient charge separation, if the structure is exposed to a solvent. The fast energy transfer can adopt the dye excitation to the actual conformation. In this sense, the probability to achieve charge separation is large enough since any dominance of unfavorable conformations that exhibit a large dye-fullerene distance is circumvented. And the slow electron transfer may realize an averaging with respect to different conformations. To confirm the reliability of our computations, ensemble measurements on the charge separation dynamics are simulated and a very good agreement with the experimental data is obtained.
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Affiliation(s)
- Thomas Plehn
- Institut für Physik, Humboldt Universität zu Berlin, Newtonstraße 15, D-12489 Berlin, Germany.
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22
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Kubas A, Hoffmann F, Heck A, Oberhofer H, Elstner M, Blumberger J. Electronic couplings for molecular charge transfer: benchmarking CDFT, FODFT, and FODFTB against high-level ab initio calculations. J Chem Phys 2014; 140:104105. [PMID: 24628150 DOI: 10.1063/1.4867077] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We introduce a database (HAB11) of electronic coupling matrix elements (H(ab)) for electron transfer in 11 π-conjugated organic homo-dimer cations. High-level ab inito calculations at the multireference configuration interaction MRCI+Q level of theory, n-electron valence state perturbation theory NEVPT2, and (spin-component scaled) approximate coupled cluster model (SCS)-CC2 are reported for this database to assess the performance of three DFT methods of decreasing computational cost, including constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), and self-consistent charge density functional tight-binding (FODFTB). We find that the CDFT approach in combination with a modified PBE functional containing 50% Hartree-Fock exchange gives best results for absolute H(ab) values (mean relative unsigned error = 5.3%) and exponential distance decay constants β (4.3%). CDFT in combination with pure PBE overestimates couplings by 38.7% due to a too diffuse excess charge distribution, whereas the economic FODFT and highly cost-effective FODFTB methods underestimate couplings by 37.6% and 42.4%, respectively, due to neglect of interaction between donor and acceptor. The errors are systematic, however, and can be significantly reduced by applying a uniform scaling factor for each method. Applications to dimers outside the database, specifically rotated thiophene dimers and larger acenes up to pentacene, suggests that the same scaling procedure significantly improves the FODFT and FODFTB results for larger π-conjugated systems relevant to organic semiconductors and DNA.
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Affiliation(s)
- Adam Kubas
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Felix Hoffmann
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Alexander Heck
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Harald Oberhofer
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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23
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Heck A, Woiczikowski PB, Kubař T, Welke K, Niehaus T, Giese B, Skourtis S, Elstner M, Steinbrecher TB. Fragment Orbital Based Description of Charge Transfer in Peptides Including Backbone Orbitals. J Phys Chem B 2014; 118:4261-72. [DOI: 10.1021/jp408907g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Alexander Heck
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - P. Benjamin Woiczikowski
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Kai Welke
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Thomas Niehaus
- Department
of Physics, University of Regensburg, 93053 Regensburg, Germany
| | - Bernd Giese
- Department
of Chemistry, University of Fribourg, Chemin du Musee 9, CH-1700 Fribourg, Switzerland
| | - Spiros Skourtis
- Department
of Physics, University of Cyprus, PO Box 20537, Nicosia 1678, Cyprus
| | - Marcus Elstner
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Thomas B. Steinbrecher
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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24
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Nguyen TX, Grampp G, Yurkovskaya A, Lukzen N. Kinetics of the oxidation of thymine and thymidine by triplet 2,2'-dipyridyl in aqueous solutions at different pH values. J Phys Chem A 2013; 117:7655-60. [PMID: 23906227 PMCID: PMC3751068 DOI: 10.1021/jp4022882] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 06/21/2013] [Indexed: 01/20/2023]
Abstract
The photo-oxidation of the nucleobase, thymine (Thy), and nucleoside, thymidine (dThy), by dipyridyl (DP) has been investigated in aqueous solution using time-resolved laser flash photolysis. The pH dependence of the oxidation rate constants is measured within a large pH scale. As a consequence, the chemical reactivity of the reactants existing in solution at a certain range of pH is predicted. Bimolecular rate constants of the quenching reactions between triplet dipyridyl and thymine and thymidine are, respectively, kq = 2.4 × 10(7) M(-1) s(-1) (pH < 5.8) and kq = 1.0 × 10(7) M(-1) s(-1) (5.8 < pH < 9.8). Cyclic voltammetry was used to measure the potentials of thymine oxidation and dipyridyl reduction in water at pH < 7. Both results give hints for a proton coupled electron-transfer (PCET) reaction from thymine to triplet dipyridyl.
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Affiliation(s)
- Truong X. Nguyen
- Institute of Physical and Theoretical
Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Günter Grampp
- Institute of Physical and Theoretical
Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Alexandra
V. Yurkovskaya
- International Tomography
Center, Institutskaya 3a, 630090 Novosibirsk, Russia
- Novosibirsk State
University, Pirogova 2, 630090 Novosibirsk, Russia
| | - Nikita Lukzen
- International Tomography
Center, Institutskaya 3a, 630090 Novosibirsk, Russia
- Novosibirsk State
University, Pirogova 2, 630090 Novosibirsk, Russia
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25
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Jiang N, Kuznetsov A, Nocek JM, Hoffman BM, Crane BR, Hu X, Beratan DN. Distance-independent charge recombination kinetics in cytochrome c-cytochrome c peroxidase complexes: compensating changes in the electronic coupling and reorganization energies. J Phys Chem B 2013; 117:9129-41. [PMID: 23895339 PMCID: PMC3809023 DOI: 10.1021/jp401551t] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Charge recombination rate constants vary no more than 3-fold for interprotein ET in the Zn-substituted wild type (WT) cytochrome c peroxidase (CcP):cytochrome c (Cc) complex and in complexes with four mutants of the Cc protein (i.e., F82S, F82W, F82Y, and F82I), despite large differences in the ET distance. Theoretical analysis indicates that charge recombination for all complexes involves a combination of tunneling and hopping via Trp191. For three of the five structures (WT and F82S(W)), the protein favors hopping more than that in the other two structures that have longer heme → ZnP distances (F82Y(I)). Experimentally observed biexponential ET kinetics is explained by the complex locking in alternative coupling pathways, where the acceptor hole state is either primarily localized on ZnP (slow phase) or on Trp191 (fast phase). The large conformational differences between the CcP:Cc interface for the F82Y(I) mutants compared to that the WT and F82S(W) complexes are predicted to change the reorganization energies for the CcP:Cc ET reactions because of changes in solvent exposure and interprotein ET distances. Since the recombination reaction is likely to occur in the inverted Marcus regime, an increased reorganization energy compensates the decreased role for hopping recombination (and the longer transfer distance) in the F82Y(I) mutants. Taken together, coupling pathway and reorganization energy effects for the five protein complexes explain the observed insensitivity of recombination kinetics to donor-acceptor distance and docking pose and also reveals how hopping through aromatic residues can accelerate long-range ET.
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Affiliation(s)
- Nan Jiang
- Department of Chemistry, Duke University, Durham, NC 27708
| | | | - Judith M. Nocek
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Xiangqian Hu
- Department of Chemistry, Duke University, Durham, NC 27708
| | - David N. Beratan
- Department of Chemistry, Duke University, Durham, NC 27708
- Department of Biochemistry, Duke University, Durham, NC 27708
- Department of Physics, Duke University, Durham, NC 27708
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26
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Kubař T, Elstner M. A hybrid approach to simulation of electron transfer in complex molecular systems. J R Soc Interface 2013; 10:20130415. [PMID: 23883952 DOI: 10.1098/rsif.2013.0415] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Electron transfer (ET) reactions in biomolecular systems represent an important class of processes at the interface of physics, chemistry and biology. The theoretical description of these reactions constitutes a huge challenge because extensive systems require a quantum-mechanical treatment and a broad range of time scales are involved. Thus, only small model systems may be investigated with the modern density functional theory techniques combined with non-adiabatic dynamics algorithms. On the other hand, model calculations based on Marcus's seminal theory describe the ET involving several assumptions that may not always be met. We review a multi-scale method that combines a non-adiabatic propagation scheme and a linear scaling quantum-chemical method with a molecular mechanics force field in such a way that an unbiased description of the dynamics of excess electron is achieved and the number of degrees of freedom is reduced effectively at the same time. ET reactions taking nanoseconds in systems with hundreds of quantum atoms can be simulated, bridging the gap between non-adiabatic ab initio simulations and model approaches such as the Marcus theory. A major recent application is hole transfer in DNA, which represents an archetypal ET reaction in a polarizable medium. Ongoing work focuses on hole transfer in proteins, peptides and organic semi-conductors.
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Affiliation(s)
- Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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27
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McCullagh M, Voth GA. Unraveling the Role of the Protein Environment for [FeFe]-Hydrogenase: A New Application of Coarse-Graining. J Phys Chem B 2013; 117:4062-71. [DOI: 10.1021/jp402441s] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Martin McCullagh
- Department of Chemistry,
James Franck Institute, Institute
for Biophysical Dynamics, and Computation Institute, The University of Chicago, Chicago, Illinois 60637,
United States
| | - Gregory A. Voth
- Department of Chemistry,
James Franck Institute, Institute
for Biophysical Dynamics, and Computation Institute, The University of Chicago, Chicago, Illinois 60637,
United States
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28
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Paltrinieri L, Borsari M, Ranieri A, Battistuzzi G, Corni S, Bortolotti CA. The Active Site Loop Modulates the Reorganization Energy of Blue Copper Proteins by Controlling the Dynamic Interplay with Solvent. J Phys Chem Lett 2013; 4:710-715. [PMID: 26281923 DOI: 10.1021/jz302125k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Understanding the factors governing the rate of electron transfer processes in proteins is crucial not only to a deeper understanding of redox processes in living organisms but also for the design of efficient devices featuring biological molecules. Here, molecular dynamics simulations performed on native azurin and four chimeric cupredoxins allow for the calculation of the reorganization energy and of structure-related quantities that were used to clarify the molecular determinants to the dynamics/function relationship in blue copper proteins. We find that the dynamics of the small, metal-binding loop region controls the outer-sphere reorganization energy not only by determining the exposure of the active site to solvent but also through the modulation of the redox-dependent rearrangement of the whole protein scaffold and of the surrounding water molecules.
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Affiliation(s)
| | | | | | | | - Stefano Corni
- ¶CNR-Nano Institute of Nanoscience, via Campi 213/A, 41125 Modena, Italy
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29
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Skourtis SS. Reviewprobing protein electron transfer mechanisms from the molecular to the cellular length scales. Biopolymers 2013; 100:82-92. [DOI: 10.1002/bip.22169] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 09/14/2012] [Accepted: 09/23/2012] [Indexed: 11/10/2022]
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30
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Amadei A, Daidone I, Bortolotti CA. A general statistical mechanical approach for modeling redox thermodynamics: the reaction and reorganization free energies. RSC Adv 2013. [DOI: 10.1039/c3ra42842g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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31
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Blumberger J, McKenna KP. Constrained density functional theory applied to electron tunnelling between defects in MgO. Phys Chem Chem Phys 2013; 15:2184-96. [DOI: 10.1039/c2cp42537h] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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32
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Oberhofer H, Blumberger J. Revisiting electronic couplings and incoherent hopping models for electron transport in crystalline C60 at ambient temperatures. Phys Chem Chem Phys 2012; 14:13846-52. [PMID: 22858858 DOI: 10.1039/c2cp41348e] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We assess the validity of incoherent hopping models that have previously been used to describe electron transport in crystalline C(60) at room temperature. To this end we present new density functional theory based calculations of the electron transfer parameter defining these models. Specifically, we report electronic coupling matrix elements for several ten thousand configurations that are thermally accessible to the C(60) molecules through rotational diffusion around their lattice sites. We find that the root-mean-square fluctuations of the electronic coupling matrix element (11 meV) are almost as large as the average value (14 meV) and that the distribution is well approximated by a Gaussian. Importantly, due to the small reorganisation energy of the C(60) dimer (≈0.1 eV), the ET is almost activationless for the majority of configurations. Yet, for a small but significant fraction of orientations the coupling is so strong compared to reorganisation energy that no charge-localised state exists, a situation that is aggravated if zero-point motion of the nuclei is taken into account. The present calculations indicate that standard hopping models do not provide a sound description of electron transport in C(60), which might be the case for many other organics as well, and that approaches are needed that solve the electron dynamics directly.
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Affiliation(s)
- Harald Oberhofer
- Theoretical Chemistry, TU Munich, Lichtenbergstr. 4, D-85747 Garching, Germany
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33
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Lauz M, Eckhardt S, Fromm KM, Giese B. The influence of dipole moments on the mechanism of electron transfer through helical peptides. Phys Chem Chem Phys 2012; 14:13785-8. [PMID: 22729294 DOI: 10.1039/c2cp41159h] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The life time of aromatic radical cations is limited by reactions like β-elimination, dimerization, and addition to the solvent. Here we show that the attachment of such a radical cation to the C-terminal end of an α-/3(10)-helical peptide further reduces its life time by two orders of magnitude. For PPII-helical peptides, such an effect is only observed if the peptide contains an adjacent electron donor like tyrosine, which enables electron transfer (ET) through the peptide. In order to explain the special role of α-/3(10)-helical peptides, it is assumed that the aromatic radical cation injects a positive charge into an adjacent amide group. This is in accord with quantum chemical calculations and electrochemical experiments in the literature showing a decrease in the amide redox potentials caused by the dipole moments of long α-/3(10)-helical peptides. Rate measurements are in accord with a mechanism for a multi-step ET through α-/3(10)-helical peptides that uses the amide groups or H-bonds as stepping stones.
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Affiliation(s)
- Miriam Lauz
- University of Fribourg, Department of Chemistry, 1700 Fribourg, Switzerland
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