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Cao Y, Zhu W, Wei H, Ma C, Lin Y, Zhu JJ. Stable and Monochromatic All-Inorganic Halide Perovskite Assisted by Hollow Carbon Nitride Nanosphere for Ratiometric Electrochemiluminescence Bioanalysis. Anal Chem 2020; 92:4123-4130. [DOI: 10.1021/acs.analchem.0c00070] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yue Cao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Wenlei Zhu
- School of Mechanical and Materials Engineering, Washington State University, Pullman, Washington 99164, United States
| | - Huifang Wei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Cheng Ma
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Yuehe Lin
- School of Mechanical and Materials Engineering, Washington State University, Pullman, Washington 99164, United States
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
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2
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Martin DR, Dinpajooh M, Matyushov DV. Polarizability of the Active Site in Enzymatic Catalysis: Cytochrome c. J Phys Chem B 2019; 123:10691-10699. [DOI: 10.1021/acs.jpcb.9b09236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Mohammadhasan Dinpajooh
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Landi A, Borrelli R, Capobianco A, Peluso A. Transient and Enduring Electronic Resonances Drive Coherent Long Distance Charge Transport in Molecular Wires. J Phys Chem Lett 2019; 10:1845-1851. [PMID: 30939015 DOI: 10.1021/acs.jpclett.9b00650] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
It is shown that the yields of oxidative damage observed in double-stranded DNA oligomers consisting of two guanines separated by adenine-thymine (A:T) n bridges of various lengths are reliably accounted for by a multistep mechanism, in which transient and nontransient electronic resonances induce charge transport and solvent relaxation stabilizes the hole transfer products. The proposed multistep mechanism leads to results in excellent agreement with the observed yield ratios for both the short and the long distance regime; the almost distance independence of yield ratios for longer bridges ( n ≥ 3) is the consequence of the significant energy decrease of the electronic levels of the bridge, which, as the bridge length increases, become quasi-degenerate with those of the acceptor and donor groups (enduring resonance). These results provide significant guidelines for the design of novel DNA sequences to be employed in organic electronics.
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Affiliation(s)
- Alessandro Landi
- Dipartimento di Chimica e Biologia , Università di Salerno , I-84084 Fisciano , Salerno , Italy
| | - Raffaele Borrelli
- Department of Agricultural, Forestry and Food Science , University of Torino , Via Leonardo da Vinci 44 , I-10095 Grugliasco , Italy
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia , Università di Salerno , I-84084 Fisciano , Salerno , Italy
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia , Università di Salerno , I-84084 Fisciano , Salerno , Italy
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Xu T, Wang W, Yin S. Explicit Method To Evaluate the External Reorganization Energy of Charge-Transfer Reactions in Oligoacene Crystals Using the State-Specific Polarizable Force Field. J Phys Chem A 2018; 122:8957-8964. [DOI: 10.1021/acs.jpca.8b08998] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tao Xu
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an City 710119, People’s Republic of China
| | - Wenliang Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an City 710119, People’s Republic of China
| | - Shiwei Yin
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an City 710119, People’s Republic of China
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Corbella M, Voityuk AA, Curutchet C. How abasic sites impact hole transfer dynamics in GC-rich DNA sequences. Phys Chem Chem Phys 2018; 20:23123-23131. [DOI: 10.1039/c8cp03572e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hole transfer dynamics through GC-rich DNA duplexes containing abasic sites is strongly modulated by the nature of the unpaired nucleobase.
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Affiliation(s)
- Marina Corbella
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Química Teòrica i Computacional (IQTC-UB)
- Universitat de Barcelona
- 08028 Barcelona
- Spain
| | - Alexander A. Voityuk
- Institució Catalana de Recerca i Estudis Avançats (ICREA)
- 08010 Barcelona
- Spain
- Institut de Química Computacional i Catàlisi and Departament de Química
- Universitat de Girona
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Química Teòrica i Computacional (IQTC-UB)
- Universitat de Barcelona
- 08028 Barcelona
- Spain
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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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Zhang Y, Dood J, Beckstead AA, Li XB, Nguyen KV, Burrows CJ, Improta R, Kohler B. Photoinduced Electron Transfer in DNA: Charge Shift Dynamics Between 8-Oxo-Guanine Anion and Adenine. J Phys Chem B 2015; 119:7491-502. [PMID: 25660103 DOI: 10.1021/jp511220x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Femtosecond time-resolved IR spectroscopy is used to investigate the excited-state dynamics of a dinucleotide containing an 8-oxoguanine anion at the 5'-end and neutral adenine at the 3'-end. UV excitation of the dinucleotide transfers an electron from deprotonated 8-oxoguanine to its π-stacked neighbor adenine in less than 1 ps, generating a neutral 8-oxoguanine radical and an adenine radical anion. These species are identified by the excellent agreement between the experimental and calculated IR difference spectra. The quantum efficiency of this ultrafast charge shift reaction approaches unity. Back electron transfer from the adenine radical anion to the 8-oxguanine neutral radical occurs in 9 ps, or approximately 6 times faster than between the adenine radical anion and the 8-oxoguanine radical cation (Zhang, Y. et al. Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 11612-11617). The large asymmetry in forward and back electron transfer rates is fully rationalized by semiclassical nonadiabatic electron transfer theory. Forward electron transfer is ultrafast because the driving force is nearly equal to the reorganization energy, which is estimated to lie between 1 and 2 eV. Back electron transfer is highly exergonic and takes place much more slowly in the Marcus inverted region.
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Affiliation(s)
- Yuyuan Zhang
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Jordan Dood
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Ashley A Beckstead
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Xi-Bo Li
- ‡Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Khiem V Nguyen
- ‡Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Cynthia J Burrows
- ‡Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Roberto Improta
- §CNR-Consiglio Nazionale delle Ricerche Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, 80136 Napoli, Italy
| | - Bern Kohler
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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Cisneros GA, Karttunen M, Ren P, Sagui C. Classical electrostatics for biomolecular simulations. Chem Rev 2014; 114:779-814. [PMID: 23981057 PMCID: PMC3947274 DOI: 10.1021/cr300461d] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Barnett RN, Joseph J, Landman U, Schuster GB. Oxidative Thymine Mutation in DNA: Water-Wire-Mediated Proton-Coupled Electron Transfer. J Am Chem Soc 2013; 135:3904-14. [DOI: 10.1021/ja311282k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Robert N. Barnett
- School of Physics, Georgia Institute of Technology, Atlanta,
Georgia 30332-0430, United States
| | - Joshy Joseph
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Uzi Landman
- School of Physics, Georgia Institute of Technology, Atlanta,
Georgia 30332-0430, United States
| | - Gary B. Schuster
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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Abstract
Electrostatic interactions are crucial for both the accuracy and performance of atomistic biomolecular simulations. In this chapter we review well-established methods and current developments aiming at efficiency and accuracy. Specifically, we review the classical Ewald summations, particle-particle particle-method particle-method Ewald algorithms, multigrid, fast multipole, and local methods. We also highlight some recent developments targeting more accurate, yet classical, representation of the molecular charge distribution.
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11
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Yao XX, Ji CG, Xie DQ, Zhang JZ. Molecular dynamics study of DNA binding by INT-DBD under a polarized force field. J Comput Chem 2013; 34:1136-42. [DOI: 10.1002/jcc.23244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 11/08/2012] [Accepted: 12/30/2012] [Indexed: 11/06/2022]
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Abstract
This chapter provides an overview of the most common methods for including an explicit description of electronic polarization in molecular mechanics force fields: the induced point dipole, shell, and fluctuating charge models. The importance of including polarization effects in biomolecular simulations is discussed, and some of the most important achievements in the development of polarizable biomolecular force fields to date are highlighted.
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Affiliation(s)
- Hanne S Antila
- Department of Chemistry, Aalto University, Espoo, Finland
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Siriwong K, Voityuk AA. Electron transfer in DNA. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1102] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Lu Y, Lan Z, Thiel W. Monomeric adenine decay dynamics influenced by the DNA environment. J Comput Chem 2012; 33:1225-35. [DOI: 10.1002/jcc.22952] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 01/09/2012] [Accepted: 01/16/2012] [Indexed: 01/25/2023]
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Kabelác M, Zimandl F, Fessl T, Chval Z, Lankas F. A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics. Phys Chem Chem Phys 2010; 12:9677-84. [PMID: 20535407 DOI: 10.1039/c004020g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Molecular dynamics (MD) simulations and ab initio quantum chemical calculations were employed to investigate the structure, dynamics and interactions of the QSY 21 nonfluorescent quencher and the fluorescence dye Rhodamine 6G bound to a B-DNA decamer. For QSY 21, two binding motifs were observed. In the first motif, the central xanthene ring is stacked on one base of the adjacent cytosine-guanine DNA base pair, whereas one of the 2,3-dihydro-1-indolyl aromatic side rings is stacked on the other base. In the second motif, the QSY 21 stacking interaction with the DNA base pair is mediated only by one of the side rings. Several transitions between the motifs are observed during a MD simulation. The ab initio calculations show that none of these motifs is energetically preferred. Two binding motifs were found also for Rhodamine 6G, with the xanthene ring stacked predominantly either on the cytosine or on the guanine. These results suggest that the side rings of QSY 21 play a crucial role in its stacking on the DNA and indicate novel binding mode absent in the case of Rhodamine 6G, which lacks aromatic side rings.
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Affiliation(s)
- Martin Kabelác
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
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Affiliation(s)
- Joseph C. Genereux
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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Treesuwan W, Wittayanarakul K, Anthony NG, Huchet G, Alniss H, Hannongbua S, Khalaf AI, Suckling CJ, Parkinson JA, Mackay SP. A detailed binding free energy study of 2:1 ligand-DNA complex formation by experiment and simulation. Phys Chem Chem Phys 2009; 11:10682-93. [PMID: 20145812 DOI: 10.1039/b910574c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In 2004, we used NMR to solve the structure of the minor groove binder thiazotropsin A bound in a 2:1 complex to the DNA duplex, d(CGACTAGTCG)2. In this current work, we have combined theory and experiment to confirm the binding thermodynamics of this system. Molecular dynamics simulations that use polarizable or non-polarizable force fields with single and separate trajectory approaches have been used to explore complexation at the molecular level. We have shown that the binding process invokes large conformational changes in both the receptor and ligand, which is reflected by large adaptation energies. This is compensated for by the net binding free energy, which is enthalpy driven and entropically opposed. Such a conformational change upon binding directly impacts on how the process must be simulated in order to yield accurate results. Our MM-PBSA binding calculations from snapshots obtained from MD simulations of the polarizable force field using separate trajectories yield an absolute binding free energy (-15.4 kcal mol(-1)) very close to that determined by isothermal titration calorimetry (-10.2 kcal mol(-1)). Analysis of the major energy components reveals that favorable non-bonded van der Waals and electrostatic interactions contribute predominantly to the enthalpy term, whilst the unfavorable entropy appears to be driven by stabilization of the complex and the associated loss of conformational freedom. Our results have led to a deeper understanding of the nature of side-by-side minor groove ligand binding, which has significant implications for structure-based ligand development.
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Affiliation(s)
- Witcha Treesuwan
- Chemistry Department and Center of Nanotechnology, Kasetsart University, Bangkok 10900, Thailand
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Cieplak P, Dupradeau FY, Duan Y, Wang J. Polarization effects in molecular mechanical force fields. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:333102. [PMID: 21828594 PMCID: PMC4020598 DOI: 10.1088/0953-8984/21/33/333102] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component-polarization energy-and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations.
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Affiliation(s)
- Piotr Cieplak
- Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92120, USA
| | - François-Yves Dupradeau
- UMR CNRS 6219—Faculté de Pharmacie, Université de Picardie Jules Verne, 1 rue des Louvels, F-80037 Amiens, France
| | - Yong Duan
- Genome Center and Department of Applied Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Junmei Wang
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Boulevard, ND9.136, Dallas, TX 75390-9050, USA
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