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Lu Y, Shen Z, Xu Y, Lin H, Shen L, Jin Y, Guo Y, Lu J, Li L, Zhuang Y, Jin Y, Zhuang W, Huang W, Dong X, Dai H, Che J. Discovery of New Phenyltetrazolium Derivatives as Ferroptosis Inhibitors for Treating Ischemic Stroke: An Example Development from Free Radical Scavengers. J Med Chem 2024; 67:11712-11731. [PMID: 38996382 DOI: 10.1021/acs.jmedchem.4c00211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Ferroptosis is a promising therapeutic target for injury-related diseases, yet diversity in ferroptosis inhibitors remains limited. In this study, initial structure optimization led us to focus on the bond dissociation enthalpy (BDE) of the N-H bond and the residency time of radical scavengers in a phospholipid bilayer, which may play an important role in ferroptosis inhibition potency. This led to the discovery of compound D1, exhibiting potent ferroptosis inhibition, high radical scavenging, and moderate membrane permeability. D1 demonstrated significant neuroprotection in an oxygen glucose deprivation/reoxygenation (OGD/R) model and reduced infarct volume in an in vivo stroke model upon intravenous treatment. Further screening based on this strategy identified NecroX-7 and Eriodictyol-7-O-glucoside as novel ferroptosis inhibitors with highly polar structural characteristics. This approach bridges the gap between free radical scavengers and ferroptosis inhibitors, providing a foundation for research and insights into novel ferroptosis inhibitor development.
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Affiliation(s)
- Yang Lu
- Department of Pharmacy, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zexu Shen
- Department of Pharmacy, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Yaping Xu
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Haoran Lin
- Department of Pharmacy, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Liteng Shen
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yizhen Jin
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu Guo
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jialiang Lu
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Linjie Li
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuxin Zhuang
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuheng Jin
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Weihao Zhuang
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenhai Huang
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Institute of Materia Medica, Hangzhou Medical College, Hangzhou 310013, PR China
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310013, China
| | - Xiaowu Dong
- Department of Pharmacy, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China
- National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Haibin Dai
- Department of Pharmacy, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Jinxin Che
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China
- National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
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Sheng XH, Han LC, Gong A, Meng XS, Wang XH, Teng LS, Sun XH, Xu KC, Liu ZH, Wang T, Ma JP, Zhang L. Discovery of Novel Ortho-Aminophenol Derivatives Targeting Lipid Peroxidation with Potent Antiferroptotic Activities. J Med Chem 2024; 67:9536-9551. [PMID: 38822802 DOI: 10.1021/acs.jmedchem.4c00600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2024]
Abstract
The concept of ferroptosis inhibition has gained growing recognition as a promising therapeutic strategy for addressing a wide range of diseases. Here, we present the discovery of four series of ortho-aminophenol derivatives as potential ferroptosis inhibitors beginning with the endogenous substance 3-hydroxyanthranilic acid (3-HA) by employing quantum chemistry techniques, in vitro and in vivo assays. Our findings reveal that these ortho-aminophenol derivatives exhibit unique intra-H bond interactions, compelling ortho-amines to achieve enhanced alignment with the aromatic π-system, thereby expanding their activity. Notably, compounds from all four series display remarkable activity against RSL3-induced ferroptosis, showcasing an activity 100 times more than that of 3-HA. Furthermore, these compounds also demonstrate robust in vivo efficacy in protecting mice from kidney ischemia-reperfusion injury and acetaminophen-induced hepatotoxicity. In summary, we provide four distinct series of active scaffolds that significantly expand the chemical space of ferroptosis inhibitors, serving as valuable insights for future structural modifications.
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Affiliation(s)
- Xie-Huang Sheng
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Li-Cong Han
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Ao Gong
- Second Clinical Medical College of Shandong University of Traditional Chinese Medicine, Jinan 250001, China
| | - Xiang-Shuai Meng
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Xin-Hui Wang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Lin-Song Teng
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Tissue Engineering Laboratory, Department of Radiology, Shandong First Medical University, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan 250014, China
| | - Xiao-Han Sun
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Kuo-Chen Xu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Tissue Engineering Laboratory, Department of Radiology, Shandong First Medical University, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan 250014, China
| | - Zhao-Hua Liu
- The Model Animal Research Center, Cheeloo College of Medicine, Shandong University, Jinan 250014, China
| | - Ting Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Shandong First Medical University, Jinan 250014, China
| | - Jian-Ping Ma
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Lei Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Tissue Engineering Laboratory, Department of Radiology, Shandong First Medical University, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan 250014, China
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Sheng XH, Han LC, Ma XJ, Gong A, Hao MZ, Zhu H, Meng XS, Wang T, Sun CH, Ma JP, Zhang L. Design, synthesis, and biological evaluation of 2-amino-6-methyl-phenol derivatives targeting lipid peroxidation with potent anti-ferroptotic activities. Eur J Med Chem 2024; 264:115997. [PMID: 38056303 DOI: 10.1016/j.ejmech.2023.115997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023]
Abstract
The suppression of ferroptosis is emerging as a promising therapeutic strategy for effectively treating a wide range of diseases, including neurodegenerative disorders, organ ischemia-reperfusion injury, and inflammatory conditions. However, the clinical utility of ferroptosis inhibitors is significantly impeded by the limited availability of rational drug designs. In our previous study, we successfully unraveled the efficacy of ferrostatin-1 (Fer-1) attributed to the synergistic effect of its ortho-diamine (-NH) moiety. In this study, we present the discovery of the ortho-hydroxyl-amino moiety as a novel scaffold for ferroptosis inhibitors, employing quantum chemistry as well as in vitro and in vivo assays. 2-amino-6-methylphenol derivatives demonstrated remarkable inhibition of RSL3-induced ferroptosis, exhibiting EC50 values ranging from 25 nM to 207 nM. These compounds do not appear to modulate iron homeostasis or lipid reactive oxygen species (ROS) generation pathways. Nevertheless, they effectively prevent the accumulation of lipid peroxides in living cells. Furthermore, compound 13 exhibits good in vivo activities as it effectively protect mice from kidney ischemia-reperfusion injury. In summary, compound 13 has been identified as a potent ferroptosis inhibitor, warranting further investigation as a promising lead compound.
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Affiliation(s)
- Xie-Huang Sheng
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Li-Cong Han
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Xiao-Jie Ma
- Department of Rheumatology and Immunology, Shandong University of Traditional Chinese Medicine, Jinan, 250011, China
| | - Ao Gong
- Second Clinical Medical College of Shandong University of Traditional Chinese Medicine, Jinan, 250001, China
| | - Meng-Zhu Hao
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Hao Zhu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Xiang-Shuai Meng
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Ting Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250014, China
| | - Chang-Hua Sun
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Jian-Ping Ma
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China.
| | - Lei Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Tissue Engineering Laboratory, Department of Radiology, Shandong First Medical University, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, 250014, China.
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4
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Ćehić M, Nikšić-Franjić I. Reactions of a hydrogen atom with haloacetates in aqueous solutions: Computational evidence for proton-coupled electron transfer and competing mechanisms. J Comput Chem 2023; 44:2212-2222. [PMID: 37452597 DOI: 10.1002/jcc.27191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
A computational study of the mechanisms and kinetics of the aqueous reactions of a hydrogen atom with haloacetates is presented. Several mechanisms in the close competition are observed, such as proton-coupled electron transfer (PCET), hydrogen atom transfer (HAT), and halogen abstraction (XA). Computations predict that dechlorination takes place via PCET mechanisms and not via XA, as stated earlier, while XA is the fastest mechanism forIAc - . The reaction rate constants are reasonably well predicted within the theoretically most reliable canonical variational transition state theory with small curvature tunneling corrections and compared with the experimental ones. To reproduce the experimental rate constants of the debromination process it is necessary to include the PCET and XA cumulative values. Small curvature tunneling corrections to the rate constants are the highest for HAT and PCET mechanisms, up to 70 times larger than the Wigner, while variational effects for XA mechanisms are very small.
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Affiliation(s)
- Mirsada Ćehić
- Chair of Environmental Protection, University of Applied Sciences on Security and Safety, VSS, Zagreb, Croatia
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Bryenton KR, Adeleke AA, Dale SG, Johnson ER. Delocalization error: The greatest outstanding challenge in density‐functional theory. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kyle R. Bryenton
- Department of Physics and Atmospheric Science Dalhousie University Halifax Nova Scotia Canada
| | | | - Stephen G. Dale
- Queensland Micro‐ and Nanotechnology Centre Griffith University Nathan Queensland Australia
| | - Erin R. Johnson
- Department of Physics and Atmospheric Science Dalhousie University Halifax Nova Scotia Canada
- Department of Chemistry Dalhousie University Halifax Nova Scotia Canada
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Tzeliou CE, Mermigki MA, Tzeli D. Review on the QM/MM Methodologies and Their Application to Metalloproteins. Molecules 2022; 27:molecules27092660. [PMID: 35566011 PMCID: PMC9105939 DOI: 10.3390/molecules27092660] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/12/2022] [Accepted: 04/18/2022] [Indexed: 12/04/2022] Open
Abstract
The multiscaling quantum mechanics/molecular mechanics (QM/MM) approach was introduced in 1976, while the extensive acceptance of this methodology started in the 1990s. The combination of QM/MM approach with molecular dynamics (MD) simulation, otherwise known as the QM/MM/MD approach, is a powerful and promising tool for the investigation of chemical reactions’ mechanism of complex molecular systems, drug delivery, properties of molecular devices, organic electronics, etc. In the present review, the main methodologies in the multiscaling approaches, i.e., density functional theory (DFT), semiempirical methodologies (SE), MD simulations, MM, and their new advances are discussed in short. Then, a review on calculations and reactions on metalloproteins is presented, where particular attention is given to nitrogenase that catalyzes the conversion of atmospheric nitrogen molecules N₂ into NH₃ through the process known as nitrogen fixation and the FeMo-cofactor.
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Affiliation(s)
- Christina Eleftheria Tzeliou
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece; (C.E.T.); (M.A.M.)
| | - Markella Aliki Mermigki
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece; (C.E.T.); (M.A.M.)
| | - Demeter Tzeli
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece; (C.E.T.); (M.A.M.)
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 116 35 Athens, Greece
- Correspondence: ; Tel.: +30-210-727-4307
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Wang Y, Qin RC, Wang D, Liu CG. Reduction of N2 to NH3 catalyzed by a Keggin-type polyoxometalate-supported dual-atom catalyst. Inorg Chem Front 2022. [DOI: 10.1039/d1qi00752a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the present paper, a polyoxometalate-supported dual-atom catalyst has been designed for the nitrogen reduction reaction based on our density functional theory calculations.
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Affiliation(s)
- Yu Wang
- College of Chemical Engineering, Northeast Electric Power University, Jilin City, 132012, P. R. China
- State Key Lab of Urban Water Resource and Environment, School of Science, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
| | - Rui-Cheng Qin
- Department of Chemistry, Faculty of Science, Beihua University, Jilin City, 132013, P. R. China
| | - Dan Wang
- Department of Chemistry, Faculty of Science, Beihua University, Jilin City, 132013, P. R. China
| | - Chun-Guang Liu
- Department of Chemistry, Faculty of Science, Beihua University, Jilin City, 132013, P. R. China
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Brito J, Hlushko H, Abbott A, Aliakseyeu A, Hlushko R, Sukhishvili SA. Integrating Antioxidant Functionality into Polymer Materials: Fundamentals, Strategies, and Applications. ACS APPLIED MATERIALS & INTERFACES 2021; 13:41372-41395. [PMID: 34448558 DOI: 10.1021/acsami.1c08061] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
While antioxidants are widely known as natural components of healthy food and drinks or as additives to commercial polymer materials to prevent their degradation, recent years have seen increasing interest in enhancing the antioxidant functionality of newly developed polymer materials and coatings. This paper provides a critical overview and comparative analysis of multiple ways of integrating antioxidants within diverse polymer materials, including bulk films, electrospun fibers, and self-assembled coatings. Polyphenolic antioxidant moieties with varied molecular architecture are in the focus of this Review, because of their abundance, nontoxic nature, and potent antioxidant activity. Polymer materials with integrated polyphenolic functionality offer opportunities and challenges that span from the fundamentals to their applications. In addition to the traditional blending of antioxidants with polymer materials, developments in surface grafting and assembly via noncovalent interaction for controlling localization versus migration of antioxidant molecules are discussed. The versatile chemistry of polyphenolic antioxidants offers numerous possibilities for programmed inclusion of these molecules in polymer materials using not only van der Waals interactions or covalent tethering to polymers, but also via their hydrogen-bonding assembly with neutral molecules. An understanding and rational use of interactions of polyphenol moieties with surrounding molecules can enable precise control of concentration and retention versus delivery rate of antioxidants in polymer materials that are critical in food packaging, biomedical, and environmental applications.
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Affiliation(s)
- Jordan Brito
- Department of Materials Science & Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Hanna Hlushko
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Ashleigh Abbott
- Department of Materials Science & Engineering, Missouri University of Science & Technology, Rolla, Missouri 65409, United States
| | - Aliaksei Aliakseyeu
- Department of Materials Science & Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Raman Hlushko
- Department of Materials Science & Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Svetlana A Sukhishvili
- Department of Materials Science & Engineering, Texas A&M University, College Station, Texas 77843, United States
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9
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Density functional theory studies of the antioxidants-a review. J Mol Model 2021; 27:271. [PMID: 34463834 DOI: 10.1007/s00894-021-04891-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/23/2021] [Indexed: 10/20/2022]
Abstract
The following review article attempts to compare the antioxidant activity of the compounds. For this purpose, density functional theory/Becke three-parameter Lee-Yang-Parr (DFT/B3LYP) methodology was carried out instead of using pharmacological methodologies because of economic benefits and high accuracy. This methodology filtrates the compounds with the lowest antioxidant activity. At first, the Koopmans' theorem was carried out to calculate some descriptors to compare antioxidants. The energy of the highest occupied molecular orbitals (HOMO) was accepted as the best indicator, and then some studies confirmed that the highest occupied molecular orbital/lowest unoccupied molecular orbital (HOMO-LUMO) energy gap is the more precise descriptor. Although it would be better to compare spin density distribution (SDD) on the oxygen of the corresponding radical in the polarizable continuum model (PCM) to evaluate their capability to chain reaction inhibition. Next, it was mentioned that in the multi-target directed ligands (MTDLs), the antioxidant is connected to other moieties in para positions to create better antioxidants or novel hybrid compounds. Indeed, SDD was introduced as a descriptor for MTDL antioxidant effectiveness. Then, the relation between antioxidants and aromaticity was investigated. The more the aromaticity of an antioxidant, the more stable the corresponding radical is. Subsequently, in preferred antioxidant activity, it was defined that the hydrogen atom transfer (HAT) mechanism is more favored in metabolism phase I. It has been seen that the solvent model can change the antioxidant mechanism. Therefore, the solvent model is more important than the chemical structure of antioxidants, and an ideal antioxidant should be evaluated in PCM for pharmacological evaluations.
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10
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Price AJA, Bryenton KR, Johnson ER. Requirements for an accurate dispersion-corrected density functional. J Chem Phys 2021; 154:230902. [PMID: 34241263 DOI: 10.1063/5.0050993] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Post-self-consistent dispersion corrections are now the norm when applying density-functional theory to systems where non-covalent interactions play an important role. However, there is a wide range of base functionals and dispersion corrections available from which to choose. In this work, we opine on the most desirable requirements to ensure that both the base functional and dispersion correction, individually, are as accurate as possible for non-bonded repulsion and dispersion attraction. The base functional should be dispersionless, numerically stable, and involve minimal delocalization error. Simultaneously, the dispersion correction should include finite damping, higher-order pairwise dispersion terms, and electronic many-body effects. These criteria are essential for avoiding reliance on error cancellation and obtaining correct results from correct physics.
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Affiliation(s)
- Alastair J A Price
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyle R Bryenton
- Department of Physics and Atmospheric Science, Dalhousie University, 6310 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
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12
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Chazelas P, Steichen C, Favreau F, Trouillas P, Hannaert P, Thuillier R, Giraud S, Hauet T, Guillard J. Oxidative Stress Evaluation in Ischemia Reperfusion Models: Characteristics, Limits and Perspectives. Int J Mol Sci 2021; 22:ijms22052366. [PMID: 33673423 PMCID: PMC7956779 DOI: 10.3390/ijms22052366] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/14/2022] Open
Abstract
Ischemia reperfusion injury is a complex process consisting of a seemingly chaotic but actually organized and compartmentalized shutdown of cell function, of which oxidative stress is a key component. Studying oxidative stress, which results in an imbalance between reactive oxygen species (ROS) production and antioxidant defense activity, is a multi-faceted issue, particularly considering the double function of ROS, assuming roles as physiological intracellular signals and as mediators of cellular component damage. Herein, we propose a comprehensive overview of the tools available to explore oxidative stress, particularly in the study of ischemia reperfusion. Applying chemistry as well as biology, we present the different models currently developed to study oxidative stress, spanning the vitro and the silico, discussing the advantages and the drawbacks of each set-up, including the issues relating to the use of in vitro hypoxia as a surrogate for ischemia. Having identified the limitations of historical models, we shall study new paradigms, including the use of stem cell-derived organoids, as a bridge between the in vitro and the in vivo comprising 3D intercellular interactions in vivo and versatile pathway investigations in vitro. We shall conclude this review by distancing ourselves from "wet" biology and reviewing the in silico, computer-based, mathematical modeling, and numerical simulation options: (a) molecular modeling with quantum chemistry and molecular dynamic algorithms, which facilitates the study of molecule-to-molecule interactions, and the integration of a compound in a dynamic environment (the plasma membrane...); (b) integrative systemic models, which can include many facets of complex mechanisms such as oxidative stress or ischemia reperfusion and help to formulate integrated predictions and to enhance understanding of dynamic interaction between pathways.
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Affiliation(s)
- Pauline Chazelas
- Maintenance Myélinique et Neuropathies Périphériques, Université de Limoges, EA 6309, 87032 Limoges, France; (P.C.); (F.F.)
- Laboratoire de Biochimie et Génétique Moléculaire, CHU de Limoges, 87042 Limoges, France
| | - Clara Steichen
- INSERM U1082, IRTOMIT, 86021 Poitiers, France; (C.S.); (P.H.); (R.T.); (S.G.); (T.H.)
- Faculté de Médecine et de Pharmacie, Université de Poitiers, 86074 Poitiers, France
| | - Frédéric Favreau
- Maintenance Myélinique et Neuropathies Périphériques, Université de Limoges, EA 6309, 87032 Limoges, France; (P.C.); (F.F.)
- Laboratoire de Biochimie et Génétique Moléculaire, CHU de Limoges, 87042 Limoges, France
| | - Patrick Trouillas
- INSERM U1248, IPPRITT, Université de Limoges, 87032 Limoges, France;
- RCPTM, University Palacký of Olomouc, 771 47 Olomouc, Czech Republic
| | - Patrick Hannaert
- INSERM U1082, IRTOMIT, 86021 Poitiers, France; (C.S.); (P.H.); (R.T.); (S.G.); (T.H.)
| | - Raphaël Thuillier
- INSERM U1082, IRTOMIT, 86021 Poitiers, France; (C.S.); (P.H.); (R.T.); (S.G.); (T.H.)
- Faculté de Médecine et de Pharmacie, Université de Poitiers, 86074 Poitiers, France
- Service de Biochimie, CHU de Poitiers, 86021 Poitiers, France
| | - Sébastien Giraud
- INSERM U1082, IRTOMIT, 86021 Poitiers, France; (C.S.); (P.H.); (R.T.); (S.G.); (T.H.)
- Service de Biochimie, CHU de Poitiers, 86021 Poitiers, France
| | - Thierry Hauet
- INSERM U1082, IRTOMIT, 86021 Poitiers, France; (C.S.); (P.H.); (R.T.); (S.G.); (T.H.)
- Faculté de Médecine et de Pharmacie, Université de Poitiers, 86074 Poitiers, France
- Service de Biochimie, CHU de Poitiers, 86021 Poitiers, France
- FHU SUPORT Survival Optimization in Organ Transplantation, 86021 Poitiers, France
- IBiSA Plateforme Modélisation Préclinique-Innovations Chirurgicale et Technologique (MOPICT), Do-maine Expérimental du Magneraud, 17700 Surgères, France
| | - Jérôme Guillard
- UMR CNRS 7285 IC2MP, Team 5 Chemistry, Université de Poitiers, 86073 Poitiers, France
- Correspondence: ; Tel.: +33-5-49-44-38-59
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13
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Amić A, Milenković D, Marković Z, Cagardová D, Rodríguez-Guerra Pedregal J, Dimitrić Marković JM. Impact of the phenolic O–H vs. C-ring C–H bond cleavage on the antioxidant potency of dihydrokaempferol. NEW J CHEM 2021. [DOI: 10.1039/d1nj00690h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to correctly estimate hydrogen atom abstraction from polyphenols, kinetic analysis including suitable tunneling effects should be mandatory.
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Affiliation(s)
- Ana Amić
- Department of Chemistry
- Josip Juraj Strossmayer University of Osijek
- 31000 Osijek
- Croatia
| | - Dejan Milenković
- Institute for Information Technologies
- Department of Science
- University of Kragujevac
- 34000 Kragujevac
- Serbia
| | - Zoran Marković
- Institute for Information Technologies
- Department of Science
- University of Kragujevac
- 34000 Kragujevac
- Serbia
| | - Denisa Cagardová
- Institute of Physical Chemistry and Chemical Physics
- Department of Chemical Physics
- Slovak University of Technology in Bratislava
- SK-812 37 Bratislava
- Slovak Republic
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14
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Handojo L, Zunita M, Indarto A. Molecular Study of Phenyl Formation on ZSM-5: Comparison between Surface and Gas Phase Reactions. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2018.1441883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Lienda Handojo
- Department of Chemical Engineering, Institut Teknologi Bandung, Bandung, Indonesia
| | - Megawati Zunita
- Department of Chemical Engineering, Institut Teknologi Bandung, Bandung, Indonesia
| | - Antonius Indarto
- Department of Chemical Engineering, Institut Teknologi Bandung, Bandung, Indonesia
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15
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Torralba-Sanchez TL, Bylaska EJ, Salter-Blanc AJ, Meisenheimer DE, Lyon MA, Tratnyek PG. Reduction of 1,2,3-trichloropropane (TCP): pathways and mechanisms from computational chemistry calculations. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:606-616. [PMID: 31990012 DOI: 10.1039/c9em00557a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The characteristic pathway for degradation of halogenated aliphatic compounds in groundwater or other environments with relatively anoxic and/or reducing conditions is reductive dechlorination. For 1,2-dihalocarbons, reductive dechlorination can include hydrogenolysis and dehydrohalogenation, the relative significance of which depends on various structural and energetic factors. To better understand how these factors influence the degradation rates and products of the lesser halogenated hydrocarbons (in contrast to the widely studied per-halogenated hydrocarbons, like trichloroethylene and carbon tetrachloride), density functional theory calculations were performed to compare all of the possible pathways for reduction and elimination of 1,2,3-trichloropropane (TCP). The results showed that free energies of each species and reaction step are similar for all levels of theory, although B3LYP differed from the others. In all cases, the reaction coordinate diagrams suggest that β-elimination of TCP to allyl chloride followed by hydrogenolysis to propene is the thermodynamically favored pathway. This result is consistent with experimental results obtained using TCP, 1,2-dichloropropane, and 1,3-dichloropropane in batch experiments with zerovalent zinc (Zn0, ZVI) as a reductant.
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Affiliation(s)
- Tifany L Torralba-Sanchez
- OHSU-PSU School of Public Health, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
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16
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Yang J, Peng XL, Sun ZZ, Feng S, Ding WL, He HY, Li ZS. Understanding the effects of the co-sensitizing ratio on the surface potential, electron injection efficiency, and Förster resonance energy transfer. Phys Chem Chem Phys 2020; 22:5568-5576. [DOI: 10.1039/c9cp06028f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multiple absorbers that function in different absorption regions (near infra-red (NIR) and UV-Visible (UV-Vis)) have been widely used in solar cell applications to enhance the light-harvesting.
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Affiliation(s)
- Jie Yang
- Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials
- Key Laboratory of Cluster Science of Ministry of Education
- School of Chemistry
- Beijing Key Laboratory for Chemical Power Source and Green Catalysis
- School of Chemistry
| | - Xing-Liang Peng
- MOE Key Laboratory of Organic OptoElectronics and Molecular Engineering
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- People's Republic of China
| | - Zhu-Zhu Sun
- Energy-Saving Building Materials Innovative Collaboration Center of Henan Province
- Xinyang Normal University
- Xinyang
- China
| | - Shuai Feng
- College of Chemistry and Chemical Engineering
- Taishan University
- Taian
- China
| | - Wei-Lu Ding
- Beijing Key Laboratory of Ionic Liquids Clean Process
- CAS Key Laboratory of Green Process and Engineering
- State Key Laboratory of Multiphase Complex Systems
- Institute of Process Engineering
- Chinese Academy of Sciences
| | - Hong-Yan He
- Beijing Key Laboratory of Ionic Liquids Clean Process
- CAS Key Laboratory of Green Process and Engineering
- State Key Laboratory of Multiphase Complex Systems
- Institute of Process Engineering
- Chinese Academy of Sciences
| | - Ze-Sheng Li
- Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials
- Key Laboratory of Cluster Science of Ministry of Education
- School of Chemistry
- Beijing Key Laboratory for Chemical Power Source and Green Catalysis
- School of Chemistry
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17
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Li YZ, Zhou XL, Huo BQ, Chen DZ, Liu ZH, Sheng XH. Reactions of the Lipid Hydroperoxides With Aminic Antioxidants: The Influence of Stereoelectronic and Resonance Effects on Hydrogen Atom Transfer. Front Chem 2019; 7:850. [PMID: 31921773 PMCID: PMC6927943 DOI: 10.3389/fchem.2019.00850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/22/2019] [Indexed: 01/31/2023] Open
Abstract
Aminic radical-trapping antioxidants (RTAs), as one of the most important antioxidants, have not received sufficient attention yet. But, an increasing number of aminic RTAs have been identified as ferroptosis inhibitors in recent years, which can potentially mediate many pathological states including inflammation, cancer, neurodegenerative disease, as well as ocular and kidney degeneration. This highlights the importance of aminic RTAs in the field of medicine. Herein, we systematically explored the radical scavenging mechanism of aminic RTAs with a quantum chemical method, particularly emphasizing the role of stereoelectronic factors and resonance factors on the transfer of H-atom and the stability to one-electron oxidation. These theoretical results elucidate the diversity of free radical scavenging mechanisms for aminic RTAs, and has significant implications for the rational design of new aminic RTAs.
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Affiliation(s)
- Yu-Zhen Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, China
| | - Xiao-Lu Zhou
- Key Laboratory of Systems Bioengineering, Ministry of Education, Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Bao-Qi Huo
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, China
| | - De-Zhan Chen
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, China
| | - Zhao-Hua Liu
- Center for New Drug Evaluation, School of Pharmaceutical Sciences of Shandong University, Jinan, China
| | - Xie-Huang Sheng
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, China
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18
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Sheng XH, Cui CC, Shan C, Li YZ, Sheng DH, Sun B, Chen DZ. O-Phenylenediamine: a privileged pharmacophore of ferrostatins for radical-trapping reactivity in blocking ferroptosis. Org Biomol Chem 2018; 16:3952-3960. [DOI: 10.1039/c8ob00546j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ferroptosis is a non-apoptotic, iron dependent form of regulated cell death that is characterized by the accumulation of lipid hydroperoxides.
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Affiliation(s)
- Xie-Huang Sheng
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Cheng-Cheng Cui
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chao Shan
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Yu-Zhen Li
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Duo-Hong Sheng
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- P. R. China
| | - Bin Sun
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - De-Zhan Chen
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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19
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Aazaad B, Lakshmipathi S. Reaction of Pentanol isomers with OH radical – A theoretical perspective. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1414966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Basheer Aazaad
- Department of Physics, Bharathiar University, Coimbatore, India
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20
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Hu YC, Ding WL, Peng XL, Li ZS. Extending donor size in D-A-π-A organic dye for dye sensitized solar cells: Anti-aggregation and improving electron injection. J Mol Graph Model 2017; 77:322-329. [DOI: 10.1016/j.jmgm.2017.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/30/2017] [Accepted: 09/01/2017] [Indexed: 10/18/2022]
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21
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Zhang H, Wu W, Mo Y. Study of proton-coupled electron transfer (PCET) with four explicit diabatic states at the ab initio level. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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22
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23
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Vilella-Arribas L, García-Melchor M, Balcells D, Lledós A, López JA, Sancho S, Villarroya BE, del Río MP, Ciriano MA, Tejel C. Rhodium Complexes Promoting C−O Bond Formation in Reactions with Oxygen: The Role of Superoxo Species. Chemistry 2017; 23:5232-5243. [DOI: 10.1002/chem.201605959] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Laia Vilella-Arribas
- Departament de Química; Universitat Autònoma de Barcelona; Cerdanyola del Vallès 08193 Barcelona Spain
| | - Max García-Melchor
- School of Chemistry; Trinity College Dublin; College Green Dublin 2 Ireland
| | - David Balcells
- Centre for Theoretical and Computational Chemistry (CTCC) and Department of Chemistry; University of Oslo; P.O. Box 1033, Blindern 0315 Oslo Norway
| | - Agustí Lledós
- Departament de Química; Universitat Autònoma de Barcelona; Cerdanyola del Vallès 08193 Barcelona Spain
| | - José A. López
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálsis Homogénea (ISQCH); CSIC Universidad de Zaragoza; Pedro Cerbuna 12 50009 Zaragoza Spain
| | - Sofía Sancho
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálsis Homogénea (ISQCH); CSIC Universidad de Zaragoza; Pedro Cerbuna 12 50009 Zaragoza Spain
| | - B. Eva Villarroya
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálsis Homogénea (ISQCH); CSIC Universidad de Zaragoza; Pedro Cerbuna 12 50009 Zaragoza Spain
| | - M. Pilar del Río
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálsis Homogénea (ISQCH); CSIC Universidad de Zaragoza; Pedro Cerbuna 12 50009 Zaragoza Spain
| | - Miguel A. Ciriano
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálsis Homogénea (ISQCH); CSIC Universidad de Zaragoza; Pedro Cerbuna 12 50009 Zaragoza Spain
| | - Cristina Tejel
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálsis Homogénea (ISQCH); CSIC Universidad de Zaragoza; Pedro Cerbuna 12 50009 Zaragoza Spain
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25
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Sheng X, Shan C, Liu J, Yang J, Sun B, Chen D. Theoretical insights into the mechanism of ferroptosis suppression via inactivation of a lipid peroxide radical by liproxstatin-1. Phys Chem Chem Phys 2017; 19:13153-13159. [DOI: 10.1039/c7cp00804j] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ferroptosis is a recently discovered iron-dependent form of non-apoptotic cell death caused by the accumulation of membrane lipid peroxidation products, which is involved in various pathological conditions of the brain, kidneys, liver and heart.
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Affiliation(s)
- Xiehuang Sheng
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chao Shan
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Jianbiao Liu
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Jintong Yang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Bin Sun
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Dezhan Chen
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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26
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Ljubić I, Sabljić A, Bonifačić M. Reactions of 2-Propanol Radical with Halogenated Organics in Aqueous Solution: Theoretical Evidence for Proton-Coupled Electron Transfer and Competing Mechanisms. J Phys Chem B 2016; 120:11810-11820. [DOI: 10.1021/acs.jpcb.6b08765] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ivan Ljubić
- Department of Physical
Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10000 Zagreb, Croatia
| | - Aleksandar Sabljić
- Department of Physical
Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10000 Zagreb, Croatia
| | - Marija Bonifačić
- Department of Physical
Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10000 Zagreb, Croatia
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27
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Jiang YY, Man X, Bi S. Advances in theoretical study on transition-metal-catalyzed C−H activation. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0330-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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28
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Aazaad B, Mano Priya A, Senthilkumar L. Addition and abstraction reaction mechanism of 2,4,5-trimethylphenol with OH radical – A first principle study. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Miller DC, Tarantino KT, Knowles RR. Proton-Coupled Electron Transfer in Organic Synthesis: Fundamentals, Applications, and Opportunities. Top Curr Chem (Cham) 2016; 374:30. [PMID: 27573270 PMCID: PMC5107260 DOI: 10.1007/s41061-016-0030-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/21/2016] [Indexed: 10/21/2022]
Abstract
Proton-coupled electron transfers (PCETs) are unconventional redox processes in which both protons and electrons are exchanged, often in a concerted elementary step. While PCET is now recognized to play a central a role in biological redox catalysis and inorganic energy conversion technologies, its applications in organic synthesis are only beginning to be explored. In this chapter, we aim to highlight the origins, development, and evolution of the PCET processes most relevant to applications in organic synthesis. Particular emphasis is given to the ability of PCET to serve as a non-classical mechanism for homolytic bond activation that is complimentary to more traditional hydrogen atom transfer processes, enabling the direct generation of valuable organic radical intermediates directly from their native functional group precursors under comparatively mild catalytic conditions. The synthetically advantageous features of PCET reactivity are described in detail, along with examples from the literature describing the PCET activation of common organic functional groups.
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Affiliation(s)
- David C Miller
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Kyle T Tarantino
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Robert R Knowles
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.
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31
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Zhao S, Zhang RB, Li ZS. A new understanding towards the reactivity of DNA peroxy radicals. Phys Chem Chem Phys 2016; 18:23763-8. [DOI: 10.1039/c6cp04720c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
New radical reaction paths for the formation of DNA oxidation products are suggested, which are strongly different from the previously suggested paths with the tetraoxide intermediate.
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Affiliation(s)
- Shuang Zhao
- School of Chemistry
- Beijing Institute of Technology
- 100081 Beijing
- China
| | - Ru-bo Zhang
- School of Chemistry
- Beijing Institute of Technology
- 100081 Beijing
- China
| | - Ze-sheng Li
- School of Chemistry
- Beijing Institute of Technology
- 100081 Beijing
- China
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32
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Pabis A, Paluch P, Szala J, Paneth P. A DFT Study of the Kinetic Isotope Effects on the Competing SN2 and E2 Reactions between Hypochlorite Anion and Ethyl Chloride. J Chem Theory Comput 2015; 5:33-6. [PMID: 26609818 DOI: 10.1021/ct800412h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Kinetic isotope effects (KIEs) on the two alternative reactions, SN2 and E2, between hypochlorite anion and ethyl chloride in water have been studied theoretically using B3LYP and M06-2X functionals. It has been found that the latter one yields more correct geometries and energetics. Although, in the qualitative sense, KIEs obtained using both DFT functionals are in agreement, interpretation of some of them, like (18)O-KIE in the present case, leads to different mechanistic conclusions.
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Affiliation(s)
- Anna Pabis
- Faculty of Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Piotr Paluch
- Faculty of Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Joanna Szala
- Faculty of Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Piotr Paneth
- Faculty of Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
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33
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Abstract
An enormous variety of biological redox reactions are accompanied by changes in proton content at enzyme active sites, in their associated cofactors, in substrates and/or products, and between protein interfaces. Understanding this breadth of reactivity is an ongoing chemical challenge. A great many workers have developed and investigated biomimetic model complexes to build new ways of thinking about the mechanistic underpinnings of such complex biological proton-coupled electron transfer (PCET) reactions. Of particular importance are those model reactions that involve transfer of one proton (H(+)) and one electron (e(-)), which is equivalent to transfer of a hydrogen atom (H(•)). In this Current Topic, we review key concepts in PCET reactivity and describe important advances in biomimetic PCET chemistry, with a special emphasis on research that has enhanced efforts to understand biological PCET reactions.
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Affiliation(s)
- Jeffrey J. Warren
- Simon Fraser University, Department of Chemistry, 8888 University Drive, Burnaby BC, Canada V5A 1S6
| | - James M. Mayer
- Yale University, Department of Chemistry, P.O. Box 208107, 225 Prospect Street, New Haven, CT 06520-8107
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Wang H, Chen X, Fang W. Excited-state proton coupled electron transfer between photolyase and the damaged DNA through water wire: a photo-repair mechanism. Phys Chem Chem Phys 2014; 16:25432-41. [PMID: 25341360 DOI: 10.1039/c4cp04130e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photolyase enzyme absorbs blue light to repair damaged DNA through a cyclic electron transfer reaction. A description of the underlying mechanism has proven to be a challenging issue for both experimental and theoretical studies. In the present work, combined CASPT2//CASSCF/AMBER (QM/MM) calculations have been performed for damaged DNA in photolyase. A proton-coupled electron transfer (PCET) mechanism has been determined for restoring cyclobutane pyrimidine dimer (CPD) to two normal thymine bases by irradiation of photolyase. A well-defined water wire between FADH(-) and CPD was determined as a bridge to assist the PCET process within FADH(-) and thereby trigger the forward electron transfer to CPD. The subsequent CPD splitting and the alternation of the H-bond pattern proceed in a concerted way, which makes the productive backward electron transfer occur on an ultrafast timescale. A local minimum of SCT((1)ππ*)-LMin was identified on the pathway of the futile backward electron transfer (BET), which is stabilized by the strong H-bond interaction between the water wire and CPD. As a result, the futile BET process is endothermic by ∼18.0 kcal mol(-1), which is responsible for a 2.4 ns timescale inferred experimentally for the futile BET process. Besides the unbiased interpretation for the majority of the experimental findings, the present study provides a new excited-state PCET mechanism, which leads to a significant step toward a deeper understanding of the photo-repair process of damaged-DNA by the photolyase enzyme.
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Affiliation(s)
- Hongjuan Wang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, Department of Chemistry, Beijing Normal University, Xin-wai-da-jie No. 19, Beijing, 100875, China.
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35
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Chen X, Ma G, Sun W, Dai H, Xiao D, Zhang Y, Qin X, Liu Y, Bu Y. Water Promoting Electron Hole Transport between Tyrosine and Cysteine in Proteins via a Special Mechanism: Double Proton Coupled Electron Transfer. J Am Chem Soc 2014; 136:4515-24. [DOI: 10.1021/ja406340z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xiaohua Chen
- School
of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, China
| | - Guangcai Ma
- School
of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Weichao Sun
- School
of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, China
| | - Hongjing Dai
- School
of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, China
| | - Dong Xiao
- School
of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, China
| | - Yanfang Zhang
- School
of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, China
| | - Xin Qin
- School
of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, China
| | - Yongjun Liu
- School
of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yuxiang Bu
- School
of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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36
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Inagaki T, Yamamoto T. Critical Role of Deep Hydrogen Tunneling to Accelerate the Antioxidant Reaction of Ubiquinol and Vitamin E. J Phys Chem B 2014; 118:937-50. [DOI: 10.1021/jp410263f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Taichi Inagaki
- Department of
Chemistry, Graduate School of
Science, Kyoto University, Kyoto 606-8502, Japan
| | - Takeshi Yamamoto
- Department of
Chemistry, Graduate School of
Science, Kyoto University, Kyoto 606-8502, Japan
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37
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Anouar EH, Raweh S, Bayach I, Taha M, Baharudin MS, Di Meo F, Hasan MH, Adam A, Ismail NH, Weber JFF, Trouillas P. Antioxidant properties of phenolic Schiff bases: structure-activity relationship and mechanism of action. J Comput Aided Mol Des 2013; 27:951-64. [PMID: 24243063 DOI: 10.1007/s10822-013-9692-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 11/09/2013] [Indexed: 11/27/2022]
Abstract
Phenolic Schiff bases are known for their diverse biological activities and ability to scavenge free radicals. To elucidate (1) the structure-antioxidant activity relationship of a series of thirty synthetic derivatives of 2-methoxybezohydrazide phenolic Schiff bases and (2) to determine the major mechanism involved in free radical scavenging, we used density functional theory calculations (B3P86/6-31+(d,p)) within polarizable continuum model. The results showed the importance of the bond dissociation enthalpies (BDEs) related to the first and second (BDEd) hydrogen atom transfer (intrinsic parameters) for rationalizing the antioxidant activity. In addition to the number of OH groups, the presence of a bromine substituent plays an interesting role in modulating the antioxidant activity. Theoretical thermodynamic and kinetic studies demonstrated that the free radical scavenging by these Schiff bases mainly proceeds through proton-coupled electron transfer rather than sequential proton loss electron transfer, the latter mechanism being only feasible at relatively high pH.
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Affiliation(s)
- El Hassane Anouar
- Atta-ur-Rahman Institute for Natural Product Discovery (RiND), Universiti Teknologi MARA, Kampus Puncak Alam, 42300 Bandar Puncak Alam, Shah Alam, Selangor DE, Malaysia,
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38
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Usharani D, Lacy DC, Borovik AS, Shaik S. Dichotomous hydrogen atom transfer vs proton-coupled electron transfer during activation of X-H bonds (X = C, N, O) by nonheme iron-oxo complexes of variable basicity. J Am Chem Soc 2013; 135:17090-104. [PMID: 24124906 PMCID: PMC3876471 DOI: 10.1021/ja408073m] [Citation(s) in RCA: 191] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We describe herein the hydrogen-atom transfer (HAT)/proton-coupled electron-transfer (PCET) reactivity for Fe(IV)-oxo and Fe(III)-oxo complexes (1-4) that activate C-H, N-H, and O-H bonds in 9,10-dihydroanthracene (S1), dimethylformamide (S2), 1,2-diphenylhydrazine (S3), p-methoxyphenol (S4), and 1,4-cyclohexadiene (S5). In 1-3, the iron is pentacoordinated by tris[N'-tert-butylureaylato)-N-ethylene]aminato ([H3buea](3-)) or its derivatives. These complexes are basic, in the order 3 ≫ 1 > 2. Oxidant 4, [Fe(IV)N4Py(O)](2+) (N4Py: N,N-bis(2-pyridylmethyl)bis(2-pyridyl)methylamine), is the least basic oxidant. The DFT results match experimental trends and exhibit a mechanistic spectrum ranging from concerted HAT and PCET reactions to concerted-asynchronous proton transfer (PT)/electron transfer (ET) mechanisms, all the way to PT. The singly occupied orbital along the O···H···X (X = C, N, O) moiety in the TS shows clearly that in the PCET cases, the electron is transferred separately from the proton. The Bell-Evans-Polanyi principle does not account for the observed reactivity pattern, as evidenced by the scatter in the plot of calculated barrier vs reactions driving forces. However, a plot of the deformation energy in the TS vs the respective barrier provides a clear signature of the HAT/PCET dichotomy. Thus, in all C-H bond activations, the barrier derives from the deformation energy required to create the TS, whereas in N-H/O-H bond activations, the deformation energy is much larger than the corresponding barrier, indicating the presence of a stabilizing interaction between the TS fragments. A valence bond model is used to link the observed results with the basicity/acidity of the reactants.
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Affiliation(s)
- Dandamudi Usharani
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - David C. Lacy
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - A. S. Borovik
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Sason Shaik
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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39
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Karasulu B, Patil M, Thiel W. Amine oxidation mediated by lysine-specific demethylase 1: quantum mechanics/molecular mechanics insights into mechanism and role of lysine 661. J Am Chem Soc 2013; 135:13400-13. [PMID: 23988016 DOI: 10.1021/ja403582u] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report classical molecular dynamics (MD) simulations and combined quantum mechanics/molecular mechanics (QM/MM) calculations to elucidate the catalytic mechanism of the rate-determining amine oxidation step in the lysine-specific demethylase 1 (LSD1)-catalyzed demethylation of the histone tail lysine (H3K4), with flavin adenine dinucleotide (FAD) acting as cofactor. The oxidation of substrate lysine (sLys) involves the cleavage of an α-CH bond accompanied by the transfer of a hydride ion equivalent to FAD, leading to an imine intermediate. This hydride transfer pathway is shown to be clearly favored for sLys oxidation over other proposed mechanisms, including the radical (or single-electron transfer) route as well as carbanion and polar-nucleophilic mechanisms. MD simulations on six NVT ensembles (covering different protonation states of sLys and K661 as well as the K661M mutant) identify two possible orientations of the reacting sLys and FAD subunits (called "downward" and "upward"). Calculations at the QM(B3LYP-D/6-31G*)/CHARMM22 level provide molecular-level insights into the mechanism, helping to understand how LSD1 achieves the activation of the rather inert methyl-CH bond in a metal-free environment. Factors such as proper alignment of sLys (downward orientation), transition-state stabilization (due to the protein environment and favorable orbital interactions), and product stabilization via adduct formation are found to be crucial for facilitating the oxidative α-CH bond cleavage. The current study also sheds light on the role of important active-site residues (Y761, K661, and W695) and of the conserved water-bridge motif. The steric influence of Y761 helps to position the reaction partners properly, K661 is predicted to get deprotonated prior to substrate binding and to act as an active-site base that accepts a proton from sLys to enable the subsequent amine oxidation, and the water bridge that is stabilized by K661 and W695 mediates this proton transfer.
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Affiliation(s)
- Bora Karasulu
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
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40
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Di Meo F, Lemaur V, Cornil J, Lazzaroni R, Duroux JL, Olivier Y, Trouillas P. Free radical scavenging by natural polyphenols: atom versus electron transfer. J Phys Chem A 2013; 117:2082-92. [PMID: 23418927 DOI: 10.1021/jp3116319] [Citation(s) in RCA: 176] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polyphenols (synthetically modified or directly provided by human diet) scavenge free radicals by H-atom transfer and may thus decrease noxious effects due to oxidative stress. Free radical scavenging by polyphenols has been widely theoretically studied from the thermodynamic point of view whereas the kinetic point of view has been much less addressed. The present study describes kinetic-based structure-activity relationship for quercetin. This compound is very characteristic of the wide flavonoid subclass of polyphenols. H-atom transfer is a mechanism based on either atom or electron transfer. This is analyzed here by quantum chemical calculations, which support the knowledge acquired from experimental studies. The competition between the different processes is discussed in terms of the nature of the prereaction complexes, the pH, the formation of activated-deprotonated forms, and the atom- and electron-transfer efficiency. The role of the catechol moiety and the 3-OH group of quercetin as scavengers of different types of free radicals (CH3OO(•), CH3O(•), (•)OH, and (•)CH2OH) is rationalized. Identifying the exact mechanism and accurately evaluating kinetics is of fundamental importance to understand antioxidant behavior in physiological environments.
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Affiliation(s)
- Florent Di Meo
- Laboratoire de Chimie des Substances Naturelles EA-1069, Faculté de Pharmacie, Université de Limoges, 2 rue du Docteur Marcland, Limoges Cedex, France
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41
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Sviatenko LK, Gorb L, Hill FC, Leszczynski J. Theoretical study of ionization and one-electron oxidation potentials ofN-heterocyclic compounds. J Comput Chem 2013; 34:1094-100. [DOI: 10.1002/jcc.23228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 11/12/2012] [Accepted: 12/16/2012] [Indexed: 11/08/2022]
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42
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Sharma AK, Sunoj RB. Refined Transition-State Models for Proline-Catalyzed Asymmetric Michael Reactions under Basic and Base-Free Conditions. J Org Chem 2012. [DOI: 10.1021/jo3023654] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Akhilesh K. Sharma
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Raghavan B. Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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43
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Cembran A, Provorse MR, Wang C, Wu W, Gao J. The Third Dimension of a More O'Ferrall-Jencks Diagram for Hydrogen Atom Transfer in the Isoelectronic Hydrogen Exchange Reactions of (PhX)(2)H(•) with X = O, NH, and CH(2). J Chem Theory Comput 2012; 8:4347-4358. [PMID: 23226989 PMCID: PMC3516191 DOI: 10.1021/ct3004595] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A critical element in theoretical characterization of the mechanism of proton-coupled electron transfer (PCET) reactions, including hydrogen atom transfer (HAT), is the formulation of the electron and proton localized diabatic states, based on which a More O'Ferrall-Jencks diagram can be represented to determine the step-wise and concerted nature of the reaction. Although the More O'Ferrall-Jencks diabatic states have often been used empirically to develop theoretical models for PCET reactions, the potential energy surfaces for these states have never been determined directly based on first principles calculations using electronic structure theory. The difficulty is due to a lack of practical method to constrain electron and proton localized diabatic states in wave function or density functional theory calculations. Employing a multistate density functional theory (MSDFT), in which the electron and proton localized diabatic configurations are constructed through block-localization of Kohn-Sham orbitals, we show that distinction between concerted proton-electron transfer (CPET) and HAT, which are not distinguishable experimentally from phenomenological kinetic data, can be made by examining the third dimension of a More O'Ferrall-Jencks diagram that includes both the ground and excited state potential surfaces. In addition, we formulate a pair of effective two-state valence bond models to represent the CPET and HAT mechanisms. We found that the lower energy of the CPET and HAT effective diabatic states at the intersection point can be used as an energetic criterion to distinguish the two mechanisms. In the isoelectronic series of hydrogen exchange reaction in (PhX)(2)H(•), where X = O, NH, and CH(2), there is a continuous transition from a CPET mechanism for the phenoxy radical-phenol pair to a HAT process for benzyl radical and toluene, while the reaction between PhNH(2) and PhNH(•) has a mechanism intermediate of CPET and HAT. The electronically nonadiabatic nature of the CPET mechanism in the phenol system can be attributed to the overlap interactions between the ground and excited state surfaces, resulting in roughly orthogonal minimum energy paths on the adiabatic ground and excited state potential energy surfaces. On the other hand, the minimum energy path on the adiabatic ground state for the HAT mechanism coincides with that on the excited state, producing a large electronic coupling that separates the two surfaces by more than 120 kcal/mol.
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Affiliation(s)
- Alessandro Cembran
- Department of Chemistry, Digital Technology Center and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
| | - Makenzie R. Provorse
- Department of Chemistry, Digital Technology Center and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
| | - Changwei Wang
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Jiali Gao
- Department of Chemistry, Digital Technology Center and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
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44
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Jose D, Datta A. Tunneling Governs Intramolecular Proton Transfer in Thiotropolone at Room Temperature. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203355] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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45
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Jose D, Datta A. Tunneling Governs Intramolecular Proton Transfer in Thiotropolone at Room Temperature. Angew Chem Int Ed Engl 2012; 51:9389-92. [DOI: 10.1002/anie.201203355] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/26/2012] [Indexed: 11/11/2022]
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46
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Weinberg DR, Gagliardi CJ, Hull JF, Murphy CF, Kent CA, Westlake BC, Paul A, Ess DH, McCafferty DG, Meyer TJ. Proton-Coupled Electron Transfer. Chem Rev 2012; 112:4016-93. [DOI: 10.1021/cr200177j] [Citation(s) in RCA: 1125] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- David R. Weinberg
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
- Department of Physical and Environmental
Sciences, Colorado Mesa University, 1100 North Avenue, Grand Junction,
Colorado 81501-3122, United States
| | - Christopher J. Gagliardi
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Jonathan F. Hull
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Christine Fecenko Murphy
- Department
of Chemistry, B219
Levine Science Research Center, Box 90354, Duke University, Durham,
North Carolina 27708-0354, United States
| | - Caleb A. Kent
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Brittany C. Westlake
- The American Chemical Society,
1155 Sixteenth Street NW, Washington, District of Columbia 20036,
United States
| | - Amit Paul
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Daniel H. Ess
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Dewey Granville McCafferty
- Department
of Chemistry, B219
Levine Science Research Center, Box 90354, Duke University, Durham,
North Carolina 27708-0354, United States
| | - Thomas J. Meyer
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
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47
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Lai W, Li C, Chen H, Shaik S. Hydrogen-abstraction reactivity patterns from A to Y: the valence bond way. Angew Chem Int Ed Engl 2012; 51:5556-78. [PMID: 22566272 DOI: 10.1002/anie.201108398] [Citation(s) in RCA: 212] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Indexed: 01/06/2023]
Abstract
"Give us insight, not numbers" was Coulson's admonition to theoretical chemists. This Review shows that the valence bond (VB)-model provides insights and some good numbers for one of the fundamental reactions in nature, the hydrogen-atom transfer (HAT). The VB model is applied to over 50 reactions from the simplest H + H(2) process, to P450 hydroxylations and H-transfers among closed-shell molecules; for each system the barriers are estimated from raw data. The model creates a bridge to the Marcus equation and shows that H-atom abstraction by a closed-shell molecule requires a higher barrier owing to the additional promotion energy needed to prepare the abstractor for H-abstraction. Under certain conditions, a closed-shell abstractor can bypass this penalty through a proton-coupled electron transfer (PCET) mechanism. The VB model links the HAT and PCET mechanisms conceptually and shows the consequences that this linking has for H-abstraction reactivity.
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Affiliation(s)
- Wenzhen Lai
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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48
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Lai W, Li C, Chen H, Shaik S. Wasserstoffatomabstraktion von A bis Y: Reaktionsmuster nach der Valenzstrukturtheorie. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108398] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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49
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Li C, Danovich D, Shaik S. Blended hydrogen atom abstraction and proton-coupled electron transfer mechanisms of closed-shell molecules. Chem Sci 2012. [DOI: 10.1039/c2sc20115a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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50
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Huff GS, Doncheva IS, Brinkley DW, Angeles-Boza AM, Mukherjee A, Cramer CJ, Roth JP. Experimental and Computational Investigations of Oxygen Reactivity in a Heme and Tyrosyl Radical-Containing Fatty Acid α-(Di)oxygenase. Biochemistry 2011; 50:7375-89. [DOI: 10.1021/bi201016h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Gregory S. Huff
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Irina S. Doncheva
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - David W. Brinkley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Alfredo M. Angeles-Boza
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Arnab Mukherjee
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Christopher J. Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis,
Minnesota 55455, United States
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
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