51
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Summers TJ, Cheng Q, DeYonker NJ. A transition state “trapped”? QM-cluster models of engineered threonyl-tRNA synthetase. Org Biomol Chem 2018; 16:4090-4100. [DOI: 10.1039/c8ob00540k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
QM-cluster models demonstrate how protein bioengineering alters the local energy landscape of p-biphenylalanine to stabilize a transition state analogue.
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Affiliation(s)
| | - Qianyi Cheng
- The Department of Chemistry
- The University of Memphis
- Memphis
- USA
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52
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Zhou S, Yue L, Schlangen M, Schwarz H. Electronic Origin of the Competitive Mechanisms in the Thermal Activation of Methane by the Heteronuclear Cluster Oxide [Al 2 ZnO 4 ] .. Angew Chem Int Ed Engl 2017; 56:14297-14300. [PMID: 28570779 DOI: 10.1002/anie.201704979] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Indexed: 11/08/2022]
Abstract
The thermal gas-phase reactions of [Al2 ZnO4 ].+ with methane have been explored by using FT-ICR mass spectrometry complemented by high-level quantum chemical calculations. Two competitive mechanisms, that is, hydrogen-atom transfer (HAT) and proton-coupled electron transfer (PCET) are operative. Interestingly, while the HAT process is influenced by the polarity of the transition structure, both the ionic nature of the metal-oxygen bond and the structural rigidity of the cluster oxide affect the PCET pathway. As compared to the previously reported homonuclear [Al2 O3 ].+ and [ZnO].+ , the heteronuclear oxide [Al2 ZnO4 ].+ exhibits a much higher chemoselectivity towards methane. The electronic origins of the doping effect have been explored.
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Affiliation(s)
- Shaodong Zhou
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Lei Yue
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Maria Schlangen
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Helmut Schwarz
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany
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53
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Zhou S, Firouzbakht M, Schlangen M, Kaupp M, Schwarz H. On the Electronic Origin of Remarkable Ligand Effects on the Reactivities of [NiL] + Complexes (L=C 6 H 5 , C 5 H 4 N, CN) towards Methane. Chemistry 2017; 23:14430-14433. [PMID: 28865112 DOI: 10.1002/chem.201703767] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Indexed: 11/07/2022]
Abstract
The gas-phase reactions of [NiL]+ (L=C6 H5 , C5 H4 N, CN) with methane have been explored by using electrospray-ionization mass spectrometry (ESI-MS) complemented by quantum chemical calculations. Though the phenyl Ni complex [Ni(C6 H5 )]+ exclusively abstracts one hydrogen atom from methane at ambient conditions, the cyano Ni complex [Ni(CN)]+ brings about both H-atom abstraction and ligand exchange to generate [Ni(CH3 )]+ . In contrast, the complex 2-pyridinyl Ni [Ni(C5 H4 N)]+ is inert towards this substrate. The presence of the empty 4s(Ni) orbital dominates the proton-coupled electron transfer (PCET) processes for the investigated systems.
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Affiliation(s)
- Shaodong Zhou
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany.,Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Marjan Firouzbakht
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Maria Schlangen
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Martin Kaupp
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Helmut Schwarz
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany
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54
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Liao RZ, Siegbahn PE. Possible water association and oxidation mechanisms for a recently synthesized Mn4Ca-complex. J Catal 2017. [DOI: 10.1016/j.jcat.2017.07.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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55
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Qin X, Deng L, Hu C, Li L, Chen X. Copper-Containing Nitrite Reductase Employing Proton-Coupled Spin-Exchanged Electron-Transfer and Multiproton Synchronized Transfer to Reduce Nitrite. Chemistry 2017; 23:14900-14910. [DOI: 10.1002/chem.201703221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Xin Qin
- National-Municipal Joint Engineering Laboratory for Chemical; Process Intensification and Reaction; School of Chemistry and Chemical Engineering; Chongqing University; Chongqing 401331 P.R. China
| | - Li Deng
- National-Municipal Joint Engineering Laboratory for Chemical; Process Intensification and Reaction; School of Chemistry and Chemical Engineering; Chongqing University; Chongqing 401331 P.R. China
| | - Caihong Hu
- National-Municipal Joint Engineering Laboratory for Chemical; Process Intensification and Reaction; School of Chemistry and Chemical Engineering; Chongqing University; Chongqing 401331 P.R. China
| | - Li Li
- National-Municipal Joint Engineering Laboratory for Chemical; Process Intensification and Reaction; School of Chemistry and Chemical Engineering; Chongqing University; Chongqing 401331 P.R. China
| | - Xiaohua Chen
- National-Municipal Joint Engineering Laboratory for Chemical; Process Intensification and Reaction; School of Chemistry and Chemical Engineering; Chongqing University; Chongqing 401331 P.R. China
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56
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Moa S, Himo F. Quantum chemical study of mechanism and stereoselectivity of secondary alcohol dehydrogenase. J Inorg Biochem 2017; 175:259-266. [PMID: 28803132 DOI: 10.1016/j.jinorgbio.2017.07.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/02/2017] [Accepted: 07/18/2017] [Indexed: 11/17/2022]
Abstract
Secondary alcohol dehydrogenase from Thermoanaerobacter brockii (TbSADH) is a Zn- and NADP-dependent enzyme that catalyses the reversible transformation of secondary alcohols into ketones. It is of potential biocatalytic interest as it can be used in the synthesis of chiral alcohols by asymmetric reduction of ketones. In this paper, density functional theory calculations are employed to elucidate the origins of the enantioselectivity of TbSADH using a large model of the active site and considering two different substrates, 2-butanol and 3-hexanol. For these two substrates the enzyme has experimentally been shown to have the opposite enantioselectivity. The energy profiles for the reactions are calculated and the stationary points along the reaction path are characterised. The calculations first confirm that the general mechanism proposed for other alcohol dehydrogenases is energetically viable. In this mechanism, a proton is first transferred from the substrate to a histidine residue at the surface, followed by a hydride transfer to the NADP cofactor. The calculated overall energy barrier is consistent with the measured rate constant. Very importantly, the calculations are able to reproduce and rationalise the enantioselectivity of the enzyme for both substrates. The detailed characterisation of the energies and geometries of the involved transition states will be valuable in the rational engineering of TbSADH to expand its utility in biocatalysis.
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Affiliation(s)
- Sara Moa
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.
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57
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Zhou S, Yue L, Schlangen M, Schwarz H. Elektronische Ursache konkurrierender Mechanismen bei der thermischen Aktivierung von Methan durch das heteronukleare Clusteroxid [Al2
ZnO4
].+. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704979] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shaodong Zhou
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Lei Yue
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Maria Schlangen
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Helmut Schwarz
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
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58
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Sheng X, Zhu W, Huddleston J, Xiang DF, Raushel FM, Richards NGJ, Himo F. A Combined Experimental-Theoretical Study of the LigW-Catalyzed Decarboxylation of 5-Carboxyvanillate in the Metabolic Pathway for Lignin Degradation. ACS Catal 2017. [DOI: 10.1021/acscatal.7b01166] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiang Sheng
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Wen Zhu
- School
of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
| | - Jamison Huddleston
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Dao Fen Xiang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | | | - Fahmi Himo
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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59
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Wang X, Wang S, Gu C, Zhang W, Zheng H, Zhang J, Lu G, Zhang YM, Li M, Zhang SXA. Reversible Bond/Cation-Coupled Electron Transfer on Phenylenediamine-Based Rhodamine B and Its Application on Electrochromism. ACS APPLIED MATERIALS & INTERFACES 2017; 9:20196-20204. [PMID: 28535036 DOI: 10.1021/acsami.7b03199] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A biomimetic system on reversible bond-coupled electron transfer (BCET) has been proposed and investigated in a switchable Rh-N molecule with redox active subunits. We discover that energy barrier of C-N bond breaking is reduced dramatically to less than 1/7 (from 40.4 to 5.5 kcal/mol), and 1/3 of the oxidation potential is simultaneously lowered (from 0.67 to 0.43 V) with the oxidation of Rh-N. The concept, cation-coupled electron transfer (CCET), is highly recommended by analyzing existing proton coupled electron transfer (PCET) and metal coupled electron transfer (MCET) along with aforementioned BCET, which have same characteristic of transferring positive charges, such as proton, metal ion, and organic cation. Molecular switch can be controlled directly by electricity through BCET process. Solid electrochromic device was fabricated with extremely high coloration efficiency (720 cm2/C), great reversibility (no degradation for 600 cycles), and quick respond time (30 ms).
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Affiliation(s)
- Xiaojun Wang
- State Key Lab of Supramolecular Structure and Materials, Jilin University , Changchun, 130012, P. R. China
- College of Chemistry, Jilin University , Changchun, 130012, P. R. China
| | - Shuo Wang
- College of Chemistry, Jilin University , Changchun, 130012, P. R. China
| | - Chang Gu
- College of Chemistry, Jilin University , Changchun, 130012, P. R. China
| | - Weiran Zhang
- State Key Lab of Supramolecular Structure and Materials, Jilin University , Changchun, 130012, P. R. China
- College of Chemistry, Jilin University , Changchun, 130012, P. R. China
| | - Hongzhi Zheng
- College of Chemistry, Jilin University , Changchun, 130012, P. R. China
| | - Jingjing Zhang
- College of Chemistry, Jilin University , Changchun, 130012, P. R. China
| | - Geyu Lu
- College of Electron Science and Engineering, Jilin University , Changchun 130012, P. R. China
| | - Yu-Mo Zhang
- College of Chemistry, Jilin University , Changchun, 130012, P. R. China
| | - Minjie Li
- State Key Lab of Supramolecular Structure and Materials, Jilin University , Changchun, 130012, P. R. China
- College of Chemistry, Jilin University , Changchun, 130012, P. R. China
| | - Sean Xiao-An Zhang
- State Key Lab of Supramolecular Structure and Materials, Jilin University , Changchun, 130012, P. R. China
- College of Chemistry, Jilin University , Changchun, 130012, P. R. China
- Department of Chemistry and Pharmacy, Zhuhai College of Jilin University , Zhuhai, 519041, P. R. China
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60
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Abstract
The quantum chemical cluster approach is a powerful method for investigating enzymatic reactions. Over the past two decades, a large number of highly diverse systems have been studied and a great wealth of mechanistic insight has been developed using this technique. This Perspective reviews the current status of the methodology. The latest technical developments are highlighted, and challenges are discussed. Some recent applications are presented to illustrate the capabilities and progress of this approach, and likely future directions are outlined.
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Affiliation(s)
- Fahmi Himo
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University , SE-106 91 Stockholm, Sweden
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61
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Yu MJ, Chen SL. From NAD + to Nickel Pincer Complex: A Significant Cofactor Evolution Presented by Lactate Racemase. Chemistry 2017; 23:7545-7557. [PMID: 28374531 DOI: 10.1002/chem.201700405] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Indexed: 02/02/2023]
Abstract
Lactate racemase (LarA), a new nickel enzyme discovered recently, catalyzes the racemization between d- and l-lactates with a novel nickel pincer cofactor (Ni-PTTMN) derived from nicotinic acid. In this study, by using DFT and a 200-atom active-site model, LarA is revealed to employ a modified proton-coupled hydride-transfer mechanism in which a hydride is transferred to a cofactor pyridine carbon from the substrate α-carbon along with proton transfer from the substrate hydroxy group to a histidine, and then moved back from the opposite side. Tyr294 and Lys298 provide significant acceleration effects by orientating substrates and stabilizing the negative charge developing at the substrate hydroxy oxygen. The barrier was determined to be 12.0 kcal mol-1 , which reveals enhanced racemase activity relative to the LarA reaction using NAD+ -like cofactors. Compared with NAD+ , Ni-PTTMN has a stronger hydride-addition reactivity in moderate and high environmental polarity and may fit perfectly the moderately polar active site of LarA.
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Affiliation(s)
- Ming-Jia Yu
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P.R. China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P.R. China
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62
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Zhou S, Li J, Firouzbakht M, Schlangen M, Schwarz H. Sequential Gas-Phase Activation of Carbon Dioxide and Methane by [Re(CO) 2] +: The Sequence of Events Matters! J Am Chem Soc 2017; 139:6169-6176. [PMID: 28403605 DOI: 10.1021/jacs.7b01255] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The potential of carbonyl rhenium complexes in activating and coupling carbon dioxide and methane has been explored by using a combination of gas-phase experiments (FT-ICR mass spectrometry) and high-level quantum chemical calculations. While the complexes [Re(CO)x]+ (x = 0, 1, 3) are thermally unreactive toward CO2, [Re(CO)2]+ abstracts one oxygen atom from this substrate spontaneously at ambient conditions. Based on 13C and 18O labeling experiments, the newly generated CO ligand is preferentially eliminated, and two mechanistic scenarios are considered to account for this unexpected finding. The oxo complex [ORe(CO)2]+ reacts further with CH4 to produce the dihydridomethylene complex [ORe(CO)(CH2)(H)2]+. However, coupling of the CO and CH2 ligands to form CH2═C═O does not take place. Further, the complexes [Re(CO)x(CH2)]+ (x = 1, 2), generated in the thermal reaction of [Re(CO)x]+ (x = 1, 2) with CH4, are inert toward CO2. Mechanistic insight on the origin of this remarkable reactivity pattern has been derived from detailed quantum chemical calculations.
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Affiliation(s)
- Shaodong Zhou
- Institut für Chemie, Technische Universität Berlin , Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Jilai Li
- Institut für Chemie, Technische Universität Berlin , Straße des 17. Juni 135, 10623 Berlin, Germany.,Institute of Theoretical Chemistry, Jilin University , Changchun 130023, People's Republic of China
| | - Marjan Firouzbakht
- Institut für Chemie, Technische Universität Berlin , Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Maria Schlangen
- Institut für Chemie, Technische Universität Berlin , Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Helmut Schwarz
- Institut für Chemie, Technische Universität Berlin , Straße des 17. Juni 135, 10623 Berlin, Germany
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63
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64
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Khadem-Maaref M, Mehrnejad F, Phirouznia A. Effects of metal-ion replacement on pyrazinamidase activity: A quantum mechanical study. J Mol Graph Model 2017; 73:24-29. [PMID: 28214629 DOI: 10.1016/j.jmgm.2017.01.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/27/2017] [Accepted: 01/30/2017] [Indexed: 11/26/2022]
Abstract
Pyrazinamidase (PZase), a metalloenzyme, is responsible for acidic modification of pyrazinamide (PZA), a drug used in tuberculosis treatment. The metal coordination site of the enzyme is able to coordinate various divalent metal cofactors. Previous experimental studies have demonstrated that metal ions, such as Co2+, Mn2+, and Zn2+, are able to reactivate metal-depleted PZase, while others including Cu2+, Fe2+, and Mg2+, cannot restore activity. In this study, we investigated binding of various metal ions to the metal coordination site (MCS) of the enzyme using quantum mechanical calculations. We calculated the metal-ligand (residue) binding energy and the atomic partial charges in the presence of various ions. The results indicated that the tendency of alkaline earth metals to bind to PZase MCS is very low and not suitable for enzyme structural and catalytic function. In contrast, Co2+ and Ni2+ ions have very high binding affinity and are favorable to the structural and functional properties of the enzyme. Furthermore, we observed that the rate at which Ni2+, Co2+ and Fe2+ ions in PZase MCS polarize the OH bond of coordinated water molecules is much higher than the polarization rate created by other ions. This finding suggests that the coordination of Ni2+, Co2+, or Fe2+ to PZase facilitates the deprotonation of coordinated water molecules to generate a nucleophile that catalyzes the enzymatic reaction.
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Affiliation(s)
- Mahmoud Khadem-Maaref
- Department of Physics, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran.
| | - Arash Phirouznia
- Department of Physics, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran.
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65
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Gunner MR, Koder R. The design features cells use to build their transmembrane proton gradient. Phys Biol 2017; 14:013001. [DOI: 10.1088/1478-3975/14/1/013001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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66
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Sheng X, Himo F. Theoretical Study of Enzyme Promiscuity: Mechanisms of Hydration and Carboxylation Activities of Phenolic Acid Decarboxylase. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03249] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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67
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Influence of iron doping on tetravalent nickel content in catalytic oxygen evolving films. Proc Natl Acad Sci U S A 2017; 114:1486-1491. [PMID: 28137835 DOI: 10.1073/pnas.1620787114] [Citation(s) in RCA: 226] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Iron doping of nickel oxide films results in enhanced activity for promoting the oxygen evolution reaction (OER). Whereas this enhanced activity has been ascribed to a unique iron site within the nickel oxide matrix, we show here that Fe doping influences the Ni valency. The percent of Fe3+ doping promotes the formation of formal Ni4+, which in turn directly correlates with an enhanced activity of the catalyst in promoting OER. The role of Fe3+ is consistent with its behavior as a superior Lewis acid.
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68
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Yamamoto K, Takatsuka K. Photoinduced Charge Separation Catalyzed by Manganese Oxides onto a Y-Shaped Branching Acceptor Efficiently Preventing Charge Recombination. Chemphyschem 2017; 18:537-548. [DOI: 10.1002/cphc.201601237] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/27/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Kentaro Yamamoto
- Fukui Institute for Fundamental Chemistry; Kyoto University; Takano-Nishihiraki-cho 34-4, Sakyou-ku Kyoto 606-8103 Japan
| | - Kazuo Takatsuka
- Fukui Institute for Fundamental Chemistry; Kyoto University; Takano-Nishihiraki-cho 34-4, Sakyou-ku Kyoto 606-8103 Japan
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69
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Adam SM, Garcia-Bosch I, Schaefer AW, Sharma SK, Siegler MA, Solomon EI, Karlin KD. Critical Aspects of Heme-Peroxo-Cu Complex Structure and Nature of Proton Source Dictate Metal-O(peroxo) Breakage versus Reductive O-O Cleavage Chemistry. J Am Chem Soc 2017; 139:472-481. [PMID: 28029788 PMCID: PMC5274545 DOI: 10.1021/jacs.6b11322] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The 4H+/4e- reduction of O2 to water, a key fuel-cell reaction also carried out in biology by oxidase enzymes, includes the critical O-O bond reductive cleavage step. Mechanistic investigations on active-site model compounds, which are synthesized by rational design to incorporate systematic variations, can focus on and resolve answers to fundamental questions, including protonation and/or H-bonding aspects, which accompany electron transfer. Here, we describe the nature and comparative reactivity of two low-spin heme-peroxo-Cu complexes, LS-4DCHIm, [(DCHIm)F8FeIII-(O22-)-CuII(DCHIm)4]+, and LS-3DCHIm, [(DCHIm)F8FeIII-(O22-)-CuII(DCHIm)3]+ (F8 = tetrakis(2,6-difluorophenyl)-porphyrinate; DCHIm = 1,5-dicyclohexylimidazole), toward different proton (4-nitrophenol and [DMF·H+](CF3SO3-)) (DMF = dimethyl-formamide) or electron (decamethylferrocene (Fc*)) sources. Spectroscopic reactivity studies show that differences in structure and electronic properties of LS-3DCHIm and LS-4DCHIm lead to significant differences in behavior. LS-3DCHIm is resistant to reduction, is unreactive toward weakly acidic 4-NO2-phenol, and stronger acids cleave the metal-O bonds, releasing H2O2. By contrast, LS-4DCHIm forms an adduct with 4-NO2-phenol, which includes an H-bond to the peroxo O-atom distal to Fe (resonance Raman (rR) spectroscopy and DFT). With addition of Fc* (2 equiv overall required), O-O reductive cleavage occurs, giving water, Fe(III), and Cu(II) products; however, a kinetic study reveals a one-electron rate-determining process, ket = 1.6 M-1 s-1 (-90 °C). The intermediacy of a high-valent [(DCHIm)F8FeIV═O] species is thus implied, and separate experiments show that one-electron reduction-protonation of [(DCHIm)F8FeIV═O] occurs faster (ket2 = 5.0 M-1 s-1), consistent with the overall postulated mechanism. The importance of the H-bonding interaction as a prerequisite for reductive cleavage is highlighted.
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Affiliation(s)
- Suzanne M. Adam
- Johns Hopkins University, Baltimore, Maryland 21218, United States
| | | | - Andrew W. Schaefer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Savita K. Sharma
- Johns Hopkins University, Baltimore, Maryland 21218, United States
| | | | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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70
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Sun X, Zhou S, Schlangen M, Schwarz H. Thermal Methane Activation by the Metal-Free Cluster Cation [Si 2 O 4 ] .. Chemistry 2017; 23:1498-1501. [PMID: 27943447 DOI: 10.1002/chem.201605496] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Indexed: 02/05/2023]
Abstract
The thermal reaction of methane with the metal-free cluster cation [Si2 O4 ].+ has been examined by using Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry. In addition to generating a methyl radical via hydrogen-atom abstraction, [Si2 O4 ].+ can selectively oxidize methane to formaldehyde. The mechanisms of these rather efficient reactions have been elucidated by high-level quantum-chemical calculations.
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Affiliation(s)
- Xiaoyan Sun
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Shaodong Zhou
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Maria Schlangen
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Helmut Schwarz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
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71
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Guo Y, Li H, He LL, Zhao DX, Gong LD, Yang ZZ. The open-cubane oxo–oxyl coupling mechanism dominates photosynthetic oxygen evolution: a comprehensive DFT investigation on O–O bond formation in the S4state. Phys Chem Chem Phys 2017; 19:13909-13923. [DOI: 10.1039/c7cp01617d] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
How is O2created in nature? Comprehensive DFT investigations determine the dominance of the open-cubane oxo–oxyl coupling mechanism over alternative possibilities.
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Affiliation(s)
- Yu Guo
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
| | - Hui Li
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
| | - Lan-Lan He
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
| | - Li-Dong Gong
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
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72
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Ge X, Sun F, Liu X, Chen X, Qian C, Zhou S. Combined experimental/theoretical study on d-glucosamine promoted regioselective sulfenylation of indoles catalyzed by copper. NEW J CHEM 2017. [DOI: 10.1039/c7nj02784b] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combined experimental/theoretical investigation on the d-glucosamine promoted sulfenylation of indoles at the C3 position with sodium sulfinates catalyzed by copper is presented.
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Affiliation(s)
- Xin Ge
- School of Chemical and Material Engineering
- Jiangnan University
- Wuxi
- P. R. China
- Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology
| | - Fengli Sun
- School of Chemical and Material Engineering
- Jiangnan University
- Wuxi
- P. R. China
| | - Xuemin Liu
- School of Chemical and Material Engineering
- Jiangnan University
- Wuxi
- P. R. China
| | - Xinzhi Chen
- Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- P. R. China
| | - Chao Qian
- Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- P. R. China
| | - Shaodong Zhou
- Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- P. R. China
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73
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Blomberg MRA. Can Reduction of NO to N2O in Cytochrome c Dependent Nitric Oxide Reductase Proceed through a Trans-Mechanism? Biochemistry 2016; 56:120-131. [DOI: 10.1021/acs.biochem.6b00788] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Margareta R. A. Blomberg
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
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74
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Zhang X, Chung LW. Alternative Mechanistic Strategy for Enzyme Catalysis in a Ni-Dependent Lactate Racemase (LarA): Intermediate Destabilization by the Cofactor. Chemistry 2016; 23:3623-3630. [DOI: 10.1002/chem.201604893] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Xiaoyong Zhang
- Department of Chemistry; South University of Science and Technology of China; Shenzhen 518055 P. R. China
| | - Lung W. Chung
- Department of Chemistry; South University of Science and Technology of China; Shenzhen 518055 P. R. China
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75
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Zhou S, Li J, Schlangen M, Schwarz H. Ursachen der unterschiedlichen Reaktivität von [AlCeO
x
]
+
(
x=
2
–
4) gegenüber Methan in Abhängigkeit vom Sauerstoffgehalt. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shaodong Zhou
- Institut für Chemie Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Jilai Li
- Institut für Chemie Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
- Institute of Theoretical Chemistry Jilin University Changchun 130023 VR China
| | - Maria Schlangen
- Institut für Chemie Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Helmut Schwarz
- Institut für Chemie Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
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76
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Zhou S, Li J, Schlangen M, Schwarz H. On the Origin of the Remarkably Variable Reactivities of [AlCeO
x
]+
(x=
2-
4) towards Methane as a Function of Oxygen Content. Angew Chem Int Ed Engl 2016; 56:413-416. [DOI: 10.1002/anie.201610424] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Shaodong Zhou
- Institut für Chemie; Technische Universität Berlin; Strasse des 17. Juni 135 10623 Berlin Germany
| | - Jilai Li
- Institut für Chemie; Technische Universität Berlin; Strasse des 17. Juni 135 10623 Berlin Germany
- Institute of Theoretical Chemistry; Jilin University; Changchun 130023 P.R. China
| | - Maria Schlangen
- Institut für Chemie; Technische Universität Berlin; Strasse des 17. Juni 135 10623 Berlin Germany
| | - Helmut Schwarz
- Institut für Chemie; Technische Universität Berlin; Strasse des 17. Juni 135 10623 Berlin Germany
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77
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Lind MES, Himo F. Quantum Chemical Modeling of Enantioconvergency in Soluble Epoxide Hydrolase. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01562] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Maria E. S. Lind
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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78
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Zhou S, Li J, Schlangen M, Schwarz H. Zum Ursprung der effizienten thermischen Chemisorption von Methan durch den heteronuklearen Metalloxidcluster [Al2
TaO5
]+. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608999] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shaodong Zhou
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Jilai Li
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
- Institute of Theoretical Chemistry; Jilin University; Changchun 130023 VR China
| | - Maria Schlangen
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Helmut Schwarz
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
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79
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Zhou S, Li J, Schlangen M, Schwarz H. The Origin of the Efficient, Thermal Chemisorption of Methane by the Heteronuclear Metal‐Oxide Cluster [Al
2
TaO
5
]
+. Angew Chem Int Ed Engl 2016; 55:14867-14871. [DOI: 10.1002/anie.201608999] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/04/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Shaodong Zhou
- Institut für Chemie Technische Universität Berlin Strasse des 17. Juni 135 10623 Berlin Germany
| | - Jilai Li
- Institut für Chemie Technische Universität Berlin Strasse des 17. Juni 135 10623 Berlin Germany
- Institute of Theoretical Chemistry Jilin University Changchun 130023 P.R. China
| | - Maria Schlangen
- Institut für Chemie Technische Universität Berlin Strasse des 17. Juni 135 10623 Berlin Germany
| | - Helmut Schwarz
- Institut für Chemie Technische Universität Berlin Strasse des 17. Juni 135 10623 Berlin Germany
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80
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Zhou S, Li J, Schlangen M, Schwarz H. Thermal Dehydrogenation of Methane by [ReN]
+. Angew Chem Int Ed Engl 2016; 55:14863-14866. [DOI: 10.1002/anie.201607960] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Shaodong Zhou
- Institut für Chemie Technische Universität Berlin Strasse des 17. Juni 135 10623 Berlin Germany
| | - Jilai Li
- Institut für Chemie Technische Universität Berlin Strasse des 17. Juni 135 10623 Berlin Germany
- Institute of Theoretical Chemistry Jilin University P.R. China
| | - Maria Schlangen
- Institut für Chemie Technische Universität Berlin Strasse des 17. Juni 135 10623 Berlin Germany
| | - Helmut Schwarz
- Institut für Chemie Technische Universität Berlin Strasse des 17. Juni 135 10623 Berlin Germany
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81
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Zhou S, Li J, Schlangen M, Schwarz H. Thermische Dehydrierung von Methan durch [ReN]+. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607960] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shaodong Zhou
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Jilai Li
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
- Institute of Theoretical Chemistry; Jilin University; VR China
| | - Maria Schlangen
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Helmut Schwarz
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
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82
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Sun X, Zhou S, Schlangen M, Schwarz H. Thermal Methane Activation by [Si 2 O 5 ] .+ and [Si 2 O 5 H 2 ] .+ : Reactivity Enhancement by Hydrogenation. Angew Chem Int Ed Engl 2016; 55:13345-13348. [PMID: 27650136 DOI: 10.1002/anie.201607864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Indexed: 11/09/2022]
Abstract
The thermal reactions of methane with the oxygen-rich cluster cations [Si2 O5 ]⋅+ and [Si2 O5 H2 ]⋅+ have been examined using Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry in conjunction with state-of-the-art quantum chemical calculations. In contrast to the inertness of [Si2 O5 ].+ towards methane, the hydrogenated cluster [Si2 O5 H2 ].+ brings about hydrogen-atom transfer (HAT) from methane with an efficiency of 28 % relative to the collision rate. The mechanisms of this process have been investigated in detail and the reasons for the striking reactivity difference of the two cluster ions have been revealed.
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Affiliation(s)
- Xiaoyan Sun
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Shaodong Zhou
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Maria Schlangen
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Helmut Schwarz
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany.
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83
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Sun X, Zhou S, Schlangen M, Schwarz H. Thermische Methanaktivierung durch [Si2
O5
].+
und [Si2
O5
H2
].+
: Reaktivitätssteigerung durch Hydrierung. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xiaoyan Sun
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Shaodong Zhou
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Maria Schlangen
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Helmut Schwarz
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
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84
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Barman P, Faponle AS, Vardhaman AK, Angelone D, Löhr AM, Browne WR, Comba P, Sastri CV, de Visser SP. Influence of Ligand Architecture in Tuning Reaction Bifurcation Pathways for Chlorite Oxidation by Non-Heme Iron Complexes. Inorg Chem 2016; 55:10170-10181. [PMID: 27704794 DOI: 10.1021/acs.inorgchem.6b01384] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction bifurcation processes are often encountered in the oxidation of substrates by enzymes and generally lead to a mixture of products. One particular bifurcation process that is common in biology relates to electron transfer versus oxygen atom transfer by high-valent iron(IV)-oxo complexes, which nature uses for the oxidation of metabolites and drugs. In biomimicry and bioremediation, an important reaction relates to the detoxification of ClOx- in water, which can lead to a mixture of products through bifurcated reactions. Herein we report the first three water-soluble non-heme iron(II) complexes that can generate chlorine dioxide from chlorite at ambient temperature and physiological pH. These complexes are highly active oxygenation oxidants and convert ClO2- into either ClO2 or ClO3¯ via high-valent iron(IV)-oxo intermediates. We characterize the short-lived iron(IV)-oxo species and establish rate constants for the bifurcation mechanism leading to ClO2 and ClO3- products. We show that the ligand architecture of the metal center plays a dominant role by lowering the reduction potential of the metal center. Our experiments are supported by computational modeling, and a predictive valence bond model highlights the various factors relating to the substrate and oxidant that determine the bifurcation pathway and explains the origins of the product distributions. Our combined kinetic, spectroscopic, and computational studies reveal the key components necessary for the future development of efficient chlorite oxidation catalysts.
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Affiliation(s)
- Prasenjit Barman
- Department of Chemistry, Indian Institute of Technology Guwahati , Guwahati 781 039, Assam, India
| | - Abayomi S Faponle
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Anil Kumar Vardhaman
- Department of Chemistry, Indian Institute of Technology Guwahati , Guwahati 781 039, Assam, India
| | - Davide Angelone
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Anna-Maria Löhr
- Anorganisch-Chemisches Institut and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University , Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Wesley R Browne
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Peter Comba
- Anorganisch-Chemisches Institut and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University , Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati , Guwahati 781 039, Assam, India
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
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85
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Lan CL, Chen SL. The Decarboxylation of α,β-Unsaturated Acid Catalyzed by Prenylated FMN-Dependent Ferulic Acid Decarboxylase and the Enzyme Inhibition. J Org Chem 2016; 81:9289-9295. [PMID: 27618344 DOI: 10.1021/acs.joc.6b01872] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ferulic acid decarboxylase (Fdc1) is able to catalyze the decarboxylation of α,β-unsaturated acids using a novel cofactor, prenylated flavin mononucleotide (PrFMN). Using density functional theory calculations, we here have investigated the Fdc1 reaction mechanism with the substrate of α-methylcinnamic acid. It is demonstrated that Fdc1 employs a 1,3-dipolar cycloaddition mechanism involving four concerted steps, where the Glu282 acts as a crucial proton donor to protonate the α carbon (Cα). The last step, the decomposition of a pyrrolidine species, is rate-limiting with an overall barrier of 18.9 kcal mol-1. Furthermore, when α-hydroxycinnamic acid is used, the Glu282 is found to have another face to transport the hydroxyl proton to the Cβ atom to promote the tautomerization from enol intermediate to ketone species leading to the inhibition of the Fdc1 enzyme. The PrFMN roles are also discussed in detail.
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Affiliation(s)
- Cui-Lan Lan
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology , Beijing 100081, China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology , Beijing 100081, China
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86
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Zhou S, Li J, Schlangen M, Schwarz H. Effiziente, thermische Aktivierung von Methan durch TaN+
unter C-N-Kupplung. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606259] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shaodong Zhou
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Jilai Li
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
- Institute of Theoretical Chemistry; Jilin University; Changchun 130023 VR China
| | - Maria Schlangen
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Helmut Schwarz
- Institut für Chemie; Technische Universität Berlin; Straße des 17. Juni 135 10623 Berlin Deutschland
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87
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Zhou S, Li J, Schlangen M, Schwarz H. Efficient Room-Temperature Activation of Methane by TaN+
under C−N Coupling. Angew Chem Int Ed Engl 2016; 55:11678-81. [DOI: 10.1002/anie.201606259] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Shaodong Zhou
- Institut für Chemie; Technische Universität Berlin; Strasse des 17. Juni 135 10623 Berlin Germany
| | - Jilai Li
- Institut für Chemie; Technische Universität Berlin; Strasse des 17. Juni 135 10623 Berlin Germany
- Institute of Theoretical Chemistry; Jilin University; Changchun 130023 P.R. China
| | - Maria Schlangen
- Institut für Chemie; Technische Universität Berlin; Strasse des 17. Juni 135 10623 Berlin Germany
| | - Helmut Schwarz
- Institut für Chemie; Technische Universität Berlin; Strasse des 17. Juni 135 10623 Berlin Germany
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88
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Siegbahn PEM. Model Calculations Suggest that the Central Carbon in the FeMo-Cofactor of Nitrogenase Becomes Protonated in the Process of Nitrogen Fixation. J Am Chem Soc 2016; 138:10485-95. [DOI: 10.1021/jacs.6b03846] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Per E. M. Siegbahn
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
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89
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Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase. Proc Natl Acad Sci U S A 2016; 113:7420-5. [PMID: 27339133 DOI: 10.1073/pnas.1601982113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytochrome c oxidase (CcO) reduces oxygen to water and uses the released free energy to pump protons across the membrane. We have used multiscale reactive molecular dynamics simulations to explicitly characterize (with free-energy profiles and calculated rates) the internal proton transport events that enable proton pumping during first steps of oxidation of the fully reduced enzyme. Our results show that proton transport from amino acid residue E286 to both the pump loading site (PLS) and to the binuclear center (BNC) are thermodynamically driven by electron transfer from heme a to the BNC, but that the former (i.e., pumping) is kinetically favored whereas the latter (i.e., transfer of the chemical proton) is rate-limiting. The calculated rates agree with experimental measurements. The backflow of the pumped proton from the PLS to E286 and from E286 to the inside of the membrane is prevented by large free-energy barriers for the backflow reactions. Proton transport from E286 to the PLS through the hydrophobic cavity and from D132 to E286 through the D-channel are found to be strongly coupled to dynamical hydration changes in the corresponding pathways and, importantly, vice versa.
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90
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Shakib F, Hanna G. Mixed Quantum-Classical Liouville Approach for Calculating Proton-Coupled Electron-Transfer Rate Constants. J Chem Theory Comput 2016; 12:3020-9. [DOI: 10.1021/acs.jctc.6b00362] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Farnaz Shakib
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Gabriel Hanna
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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91
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Blomberg MRA, Siegbahn PEM. Improved free energy profile for reduction of NO in cytochrome c dependent nitric oxide reductase (cNOR). J Comput Chem 2016; 37:1810-8. [DOI: 10.1002/jcc.24396] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 03/31/2016] [Accepted: 04/02/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Margareta R. A. Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory; Stockholm University; Stockholm SE-106 91 Sweden
| | - Per E. M. Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory; Stockholm University; Stockholm SE-106 91 Sweden
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92
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Jackson MN, Surendranath Y. Donor-Dependent Kinetics of Interfacial Proton-Coupled Electron Transfer. J Am Chem Soc 2016; 138:3228-34. [PMID: 26862666 DOI: 10.1021/jacs.6b00167] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The effect of the proton donor on the kinetics of interfacial concerted proton-electron transfer (CPET) to polycrystalline Au was probed indirectly by studying the rate of hydrogen evolution from trialkylammonium donors with different steric profiles, but the same pKa. Detailed kinetic studies point to a mechanism for HER catalysis that involves rate-limiting CPET from the proton donor to the electrode surface, allowing this catalytic reaction to serve as a proxy for the rate of interfacial CPET. In acetonitrile electrolyte, triethylammonium (TEAH(+)) displays up to 20-fold faster CPET kinetics than diisopropylethylammonium (DIPEAH(+)) at all measured potentials. In aqueous electrolyte, this steric constraint is largely lifted, suggesting a key role for water in mediating interfacial CPET. In acetonitrile, TEAH(+) also displays a much larger transfer coefficient (β = 0.7) than DIPEAH(+) (β = 0.4), and TEAH(+) displays a potential-dependent H/D kinetic isotope effect that is not observed for DIPEAH(+). These results demonstrate that proton donor structure strongly impacts the free energy landscape for CPET to extended solid surfaces and highlight the crucial role of the proton donor in the kinetics of electrocatalytic energy conversion reactions.
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Affiliation(s)
- Megan N Jackson
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Yogesh Surendranath
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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93
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Molecular simulation and modeling of complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:915-21. [PMID: 26780586 DOI: 10.1016/j.bbabio.2016.01.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 11/23/2022]
Abstract
Molecular modeling and molecular dynamics simulations play an important role in the functional characterization of complex I. With its large size and complicated function, linking quinone reduction to proton pumping across a membrane, complex I poses unique modeling challenges. Nonetheless, simulations have already helped in the identification of possible proton transfer pathways. Simulations have also shed light on the coupling between electron and proton transfer, thus pointing the way in the search for the mechanistic principles underlying the proton pump. In addition to reviewing what has already been achieved in complex I modeling, we aim here to identify pressing issues and to provide guidance for future research to harness the power of modeling in the functional characterization of complex I. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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94
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Blomberg MRA. Mechanism of Oxygen Reduction in Cytochrome c Oxidase and the Role of the Active Site Tyrosine. Biochemistry 2016; 55:489-500. [PMID: 26690322 DOI: 10.1021/acs.biochem.5b01205] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome c oxidase, the terminal enzyme in the respiratory chain, reduces molecular oxygen to water and stores the released energy through electrogenic chemistry and proton pumping across the membrane. Apart from the heme-copper binuclear center, there is a conserved tyrosine residue in the active site (BNC). The tyrosine delivers both an electron and a proton during the O-O bond cleavage step, forming a tyrosyl radical. The catalytic cycle then occurs in four reduction steps, each taking up one proton for the chemistry (water formation) and one proton to be pumped. It is here suggested that in three of the reduction steps the chemical proton enters the center of the BNC, leaving the tyrosine unprotonated with radical character. The reproprotonation of the tyrosine occurs first in the final reduction step before binding the next oxygen molecule. It is also suggested that this reduction mechanism and the presence of the tyrosine are essential for the proton pumping. Density functional theory calculations on large cluster models of the active site show that only the intermediates with the proton in the center of the BNC and with an unprotonated tyrosyl radical have a high electron affinity of similar size as the electron donor, which is essential for the ability to take up two protons per electron and thus for the proton pumping. This type of reduction mechanism is also the only one that gives a free energy profile in accordance with experimental observations for the amount of proton pumping in the working enzyme.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91, Stockholm, Sweden
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95
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Jayapal P, Ansari A, Rajaraman G. Computational Examination on the Active Site Structure of a (Peroxo)diiron(III) Intermediate in the Amine Oxygenase AurF. Inorg Chem 2015; 54:11077-82. [PMID: 26588098 DOI: 10.1021/acs.inorgchem.5b00872] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this work, we report the first computational investigation on the structure and properties of the (peroxo)diiron(III) intermediate of the AurF enzyme. Our calculations predict that, in the oxidized state of the AurF enzyme, the peroxo ligand is depicted in a μ-1,1-coordination mode with a protonated bridging ligand and is not in a μ-η(2):η(2) or μ-1,2 mode. Computed spectral data for the μ-1,1-coordination mode correlate well with experimental observations and unravel the potential of the energetics-spectroscopic approach adapted here.
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Affiliation(s)
- Prabha Jayapal
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
| | - Azaj Ansari
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
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96
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Blumberger J. Recent Advances in the Theory and Molecular Simulation of Biological Electron Transfer Reactions. Chem Rev 2015; 115:11191-238. [DOI: 10.1021/acs.chemrev.5b00298] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jochen Blumberger
- Department of Physics and
Astronomy, University College London, Gower Street, London WC1E 6BT, U.K
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97
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Sheng X, Lind MES, Himo F. Theoretical study of the reaction mechanism of phenolic acid decarboxylase. FEBS J 2015; 282:4703-13. [PMID: 26408050 DOI: 10.1111/febs.13525] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 09/01/2015] [Accepted: 09/22/2015] [Indexed: 12/13/2022]
Abstract
The cofactor-free phenolic acid decarboxylases (PADs) catalyze the non-oxidative decarboxylation of phenolic acids to their corresponding p-vinyl derivatives. Phenolic acids are toxic to some organisms, and a number of them have evolved the ability to transform these compounds, including PAD-catalyzed reactions. Since the vinyl derivative products can be used as polymer precursors and are also of interest in the food-processing industry, PADs might have potential applications as biocatalysts. We have investigated the detailed reaction mechanism of PAD from Bacillus subtilis using quantum chemical methodology. A number of different mechanistic scenarios have been considered and evaluated on the basis of their energy profiles. The calculations support a mechanism in which a quinone methide intermediate is formed by protonation of the substrate double bond, followed by C-C bond cleavage. A different substrate orientation in the active site is suggested compared to the literature proposal. This suggestion is analogous to other enzymes with p-hydroxylated aromatic compounds as substrates, such as hydroxycinnamoyl-CoA hydratase-lyase and vanillyl alcohol oxidase. Furthermore, on the basis of the calculations, a different active site residue compared to previous proposals is suggested to act as the general acid in the reaction. The mechanism put forward here is consistent with the available mutagenesis experiments and the calculated energy barrier is in agreement with measured rate constants. The detailed mechanistic understanding developed here might be extended to other members of the family of PAD-type enzymes. It could also be useful to rationalize the recently developed alternative promiscuous reactivities of these enzymes.
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Affiliation(s)
- Xiang Sheng
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Sweden
| | - Maria E S Lind
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Sweden
| | - Fahmi Himo
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Sweden
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98
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Proton transfer in the K-channel analog of B-type Cytochrome c oxidase from Thermus thermophilus. Biophys J 2015; 107:2177-84. [PMID: 25418102 DOI: 10.1016/j.bpj.2014.09.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/03/2014] [Accepted: 09/11/2014] [Indexed: 01/08/2023] Open
Abstract
A key enzyme in aerobic metabolism is cytochrome c oxidase (CcO), which catalyzes the reduction of molecular oxygen to water in the mitochondrial and bacterial membranes. Substrate electrons and protons are taken up from different sides of the membrane and protons are pumped across the membrane, thereby generating an electrochemical gradient. The well-studied A-type CcO uses two different entry channels for protons: the D-channel for all pumped and two consumed protons, and the K-channel for the other two consumed protons. In contrast, the B-type CcO uses only a single proton input channel for all consumed and pumped protons. It has the same location as the A-type K-channel (and thus is named the K-channel analog) without sharing any significant sequence homology. In this study, we performed molecular-dynamics simulations and electrostatic calculations to characterize the K-channel analog in terms of its energetic requirements and functionalities. The function of Glu-15B as a proton sink at the channel entrance is demonstrated by its rotational movement out of the channel when it is deprotonated and by its high pKA value when it points inside the channel. Tyr-244 in the middle of the channel is identified as the valve that ensures unidirectional proton transfer, as it moves inside the hydrogen-bond gap of the K-channel analog only while being deprotonated. The electrostatic energy landscape was calculated for all proton-transfer steps in the K-channel analog, which functions via proton-hole transfer. Overall, the K-channel analog has a very stable geometry without large energy barriers.
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99
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Zhang HM, Chen SL. Include Dispersion in Quantum Chemical Modeling of Enzymatic Reactions: The Case of Isoaspartyl Dipeptidase. J Chem Theory Comput 2015; 11:2525-35. [DOI: 10.1021/acs.jctc.5b00246] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hai-Mei Zhang
- Key Laboratory
of Cluster
Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic
Conversion Materials, School of Chemistry, Beijing Institute of Technology, Beijing 100081, China
| | - Shi-Lu Chen
- Key Laboratory
of Cluster
Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic
Conversion Materials, School of Chemistry, Beijing Institute of Technology, Beijing 100081, China
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100
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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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