A QM/MM study of nitric oxide reductase-catalysed N2O formation

被引：8

作者：

Shoji, Mitsuo ^{[1
,2
]}

Hanaoka, Kyohei ^{[1
]}

Kondo, Daiki ^{[1
]}

Sato, Akimasa ^{[1
]}

Umeda, Hiroaki ^{[2
]}

Kamiya, Katsumasa ^{[1
]}

Shiraishi, Kenji ^{[1
]}

机构：

[1] Univ Tsukuba, Grad Sch Pure & Appl Sci, Tsukuba, Ibaraki, Japan

[2] Univ Tsukuba, Ctr Computat Sci, Tsukuba, Ibaraki, Japan

来源：

MOLECULAR PHYSICS | 2014年 / 112卷 / 3-4期

关键词：

nitric oxide reductase; QM; MM; nitrous oxide; N2O; nitric oxide; NO; HEME-COPPER OXIDASE; PARACOCCUS-DENITRIFICANS;

D O I：

10.1080/00268976.2013.830200

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

Nitrous oxide (N2O), with a greenhouse effect 300 times that of CO2, is increasingly eliminated into the atmosphere. Using a hybrid quantum mechanics/molecular mechanics (QM/MM) method, we examined nitric oxide reductase-catalysed N2O formation, which includes two important chemical reactions of N-N bond formation and N-O bond cleavage. The N-N bond formation has no activation barrier, but N-O bond cleavage exhibits an activation barrier of 20.9 kcal.mol(-1) at the QM/MM level. We show that the N-O bond cleavage occurs via a hyponitrous intermediate (Fe-B (II; s = 4/2)/N2O2 (-1; s = 1/2)/Fe-b3(III; s = -1/2)), with bidentate coordination between Glu211 and a non-heme iron atom. The Glu211 coordination decreases the N-O bond cleavage energy barrier by inhibiting the formation of stable, five-membered ring intermediate (Fe-B-O-1-N-1-N-2-O-2-).

引用

页码：393 / 397

页数：5

共 50 条

[1] Electroanalytical characterization of the direct Marinobacter hydrocarbonoclasticus nitric oxide reductase-catalysed nitric oxide and dioxygen reduction
Gomes, Filipa O.
Maia, Luisa B.
Cordas, Cristina
Moura, Isabel
Delerue-Matos, Cristina
Moura, Jose J. G.
Morais, Simone
BIOELECTROCHEMISTRY, 2019, 125 : 8 - 14
[2] Mechanism for N2O Generation in Bacterial Nitric Oxide Reductase: A Quantum Chemical Study
Blomberg, Margareta R. A.
Siegbahn, Per E. M.
BIOCHEMISTRY, 2012, 51 (25) : 5173 - 5186
[3] Structural Basis of Biological N2O Generation by Bacterial Nitric Oxide Reductase
Hino, Tomoya
Matsumoto, Yushi
Nagano, Shingo
Sugimoto, Hiroshi
Fukumori, Yoshihiro
Murata, Takeshi
Iwata, So
Shiro, Yoshitsugu
SCIENCE, 2010, 330 (6011) : 1666 - 1670
[4] Mineral-catalysed formation of marine NO and N2O on the anoxic early Earth
Buessecker, Steffen
Imanaka, Hiroshi
Ely, Tucker
Hu, Renyu
Romaniello, Stephen J.
Cadillo-Quiroz, Hinsby
NATURE GEOSCIENCE, 2022, 15 (12) : 1056 - +
[5] The formation of N2O during the chemisorptions of nitric oxide at platinum surfaces at low temperature:: a comment on the mechanism
Roberts, MW
CATALYSIS LETTERS, 2004, 93 (1-2) : 29 - 30
[6] The Formation of N2O During the Chemisorptions of Nitric Oxide at Platinum Surfaces at Low Temperature: A Comment on the Mechanism
M.W. Roberts
Catalysis Letters, 2004, 93 : 29 - 30
[7] Isotopic Fractionation by a Fungal P450 Nitric Oxide Reductase during the Production of N2O
Yang, Hui
Gandhi, Hasand
Ostrom, Nathaniel E.
Hegg, Eric L.
ENVIRONMENTAL SCIENCE & TECHNOLOGY, 2014, 48 (18) : 10707 - 10715
[8] Kinetics of nitrous oxide (N2O) formation and reduction by Paracoccus pantotrophus
Read-Daily, B. L.
Sabba, F.
Pavissich, J. P.
Nerenberg, R.
AMB EXPRESS, 2016, 6
[9] Mechanisms of nitrous oxide (N2O) formation and reduction in denitrifying biofilms
Sabba, Fabrizio
Picioreanu, Cristian
Nerenberg, Robert
BIOTECHNOLOGY AND BIOENGINEERING, 2017, 114 (12) : 2753 - 2761
[10] Can Reduction of NO to N2O in Cytochrome c Dependent Nitric Oxide Reductase Proceed through a Trans-Mechanism?
Blomberg, Margareta R. A.
BIOCHEMISTRY, 2017, 56 (01) : 120 - 131

← 1 2 3 4 5 →