title: Theoretical study on reaction mechanisms of nitrite reduction by copper nitrite complexes: toward understanding and controlling possible mechanisms of copper nitrite reductase.
abstract: Using density functional theory, we studied denitrification reaction mechanisms of copper adducts of tris(pyrazolyl)methane and hydrotris(pyrazolyl)borate models of a copper nitrite reductase (Cu-NiR), and herein propose several possible reaction pathways, including some parts that have never been examined previously. Because electron and proton transfer reactions participate in the enzymatic cycles of Cu-NiR, the Gibbs energy of a proton in solution, G(H(+)), and the redox potential, Eredox, of the model Cu-NiR are also evaluated. Although the pathway where a nitrite is provided as HNO2 is energetically preferable, a well-known reaction pathway passing through the resting state with an active site occupied by a water molecule where nitrite is provided as NO2(-) is the main recognized pathway under normal conditions. These features do not change whether the electron transfer occurs before production of NO or not. However, our results suggest that the pathway involving HNO2 might become dominant under low pH conditions in conjunction with experimental results.
authors.affiliation: †Computational Science Group, Mitsui Chemicals, Inc., 580-32 Nagaura, Sodegaura, Chiba 299-0265, Japan.
authors.forename: Shintaro
authors.initials: S
authors.lastname: Maekawa
authors.affiliation: ‡RIKEN, Advanced Institute for Computational Science, 7-1-26, Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan.
authors.forename: Toru
authors.initials: T
authors.lastname: Matsui
authors.affiliation: ‡RIKEN, Advanced Institute for Computational Science, 7-1-26, Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan.
authors.forename: Kimihiko
authors.initials: K
authors.lastname: Hirao
authors.affiliation: §Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.|∥CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawagoe, Saitama 332-0012, Japan.
authors.forename: Yasuteru
authors.initials: Y
authors.lastname: Shigeta
mesh_terms: D040761:Biomimetic Materials / Q000737:chemistry*; D001881:Borates / Q000737:chemistry; D020134:Catalytic Domain; D003300:Copper / Q000737:chemistry*; D004579:Electron Transport; D008958:Models, Molecular; D009572:Nitrite Reductases / Q000737:chemistry*; D009573:Nitrites / Q000737:chemistry*; D009942:Organometallic Compounds / Q000737:chemistry*; D011720:Pyrazoles / Q000737:chemistry; D011789:Quantum Theory
chemical_list: D001881:Borates; D009573:Nitrites; D009942:Organometallic Compounds; D011720:Pyrazoles; C515919:hydrotris(pyrazolyl)borate; C515920:tris(pyrazolyl)methane; D003300:Copper; D009572:Nitrite Reductases; C052695:nitrite reductase, copper-containing