scholarly journals Nitric oxide coupling to generate N2O promoted by a single-heme system as examined by density functional theory

Nitric Oxide ◽  
2016 ◽  
Vol 60 ◽  
pp. 69-75 ◽  
Author(s):  
Jun Yi ◽  
Adam L.O. Campbell ◽  
George B. Richter-Addo
Keyword(s):  
Nitric Oxide ◽  
Density Functional Theory ◽  
Density Functional ◽  
Functional Theory

A flat-lying dimer as a key intermediate in NO reduction on Cu(100)

2021 ◽  
Author(s):  
Kenta Kuroishi ◽  
Muhammad Rifqi Al Fauzan ◽  
Ngoc Thanh Pham ◽  
Yuelin Wang ◽  
Yuji Hamamoto ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Density Functional Theory ◽  
Scanning Tunneling Microscope ◽  
Density Functional ◽  
No Reduction ◽  
Density Functional Theory Calculations ◽  
Scanning Tunneling ◽  
Functional Theory ◽  
Tunneling Microscope ◽  
Electron Energy Loss

The reaction of nitric oxide (NO) on Cu(100) is studied by scanning tunneling microscope, electron energy loss spectroscopy and density functional theory calculations. The NO molecules adsorb mainly as monomers...

scholarly journals Insight into Trimeric Formation of Nitric Oxide on Cu(111): A Density Functional Theory Study

2020 ◽  
Vol 124 (5) ◽  
pp. 2968-2977 ◽  
Author(s):  
Thanh Ngoc Pham ◽  
Yuji Hamamoto ◽  
Kouji Inagaki ◽  
Do Ngoc Son ◽  
Ikutaro Hamada ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Density Functional Theory ◽  
Density Functional ◽  
Density Functional Theory Study ◽  
Functional Theory ◽  
Insight Into

PLANE-WAVE PSEUDOPOTENTIAL DENSITY FUNCTIONAL THEORY PERIODIC SLAB CALCULATIONS OF NO ADSORPTION ON Ag(001) SURFACE

2010 ◽  
Vol 09 (04) ◽  
pp. 701-709
Author(s):  
H. AGHAIE ◽  
M. R. GHOLAMI ◽  
F. KHAZALI ◽  
K. ZARE ◽  
M. MONAJJEMI ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Density Functional Theory ◽  
Plane Wave ◽  
Density Functional ◽  
Hollow Site ◽  
Generalized Gradient ◽  
No Adsorption ◽  
Functional Theory ◽  
Adsorption Sites ◽  
Generalized Gradient Approximation

Plane-wave pseudopotential density functional theory (DFT) periodic slab calculations were performed using the generalized gradient approximation (GGA) to investigate the adsorption of nitric oxide (NO) on the (001) surface of Ag . We examined three different adsorption sites perpendicular with respect to the surface and a position that the axis of NO molecule was tilted from the upright. The adsorption of NO in the fourfold hollow site was favored, with a binding energy of 45.47 kJ/mol.

Interaction of Nitric Oxide and Nitric Oxide Dimer with Silver Clusters

2005 ◽  
Vol 1 (4) ◽  
pp. 253-258 ◽  
Author(s):  
V.E. Matulis ◽  
O.A. Ivashkevich ◽  
V.S. Gurin
Keyword(s):  
Nitric Oxide ◽  
Density Functional Theory ◽  
Cluster Model ◽  
Density Functional ◽  
Bond Formation ◽  
Silver Cluster ◽  
Silver Clusters ◽  
Functional Theory ◽  
Nitric Oxide Dimer

Study of interaction of NO and (NO)2 molecules with silver clusters has been carried out using the hybrid method S2LYP based on density functional theory (DFT). The role of cluster charge and site of adsorption on N–O stretch frequency, adsorption energy and geometry has been investigated. Four cluster models of different size have been used for simulation of (NO)2 adsorption on Ag{111} surface. The pronounced effect of N–N bond shortening in comparison with gaseous (NO)2 has been found due to adsorption of (NO)2 on silver cluster. This phenomenon is important as possible pathway of N–N bond formation in catalytic fragmentation of NO molecule. The calculations showed that the silver octamer is the best candidate for simulation of formation and fragmentation of (NO)2 on Ag{111} surface within the cluster model.

Density functional theory (DFT) and combined quantum mechanical/molecular mechanics (QM/MM) studies on the oxygen activation step in nitric oxide synthase enzymes

2009 ◽  
Vol 37 (2) ◽  
pp. 373-377 ◽  
Author(s):  
Sam P. de Visser
Keyword(s):  
Nitric Oxide ◽  
Density Functional Theory ◽  
Cytochrome P450 ◽  
Density Functional ◽  
Catalytic Cycle ◽  
Theoretical Studies ◽  
Cytochrome P450 Enzymes ◽  
Compound I ◽  
Functional Theory ◽  
Oxide Synthase

In this review paper, we will give an overview of recent theoretical studies on the catalytic cycle(s) of NOS (nitric oxide synthase) enzymes and in particular on the later stages of these cycles where experimental work is difficult due to the short lifetime of intermediates. NOS enzymes are vital for human health and are involved in the biosynthesis of toxic nitric oxide. Despite many experimental efforts in the field, the catalytic cycle of this important enzyme is still surrounded by many unknowns and controversies. Our theoretical studies were focused on the grey zones of the catalytic cycle, where intermediates are short-lived and experimental detection is impossible. Thus combined QM/MM (quantum mechanics/molecular mechanics) as well as DFT (density functional theory) studies on NOS enzymes and active site models have established a novel mechanism of oxygen activation and the conversion of L-arginine into Nω-hydroxo-arginine. Although NOS enzymes show many structural similarities to cytochrome P450 enzymes, it has long been anticipated that therefore they should have a similar catalytic cycle where molecular oxygen binds to a haem centre and is converted into an Fe(IV)-oxo haem(+•) active species (Compound I). Compound I, however, is elusive in the cytochrome P450s as well as in NOS enzymes, but indirect experimental evidence on cytochrome P450 systems combined with theoretical modelling have shown it to be the oxidant responsible for hydroxylation reactions in cytochrome P450 enzymes. By contrast, in the first catalytic cycle of NOS it has been shown that Compound I is first reduced to Compound II before the hydroxylation of arginine. Furthermore, substrate arginine in NOS enzymes appears to have a dual function, namely first as a proton donor in the catalytic cycle to convert the ferric-superoxo into a ferric-hydroperoxo complex and secondly as the substrate that is hydroxylated in the process leading to Nω-hydroxo-arginine.

Basis set superposition error in MP2 and density-functional theory: A case of methane-nitric oxide association

2005 ◽  
Vol 123 (13) ◽  
pp. 134107 ◽  
Author(s):  
Rachel Crespo-Otero ◽  
Luis Alberto Montero ◽  
Wolf-Dieter Stohrer ◽  
José M. García de la Vega
Keyword(s):  
Nitric Oxide ◽  
Density Functional Theory ◽  
Density Functional ◽  
Basis Set ◽  
Functional Theory ◽  
Basis Set Superposition Error
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