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

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.

Author(s):  
Kenta Kuroishi ◽  
Muhammad Rifqi Al Fauzan ◽  
Ngoc Thanh Pham ◽  
Yuelin Wang ◽  
Yuji Hamamoto ◽  
...  

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...


2020 ◽  
Vol 44 (5) ◽  
pp. 1254-1264
Author(s):  
Shaya AL-RAQA ◽  
İpek ÖMEROĞLU ◽  
Doğan ERBAHAR ◽  
Mahmut DURMUŞ

Phenyl-4,4-di(3,6-dibutoxyphthalonitrile) (3) was synthesized by the reaction of 1,4-phenylenebisboronic acid (1) and 4-bromo-3,6-dibutoxyphthalonitrile (2), using Suzuki cross-coupling reaction. The newly synthesized compound (3) was characterized by FT-IR, MALDI-MS, ESI-MS, 1H-NMR, 13C-NMR, and 13C-DEPT-135-NMR. The fluorescence property of phenyl-4,4-di(3,6- dibutoxyphthalonitrile) (3) towards various metal ions was investigated by fluorescence spectroscopy, and it was observed thatthe compound (3) displayed a significantly ‘turn-off’ response to Fe3+, which was referred to 1:2 complex formation between ligand (3) and Fe3+. The compound was also studied via density functional theory calculations revealing the interaction mechanism of the molecule with Fe3+ ions.


2019 ◽  
Vol 48 (1) ◽  
pp. 168-175 ◽  
Author(s):  
Chao Deng ◽  
Yingxin Sun ◽  
Yi Ren ◽  
Weihua Zhang

Density functional theory calculations were carried out to study the reaction mechanism of the Rh(iii)-catalyzed regioselective C–H cyanation of indole and indoline with N-cyano-N-phenyl-para-methylbenzenesulfonamide (NCTS).


2007 ◽  
Vol 06 (01) ◽  
pp. 1-12 ◽  
Author(s):  
JIAN-HUA XU ◽  
LAI-CAI LI ◽  
YAN ZHENG ◽  
JUN-LING LIU ◽  
XIN WANG

The reaction mechanisms of HNCS with CH 2 CH radical have been investigated by density functional theory (DFT). The geometries and harmonic frequencies of the reactants, intermediates, transition states and products have been calculated at the B3LYP/6-311++G(d,p) level. The results show that the reaction is very complicated. Nine possible reaction pathways were identified. The results show that the most feasible reaction channel is the hydrogen-transfer pathway CH 2 CH + HNCS → IMA1 → TSA1 → CH 2 CHH + NCS . The pathway VIC C-S addition channel ( CH 2 CH + HNCS → TSD5 → IMD4 → TSD9 → CH 2 CHS + CNH ) can also occur easily. Ethene and radical NCS is the main product of the studied reaction, and product P8 ( CH 2 CHS and CNH ) may also be observed. Compared with our previous study on the reaction HNCS + CH 2 CH , the present reaction is easier to proceed.


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