Strong Trans Influence Methoxymethyl Ligand in B12Cobaloxime and Imine/Oxime Model Complexes:  Structural, Spectroscopic, and Molecular Mechanics Investigations

1998 ◽  
Vol 37 (26) ◽  
pp. 6890-6897 ◽  
Author(s):  
Renzo Cini ◽  
Scott J. Moore ◽  
Luigi G. Marzilli
2004 ◽  
Vol 82 (11) ◽  
pp. 1619-1624 ◽  
Author(s):  
Lilian W Paes ◽  
Roberto B Faria ◽  
Juan O Machuca-Herrera ◽  
Ademir Neves ◽  
Sérgio P Machado

Purple acid phosphatases (PAPs) constitute a new class of metalloenzymes that catalyze the hydrolysis of certain phosphate esters, including nucleoside di- and triphosphates and aryl phosphates, under acidic conditions. To provide some insight into these metalloenzymes we have performed quantum chemical and molecular mechanics calculations based on the mixed-valence [FeIIFeIII(BPBPMP)(OAc)2]+ model complex (1) (H2BPBPMP = 2-bis[{(2-pyridylmethyl)-aminomethyl}-6-{(2-hydroxybenzyl)-(2-pyridylmethyl)}-aminomethyl]-4-methylphenol). The geometric and the vibrational parameters calculated by molecular mechanics show that the force fields established in this work reproduce the binuclear iron core with µ-phenoxo or µ-alkoxo and di-µ-acetate bridges presented in the PAPs model complexes. The atomic orbital analysis of the SOMO contributions indicated that the FeIII atom and the terminal phenolate are involved in the phenolate to FeIII charge transfer electronic transition in 1 as argued from electronic spectroscopic data in the PAPs. Key words: mixed-valence FeIIFeIII complex, purple acid phosphatases, molecular modeling.


1989 ◽  
Vol 86 ◽  
pp. 945-954 ◽  
Author(s):  
F. Bayard ◽  
D. Decoret ◽  
D. Pattou ◽  
J. Royer ◽  
A. Satrallah ◽  
...  

2020 ◽  
Author(s):  
Zenghui Yang

Quantum mechanics/molecular mechanics (QM/MM) methods partition the system into active and environmental regions and treat them with different levels of theory, achieving accuracy and efficiency at the same time. Adaptive-partitioning (AP) QM/MM methods allow on-the-fly changes to the QM/MM partitioning of the system. Many of the available energy-based AP-QM/MM methods partition the system according to distances to pre-chosen centers of active regions. For such AP-QM/MM methods, I develop an adaptive-center (AC) method that allows on-the-fly determination of the centers of active regions according to general geometrical or potential-related criteria, extending the range of application of energy-based AP-QM/MM methods to systems where active regions may occur or vanish during the simulation.


Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.


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