Performance Evaluation of the Three-Layer ONIOM Method:  Case Study for a Zwitterionic Peptide

Abstract

The performance of the three-layer ONIOM method was systematically investigated by comparing the optimized geometries and calculated deprotonation energy of a zwitterionic peptide molecule, NH3(+)-CH(n)Bu-CO-NH-CH2-CO-NH-CH(n)Bu-COO(-), using all possible combinations of B3LYP/6-31G* as the high-level quantum (HQ), AM1 as the low-level quantum (LQ), and Amber as the MM method. Results show that the three-layer ONIOM(HQ:LQ:MM) method, which includes a medium-level quantum method in the middle system to take into account the electronic effects of the middle layer and to keep the problematic QM-MM boundary away from the action region, is more reliable and more stable than the QM:MM:MM or generic QM/MM method and is the best compromise between accuracy and computational cost.

Multi-state extrapolation of UV/Vis absorption spectra with QM/QM hybrid methods

“…[25][26][27][28][29][30][35][36][37] Hence, let us briefly review ONIOM for two layers and introduce the notation that we will use throughout the paper. Following the layer separation in Figure 1, open valencies resulting from the severing of covalent bonds are capped with link atoms (usually hydrogens), e.g., X Y −→ X-H.…”

“…[10][11][12][13][14][15][16] The use of QM/QM methods has also been extended in recent times to excited state calculations. [17][18][19][20][21][22][23][24] One of the most successful hybrid methods is ONIOM (Our own N-layered Integrated molecular Orbital molecular Mechanics), [25][26][27][28][29][30] which is briefly described in Sec. II.…”

Binding of huperzine A and galanthamine to acetylcholinesterase, based on ONIOM method

“…To understand the interaction of AChE and the drugs (GAL and HUP A), an ONIOM (our own nlayered integrated molecular orbital and molecular mechanics) method 15,16 has been applied. This method is based on the idea that molecular calculations at the active center of a biomolecular complex can be performed with methods of higher accuracy, and the remaining protein is treated with a lower level of calculations.…”

Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM

“…Still, both link atom and localized orbital significantly perturb the studied system, necessitating a careful choice of the boundary and its distance to the actual bond breaking or making to achieve energy convergence in the calculation. It is therefore recommended to place any QM/MM boundary at least three bonds away from the bond broken or made, otherwise a discontinuous PES may result (104). Furthermore, because charge transfer through the QM/MM boundary is neglected, it would be incorrect to cut any bonds for which charge transfer is expected, such as a conjugated or coordination bond.…”