ONIOM:  A Multilayered Integrated MO + MM Method for Geometry Optimizations and Single Point Energy Predictions. A Test for Diels−Alder Reactions and Pt(P(t-Bu)₃)₂ + H₂ Oxidative Addition

Abstract

The new ONIOM (our own n-layered integrated molecular orbital and molecular mechanics) approach has been proposed and shown to be successful in reproducing benchmark calculations and experimental results. ONIOM3, a three-layered version, divides a system into an active part treated at a very high level of ab initio molecular orbital theory like CCSD(T), a semiactive part that includes important electronic contributions and is treated at the HF or MP2 level, and a nonactive part that is handled using force field approaches. The three-layered scheme allows us to study a larger system more accurately than the previously proposed two-layered schemes IMOMO, which can treat a medium size system very accurately, and IMOMM, which can handle a very large system with modest accuracy. This three-layered scheme has been applied to activation barriers for the Diels−Alder reaction of acrolein + isoprene, acrolein + 2-tert-butyl-1,3-butadiene, and ethylene + 1,4-di-tert-butyl-1,3-butadiene. In general, the results for both geometry optimizations and single point energy calculations agree well with benchmark predictions and experimental results. The scheme has also been applied to the transition state for the oxidative addition of H2 to Pt(P(t-Bu)3)2. The activation energy of this 83-atom reaction is predicted to be 14.2 kcal/mol with the ONIOM3(CCSD(T):MP2:MM3) method.

Modeling Heat Dissipation at the Nanoscale: An Embedding Approach for Chemical Reaction Dynamics on Metal Surfaces

“…The contribution of elastic substrate-substrate interaction is supplied by V Me , which denotes an energy from a large bath-like MM region described at the level of many-body CIPs. Equation (1) bears similarities to the ONIOM scheme of Morokuma and coworkers, [22] but avoids the construction of finite QM clusters entirely by treating the embedded region twice at the same level of theory. This crucial difference exploiting the short-rangedness of V ∆QM avoids boundary effects and yields a quantum mechanical manybody augmentation of the CIP V Me that fully captures the chemistry of bond breaking and making.…”

Transition States in a Protein Environment − ONIOM QM:MM Modeling of Isopenicillin N Synthesis

“…[5][6][7][8] In the present QM:MM model, the metal center, i.e., iron, iron ligands and substrate, is treated by density-functional theory (DFT), while the rest of the enzyme is treated by a classical force field. The two-layer approach is not only computationally efficient, but also makes it easier to separate effects from the metal center from those of the surrounding protein because they are described at different computational levels.…”

Modeling the Absorption Spectrum of Tryptophan in Proteins

“…Traditionally, protein dynamics are studied through classical MD simulations, and classical force fields such as CHARMM 22 and AMBER 21 are used extensively to study the structure and dynamics of proteins. Hybrid quantum mechanics/ molecular mechanics (QM/MM) methods, such as ONIOM, 28 provide a compromise between fully quantum and classical approaches, resulting in improved structural predictions. The main thrust of this paper is to address the problem of computing the excited states of the chromophore within the environment of the protein.…”