Quantum mechanical/quantum mechanical methods. I. A divide and conquer strategy for solving the Schrödinger equation for large molecular systems using a composite density functional–semiempirical Hamiltonian

Westerhoff, Lance M.; Merz, Kenneth M.

doi:10.1063/1.1290608

Cited by 74 publications

(51 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Methods of this type have been pioneered by Morokuma and coworkers with their IMOMO/ONIOM series of models (see, e.g., refs. 68 and 69), but others have also developed similar techniques, including Gogonea et al, who have introduced a combined ab initio DFT/semiempirical QM algorithm, 70 and Hong et al, who describe a DFT method in which the electronic density of the environment is either frozen or constrained. 71 To finish this section it is perhaps worth restating the advantage that QM/MM methods have over pure QM methods for treating large molecular systems.…”

Section: Hybrid Potential Methodsmentioning

confidence: 99%

Simulating enzyme reactions: Challenges and perspectives

2001

View full text Add to dashboard Cite

Elucidating how enzymes enhance the rates of the reactions that they catalyze is a major goal of contemporary biochemistry, and it is an area in which computational and theoretical techniques can make a major contribution. This article outlines some of the processes that need to be investigated if enzyme catalysis is to be understood, reviews the current state-of-the-art in enzyme simulation work, and highlights challenges for the future.

show abstract

Section: Hybrid Potential Methodsmentioning

confidence: 99%

Simulating enzyme reactions: Challenges and perspectives

2001

View full text Add to dashboard Cite

show abstract

“…10,11 For large systems an alternative is the combination of a density functional as QM method with a semiempirical method or density-functional tight-binding (DFTB) as QM' method. [12][13][14] The flexibility of the ONIOM QM:QM' scheme makes it possible to choose an optimum combination of QM and QM' for a wide range of different phenomena.…”

Section: Introductionmentioning

confidence: 99%

Understanding cross‐boundary events in ONIOM QM:QM' calculations

Lundberg

2011

J Comput Chem

View full text Add to dashboard Cite

QM:QM' models, where QM' is a fast molecular orbital method, offers advantages over standard QM:MM models, especially in the description of charge transfer and mutual polarization between layers. The ONIOM QM:QM' scheme also allows for reactions across the layer boundary, but the understanding of these events is limited. To explain the factors that affect cross-boundary events, a set of proton transfer processes, including the acylation reaction in serine protease, have been investigated. For reactions inside out, i.e., when a group breaks a bond in the high layer and forms a new bond with a group in the low layer, QM' methods that are overbinding relative to the QM method, e.g., Hartree-Fock vs B3LYP, can severely overestimate the exothermicity of the reaction. This might lead to artificial reactivity across the QM:QM' boundary, a phenomenon called model escape. The accuracy for reactions that occur outside in, i.e., when a group in the low layer forms a new bond with the high layer, is mainly determined by the QM' calculation. Cross-boundary reactions should generally be avoided in the present ONIOM scheme. Fortunately, a better understanding of these events makes it easy to design stable ONIOM QM:QM' models, e.g.,

show abstract

“…Other authors have developed this work adding more sophisticated buffer regions and extending applicability to other ab initio and quantum chemistry methods [15]. Recent large scale efforts have shown promising results [16,17,18,19,20,21,22]. One of the principle challenges when using divide and conquer methods is the selection of subsystems.…”

Section: Introductionmentioning

confidence: 99%

The potential, limitations, and challenges of divide and conquer quantum electronic structure calculations on energetic materials.

Tucker¹,

Magyar²

2012

View full text Add to dashboard Cite

High explosives are an important class of energetic materials used in many weapons applications. Even with modern computers, the simulation of the dynamic chemical reactions and energy release is exceedingly challenging. While the scale of the detonation process may be macroscopic, the dynamic bond breaking responsible for the explosive release of energy is fundamentally quantum mechanical. Thus, any method that does not adequately describe bonding is destined to lack predictive capability on some level. Performing quantum mechanics calculations on systems with more than dozens of atoms is a gargantuan task, and severe approximation schemes must be employed in practical calculations. We have developed and tested a divide and conquer (DnC) scheme to obtain total energies, forces, and harmonic frequencies within semi-empirical quantum mechanics. The method is intended as an approximate but faster solution to the full problem and is possible due to the sparsity of the density matrix in many applications. The resulting total energy calculation scales linearly as the number of subsystems, and the method provides a path-forward to quantum mechanical simulations of millions of atoms. 3This page intentionally left blank.4

show abstract

Quantum mechanical/quantum mechanical methods. I. A divide and conquer strategy for solving the Schrödinger equation for large molecular systems using a composite density functional–semiempirical Hamiltonian

Cited by 74 publications

References 17 publications

Simulating enzyme reactions: Challenges and perspectives

Simulating enzyme reactions: Challenges and perspectives

Understanding cross‐boundary events in ONIOM QM:QM' calculations

The potential, limitations, and challenges of divide and conquer quantum electronic structure calculations on energetic materials.

Contact Info

Product

Resources

About