Properties of a Method for Performing Adaptive, Multilevel QM Simulations of Complex Chemical Reactions in the Gas-Phase

Guthrie, Malcolm; Daigle, April D.; Salazar, Michael R.

doi:10.1021/ct900449q

Cited by 10 publications

(8 citation statements)

References 49 publications

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“…Another highly desirable extension is to combine the FB scheme with the adaptive‐QM/MM algorithms, which treat the on‐the‐fly exchanges of atoms between the QM and MM subsystems. The combination of the FB and adaptive methods will lead to the open‐boundary QM/MM, which permits dynamical transfers of both partial charges and atoms at the same time between the QM and MM subsystem in MD simulations.…”

Section: Discussionmentioning

confidence: 99%

Molecular dynamics simulations of ion solvation by flexible‐boundary QM/MM: On‐the‐fly partial charge transfer between QM and MM subsystems

Pezeshki

Lin

2014

J Comput Chem

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The flexible-boundary (FB) quantum mechanical/molecular mechanical (QM/MM) scheme accounts for partial charge transfer between the QM and MM subsystems. Previous calculations have demonstrated excellent performance of FB-QM/MM in geometry optimizations. This article reports an implementation to extend FB-QM/MM to molecular dynamics simulations. To prevent atoms from getting unreasonably close, which can lead to polarization catastrophe, empirical correcting functions are introduced to provide additive penalty energies for the involved atom pairs and to improve the descriptions of the repulsive exchange forces in FB-QM/MM calculations. Test calculations are carried out for chloride, lithium, sodium, and ammonium ions solvated in water. Comparisons with conventional QM/MM calculations suggest that the FB treatment provides reasonably good results for the charge distributions of the atoms in the QM subsystems and for the solvation shell structural properties, albeit smaller QM subsystems have been used in the FB-QM/MM dynamics simulations.

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Section: Discussionmentioning

confidence: 99%

Molecular dynamics simulations of ion solvation by flexible‐boundary QM/MM: On‐the‐fly partial charge transfer between QM and MM subsystems

Pezeshki

Lin

2014

J Comput Chem

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“…By adaptive resolution it is meant that the space is partitioned in regions characterized by different molecular resolutions where molecules can freely diffuse changing their representation according to the region where they are instantaneously located. In the last few years several approaches have been presented and they are characterized by different levels of theoretical sophistication and computational complexity [1][2][3][4][5][6]. The interest in this kind of approach arises from the fact that it may efficiently tackle the problem of interplay between different scales.…”

Section: Introductionmentioning

confidence: 99%

“…Obviously the approach here is suited only for a class of problems and, as it is designed now, certainly not for those problems where the quantum mechanics refers to electrons. It must be noted that practical methods [6,16,17] which couple the two regimes when electrons are considered suffer from the same conceptual limitations underlined in this work and base their validity on numerical criteria only. In this specific case the conceptual discontinuity is in the arbitrary cut off of the electron wavefunction and in the non conservation of the number of electrons as the system evolves in time.…”

Section: Introductionmentioning

confidence: 99%

Classical to Path-Integral Adaptive Resolution in Molecular Simulation: Towards a Smooth Quantum-Classical Coupling

Poma

Site

2010

Phys. Rev. Lett.

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Simulations that couple different classical molecular models in an adaptive way by changing the number of degrees of freedom on the fly, are available within reasonably consistent theoretical frameworks. The same does not occur when it comes to classical-quantum adaptivity. The main reason for this is the difficulty in describing a continuous transition between the two different kind of physical principles: probabilistic for the quantum and deterministic for the classical. Here we report the basic principles of an algorithm that allows for a continuous and smooth transition by employing the path integral description of atoms.

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“…Adaptive methods allow atoms, or groups of atoms, to enter or leave the “active zone” which is typically centered on the QM core . In adaptive schemes, the partitioning of the entire system into QM and MM regions is not rigid, and the molecules are continually being repartitioned into QM and MM subsystems . The repartitioning of the QM and MM regions was initially accomplished by adopting a geometric criterion in the form of a distance cut‐off, R QM .…”

Section: Introductionmentioning

confidence: 99%

Toward more efficient density‐based adaptive QM/MM methods

Zheng¹,

Kuriappan²,

Waller³

2016

Int J of Quantum Chemistry

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Funding informationDeutsche Forschungsgemeinschaft (DFG).Adaptive QM/MM (quantum mechanical/molecular mechanical) methods repartition molecules on-the-fly into the QM and MM regions based on a partitioning criterion. A density-based partitioning scheme offers a unique way of carrying out QM and MM assignments on the presence/ absence of (non) covalent interactions between non-QM core molecules and the QM core. Here, we present two improvements to promote our density-based adaptive partitioning strategy for adaptive QM/MM calculations. First, bond formation/breaking processes between non-QM core molecules and the QM core are monitored using a density-based descriptor, to define an adaptive QM core region on the fly. Second, the density-based adaptive QM/MM partitioning scheme is made efficient enough for large systems by utilizating an adaptive search region and a Voronoi style-partitioning scheme. The adaptive search region is used to preselect the subset of molecules that may interact strongly enough with the QM core region, and then a density-based interaction calculation is only carried out on this subset. A Voronoi style-partitioning scheme achieves an efficient assignment of the density-based interactions. K E Y W O R D S adaptive multiscale modeling, density-based adaptive, noncovalent interactions, Voronoi partitioning 1 | I N T R O D U C T I O N Hybrid quantum mechanical/molecular mechanical (QM/MM) methods allow accurate calculations on large complex systems by describing the chemically most relevant (active) region with a high-level electronic structure method, while the remaining environment is modeled bylower-level methods. [1][2][3][4][5][6][7] The chemically relevant part is usually small, such as a solute, an enzyme's active site, [8,9] or a local defect in a material. [10] In traditional QM/MM methods, the contents of these regions are fixed and cannot change during a geometry optimization or molecular dynamics simulation. [11] This fixed composition of the two regions is not ideal for systems such as complex gas-phase reactive systems, solution processes, diffusion through liquid or solid, defect propagation, or reactions on catalytic surfaces such as nanoparticles.A number of so-called adaptive QM/MM schemes have been developed to effectively expand the research areas for traditional QM/ MM methodology. Adaptive methods allow atoms, or groups of atoms, to enter or leave the "active zone" which is typically centered on the QM core. [12][13][14][15][16][17][18][19][20][21][22][23][24][25] In adaptive schemes, the partitioning of the entire system into QM and MM regions is not rigid, and the molecules are continually being repartitioned into QM and MM subsystems. [26][27][28][29][30] The repartitioning of the QM and MM regions was initially accomplished by adopting a geometric criterion in the form of a distance cutoff, R QM . [14,[17][18][19][20][21] For each of the molecules in a given molecular system, assignment of QM versus MM character is determined by its distance from a predefined QM core r...

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Properties of a Method for Performing Adaptive, Multilevel QM Simulations of Complex Chemical Reactions in the Gas-Phase

Cited by 10 publications

References 49 publications

Molecular dynamics simulations of ion solvation by flexible‐boundary QM/MM: On‐the‐fly partial charge transfer between QM and MM subsystems

Molecular dynamics simulations of ion solvation by flexible‐boundary QM/MM: On‐the‐fly partial charge transfer between QM and MM subsystems

Classical to Path-Integral Adaptive Resolution in Molecular Simulation: Towards a Smooth Quantum-Classical Coupling

Toward more efficient density‐based adaptive QM/MM methods

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