One-electron quantum capping potential for hybrid QM/MM studies of silicate molecules and solids

Jardillier, Nicolas; Goursot, Annick

doi:10.1016/j.cplett.2008.01.073

Cited by 15 publications

(5 citation statements)

References 28 publications

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“…(f) Quantum capping potentials: The saturation of dangling bonds with effective potentials has already been attempted by DiLabio et al – in an approach that is similar to the one proposed in this work. A conventional pseudopotential is used to truncate the quantum region, using a local part and nonlocal angular-momentum-dependent projectors.…”

Section: Introductionmentioning

confidence: 93%

Optimization of Capping Potentials for Spectroscopic Parameters in Hybrid Quantum Mechanical/Mechanical Modeling Calculations

Komin

Sebastiani

2009

J. Chem. Theory Comput.

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We present a capping scheme for hybrid calculations which is designed for a systematic optimization to reproduce the molecular structure, frontier bond potential, and spectroscopic properties for the quantum subsystem. Our technique is capable of reducing the perturbations of the electronic structure which are normally caused by conventional link atoms between quantum and classical regions. Specifically, we propose analytic effective core potentials with a small set of adjustable parameters, which are optimized to reproduce the full-quantum-mechanical (full-QM) properties in the direct environment of the bond cleavage. The capping potentials are conceptually simple and easy to employ in most instances without significant code modifications. They do not require any further external geometry constraints and yield also reasonable results for the potential energy surface. We benchmark these potentials for a series of chemically and biologically relevant molecules calculating NMR chemical shifts, protonation energies, and optimized geometries. Our optimized QM/mechanical modeling (MM) potentials are another step toward a realistic first-principles prediction of spectroscopic parameters in complex chemical environments using hybrid QM/MM calculations.

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Section: Introductionmentioning

confidence: 93%

Optimization of Capping Potentials for Spectroscopic Parameters in Hybrid Quantum Mechanical/Mechanical Modeling Calculations

Komin

Sebastiani

2009

J. Chem. Theory Comput.

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“…Note that for heavier elements scalar relativistic effects must be taken into account either by effective core potentials (ECPs) or by model core potentials (MCPs) [50]. The ECP approach can also be used for the introduction of capping potentials [51] in QM/MM calculations. We also recommend the PBE functional for QM/MM calculation because analytic ADFT kernel formulas [52] are implemented in deMon2k.…”

Section: Energies and Gradientsmentioning

confidence: 99%

Chapter 1. QM/MM with Auxiliary DFT in deMon2k

Samaniego-Rojas¹,

Hernández-Segura²,

López-Sosa³

et al. 2021

Theoretical and Computational Chemistry Series

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This chapter describes the theoretical background of the Quantum Mechanical/Molecular Mechanical (QM/MM) implementation in deMon2k within the framework of Auxiliary Density Functional Theory (ADFT). It aims to give the reader an overview of the current state-of-the-art of this QM/MM implementation and perspectives for its future development. To this end, we first derive the ADFT working equations for the QM and QM/MM energy and gradient expressions.Based on the joined QM/MM gradient expression, we present algorithms for QM/MM structure optimizations, transition state searches and molecular dynamics simulations. The use of auxiliary density perturbation theory (ADPT) in the framework of QM/MM is discussed on illustrative example implementations including analytic second-order ADFT energy derivatives, nuclear magnetic resonance chemical shift calculations and excited state calculations by time-dependent ADFT. The chapter closes with the description of a transformation program to generate deMon2k QM/MM inputs.

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“…For the capping potentials efficient half-numerical effective core potential (ECP) and model core potential (MCP) integral routines are available in deMon2k [60]. The capping potential is used in combination with an optimized basis set [61,62]. The advantage of this approach is that optimization or molecular dynamics can be performed per se without adding spurious atoms to the system.…”

Section: In-demon2k Qm/mmmentioning

confidence: 99%

QM/MM Calculations with deMon2k

et al. 2015

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Abstract:The density functional code deMon2k employs a fitted density throughout (Auxiliary Density Functional Theory), which offers a great speed advantage without OPEN ACCESSMolecules 2015, 20 4781 sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM) approaches are reviewed. Following an overview of the basic features of deMon2k that make it efficient while retaining accuracy, three QM/MM implementations are compared and contrasted. In the first, deMon2k is interfaced with the CHARMM MM code (CHARMM-deMon2k); in the second MM is coded directly within the deMon2k software; and in the third the Chemistry in Ruby (Cuby) wrapper is used to drive the calculations. Cuby is also used in the context of constrained-DFT/MM calculations. Each of these implementations is described briefly; pros and cons are discussed and a few recent applications are described briefly. Applications include solvated ions and biomolecules, polyglutamine peptides important in polyQ neurodegenerative diseases, copper monooxygenases and ultra-rapid electron transfer in cryptochromes.

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One-electron quantum capping potential for hybrid QM/MM studies of silicate molecules and solids

Cited by 15 publications

References 28 publications

Optimization of Capping Potentials for Spectroscopic Parameters in Hybrid Quantum Mechanical/Mechanical Modeling Calculations

Optimization of Capping Potentials for Spectroscopic Parameters in Hybrid Quantum Mechanical/Mechanical Modeling Calculations

Chapter 1. QM/MM with Auxiliary DFT in deMon2k

QM/MM Calculations with deMon2k

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