Multilevel X-Pol: A Fragment-Based Method with Mixed Quantum Mechanical Representations of Different Fragments

Wang, Yingjie; Sosa, Carlos; Cembran, Alessandro; Truhlar, Donald G.; Gao, Jiali

doi:10.1021/jp212399g

Cited by 36 publications

(41 citation statements)

References 85 publications

(236 reference statements)

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“…For completeness, we first provide a brief summary of the fragment‐based X‐Pol density embedding scheme, which may be considered as a generalization of combined QM/MM approaches to a multilayer QM representation of the system. [ 47 ] Then, we describe the present DF approach for treatment of interfragment electrostatic interactions, particularly useful for fragments in close contact. The method is closely related to the general approach used in linear scaling electronic structure method and DFT calculations.…”

Section: Methodsmentioning

confidence: 99%

A self‐consistent coulomb bath model using density fitting

Chen

Suo

et al. 2020

J Comput Chem

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A self-consistent Coulomb bath model is presented to provide an accurate and efficient way of performing calculations for interfragment electrostatic and polarization interactions. In this method, a condensed-phase system is partitioned into molecular fragment blocks. Each fragment is embedded in the Coulomb bath due to other fragments. Importantly, the present Coulomb bath is represented using a density fitting method in which the electron densities of molecular fragments are fitted using an atom-centered auxiliary basis set of Gaussian type. The Coulomb bath is incorporated into an effective Hamiltonian for each fragment, with which the electron density is optimized through an iterative double self-consistent field (DSCF) procedure to realize the mutual many-body polarization effects. In this work, the accuracy of interfragment interaction energies enumerated using the Coulomb bath is tested, showing a good agreement with the exact results from an energy decomposition analysis. The qualitative features of many-body polarization effects are visualized by electron density difference plots. It is also shown that the present DSCF method can yield fast and robust convergence with near-linear scaling in performance with increase in system size. K E Y W O R D Scoulomb bath mode, density fitting, fragment-based method

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Section: Methodsmentioning

confidence: 99%

A self‐consistent coulomb bath model using density fitting

Chen

Suo

et al. 2020

J Comput Chem

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“…12 In practice, Δ H ( Q , R [ t ]) can be evaluated using a combined QM/MM potential, or by a mixed fragmental QM model in which the solute and its nearest neighbors are described by a high-level theory embedded in the solvent environment to model long-range electrostatic effects. 89 In the latter case, short-range repulsion, dispersion, and charge transfer effects between the oscillator and solvent molecules in close proximity are naturally included in the QM model. For the present HCl–water clusters, the entire system is treated quantum-mechanically using two QM methods: M06-2X 90 /cc-pVTZ and CCSD(T)-F12B 91–93 /cc-pVTZ.…”

Section: Methodsmentioning

confidence: 99%

Perturbation Approach for Computing Infrared Spectra of the Local Mode of Probe Molecules

Xue

Grofe

Yin

et al. 2016

J. Chem. Theory Comput.

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Linear and two-dimensional infrared (IR) spectroscopy of site-specific probe molecules provides an opportunity to gain a molecular-level understanding of the local hydrogen-bonding network, conformational dynamics, and long-range electrostatic interactions in condensed-phase and biological systems. A challenge in computation is to determine the time-dependent vibrational frequencies that incorporate explicitly both nuclear quantum effects of vibrational motions and an electronic structural representation of the potential energy surface. In this paper, a nuclear quantum vibrational perturbation (QVP) method is described for efficiently determining the instantaneous vibrational frequency of a chromophore in molecular dynamics simulations. Computational efficiency is achieved through the use of (a) discrete variable representation of the vibrational wave functions, (b) a perturbation theory to evaluate the vibrational energy shifts due to solvent dynamic fluctuations, and (c) a combined QM/MM potential for the systems. It was found that first-order perturbation is sufficiently accurate, enabling time-dependent vibrational frequencies to be obtained on the fly in molecular dynamics. The QVP method is illustrated in the mode-specific linear and 2D-IR spectra of the H–Cl stretching frequency in the HCl–water clusters and the carbonyl stretching vibration of acetone in aqueous solution. To further reduce computational cost, a hybrid strategy was proposed, and it was found that the computed vibrational spectral peak position and line shape are in agreement with experimental results. In addition, it was found that anharmonicity is significant in the H–Cl stretching mode, and hydrogen-bonding interactions further enhance anharmonic effects. The present QVP method complements other computational approaches, including path integral-based molecular dynamics, and represents a major improvement over the electrostatics-based spectroscopic mapping procedures.

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“…they aim to treat the entire system at the same level of theory. Famous examples are, for instance, the Fragment Molecular Orbital approach 6,7 , the X-Pol method [8][9][10][11][12][13][14][15] , the Molecular Tailoring Approach [16][17][18][19] , or subsystem DFT 20,21 . Embedding methods, on the other hand, aim to split the system into a target region and an environment, each treated at different computational cost.…”

Section: Introductionmentioning

confidence: 99%

Complexity Reduction in Density Functional Theory Calculations of Large Systems: System Partitioning and Fragment Embedding

Dawson

Mohr

Ratcliff

et al. 2020

J. Chem. Theory Comput.

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With the development of low order scaling methods for performing Kohn-Sham Density Functional Theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an increase in the size of system treated comes an increase in complexity, making it challenging to analyze such large systems and determine the cause of emergent properties. To address this issue, in this paper we present a systematic complexity reduction methodology which can break down large systems into their constituent fragments, and quantify inter-fragment interactions. The methodology proposed here requires no a priori information or user interaction, allowing a single workflow to be automatically applied to any system of interest. We apply this approach to a variety of different systems, and show how it allows for the derivation of new system descriptors, the design of QM/MM partitioning schemes, and the novel application of graph metrics to molecules and materials.

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Multilevel X-Pol: A Fragment-Based Method with Mixed Quantum Mechanical Representations of Different Fragments

Cited by 36 publications

References 85 publications

A self‐consistent coulomb bath model using density fitting

A self‐consistent coulomb bath model using density fitting

Perturbation Approach for Computing Infrared Spectra of the Local Mode of Probe Molecules

Complexity Reduction in Density Functional Theory Calculations of Large Systems: System Partitioning and Fragment Embedding

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