Explicit Polarization Theory

Wang, Yingjie; Mazack, Michael J. M.; Truhlar, Donald G.; Gao, Jiali

doi:10.1201/b21343-5

Cited by 3 publications

(1 citation statement)

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“…For the derivation of charges, we focused on perhaps the most commonly used basis set, 6-31G*, and employed both Hartree–Fock (HF) and the density functional theory exchange correlation function, B3LYP. Although the former method is the one most traditionally used for this task, because of a fortuitous cancellation of errors, 22 B3LYP is also employed. 23 The other charge derivation procedure we tested is the semiempirical QM approach using the AM1-BCC charge method, 12 as used by programs such as MOPAC.…”

Section: Methodsmentioning

confidence: 99%

Comparison of Charge Derivation Methods Applied to Amino Acid Parameterization

2018

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When using non-natural amino acids in computational simulations of proteins, it is necessary to ensure appropriate parameterization of the new amino acids toward the creation of appropriate input files. In particular, the charges on the atoms may have to be derived de novo and ad hoc for the new species. As there are many variables in the charge derivation process, an investigation was devised to compare different approaches and determine their effect on simulations. This was done with the purpose to identify the methods which produced results compatible with the existing parameters. It was found in this study that all analyzed charge derivation methods reproduce with sufficient accuracy the literature values and can be used with confidence when parameterizing novel species.

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Section: Methodsmentioning

confidence: 99%

Comparison of Charge Derivation Methods Applied to Amino Acid Parameterization

2018

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Analytic gradient for the QM/MM-Ewald method using charges derived from the electrostatic potential: Theory, implementation, and application to ab initio molecular dynamics simulation of the aqueous electron

Holden

Rana

Herbert

2019

The Journal of Chemical Physics

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We report an implementation of periodic boundary conditions for mixed quantum mechanics/molecular mechanics (QM/MM) simulations, in which atomic partial charges are used to represent periodic images of the QM region. These charges are incorporated into the Fock matrix in a manner that preserves the variational nature of the self-consistent field procedure, and their interactions with the MM charges are summed using the conventional Ewald technique. To ensure that the procedure is stable in arbitrary basis sets, the atomic charges are derived by least-squares fit to the electrostatic potential generated by the QM region. We formulate and implement analytic energy gradients for the QM/MM-Ewald method and demonstrate that stable molecular dynamics simulations are thereby obtained. As a proof-of-concept application, we perform QM/MM simulations of a hydrated electron in bulk liquid water at the level of Hartree-Fock theory plus empirical dispersion. These simulations demonstrate that the “cavity model” of the aqueous electron, in which the spin density of the anionic defect is localized within an excluded volume in the liquid, is stable at room temperature on a time scale of at least several picoseconds. These results validate cavity-forming pseudopotential models of e−(aq) that have previously been derived from static-exchange Hartree-Fock calculations, and cast doubt upon whether non-cavity-forming pseudopotentials are faithful to the underlying Hartree-Fock calculation from which they were obtained.

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Fantasy versus reality in fragment-based quantum chemistry

Herbert

2019

The Journal of Chemical Physics

137

205

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Since the introduction of the fragment molecular orbital method 20 years ago, fragment-based approaches have occupied a small but growing niche in quantum chemistry. These methods decompose a large molecular system into subsystems small enough to be amenable to electronic structure calculations, following which the subsystem information is reassembled in order to approximate an otherwise intractable supersystem calculation. Fragmentation sidesteps the steep rise (with respect to system size) in the cost of ab initio calculations, replacing it with a distributed cost across numerous computer processors. Such methods are attractive, in part, because they are easily parallelizable and therefore readily amenable to exascale computing. As such, there has been hope that distributed computing might offer the proverbial “free lunch” in quantum chemistry, with the entrée being high-level calculations on very large systems. While fragment-based quantum chemistry can count many success stories, there also exists a seedy underbelly of rarely acknowledged problems. As these methods begin to mature, it is time to have a serious conversation about what they can and cannot be expected to accomplish in the near future. Both successes and challenges are highlighted in this Perspective.

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Explicit Polarization Theory

Cited by 3 publications

References 0 publications

Comparison of Charge Derivation Methods Applied to Amino Acid Parameterization

Comparison of Charge Derivation Methods Applied to Amino Acid Parameterization

Analytic gradient for the QM/MM-Ewald method using charges derived from the electrostatic potential: Theory, implementation, and application to ab initio molecular dynamics simulation of the aqueous electron

Fantasy versus reality in fragment-based quantum chemistry

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