Self-Parametrizing System-Focused Atomistic Models

Brunken, Christoph; Reiher, Markus

doi:10.1021/acs.jctc.9b00855

Cited by 34 publications

(101 citation statements)

References 165 publications

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“…Dihedral (15–24%) and bonded terms (− 29 to +24%) can also play a significant role in some force fields. Therefore, the employment of either tailored MM’ fields [58,76,77], or force fields that were completely derived from QM [85–89] will most likely play a more important role in the future of multi-scale applications that combine MM with QM.…”

Section: Discussionmentioning

confidence: 99%

On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces

König

Riniker

2020

Interface Focus.

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Force fields based on molecular mechanics (MM) are the main computational tool to study the relationship between protein structure and function at the molecular level. To validate the quality of such force fields, high-level quantum-mechanical (QM) data are employed to test their capability to reproduce the features of all major conformational substates of a series of blocked amino acids. The phase-space overlap between MM and QM is quantified in terms of the average structural reorganization energies over all energy minima. Here, the structural reorganization energy is the MM potential-energy difference between the structure of the respective QM energy minimum and the structure of the closest MM energy minimum. Thus, it serves as a measure for the relative probability of visiting the QM minimum during an MM simulation. We evaluate variants of the AMBER, CHARMM, GROMOS and OPLS biomolecular force fields. In addition, the two blocked amino acids alanine and serine are used to demonstrate the dependence of the measured agreement on the QM method, the phase, and the conformational preferences. Blocked serine serves as an example to discuss possible improvements of the force fields, such as including polarization with Drude particles, or using tailored force fields. The results show that none of the evaluated force fields satisfactorily reproduces all energy minima. By decomposing the average structural reorganization energies in terms of individual energy terms, we can further assess the individual weaknesses of the parametrization strategies of each force field. The dominant problem for most force fields appears to be the van der Waals parameters, followed to a lesser degree by dihedral and bonded terms. Our results show that performing a simple QM energy optimization from an MM-optimized structure can be a first test of the validity of a force field for a particular target molecule.

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Section: Discussionmentioning

confidence: 99%

On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces

König

Riniker

2020

Interface Focus.

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“…The FF parameters that we obtained in this way performed significantly worse than the manually refined parameters, which is why we focus only on the latter in this work. Other possible alternatives to obtaining FFs for challenging systems include QM-derived FFs [62,63] and machine-learning-based potentials [64,65].…”

Section: Parameter Setupmentioning

confidence: 99%

A Force Field for a Manganese-Vanadium Water Oxidation Catalyst: Redox Potentials in Solution as Showcase

et al. 2021

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We present a molecular mechanics force field in AMBER format for the mixed-valence manganese vanadium oxide cluster [Mn4V4O17(OAc)3]3−—a synthetic analogue of the oxygen-evolving complex that catalyzes the water oxidation reaction in photosystem II—with parameter sets for two different oxidation states. Most force field parameters involving metal atoms have been newly parametrized and the harmonic terms refined using hybrid quantum mechanics/molecular mechanics reference simulations, although some parameters were adapted from pre-existing force fields of vanadate cages and manganese oxo dimers. The characteristic Jahn–Teller distortions of d4 MnIII ions in octahedral environments are recovered by the force field. As an application, the developed parameters have been used to calculate the redox potential of the [MnIIIMn3IV] ⇌ [Mn4IV]+e− half-reaction in acetonitrile by means of Marcus theory.

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“…Die Möglichkeiten, die sich mit einem solchen Ansatz ergeben, wurden bereits an mehreren Testsystemen gezeigt. [31][32][33][34][35]…”

Section: Dynamik Angeregter Zuständeunclassified

Trendbericht Theoretische Chemie 1/2: Lichtgetriebene Reaktionen unter der Theorielupe

Faraji¹

2021

Nachr Chem

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Photoinduzierte Prozesse sind elementar in unserem Leben und Techniken zur Umwandlung von Energie, etwa von Sonnenlicht in Strom. Moderne Ultrakurzzeitspektroskopie ermöglicht es, solche chemischen Prozesse in Echtzeit zu beobachten. Aber nur im Wechselspiel aus Theorie und Experiment lassen sich die experimentellen Beobachtungen in ein mechanistisches Bild übersetzen. Daher ist eine realistische theoretische Beschreibung unentbehrlich.

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Self-Parametrizing System-Focused Atomistic Models

Cited by 34 publications

References 165 publications

On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces

On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces

A Force Field for a Manganese-Vanadium Water Oxidation Catalyst: Redox Potentials in Solution as Showcase

Trendbericht Theoretische Chemie 1/2: Lichtgetriebene Reaktionen unter der Theorielupe

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