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Probing Proton Transfer Reactions in Molecular Dynamics—A Crucial Prerequisite for QM/MM Simulations Using Dissociative Models

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Quantum Modeling of Complex Molecular Systems

Part of the book series: Challenges and Advances in Computational Chemistry and Physics ((COCH,volume 21))

Abstract

The classical modeling of proton transfer reactions in chemical simulations requires the application of reactive force field formulations. A common feature of these dissociative potential models of aqueous systems is the possibility to transfer protons between water, oxonium and hydroxide ions. Since molecules undergo a change of their composition as the simulation progresses, the respective topology defining which atoms form a molecular unit at a given configuration becomes time-dependent. Knowledge of this variable topology is a key prerequisite to apply dissociative models in the framework of hybrid quantum mechanical/molecular mechanical (QM/MM) simulation studies. In order to effectively execute QM/MM simulations, the simulation software has to be able to independently monitor all occurring bond formation and cleavage events and automatically adjust the respective topology information, thereby discriminating between short-time fluctuations and sustained proton transfer events. The properties of a simple yet effective automated topology update criterion developed for excess protons are presented and its performance for hydroxide containing solutions and systems containing excess protons is compared. Furthermore, the influence of deuteration of the different systems is discussed. The data clearly demonstrates that it is possible to apply a global setting for the automated topology update of both proton and proton-hole migration.

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Abbreviations

CPMD:

Car--Parrinello molecular dynamics

DFT:

Density functional theory

QM:

Quantum mechanical

MM:

Molecular mechanical

QM/MM:

Quantum mechanical/molecular mechanical

MD:

Molecular dynamics

PT:

Proton transfer

MS-EVB:

Multistate empirical valence bond

HPC:

High-performance computing

ATU:

Automated topology update

PTM:

Proton transfer maps

PH:

Proton-hole

NQE:

Nuclear quantum effects

sOSS2:

Scaled Ojamäe-Shavitt-Singer

PIMD:

Path-integral molecular dynamics

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Acknowledgments

This work was supported by the Austrian Ministry of Science BMWF as part of the Konjunkturpaket II of the Focal Point Scientific Computing at the University of Innsbruck.

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  1. Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria

    Thomas S. Hofer

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Editors and Affiliations

  1. UMR 7565—SRSMC, Université de Lorraine, Nancy-Vandoeuvre, France

    Jean-Louis Rivail

  2. UMR 7565—SRSMC, Université de Lorraine, Nancy-Vandoeuvre, France

    Manuel Ruiz-Lopez

  3. UMR 7565—SRSMC, Université de Lorraine, Nancy-Vandoeuvre, France

    Xavier Assfeld

Appendix: Simulation Protocol

Appendix: Simulation Protocol

Starting structures for all simulations have been prepared by pre–equilibration of a number of simulations systems with an adequate number of water molecules employing periodic, cubic simulation cells for 100 000 MD steps. The velocity-Verlet algorithm has been employed to integrate the equations of motion with a time step of 0.2 fs. The Nose Hoover thermostat [42, 64] was employed to maintain constant temperature of 298.15 K. To account for long-range Coulombic interactions, the Wolf summation technique [108] with a cutoff distance of 10.0 Å was applied as defined in the Garofalini model [57, 106]. The proton transfer update criterion \(\rho\) was set to the recommended value of 0.585 [40].

Next, random water molecules have been adjusted to form H3O+ and OH− ions or have been replaced by Na+ and Cl− ions as required. 1 M HCl and NaOH systems have been generated by replacing random water molecules with Na+ or Cl− and by adding/deleting hydrogen atoms to/from another randomly chosen water molecule, yielding net stochiometries of 17 HCl and 18 NaOH molecules per 1000 water molecules. For deuterated systems each hydrogen atoms was replaced by deuterium.

The solutions have then been equilibrated for at least 1 000 000 MD steps (200 ps). Data sampling has been performed for 1 500 000 and 2 500 000 MD steps in case of acidified and basic systems, respectively, corresponding to sampling times of 300 and 500 ps. To tightly monitor all occurring proton transfer events data sampling was performed every tenth MD step, leading to trajectory file sizes of approximately 60–110 GB per system, respectively.

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Hofer, T.S. (2015). Probing Proton Transfer Reactions in Molecular Dynamics—A Crucial Prerequisite for QM/MM Simulations Using Dissociative Models. In: Rivail, JL., Ruiz-Lopez, M., Assfeld, X. (eds) Quantum Modeling of Complex Molecular Systems. Challenges and Advances in Computational Chemistry and Physics, vol 21. Springer, Cham. https://doi.org/10.1007/978-3-319-21626-3_4

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