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An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations

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Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56125 Pisa, Italy, and Computational Science, Department of Chemistry and Applied Biosciences, ETH Zürich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
Cite this: J. Chem. Theory Comput. 2006, 2, 5, 1370–1378
Publication Date (Web):August 5, 2006
https://doi.org/10.1021/ct6001169
Copyright © 2006 American Chemical Society

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    Abstract

    A new linear-scaling method based on a multigrid approach to treat long-range electrostatic interactions in hybrid quantum mechanics/molecular mechanics (QM/MM) simulations is described. The scheme has been implemented in the context of a QM calculation based on density functional theory (DFT). The method is tested on an analytical model to validate the new algorithm. Two realistic problems in α-quartz crystals and a zwitterionic dipeptide (GLY-ALA) in water have been chosen as further tests. Results from QM/MM calculations with periodic boundary conditions (PBC) show that the use of PBC is essential when studying highly ordered crystal structures, unless a carefully designed MM crystal is used for the calculation. With a general shaped MM subsystem, the absence of PBC leads to an incorrect description of Kohn−Sham band gaps and charge density. The present method allows periodic boundary conditions to be used in molecular simulations of biological and material science systems.

    *

     Corresponding author fax:  +41919138817; e-mail: [email protected].

     Scuola Normale Superiore di Pisa.

     ETH Zürich.

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    84. Y. Kawashima, K. Ishimura, M. Shiga. Ab initio quantum mechanics/molecular mechanics method with periodic boundaries employing Ewald summation technique to electron-charge interaction: Treatment of the surface-dipole term. The Journal of Chemical Physics 2019, 150 (12) https://doi.org/10.1063/1.5048451
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    86. F. Zipoli, M. Hijazi, R. Petraglia, V. Weber, T. Laino. Semiempirical molecular dynamics (SEMD) simulations: Parameterization and validation for biological systems precursors. IBM Journal of Research and Development 2018, 62 (6) , 5:1-5:9. https://doi.org/10.1147/JRD.2018.2887388
    87. Angelo Spinello, Matic Pavlin, Lorenzo Casalino, Alessandra Magistrato. A Dehydrogenase Dual Hydrogen Abstraction Mechanism Promotes Estrogen Biosynthesis: Can We Expand the Functional Annotation of the Aromatase Enzyme?. Chemistry – A European Journal 2018, 24 (42) , 10840-10849. https://doi.org/10.1002/chem.201802025
    88. C. Richard A. Catlow, John Buckeridge, Matthew R. Farrow, Andrew J. Logsdail, Alexey A. Sokol. Quantum Mechanical/Molecular Mechanical ( QM / MM ) Approaches. 2017, 647-680. https://doi.org/10.1002/9783527691036.hsscvol5012
    89. R. Gonçalves, W.A. Christinelli, A.B. Trench, A. Cuesta, E.C. Pereira. Properties improvement of poly(o-methoxyaniline) based supercapacitors: experimental and theoretical behaviour study of self-doping effect. Electrochimica Acta 2017, 228 , 57-65. https://doi.org/10.1016/j.electacta.2016.12.188
    90. Gerald Monard, Jean-Louis Rivail. Solvent Effects in Quantum Chemistry. 2017, 727-739. https://doi.org/10.1007/978-3-319-27282-5_15
    91. Adhitya Mangala Putra Moeljadi, Rochus Schmid, Hajime Hirao. Dioxygen binding to Fe-MOF-74: microscopic insights from periodic QM/MM calculations. Canadian Journal of Chemistry 2016, 94 (12) , 1144-1150. https://doi.org/10.1139/cjc-2016-0284
    92. Ruibin Liang, Jessica M. J. Swanson, Jesper J. Madsen, Mei Hong, William F. DeGrado, Gregory A. Voth. Acid activation mechanism of the influenza A M2 proton channel. Proceedings of the National Academy of Sciences 2016, 113 (45) https://doi.org/10.1073/pnas.1615471113
    93. Isaac J. Sugden, David F. Plant, Robert G. Bell. Impact scenarios in boron carbide: A computational study. Journal of Theoretical and Computational Chemistry 2016, 15 (07) , 1650055. https://doi.org/10.1142/S0219633616500553
    94. Diego Hunt, Veronica M Sanchez, Damián A Scherlis. A quantum-mechanics molecular-mechanics scheme for extended systems. Journal of Physics: Condensed Matter 2016, 28 (33) , 335201. https://doi.org/10.1088/0953-8984/28/33/335201
    95. Sudhir K. Sahoo, Nisanth N. Nair. CPMD/GULP QM/MM interface for modeling periodic solids: Implementation and its application in the study of Y‐zeolite supported Rh n clusters. Journal of Computational Chemistry 2016, 37 (18) , 1657-1667. https://doi.org/10.1002/jcc.24379
    96. Eric G. Kratz, Robert E. Duke, G. Andrés Cisneros. Long-range electrostatic corrections in multipolar/polarizable QM/MM simulations. Theoretical Chemistry Accounts 2016, 135 (7) https://doi.org/10.1007/s00214-016-1923-8
    97. Andrea Mirats, Jorge Alí-Torres, Luis Rodríguez-Santiago, Mariona Sodupe. Stability of transient Cu+Aβ (1–16) species and influence of coordination and peptide configuration on superoxide formation. Theoretical Chemistry Accounts 2016, 135 (3) https://doi.org/10.1007/s00214-016-1836-6
    98. Sangyun Lee, Jessica M.J. Swanson, Gregory A. Voth. Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter. Biophysical Journal 2016, 110 (6) , 1334-1345. https://doi.org/10.1016/j.bpj.2016.02.014
    99. Riccardo Petraglia, Adrien Nicolaï, Matthew D. Wodrich, Michele Ceriotti, Clemence Corminboeuf. Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry. Journal of Computational Chemistry 2016, 37 (1) , 83-92. https://doi.org/10.1002/jcc.24025
    100. K. Doll, T. Jacob. QM/MM description of periodic systems. Journal of Theoretical and Computational Chemistry 2015, 14 (07) , 1550054. https://doi.org/10.1142/S0219633615500546
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