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WIREs Comput Mol Sci
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Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials

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Abstract Quantum mechanics/molecular mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is in the investigation of reaction mechanisms in condensed‐phase and biological systems. The combination of QM and MM methods to represent a system gives rise to several challenges that need to be addressed. The increase in computational speed has allowed the expanded use of more complicated and accurate methods for both QM and MM simulations. Here, we review some approaches that address several common challenges encountered in QM/MM simulations with advanced polarizable potentials, from methods to account for boundary across covalent bonds and long‐range effects, to polarization and advanced embedding potentials. This article is categorized under: Electronic Structure Theory > Combined QM/MM Methods Molecular and Statistical Mechanics > Molecular Interactions Software > Simulation Methods
Main protease of SARS‐CoV2 in a box of water.10 The whole protein (left) and a close‐up in the active site (right) are shown. Histidine 41 and cysteine 145 amino acid residues are represented by balls and cylinders. PDB: 6LU711
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(a) Reaction scheme for the N‐tert‐butoxycarbonylation of aniline for the step‐wise mechanism. (b) Minimum energy path for configuration C2, Scheme 1c. (c) Minimum energy path for Scheme c for configuration C2 without the AMOEBA polarization term. (d) Reaction scheme for the N‐tert‐butoxycarbonylation of aniline for the concerted mechanism. (e) Minimum energy path for configuration C2, Scheme 1d. (f) Minimum energy path for Scheme d for configuration C2 without the AMOEBA polarization termSource: Adapted from E.A. Vazquez‐Montelongo, J.E. Vazquez‐Cervantes, G.A. Cisneros, Polarizable ab initio QM/MM study of the reaction mechanism of N‐tert‐butyloxycarbonylation of aniline in [EMIm][BF4]. Molecules 2018, 23, 283025
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Relative energies obtained by NEB (blue, square) and QSM (red, circle), and QSM using the restrained‐MM method (green, triangle) along the reaction coordinate (left), and total wall time required for the optimization in hours (right). The wall time for MM calculations, QM calculations, and for system calls are depicted above the wall time bars (right)Source: Reprinted with permission from H. Gökcan, E. Antonio Vázquez‐Montelongo, G. Andrés Cisneros, J. Chem. Theory Comput. 2019, 15 (5), 3056–3065. Copyright (2019) American Chemical Society
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Flowchart of QSM algorithm implemented within LICHEMSource: Reprinted with permission from H. Gökcan, E. Antonio Vázquez‐Montelongo, G. Andrés Cisneros, J. Chem. Theory Comput. 2019, 15 (5), 3056–3065. Copyright (2020) American Chemical Society
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Errors per cluster with respect to SAPT. The errors corresponding to the coulomb interaction energy are depicted on the first column, and the errors corresponding to the exchange interaction energy are given on the second column. The computed errors for the sum of dispersion and polarization energies are depicted on the third, while the error for total energy is given on the fourth columnSource: Reprinted with permission from J. Phys. Chem. Lett. 2018, 9 (11), 3062–3067. Copyright 2018 American Chemical Society
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Polarization of the QM subsystem for one QM water by one GEM waterSource: Adapted with permission from J. Phys. Chem. B 2006, 110, 28, 13682–13684. Copyright 2006 American Chemical Society
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LREC damping function with s = 2 and s = 3. Increasing the exponent moves the inflection point of the LREC function closer to the cutoff radiusSource: Reprinted with permission from E.G. Kratz, R.E. Duke, G.A. Cisneros, Long‐range electrostatic corrections in multipolar/polarizable QM/MM simulations. Theor. Chem. Acc. 2016, 135, 166
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Relative energies (ΔE, in kcal/mol) of computed stationary points along the stepwise dissociative pathway of UDG, based on a constrained and truncated QM model of the UDG active site. Values corrected for zero‐point energy vibration (ZPVE) are shown in parentheses (ΔEZPVE, in kcal/mol). Geometries of all stationary points were optimized at the ωB97X‐D/6–31+G(d) levelSource: Reprinted with permission from J. Am. Chem. Soc. 2019, 141, 35, 13739–13743. Copyright 2019 American Chemical Society95
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(a) Molecular schematic representation of the pseudobond approach for polarizable QM/MM optimization, with QM (MM) atoms in the green(blue) shaded regions, and boundary atoms shaded in purple. In this approach, a polarizable QM/MM involves four calculations: (b) QM polarized by the static MM field (blue shaded region), (c) MM without charges on QM (green circle) or boundary atoms (purple shaded atoms), (d) MM polarization including static (approximate) QM field (green and purple shaded regions), (e) MM optimization with static field from QM and boundary atoms (green and purple shaded regions)66
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Representation of (a) link atom approaches: Simple link atom80, 81 (left) and double link atom (right),82 and frozen localized orbitals where gray orbitals are kept frozen while plain white orbitals are optimized during QM optimization: (b) LSCF,83–88 (c) GHO methods89,90
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(a) Pictorial representation of the TO dye buried in the DNA double helix, embedded in a sphere of water (16,500 atoms). The different colors represent the differences for each of the QM/MM partition schemes employed. (b) The DNA structure is highlighted in a ball‐and‐stick representation, leaving the first water solvation shell around the TO dye. The QM subsystem defined in this work, tagged as QM/MM(PB) and made up of the TO dye and the four closest nucleobases (NBs) is zoomed out and represented in licorice style in the blue square. (c) NTOs and excitation energies relative to the ππ* bright excitation of the TO dye embedded in different environments, from vacuum to the QM/MM(PB) partition scheme. H and P denote the hole and particle, respectivelySource: Reproduction from D. Loco, L. Lagardère, G. A. Cisneros, G. Scalmani, M. Frisch, F. Lipparini, B. Mennucci, J.P. Piquemal, Chem. Sci., 2019, 10, 7200—Published by The Royal Society of Chemistry75
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Software > Simulation Methods
Molecular and Statistical Mechanics > Molecular Interactions
Electronic Structure Theory > Combined QM/MM Methods

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