ONIOM-XS: an extension of the ONIOM method for molecular simulation in condensed phase

Kerdcharoen, Teerakiat; Morokuma, Keiji

doi:10.1016/s0009-2614(02)00210-5

Cited by 202 publications

(223 citation statements)

References 22 publications

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“…An important issue that arises in simulating liquid-state phenomena and diffusion through solids is the adaptive movement of the quantum mechanical region, which is called the "hot spot" [50,77,116,178]. Algorithms have been reported for liquid-phase simulation that allows water molecules to enter and leave the QM region dynamically.…”

Section: Adaptive Qm/mmmentioning

confidence: 99%

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QM/MM: what have we learned, where are we, and where do we go from here?

2006

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This paper briefly reviews the current status of the most popular methods for combined quantum mechanical/molecular mechanical (QM/MM) calculations, including their advantages and disadvantages. There is a special emphasis on very general link-atom methods and various ways to treat the charge near the boundary. Mechanical and electric embedding are contrasted. We consider methods applicable to gas-phase organic chemistry, liquid-phase organic and organometallic chemistry, biochemistry, and solid-state chemistry. Then we review some recent tests of QM/MM methods and summarize what we learn about QM/MM from these studies. We also discuss some available software. Finally, we present a few comments about future directions of research in this exciting area, where we focus on more intimate blends of QM with MM.

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Section: Adaptive Qm/mmmentioning

confidence: 99%

“…Despite its success, this treatment lacks a unique definition for the energy, which is obtained by integration of the force. Later, Kerdcharoen and Morokuma [116] described another scheme to cope with the discontinuity. In their scheme, two QM/MM calculations are performed for a given configuration of the whole system.…”

Section: Adaptive Qm/mmmentioning

confidence: 99%

QM/MM: what have we learned, where are we, and where do we go from here?

2006

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“…The QM subsystem was described at the RIMP2 level of theory, 177,178 with a def2-SVP basis set 213 for the ion and a 6-31G(d,p) basis set 214,215 for water, along with a rigid SPC/E-like geometry for the water molecules. The MM subsystem was described in the same way as in the MM calculations (see above), and the coupling between the two subsystems relied on a progressive interaction switching 216 and a classical electrostatic coupling based on Mulliken charges 217,218 (see Sec. II I for more details).…”

Section: B Thermodynamic Cyclementioning

confidence: 99%

Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration

Hofer

Hünenberger

2018

The Journal of Chemical Physics

104

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The absolute intrinsic hydration free energy G • H + ,wat of the proton, the surface electric potential jump χ • wat upon entering bulk water, and the absolute redox potential V • H + ,wat of the reference hydrogen electrode are cornerstone quantities for formulating single-ion thermodynamics on absolute scales. They can be easily calculated from each other but remain fundamentally elusive, i.e., they cannot be determined experimentally without invoking some extra-thermodynamic assumption (ETA). The Born model provides a natural framework to formulate such an assumption (Born ETA), as it automatically factors out the contribution of crossing the water surface from the hydration free energy. However, this model describes the short-range solvation inaccurately and relies on the choice of arbitrary ion-size parameters. In the present study, both shortcomings are alleviated by performing first-principle calculations of the hydration free energies of the sodium (Na + ) and potassium (K + ) ions. The calculations rely on thermodynamic integration based on quantum-mechanical molecular-mechanical (QM/MM) molecular dynamics (MD) simulations involving the ion and 2000 water molecules. The ion and its first hydration shell are described using a correlated ab initio method, namely resolution-of-identity second-order Møller-Plesset perturbation (RIMP2). The next hydration shells are described using the extended simple point charge water model (SPC/E). The hydration free energy is first calculated at the MM level and subsequently increased by a quantization term accounting for the transformation to a QM/MM description. It is also corrected for finite-size, approximate-electrostatics, and potentialsummation errors, as well as standard-state definition. These computationally intensive simulations provide accurate first-principle estimates for G • H + ,wat , χ • wat , and V • H + ,wat , reported with statistical errors based on a confidence interval of 99%. The values obtained from the independent Na + and K + simulations are in excellent agreement. In particular, the difference between the two hydration free energies, which is not an elusive quantity, is 73.9 ± 5.4 kJ mol 1 (K + minus Na + ), to be compared with the experimental value of 71.7 ± 2.8 kJ mol 1 . The calculated values of G • H + ,wat , χ • wat , and V • H + ,wat ( 1096.7 ± 6.1 kJ mol 1 , 0.10 ± 0.10 V, and 4.32 ± 0.06 V, respectively, averaging over the two ions) are also in remarkable agreement with the values recommended by Reif and Hünenberger based on a thorough analysis of the experimental literature ( 1100 ± 5 kJ mol 1 , 0.13 ± 0.10 V, and 4.28 ± 0.13 V, respectively). The QM/MM MD simulations are also shown to provide an accurate description of the hydration structure, dynamics, and energetics. Published by AIP Publishing.

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“…Adaptive resolution methods address this issue by dynamically assigning molecules HR or LR character based on their proximity to the active site. [6][7][8][9][10][11][12][13] Generally, this procedure involves a transition region that connects smoothly the active and environment regions (T-region, Figure 1). The solvent molecules in the T-region have partial HR and partial LR character, and the description of each solvent molecule s smoothly changes from HR to LR (or vice versa) as it moves across the region.…”

Section: Introductionmentioning

confidence: 99%

Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials

Boereboom

Potestio

Donadio

et al. 2016

J. Chem. Theory Comput.

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Adaptive quantum mechanical (QM) / molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution by describing reactive subregions with an accurate many-body potential energy expression (QM) while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the many-body QM potential. It would be desirable to model such system 1 using an adaptive Hamiltonian, but so far it has resulted in distorted structures at the boundary between the two regions. Here, we propose a Hamiltonian scheme to describe adaptively solvent diffusion across a multi-scale boundary separating configurational potentials that cannot be expressed by a multi-body expansion. The adaptive expressions are entirely general, and complimentary to all standard (non-adaptive) QM/MM embedding schemes available. We demonstrate the validity of our approach on a system described by two different MM potentials (MM/MM'), in which long-range interactions are treated by many-body Ewald summation. Our Hamiltonian approach provides both energy conservation and the correct solvent structure everywhere in the system, thus enabling microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties.

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ONIOM-XS: an extension of the ONIOM method for molecular simulation in condensed phase

Cited by 202 publications

References 22 publications

QM/MM: what have we learned, where are we, and where do we go from here?

QM/MM: what have we learned, where are we, and where do we go from here?

Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration

Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials

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