Molecular systems with open boundaries: Theory and simulation

Site, Luigi Delle; Praprotnik, Matej

doi:10.1016/j.physrep.2017.05.007

Cited by 79 publications

(119 citation statements)

References 277 publications

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“…110 and 153-157), employed here in conjunction with TI. The QM/MM MD simulations rely on the quantum-mechanical charge field (QMCF) approach, 158,159 which belongs to the family of adaptive QM/MM methods 148,149,160 and has been applied with success in the past to investigations of solvated ions, 153,154 molecules, 161,162 coordination complexes, 163,164 and biomolecular systems. 165,166 Single-determinantal approaches such as ab initio HartreeFock 167,168 (HF) or DFT 169,170 have a limited accuracy/reliability 120,[123][124][125][126][127]155,[171][172][173][174][175][176] in the description of hydration phenomena.…”

Section: Introductionmentioning

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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Section: Introductionmentioning

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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“…To perform a truly open grand-canonical molecular simulations one should take recourse to the open boundary molecular dynamics (OBMD) [57,116,[136][137][138] that permits simulations directly in the grand-canonical ensemble. The OBMD method combines features of AdResS and open MD [139,140], which enable the exchange of energy, momentum, and matter with the external environment through the imposed arbitrary time-dependent external pressure tensor.…”

Section: Discussionmentioning

confidence: 99%

“…Only recently it became feasible to set up an all-atom MD simulation for a larger set of DNA molecules [51,53] characterized by a single packing geometry with only a partial characterization of the DNA countercharge and solvent ordering. This approach has been later extended by the applications of the multiscale MD technique AdResS (Adaptive Resolution Scheme) [54][55][56][57][58][59][60][61][62][63][64][65][66][67], which has been already successfully applied to various biological systems [68][69][70][71][72][73][74][75][76][77], enabling a concurrent and consistent coupling between the atomistic (AT) and the coarse-grained (CG) representations with a key feature of allowing molecules to freely move not only in real space but also in the resolution space across different regions and change their resolution on the fly according to their position in the computational domain.…”

Section: Simulating Dna Arraysmentioning

confidence: 99%

“…On the other hand, top-down approaches such as MARTINI [103] focusing on thermodynamic properties can also be applied. However, due to the reduction of degrees of freedom associated with coarse graining, the CG interactions are softer leading to reduced viscosity [55,57,115]. As a result, the CG models frequently display accelerated dynamics.…”

Section: Adress-single Dnamentioning

confidence: 99%

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Molecular Dynamics Simulation of High Density DNA Arrays

2018

Self Cite

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Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between them remains less well understood. Since at high DNA densities, i.e., small interaxial spacings, one can neither neglect the atomic details of the interacting macromolecular surfaces nor the atomic details of the intervening ionic solution, the atomistic resolution is a sine qua non to properly describe and analyze the interactions between DNA molecules. In fact, in order to properly understand the details of the observed osmotic equation of state, one needs to implement multiple levels of organization, spanning the range from the molecular order of DNA itself, the possible ordering of counterions, and then all the way to the induced molecular ordering of the aqueous solvent, all coupled together by electrostatic, steric, thermal and direct hydrogen-bonding interactions. Multiscale simulations therefore appear as singularly suited to connect the microscopic details of this system with its macroscopic thermodynamic behavior. We review the details of the simulation of dense atomistically resolved DNA arrays with different packing symmetries and the ensuing osmotic equation of state obtained by enclosing a DNA array in a monovalent salt and multivalent (spermidine) counterions within a solvent permeable membrane, mimicking the behavior of DNA arrays subjected to external osmotic stress. By varying the DNA density, the local packing symmetry, and the counterion type, we are able to analyze the osmotic equation of state together with the full structural characterization of the DNA subphase, the counterion distribution and the solvent structural order in terms of its different order parameters and consequently identify the most important contribution to the DNA-DNA interactions at high DNA densities.

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“…In this study we employ the Grand Canonical Adaptive Resolution Simulation Scheme (GC-AdResS) for molecular dynamics [25,26,[28][29][30]38]. Two regions of a simulation box having different resolution regions: 1. atomistic (AT) and 2. a coarse-grained (CG) system can be linked using this multi-resolution simulation method.…”

Section: Methodsmentioning

confidence: 99%

Ionic Liquids Treated within the Grand Canonical Adaptive Resolution Molecular Dynamics Technique

Jabes¹,

Krekeler

2018

Computation

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Abstract:We use the Grand Canonical Adaptive Resolution Molecular Dynamics Technique (GC-AdResS) to examine the essential degrees of freedom necessary for reproducing the structural properties of the imidazolium class of ionic liquids. In this technique, the atomistic details are treated as an open sub-region of the system while the surrounding environment is modelled as a generic coarse-grained model. We systematically characterize the spatial quantities such as intramolecular, intermolecular radial distribution functions, other structural and orientational properties of ILs. The spatial quantities computed in an open sub-region of the system are in excellent agreement with the equivalent quantities calculated in a full atomistic simulation, suggesting that the atomistic degrees of freedom outside the sub-region are negligible. The size of the sub-region considered in this study is 2 nm, which is essentially the size of a few ions. Insight from the study suggests that a higher degree of spatial locality seems to play a crucial role in characterizing the properties of imidazolium based ionic liquids.

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Molecular systems with open boundaries: Theory and simulation

Cited by 79 publications

References 277 publications

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

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

Molecular Dynamics Simulation of High Density DNA Arrays

Ionic Liquids Treated within the Grand Canonical Adaptive Resolution Molecular Dynamics Technique

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