Effects of a More Accurate Polarizable Hamiltonian on Polymorph Free Energies Computed Efficiently by Reweighting Point-Charge Potentials

Dybeck, Eric; Schieber, Natalie P.; Shirts, Michael R.

doi:10.1021/acs.jctc.6b00397

Cited by 28 publications

(77 citation statements)

References 121 publications

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“…On the other hand, these Lennard-Jones interaction parameters may have a strong impact 195,200,201 on the convergence properties of the computationally intensive ∆G qua calculation (Sec. II F).…”

Section: J Optimization Of the Lennard-jones Interaction Parametersmentioning

confidence: 99%

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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: J Optimization Of the Lennard-jones Interaction Parametersmentioning

confidence: 99%

“…199 The advantage of adjusting the parameters of the MM model to improve the convergence has also been noted in this context. 195,200,201 This approach was also applied in the BOMD study of Refs. 112 and 113.…”

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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“…Including more advanced effects such as anisotropic multipoles, intermolecular polarization, and QM electron correlations can significantly change the lattice energy landscape and therefore the relative ranking of different predicted structures. In some cases, the lattice minima in a cheaper potential can completely restructure when more accurate interaction effects are included [119].…”

Section: Sensitivity To the Hamiltonianmentioning

confidence: 99%

“…Additionally, these systems had well-characterized structures for both the high and low temperature form in the Cambridge Structural Database (CSD). The experimentally determined polymorphic transition temperatures and CSD refcodes for each crystal are shown in Table B interactions [119]. Additionally, the large supercells accommodate between 32-96 independently moving molecules in each system which approximates real crystals better than single unit cells.…”

Section: Initial System Structuresmentioning

confidence: 99%

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Capturing the Role of Temperature and Entropy in Crystal Polymorphs Through Molecular Simulations

Dybeck

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AcknowledgementsI would like to acknowledge the guidance and support provided by my advisor MichaelShirts. I would also like to thank Levi Naden, Natalie Schieber, Nate Abraham and the entire Shirts group for their help and technical support during my research. I also would like to acknowledge the UVA high performance computing team for the computational resources necessary to complete this work. Finally, I would like to acknowledge the endless love and support that my friends and family provided me during this challenging Ph.D. journey.iii AbstractThe presence of multiple stable crystal structures in solid organic materials can limit their commercial viability when two or more observable polymorphs exhibit markedly different physical properties. Unintended restructuring events have hindered pharmaceutical solid form development in numerous therapeutic candidates and have led to costly market recalls.Conversely, intentional synthesis of a metastable form has led to significantly more favorable performance in numerous materials.Current computational methods for predicting polymorphic behavior evaluate candidate crystal structures based on the minimized lattice energy. However, these static lattice energybased approaches generate far more lattice energy minima than there are experimentally observed structures. Thermal motion of the crystals under working conditions has the potential to explain why many of these lattice minima are not observed experimentally. Lattice minima that are identified from a static crystal structure prediction can ultimately be unstable at experimental conditions through either temperature-mediated stability reranking, kinetic interconversion of multiple minima, or inaccuracies of the energy function in producing the real crystal ensemble.In this work, we explore the role of thermal motion in eliminating candidate crystal structures using fully atomistic molecular dynamics simulations. Enthalpically favorable structures with low entropy will become unfavorable at high temperatures through temperaturemediated stability reranking. Our simulations correctly identify the high temperature solid form as having a larger entropy than the low temperature form in twelve small molecule organic systems with known temperature-mediated transformations. The estimated entropy differences in the classical point-charge potential are significantly closer to experimental measurements than estimated enthalpy differences. This result suggests that entropy difference estimates are less sensitive to the complexity of the simulation potential than the corresponding enthalpy estimates. We additionally find that a cheaper harmonic approximation provides a sufficient estimate of entropic contributions in small rigid molecules. However, entropies with iv the harmonic approximation diverge from molecular dynamics-derived entropies in systems with multiple rotatable degrees of freedom or dynamically disordered crystalline structures.We additionally probe the sensitivity of the stability estimates to the energy function ...

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Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state

Gheta,

Bonin,

Gerlach

et al. 2023

J Comput Aided Mol Des

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Effects of a More Accurate Polarizable Hamiltonian on Polymorph Free Energies Computed Efficiently by Reweighting Point-Charge Potentials

Cited by 28 publications

References 121 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

Capturing the Role of Temperature and Entropy in Crystal Polymorphs Through Molecular Simulations

Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state

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