Free Energy Calculations

Chipot, Christophe; Pohorille, Andrew

doi:10.1007/978-3-540-38448-9

Cited by 759 publications

(38 citation statements)

References 9 publications

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“…This implies that the molecules, if they are free to rotate in place, could lower their energy by aligning with the electric field of the cavity mode, which could possibly lead to self-organization (for the example system above, this also requires breaking of the overall spherical symmetry). The details of this effect depend on the precise setup, such as the cavity material and shape, molecular and solvent properties, etc., and would require a more complete treatment taking thermodynamical effects and free energy into account [111,112], which is beyond the scope of the current work. However, we mention that it has recently been shown that strong coupling and the associated formation of polaritons itself could lead to alignment due to the associated decrease of the lower polariton energy, provided that a significant fraction of molecules are excited to lower polariton states [29,113].…”

Section: Collective Effectsmentioning

confidence: 99%

Cavity Casimir-Polder Forces and Their Effects in Ground-State Chemical Reactivity

et al. 2019

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Here we present a fundamental study on how the ground-state chemical reactivity of a molecule can be modified in a QED scenario, i.e., when it is placed inside a cavity and there is strong coupling between the cavity field and vibrational modes within the molecule. We work with a model system for the molecule (Shin-Metiu model) in which nuclear, electronic and photonic degrees of freedom are treated on the same footing. This simplified model allows the comparison of exact quantum reaction rate calculations with predictions emerging from transition state theory based on the cavity Born-Oppenheimer approach. We demonstrate that QED effects are indeed able to significantly modify activation barriers in chemical reactions and, as a consequence, reaction rates. The critical physical parameter controlling this effect is the permanent dipole of the molecule and how this magnitude changes along the reaction coordinate. We show that the effective coupling can lead to significant single-molecule energy shifts in an experimentally available nanoparticle-on-mirror cavity. We then apply the validated theory to a realistic case (internal rotation in the 1,2-dichloroethane molecule), showing how reactions can be inhibited or catalyzed depending on the profile of the molecular dipole. Furthermore, we discuss the absence of resonance effects in this process, which can be understood through its connection to Casimir-Polder forces. Finally, we treat the case of many-molecule strong coupling, and find collective modifications of reaction rates if the molecular permanent dipole moments are oriented with respected to the cavity field. This demonstrates that collective coupling can also provide a mechanism for modifying ground-state chemical reactivity of an ensemble of molecules coupled to a cavity mode. * javier.galego@uam.es † claudia.climent@uam.es ‡ fj.garcia@uam.es § johannes.feist@uam.es pling. This leads to many interesting effects such as collective protection of polaritons and changes in chemical reactivity [19,20], cavity-induced nonadiabatic phenomena [21,28,34], and the opening of novel reaction pathways in photochemistry [23].

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Section: Collective Effectsmentioning

confidence: 99%

Cavity Casimir-Polder Forces and Their Effects in Ground-State Chemical Reactivity

et al. 2019

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“…Functional uncertainty quantification (FUQ) can, in principle, be used to assess the uncertainties originating from approximate input constitutive laws, correct predictions if a more accurate function becomes available, and rank when and where to replace a low-fidelity model used in a simulation with one of higher fidelity in order to reduce prediction error by running additional simulations. This paper introduces a computationally efficient method to compute FDs in MD simulations involving two-body interatomic potentials, extending ideas from thermodynamic integration and free-energy perturbation methods [21,22]. The FD quantifies how a quantity of interest (QoI) -in this case the total potential energy or pressure computed from an MD simulation in the canonical ensemble -depends on the input function, here the Lennard-Jones (LJ) two-body pair potential.…”

Section: Introductionmentioning

confidence: 99%

Error correction in multi-fidelity molecular dynamics simulations using functional uncertainty quantification

Reeve

Strachan

2017

Journal of Computational Physics

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We use functional, Fréchet, derivatives to quantify how thermodynamic outputs of a molecular dynamics (MD) simulation depend on the potential used to compute atomic interactions. Our approach quantifies the sensitivity of the quantities of interest with respect to the input functions as opposed to its parameters as is done in typical uncertainty quantification methods. We show that the functional sensitivity of the average potential energy and pressure in isothermal, isochoric MD simulations using Lennard-Jones two-body interactions can be used to accurately predict those properties for other interatomic potentials (with different functional forms) without re-running the simulations. This is demonstrated under three different thermodynamic conditions, namely a crystal at room temperature, a liquid at ambient pressure, and a high pressure liquid. The method provides accurate predictions as long as the change in potential does not significantly affect the region in phase space explored by the simulation. The functional uncertainty quantification approach can be used to estimate the uncertainties associated with constitutive models used in the simulation and to correct predictions if a more accurate representation becomes available.

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“…Unfortunately, it is very hard to calculate the absolute free energy of real systems because we don’t know their partition functions. Free energy calculations allow us to bypass this problem, but require at least two states: a reference state whose free energy can be analytically or numerically found, and a final state of interest 36, 37 . We chose to calculate the free energy difference using alchemical free energy calculations, a method in which we simulate a series of non-physical intermediates between the end states 38 .…”

Section: Theorymentioning

confidence: 99%

Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules

Matos

Mobley

2018

F1000Res

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Background: Solubility is a physical property of high importance to the pharmaceutical industry, the prediction of which for potential drugs has so far been a hard task. We attempted to predict the solubility of acetylsalicylic acid (ASA) by estimating the absolute chemical potentials of its most stable polymorph and of solutions with different concentrations of the drug molecule. Methods: Chemical potentials were estimated from all-atom molecular dynamics simulations. We used the Einstein molecule method (EMM) to predict the absolute chemical potential of the solid and solvation free energy calculations to predict the excess chemical potentials of the liquid-phase systems. Results: Reliable estimations of the chemical potentials for the solid and for a single ASA molecule using the EMM required an extremely large number of intermediate states for the free energy calculations, meaning that the calculations were extremely demanding computationally. Despite the computational cost, however, the computed value did not agree well with the experimental value, potentially due to limitations with the underlying energy model. Perhaps better values could be obtained with a better energy model; however, it seems likely computational cost may remain a limiting factor for use of this particular approach to solubility estimation. Conclusions: Solubility prediction of drug-like solids remains computationally challenging, and it appears that both the underlying energy model and the computational approach applied may need improvement before the approach is suitable for routine use.

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Free Energy Calculations

Cited by 759 publications

References 9 publications

Cavity Casimir-Polder Forces and Their Effects in Ground-State Chemical Reactivity

Cavity Casimir-Polder Forces and Their Effects in Ground-State Chemical Reactivity

Error correction in multi-fidelity molecular dynamics simulations using functional uncertainty quantification

Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules

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