59,054 research outputs found
Efficient construction of free energy profiles of breathing metal–organic frameworks using advanced molecular dynamics simulations
In order to reliably predict and understand the breathing behavior of highly flexible metal–organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials
Frequency adaptive metadynamics for the calculation of rare-event kinetics
The ability to predict accurate thermodynamic and kinetic properties in
biomolecular systems is of both scientific and practical utility. While both
remain very difficult, predictions of kinetics are particularly difficult
because rates, in contrast to free energies, depend on the route taken and are
thus not amenable to all enhanced sampling methods. It has recently been
demonstrated that it is possible to recover kinetics through so called
`infrequent metadynamics' simulations, where the simulations are biased in a
way that minimally corrupts the dynamics of moving between metastable states.
This method, however, requires the bias to be added slowly, thus hampering
applications to processes with only modest separations of timescales. Here we
present a frequency-adaptive strategy which bridges normal and infrequent
metadynamics. We show that this strategy can improve the precision and accuracy
of rate calculations at fixed computational cost, and should be able to extend
rate calculations for much slower kinetic processes.Comment: 15 pages, 2 figures, 2 table
An efficient Monte Carlo method for calculating ab initio transition state theory reaction rates in solution
In this article, we propose an efficient method for sampling the relevant
state space in condensed phase reactions. In the present method, the reaction
is described by solving the electronic Schr\"{o}dinger equation for the solute
atoms in the presence of explicit solvent molecules. The sampling algorithm
uses a molecular mechanics guiding potential in combination with simulated
tempering ideas and allows thorough exploration of the solvent state space in
the context of an ab initio calculation even when the dielectric relaxation
time of the solvent is long. The method is applied to the study of the double
proton transfer reaction that takes place between a molecule of acetic acid and
a molecule of methanol in tetrahydrofuran. It is demonstrated that calculations
of rates of chemical transformations occurring in solvents of medium polarity
can be performed with an increase in the cpu time of factors ranging from 4 to
15 with respect to gas-phase calculations.Comment: 15 pages, 9 figures. To appear in J. Chem. Phy
Coupling different levels of resolution in molecular simulations
Simulation schemes that allow to change molecular representation in a
subvolume of the simulation box while preserving the equilibrium with the
surrounding introduce conceptual problems of thermodynamic consistency. In this
work we present a general scheme based on thermodynamic arguments which ensures
thermodynamic equilibrium among the molecules of different representation. The
robustness of the algorithm is tested for two examples, namely an adaptive
resolution simulation, atomistic/coarse-grained, for a liquid of tetrahedral
molecules and an adaptive resolution simulation of a binary mixture of
tetrahedral molecules and spherical solutes
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