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“Free energy barriers from biased molecular dynamics simulations”. Bal KM, Fukuhara S, Shibuta Y, Neyts EC, Journal Of Chemical Physics 153, 114118 (2020). http://doi.org/10.1063/5.0020240
Abstract: Atomistic simulation methods for the quantification of free energies are in wide use. These methods operate by sampling the probability density of a system along a small set of suitable collective variables (CVs), which is, in turn, expressed in the form of a free energy surface (FES). This definition of the FES can capture the relative stability of metastable states but not that of the transition state because the barrier height is not invariant to the choice of CVs. Free energy barriers therefore cannot be consistently computed from the FES. Here, we present a simple approach to calculate the gauge correction necessary to eliminate this inconsistency. Using our procedure, the standard FES as well as its gauge-corrected counterpart can be obtained by reweighing the same simulated trajectory at little additional cost. We apply the method to a number of systems—a particle solvated in a Lennard-Jones fluid, a Diels–Alder reaction, and crystallization of liquid sodium—to demonstrate its ability to produce consistent free energy barriers that correctly capture the kinetics of chemical or physical transformations, and discuss the additional demands it puts on the chosen CVs. Because the FES can be converged at relatively short (sub-ns) time scales, a free energy-based description of reaction kinetics is a particularly attractive option to study chemical processes at more expensive quantum mechanical levels of theory.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.4
DOI: 10.1063/5.0020240
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“Stable single-layers of calcium halides (CaX₂, X = F, Cl, Br, I)”. Baskurt M, Yagmurcukardes M, Peeters FM, Sahin H, Journal Of Chemical Physics 152, 164116 (2020). http://doi.org/10.1063/5.0006011
Abstract: By means of density functional theory based first-principles calculations, the structural, vibrational, and electronic properties of 1H- and 1T-phases of single-layer CaX2 (X = F, Cl, Br, or I) structures are investigated. Our results reveal that both the 1H- and 1T-phases are dynamically stable in terms of their phonon band dispersions with the latter being the energetically favorable phase for all single-layers. In both phases of single-layer CaX2 structures, significant phonon softening occurs as the atomic radius increases. In addition, each structural phase exhibits distinctive Raman active modes that enable one to characterize either the phase or the structure via Raman spectroscopy. The electronic band dispersions of single-layer CaX2 structures reveal that all structures are indirect bandgap insulators with a decrease in bandgaps from fluorite to iodide crystals. Furthermore, the calculated linear elastic constants, in-plane stiffness, and Poisson ratio indicate the ultra-soft nature of CaX2 single-layers, which is quite important for their nanoelastic applications. Overall, our study reveals that with their dynamically stable 1T- and 1H-phases, single-layers of CaX2 crystals can be alternative ultra-thin insulators.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 4.4
Times cited: 14
DOI: 10.1063/5.0006011
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“Quantitative morphometric analysis of single gold nanoparticles by optical extinction microscopy: Material permittivity and surface damping effects”. Payne LM, Masia F, Zilli A, Albrecht W, Borri P, Langbein W, Journal Of Chemical Physics 154, 044702 (2021). http://doi.org/10.1063/5.0031012
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.965
DOI: 10.1063/5.0031012
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“Abnormal in-plane permittivity and ferroelectricity of confined water : from sub-nanometer channels to bulk”. Hamid I, Jalali H, Peeters FM, Neek-Amal M, Journal Of Chemical Physics 154, 114503 (2021). http://doi.org/10.1063/5.0038359
Abstract: Dielectric properties of nano-confined water are important in several areas of science, i.e., it is relevant in the dielectric double layer that exists in practically all heterogeneous fluid-based systems. Molecular dynamics simulations are used to predict the in-plane dielectric properties of confined water in planar channels of width ranging from sub-nanometer to bulk. Because of suppressed rotational degrees of freedom near the confining walls, the dipole of the water molecules tends to be aligned parallel to the walls, which results in a strongly enhanced in-plane dielectric constant (epsilon (parallel to)) reaching values of about 120 for channels with height 8 angstrom < h < 10 angstrom. With the increase in the width of the channel, we predict that epsilon (parallel to) decreases nonlinearly and reaches the bulk value for h > 70 angstrom. A stratified continuum model is proposed that reproduces the h > 10 angstrom dependence of epsilon (parallel to). For sub-nanometer height channels, abnormal behavior of epsilon (parallel to) is found with two orders of magnitude reduction of epsilon (parallel to) around h similar to 7.5 angstrom, which is attributed to the formation of a particular ice phase that exhibits long-time (similar to mu s) stable ferroelectricity. This is of particular importance for the understanding of the influence of confined water on the functioning of biological systems.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.965
Times cited: 13
DOI: 10.1063/5.0038359
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“Extending and validating bubble nucleation rate predictions in a Lennard-Jones fluid with enhanced sampling methods and transition state theory”. Bal KM, Neyts EC, Journal Of Chemical Physics 157, 184113 (2022). http://doi.org/10.1063/5.0120136
Abstract: We calculate bubble nucleation rates in a Lennard-Jones fluid through explicit molecular dynamics simulations. Our approach-based on a recent free energy method (dubbed reweighted Jarzynski sampling), transition state theory, and a simple recrossing correction-allows us to probe a fairly wide range of rates in several superheated and cavitation regimes in a consistent manner. Rate predictions from this approach bridge disparate independent literature studies on the same model system. As such, we find that rate predictions based on classical nucleation theory, direct brute force molecular dynamics simulations, and seeding are consistent with our approach and one another. Published rates derived from forward flux sampling simulations are, however, found to be outliers. This study serves two purposes: First, we validate the reliability of common modeling techniques and extrapolation approaches on a paradigmatic problem in materials science and chemical physics. Second, we further test our highly generic recipe for rate calculations, and establish its applicability to nucleation processes.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.4
DOI: 10.1063/5.0120136
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“Nucleation rates from small scale atomistic simulations and transition state theory”. Bal KM, Journal Of Chemical Physics 155, 144111 (2021). http://doi.org/10.1063/5.0063398
Abstract: The evaluation of nucleation rates from molecular dynamics trajectories is hampered by the slow nucleation time scale and impact of finite size effects. Here, we show that accurate nucleation rates can be obtained in a very general fashion relying only on the free energy barrier, transition state theory, and a simple dynamical correction for diffusive recrossing. In this setup, the time scale problem is overcome by using enhanced sampling methods, in casu metadynamics, whereas the impact of finite size effects can be naturally circumvented by reconstructing the free energy surface from an appropriate ensemble. Approximations from classical nucleation theory are avoided. We demonstrate the accuracy of the approach by calculating macroscopic rates of droplet nucleation from argon vapor, spanning 16 orders of magnitude and in excellent agreement with literature results, all from simulations of very small (512 atom) systems.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.965
DOI: 10.1063/5.0063398
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“Partial hydrolysis of diphosphonate ester during the formation of hybrid Tio₂, nanoparticles : role of acid concentration”. Ramesha BM, Pawlak B, Arenas Esteban D, Reekmans G, Bals S, Marchal W, Carleer R, Adriaensens P, Meynen V, ChemPhysChem : a European journal of chemical physics and physical chemistry , e202300437 (2023). http://doi.org/10.1002/CPHC.202300437
Abstract: In the present work, a method was utilized to control the in‐situ partial hydrolysis of a diphosphonate ester in presence of a titania precursor and in function of acid content and its impact on the hybrid nanoparticles was assessed. The hydrolysis degree of organodiphosphonate ester linkers during the formation of hybrid organic‐inorganic metal oxide nanoparticles, are relatively underexplored . Quantitative solution NMR spectroscopy revealed that during the synthesis of TiO2 nanoparticles, an increase in acid concentration introduces a higher degree of partial hydrolysis of the TEPD linker into diverse acid/ester derivatives of TEPD. Increasing the HCl/Ti ratio from 1 to 3, resulted in an increase in degree of partial hydrolysis of the TEPD linker in solution from 4% to 18.8% under the here applied conditions. As a result of the difference in partial hydrolysis, the linker‐TiO2 bonding was altered. Upon subsequent drying of the colloidal TiO2 solution, different textures, at nanoscale and macroscopic scale, were obtained dependent on the HCl/Ti ratio and thus the degree of hydrolysis of TEPD. Understanding such linker‐TiO2 nanoparticle surface dynamics is crucial for making hybrid organic‐inorganic materials (i.e. (porous) metal phosphonates) employed in applications such as electronic/photonic devices, separation technology and heterogeneous catalysts.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Laboratory of adsorption and catalysis (LADCA)
Impact Factor: 2.9
DOI: 10.1002/CPHC.202300437
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