105 research outputs found
Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions
Determining the solvation free energies of single ions in water is one of the
most fundamental problems in physical chemistry and yet many unresolved
questions remain. In particular, the ability to decompose the solvation free
energy into simple and intuitive contributions will have important implications
for models of electrolyte solution. Here, we provide definitions of the various
types of single ion solvation free energies based on different simulation
protocols. We calculate solvation free energies of charged hard spheres using
density functional theory interaction potentials with molecular dynamics
simulation (DFT-MD) and isolate the effects of charge and cavitation, comparing
to the Born (linear response) model. We show that using uncorrected Ewald
summation leads to unphysical values for the single ion solvation free energy
and that charging free energies for cations are approximately linear as a
function of charge but that there is a small non-linearity for small anions.
The charge hydration asymmetry (CHA) for hard spheres, determined with quantum
mechanics, is much larger than for the analogous real ions. This suggests that
real ions, particularly anions, are significantly more complex than simple
charged hard spheres, a commonly employed representation.Comment: 28 pages, 5 figure
Real single ion solvation free energies with quantum mechanical simulation
Single ion solvation free energies are one of the most important properties
of electrolyte solutions and yet there is ongoing debate about what these
values are. Only the values for neutral ion pairs are known. Here, we use DFT
interaction potentials with molecular dynamics simulation (DFT-MD) combined
with a modified version of the quasi-chemical theory (QCT) to calculate these
energies for the lithium and fluoride ions. A method to correct for the error
in the DFT functional is developed and very good agreement with the
experimental value for the lithium fluoride pair is obtained. Moreover, this
method partitions the energies into physically intuitive terms such as surface
potential, cavity and charging energies which are amenable to descriptions with
reduced models. Our research suggests that lithium's solvation free energy is
dominated by the free energetics of a charged hard sphere, whereas fluoride
exhibits significant quantum mechanical behavior that cannot be simply
described with a reduced model.Comment: 13 pages, 4 figure
Mass Density Fluctuations in Quantum and Classical descriptions of Liquid Water
First principles molecular dynamics simulation protocol is established using
revised functional of Perdew-Burke-Ernzerhof (revPBE) in conjunction with
Grimme's third generation of dispersion (D3) correction to describe properties
of water at ambient conditions. This study also demonstrates the consistency of
the structure of water across both isobaric (NpT) and isothermal (NVT)
ensembles. Going beyond the standard structural benchmarks for liquid water, we
compute properties that are connected to both local structure and mass density
uctuations that are related to concepts of solvation and hydrophobicity. We
directly compare our revPBE results to the Becke-Lee-Yang-Parr (BLYP) plus
Grimme dispersion corrections (D2) and both the empirical fixed charged model
(SPC/E) and many body interaction potential model (MB-pol) to further our
understanding of how the computed properties herein depend on the form of the
interaction potential
ENHANCED GRAVITROPISM 2 coordinates molecular adaptations to gravistimulation in the elongation zone of barley roots
Root gravitropism includes gravity perception in the root cap, signal transduction between root cap and elongation zone, and curvature response in the elongation zone. The barley (Hordeum vulgare) mutant enhanced gravitropism 2 (egt2) displays a hypergravitropic root phenotype. We compared the transcriptomic reprogramming of the root cap, the meristem, and the elongation zone of wild-type (WT) and egt2 seminal roots upon gravistimulation in a time-course experiment and identified direct interaction partners of EGT2 by yeast-two-hybrid screening and bimolecular fluorescence complementation validation. We demonstrated that the elongation zone is subjected to most transcriptomic changes after gravistimulation. Here, 33% of graviregulated genes are also transcriptionally controlled by EGT2, suggesting a central role of this gene in controlling the molecular networks associated with gravitropic bending. Gene co-expression analyses suggested a role of EGT2 in cell wall and reactive oxygen species-related processes, in which direct interaction partners of EGT2 regulated by EGT2 and gravity might be involved. Taken together, this study demonstrated the central role of EGT2 and its interaction partners in the networks controlling root zone-specific transcriptomic reprogramming of barley roots upon gravistimulation. These findings can contribute to the development of novel root idiotypes leading to improved crop performance
Understanding the scale of the single ion free energy: a critical test of the tetra-phenyl arsonium and tetra-phenyl borate assumption
The tetra-phenyl arsonium and tetra-phenyl borate (TATB) assumption is a commonly used extra-thermodynamic assumption that allows single ion free energies to be split into cationic and anionic contributions. The assumption is that the values for the TATB salt can be divided equally. This is justified by arguing that these large hydrophobic ions will cause a symmetric response in water. Experimental and classical simulation work has raised potential flaws with this assumption, indicating that hydrogen bonding with the phenyl ring may favor the solvation of the TB anion. Here, we perform ab initio molecular dynamics simulations of these ions in bulk water demonstrating that there are significant structural differences. We quantify our findings by reproducing the experimentally observed vibrational shift for the TB anion and confirm that this is associated with hydrogen bonding with the phenyl rings. Finally, we demonstrate that this results in a substantial energetic preference of the water to solvate the anion. Our results suggest that the validity of the TATB assumption, which is still widely used today, should be reconsidered experimentally in order to properly reference single ion solvation free energy, enthalpy, and entropy
Quantifying the hydration structure of sodium and potassium ions: taking additional steps on Jacob's Ladder
The ability to reproduce the experimental structure of water around the sodium and potassium ions is a key test of the quality of interaction potentials due to the central importance of these ions in a wide range of important phenomena. Here, we simulate the Na+ and K+ ions in bulk water using three density functional theory functionals: (1) the generalized gradient approximation (GGA) based dispersion corrected revised Perdew, Burke, and Ernzerhof functional (revPBE-D3) (2) the recently developed strongly constrained and appropriately normed (SCAN) functional (3) the random phase approximation (RPA) functional for potassium. We compare with experimental X-ray diffraction (XRD) and X-ray absorption fine structure (EXAFS) measurements to demonstrate that SCAN accurately reproduces key structural details of the hydration structure around the sodium and potassium cations, whereas revPBE-D3 fails to do so. However, we show that SCAN provides a worse description of pure water in comparison with revPBE-D3. RPA also shows an improvement for K+, but slow convergence prevents rigorous comparison. Finally, we analyse cluster energetics to show SCAN and RPA have smaller fluctuations of the mean error of ion-water cluster binding energies compared with revPBE-D3
A path integral methodology for obtaining thermodynamic properties of nonadiabatic systems using Gaussian mixture distributions
This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. The following article appeared in Raymond, N., Iouchtchenko, D., Roy, P.-N., & Nooijen, M. (2018). A path integral methodology for obtaining thermodynamic properties of nonadiabatic systems using Gaussian mixture distributions. The Journal of Chemical Physics, 148(19), 194110 and may be found at https://doi.org/10.1063/1.5025058We introduce a new path integral Monte Carlo method for investigating nonadiabatic systems in thermal equilibrium and demonstrate an approach to reducing stochastic error. We derive a general path integral expression for the partition function in a product basis of continuous nuclear and discrete electronic degrees of freedom without the use of any mapping schemes. We separate our Hamiltonian into a harmonic portion and a coupling portion; the partition function can then be calculated as the product of a Monte Carlo estimator (of the coupling contribution to the partition function) and a normalization factor (that is evaluated analytically). A Gaussian mixture model is used to evaluate the Monte Carlo estimator in a computationally efficient manner. Using two model systems, we demonstrate our approach to reduce the stochastic error associated with the Monte Carlo estimator. We show that the selection of the harmonic oscillators comprising the sampling distribution directly affects the efficiency of the method. Our results demonstrate that our path integral Monte Carlo method’s deviation from exact Trotter calculations is dominated by the choice of the sampling distribution. By improving the sampling distribution, we can drastically reduce the stochastic error leading to lower computational cost.Natural Sciences and Engineering Research Council of Canada (NSERC)
Ontario Ministry of Research and Innovation (MRI)
Canada Foundation for Innovation (CFI)
Canada Research Chair progra
- …