arXiv subjects

J. Daniel Gezelter

Publications and source records attributed to J. Daniel Gezelter.

11 recordsLinked to original sources

arXiv2026

Separation of Flexible Enantiomers Using Shear Flow

Mechanical separation of enantiomers is an attractive alternative to synthetic methods for producing enantiopure samples. Shear flow that produces solution vorticity has been shown to be a viable means for separating chiral objects on the micro- to nano-scale due to the tensorial nature of the interactions between chiral objects and the surrounding fluid. A recently-developed theory of molecular pitch characterizes these interactions using the resistance tensor and predicts the shear-induced separation of drug-like molecules from their optimized molecular geometries. We present a molecular dynamics study on the effects of incorporating molecular flexibility into the molecular pitch framework. We also evaluate the potential for enantiomeric separation of two drug molecules: bicalutamide (Casodex) and montelukast sodium (Singulair). Simulations reveal the emergence of flexibility-induced pitch distributions that result from conformational changes occurring in a realistic solvent environment. However, these distributions are weakly influenced by the solvent identity and the shearing process, producing mean scalar pitch values that are close to those from optimized gas phase structures. Despite the opposing effect of translational diffusion at the molecular scale, racemic mixtures of flexible enantiomers show linear rates of separation at the 10 ns timescale, and we predict that cm-scale separation can be achieved within hours. Additionally, we provide estimates for parameters of a Taylor-Couette device for generating laminar shear flow, as well as considerations for future experiments.

physics.chem-ph↗

arXiv2026

Elucidating Trace Gas Interactions with Ice Surfaces using Molecular Dynamics

Recent experimental work carried out by Yettapu, Manning, and Cyran on ice / vapor interfaces revealed changes in sum frequency generation (SFG) signals at ~ 3170 cm$^{-1}$ depending on whether acetone or methanol was adsorbed onto the ice at 223 K. They linked the transformation of that signal to the induced melting of the ice crystal. We present molecular dynamics modeling of their experiments using methanol and acetone layers adsorbed on the basal facet of a proton-ordered Ice-Ih crystal at temperatures of 223 K and 265 K. The width of the quasi-liquid layer (QLL), O-H bond frequencies, calculated SFG signals, and hydrogen bonding statistics all indicate changes due to the presence of the adsorbates. While we see no significant adsorbate-based differences in QLL formation, we find at 223 K that acetone preserves under-coordinated waters that are associated with a secondary water with a low frequency O-H bond, while methanol integrates more fully into the hydrogen bonding network, resulting in a narrower distribution of O-H bond frequencies. This change in hydrogen bonding produces a local modification of the electric field, which may contribute to the difference in the experimental SFG signals at low frequencies.

physics.chem-ph↗

arXiv2025

Molecular dynamics of ice-active solutions at ice-water interfaces

Small molecules that interact strongly with water were the subject of this molecular dynamics (MD) study. These solutes include a cryoprotectant (DMSO), a polyalcohol [CH$_2$(OH)$_2$], carboxylic acid conjugates (HCOOH and HCOONa), an ammonium salt (NH$_4$Cl), and two alkyl halide salts (NaCl and NaF). MD simulations were carried out for bulk supercooled liquids and solutions in contact with ice. Solute and water hydrogen bonding, orientational and translational order, and hydrogen bond jump dynamics were compared in bulk and as a function of distance from the solute molecules. Reverse non-equilibrium molecular dynamics (RNEMD) simulations were used to determine interfacial widths, friction coefficients ($κ$) with ice, and solution phase viscosities ($η$). Ionic solutes were found to reduce orientational and translational ordering near the ice interfaces. However, in bulk liquids, we find a correlation between orientational ordering and the statistics of water hydrogen bonds -- a donor-acceptor imbalance in water has the greatest impact on ordering in the bulk liquids. Although ionic solutions exhibited similar effects on the water structure, the effect on dynamics depends most directly on donor-acceptor imbalance. Solutes that are hydrogen bond acceptors were found to slow hydrogen bond lifetimes relative to hydrogen bond donors. We also observed a direct correlation between the liquid phase hydrogen-bond jump times and shear viscosity. Finally, of all the solutes studied, only DMSO and sodium formate exhibited increased friction at the ice-water interface.

physics.chem-ph↗

arXiv2024

A Reverse Non-Equilibrium Molecular Dynamics (RNEMD) Algorithm for Coupled Mass and Heat Transport in Mixtures

We present a new method for introducing stable non-equilibrium concentration gradients in molecular dynamics simulations of mixtures. This method extends earlier Reverse Non-Equilibrium Molecular Dynamics (RNEMD) methods which use kinetic energy scaling moves to create temperature or velocity gradients. In the new scaled particle flux (SPF-RNEMD) algorithm, energies and forces are computed simultaneously for a molecule existing in two non-adjacent regions of a simulation box, and the system evolves under a linear combination of these interactions. A continuously increasing particle scaling variable is responsible for migration of the molecule between the regions as the simulation progresses, allowing for simulations under an applied particle flux. To test the method, we investigate diffusivity in mixtures of identical, but distinguishable particles, and in a simple mixture of multiple Lennard-Jones particles. The resulting concentration gradients provide Fick diffusion constants for mixtures. We also discuss using the new method to obtain coupled transport properties using simultaneous particle and thermal fluxes to compute the temperature dependence of the diffusion coefficient and activation energies for diffusion from a single simulation. Lastly, we demonstrate the use of this new method in interfacial systems by computing the diffusive permeability for a molecular fluid moving through a nanoporous graphene membrane.

physics.chem-ph↗

arXiv2023

Heat Transfer in Gold Interfaces Capped with Thiolated Polyethylene Glycol: A Molecular Dynamics Study

Reverse non-equilibrium molecular dynamics (RNEMD) simulations were used to study heat transport in solvated gold interfaces which have been functionalized with a low molecular weight thiolated polyethylene glycol (PEG). The gold interfaces studied included (111), (110), and (100) facets, as well as spherical nanoparticles with radii of 10 and 20 Å. The embedded atom model (EAM) and the polarizable density-readjusted embedded atom model (DR-EAM) were implemented to determine the effect of metal polarizability on heat transport properties. We find that the interfacial thermal conductance values for thiolated PEG capped interfaces are higher than those for pristine gold interfaces. Hydrogen bonding between the thiolated PEG and solvent differs between planar facets and the nanospheres, suggesting one mechanism for enhanced transfer of energy, while the covalent gold sulfur bond appears to create the largest barrier to thermal conduction. Through analysis of vibrational power spectra, we find an enhanced population at low frequency heat carrying modes for the nanospheres, which may also explain the higher mean G value.

physics.chem-ph↗

arXiv2023

A Theory of Pitch for the Hydrodynamic Properties of Molecules, Helices, and Achiral Swimmers at Low Reynolds Number

We present a theory for pitch, a matrix property which is linked to the coupling of rotational and translational motion of rigid bodies at low Reynolds number. The pitch matrix is a geometric property of objects in contact with a surrounding fluid, and it can be decomposed into three principal axes of pitch and their associated \textit{moments of pitch}. The moments of pitch predict the translational motion in a direction parallel to each pitch axis when the object is rotated around that axis, and can be used to explain translational drift, particularly for rotating helices. We also provide a symmetrized boundary element model for blocks of the resistance tensor, allowing calculation of the pitch matrix for arbitrary rigid bodies. We analyze a range of chiral objects, including chiral molecules and helices. Chiral objects with a $C_n$ symmetry axis with $n > 2$ show additional symmetries in their pitch matrices. We also show that some achiral objects have non-vanishing pitch matrices, and use this result to explain recent observations of achiral microswimmers. We also discuss the small, but non-zero pitch of Lord Kelvin's isotropic helicoid.

physics.chem-ph↗

arXiv2019

Polarizable Potentials For Metals: The Density Readjusting Embedded Atom Method (DR-EAM)

In simulations of metallic interfaces, a critical aspect of metallic behavior is missing from the some of the most widely used classical molecular dynamics force fields. We present a modification of the embedded atom method (EAM) which allows for electronic polarization of the metal by treating the valence density around each atom as a fluctuating dynamical quantity. The densities are represented by a set of additional fluctuating variables (and their conjugate momenta) which are propagated along with the nuclear coordinates. This ``density readjusting EAM'' (DR-EAM) preserves nearly all of the useful qualities of traditional EAM, including bulk elastic properties and surface energies. However, it also allows valence electron density to migrate through the metal in response to external perturbations. We show that DR-EAM can successfully model polarization in response to external charges, capturing the image charge effect in atomistic simulations. DR-EAM also captures some of the behavior of metals in the presence of uniform electric fields, predicting surface charging and shielding internal to the metal. We further show that it predicts charge transfer between the constituent atoms in alloys, leading to novel predictions about unit cell geometries in layered L$1_0$ structures.

cond-mat.mtrl-sci↗

arXiv2016

CO-Induced Restructuring on Stepped Pt Surfaces: A Molecular Dynamics Study

The effects of plateau width and step edge kinking on carbon monoxide (CO)-induced restructuring of platinum surfaces were explored using molecular dynamics (MD) simulations. Platinum crystals displaying four different vicinal surfaces [(321), (765), (112), and (557)] were constructed and exposed to partial coverages of carbon monoxide. Platinum-CO interactions were fit to recent experimental data and density functional theory (DFT) calculations, providing a classical interaction model that captures the atop binding preference on Pt. The differences in Pt-Pt binding strength between edge atoms on the various facets were found to play a significant role in step edge wandering and reconstruction events. Because the mechanism for step doubling relies on a stochastic meeting of two wandering edges, the widths of the plateaus on the original surfaces was also found to play a role in these reconstructions. On the Pt(321) surfaces, the CO adsorbate was found to assist in reordering the kinked step edges into straight {100} edge segments.

physics.chem-ph↗

arXiv2016

Real space electrostatics for multipoles. III. Dielectric Properties

In the first two papers in this series, we developed new shifted potential (SP), gradient shifted force (GSF), and Taylor shifted force (TSF) real-space methods for multipole interactions in condensed phase simulations. Here, we discuss the dielectric properties of fluids that emerge from simulations using these methods. Most electrostatic methods (including the Ewald sum) require correction to the conducting boundary fluctuation formula for the static dielectric constants, and we discuss the derivation of these corrections for the new real space methods. For quadrupolar fluids, the analogous material property is the quadrupolar susceptibility. As in the dipolar case, the fluctuation formula for the quadrupolar susceptibility has corrections that depend on the electrostatic method being utilized. One of the most important effects measured by both the static dielectric and quadrupolar susceptibility is the ability to screen charges embedded in the fluid. We use potentials of mean force between solvated ions to discuss how geometric factors can lead to distance-dependent screening in both quadrupolar and dipolar fluids.

physics.chem-ph↗

arXiv2016

Interfacial Thermal Conductance of Thiolate-Protected Gold Nanospheres

Molecular dynamics simulations of thiolate-protected and solvated gold nanoparticles were carried out in the presence of a non-equilibrium heat flux between the solvent and the core of the particle. The interfacial thermal conductance ($G$) was computed for these interfaces, and the behavior of the thermal conductance was studied as a function of particle size, ligand flexibility, and ligand chain length. In all cases, thermal conductance of the ligand-protected particles was higher than the bare metal-solvent interface. A number of mechanisms for the enhanced conductance were investigated, including thiolate-driven corrugation of the metal surface, solvent ordering at the interface, solvent-ligand interpenetration, and ligand ordering relative to the particle surface. Only the smallest particles exhibited significant corrugation. All ligands permitted substantial solvent-ligand interpenetration, and ligand chain length has a significant influence on the orientational ordering of interfacial solvent. Solvent-ligand vibrational overlap, particularly in the low frequency range ($< 80 \mathrm{cm}^{-1}$) was significantly altered by ligand rigidity, and had direct influence on the interfacial thermal conductance.

physics.chem-ph↗

arXiv2015

The different facets of ice have different hydrophilicities: Friction at water / ice-I$_\mathrm{h}$ interfaces

We present evidence that the prismatic and secondary prism facets of ice-I$_\mathrm{h}$ crystals possess structural features that can reduce the effective hydrophilicity of the ice/water interface. The spreading dynamics of liquid water droplets on ice facets exhibits long-time behavior that differs for the prismatic $\{10\bar{1}0\}$ and secondary prism $\{11\bar{2}0\}$ facets when compared with the basal $\{0001\}$ and pyramidal $\{20\bar{2}1\}$ facets. We also present the results of simulations of solid-liquid friction of the same four crystal facets being drawn through liquid water, and find that the two prismatic facets exhibit roughly half the solid-liquid friction of the basal and pyramidal facets. These simulations provide evidence that the two prismatic faces have a significantly smaller effective surface area in contact with the liquid water. The ice / water interfacial widths for all four crystal facets are similar (using both structural and dynamic measures), and were found to be independent of the shear rate. Additionally, decomposition of orientational time correlation functions show position-dependence for the short- and longer-time decay components close to the interface.

physics.chem-ph↗