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John D. Weeks

Publications and source records attributed to John D. Weeks.

At least 19 recordsLinked to original sources

Response Theory for Static and Dynamic Solvation of Ionic and Dipolar Solutes in Water

The response of polar solvents to ions and polar molecules dictates many fundamental molecular processes. To understand such electrostatically-driven solvation processes, one ideally would probe the dielectric response of a solvent to an idealized point test charge or dipole solute, as envisioned in classic continuum treatments of the problem. However, this is difficult in simulations using standard atomically-detailed solvent models with embedded point charges due to possible overlap with the test charge that lead to singular interaction energies. This problem is traditionally avoided for a realistic charged solute by introducing an excluded volume core that shields its embedded point charge or dipole from the charges in the solvent. However, this core introduces additional molecular-scale perturbations of the solvent density that complicate the interpretation of solvent dielectric response. In this work, we avoid these complications through the use of Gaussian-smoothed test charges and dipoles. Gaussian charges and dipoles can be readily inserted anywhere into an atomistic solvent model without encountering infinite energies. If the Gaussian-smoothing is on the scale of molecular correlations in the solvent, both the thermodynamic and dynamic solvation response is linear. Using this observation, we construct accurate predictive theories for solvation free energies and solvation dynamics for insertion of Gaussian charges and dipoles in polar solvents and demonstrate the accuracy of the theories for a widely-used model of water. Our results suggest that Gaussian test charge distributions can be used as an informative probe of dielectric response in molecular models, and our theories can be used to analytically predict the largest component of solvation free energies of charged and polar solutes.

physics.chem-ph

Quantifying the relevance of long-range forces for crystal nucleation in water

Understanding nucleation from aqueous solutions is of fundamental importance in a multitude of fields, ranging from materials science to biophysics. The complex solvent-mediated interactions in aqueous solutions hamper the development of a simple physical picture elucidating the roles of different interactions in nucleation processes. In this work we make use of three complementary techniques to disentangle the role played by short and long-range interactions in solvent mediated nucleation. Specifically, the first approach we utilize is the local molecular field (LMF) theory to renormalize long-range Coulomb electrostatics. Secondly, we use well-tempered metadynamics to speed up rare events governed by short-range interactions. Thirdly, deep learning-based State Predictive Information Bottleneck approach is employed in analyzing the reaction coordinate of the nucleation processes obtained from LMF treatment coupled with well-tempered metadynamics. We find that the two-step nucleation mechanism can largely be captured by the short-range interactions, while the long-range interactions further contribute to the stability of the primary crystal state at ambient conditions. Furthermore, by analyzing the reaction coordinate obtained from combined LMF-metadynamics treatment, we discern the fluctuations on different time scales, highlighting the need for long-range interactions when accounting for metastability.

cond-mat.soft

Influence of long range forces on the transition states and dynamics of NaCl ion-pair dissociation in water

We study NaCl ion-pair dissociation in a dilute aqueous solution using computer simulations both for the full system with long range Coulomb interactions and for a well chosen reference system with short range intermolecular interactions. Analyzing results using concepts from Local Molecular Field (LMF) theory and the recently proposed AI-based analysis tool "State predictive information bottleneck" (SPIB) we show that the system with short range interactions can accurately reproduce the transition rate for the dissociation process, the dynamics for moving between the underlying metastable states, and the transition state ensemble. Contributions from long range interactions can be largely neglected for these processes because long range forces from the direct interionic Coulomb interactions are almost completely canceled ($>90\%$) by those from solvent interactions over the length scale where the transition takes place. Thus for this important monovalent ion-pair system, short range forces alone are able to capture detailed consequences of the collective solvent motion, allowing the use of physically suggestive and computationally efficient short range models for the disassociation event. We believe that the framework here should be applicable to disentangling mechanisms for more complex processes such as multivalent ion disassociation, where previous work has suggested that long range contributions may be more important.

physics.chem-ph

The Influence of Distant Boundaries on the Solvation of Charged Particles

The long-ranged nature of the Coulomb potential requires a proper accounting for the influence of even distant electrostatic boundaries in the determination of the solvation free energy of a charged solute. We introduce an exact rewriting of the free energy change upon charging a solute that explicitly isolates the contribution from these boundaries and quantifies the impact of the different boundaries on the free energy. We demonstrate the importance and advantages of appropriately referencing the electrostatic potential to that of the vacuum through the study of several simple model charge distributions, for which we can isolate an analytic contribution from the boundaries that can be readily evaluated in computer simulations of molecular systems. Finally, we highlight that the constant potential of the bulk dielectric phase - the Bethe potential - cannot contribute to the solvation thermodynamics of a single charged solute when the charge distributions of the solvent and solute do not overlap in relevant configurations. But when the charge distribution of a single solute can overlap with the intramolecular charge distribution of solvent molecules, as is the case in electron holography, for example, the Bethe potential is needed when comparing to experiment. Our work may also provide insight into the validity of "extra thermodynamic assumptions" traditionally made during the experimental determination of single ion solvation free energies.

cond-mat.stat-mech

Dissecting Hydrophobic Hydration and Association

We use appropriately defined short ranged reference models of liquid water to clarify the different roles local hydrogen bonding, van der Waals attractions, and long ranged electrostatic interactions play in the solvation and association of apolar solutes in water. While local hydrogen bonding in- teractions dominate hydrophobic effects involving small solutes, longer ranged electrostatic and dis- persion interactions are found to be increasingly important in the description of interfacial structure around large solutes. The hydrogen bond network sets the solute length scale at which a crossover in solvation behavior between these small and large length scale regimes is observed. Unbalanced long ranged forces acting on interfacial water molecules are also important in hydrophobic association, illustrated here by analysis of the association of model methane and buckminsterfullerene solutes.

cond-mat.stat-mech

Hydrophobicity Scaling of Aqueous Interfaces by an Electrostatic Mapping

An understanding of the hydrophobicity of complex heterogeneous molecular assemblies is crucial to characterize and predict interactions between biomolecules. As such, uncovering the subtleties of assembly processes hinges on an accurate classification of the relevant interfaces involved, and much effort has been spent on developing so-called "hydrophobicity maps." In this work, we introduce a novel electrostatics-based mapping of aqueous interfaces that focuses on the collective, long-wavelength electrostatic response of water to the presence of nearby surfaces. In addition to distinguishing between hydrophobic and hydrophilic regions of heterogeneous surfaces, this electrostatic mapping can also differentiate between hydrophilic regions that polarize nearby waters in opposing directions. We therefore expect this approach to find use in predicting the location of possible water-mediated hydrophilic interactions, in addition to the more commonly emphasized hydrophobic interactions that can also be of significant importance.

cond-mat.soft

Deconstructing classical water models at interfaces and in bulk

Using concepts from perturbation and local molecular field theories of liquids we divide the potential of the SPC/E water model into short and long ranged parts. The short ranged parts define a minimal reference network model that captures very well the structure of the local hydrogen bond network in bulk water while ignoring effects of the remaining long ranged interactions. This deconstruction can provide insight into the different roles that the local hydrogen bond network, dispersion forces, and long ranged dipolar interactions play in determining a variety of properties of SPC/E and related classical models of water. Here we focus on the anomalous behavior of the internal pressure and the temperature dependence of the density of bulk water. We further utilize these short ranged models along with local molecular field theory to quantify the influence of these interactions on the structure of hydrophobic interfaces and the crossover from small to large scale hydration behavior. The implications of our findings for theories of hydrophobicity and possible refinements of classical water models are also discussed.

cond-mat.stat-mech

On the efficient and accurate short-ranged simulations of uniform polar molecular liquids

We show that spherical truncations of the 1/r interactions in models for water and acetonitrile yield very accurate results in bulk simulations for all site-site pair correlation functions as well as dipole-dipole correlation functions. This good performance in bulk simulations contrasts with the generally poor results found with the use of such truncations in nonuniform molecular systems. We argue that Local Molecular Field (LMF) theory provides a general theoretical framework that gives the necessary corrections to simple truncations in most nonuniform environments and explains the accuracy of spherical truncations in uniform environments by showing that these corrections are very small. LMF theory is derived from the exact Yvon-Born-Green (YBG) hierarchy by making physically-motivated and well-founded approximations. New and technically interesting derivations of both the YBG hierarchy and LMF theory for a variety of site-site molecular models are presented in appendices. The main paper focuses on understanding the accuracy of these spherical truncations in uniform systems both phenomenologically and quantitatively using LMF theory.

cond-mat.stat-mech

Acetonitrile on silica surfaces and at its liquid-vapor interface: structural correlations and collective dynamics

Solvent structure and dynamics of acetonitrile at its liquid-vapor (LV) interface and at the acetonitrile-silica (LS) interface are studied by means of molecular dynamics simulations. We set up the interfacial system and treat the long-ranged electrostatics carefully to obtain both stable LV and LS interfaces within the same system. Single molecule (singlet) and correlated density orientational profiles and singlet and collective reorientational dynamics are reported for both interfaces. At the LS interface acetonitrile forms layers. The closest sublayer is dominated by nitrogen atoms bonding to the hydrogen sites of the silica surface. The singlet molecular reorientation is strongly hindered when close to the silica surface, but at the LV interface it relaxes much faster than in the bulk. Antiparallel correlations between acetonitrile molecules at the LV interface are even stronger than in the bulk liquid phase. This strong antiparallel correlation disappears at the LS interface. The collective reorientational relaxation of the first layer acetonitrile is much faster than the singlet reorientational relaxation but it is still slower than in the bulk. These results are interpreted with reference to a variety of recent experiments. We found that defining interface properties based on the distribution of positions of different choices of atoms or sites within the molecule leads to apparently different orientational profiles, especially at the LV interface. We provide a general formulation showing that this ambiguity arises when the size of the molecule is comparable to the interfacial width and is particularly significant when there is a large difference in density at the upper and lower boundaries of the interface. We finally analyze the effect of electrostatics to show the necessity of properly treating long-ranged electrostatics for simulations of interfacial systems.

cond-mat.mtrl-sci

Efficient solutions of self-consistent mean field equations for dewetting and electrostatics in nonuniform liquids

We use a new configuration-based version of linear response theory to efficiently solve self-consistent mean field equations relating an effective single particle potential to the induced density. The versatility and accuracy of the method is illustrated by applications to dewetting of a hard sphere solute in a Lennard-Jones fluid, the interplay between local hydrogen bond structure and electrostatics for water confined between two hydrophobic walls, and to ion pairing in ionic solutions. Simulation time has been reduced by more than an order of magnitude over previous methods.

cond-mat.stat-mech

Accurate Thermodynamics for Short-Ranged Truncations of Coulomb Interactions in Site-Site Molecular Models

Coulomb interactions are present in a wide variety of all-atom force fields. Spherical truncations of these interactions permit fast simulations but are problematic due to their incorrect thermodynamics. Herein we demonstrate that simple analytical corrections for the thermodynamics of uniform truncated systems are possible. In particular results for the SPC/E water model treated with spherically-truncated Coulomb interactions suggested by local molecular field theory [Proc. Nat. Acad. Sci. USA 105, 19136 (2008)] are presented. We extend results developed by Chandler [J. Chem. Phys. 65, 2925 (1976)] so that we may treat the thermodynamics of mixtures of flexible charged and uncharged molecules simulated with spherical truncations. We show that the energy and pressure of spherically-truncated bulk SPC/E water are easily corrected using exact second-moment-like conditions on long-ranged structure. Furthermore, applying the pressure correction as an external pressure removes the density errors observed by other research groups in NPT simulations of spherically-truncated bulk species.

cond-mat.stat-mech

Exact relations between charge-density functions determining the total Coulomb energy and the dielectric constant for a mixture of neutral and charged site-site molecules

We extend results developed by Chandler [J. Chem. Phys. 65, 2925 (1976)] for the dielectric constant of neutral site-site molecular models to mixtures of both charged and uncharged molecules. This provides a unified derivation connecting the Stillinger-Lovett moment conditions for ions to standard results for the dielectric constant for polar species and yields exact expressions for the small-k expansion of the two-point intermolecular charge-density function used to determine the total Coulomb energy. The latter is useful in determining corrections to the thermodynamics of uniform site-site molecular models simulated with spherically truncated Coulomb interactions.

cond-mat.stat-mech

Orbital-Free Density Functional Theory: Linear Scaling Methods for Kinetic Potentials, and Applications to Solid Al and S

In orbital-free density functional theory the kinetic potential (KP), the functional derivative of the kinetic energy density functional, appears in the Euler equation for the electron density and may be more amenable to simple approximations. We study properties of two solid-state systems, Al and Si, using two nonlocal KPs that gave good results for atoms. Very accurate results are found for Al, but results for Si are much less satisfactory, illustrating the general need for a better treatment of extended covalent systems. A different integration pathway in the KP formalism may prove useful in attacking this fundamental problem.

cond-mat.other

Equilibrium and nonequilibrium effects in the collapse of a model polypeptide

We present results of molecular simulations of a model protein whose hydrophobic collapse proceeds as a cascade of downhill transitions between distinct intermediate states. Different intermediates are stabilized by means of appropriate harmonic constraints, allowing explicit calculation of the equilibrium free energy landscape. Nonequilibrium collapse trajectories are simulated independently and compared to diffusion on the calculated free energy surface. We find that collapse generally adheres to this surface, but quantitative agreement is complicated by nonequilibrium effects and by dependence of the diffusion coefficient on position on the surface.

cond-mat.soft

Dynamic interfaces in an organic thin film

Low-dimensional boundaries between phases and domains in organic thin films are important in charge transport and recombination. Here, fluctuations of interfacial boundaries in an organic thin film, acridine-9-carboxylic acid (ACA) on Ag(111), have been visualized in real time, and measured quantitatively, using Scanning Tunneling Microscopy. The boundaries fluctuate via molecular exchange with exchange time constants of 10-30 ms at room temperature, yielding length mode fluctuations that should yield characteristic f-1/2 signatures for frequencies less than ~100 Hz. Although ACA has highly anisotropic intermolecular interactions, it forms islands that are compact in shape with crystallographically distinct boundaries that have essentially identical thermodynamic and kinetic properties . The physical basis of the modified symmetry is shown to arise from significantly different substrate interactions induced by alternating orientations of successive molecules in the condensed phase. Incorporating this additional set of interactions in a lattice gas model leads to effective multi-component behavior, as in the Blume-Emery-Griffiths (BEG) model, and can straightforwardly reproduce the experimentally observed isotropic behavior. The general multi-component description allows the domain shapes and boundary fluctuations to be tuned from isotropic to highly anisotropic in terms of the balance between intermolecular interactions and molecule-substrate interactions. Key words: Organic thin film, fluctuations, STM, molecular interactions, diffusion kinetics, phase coexistence

cond-mat.mtrl-sci

Local molecular field theory for the treatment of electrostatics

We examine in detail the theoretical underpinnings of previous successful applications of local molecular field (LMF) theory to charged systems. LMF theory generally accounts for the averaged effects of long-ranged components of the intermolecular interactions by using an effective or restructured external field. The derivation starts from the exact Yvon-Born-Green hierarchy and shows that the approximation can be very accurate when the interactions averaged over are slowly varying at characteristic nearest-neighbor distances. Application of LMF theory to Coulomb interactions alone allows for great simplifications of the governing equations. LMF theory then reduces to a single equation for a restructured electrostatic potential that satisfies Poisson's equation defined with a smoothed charge density. Because of this charge smoothing by a Gaussian of width sigma, this equation may be solved more simply than the detailed simulation geometry might suggest. Proper choice of the smoothing length sigma plays a major role in ensuring the accuracy of this approximation. We examine the results of a basic confinement of water between corrugated wall and justify the simple LMF equation used in a previous publication. We further generalize these results to confinements that include fixed charges in order to demonstrate the broader impact of charge smoothing by sigma. The slowly-varying part of the restructured electrostatic potential will be more symmetric than the local details of confinements.

cond-mat.stat-mech

Interplay of local hydrogen-bonding and long-ranged dipolar forces in simulations of confined water

Spherical truncations of Coulomb interactions in standard models for water permit efficient molecular simulations and can give remarkably accurate results for the structure of the uniform liquid. However truncations are known to produce significant errors in nonuniform systems, particularly for electrostatic properties. Local molecular field (LMF) theory corrects such truncations by use of an effective or restructured electrostatic potential that accounts for effects of the remaining long-ranged interactions through a density-weighted mean field average and satisfies a modified Poisson's equation defined with a Gaussian-smoothed charge density. We apply LMF theory to three simple molecular systems that exhibit different aspects of the failure of a naive application of spherical truncations -- water confined between hydrophobic walls, water confined between atomically-corrugated hydrophilic walls, and water confined between hydrophobic walls with an applied electric field. Spherical truncations of 1/r fail spectacularly for the final system in particular, and LMF theory corrects the failings for all three. Further, LMF theory provides a more intuitive way to understand the balance between local hydrogen bonding and longer-ranged electrostatics in molecular simulations involving water.

cond-mat.stat-mech

A new approach for efficient simulation of Coulomb interactions in ionic fluids

We propose a simplified version of local molecular field (LMF) theory to treat Coulomb interactions in simulations of ionic fluids. LMF theory relies on splitting the Coulomb potential into a short-ranged part that combines with other short-ranged core interactions and is simulated explicitly. The averaged effects of the remaining long-ranged part are taken into account through a self-consistently determined effective external field. The theory contains an adjustable length parameter sigma that specifies the cut-off distance for the short-ranged interaction. This can be chosen to minimize the errors resulting from the mean-field treatment of the complementary long-ranged part. Here we suggest that in many cases an accurate approximation to the effective field can be obtained directly from the equilibrium charge density given by the Debye theory of screening, thus eliminating the need for a self-consistent treatment. In the limit sigma -> 0, this assumption reduces to the classical Debye approximation. We examine the numerical performance of this approximation for a simple model of a symmetric ionic mixture. Our results for thermodynamic and structural properties of uniform ionic mixtures agree well with similar results of Ewald simulations of the full ionic system. In addition we have used the simplified theory in a grand-canonical simulation of a nonuniform ionic mixture where an ion has been fixed at the origin. Simulations using short-ranged truncations of the Coulomb interactions alone do not satisfy the exact condition of complete screening of the fixed ion, but this condition is recovered when the effective field is taken into account. We argue that this simplified approach can also be used in the simulations of more complex nonuniform systems.

cond-mat.stat-mech