Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics

Molecular Simulations of Thermal Transport across Iron Oxide-Hydrocarbon Interfaces

The rational design of dielectric fluids for immersion cooling of batteries requires a molecular-level understanding of the heat flow across the battery casing/dielectric fluid interface. Here, we use nonequilibrium molecular dynamics (NEMD) simulations to quantify the interfacial thermal resistance (ITR) between hematite and poly-α-olefin (PAO), which are representative of the outer surface of the steel battery casing and a synthetic hydrocarbon dielectric fluid, respectively. After identifying the most suitable force fields to model the thermal properties of the individual components, we then compared different solid-liquid interaction potentials for the calculation of the ITR. These potentials resulted in a wide range of ITR values (4-21 K m2 GW-1), with stronger solid-liquid interactions leading to lower ITR. The increase in ITR is correlated with an increase in density of the fluid layer closest to the surface. Since the ITR has not been experimentally measured for the hematite/PAO interface, we validate the solid-liquid interaction potential using the work of adhesion calculated using the dry-surface method. The work of adhesion calculations from the simulations were compared to those derived from experimental contact angle measurements for PAO on steel. We find that all of the solid-liquid potentials overestimate the experimental work of adhesion. The experiments and simulations can only be reconciled by further reducing the strength of the interfacial interactions. This suggests some screening of the solid-liquid interactions, which may be due to the presence of an interfacial water layer between PAO and steel in the contact angle experiments. Using the solid-liquid interaction potential that reproduces the experimental work of adhesion, we obtain a higher ITR (33 K m2 GW-1), suggesting inefficient thermal transport. The results of this study demonstrate the potential for NEMD simulations to improve understanding of the nanoscale thermal transport across industrially important interfaces. This study represents an important step toward the rational design of more effective fluids for immersion cooling systems for electric vehicles and other applications where thermal management is of high importance.

Monte Carlo simulation of an ammonia adsorption refrigeration system based on calcium chloride impregnated nanoporous carbon

We use Monte Carlo simulations to investigate the effect of incorporating calcium chloride salt into nanoporous carbon on the performance of an ammonia-carbon adsorption refrigeration system. Simulations of ideal carbon slit-pores with pore sizes of 1, 2, and 3 nm, each containing calcium chloride with ion densities of 0.0, 0.25, and 0.5 nm-3, were carried out at temperatures between 0 and 30 °C and ammonia pressures up to 15.0 bar. The results reveal that ideal 1 nm pores are able to achieve a good refrigeration performance using waste heat below 100 °C to drive the process, but adding salt to these pores increases the waste heat temperature required beyond 100 °C. However, ideal 2 nm pores require the addition of 0.25 nm-3 salt to achieve a similar performance, while the 3 nm pores were unable to achieve a satisfactory refrigeration performance. Considering that real nanoporous carbons usually feature a variety of specific adsorption sites and non-ideal geometries that should have a similar impact to adding salt, these results indicate that nanoporous carbons with pores in the range of 1-2 nm are likely to hold the most promise for adsorption refrigeration applications and that the addition of salt may not always be helpful.

Molecular dynamics simulation for phase transition of CsPbI3 perovskite with the Buckingham potential

The CsPbI3 perovskite is a promising candidate for photovoltaic applications, for which several critical phase transitions govern both its efficiency and stability. Large-scale molecular dynamics simulations are valuable in understanding the microscopic mechanisms of these transitions, in which the accuracy of the simulation heavily depends on the empirical potential. This study parameterizes two efficient and stable empirical potentials for the CsPbI3 perovskite. In these two empirical potentials, the short-ranged repulsive interaction is described by the Lennard-Jones model or the Buckingham model, while the long-ranged Coulomb interaction is summed by the damped shifted force method. Our molecular dynamics simulations show that these two empirical potentials accurately capture the γ ↔ β ↔ α and δ → α phase transitions for the CsPbI3 perovskite. Furthermore, they are up to two orders of magnitude more efficient than previous empirical models, owing to the high efficiency of the damped shifted force truncation treatment for the Coulomb interaction.

On the Relationship between Water Adsorption and Surface Chemistry in Soda-lime Silicate Glasses

Understanding how the surface structure affects the bioactivity and degradation rate of the glass is one of the primary challenges in developing new bioactive materials. Here, classical and reactive molecular dynamics simulations are used to investigate the relationship between local surface chemistry and local adsorption energies of water on three soda-lime silicate glasses. The compositions of the glasses, (SiO2)65-x(CaO)35(Na2O)x with x=5, 10, and 15, were chosen for their bioactive properties. Analysis of the glass surface structure, compared to the bulk structure, showed that the surface is rich in modifiers and non-bridging oxygen atoms, which were correlated with local adsorption energies. The reactivity of the glasses is found to increase with higher Na2O content, attributed to elevated Na cations and undercoordinated species at the glass surfaces. The current work provides insights into the relationship between the surface structure, chemistry, and properties in these bioactive glasses and offers a step toward their rational design.

Impact of adsorption on thermal conductivity dynamics of adsorbate and adsorbent: Molecular dynamics study of methane and Cu-BTC

Understanding changes in thermodynamic and transport properties during adsorption is crucial for the thermal management of metal-organic frameworks, which also imposes significant challenges for improved performance and energy density of adsorption system. Because of phase transitions in the intermolecular interactions involved in the adsorption phenomena, transport properties including the thermal conductivity exhibit interesting behaviors, yet fully understood. This study employs detailed molecular dynamics simulations to replicate the methane/Cu-BTC adsorption phenomenon for the evaluation of their thermal conductivities across different pressures and temperatures. The molecular simulations show that the thermal conductivities of both the adsorbent (Cu-BTC) and adsorbate (methane, adsorbed phase) vary notably during adsorption processes. Using the concepts of the change in the degree of free movements of the adsorbate molecules and atomic vibration of adsorbent, the reduction of the adsorbate thermal conductivity (∼70-93%) and increase thermal conductivity of the adsorbent (up to 3 times) in Cu-BTC+CH4 pair are explained.

Effects of Surface Charge Distribution and Electrolyte Ions on the Nonlinear Spectra of Model Solid-Water Interfaces

Molecular dynamics simulations of model charged solid/water interfaces were carried out to provide insight about the relationship between the second-order nonlinear susceptibility χ(2) and the structure of the interfacial water layer. The results of the calculations reveal that the density fluctuations of water extend to about 12 Å from the surface regardless of the system, while the orientational ordering of molecules is long-ranged and is sensitive to the presence of electrolytes. The charge localization on the surface was found to affect only the high-frequency part of the Im[χ(2)] spectrum, and the addition of salt has very little effect on the spectrum of the first water layer. For solid/neat water interfaces, the spectroscopically active part of the liquid phase has a thickness largely exceeding the region of density fluctuations, and this long-ranged nonlinear activity is mediated by the electric field of the molecules. The electrolyte ions and their hydration shells act in a destructive way on the molecular field. This effect, combined with the screening of the surface charge by ions, drastically reduces the thickness of the spectroscopic diffuse layer. There is an electrolyte concentration at which the nonlinear response of the diffuse layer is suppressed and the χ(2) spectrum of the interface essentially coincides with that of the first water layer.

Unification of Ewald and shifted force methods to calculate Coulomb interactions in molecular simulations

Three new Ewald series are derived using a new strategy that does not start with a proposed charge spreading function. Of these, the Ewald series produced using shifted potential interactions for the Ewald real space series converges relatively slowly, while the corresponding expression using a shifted force (SF) interaction does not converge. A comparison is made between several approximations of the Ewald method and the SF route to include Coulomb interactions in molecular dynamics (MD) computer simulations. MD simulations of a model bulk molten salt and water were carried out. The recently derived α' variant of Ewald, by K. D. Hammonds and D. M. Heyes [J. Chem. Phys. 157, 074108 (2022)], has been developed analytically and found to be more accurate and computationally efficient than SF in part due to the smaller real space truncation distance that can be used. In addition, with α', the number of reciprocal lattice vectors required is reduced considerably compared with the standard Ewald implementations to give the same accuracy. The invention of the α' method shifts the computational balance back toward using an Ewald construction. The SF method shows greater errors in the Coulomb pressure and time dependent fluctuation properties compared to α'. It does not conserve the shadow Hamiltonian in a microcanonical MD simulation, whereas the α' method does, which facilitates long time stability and insignificant drift of properties over time. The speed of the Ewald computer code is improved by using a new lookup table method.

Analytic Gradients for the Electrostatic Embedding QM/MM Model in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted Charge Operators

Long-range electrostatic effects are fundamental for describing chemical reactivity in the condensed phase. Here, we present the methodology of an efficient quantum mechanical/molecular mechanical (QM/MM) model in periodic boundary conditions (PBC) compatible with QM/MM boundaries at chemical bonds. The method combines electrostatic potential fitted charge operators and electrostatic potentials derived from the smooth particle-mesh Ewald (PME) sum approach. The total energy and its analytic first derivatives with respect to QM, MM, and lattice vectors allow QM/MM molecular dynamics (MD) in the most common thermodynamic ensembles. We demonstrate the robustness of the method by performing a QM/MM MD equilibration of methanol in water. We simulate the cis/trans isomerization free-energy profiles in water of proline amino acid and a proline-containing oligopeptide, showing a correct description of the reaction barrier. Our PBC-compatible QM/MM model can efficiently be used to study the chemical reactivity in the condensed phase and enzymatic catalysis.

Atomistic modeling of electromechanical properties of piezoelectric zinc oxide nanowires

Currently, numerous articles are devoted to examining the influence of geometry and charge distribution on the mechanical properties and structural stability of piezoelectric nanowires (NWs). The varied modeling techniques adopted in earlier molecular dynamics (MD) works dictated the outcome of the different efforts. In this article, comprehensive MD studies are conducted to determine the influence of varied interatomic potentials (partially charged rigid ion model, [PCRIM] ReaxFF, charged optimized many-body [COMB], and Buckingham), geometrical parameters (cross-section geometry, wire diameter, and length), and charge distribution (uniform full charges versus partially charged surface atoms) on the resulting mechanical properties and structural stability of zinc oxide (ZnO) NWs. Our optimized parameters for the Buckingham interatomic potential are in good agreement with the existing experimental results. Furthermore, we found that the incorrect selection of interatomic potentials could lead to excessive overestimate (61%) of the elastic modulus of the NW. While NW length was found to dictate the strain distribution along the wire, impacting its predicted properties, the cross-section shape did not play a major role. Assigning uniform charges for both the core and surface atoms of ZnO NWs leads to a drastic decrease in fracture properties.

Efficient Assessment of 'Instantaneous pK' Values from Molecular Dynamics Simulations

We present a molecular simulation approach to studying the role of local and momentary molecular environment for potential acid-base reactions. For this, we combine thermodynamic considerations on the pK of ionic species with rapid sampling of energy changes related to (de)protonation. Using dispersed carbonate ions in water as a reference, our approach aims at the fast assessment of the momentary protonation energy, and thus the 'instantaneous pK', of calcium-carbonate ion aggregates. The latter include transient complexes that are elusive to long sampling runs. This motivated the elaboration of approximate, yet particularly fast assessable sampling strategies. Along this line, we were able to characterize instantaneous pK values at a statistical accuracy of 0.4 pK units within sampling runs of only 10 ps duration, whereas statistical errors reduce to 0.1 pK units in 75 ps sampling runs, respectively. This readily enabled the required time resolution for the characterization of [Cax (CO3 )y ]2(x-y) aggregates with x=1,2 and y=1,2,3, respectively. In turn, the analysis of the pH-dependent nature of calcite-water interfaces and dynamically ordered liquid-like oxyanion polymers (dollop) domains is outlined at 10 ps resolution.

A cutoff-based method with charge-distribution-data driven pair potentials for efficiently estimating electrostatic interactions in molecular systems

We introduce a simple cutoff-based method for precise electrostatic energy calculations in the molecular dynamics (MD) simulations of point-particle systems. Our method employs a theoretically derived smooth pair potential function to define electrostatic energy, offering stability and computational efficiency in MD simulations. Instead of imposing specific physical conditions, such as dielectric environments or charge neutrality, we focus on the relationship represented by a single summation formula of charge-weighted pair potentials. This approach allows an accurate energy approximation for each particle, enabling a straightforward error analysis. The resulting particle-dependent pair potential captures the charge distribution information, making it suitable for heterogeneous systems and ensuring an enhanced accuracy through distant information inclusion. Numerical investigations of the Madelung constants of crystalline systems validate the method's accuracy.

Microstructure-driven mechanical and electromechanical phenomena in additively manufactured nanocrystalline zinc oxide

Advances in nanoscale additive manufacturing (AM) offer great opportunities to expand nanotechnologies; however, the size effects in these printed remain largely unexplored. Using bothin situnanomechanical and electrical experiments and molecular dynamics (MD) simulations, this study investigates additively manufactured nano-architected nanocrystalline ZnO (nc-ZnO) with ∼7 nm grains and dimensions spanning 0.25-4μm. These nano-scale ceramics are fabricated through printing and subsequent burning of metal ion-containing hydrogels to produce oxide structures. Electromechanical behavior is shown to result from random ordering in the microstructure and can be modeled through a statistical treatment. A size effect in the failure behavior of AM nc-ZnO is also observed and characterized by the changes in deformation behavior and suppression of brittle failure. MD simulations provide insights to the role of grain boundaries and grain boundary plasticity on both electromechanical behavior and failure mechanisms in nc-ZnO. The frameworks developed in this paper extend to other AM nanocrystalline materials and provide quantification of microstructurally-drive limitations to precision in materials property design.

Properties of water and argon clusters developed in supersonic expansions

Using adiabatic molecular dynamics coupled with the fluid dynamics equations, we model nucleation in an expanding beam of water vapor and argon on a microsecond scale. The size distribution of clusters, their temperature, and pickup cross sections in dependence on velocity are investigated and compared to the geometric cross sections and the experiment. The clusters are warmer than the expanding gas because of the time scale of relaxation processes. We also suggest that their translational and rotational kinetic energies are modified due to evaporative cooling. The pickup cross sections determined for the final clusters using molecules of the same kind increase with decreasing velocity, still obeying the (a+bN1/3)2 law.

First-principles molten salt phase diagrams through thermodynamic integration

Precise prediction of phase diagrams in molecular dynamics simulations is challenging due to the simultaneous need for long time and large length scales and accurate interatomic potentials. We show that thermodynamic integration from low-cost force fields to neural network potentials trained using density-functional theory (DFT) enables rapid first-principles prediction of the solid-liquid phase boundary in the model salt NaCl. We use this technique to compare the accuracy of several DFT exchange-correlation functionals for predicting the NaCl phase boundary and find that the inclusion of dispersion interactions is critical to obtain good agreement with experiment. Importantly, our approach introduces a method to predict solid-liquid phase boundaries for any material at an ab initio level of accuracy, with the majority of the computational cost at the level of classical potentials.

Learning molecular dynamics: predicting the dynamics of glasses by a machine learning simulator

Many-body dynamics of atoms such as glass dynamics is generally governed by complex (and sometimes unknown) physics laws. This challenges the construction of atom dynamics simulations that both (i) capture the physics laws and (ii) run with little computation cost. Here, based on graph neural network (GNN), we introduce an observation-based graph network (OGN) framework to "bypass all physics laws" to simulate complex glass dynamics solely from their static structure. By taking the example of molecular dynamics (MD) simulations, we successfully apply the OGN to predict atom trajectories evolving up to a few hundred timesteps and ranging over different families of complex atomistic systems, which implies that the atom dynamics is largely encoded in their static structure in disordered phases and, furthermore, allows us to explore the capacity of OGN simulations that is potentially generic to many-body dynamics. Importantly, unlike traditional numerical simulations, the OGN simulations bypass the numerical constraint of small integration timestep by a multiplier of ≥5 to conserve energy and momentum until hundreds of timesteps, thus leapfrogging the execution speed of MD simulations for a modest timescale.

Interfaces in reinforced epoxy resins: from molecular scale understanding towards mechanical properties

CONTEXT

We report on atomic level of detail analyses of polymer composite models featuring epoxy resin interfaces to silica, iron oxide, and cellulose layers. Using "reactive" molecular dynamics simulations to explore epoxy network formation, resin hardening is investigated in an unprejudiced manner. This allows the detailed characterization of salt-bridges and hydrogen bonds at the interfaces. Moreover, our sandwich-type composite systems are subjected to tensile testing along the interface normal. To elucidate the role of relaxation processes, we contrast (i) direct dissociation of the epoxy-metal oxide/cellulose contact layer, (ii) constant strain-rate molecular dynamics studies featuring (visco-)elastic deformation and bond rupture of the epoxy resin, and (iii) extrapolated relaxation dynamics mimicking quasi-static conditions. While the fracture mechanism is clearly identified as interface dissociation of the composite constituents, we still find damaging of the nearby polymer phase. The observed plastic deformation and local cavitation are rationalized from the comparably large stress required for the dissociation of salt-bridges, hydrogen bonds, and van der Waals contacts. Indeed, the delamination of the contact layers of epoxy resins with slabs of silica, magnetite, and cellulose call for a maximum stress of 33, 26, and 21 MPa, respectively, as compared to 84 MPa required for bulk epoxy yielding.

METHODS

Molecular dynamics simulations using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code were augmented by a Monte Carlo-type procedure to probe epoxy bond formation (Macromolecules 53(22): 9698-9705). The underlying interaction models are split into conventional Generalized Amber Force Fields (GAFF) for non-reacting moieties and a recently developed reactive molecular mechanics potential enabling epoxy bond formation and cleavage (ACS Polymers Au 1(3): 165-174).

Thermal Stability and CO Permeability of [C4C1Pyr][NTf2]/Pd(111) Model SCILLs: from UHV to Ambient Pressure

Solid catalysts with ionic liquid layers (SCILLs) are heterogeneous catalysts which benefit significantly in terms of selectivity from a thin coating of an ionic liquid (IL). In the present work, we study the interaction of CO with a Pd model SCILL consisting of a 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)-imide ([C4C1Pyr][NTf2]) film deposited on Pd(111). We investigate the CO permeability and stability of the IL film via pressure modulation experiments by infrared reflection absorption spectroscopy (IRAS) in ultrahigh vacuum (UHV) and at ambient pressure conditions by time-resolved, temperature-programmed, and polarization-modulated (PM) IRAS experiments. In addition, we performed molecular dynamics (MD) simulations to identify adsorption motifs, their abundance, and the influence of CO. We find a strongly bound IL wetting monolayer (ML) and a potentially dewetting multilayer. Molecular reorientation of the IL at the interface and multilayer dewetting allow for the accumulation of CO at the metal/IL interface. Our results confirm that co-adsorption of CO changes the molecular structure of the IL wetting layer which confirms the importance to study model SCILL systems under in situ conditions.

Graphical abstract

Local Molecular Field Theory for Coulomb Interactions in Aqueous Solutions

Coulomb interactions play a crucial role in a wide array of processes in aqueous solutions but present conceptual and computational challenges to both theory and simulations. We review recent developments in an approach addressing these challenges─local molecular field (LMF) theory. LMF theory exploits an exact and physically suggestive separation of intermolecular Coulomb interactions into strong short-range and uniformly slowly varying long-range components. This allows us to accurately determine the averaged effects of the long-range components on the short-range structure using effective single particle fields and analytical corrections, greatly reducing the need for complex lattice summation techniques used in most standard approaches. The simplest use of these ideas in aqueous solutions leads to the short solvent (SS) model, where both solvent-solvent and solute-solvent Coulomb interactions have only short-range components. Here we use the SS model to give a simple description of pairing of nucleobases and biologically relevant ions in water.

A perspective on the microscopic pressure (stress) tensor: History, current understanding, and future challenges

The pressure tensor (equivalent to the negative stress tensor) at both microscopic and macroscopic levels is fundamental to many aspects of engineering and science, including fluid dynamics, solid mechanics, biophysics, and thermodynamics. In this Perspective, we review methods to calculate the microscopic pressure tensor. Connections between different pressure forms for equilibrium and nonequilibrium systems are established. We also point out several challenges in the field, including the historical controversies over the definition of the microscopic pressure tensor; the difficulties with many-body and long-range potentials; the insufficiency of software and computational tools; and the lack of experimental routes to probe the pressure tensor at the nanoscale. Possible future directions are suggested.

New Prediction Model of Surface and Interfacial Energies Based on COSMO-UCE

The nature and strength of intermolecular and surface forces are the key factors that influence the solvation, adhesion and wetting phenomena. The universal cohesive energy prediction equation based on conductor-like screening model (COSMO-UCE) was extended from like molecules (pure liquids) to unlike molecules (dissimilar liquids). A new molecular-thermodynamic model of interfacial tension (IFT) for liquid-liquid and solid-liquid systems was developed in this work, which can predict the surface free energy of solid materials and interfacial energy directly through cohesive energy calculations based on COSMO-UCE. The applications of this model in prediction of IFT for water-organic, solid (n-hexatriacontane, polytetrafluoroethylene(PTFE) and octadecyl-amine monolayer)-liquid systems have been verified extensively with successful results; which indicates that this is a straightforward and reliable model of surface and interfacial energies through predicting intermolecular interactions based on merely molecular structure (profiles of surface segment charge density), the dimensionless wetting coefficient R_A/C can characterize the wetting behavior (poor adhesive (non-wetting), wetting, spreading) of liquids on the surface of solid materials very well.

Accurate estimation of dynamical quantities for nonequilibrium nanoscale systems

Fluctuations of dynamical quantities are fundamental and inevitable. For the booming research in nanotechnology, huge relative fluctuation comes with the reduction of system size, leading to large uncertainty for the estimates of dynamical quantities. Thus, increasing statistical efficiency, i.e., reducing the number of samples required to achieve a given accuracy, is of great significance for accurate estimation. Here we propose a theory as a fundamental solution for such problem by constructing auxiliary path for each real path. The states on auxiliary paths constitute canonical ensemble and share the same macroscopic properties (NVT) with the initial states of the real path. By implementing the theory in molecular dynamics simulations, we obtain a nanoscale Couette flow field with an accuracy of 0.2μm/s with relative standard error <0.1. The required number of samples is reduced by 12 orders compared to conventional method. The predicted thermolubric behavior of water sliding on a self-assembled surface is directly validated by experiment under the same velocity. This theory only assumes the system is initially in thermal equilibrium, then driven from that equilibrium by an external perturbation. It could serve as a general approach for extracting the accurate estimate of dynamical quantities from large fluctuations to provide insights on atomic level under experimental conditions, and benefit the studies on mass transport through (biological) nanochannels and fluid film lubrication of nanometer thickness.

Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference

In molecular simulations, it is essential to properly calculate the electrostatic interactions of particles in the physical system of interest. Here we consider a method called the non-Ewald method, which does not rely on the standard Ewald method with periodic boundary conditions, but instead relies on the cutoff-based techniques. We focus on the physicochemical and mathematical conceptual aspects of the method in order to gain a deeper understanding of the simulation methodology. In particular, we take into account the reaction field (RF) method, the isotropic periodic sum (IPS) method, and the zero-multipole summation method (ZMM). These cutoff-based methods are based on different physical ideas and are completely distinguishable in their underlying concepts. The RF and IPS methods are "additive" methods that incorporate information outside the cutoff region, via dielectric medium and isotropic boundary condition, respectively. In contrast, the ZMM is a "subtraction" method that tries to remove the artificial effects, generated near the boundary, from the cutoff sphere. Nonetheless, we find physical and/or mathematical similarities between these methods. In particular, the modified RF method can be derived by the principle of neutralization utilized in the ZMM, and we also found a direct relationship between IPS and ZMM.

A New Formulation for the Concerted Alchemical Calculation of van der Waals and Coulomb Components of Solvation Free Energies

Alchemical free energy calculations via molecular dynamics have been widely used to obtain thermodynamic properties related to protein-ligand binding and solute-solvent interactions. Although soft-core modeling is the most common approach, the linear basis function (LBF) methodology [Naden, L. N.; et al. J. Chem. Theory Comput.2014, 10 (3), 1128; 2015, 11 (6), 2536] has emerged as a suitable alternative. It overcomes the end-point singularity of the scaling method while maintaining essential advantages such as ease of implementation and high flexibility for postprocessing analysis. In the present work, we propose a simple LBF variant and formulate an efficient protocol for evaluating van der Waals and Coulomb components of an alchemical transformation in tandem, in contrast to the prevalent sequential evaluation mode. To validate our proposal, which results from a careful optimization study, we performed solvation free energy calculations and obtained octanol-water partition coefficients of small organic molecules. Comparisons with results obtained via the sequential mode using either another LBF approach or the soft-core model attest to the effectiveness and correctness of our method. In addition, we show that a reaction field model with an infinite dielectric constant can provide very accurate hydration free energies when used instead of a lattice-sum method to model solute-solvent electrostatics.

Molecular Simulations and Network Analyses of Surface/Interface Effects in Epoxy Resins: How Bonding Adapts to Boundary Conditions

In this study, we unravel the atomic structure of a covalent resin near boundaries such as surfaces and composite constituents. For this, a molecular simulation analysis of epoxy resin hardening under various boundary conditions was performed. On the atomic level of detail, molecular dynamics simulations were employed to study crosslinking reactions and self-organization of the polymer network within nm scale slab models. The resulting structures were then coarsened into a graph theoretical description for connectivity analysis of the nodes and combined with characterization of the node-to-node vector orientation. On this basis, we show that the local bonding of epoxy resins near interfaces tends to avoid under-coordinated linker sites. For both epoxy-vacuum surface models and epoxy-silica/epoxy cellulose interfaces, we find almost fully cured polymer networks. These feature a local increase in network linking lateral to the surface/interface, rather than the dangling of unreacted epoxy groups. Consequently, interface tension is low (as compared to the work of separating bulk epoxy), and the reactivity of the resin surface appears negligible.

Optimization of the Ewald method for calculating Coulomb interactions in molecular simulations

Practical implementations of the Ewald method used to compute Coulomb interactions in molecular dynamics simulations are hampered by the requirement to truncate its reciprocal space series. It is shown that this can be mitigated by representing the contributions from the neglected reciprocal lattice vector terms as a simple modification of the real space expression in which the real and reciprocal space series have slightly different charge spreading parameters. This procedure, called the α′ method, enables significantly fewer reciprocal lattice vectors to be taken than is currently typical for Ewald, with negligible additional computational cost, which is validated on model systems representing different classes of charged system, a CsI crystal and melt, water, and a room temperature ionic liquid. A procedure for computing accurate energies and forces based on a periodic sampling of an additional number of reciprocal lattice vectors is also proposed and validated by the simulations. The convergence characteristics of expressions for the pressure based on the forces and the potential energy are compared, which is a useful assessment of the accuracy of the simulations in reproducing the Coulomb interaction. The techniques developed in this work can reduce significantly the total computer simulation times for medium sized charged systems, by factors of up to ∼5 for those in the classes studied here.

Computing the Work of Solid-Liquid Adhesion in Systems with Damped Coulomb Interactions via Molecular Dynamics: Approaches and Insights

Recently, the dry-surface method [Langmuir2016, 31, 8335−8345] has been developed to compute the work of adhesion of solid–liquid and other interfaces using molecular dynamics via thermodynamic integration. Unfortunately, when long-range Coulombic interactions are present in the interface, a special treatment is required, such as solving additional Poisson equations, which is usually not implemented in generic molecular dynamics software, or as fixing some groups of atoms in place, which is undesirable most of the time. In this work, we replace the long-range Coulombic interactions with damped Coulomb interactions, and explore several thermal integration paths. We demonstrate that regardless of the integration path, the same work of adhesion values are obtained as long as the path is reversible, but the numerical efficiency differs vastly. Simple scaling of the interactions is most efficient, requiring as little as 8 sampling points, followed by changing the Coulomb damping parameter, while modifying the Coulomb interaction cutoff length performs worst. We also demonstrate that switching long-range Coulombic interactions to damped ones results in a higher work of adhesion by about 10 mJ/m² because of slightly different liquid molecule orientation at the solid–liquid interface, and this value is mostly unchanged for surfaces with substantially different Coulombic interactions at the solid–liquid interface. Finally, even though it is possible to split the work of adhesion into van der Waals and Coulomb components, it is known that the specific per-component values are highly dependent on the integration path. We obtain an extreme case, which demonstrates that caution should be taken even when restricting to qualitative comparison.

Notes on the Treatment of Charged Particles for Studying Cyclotide/Membrane Interactions with Dissipative Particle Dynamics

Different charge treatment approaches are examined for cyclotide-induced plasma membrane disruption by lipid extraction studied with dissipative particle dynamics. A pure Coulomb approach with truncated forces tuned to avoid individual strong ion pairing still reveals hidden statistical pairing effects that may lead to artificial membrane stabilization or distortion of cyclotide activity depending on the cyclotide's charge state. While qualitative behavior is not affected in an apparent manner, more sensitive quantitative evaluations can be systematically biased. The findings suggest a charge smearing of point charges by an adequate charge distribution. For large mesoscopic simulation boxes, approximations for the Ewald sum to account for mirror charges due to periodic boundary conditions are of negligible influence.

Investigating finite-size effects in molecular dynamics simulations of ion diffusion, heat transport, and thermal motion in superionic materials

The effects of the finite size of the simulation box in equilibrium molecular dynamics simulations are investigated for prototypical superionic conductors of different types, namely, the fluorite-structure materials PbF₂, CaF₂, and UO₂ (type II), and the α phase of AgI (type I). Largely validated empirical force-fields are employed to run ns-long simulations and extract general trends for several properties, at increasing size and in a wide temperature range. This work shows that, for the considered type-II superionic conductors, the diffusivity dramatically depends on the system size and that the superionic regime is shifted to larger temperatures in smaller cells. Furthermore, only simulations of several hundred atoms are able to capture the experimentally observed, characteristic change in the activation energy of the diffusion process, occurring at the order-disorder transition to the superionic regime. Finite-size effects on ion diffusion are instead much weaker in α-AgI. The thermal conductivity is found generally smaller for smaller cells, where the temperature-independent (Allen-Feldman) regime is also reached at significantly lower temperatures. The finite-size effects on the thermal motion of the non-mobile ions composing the solid matrix follow the simple law that holds for solids.

Cleaving Method for Molecular Crystals and Its Application to Calculation of the Surface Free Energy of Crystalline β-d-Mannitol at Room Temperature

Calculation of the surface free energy (SFE) is an important application of the thermodynamic integration (TI) methodology, which was mainly employed for atomic crystals (such as Lennard–Jones or metals). In this work, we present the calculation of the SFE of a molecular crystal using the cleaving technique which we implemented in the LAMMPS molecular dynamics package. We apply this methodology to a crystal of β-d-mannitol at room temperature and report the results for two types of force fields belonging to the GROMOS family: all atoms and united atoms. The results show strong dependence on the type of force field used, highlighting the need for the development of better force fields to model the surface properties of molecular crystals. In particular, we observe that the united-atoms force field, despite its higher degree of coarse graining compared to the all-atoms force field, produces SFE results in better agreement with the experimental results from inverse gas chromatography measurements.

Pyridine interaction with γ-CuI: synergy between molecular dynamics and molecular orbital approaches to molecule/surface interactions

We have used a synergistic computational approach merging Molecular Dynamics (MD) simulations with density functional theory (DFT) to investigate the mechanistic aspects of chemisorption of pyridine (Py) molecules on copper iodide. The presence of both positive and negative ions at the metal halide surface presents a chemical environment in which pyridine molecules may act as charge donors and/or acceptors. Computational results reveal that Py molecules interact with the γ-CuI(111) surface owing to a combination of noncovalent Cu⋯N, Cu/I⋯π/π*, and hydrogen bonding interactions as determined via Natural Bonding Orbitals (NBO). Introduction of surface defect sites alters the interaction dynamics, resulting in a "localizing effect" in which the Py molecules clump together within the defect site. Significant enhancement of hydrogen bonding between C-H σ* and I 6p orbitals results in more tightly surface-bound Py molecules. Our findings provide a platform for understanding the interaction between Py and Py-derivative vapors and metal-based surfaces that contain both electron acceptor and donor atoms.

Electric Potential of Citrate-Capped Gold Nanoparticles Is Affected by Poly(allylamine hydrochloride) and Salt Concentration

The structure near polyelectrolyte-coated gold nanoparticles (AuNPs) is of significant interest because of the increased use of AuNPs in technological applications and the possibility that the acquisition of polyelectrolytes can lead to novel chemistry in downstream environments. We use all-atom molecular dynamics (MD) simulations to reveal the electric potential around citrate-capped gold nanoparticles (cit-AuNPs) and poly(allylamine hydrochloride) (PAH)-wrapped cit-AuNP (PAH-AuNP). We focus on the effects of the overall ionic strength and the shape of the electric potential. The ionic number distributions for both cit-AuNP and PAH-AuNP are calculated using MD simulations at varying salt concentrations (0, 0.001, 0.005, 0.01, 0.05, 0.1, and 0.2 M NaCl). The net charge distribution (Z(r)) around the nanoparticle is determined from the ionic number distribution observed in the simulations and allows for the calculation of the electric potential (ϕ(r)). We find that the magnitude of ϕ(r) decreases with increasing salt concentration and upon wrapping by PAH. Using a hydrodynamic radius (R_H) estimated from the literature and fits to the Debye-Hü̈ckel expression, we found and report the ζ potential for both cit-AuNP and PAH-AuNP at varying salt concentrations. For example, at 0.001 M NaCl, MD simulations suggest that ζ = -25.5 mV for cit-AuNP. Upon wrapping of cit-AuNP by one PAH chain, the resulting PAH-AuNP exhibits a reduced ζ potential (ζ = -8.6 mV). We also compare our MD simulation results for ϕ(r) to the classic Poisson-Boltzmann equation (PBE) approximation and the well-known Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. We find agreement with the limiting regimes─with respect to surface charge, salt concentration and particle size─in which the assumptions of the PBE and DLVO theory are known to be satisfied.

Molecular Picture of the Effect of Cosolvent Crowding on Ligand Binding and Dispersed Solvation Dynamics in G-Quadruplex DNA

Understanding molecular interactions and dynamics of proteins and DNA in a cell-like crowded environment is crucial for predicting their functions within the cell. Noncanonical G-quadruplex DNA (GqDNA) structures adopt various topologies that were shown to be strongly affected by molecular crowding. However, it is unknown how such crowding affects the solvation dynamics in GqDNA. Here, we study the effect of cosolvent (acetonitrile) crowding on ligand (DAPI) solvation dynamics within human telomeric antiparallel GqDNA through direct comparison of time-resolved fluorescence Stokes shift (TRFSS) experiments and molecular dynamics (MD) simulations results. We show that ligand binding affinity to GqDNA is drastically affected by acetonitrile (ACN). Solvation dynamics probed by DAPI in GqDNA groove show dispersed dynamics from ∼100 fs to 10 ns in the absence and presence of 20% and 40% (v/v) ACN. The nature of dynamics remain similar in buffer and 20% ACN, although in 40% ACN, distinct dynamics is observed in <100 ps. MD simulations performed on GqDNA/DAPI complex reveal preferential solvation of ligand by ACN, particularly in 40% ACN. Simulated solvation time-correlation functions calculated from MD trajectories compare very well to the overall solvation dynamics of DAPI in GqDNA, observed in experiments. Linear response decomposition of simulated solvation correlation functions unfolds the origin of dispersed dynamics, showing that the slower dynamics is dominated by DNA-motion in the presence of ACN (and also by the ACN dynamics at higher concentration). However, water-DNA coupled motion controls the slow dynamics in the absence of ACN. Our data, thus, unravel a detailed molecular picture showing that though ACN crowding affect ligand binding affinity to GqDNA significantly, the overall dispersed solvation dynamics in GqDNA remain similar in the absence and the presence of 20% ACN, albeit with a small effect on the dynamics in the presence of 40% ACN due to preferential solvation of ligand by ACN.

High Directional Water Transport Graphene Oxide Biphilic Stack

Understanding the nature of water transport in nanoscale is of high importance. Graphene properties such as mass flow rate, stability, filtration efficiency, and selectivity have been studied in various fields. It is a widely held view that the hydrophilicity of graphene oxide enhances the water transport properties. In this study, it is shown that despite this belief, a combination of graphene and graphene oxide can yield superior transport properties including high mass flow rate and directionality. Firstly, different membrane characteristics such as the smallest pore diameter for water molecules sieving and mass flow rate have been evaluated. Furthermore, a combination of graphene and graphene oxide, a biphilic stack of hydrophobic and hydrophilic layers, are used to evaluate the mass flow rates and results are compared with that of normal graphene oxide laminates. The proposed structure acts like a water diode i.e. conduct water molecules in a desired direction and increases the mass flow rate several times. The effect of interatomic potential, oxidation level and charge, and the spacing between layers on both mass flow rate and directionality are examined. It is found that an optimized structure conducts water in a desired direction and increases the mass flow rate up to 10 times for the small interlayer distance of 7 Å compared to the normal graphene oxide laminates. The given structures can be used in a wide range of filtration applications where selective water sieving with high mass flow rate is desired.

Computational Screening of Physical Solvents for CO2 Pre-combustion Capture

A computational scheme was used to screen physical solvents for CO₂ pre-combustion capture by integrating the commercial NIST database, an in-house computational database, chem-informatics, and molecular modeling. A commercially available screened hydrophobic solvent, diethyl sebacate, was identified from the screening with favorable physical properties and promising absorption performance. The promising performance to use diethyl sebacate in CO₂ pre-combustion capture has also been confirmed from experiments. Water loading in diethyl sebacate is very low, and therefore, water is kept with H₂ in the gas stream. The favorable CO₂ interaction with diethyl sebacate and the intermediate solvent free volume fraction leads to both high CO₂ solubility and high CO₂/H₂ solubility selectivity in diethyl sebacate. An in-house NETL computational database was built to characterize CO₂, H₂, N₂, and H₂O interactions with 202 different chemical functional groups. It was found that 13% of the functional groups belong to the strong interaction category with the CO₂ interaction energy between -15 and -21 kJ/mol; 62% of the functional groups interact intermediately with CO₂ (-8 to -15 kJ/mol). The remaining 25% of functional groups interact weakly with CO₂ (below -8 kJ/mol). In addition, calculations show that CO₂ interactions with the functional groups are stronger than N₂ and H₂ interactions but are weaker than H₂O interactions. The CO₂ and H₂O interactions with the same functional groups exhibit a very strong linear positive correlation coefficient of 0.92. The relationship between CO₂ and H₂ gas solubilities and solvent fractional free volume (FFV) has been systematically studied for seven solvents at 298.2 K. A skewed bell-shaped relation was obtained between CO₂ solubility and solvent FFV. When an organic compound has a density approximately 10% lower than its density at 298.2 K and 1 bar, it exhibits the highest CO₂ loading at that specific solvent density and FFV. Note that the solvent densities were varied using simulations, which are difficult to be obtained from the experiment. In contrast, H₂ solubility results exhibit an almost perfect positive linear correlation with the solvent FFV. The theoretical maximum and minimum physical CO₂ solubilities in any organic compound at 298.2 K were estimated to be 11 and 0.4 mol/MPa L, respectively. An examination of 182 experimental CO₂ physical solubility data and 29 simulated CO₂ physical solubilities shows that all the CO₂ physical solubility data are within the maximum and minimum with only a few exceptions. Finally, simulations suggest that in order to develop physical solvents with both high CO₂ solubility and high CO₂/H₂ solubility selectivity, the solvents should contain functional groups which are available to interact strongly with CO₂ while minimizing FFV.

A Universal Force Field for Materials, Periodic GFN-FF: Implementation and Examination

In this study, the adaption of the recently published molecular GFN-FF for periodic boundary conditions (pGFN-FF) is described through the use of neighbor lists combined with appropriate charge sums to handle any dimensionality from 1D polymers to 2D surfaces and 3D solids. Numerical integration over the Brillouin zone for the calculation of π bond orders of periodic fragments is also included. Aside from adapting the GFN-FF method to handle periodicity, improvements to the method are proposed in regard to the calculation of topological charges through the inclusion of a screened Coulomb term that leads to more physical charges and avoids a number of pathological cases. Short-range damping of three-body dispersion is also included to avoid collapse of some structures. Analytic second derivatives are also formulated with respect to both Cartesian and strain variables, including prescreening of terms to accelerate the dispersion/coordination number contribution to the Hessian. The modified pGFN-FF scheme is then applied to a wide range of different materials in order to examine how well this universal model performs.

Deciphering the molecular mechanism of water boiling at heterogeneous interfaces

Water boiling control evolution of natural geothermal systems is widely exploited in industrial processes due to the unique non-linear thermophysical behavior. Even though the properties of water both in the liquid and gas state have been extensively studied experimentally and by numerical simulations, there is still a fundamental knowledge gap in understanding the mechanism of the heterogeneous nucleate boiling controlling evaporation and condensation. In this study, the molecular mechanism of bubble nucleation at the hydrophilic and hydrophobic solid-water interface was determined by performing unbiased molecular dynamics simulations using the transition path sampling scheme. Analyzing the liquid to vapor transition path, the initiation of small void cavities (vapor bubbles nuclei) and their subsequent merging mechanism, leading to successively growing vacuum domains (vapor phase), has been elucidated. The molecular mechanism and the boiling nucleation sites' location are strongly dependent on the solid surface hydrophobicity and hydrophilicity. Then simulations reveal the impact of the surface functionality on the adsorbed thin water molecules film structuring and the location of high probability nucleation sites. Our findings provide molecular-scale insights into the computational aided design of new novel materials for more efficient heat removal and rationalizing the damage mechanisms.

New Features of the Open Source Monte Carlo Software Brick-CFCMC: Thermodynamic Integration and Hybrid Trial Moves

We present several new major features added to the Monte Carlo (MC) simulation code Brick-CFCMC for phase- and reaction equilibria calculations (https://gitlab.com/ETh_TU_Delft/Brick-CFCMC). The first one is thermodynamic integration for the computation of excess chemical potentials (μ^ex). For this purpose, we implemented the computation of the ensemble average of the derivative of the potential energy with respect to the scaling factor for intermolecular interactions (). Efficient bookkeeping is implemented so that the quantity is updated after every MC trial move with negligible computational cost. We demonstrate the accuracy and reliability of the calculation of μ^ex for sodium chloride in water. Second, we implemented hybrid MC/MD translation and rotation trial moves to increase the efficiency of sampling of the configuration space. In these trial moves, short Molecular Dynamics (MD) trajectories are performed to collectively displace or rotate all molecules in the system. These trajectories are accepted or rejected based on the total energy drift. The efficiency of these trial moves can be tuned by changing the time step and the trajectory length. The new trial moves are demonstrated using MC simulations of a viscous fluid (deep eutectic solvent).

Density-functional-theory approach to the Hamiltonian adaptive resolution simulation method

In the Hamiltonian adaptive resolution simulation method (H-AdResS) it is possible to simulate coexisting atomistic (AT) and ideal gas representations of a physical system that belong to different subdomains within the simulation box. The Hamiltonian includes a field that bridges both models by smoothly switching on (off) the intermolecular potential as particles enter (leave) the AT region. In practice, external one-body forces are calculated and applied to enforce a reference density throughout the simulation box, and the resulting external potential adds up to the Hamiltonian. This procedure suggests an apparent dependence of the final Hamiltonian on the system's thermodynamic state that challenges the method's statistical mechanics consistency. In this paper, we explicitly include an external potential that depends on the switching function. Hence, we build a grand canonical potential for this inhomogeneous system to find the equivalence between H-AdResS and density functional theory (DFT). We thus verify that the external potential inducing a constant density profile is equal to the system's excess chemical potential. Given DFT's one-to-one correspondence between external potential and equilibrium density, we find that a Hamiltonian description of the system is compatible with the numerical implementation based on enforcing the reference density across the simulation box. In the second part of the manuscript, we focus on assessing our approach's convergence and computing efficiency concerning various model parameters, including sample size and solute concentrations. To this aim, we compute the excess chemical potential of water, aqueous urea solutions and Lennard-Jones (LJ) mixtures. The results' convergence and accuracy are convincing in all cases, thus emphasising the method's robustness and capabilities.