First-principles molecular dynamics simulations at solid-liquid interfaces with a continuum solvent

Structure and dynamics of nanoconfined water and aqueous solutions

This review is devoted to discussing recent progress on the structure, thermodynamic, reactivity, and dynamics of water and aqueous systems confined within different types of nanopores, synthetic and biological. Currently, this is a branch of water science that has attracted enormous attention of researchers from different fields interested to extend the understanding of the anomalous properties of bulk water to the nanoscopic domain. From a fundamental perspective, the interactions of water and solutes with a confining surface dramatically modify the liquid's structure and, consequently, both its thermodynamical and dynamical behaviors, breaking the validity of the classical thermodynamic and phenomenological description of the transport properties of aqueous systems. Additionally, man-made nanopores and porous materials have emerged as promising solutions to challenging problems such as water purification, biosensing, nanofluidic logic and gating, and energy storage and conversion, while aquaporin, ion channels, and nuclear pore complex nanopores regulate many biological functions such as the conduction of water, the generation of action potentials, and the storage of genetic material. In this work, the more recent experimental and molecular simulations advances in this exciting and rapidly evolving field will be reported and critically discussed.

Implicit Solvation Using a Generalized Finite-Difference Approach in CRYSTAL: Implementation and Results for Molecules, Polymers, and Surfaces

We present the implementation of an implicit solvation model in the CRYSTAL code. The solvation energy is separated into two components: the electrostatic contribution arising from a self-consistent reaction field treatment obtained within a generalized finite-difference Poisson model, augmented by a nonelectrostatic contribution proportional to the solvent-accessible surface area of the solute. A discontinuous dielectric boundary is used, along with a solvent-excluded surface built from interlocking atom-centered spheres on which apparent surface point charges are mapped. The procedure is general and can be performed at both the Hartree-Fock and density functional theory levels, with pure or hybrid functionals, for systems periodic in 0, 1, and 2 directions, that is, for isolated molecules and extended polymers and surfaces. The Poisson equation resolution and apparent surface charge formalism is first validated on model analytical test cases. The good agreement obtained on solvation free energies is further confirmed by calculations performed on a large test set of 501 neutral molecules, for which a mean unsigned error of 1.3 kcal/mol is obtained when compared to the available experimental data. Importantly, the self-consistent reaction field procedure converges well for all molecules tested. This is further verified for all polymers and surfaces considered. In particular, for periodic systems, results obtained on an infinite glycine chain and on the wettability parameters of SiO₂ surfaces are in good agreement with previously published data. The size extensivity of the energetic terms involved in the electrostatic contribution to the solvation energy is also well verified. These encouraging results constitute a first step to take into account complex environments in the CRYSTAL code, potentially allowing for a more accurate modeling of complex processes for both periodic and nonperiodic systems.

Metallic Bond-Enabled Wetting Behavior at the Liquid Ga/CuGa2 Interfaces

Interface interaction can strongly modify contact angle, adsorption energy, interfacial tension, and composition of the contact area. In particular, the interfaces between gallium-based liquid metal (LM) and its intermetallic layer present many mysterious and peculiar wetting phenomena, which have not been fully realized up to now. Here in this study, we found that a gallium-based liquid metal droplet can quickly transform into a puddle on the CuGa₂ surface through a spreading-wetting procedure. The mechanism lying behind this phenomenon can be ascribed to the formation of an intermetallic CuGa₂ on Cu plate surface, which provides a stable metallic bond to induce the wetting behavior. For a quantitative evaluation of the interface force, a metallic bond-enabled wetting model is established on the basis of the density functional theory. The first-principles density functional calculations are then performed to examine the work function, density of states, and adsorption energy. The predicted results show that the work function of CuGa₂ (010) is approximately 4.47 eV, which is very comparable with that of pure liquid Ga (4.32 eV). This indicates that the valence electrons between Ga and CuGa₂ slab can exchange easily, which consequently leads to the strong valence electron hybridization and metallic bond. In addition, the adsorption energy of a single Ga atom on CuGa₂ (010) slab has a larger value than In and Sn. The tested metallic bond wetting force at the interface is proportional to the average adsorption energy of the gallium-based LM adatom, and increases with the rising content of gallium. The simulation results demonstrate excellent consistency with the experimental data in this work.

DL_MG: A Parallel Multigrid Poisson and Poisson-Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution

The solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential-a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the Poisson equation, featuring nonhomogeneous dielectric permittivities, ionic concentrations with nonlinear dependencies, and diverse boundary conditions. The analytic solutions generally used to solve the Poisson equation in vacuum (or with homogeneous permittivity) are not applicable in these circumstances, and numerical methods must be used. In this work, we present DL_MG, a flexible, scalable, and accurate solver library, developed specifically to tackle the challenges of solving the Poisson equation in modern large-scale electronic structure calculations on parallel computers. Our solver is based on the multigrid approach and uses an iterative high-order defect correction method to improve the accuracy of solutions. Using two chemically relevant model systems, we tested the accuracy and computational performance of DL_MG when solving the generalized Poisson and Poisson-Boltzmann equations, demonstrating excellent agreement with analytic solutions and efficient scaling to ∼10⁹ unknowns and 100s of CPU cores. We also applied DL_MG in actual large-scale electronic structure calculations, using the ONETEP linear-scaling electronic structure package to study a 2615 atom protein-ligand complex with routinely available computational resources. In these calculations, the overall execution time with DL_MG was not significantly greater than the time required for calculations using a conventional FFT-based solver.

Benchmarks and Dielectric Constants for Reparametrized OPLS and Polarizable Force Field Models of Chlorinated Hydrocarbons

The knowledge of dielectric response properties of the environment is of paramount importance in many theoretical embedding methods and studies of solutes and of catalytic sites and processes in condensed phases. In particular, the realistic embedding of active sites into solid/liquid and liquid/liquid interfaces is a crucial point in the context of modeling energy conversion (e.g., electrochemical, photochemical, power-to-X) processes. Recently, the finding that the dielectric permeability of liquids near solid/liquid interfaces is far from being constant but deviates strongly from the bulk value within several nanometers from the interface has raised the interest in a more fundamental understanding of the response properties near interfaces. As these questions are hard to study experimentally, reliable theoretical models are required. Here we describe a careful first-principles based reparametrization of nonpolarizable molecular mechanics force fields for a class of technological relevant organic chlorinated hydrocarbon solvents which are immiscible with water. For the solvent 1,2-dichloroethane (1,2-DCE) we also present a new polarizable force field based on the Drude oscillator model. Its parametrization needs particular attention to avoid unphysical couplings between the internal torsional degree of freedom and the Drude oscillators, which could severely skew the response properties. The performance of this new set of force fields is critically assessed based on a comprehensive molecular dynamics study.

Electrode potential dependent desolvation and resolvation of germanium(100) in contact with aqueous perchlorate electrolytes

The electrode potential dependence of the hydration layer on an n-Ge(100) surface was studied by a combination of in situ and operando electrochemical attenuated total reflection infrared (ATR-IR) spectroscopy and real space density functional theory (DFT) calculations. Constant-potential DFT calculations were coupled to a modified generalised Poisson-Boltzmann ion distribution model and applied within an ab initio molecular dynamics (AIMD) scheme. As a result, potential-dependent vibrational spectra of surface species and surface water were obtained, both experimentally and by simulations. The experimental spectra show increasing absorbance from the Ge-H stretching modes at negative potentials, which is associated with an increased negative difference absorbance of water-related OH modes. When the termination transition of germanium from OH to H termination occurs, the surface switches from hydrophilic to hydrophobic. This transition is fully reversible. During the switching, the interface water molecules are displaced from the surface forming a "hydrophobic gap". The gap thickness was experimentally estimated by a continuum electrodynamic model to be ≈2 Å. The calculations showed a shift in the centre of mass of the interface water by ≈0.9 Å due to the surface transformation. The resulting IR spectra of the interfacial water in contact with the hydrophobic Ge-H show an increased absorbance of free OH groups, and a decreased absorbance of strongly hydrogen bound water. Consequently, the surface transformation to a Ge-H terminated surface leads to a surface which is weakening the H-bond network of the interfacial water in contact.

SU-8 based pyrolytic carbon for the electrochemical detection of dopamine

Here we investigated the electrochemical properties and dopamine (DA) detection capability of SU-8 photoresist based pyrolytic carbon (PyC) as well as its biocompatibility with neural cells.

Multigrid-Based Methodology for Implicit Solvation Models in Periodic DFT

Continuum solvation models have become a widespread approach for the study of environmental effects in Density Functional Theory (DFT) methods. Adding solvation contributions mainly relies on the solution of the Generalized Poisson Equation (GPE) governing the behavior of the electrostatic potential of a system. Although multigrid methods are especially appropriate for the solution of partial differential equations, up to now, their use is not much extended in DFT-based codes because of their high memory requirements. In this Article, we report the implementation of an accelerated multigrid solver-based approach for the treatment of solvation effects in the Vienna ab initio Simulation Package (VASP). The stated implicit solvation model, named VASP-MGCM (VASP-Multigrid Continuum Model), uses an efficient and transferable algorithm for the product of sparse matrices that highly outperforms serial multigrid solvers. The calculated solvation free energies for a set of molecules, including neutral and ionic species, as well as adsorbed molecules on metallic surfaces, agree with experimental data and with simulation results obtained with other continuum models.

Charge- and thickness-dependent inplane deformation of multilayer graphene thin films

A theoretical model, verified by first-principles calculations, can describe the charge- and thickness-dependent inplane deformation of graphene thin films.

CO2 Capture and Conversion on Rutile TiO2(110) in the Water Environment: Insight by First-Principles Calculations

The conversion of CO2 by the virtue of sunlight has the great potential to produce useful fuels or valuable chemicals while decreasing CO2 emission from the traditional fossil fuels. Here, we use the first-principles calculations combined with the periodic continuum solvation model (PCSM) to explore the adsorption and reactivity of CO2 on rutile TiO2(110) in the water environment. The results exhibit that both adsorption structures and reactivity of CO2 are greatly affected by water coadsorption on rutile TiO2(110). In particular, the solvation effect can change the most stable adsorption configuration of CO2 and H2O on rutile TiO2(110). In addition, the detailed conversion mechanism of CO2 reduction is further explored in the water environment. The results reveal that the solvation effect cannot only greatly decrease the energy barrier of CO2 reduction but also affect the selectivity of the reaction processes. These results presented here show the importance of the aqueous solution, which should be helpful to understand the detailed reaction processes of photocatalysts.

Adsorption of R-OH molecules on TiO2 surfaces at the solid-liquid interface

The exploration of TiO2 surface reactivity from first-principles calculations has been almost always limited to the gas phase, even though most of the chemically relevant applications of this interface involve the solid-liquid boundary. The reason for this limitation is the complexity of the solid-liquid interface, which poses a serious challenge to standard ab initio methodologies as density functional theory (DFT). In this work we study the interaction of H2O, CH3OH, H2O2, and HCO2H with anatase (101) and rutile (110) surfaces in aqueous solution, employing a continuum solvation model in a DFT framework in periodic boundary conditions [ J. Chem. Phys. 2009 , 131 , 174108 ]. Different adsorption configurations were analyzed, examining the effect of the first water monolayer explicitly included in the simulation. For water and methanol, molecular adsorption was found to be the most stable in the presence of the solvent, while for hydrogen peroxide the preferred configuration depended on the surface. The explicit inclusion of the first water monolayer turns out to be important since it may play a role in the stabilization of the adsorbates at the interface. In general, the slightly positive adsorption energy values obtained (with respect to water) suggest that CH3OH and H2O2 will poorly adsorb from an aqueous solution at the titania surface. Among the three species investigated other than water, the formic acid was the only one to exhibit a higher affinity for the surface than H2O.