First principles and classical molecular dynamics simulations of solvated benzene

Property structure relationships in materials can be studied by a number of computational approaches such as ab initio quantum chemistry calculations, ab initio molecular dynamics (MD) simulations, classical MD and Monte-Carlo simulations, finite element modelling, etc. A choice of the computational method depends on the time and length scales and computational resources available. At the current stage of method and hardware development, ab initio quantum chemistry calculations are best suited for studying energy-structure relationships in relatively small systems consisting of tens of atoms. Ab initio MD simulations allow one to study dynamics of systems on a picosecond time scale for systems consisting of hundreds of atoms. Energy and forces in ab initio MD simulations are obtained from solving the electronic structure problem “on the fly”. Parameterization of the energy a system as a function of the relative atom positions, e. g., development of a classical force field, significantly speeds up calculations of the energies and forces in MD simulations, positioning classical MD simulations as the most suitable tool to obtain properties of the systems containing 10-10 atoms on the time scales from 10 to 10 s. However, the value of the property predictions using classical MD simulations is limited to the accuracy of the force field used, making a consistent derivation of a high quality classical force fields central to accurate prediction of the property-structure relationship from MD simulations.

The behavior of water near a graphene sheet is investigated by means of ab initio and classical molecular dynamics simulations. The wetting of the graphene sheet by ab initio water and the relation of such behavior to the strength of classical dispersion interaction between surface atoms and water are explored. The first principles simulations reveal a layered solvation structure around the graphene sheet with a significant water density in the interfacial region implying no drying or cavitation effect. It is found that the ab initio results of water density at interfaces can be reproduced reasonably well by classical simulations with a tuned dispersion potential between the surface and water molecules. Calculations of vibrational power spectrum from ab initio simulations reveal a shift of the intramolecular stretch modes to higher frequencies for interfacial water molecules when compared with those of the second solvation later or bulk-like water due to the presence of free OH modes near the graphene sheet. Also, a weakening of the water-water hydrogen bonds in the vicinity of the graphene surface is found in our ab initio simulations as reflected in the shift of intermolecular vibrational modes to lower frequencies for interfacial water molecules. The first principles calculations also reveal that the residence and orientational dynamics of interfacial water are somewhat slower than those of the second layer or bulk-like molecules. However, the lateral diffusion and hydrogen bond relaxation of interfacial water molecules are found to occur at a somewhat faster rate than that of the bulk-like water molecules. The classical molecular dynamics simulations with tuned Lennard-Jones surface-water interaction are found to produce dynamical results that are qualitatively similar to those of ab initio molecular dynamics simulations.

Ab initio and classical molecular dynamics studies of electrode reactions

The shock Hugoniot for full-density and porous ${\mathrm{CeO}}_{2}$ was investigated in the liquid regime using ab initio molecular dynamics (AIMD) simulations with Erpenbeck's approach based on the Rankine-Hugoniot jump conditions. The phase space was sampled by carrying out NVT simulations for isotherms between 6000 and 100 000 K and densities ranging from $\ensuremath{\rho}=2.5$ to $20\phantom{\rule{0.28em}{0ex}}\mathrm{g}/{\mathrm{cm}}^{3}$. The impact of on-site Coulomb interaction corrections $+U$ on the equation of state (EOS) obtained from AIMD simulations was assessed by direct comparison with results from standard density functional theory simulations. Classical molecular dynamics (CMD) simulations were also performed to model atomic-scale shock compression of larger porous ${\mathrm{CeO}}_{2}$ models. Results from AIMD and CMD compression simulations compare favorably with Z-machine shock data to 525 GPa and gas-gun data to 109 GPa for porous ${\mathrm{CeO}}_{2}$ samples. Using results from AIMD simulations, an accurate liquid-regime Mie-Gr\"uneisen EOS was built for ${\mathrm{CeO}}_{2}$. In addition, a revised multiphase SESAME-type EOS was constrained using AIMD results and experimental data generated in this work. This study demonstrates the necessity of acquiring data in the porous regime to increase the reliability of existing analytical EOS models.

We present the absolute enthalpy, entropy, heat capacity, and free energy of liquid water at ambient conditions calculated by the two-phase thermodynamic method applied to ab initio, reactive and classical molecular dynamics simulations. We find that the absolute entropy and heat capacity of liquid water from ab initio molecular dynamics (AIMD) is underestimated, but falls within the range of the flexible empirical as well as the reactive force fields. The origin of the low absolute entropy of liquid water from AIMD simulations is due to an underestimation of the translational entropy by 20% and the rotational entropy by 40% compared to the TIP3P classical water model, consistent with previous studies that reports low diffusivity and increased ordering of liquid water from AIMD simulations. Classical MD simulations with rigid water models tend to be in better agreement with experiment (in particular TIP3P yielding the best agreement), although the TIP4P-ice water model, the only empirical force field that reproduces the experimental melting temperature, has the lowest entropy, perhaps expectedly. This reiterates the limitations of existing empirical water models in simultaneously capturing the thermodynamics of solid and liquid phases. We find that the quantum corrections to heat capacity of water can be as large as 60%. Although certain water models are computed to yield good absolute free energies of water compared to experiments, they are often due to the fortuitous enthalpy-entropy cancellation, but not necessarily due to the correct descriptions of enthalpy and entropy separately.

Using classical and ab initio molecular-dynamics (MD) simulations, we have studied a calcium aluminosilicate glass of composition (SiO2)0.67–(Al2O3)0.12–(CaO)0.21. Samples with 100 and 200 atoms were generated by classical MD simulations using a potential with 3-body interactions. Although we observe, for the model with 100 atoms, finite size effects for some structural properties, these effects are substantially reduced if the glass structure is refined by the ab initio MD simulations. In addition, some structural characteristics such as the Ca–O bond length and the angular distributions are improved by the ab initio description. The structural and vibrational characteristics of these glass samples are compared to that of a glass that has been quenched from the melt using first-principles simulations. The main differences are found on the SiOSi and SiOAl angular distributions and on the apparition of high-frequency bands in the partial Ca vibrational density of states for the classically generated glass samples.

Combining theoretical and experimental approaches, we investigate the solvation properties of Li+ ions in a series of ether solvents (dimethoxyethane, diglyme, triglyme, tetraglyme, and 15-crown-5) and their subsequent effects on the solid-state lithium-sulfur reactions in subnano confinement. The ab initio and classical molecular dynamics (MD) simulations predict Li+ ion solvation structures within ether solvents in excellent agreement with experimental evidence from electrospray ionization-mass spectroscopy. An excellent correlation is also established between the Li+-solvation binding energies from the ab initio MD simulations and the lithiation overpotentials obtained from galvanostatic intermittent titration techniques (GITT). These findings convincingly indicate that a stronger solvation binding energy imposes a higher lithiation overpotential of sulfur in subnano confinement. The mechanistic understanding achieved at the electronic and atomistic level of how Li+-solvation dictates its electrochemical reactions with sulfur in subnano confinement provides invaluable guidance in designing future electrolytes and electrodes for Li-sulfur chemistry.

Results of ab initio molecular dynamics (AIMD), quantum mechanics/molecular mechanics (QM/MM), and classical molecular dynamics (CMD) simulations of Cm(3+) in liquid water at a temperature of 300 K are reported. The AIMD simulation was based on the Car-Parrinello MD scheme and GGA-PBE formulation of density functional theory. Two QM/MM simulations were performed by treating Cm(3+) and the water molecules in the first shell quantum mechanically using the PBE (QM/MM-PBE) and the hybrid PBE0 density functionals (QM/MM-PBE0). Two CMD simulations were carried out using ab initio derived pair plus three-body potentials (CMD-3B) and empirical Lennard-Jones pair potential (CMD-LJ). The AIMD and QM/MM-PBE simulations predict average first shell hydration numbers of 8, both of which disagree with recent experimental EXAFS and TRLFS value of 9. On the other hand, the average first shell hydration numbers obtained in the QM/MM-PBE0 and CMD simulations was 9, which agrees with experiment. All the simulations predicted an average first shell and second shell Cm-O bond distance of 2.49-2.53 Å and 4.67-4.75 Å respectively, both of which are in fair agreement with corresponding experimental values of 2.45-2.48 and 4.65 Å. The geometric arrangement of the 8-fold and 9-fold coordinated first shell structures corresponded to the square antiprism and tricapped trigonal prisms, respectively. The second shell hydration number for AIMD QM/MM-PBE, QM/MM-PBE0, CMD-3B, and CMD-LJ, were 15.8, 17.2, 17.7, 17.4, and 16.4 respectively, which indicates second hydration shell overcoordination compared to a recent EXAFS experimental value of 13. Save the EXAFS spectra CMD-LJ simulation, all the computed EXAFS spectra agree fairly well with experiment and a clear distinction could not be made between configurations with 8-fold and 9-fold coordinated first shells. The mechanisms responsible for the first shell associative and dissociative ligand exchange in the classical simulations have been analyzed. The first shell mean residence time was predicted to be on the nanosecond time scale. The computed diffusion constants of Cm(3+) and water are in good agreement with experimental data.

We present a comparative study of classical and ab-initio molecular dynamics (MD) simulations of methane in the liquid state. The atom wise radial distribution function (RDF) of liquid methane for both classical and ab initio simulations is calculated. It is observed that the peaks of RDF are lowered and broadened when quantum effects are considered. Also, the peaks are shifted towards the slightly lower values of intermolecular distance r. The diffusion coefficient from the slope of Mean Square Displacement (MSD) and the partial density of states has also been calculated for Quantum MD. The bond angles of the final configuration obtained after running the simulations show more fluctuations in classical MD as compared to quantum MD simulations.

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.

Due to the wide application of silica based systems ranging from microelectronics to nuclear waste disposal, detailed knowledge of water-silica interactions plays an important role in understanding fundamental processes, such as glass corrosion and the long term reliability of devices. In this dissertation, atomistic computer simulation methods have been used to explore and identify the mechanisms of water-silica reactions and the detailed processes that control the properties of the water-silica interfaces due to their ability to provide atomic level details of the structure and reaction pathways. The main challenges of the amorphous nature of the silica based systems and nano-porosity of the structures were overcome by a combination of simulation methodologies based on classical molecular dynamics (MD) simulations with Reactive Force Field (ReaxFF) and density functional theory (DFT) based ab initio MD simulations. Through the development of nanoporous amorphous silica structure models, the interactions between water and the complex unhydroxylated internal surfaces identified the unusual stability of strained siloxane bonds in high energy ring structure defects, as well as the hydroxylation reaction kinetics, which suggests the difficulty in using DFT methods to simulate Si-O bond breakage with reasonable efficiency. Another important problem addressed is the development of silica gel structures and their interfaces, which is considered to control the long term residual dissolution rate in borosilicate glasses. Through application of the ReaxFF classical MD potential, silica gel structures which mimic the development of interfacial layers during silica dissolution were created A structural model, consisting of dense silica, silica gel, and bulk water, and the related interfaces was generated, to represent the dissolution gel structure. High temperature evolution of the silica-gel-water (SGW) structure was performed through classical MD simulation of the system, and growth of the gel into the water region occurred, as well as the formation of intermediate range structural features of dense silica. Additionally, hydroxylated silica monomers (SiO4H4) and longer polymerized silica chains were formed in the water region, indicating that glass dissolution is occurring, even at short time frames. The creation of the SGW model provides a framework for a method of identifying how interfacial structures which develop at glass-water interfaces can be incorporated into atomistic models for additional analysis of the dissolution of silicates in water.

Hydrated anatase (101) titanium dioxide surfaces with oxygen vacancies have been studied using a combination of classical and ab initio molecular dynamics simulations. The reactivity of surface oxygen vacancies was investigated using ab initio calculations, showing that water molecules quickly adsorb to oxygen vacancy sites upon hydration. The oxygen vacancy then quickly reacts with the adsorbed water, forming a protonated bridging oxygen atom at the vacancy site and at a neighboring oxygen bridge. Ab initio simulations also revealed that this occurs via a short-lived hydronium ion intermediate. It was investigated how this reaction affects the structure and dynamics of water near the anatase surface. Classical molecular dynamics simulations of surfaces with and without oxygen vacancies showed that vacancies disrupt the second solvation shell, consisting of water molecules hydrogen bonded to the surface, thereby changing the local water density and diffusion as well as the binding modes for hydrogen bonding. Our findings support the hydroxylation of oxygen vacancies on anatase (101) surfaces, rather than stabilization by molecular adsorption or subsurface diffusion. The work gives new atomistic insight into water structure and surface chemistry on the catalytically relevant anatase (101) titanium dioxide surface.

Lithium thiophosphate electrolyte is a promising material for application in all-solid-state batteries. Ab initio molecular dynamics (AIMD) simulations have been used to investigate the ion conduction mechanisms in single-crystalline and glassy compounds. However, the complexity of real materials (e.g., materials with grain boundaries and multiphase glass-ceramics) causes AIMD simulations to have high computational cost. To overcome this computational limitation, we developed a new interatomic potential for classical molecular dynamics (CMD) simulations of Li solid-state electrolytes. The training datasets were generated from representative sulfide electrolytes (β-Li3PS4, γ-Li3PS4, Li4P2S6, Li7P3S11, and Li7PS6 crystals and 70Li2S-30P2S5 glass). Using the functional forms of the Class II and Stillinger-Weber potentials, all parameters were optimized by minimizing the differences in forces on atoms, stresses, and potential energies between the CMD and AIMD results. Subsequent validation showed that the optimized parameters can reproduce the dynamics of Li+ as well as the structures of the crystalline and glassy materials. The ionic conductivity of Li7P3S11 crystal was approximately five times that of the isostoichiometric 70Li2S-30P2S5 glass, indicating that CMD simulations using the developed force-field accurately reproduced the effective conduction path in Li7P3S11 from AIMD. The developed force-field parameters make it possible to simulate complex materials including amorphous-crystalline interfaces and multiphase glass-ceramics in the CMD framework.

Structure and dynamics of B2O3 melts and glasses: From ab initio to classical molecular dynamics simulations

The combination of classical and ab initio molecular dynamics simulations for computing structural and thermodynamic properties of metallic liquids is illustrated on the example of ruthenium and ruthenium-based alloys. The classical simulations used embedded atom model (EAM) potentials parametrized with the force matching method. The ab initio reference data were obtained using two electronic structure codes implementing the density functional theory plane wave/pseudopotential method. Several methodological aspects in the determination of structural and thermodynamic properties in the liquid phase are examined, first for pure ruthenium. The efficiency of this combined method is finally illustrated on the structure and the pressure of ternary alloys of platinum group metals of interest in the treatment of nuclear wastes.