Combined Ab Initio Molecular Dynamics Research Articles

Microscopic properties of liquid water from combined ab initio molecular dynamics and energy decomposition studies

The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.

Ferryl–Oxo Species Produced from Fenton’s Reagent via a Two-Step Pathway: Minimum Free-Energy Path Analysis

A mixture of ferrous ions and hydrogen peroxide, known as Fenton's reagent, is an effective oxidant and has been widely used in various industrial applications; however, there is still controversy about what the oxidizing agents are and how they are produced. In this study, we have determined minimum free-energy paths (MFEPs) from Fenton's reagent to possible oxidizing agents such as hydroxyl radicals and ferryl-oxo species by combining ab initio molecular dynamics simulations and an MFEP search method. Along the MFEPs, representative free-energy profiles of the Fenton reaction were elucidated. On the basis of the free-energy profiles, we revealed that the reaction producing ferryl-oxo species from Fenton's reagent is more energetically favorable than that yielding a free hydroxyl radical, by 24.4 kcal mol(-1), which indicates that the ferryl-oxo species is the primary oxidizing agent in reactions of Fenton's reagent. Moreover, we clarified that the ferryl-oxo species is favorably formed via a two-step reaction pathway, which reaches the product through a dihydroxyiron(IV) intermediate. The energetics charting the free-energy profiles provided valuable information for a comprehensive understanding of Fenton reactions. We concluded that a ferryl-oxo species produced from Fenton's reagent serves as the primary oxidizing agent in the Fenton reaction.

Understanding the multistate SET process in Ge-Sb-Te-based phase-change memory

Multilevel operation is a topic of much current research in the field of phase-change memory materials, representing the most feasible method for increasing memory density beyond the ultimate scaling limits of the cell size. In this work, we present a combined experimental and ab initio molecular dynamics study of the formation of intermediate states during the crystallisation of Ge2Sb2Te5 (GST). A single intermediate resistance level is formed within a narrow voltage window, and simulations suggest this consists of microscopic crystallites embedded in a bulk amorphous phase. These findings are interpreted within the framework of classical nucleation theory, and a mechanism is proposed to explain the formation of the intermediate state. Our findings suggest that it may be difficult to obtain multiple intermediate states reliably during the crystallisation of Ge2Sb2Te5 and shed light on the fundamental limitations of using this method for multilevel programming.

Structure, electronic, and optical properties of TiO2 atomic clusters: An ab initio study

Atomic clusters of TiO(2) are modeled by means of state-of-the-art techniques to characterize their structural, electronic and optical properties. We combine ab initio molecular dynamics, static density functional theory, time-dependent density functional theory, and many body techniques, to provide a deep and comprehensive characterization of these systems. TiO(2) clusters can be considered as the starting seeds for the synthesis of larger nanostructures, which are of technological interest in photocatalysis and photovoltaics. In this work, we prove that clusters with anatase symmetry are energetically stable and can be considered as the starting seeds to growth much larger and complex nanostructures. The electronic gap of these inorganic molecules is investigated, and shown to be larger than the optical gap by almost 4 eV. Therefore, strong excitonic effects appear in these systems, much more than in the corresponding bulk phase. Moreover, the use of various levels of theory demonstrates that charge transfer effects play an important role under photon absorption, and therefore the use of adiabatic functionals in time dependent density functional theory has to be carefully evaluated.

Solvent Effects and Dynamic Averaging of 195Pt NMR Shielding in Cisplatin Derivatives

The influences of solvent effects and dynamic averaging on the (195)Pt NMR shielding and chemical shifts of cisplatin and three cisplatin derivatives in aqueous solution were computed using explicit and implicit solvation models. Within the density functional theory framework, these simulations were carried out by combining ab initio molecular dynamics (aiMD) simulations for the phase space sampling with all-electron relativistic NMR shielding tensor calculations using the zeroth-order regular approximation. Structural analyses support the presence of a solvent-assisted "inverse" or "anionic" hydration previously observed in similar square-planar transition-metal complexes. Comparisons with computationally less demanding implicit solvent models show that error cancellation is ubiquitous when dealing with liquid-state NMR simulations. After aiMD averaging, the calculated chemical shifts for the four complexes are in good agreement with experiment, with relative deviations between theory and experiment of about 5% on average (1% of the Pt(II) chemical shift range).

Dynamical properties of deeply undercooled and amorphous systems: Combined classical and ab initio molecular dynamics simulations approaches

Dynamical properties of pure silicon in deeply undercooled states, and Cu–Zr bulk metallic glass are calculated from combined classical and ab initio molecular dynamics techniques. An analysis of the results indicates that a boson peak occurs in both systems but its origin is found to be different in each case.

Mechanism of Base-Promoted Dehydrochlorination of Pentachloroethane: Concerted or Stepwise?

This paper reports a first-principles molecular dynamics simulation study of the microscopic mechanism of the base-catalyzed dehydrochlorination of pentachloroethane. So far the nature of the mechanism of this reaction is not understood: the concerted and stepwise mechanisms are under debate. By combining ab initio molecular dynamics with the method of constraints, we determine the reaction mechanism and associated free energy profile. We find that the reaction barrier is in good agreement with experimental findings and reveal that the reaction proceeds via a concerted mechanism. Our simulations provide no evidence for the presence of carbanion intermediate indicative of the stepwise pathway. This microscopic understanding will provide new implications for understanding the reduction of polyhalogenated alkanes and rational design of effective materials to treat these contaminants.

Short- and medium-range order in aZr73Pt27glass: Experimental and simulation studies

The structure of a ${\text{Zr}}_{73}{\text{Pt}}_{27}$ metallic glass, which forms a ${\text{Zr}}_{5}{\text{Pt}}_{3}$ (${\text{Mn}}_{5}{\text{Si}}_{3}$-type) phase having local atomic clusters with distorted icosahedral coordination during the primary crystallization, has been investigated by means of x-ray diffraction and combining ab initio molecular-dynamics (MD) and reverse Monte Carlo (RMC) simulations. The ab initio MD simulation provides an accurate description of short-range structural and chemical ordering in the glass. A three-dimensional atomistic model of 18 000 atoms for the glass structure has been generated by the RMC method utilizing both the structure factor $S(k)$ from x-ray diffraction experiment and the partial pair-correlation functions from ab initio MD simulation. Honeycutt and Andersen index and Voronoi cell analyses, respectively, were used to characterize the short- and medium-range order in the atomistic structure models generated by ab initio MD and RMC simulations. The ab initio results show that an icosahedral type of short-range order is predominant in the glass state. Furthermore, analysis of the atomic model from the constrained RMC simulations reveals that the icosahedral-like clusters are packed in arrangements having higher-order correlations, thus establishing medium-range topological order up to two or three cluster shells.

Temperature dependent vibrational spectra and bond dynamics in hydrogenated amorphous silicon

We present the results of extensive modeling of hydrogenated amorphous silicon (a-Si:H) by combined ab initio molecular dynamics, an improved signal processing technique, and computer visualization, focusing on vibrational properties of a-Si:H. By comparing the theoretical and experimental vibrational spectra we correlate the hydrogen and silicon dynamics with the structural stability, bonding geometry, and diffusion in the a-Si:H material. Microscopic characteristics that cannot be obtained by other techniques, namely, hydrogen migration, bond switching, and silicon dangling bond passivation, are extracted from the atomic dynamics. We also demonstrate that this method offers the possibility of accessing other important macroscopic characteristics of a-Si:H and its stability in general. The approach we have developed can be used as well to model all aspects of a-Si:H dynamics, including the detrimental Staebler–Wronski effect.

Pressure Induced Friction Collapse of Rare Gas Boundary Layers Sliding over Metal Surfaces

In this Letter we show that friction of anticorrugating systems can be dramatically decreased by applying an external load. The counterintuitive behavior that deviates from the macroscopic Amonton law is dictated by quantum mechanical effects that induce a transformation from anticorrugation to corrugation in the near-surface region. We describe the load-driven modifications occurring in the potential energy surface of different rare gas-metal adsorbate systems, namely, Ar, Kr, Xe on Cu(111), and Xe on Ag(111), and we calculate the consequent friction drop for the commensurate Xe/Cu system by means of combined ab initio and classical molecular dynamics simulations.

Structure of Zr x Pt100−x (73 ≤ x ≤ 77) Metallic Glasses

The structure of hyper-eutectic ZrxPt100−x (73 ≤ x ≤ 77) metallic glasses produced by melt spinning was examined with high-energy synchrotron X-ray diffraction (HEXRD) and fluctuation electron microscopy. In addition, details of the amorphous structure were studied by combining ab initio molecular dynamics and reverse Monte Carlo simulations. Crystallization pathways in these glasses have been reported to vary dramatically with small changes in compositions; however, in the current study, the structures of the different glasses were also observed to vary with composition, particularly the prepeak in the total structure factor that occurs at a Q value of around 17 nm−1. Results from simulations and fluctuation electron microscopy suggest that the medium-range order of the amorphous structure is characterized by extended groups of Pt-centered clusters that increase in frequency, structural order, or spatial organization at higher Pt contents. These clusters may be related to the Zr5Pt3 structure, which contains Pt-centered clusters coordinated by 9Zr and 2Pt atoms.

Salt Permeation and Exclusion in Hydroxylated and Functionalized Silica Pores

We use combined ab initio molecular dynamics (AIMD), grand canonical Monte Carlo, and molecular dynamics techniques to study the effect of pore surface chemistry and confinement on the permeation of salt into silica nanopore arrays filled with water. AIMD shows that 11.6 A diameter hydroxylated silica pores are relatively stable in water, whereas amine groups on functionalized pore surfaces abstract silanol protons, turning into NH3+. Free energy calculations using an ab initio parametrized force field show that the hydroxylated pores strongly attract Na+ and repel Cl- ions. Pores lined with NH3+ have the reverse surface charge polarity. Finally, studies of ions in carbon nanotubes suggest that hydration of Cl- is more strongly frustrated by pure confinement effects than Na+.

Structure and Dynamics of the Aluminum Chlorohydrate Polymer Al13O4(OH)24 (H2O)12Cl7.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Structure and dynamics of the aluminum chlorohydrate polymer Al13O4(OH)24(H2O)12Cl7

The Al13 polymer, Al13O4(OH)24(H2O)12Cl7, is thought to be a major component of the aluminum chlorohydrate (ACH) polymer system. Although it plays important roles in various aluminum chlorohydrate applications, its structure is not well understood. We combine ab initio molecular dynamics simulations in both the gas-phase and aqueous solution, with small angle X-ray scattering experiments on a bulk ACH sample to determine the structure of Al13-mer. We find that Al13 entity is roughly spherical (∼10 Å diameter), with a central tetrahedral Al3+ ion surrounded by four shells consisting of O, OH and H2O groups. Our ab initio molecular dynamics studies indicate that such a structure is stable on the picosecond time scale in an aqueous environment.

Ab initio study of misfit dislocations at the SiC/Si(001) interface.

The high lattice mismatched SiC/Si(001) interface was investigated by means of combined classical and ab initio molecular dynamics. Among the several configurations analyzed, a dislocation network pinned at the interface was found to be the most efficient mechanism for strain relief. A detailed description of the dislocation core is given, and the related electronic properties are discussed for the most stable geometry: we found interface states localized in the gap that may be a source of failure of electronic devices.

Towards solvation simulations with a combined ab initio molecular dynamics and molecular mechanics approach

The combined quantum mechanics and molecular mechanics method has been implemented within the framework of the Projector Augmented Wave Car-Parrinello method for explicit solvent simulations. The approach has been evaluated for its ability to represent the ‘true’ intermolecular interaction potential and its ability to perform energy conserving dynamics. The combined QM/MM potential has been parameterized to reproduce 27 hydrogen bonded bimolecular interactions between a water molecule and a set of organic molecules calculated wholly at the density function theory level. For this training set, a root-mean-square deviation of 0.8kcal/mol was achieved for the interaction energies that ranged from −0.3 to −29.3kcal/mol.

Model of silica glass from combined classical and ab initio molecular-dynamics simulations

A Car-Parrinello (CP) molecular dynamics simulation of vitreous silica, combined with classical molecular dynamics, is presented. The equilibration of the liquid, quench and relaxation of the glass are performed classically using the van Beest, Kramer and van Santen (BKS) potential [12] and the resulting configuration (coordinates and velocities) is used as input for the CP simulation. A remarkable stability of the CP dynamics is observed justifying this procedure and validating the BKS potential. Several structural and electronic properties are calculated and compared with experiments.