First-principles string molecular dynamics: An efficient approach for finding chemical reaction pathways

Detecting and Directing Single Molecule Binding Events on H-Si(100) with Application to Ultradense Data Storage

Many diverse material systems are being explored to enable smaller, more capable and energy efficient devices. These bottom up approaches for atomic and molecular electronics, quantum computation, and data storage all rely on a well-developed understanding of materials at the atomic scale. Here, we report a versatile scanning tunneling microscope (STM) charge characterization technique, which reduces the influence of the typically perturbative STM tip field, to develop this understanding even further. Using this technique, we can now observe single molecule binding events to atomically defined reactive sites (fabricated on a hydrogen-terminated silicon surface) through electronic detection. We then developed a simplified error correction tool for automated hydrogen lithography, quickly directing molecular hydrogen binding events using these sites to precisely repassivate surface dangling bonds (without the use of a scanned probe). We additionally incorporated this molecular repassivation technique as the primary rewriting mechanism in ultradense atomic data storage designs (0.88 petabits per in²).

Hydrogen in beryllium oxide investigated by DFT: on the relative stability of charged-state atomic versus molecular hydrogen

The behavior of hydrogen in perfect wurtzite beryllium oxide is herein investigated by means of electronic structure calculations based on density functional theory. The formation energies of the following set of states of hydrogen (H⁰, H⁺, H^-, H₂, [Formula: see text], [Formula: see text]) are computed and their solubility is established as a function of temperature and pressure with emphasis given to conditions relevant for hydrogen-implanted materials. It is found that all magnetic states H⁰, [Formula: see text], [Formula: see text] are unstable, while the relative stability of the non-magnetic states depends on the thermodynamic conditions: H₂ prevails above temperatures around 900 K at standard pressure, which is the lowest temperature in experiments measuring the diffusion coefficient of hydrogen in wurtzite beryllium oxide. Under hydrogen implantation, the total concentration of hydrogen is fixed by the implantation source; it is found that molecular hydrogen prevails starting from a very low total concentration in hydrogen (as low as 10^-40 at.fr.). Finally, the diffusion coefficient of H₂ in beryllium oxide is calculated and the results are compared with previous experimental data.

Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations

Iterative procedures for optimizing properties of molecular models often converge slowly owing to the computational cost of accurately representing features of interest. Here, we introduce a preconditioning scheme that allows one to use a less expensive model to guide exploration of the energy landscape of a more expensive model and thus speed the discovery of locally stable states of the latter. We illustrate our approach in the contexts of energy minimization and the string method for finding transition pathways. The relation of the method to other multilevel simulation techniques and possible extensions are discussed.

Reaction sampling and reactivity prediction using the stochastic surface walking method

The new theoretical method demonstrates the ability of automated reaction sampling and activity prediction for complex organic reactions.

Hydrogen retention and diffusion in tungsten beryllide

Beryllide compounds are often used in various domains because they are more resilient to oxidation than pure beryllium and at the same time they keep some of the properties of this metal. Nevertheless, the data about their properties during atomic hydrogen exposure are very scarce: numerous experiments have been conducted in the past few years on solid hydride deposition under beryllium-seeded plasma action or on energetic hydrogen implantation into metallic beryllium; many others have been devoted to hydrogen retention and diffusion in tungsten. There have been fewer studies about hydrogen interaction with the alloys of these metals, although the beryllium-tungsten mixed compounds have been experimentally detected in laboratory experiments. This article reports on calculations carried out using first-principles density functional theory (DFT) on tungsten beryllide crystal (Be12W) taken as a model alloy. The formation and reactivity of atomic vacancies are investigated in the domain of temperature ranging from 0 to 500 K, together with atomic hydrogen retention and diffusivity in the bulk and in/out vacancies.

Current challenges in atomistic simulations of glasses for biomedical applications

Atomic-scale simulations of bioglasses are being used to tackle several challenging aspects, such as new structural markers of bioactivity, ion migration and nanosized samples.

Density functional theory study of the organic functionalization of hydrogenated silicene

Silicene, the silicon analogous of graphene, is a newly synthesized two-dimensional nanomaterial, with unique features and promising potential applications. In this paper we present density functional theory calculations of the organic functionalization of hydrogenated silicene with acetylene, ethylene, and styrene. The results are compared with previous works of the adsorption on H-Si[111]. For styrene, binding energies for the intermediate and final states as well as the energy barrier for hydrogen abstraction are rather similar for the two systems. On the other hand, results for acetylene and ethylene are surprisingly different in H-silicene: the abstraction barrier is much smaller in H-silicene than in H-Si[111]. These differences can be understood by the different electrostatic potentials due to the presence of the H atoms at the bottom of the silicene bilayer that allows the delocalization of the spin density at the reaction intermediate state.

Density functional theory study of the organic functionalization of hydrogenated silicene

Silicene, the silicon analogous of graphene, is a newly synthesized two-dimensional nanomaterial, with unique features and promising potential applications. In this paper we present density functional theory calculations of the organic functionalization of hydrogenated silicene with acetylene, ethylene, and styrene. The results are compared with previous works of the adsorption on H-Si[111]. For styrene, binding energies for the intermediate and final states as well as the energy barrier for hydrogen abstraction are rather similar for the two systems. On the other hand, results for acetylene and ethylene are surprisingly different in H-silicene: the abstraction barrier is much smaller in H-silicene than in H-Si[111]. These differences can be understood by the different electrostatic potentials due to the presence of the H atoms at the bottom of the silicene bilayer that allows the delocalization of the spin density at the reaction intermediate state.

Electric field assisted oxygen removal from the basal plane of the graphitic material

We provide a novel strategy to eliminate the epoxy group from the basal plane of graphene platelets. Given that the current reduction methods are unsatisfactory to clean the epoxides or sometimes cause undesirable structure deformations, the proposed strategy restores the original hexagonal carbon network without creating other new defects. To the best of our knowledge, the electric field mediated graphene oxide (GO) reduction has not yet been systematically investigated. The capability would permit the improvement of existing GO reduction methods and assist in the fabrication of high-quality graphitic materials.

Molecular dynamics methods for modeling complex interactions in biomaterials

The molecular dynamics method is a powerful computer simulation technique which provides access to the detailed time evolution (trajectory) of a system in specified conditions, such as a particular temperature or pressure. The full trajectory of the system can be analyzed using statistical mechanics tools to obtain thermodynamical quantities and dynamical properties; the mechanism of chemical reactions and other time-dependent processes, such as diffusion, can also be revealed in high detail. When applied to model extended and complex system such as biomaterials, MD simulations represent an invaluable tool to discover structure-activity relationships and rationalize biomedical applications.

Testing the TPSS meta-generalized-gradient-approximation exchange-correlation functional in calculations of transition states and reaction barriers

We have studied the performance of local and semilocal exchange-correlation functionals [meta-generalized-gradient-approximation (GGA)-TPSS, GGA-Perdew-Burke-Ernzerhof (PBE), and local density approximation (LDA)] in the calculation of transition states, reaction energies, and barriers for several molecular and one surface reaction, using the plane-wave pseudopotential approach. For molecular reactions, these results have been compared to all-electron Gaussian calculations using the B3LYP hybrid functional, as well as to experiment and high level quantum chemistry calculations, when available. We have found that the transition state structures are accurately identified irrespective of the level of the exchange-correlation functional, with the exception of a qualitatively incorrect LDA prediction for the H-transfer reaction in the hydrogen bonded complex between a water molecule and a OH radical. Both the meta-GGA-TPSS and the GGA-PBE functionals improve significantly the calculated LDA barrier heights. The meta-GGA-TPSS further improves systematically, albeit not always sufficiently, the GGA-PBE barriers. We have also found that, on the Si(001) surface, the meta-GGA-TPSS barriers for hydrogen adsorption agree significantly better than the corresponding GGA-PBE barriers with quantum Monte Carlo cluster results and experimental estimates.

The reaction path intrinsic reaction coordinate method and the Hamilton-Jacobi theory

The definition and location of an intrinsic reaction coordinate path is of crucial importance in many areas of theoretical chemistry. Differential equations used to define the path hitherto are complemented in this study with a variational principle of Fermat type, as Fukui [Int. J. Quantum Chem., Quantum Chem. Symp. 15, 633 (1981)] reported in a more general form some time ago. This definition is more suitable for problems where initial and final points are given. The variational definition can naturally be recast into a Hamilton-Jacobi equation. The character of the variational solution is studied via the Weierstrass necessary and sufficient conditions. The characterization of the local minima character of the intrinsic reaction coordinate is proved. Such result leads to a numerical algorithm to find intrinsic reaction coordinate paths based on the successive minimizations of the Weierstrass E-function evaluated on a guess curve connecting the initial and final points of the desired path.

Oxygen-driven unzipping of graphitic materials

Optical microscope images of graphite oxide (GO) reveal the occurrence of fault lines resulting from the oxidative processes. The fault lines and cracks of GO are also responsible for their much smaller size compared with the starting graphite materials. We propose an unzipping mechanism to explain the formation of cracks on GO and cutting of carbon nanotubes in an oxidizing acid. GO unzipping is initiated by the strain generated by the cooperative alignment of epoxy groups on a carbon lattice. We employ two small GO platelets to show that through the binding of a new epoxy group or the hopping of a nearby existing epoxy group, the unzipping process can be continued during the oxidative process of graphite. The same epoxy group binding pattern is also likely to be present in an oxidized carbon nanotube and cause its breakup.

Competing Mechanisms in the Optically Activated Functionalization of the Hydrogen-Terminated Si(111) Surface

Recent experiments have shown that organic monolayers on silicon surfaces can be formed through the optically activated surface reaction of H-terminated Si surfaces with terminally unsaturated organic molecules (Eves et al. J. Am. Chem. Soc. 2004, 126, 14318; Sun et al. J. Am. Chem. Soc. 2005, 127, 2514). Possible mechanisms for the formation of this monolayer involve the abstraction of a H atom either at the same attachment site of the molecule (Path A) or from a neighboring site (Path B). Using periodic Density Functional Theory calculations together with an efficient method for finding reaction pathways, we examine both optically activated reaction mechanisms for an alkene and an aldehyde reacting with H-Si(111). Our results show that while Path A is energetically more favorable its significant barrier is likely to limit its viability. Path B on the other hand encounters a much lower H atom abstraction barrier and appears to be more viable.

Role of Molecular Conjugation in the Surface Radical Reaction of Aldehydes with H−Si(111): First Principles Study

Within the current effort to understand and develop the organic functionalization of silicon surfaces, recent experiments have identified the radical chain reaction of unsaturated organic molecules with H-terminated silicon surfaces as a particularly promising route for controlled formation of such functionalized surfaces. Using periodic density functional theory calculations, we theoretically study and characterize the basic steps of the radical chain reaction mechanism for different aldehyde molecules (formaldehyde, benzaldehyde, propanaldehyde, propenaldehyde) reacting with the H-Si(111) surface, under the assumption that a Si dangling bond is initially present on the surface. Molecular conjugation is found to play a crucial role in the viability of the reaction, by controlling the delocalization of the spin density at the reaction intermediate. Interesting differences between our present results for aldehydes and our previous study for the reactions of alkene/alkyne molecules with H-Si(111) are observed and discussed (Takeuchi et al. J. Am. Chem. Soc. 2004, 126, 15890).

O2 and Vacancy Diffusion on Rutile(110): Pathways and Electronic Properties

The binding structures and diffusion pathways of molecular oxygen on a defective TiO2(110) surface are studied by means of a recently developed first-principles string molecular dynamics approach. A variety of molecular and dissociated O2 adsorption states are identified and the kinetics of their interconversion is analyzed. These results, as well as calculations of the electronic properties and of scanning tunneling microscopy (STM) images, are used to discuss recent experimental observations of the interactions between surface oxygen vacancies and the adsorbed oxygen molecule.

Density Functional Theory Study of One-Dimensional Growth of Styrene on the Hydrogen-Terminated Si(001)−(3 × 1) Surface

Recent experimental work has shown that the addition of styrene molecules to hydrogen-terminated Si(001) surfaces leads to the formation of one-dimensional molecular structures through a radical-initiated surface chain reaction mechanism. These nanometric structures are observed to be directed parallel to the dimer rows on the H-Si(001)-(2 x 1) surface and perpendicular to the same rows on H-Si(001)-(3 x 1). Using periodic density functional theory (DFT) calculations, we have studied the initial steps of the radical chain mechanism on the H-Si(001)-(3 x 1) surface and compared them to analogous results for H-Si(001)-(2 x 1). On the H-Si(001)-(3 x 1) surface, one of the crucial steps of the surface chain reaction, namely, the abstraction of a H atom from a nearby surface hydride unit, is found to have a somewhat smaller activation energy in the direction perpendicular to the dimer rows (H abstraction from the nearest dihydride site) than along the rows (H abstraction from a neighboring dimer). Additionally, due to the steric repulsion between the styrene molecules and the SiH2 subunits, growth along the dimer rows is not thermodynamically favorable on the (3 x 1) surface. On the other hand, due to the absence of the SiH2 subunits, growth parallel to the Si dimer rows becomes favored on the H-Si(001)-(2 x 1) surface.

Free energy profile along a discretized reaction path via the hyperplane constraint force and torque

By employing mechanical work analogies, we derive a convenient computational approach for evaluation of the free energy profile (FEP) along some discretized path defined as a sequence of hyperplanes. A hyperplane is fully specified by any of its point and a tangent vector. The FEP is obtained as an integral of two components. The translational component of the free energy is computed by integrating the hyperplane constraint force. The rotational component is evaluated via the hyperplane torque. Both ingredients--the constraint force and the hyperplane torque-are evaluated on each hyperplane independently. The integration procedure utilizes a set of reference points defining a point of rotation on each hyperplane, and these points can be chosen before or after the sampling takes place. A shift in the reference points redistributes the FEP contributions between the translational and rotational components. For systems where the FEP is dominated by the potential energy differences, reference points residing on the minimum energy path present a natural choice. We demonstrate the validity of our approach on two examples, a simple two-dimensional (2D) potential, and a seven-atom Lennard-Jones cluster. In each case, we compare the numerical FEP with the harmonic approximation estimates. Our results for the 2D potential are also verified by the data available in the literature. In both cases, the rotational component of the FEP represents a sizable contribution to the total FEP, so ignoring it would yield clearly incorrect results.

Surface Reaction of Alkynes and Alkenes with H-Si(111): A Density Functional Theory Study

Recent experiments on the addition of alkene and alkyne molecules to H-terminated silicon surfaces have provided evidence for a surface chain reaction initiated at isolated Si dangling bonds and involving an intermediate carbon radical state, which, after abstraction of a hydrogen atom from a neighboring Si-H unit, transforms into a stable adsorbed species plus a new Si dangling bond. Using periodic density functional theory (DFT) calculations, together with an efficient method for determining reaction pathways, we have studied the initial steps of this chain reaction for a few different terminal alkynes and alkenes interacting with an isolated Si dangling bond on an otherwise H-saturated Si(111) surface. Calculated minimum energy pathways (MEPs) indicate that the chain mechanism is viable in the case of C(2)H(2), whereas for C(2)H(4) the stabilization of the intermediate state is so small and the barrier for H-abstraction so (relatively) large that the molecule is more likely to desorb than to form a stable adsorbed species. For phenylacetylene and styrene, stabilization of the intermediate state and decrease of the H-abstraction barrier take place. While a stable adsorbed species exists in both cases, the overall heat of adsorption is larger for the alkyne molecules.