Hydrolysis of the amorphous silica surface. II. Calculation of activation barriers and mechanisms

Learning Adsorption Patterns on Amorphous Surfaces

The physicochemical heterogeneity found on amorphous surfaces leads to a complex interaction of adsorbate molecules with topological and undercoordinated defects, which enhance the adsorption capacity and can participate in catalytic reactions. The identification and analysis of the adsorption structure observed on amorphous surfaces require novel tools that allow the segmentation of the surfaces into complex-shaped regions that contrast with the periodic patterns found on crystalline surfaces. We propose a Random Forest (RF) classifier that segments the surface into regions that can then be further analyzed and classified to reveal the dynamics of the interaction with the adsorbate. The RF segmentation is applied to the surface density map of the adsorbed molecules and employs multiple features (intensity, gradient, and the eigenvalues of the Hessian matrix) which are nonlocal and allow a better identification of the adsorption structures. The segmentation depends on a set of parameters that specify the training set and can be tailored to serve the specific purpose of the segmentation. Here, we consider an example in which we aim to separate highly heterogeneous regions from weakly heterogeneous regions. We demonstrate that the RF segmentation is able to separate the surface into a fully connected weakly heterogeneous region (whose behavior is somehow similar to crystalline surfaces and has an exponential distribution of the residence time) and a very heterogeneous region characterized by a complex residence-time distribution, which is generated by the undercoordinated defects and is responsible for the peculiar characteristics of the amorphous surface.

Methodologies for Detecting Quantal Exocytosis in Adrenal Chromaffin Cells Through Diamond-Based MEAs

Diamond-based multiarray sensors are suitable to detect in real-time exocytosis and action potentials from cultured, spontaneously firing chromaffin cells, primary hippocampal neurons, and midbrain dopaminergic neurons. Here, we focus on how amperometric measurements of catecholamine release are performed on micrographitic diamond multiarrays (μG-D-MEAs) with high temporal and spatial resolution by 16 electrodes simultaneously.

Surface Protolysis and Its Kinetics Impact the Electrical Double Layer

Surface conductivity in the electrical double layer (EDL) is known to be affected by proton hopping and diffusion at solid-liquid interfaces. Yet, the role of surface protolysis and its kinetics on the thermodynamic and transport properties of the EDL are usually ignored as physical models consider static surfaces. Here, using a novel molecular dynamics method mimicking surface protolysis, we unveil the impact of such chemical events on the system's response. Protolysis is found to strongly affect the EDL and electrokinetic aspects with major changes in ζ potential and electro-osmotic flow.

Origin of High Friction at Graphene Step Edges on Graphite

On graphite, friction is known to be more than an order of magnitude larger at step edge defects as compared to on the basal plane, especially when the counter surface slides from the lower terrace of the step to the upper terrace. Very different mechanisms have been proposed to explain this phenomenon, including atomic interactions between the counter surface and step edge (without physical deformation) and buckling or peeling deformation of the upper graphene terrace. Here, we use atomic force microscopy (AFM) and reactive molecular dynamic (MD) simulations to capture and differentiate the mechanisms proposed to cause high friction at step edges. AFM experiments reveal the difference between cases of no deformation and buckling deformation, and the latter case is attributed to the physical stress exerted by the sliding tip. Reactive MD simulations explore the process of peeling deformation due to tribochemical bond formation between the tip and the step edge. Combining the results of AFM experiments and MD simulations, it is found that each mechanism has identifiable and characteristic features in the lateral force and vertical height profiles recorded during the step-up process. The results demonstrate that buckling and peeling deformation of the graphene edge rarely occur under typical AFM experimental conditions and thus are unlikely to be the origin of high friction at step edges in most measurements. Instead, the high step-up friction is due to stick-slip behavior facilitated by the topographical change and atomic interactions between the tip and step edge without deformation of the graphene itself.

Application of Quantum Computing to Biochemical Systems: A Look to the Future

Chemistry is considered as one of the more promising applications to science of near-term quantum computing. Recent work in transitioning classical algorithms to a quantum computer has led to great strides in improving quantum algorithms and illustrating their quantum advantage. Because of the limitations of near-term quantum computers, the most effective strategies split the work over classical and quantum computers. There is a proven set of methods in computational chemistry and materials physics that has used this same idea of splitting a complex physical system into parts that are treated at different levels of theory to obtain solutions for the complete physical system for which a brute force solution with a single method is not feasible. These methods are variously known as embedding, multi-scale, and fragment techniques and methods. We review these methods and then propose the embedding approach as a method for describing complex biochemical systems, with the parts not only treated with different levels of theory, but computed with hybrid classical and quantum algorithms. Such strategies are critical if one wants to expand the focus to biochemical molecules that contain active regions that cannot be properly explained with traditional algorithms on classical computers. While we do not solve this problem here, we provide an overview of where the field is going to enable such problems to be tackled in the future.

Quantum-chemical simulation of the adsorption-induced reduction of strength of siloxane bonds

Mechanical strength of silicate glasses is known to decrease markedly due to the adsorption of molecules from the environment, especially in aqueous alkali solutions. This effect, known as the adsorption-induced reduction of strength (AIRS), has not yet been fully understood. Here, the dependence on the chemical nature and electronic properties of adsorbates of the AIRS of siloxane bonds in silica was studied by means of quantum-chemical calculations at the wB97X-D3/def2-TZVP level of theory. A siloxane bond was modelled by H₃Si-O-SiH₃ and (HO)₃Si-O-Si(OH)₃ clusters, and the AIRS was simulated by a linear tensile deformation of the siloxane bond in the presence of the following adsorbates: OH^-, Cl^-, H₂O, H⁺ and H₃O⁺. Potential energy profiles and derivative force curves of the siloxane bond rupture were obtained. The varying effect of the adsorbates on the energy-force characteristics of the AIRS can be explained by changes in the bond lengths and electron occupancy. It is shown that the AIRS of the siloxane bonds increases with an increase in the nucleophilicity of the adsorbates, and correlates with an adsorbate-induced redistribution of electron density.

New Insights into Adsorption Behaviour of NH3 Molecules on Small (SiO2)n (n=2–7) Clusters Through Systematic Analysis of Structural and Topological Properties

The adsorption of NH3 molecules on (SiO2)n (n = 2–7) clusters was explored using various theoretical methods. The stable structures, interaction energies, and bonding properties for the various methods were evaluated in detail. Reactivity analysis and optimization results showed that a single NH3 molecule preferentially adheres to the Si atom at the edge of the clusters. It was also observed that the energy gap and hardness of the complexes decreased with an increase in the number of NH3 molecules. Topological, electron localization function, and atoms-in-molecules analyses were performed to investigate the bonding characteristics of these complexes. In addition, the results of this study were compared with those obtained for a similar system (H2O molecules adsorbed onto SiO2 clusters), and the similarities and differences between the two systems were discussed.

Ab Initio energetics of SiO bond cleavage

A multilevel approach that combines high-level ab initio quantum chemical methods applied to a molecular model of a single, strain-free SiOSi bridge has been used to derive accurate energetics for SiO bond cleavage. The calculated SiO bond dissociation energy and the activation energy for water-assisted SiO bond cleavage of 624 and 163 kJ mol^-1 , respectively, are in excellent agreement with values derived recently from experimental data. In addition, the activation energy for H₂ O-assisted SiO bond cleavage is found virtually independent of the amount of water molecules in the vicinity of the reaction site. The estimated reaction energy for this process including zero-point vibrational contribution is in the range of -5 to 19 kJ mol^-1 . © 2017 Wiley Periodicals, Inc.

H2O incorporation in the phosphorene/a-SiO2 interface: a first-principles study

Based on first-principles calculations, we investigate (i) the energetic stability and electronic properties of single-layer phosphorene (SLP) adsorbed on an amorphous SiO₂ surface (SLP/a-SiO₂), and (ii) the further incorporation of water molecules at the phosphorene/a-SiO₂ interface. In (i), we find that the phosphorene sheet binds to a-SiO₂ through van der Waals interactions, even in the presence of oxygen vacancies on the surface. The SLP/a-SiO₂ system presents a type-I band alignment, with the valence (conduction) band maximum (minimum) of the phosphorene lying within the energy gap of the a-SiO₂ substrate. The structure and the surface-potential corrugations promote the formation of electron-rich and electron-poor regions on the phosphorene sheet and at the SLP/a-SiO₂ interface. Such charge density puddles are strengthened by the presence of oxygen vacancies in a-SiO₂. In (ii), because of the amorphous structure of the surface, we consider a number of plausible geometries for H₂O embedded in the SLP/a-SiO₂ interface. There is an energetic preference for the formation of hydroxyl (OH) groups on the a-SiO₂ surface. Meanwhile, in the presence of oxygenated water or interstitial oxygen in the phosphorene sheet, we observe the formation of metastable OH bonded to the phosphorene, and the formation of energetically stable P-O-Si chemical bonds at the SLP/a-SiO₂ interface. Further x-ray absorption spectra simulations are performed, which aim to provide additional structural/electronic information on the oxygen atoms forming hydroxyl groups or P-O-Si chemical bonds at the interface region.

Graphene-based CO2 sensing and its cross-sensitivity with humidity

We present graphene-based CO₂ sensing and analyze its cross-sensitivity with humidity.

Amorphous SiO2 surface models: energetics of the dehydroxylation process, strain, ab initio atomistic thermodynamics and IR spectroscopic signatures

Realistic amorphous SiO₂ models of 2.1 × 2.1 nm with silanol densities ranging 1.1–7.2 OH per nm² are obtained by means of ab initio calculations via the dehydroxylation of a fully hydroxylated silica surface.

Resistive graphene humidity sensors with rapid and direct electrical readout

We demonstrate humidity sensing using a change of the electrical resistance of single-layer chemical vapor deposited (CVD) graphene that is placed on top of a SiO2 layer on a Si wafer. To investigate the selectivity of the sensor towards the most common constituents in air, its signal response was characterized individually for water vapor (H2O), nitrogen (N2), oxygen (O2), and argon (Ar). In order to assess the humidity sensing effect for a range from 1% relative humidity (RH) to 96% RH, the devices were characterized both in a vacuum chamber and in a humidity chamber at atmospheric pressure. The measured response and recovery times of the graphene humidity sensors are on the order of several hundred milliseconds. Density functional theory simulations are employed to further investigate the sensitivity of the graphene devices towards water vapor. The interaction between the electrostatic dipole moment of the water and the impurity bands in the SiO2 substrate leads to electrostatic doping of the graphene layer. The proposed graphene sensor provides rapid response direct electrical readout and is compatible with back end of the line (BEOL) integration on top of CMOS-based integrated circuits.

Reactive simulations of the activation barrier to dissolution of amorphous silica in water

Free energy barriers for hydrolyzation of different Si sites on amorphous silica surfaces from the Qi (i = the number of bridging oxygen atoms) to Q(j) (j = (i − 1)) reaction during dissolution to form the labeled Qij reaction; the distribution indicates the importance of including structural heterogeneity of amorphous silica surfaces in computations.

Experimental and density functional theory study of the tribochemical wear behavior of SiO2 in humid and alcohol vapor environments

This paper investigates the reaction steps involved in tribochemical wear of SiO(2) surfaces in humid ambient conditions and the mechanism of wear prevention due to alcohol adsorption. The friction and wear behaviors of SiO(2) were tested in three distinct gaseous environments at room temperature: dry argon, argon with 50% relative humidity (RH), and argon with n-pentanol vapor pressure 50% relative to the saturation pressure (P/P(sat)). Adsorbed gas molecules have significant chemical influences on the wear of the surface. The SiO(2) surface wears more readily in humid ambient compared to the dry case; however, it does not show any measurable wear in 50% P/P(sat) n-pentanol vapor at the same nominal contact load tested in the dry and humid environments. The tribochemical wear of the SiO(2) surface can be considered the Si-O-Si bond cleavage upon reactions with the impinging vapor molecules under tribological stress. DFT calculations were used to estimate the apparent activation energy needed to cleave the Si-O-Si bond at beta-cristobalite (111) and alpha-quartz (001) surfaces by reactions with impinging water and alcohol vapor molecules. The alkoxide termination of the SiO(2) surfaces increases the energy barrier required to cleave the Si-O-Si bonds when compared to hydroxyl-terminated SiO(2) surfaces.

Model for the Water−Amorphous Silica Interface: The Undissociated Surface

The physical and chemical properties of the amorphous silica-water interface are of crucial importance for a fundamental understanding of electrochemical and electrokinetic phenomena, and for various applications including chromatography, sensors, metal ion extraction, and the construction of micro- and nanoscale devices. A model for the undissociated amorphous silica-water interface reported here is a step toward a practical microscopic model of this important system. We have extended the popular BKS and SPC/E models for bulk silica and water to describe the hydrated, hydroxylated amorphous silica surface. The parameters of our model were determined using ab initio quantum chemical studies on small fragments. Our model will be useful in empirical potential studies, and as a starting point for ab initio molecular dynamics calculations. At this stage, we present a model for the undissociated surface. Our calculated value for the heat of immersion, 0.3 J x m(-2), falls within the range of reported experimental values of 0.2-0.8 J x m(-2). We also study the perturbation of water properties near the silica-water interface. The disordered surface is characterized by regions that are hydrophilic and hydrophobic, depending on the statistical variations in silanol group density.

Structure and stability of the (001) α-quartz surface

The structure and surface energies of the cleaved, reconstructed, and fully hydroxylated (001) alpha-quartz surface of various thicknesses are investigated with periodic density functional theory (DFT). The properties of the cleaved and hydroxylated surface are reproduced with a slab thickness of 18 atomic layers, while a thicker 27-layer slab is necessary for the reconstructed surface. The performance of the hybrid DFT functional B3LYP, using an atomic basis set, is compared with the generalised gradient approximation, PBE, employing plane waves. Both methodologies give similar structures and surface energies for the cleaved and reconstructed surfaces, which validates studying these surfaces with hybrid DFT. However, there is a slight difference between the PBE and B3LYP approach for the geometry of the hydrogen bonded network on the hydroxylated surface. The PBE adsorption energy of CO on a surface silanol site is in good agreement with experimental values, suggesting that this method is more accurate for hydrogen bonded structures than B3LYP. New hybrid functionals, however, yield improved weak interactions. Since these functionals also give superior activation energies, we recommend applying the new functionals to contemporary issues involving the silica surface and adsorbates on this surface.

A New Self-Consistent Empirical Interatomic Potential Model for Oxides, Silicates, and Silica-Based Glasses

A new empirical pairwise potential model for ionic and semi-ionic oxides has been developed. Its transferability and reliability have been demonstrated by testing the potentials toward the prediction of structural and mechanical properties of a wide range of silicates of technological and geological importance. The partial ionic charge model with a Morse function is used, and it allows the modeling of the quenching of melts, silicate glasses, and inorganic crystals at high-pressure and high-temperature conditions. The results obtained by molecular dynamics and free energy calculations are discussed in relation to the prediction of structural and mechanical properties of a series of soda lime silicate glasses.

A Pseudoatom Approach to Molecular Truncation: Application in ab Initio MBPT Methods

In this paper, we test the performance of the molecular truncation method of Mallik et al., which was originally applied at the semiempirical NDDO level, in ab initio MBPT methods. Pseudoatoms developed for the replacement of -OCH(3) and -OCH(2)CH(3) functional groups are used in optimizations of selected clusters, and the resulting geometries are compared to reference values taken from the full molecules. It is shown that the pseudoatoms, which consist of parametrized effective core potentials for the nearest neighbor interactions and an external charge field for long-range Coulomb effects, perform well at the MP2 and CCSD levels of theory for the suite of molecules to which they were applied. Representative timings for some of the pseudoatom-terminated clusters are presented, and it is seen that there is a significant reduction in computational time, yet the geometric configurations and deprotonation energies of the pseudoatom-terminated clusters are comparable to the more computationally expensive all-atom molecules.

From cluster to bulk: Size dependent energetics of silica and silica-water interaction

We present our computational investigations on the energetics of clusters that consist of H2O and SiO2 using first-principles Born-Oppenheimer molecular dynamics method. Cohesive energy and hydration energy of both pure (or dry) and hydroxylated (or wet) ring-structured clusters have been investigated as functions of system size. We have found clear trends of energy as the cluster size increases. Energetics of a small silica nano-rod that contains 108 atoms is also obtained as a middle reference point for size evolution. Results from cluster and nano-rod calculations are compared with values from bulk quartz calculations using the same level of theoretical treatments.

Silicate Glass and Mineral Dissolution: Calculated Reaction Paths and Activation Energies for Hydrolysis of a Q3 Si by H3O+ Using Ab Initio Methods

Molecular orbital energy minimizations were performed with the B3LYP/6-31G(d) method on a [((OH)3SiO)3SiOH-(H3O+).4(H2O)] cluster to follow the reaction path for hydrolysis of an Si-O-Si linkage via proton catalysis in a partially solvated system. The Q3 molecule was chosen (rather than Q2 or Q1) to estimate the maximum activation energy for a fully relaxed cluster representing the surface of an Al-depleted acid-etched alkali feldspar. Water molecules were included in the cluster to investigate the influence of explicit solvation on proton-transfer reactions and on the energy associated with hydroxylating the bridging oxygen atom (Obr). Single-point energy calculations were performed with the B3LYP/6-311+G(d,p) method. Proton transfer from the hydronium cation to an Obr requires sufficient energy to suggest that the Si-(OH)-Si species will occur only in trace quantities on a silica surface. Protonation of the Obr lengthens the Si-Obr bond and allows for the formation of a pentacoordinate Si intermediate ([5]Si). The energy required to form this species is the dominant component of the activation energy barrier to hydrolysis. After formation of the pentacoordinate intermediate, hydrolysis occurs via breaking the [5]Si-(OH)-Si linkage with a minimal activation energy barrier. A concerted mechanism involving stretching of the [5]Si-(OH) bond, proton transfer from the Si-(OH2)+ back to form H3O+, and a reversion of [5]Si to tetrahedral coordination was predicted. The activation energy for Q3Si hydrolysis calculated here was found to be less than that reported for Q3Si using a constrained cluster in the literature but significantly greater than the measured activation energies for the hydrolysis of Si-Obr bonds in silicate minerals. These results suggest that the rate-limiting step in silicate dissolution is not the hydrolysis of Q3Si-Obr bonds but rather the breakage of Q2 or Q1Si-Obr bonds.

Reactions and clustering of water with silica surface

The interaction between silica surface and water is an important topic in geophysics and materials science, yet little is known about the reaction process. In this study we use first-principles molecular dynamics to simulate the hydrolysis process of silica surface using large cluster models. We find that a single water molecule is stable near the surface but can easily dissociate at three-coordinated silicon atom defect sites in the presence of other water molecules. These extra molecules provide a mechanism for hydrogen transfer from the original water molecule, hence catalyzing the reaction. The two-coordinated silicon atom is inert to the water molecule, and water clusters up to pentamer could be stably adsorbed at this site at room temperature.

Theoretical Study of the Interaction between Selected Adhesives and Oxide Surfaces

We investigate the competition of the various organic components of two representative adhesive systems for reactive defect sites at model surfaces of both SiO2 and Al2O3. The reaction energies of resin monomers, curing agents, and in some cases also of additional adhesion promoters with the defects are calculated. We applied a density-functional based tight-binding method including a self-consistent correction of the Mulliken charges, which has already proven to be a useful tool for computational materials science, delivering reliable structural and energetic information.

Hydrolysis of a two-membered silica ring on the amorphous silica surface

We have combined density functional theory (DFT) with classical interatomic potential functions to model hydrolysis of amorphous silica surfaces. The water-silica interaction is described by DFT with incorporation of a long-range elastic field described by classical interatomic potentials. Both physisorption and chemisorption of water on a surface site, known as the two-membered silica ring, are studied in detail. The hybrid quantum-mechanical and classical mechanical method enables more realistic treatment of chemical processes on an extended surface than previous methods. We have studied cooperative events in the hydrolytic reactions and discovered a new reaction pathway that involves a double proton transfer process. In addition, the evaluation of the total energy in a hybrid quantum-mechanical and classical mechanical system is discussed.

Fully coordinated silica nanoclusters: (SiO2)N molecular rings

A new form of finite silica with edge-sharing SiO2 units connected in a ring is proposed. High-level density-functional calculations for (SiO2)(N), N=4-14, show the rings to be energetically more stable than the corresponding (SiO2)(N) linear chains for N>11. The rings display frequency modes in remarkable agreement with infrared bands measured on dehydrated silica surfaces indicating their potential as models of strained extended silica systems. Silica rings, if synthesized, may also be useful precursors for new bulk-silica polymorphs with tubular or porous morphologies.