Atomistic insight into salinity dependent preferential binding of polar aromatics to calcite/brine interface: implications to low salinity waterflooding.

This paper resolve the salinity-dependent interactions of polar components of crude oil at calcite-brine interface in atomic resolution. Molecular dynamics simulations carried out on the present study showed that ordered water monolayers develop immediate to a calcite substrate in contact with a saline solution. Carboxylic compounds, herein represented by benzoic acid (BA), penetrate into those hydration layers and directly linking to the calcite surface. Through a mechanism termed screening effect, development of hydrogen bonding between -COOH functional groups of BA and carbonate groups is inhibited by formation of a positively-charged Na+ layer over CaCO3 surface. Contrary to the common perception, a sodium-depleted solution potentially intensifies surface adsorption of polar hydrocarbons onto carbonate substrates; thus, shifting wetting characteristic to hydrophobic condition. In the context of enhanced oil recovery, an ion-engineered waterflooding would be more effective than injecting a solely diluted saltwater.

Ion-specific interactions at calcite-brine interfaces: a nano-scale study of the surface charge development and preferential binding of polar hydrocarbons.

This research provides an atomic-level insight into the synergic contribution of mono- and divalent ions to interfacial characteristics of calcite surfaces exposed to electrolyte solution containing organic compounds. The emphasis was placed on the ionic interactions responsible for charge developing mechanisms of calcite surfaces and also the capacity for adsorption of polar hydrocarbons, represented by benzoic acid (BA), at different brine compositions. For this purpose, molecular dynamics (MD) simulations were employed to explore the interplay of the main constituent ions of natural brines (Na+, Cl-, Mg2+, and SO42-) and BA at the interface of CaCO3. It was observed that surface accumulation of Na+ cations produces a positively charged layer immediate to the basal plane of calcite, validating the typical positive surface charge of carbonates reported by laboratory experiences. Meanwhile, a negatively charged layer appears beyond the sodium layer as a result of direct and solvent-mediated pairing of anions with Na+ cations lodged on the calcite substrate. In this process, sulfate adsorption severely diminishes surface charge to even a negative value in the case of a SO42--rich solution, providing an interpretation for the measurements reported in the literature. Our results revealed the inhibition of direct binding of BA molecules onto the calcite surface through complexation with protruding oxygen atoms of basal carbonates by the residing Na+ cations. Further, we noticed the sulfate-mediated pairing of BA molecules to the Na+ layer, which in effect intensifies surface adsorption of BA. However, BA-SO42- interaction is considerably reduced by magnesium cations shielding sulfate sites in the Mg2+-augmented brine. The findings presented in this study are of fundamental importance to advance our microscopic understanding of interfacial interactions in brine/oil/carbonate systems; with broad scientific and applied implications in the context of mobilizing organic contaminants trapped in aquifer sediments and enhancement of hydrophilicity of subsurface oil-bearing carbonate reservoirs by injecting ion-modified brine solutions.

A Deep Look into the Dynamics of Saltwater Imbibition in a Calcite Nanochannel: Temperature Impacts Capillarity Regimes.

This research concerns fundamentals of spontaneous transport of saltwater (1 mol·dm-3 NaCl solution) in nanopores of calcium carbonates. A fully atomistic model was adopted to scrutinize the temperature dependence of flow regimes during solution transport under CaCO3 nanoconfinement. The early time of capillary filling is inertia-dominated, and the solution penetrates with a near-planar meniscus at constant velocity. Following a transition period, the meniscus angle falls to a stabilized value, characterizing the capillary-viscous advancement in the calcite channel. At this stage, brine displacement follows a parabolic relationship consistent with the classical Lucas-Washburn (LW) theory. Approaching the slit outlet, the meniscus contact lines spread widely on the solid substrate and brine leaves the channel at a constant rate, in oppose to the LW law. The brine imbibition rate considerably increases at higher temperatures as a result of lower viscosity and greater tendency to form wetting layers on slit walls. We also pointed out a longer primary inertial regime and delayed onset of the viscous-capillary regime at higher temperatures. Throughout the whole span of capillary displacement, transport of sodium and chloride ions is tied to dynamics and diffusion of the water phase, even at the mineral interface. The results presented in this study are of broad implications in diverse science and technological applications.

How do ions contribute to brine-hydrophobic hydrocarbon Interfaces? An in silico study.

HYPOTHESIS: The saltwater-oil interface is of broad implication in geochemistry and petroleum disciplines. To date, the main focus has been on the surface contribution of polar, heavy compounds of crude oil, widely neglecting the role of non-polar hydrocarbons. However, non-polar compounds are expected to contribute to characteristics of oil-brine interfaces. METHODOLOGY: Utilizing molecular dynamics simulation, we aim to characterize ion behavior adjacent to hydrophobic organic phases. Concerning natural environments, NaCl, CaCl2 and Na2SO4 electrolytes at low (5 wt%) and high (15 wt%) concentrations were brought in contact with heptane and/or toluene which account for aliphatic and aromatic constituents of typical crude oils, respectively. The reproduced experimental data for interfacial tension, brines density and ions' diffusivities adequately verify our molecular calculations. FINDINGS: Ions accumulate nearby the intrinsically charge-neutral oil surfaces. A disparate surface-favoring propensity of ions causes the interfacial region to resemble an electrical layer and impose an effective surface charge onto the oil surface. Despite absence of any polar site, the effective surface charge density is hydrocarbon-dependent, with the highest and lowest values observed for toluene and heptane interfaces, respectively. Due to accumulation of toluene molecules nearby the brines, the interfacial characteristics of heptol (toluene-heptane mixture) is comparable to that of the toluene phase.

The Impact of Salinity on the Interfacial Structuring of an Aromatic Acid at the Calcite/Brine Interface: An Atomistic View on Low Salinity Effect.

This study aims to elucidate the impact of salinity on the interactions governing the adsorption of polar aromatic oil compounds onto calcite. To this end, molecular dynamics simulations were employed to assess adsorption of a model polar organic molecule (deprotonated benzoic acid, benzoate) on the calcite surface in NaCl brines of different concentration levels, namely, deionized water (DW), low-salinity water (LS, 5000 ppm), and sea water (SW; 45,000 ppm). Calcite was found to be completely covered by several well-ordered water layers. The top hydration layer is very compact and prevents direct adsorption of benzoates onto the substrate. Instead, Na+ ions form a distinct positively charged layer by adhering on the calcite substrate through inner-sphere complexion mode. Cl- ions mostly lodge on top of the adsorbed sodium cations, forming a negatively charged layer. The distribution of ions at the calcite/brine interface thus exhibits the features of an electrical double layer, composed of a Stern-like positive layer followed by a negative one. The positive charged layer attracts benzoates toward the surface. As such, the sodium ions attached onto the calcite can act as adsorption sites to connect benzoates to the surface. By increasing the salinity, more Na+ ions adsorb onto the calcite surface, and the density of benzoate molecules at the interface is enhanced as a result of more Na+ bridging ions. The monotonic salinity-dependent adsorption of benzoate molecules on calcite offers a mechanism driving additional oil recovery upon injection of diluted brine into subsurface carbonate reservoirs.

Graphene-Subgrain-Defined Oxidation of Copper.

The correlation between the crystal structure of chemical vapor deposition (CVD)-grown graphene and the crystal structure of the Cu growth substrate and their mutual effect on the oxidation of the underlying Cu are systematically explored. We report that natural oxygen or water intercalation along the graphene-Cu interface results in an orientation-dependent oxidation rate of the Cu surface, particularly noticeable for bicrystal graphene domains on the same copper grain, suggesting that the relative crystal orientation of subgrains determines the degree of Cu oxidation. Atomistic force field calculations support these observations, showing that graphene domains have preferential alignment with the Cu(111) with a smaller average height above the global Cu surface as compared to intermediate orientations, and that this is the origin of the heterogeneous oxidation rate of Cu. This work demonstrates that the natural oxidation resistance of Cu coated by graphene is highly dependent on the crystal orientation and lattice alignment of Cu and graphene, which is key information for engineering the interface configuration of the graphene-Cu system for specific functionalities in mechanical, anticorrosion, and electrical applications of CVD-grown graphene.

Multi-scale approach to first-principles electron transport beyond 100 nm.

Multi-scale computational approaches are important for studies of novel, low-dimensional electronic devices since they are able to capture the different length-scales involved in the device operation, and at the same time describe critical parts such as surfaces, defects, interfaces, gates, and applied bias, on a atomistic, quantum-chemical level. Here we present a multi-scale method which enables calculations of electronic currents in two-dimensional devices larger than 100 nm2, where multiple perturbed regions described by density functional theory (DFT) are embedded into an extended unperturbed region described by a DFT-parametrized tight-binding model. We explain the details of the method, provide examples, and point out the main challenges regarding its practical implementation. Finally we apply it to study current propagation in pristine, defected and nanoporous graphene devices, injected by chemically accurate contacts simulating scanning tunneling microscopy probes.

Bonding, structural and thermodynamic analysis of dissociative adsorption of H3O+ ion onto calcite (101⁻4) surface: CPMD and DFT calculations.

We used density functional theory (DFT) and Car-Parrinello molecular dynamics (CPMD) simulation to investigate the adsorption and bond formation of hydronium ion (H3O+) onto a [Formula: see text] calcite surface. For surface coverage of 25% to 100%, the nature of H3O+ interaction was explored through electron density and energetics in the context of bond critical points. The adsorbate-adsorbent structure was studied by simulation of pair correlation function. The results revealed that dissociation into water molecule(s) and proton(s) complements H3O+ ion(s) adsorbtion. The H2O molecule adsorbs onto the surface via its O atom, and interacts with surface calcium in a closed-shell mode; the H+ ion makes a covalent bond to the surface oxygen while maintaining H-bonding with water. Adsorption energies were diminished by 70-90 kJ mol-1 when Obridge-bonded H+ ions transferred to the Oterminal manually. While dissociative adsorption of H3O+ ions is spontaneous at all surface coverages tested, the free energy was lowest at 75% coverage. Also, protonation of a completely pre-hydrated calcite surface leads to stronger interaction of water molecules with the surface. This unique outlook on hydrating calcite provides specific insights into biomineralization of this mineral, and helps depict further pH consequences in the field of biomaterial adsorption. Graphical abstract Dissociative adsorption of hydronium ion onto the surface of calcite.

Atomic White-Out: Enabling Atomic Circuitry through Mechanically Induced Bonding of Single Hydrogen Atoms to a Silicon Surface.

We report the mechanically induced formation of a silicon-hydrogen covalent bond and its application in engineering nanoelectronic devices. We show that using the tip of a noncontact atomic force microscope (NC-AFM), a single hydrogen atom could be vertically manipulated. When applying a localized electronic excitation, a single hydrogen atom is desorbed from the hydrogen-passivated surface and can be transferred to the tip apex, as evidenced from a unique signature in frequency shift curves. In the absence of tunnel electrons and electric field in the scanning probe microscope junction at 0 V, the hydrogen atom at the tip apex is brought very close to a silicon dangling bond, inducing the mechanical formation of a silicon-hydrogen covalent bond and the passivation of the dangling bond. The functionalized tip was used to characterize silicon dangling bonds on the hydrogen-silicon surface, which was shown to enhance the scanning tunneling microscope contrast, and allowed NC-AFM imaging with atomic and chemical bond contrasts. Through examples, we show the importance of this atomic-scale mechanical manipulation technique in the engineering of the emerging technology of on-surface dangling bond based nanoelectronic devices.

Indications of chemical bond contrast in AFM images of a hydrogen-terminated silicon surface.

The origin of bond-resolved atomic force microscope images remains controversial. Moreover, most work to date has involved planar, conjugated hydrocarbon molecules on a metal substrate thereby limiting knowledge of the generality of findings made about the imaging mechanism. Here we report the study of a very different sample; a hydrogen-terminated silicon surface. A procedure to obtain a passivated hydrogen-functionalized tip is defined and evolution of atomic force microscopy images at different tip elevations are shown. At relatively large tip-sample distances, the topmost atoms appear as distinct protrusions. However, on decreasing the tip-sample distance, features consistent with the silicon covalent bonds of the surface emerge. Using a density functional tight-binding-based method to simulate atomic force microscopy images, we reproduce the experimental results. The role of the tip flexibility and the nature of bonds and false bond-like features are discussed.

Time-Resolved Imaging of Negative Differential Resistance on the Atomic Scale.

Negative differential resistance remains an attractive but elusive functionality, so far only finding niche applications. Atom scale entities have shown promising properties, but the viability of device fabrication requires a fuller understanding of electron dynamics than has been possible to date. Using an all-electronic time-resolved scanning tunneling microscopy technique and a Green's function transport model, we study an isolated dangling bond on a hydrogen terminated silicon surface. A robust negative differential resistance feature is identified as a many body phenomenon related to occupation dependent electron capture by a single atomic level. We measure all the time constants involved in this process and present atomically resolved, nanosecond time scale images to simultaneously capture the spatial and temporal variation of the observed feature.

Dispersion-correcting potentials can significantly improve the bond dissociation enthalpies and noncovalent binding energies predicted by density-functional theory.

Dispersion-correcting potentials (DCPs) are atom-centered Gaussian functions that are applied in a manner that is similar to effective core potentials. Previous work on DCPs has focussed on their use as a simple means of improving the ability of conventional density-functional theory methods to predict the binding energies of noncovalently bonded molecular dimers. We show in this work that DCPs developed for use with the LC-ωPBE functional along with 6-31+G(2d,2p) basis sets are capable of simultaneously improving predicted noncovalent binding energies of van der Waals dimer complexes and covalent bond dissociation enthalpies in molecules. Specifically, the DCPs developed herein for the C, H, N, and O atoms provide binding energies for a set of 66 noncovalently bonded molecular dimers (the "S66" set) with a mean absolute error (MAE) of 0.21 kcal/mol, which represents an improvement of more than a factor of 10 over unadorned LC-ωPBE/6-31+G(2d,2p) and almost a factor of two improvement over LC-ωPBE/6-31+G(2d,2p) used in conjunction with the "D3" pairwise dispersion energy corrections. In addition, the DCPs reduce the MAE of calculated X-H and X-Y (X,Y = C, H, N, O) bond dissociation enthalpies for a set of 40 species from 3.2 kcal/mol obtained with unadorned LC-ωPBE/6-31+G(2d,2p) to 1.6 kcal/mol. Our findings demonstrate that broad improvements to the performance of DFT methods may be achievable through the use of DCPs.

Gas doping on the topological insulator Bi2Se3 surface.

Gas molecule doping on the topological insulator Bi(2)Se(3) surface with existing Se vacancies is investigated using first-principles calculations. Consistent with experiments, NO(2) and O(2) are found to occupy the Se vacancy sites, remove vacancy-doped electrons, and restore the band structure of a perfect surface. In contrast, NO and H(2) do not favor passivation of such vacancies. Interestingly we have revealed a NO(2) dissociation process that can well explain the speculative introduced "photon-doping" effect reported by recent experiments. Experimental strategies to validate this mechanism are presented. The choice and the effect of different passivators are discussed. This step paves the way for the usage of such materials in device applications utilizing robust topological surface states.

Strong spin-filtering and spin-valve effects in a molecular V-C(60)-V contact.

Motivated by the recent achievements in the manipulation of C(60) molecules in STM experiments, we study theoretically the structure and electronic properties of a C(60) molecule in an STM tunneljunction with a magnetic tip and magnetic adatom on a Cu(111) surface using first-principles calculations. For the case of a vanadium tip/adatom, we demonstrate how spin coupling between the magnetic V atoms, mediated by the C(60), can be observed in the electronic transport, which display a strong spin-filtering effect, allowing mainly majority-spin electrons to pass (>95%). Moreover, we find a significant change in the conductance between parallel and anti-parallel spin polarizations in the junction (86%) which suggests that STM experiments should be able to characterize the magnetism and spin coupling for these systems.

Electronic transport in natively oxidized silicon nanowires.

Silicon nanowires are widely used as active functional elements in advanced electronic devices, most notably in biological sensors. While surface oxidation of the wires occurs upon exposure to a wet environment, theoretical studies are often limited to ideally crystalline, H-terminated wire models. We present an accurate computational study of the electronic and transport properties of natively oxidized, ultrathin silicon nanowires including dopant elements. Comparisons with perfectly ordered and distorted H-terminated structures reveal an unexpected interplay of effects that oxidation-induced structural distortions and electronegative Si/SiO(x) interfaces have on the conductance of B- or P-doped nanowires.

Carbon nanostructures as catalytic support for chemiluminescence of sulfur compounds in a molecular emission cavity analysis system.

The effect of different substrates including stainless steel, activated carbon, single-walled carbon nanotubes (SWCNTs), multi-walled carbon nanotubes (MWCNTs), fullerenes (C60, C70, etc.) and SWCNTs doped with iron and palladium nanoparticles were compared for catalytic chemiluminescence reaction of sulfur compounds in a flame-containing cavity of molecular emission cavity analysis (MECA) system. Different forms of CNT substrates were fabricated using electric arc-discharge method. The blue emission of excited S2 was monitored using a CCD camera. The results demonstrate that, due to the high surface area, plenty of basal planes, high thermal conductivity, and high flexibility of the carbon nanostructure as appropriate support, carbon nanostructures play an important role in catalytic chemiluminescence emission of sulfur compounds in MECA. Moreover, the presence of metallic nanoparticles doped on carbon nanostructures enhances their catalytic effect. The results revealed that under similar conditions, SWCNTs/Pd doped nanoparticles, SWCNTs/Fe doped nanoparticles, SWCNTs, MWCNTs and fullerenes have the most catalytic effects on chemiluminescence of sulfur compounds, respectively.

Efficient organometallic spin filter between single-wall carbon nanotube or graphene electrodes.

We present a theoretical study of spin transport in a class of molecular systems consisting of an organometallic benzene-vanadium cluster placed in between graphene or single-wall carbon-nanotube-model contacts. Ab initio modeling is performed by combining spin density functional theory and nonequilibrium Green's function techniques. We consider weak and strong cluster-contact bonds. Depending on the bonding we find from 73% (strong bonds) up to 99% (weak bonds) spin polarization of the electron transmission, and enhanced polarization with increased cluster length.