Energetics of atomic scale structure changes in graphene.

The presence of defects in graphene has an essential influence on its physical and chemical properties. The formation, behaviour and healing of defects are determined by energetic characteristics of atomic scale structure changes. In this article, we review recent studies devoted to atomic scale reactions during thermally activated and irradiation-induced processes in graphene. The formation energies of vacancies, adatoms and topological defects are discussed. Defect formation, healing and migration are quantified in terms of activation energies (barriers) for thermally activated processes and by threshold energies for processes occurring under electron irradiation. The energetics of defects in the graphene interior and at the edge is analysed. The effects of applied strain and a close proximity of the edge on the energetics of atomic scale reactions are overviewed. Particular attention is given to problems where further studies are required.

Epitaxial Retrieval of a Disappearing Polymorph.

Recrystallization of [PdCl2([9]aneS2O)] ([9]aneS2O = 1-oxa-4,7-dithiacyclononane), 1, and [PtCl2([9]aneS2O)], 2, by diffusion of Et2O vapor into solutions of the complexes in MeNO2 yielded three phases of 1 and two phases of 2. The known phase of 1, herein designated α-1, was obtained under ambient conditions. A second phase, designated ß-1, was initially also obtained by this method; however, following the advent of a third phase, γ-1, all subsequent efforts over a period of a year to crystallize ß-1 yielded either γ-1, obtained by carrying out the recrystallization at elevated temperature, or α-1, commonly found throughout the study. This persistent absence of a phase which could initially be crystallized with ease led us to the conclusion that ß-1 was an example of a "disappearing polymorph". The first phase obtained of 2, designated α-2, was obtained by recrystallization under ambient conditions and is isomorphous and isostructural with α-1. The second phase ß-2 was obtained by slight elevation of the recrystallization temperature and was found to be isomorphous and isostructural with ß-1. Subsequently, ß-2 was used to seed the growth of the disappearing polymorph ß-1. No third phase of 2 (γ-2) has been isolated thus far.

Isotope substitution extends the lifetime of organic molecules in transmission electron microscopy.

Structural characterisation of individual molecules by high-resolution transmission electron microscopy (HRTEM) is fundamentally limited by the element and electron energy-specific interactions of the material with the high energy electron beam. Here, the key mechanisms controlling the interactions between the e-beam and C-H bonds, present in all organic molecules, are examined, and the low atomic weight of hydrogen-resulting in its facile atomic displacement by the e-beam-is identified as the principal cause of the instability of individual organic molecules. It is demonstrated theoretically and proven experimentally that exchanging all hydrogen atoms within molecules with the deuterium isotope, and therefore doubling the atomic weight of the lightest atoms in the structure, leads to a more than two-fold increase in the stability of organic molecules in the e-beam. Substitution of H for D significantly reduces the amount of kinetic energy transferred from the e-beam to the atom (main factor contributing to stability) and also increases the barrier for bond dissociation, primarily due to the changes in the zero-point energy of the C-D vibration (minor factor). The extended lifetime of coronene-d12 , used as a model molecule, enables more precise analysis of the inter-molecular spacing and more accurate measurement of the molecular orientations.

Adsorbate-induced curvature and stiffening of graphene.

The adsorption of the alkane tetratetracontane (TTC, C44H90) on graphene induces the formation of a curved surface stabilized by a gain in adsorption energy. This effect arises from a curvature-dependent variation of a moiré pattern due to the mismatch of the carbon-carbon separation in the adsorbed molecule and the period of graphene. The effect is observed when graphene is transferred onto a deformable substrate, which in our case is the interface between water layers adsorbed on mica and an organic solvent, but is not observed on more rigid substrates such as boron nitride. Our results show that molecular adsorption can be influenced by substrate curvature, provide an example of two-dimensional molecular self-assembly on a soft, responsive interface, and demonstrate that the mechanical properties of graphene may be modified by molecular adsorption, which is of relevance to nanomechanical systems, electronics, and membrane technology.

A robust binary supramolecular organic framework (SOF) with high CO2 adsorption and selectivity.

A robust binary hydrogen-bonded supramolecular organic framework (SOF-7) has been synthesized by solvothermal reaction of 1,4-bis-(4-(3,5-dicyano-2,6-dipyridyl)dihydropyridyl)benzene (1) and 5,5'-bis-(azanediyl)-oxalyl-diisophthalic acid (2). Single crystal X-ray diffraction analysis shows that SOF-7 comprises 2 and 1,4-bis-(4-(3,5-dicyano-2,6-dipyridyl)pyridyl)benzene (3); the latter formed in situ from the oxidative dehydrogenation of 1. SOF-7 shows a three-dimensional four-fold interpenetrated structure with complementary O-H···N hydrogen bonds to form channels that are decorated with cyano and amide groups. SOF-7 exhibits excellent thermal stability and solvent and moisture durability as well as permanent porosity. The activated desolvated material SOF-7a shows high CO2 adsorption capacity and selectivity compared with other porous organic materials assembled solely through hydrogen bonding.

Analysis of high and selective uptake of CO2 in an oxamide-containing {Cu2(OOCR)4}-based metal-organic framework.

The porous framework [Cu2(H2O)2L]⋅4 H2O⋅2 DMA (H4L = oxalylbis(azanediyl)diisophthalic acid; DMA = N,N-dimethylacetamide), denoted NOTT-125, is formed by connection of {Cu2(RCOO)4} paddlewheels with the isophthalate linkers in L(4-). A single crystal structure determination reveals that NOTT-125 crystallises in monoclinic unit cell with a = 27.9161(6), b = 18.6627(4) and c = 32.3643(8) Å, ß = 112.655(3)°, space group P2(1)/c. The structure of this material shows fof topology, which can be viewed as the packing of two types of cages (cage A and cage B) in three-dimensional space. Cage A is constructed from twelve {Cu2(OOCR)4} paddlewheels and six linkers to form an ellipsoid-shaped cavity approximately 24.0 Šalong its long axis and 9.6 Šacross its central diameter. Cage B consists of six {Cu2(OOCR)4} units and twelve linkers and has a spherical diameter of 12.7 Štaking into account the van der Waals radii of the atoms. NOTT-125 incorporates oxamide functionality within the pore walls, and this, combined with high porosity in desolvated NOTT-125a, is responsible for excellent CO2 uptake (40.1 wt % at 273 K and 1 bar) and selectivity for CO2 over CH4 or N2. Grand canonical Monte Carlo (GCMC) simulations show excellent agreement with the experimental gas isotherm data, and a computational study of the specific interactions and binding energies of both CO2 and CH4 with the linkers in NOTT-125 reveals a set of strong interactions between CO2 and the oxamide motif that are not possible with a single amide.

A novel bismuth-based metal-organic framework for high volumetric methane and carbon dioxide adsorption.

Solvothermal reaction of H4L (L = biphenyl-3,3',5,5'-tetracarboxylate) and Bi(NO3)3⋅(H2O)5 in a mixture of DMF/MeCN/H2O in the presence of piperazine and nitric acid at 100 °C for 10 h affords the solvated metal-organic polymer [Bi2(L)1.5(H2O)2]⋅(DMF)3.5⋅(H2O)3 (NOTT-220-solv). A single crystal X-ray structure determination confirms that it crystallises in space group P2/c and has a neutral and non-interpenetrated structure comprising binuclear {Bi2} centres bridged by tetracarboxylate ligands. NOTT-220-solv shows a 3,6-connected network having a framework topology with a {4⋅6(2)}2{4(2)⋅6(5)⋅8(8)}{6(2)⋅8} point symbol. The desolvated material NOTT-220a shows exceptionally high adsorption uptakes for CH4 and CO2 on a volumetric basis at moderate pressures and temperatures with a CO2 uptake of 553 g L(-1) (20 bar, 293 K) with a saturation uptake of 688 g L(-1) (1 bar, 195 K). The corresponding CH4 uptake was measured as 165 V(STP)/V (20 bar, 293 K) and 189 V(STP/V) (35 bar, 293 K) with a maximum CH4 uptake for NOTT-220a recorded at 20 bar and 195 K to be 287 V(STP)/V, while H2 uptake of NOTT-220a at 20 bar, 77 K is 42 g L(-1). These gas uptakes have been modelled by grand canonical Monte Carlo (GCMC) and density functional theory (DFT) calculations, which confirm the experimental data and give insights into the nature of the binding sites of CH4 and CO2 in this porous hybrid material.

Band gap expansion, shear inversion phase change behaviour and low-voltage induced crystal oscillation in low-dimensional tin selenide crystals.

In common with rocksalt-type alkali halide phases and also semiconductors such as GeTe and SnTe, SnSe forms all-surface two atom-thick low dimensional crystals when encapsulated within single walled nanotubes (SWNTs) with diameters below ∼1.4 nm. Whereas previous density functional theory (DFT) studies indicate that optimised low-dimensional trigonal HgTe changes from a semi-metal to a semi-conductor, low-dimensional SnSe crystals typically undergo band-gap expansion. In slightly wider diameter SWNTs (∼1.4-1.6 nm), we observe that three atom thick low dimensional SnSe crystals undergo a previously unobserved form of a shear inversion phase change resulting in two discrete strain states in a section of curved nanotube. Under low-voltage (i.e. 80-100 kV) imaging conditions in a transmission electron microscope, encapsulated SnSe crystals undergo longitudinal and rotational oscillations, possibly as a result of the increase in the inelastic scattering cross-section of the sample at those voltages.

Electrostatic force between a charged sphere and a planar surface: a general solution for dielectric materials.

Using the bispherical coordinate system, an analytical solution describing the electrostatic force between a charged dielectric sphere and a planar dielectric surface is presented. This new solution exhibits excellent numerical convergence, and is sufficiently general as to allow for the presence of charge on both the sphere and the surface. The solution has been applied to two examples of sphere-plane interactions chosen from the literature, namely, (i) a charged lactose sphere interacting with a neutral glass surface and (ii) a charged polystyrene sphere interacting with a neutral graphite surface. Theory suggests that in both cases the electrostatic force makes a major contribution to the experimentally observed attraction at short sphere-plane separations, and that the force is much longer ranged than previously suggested.

Surface-charge distribution on a dielectric sphere due to an external point charge: examples of C60 and C240 fullerenes.

An analytical solution for the distribution of surface charge on a dielectric sphere due to the presence of an external point charge is presented. This solution describes how charge on the surface of the sphere is polarised in the electric field into regions of negative and positive charge. The polarisation effect (distribution of surface charge) generally varies with the separation between the sphere and the charge, and it is particularly significant at very short separations. Results obtained from the classical electrostatic model are in qualitative agreement with density functional theory calculations of charge separation in C60 and C240 fullerenes in the presence of an external point charge. This suggests that, from an electrostatic point of view, in the static electric field of external charges these molecules exhibit dielectric behaviour.

Transition metal complexes of a salen-fullerene diad: redox and catalytically active nanostructures for delivery of metals in nanotubes.

A covalently-linked salen-C60 (H2L) assembly binds a range of transition metal cations in close proximity to the fullerene cage to give complexes [M(L)] (M=Mn, Co, Ni, Cu, Zn, Pd), [MCl(L)] (M=Cr, Fe) and [V(O)L]. Attaching salen covalently to the C60 cage only marginally slows down metal binding at the salen functionality compared to metal binding to free salen. Coordination of metal cations to salen-C60 introduces to these fullerene derivatives strong absorption bands across the visible spectrum from 400 to 630 nm, the optical features of which are controlled by the nature of the transition metal. The redox properties of the metal-salen-C60 complexes are determined both by the fullerene and by the nature of the transition metal, enabling the generation of a wide range of fullerene-containing charged species, some of which possess two or more unpaired electrons. The presence of the fullerene cage enhances the affinity of these complexes for carbon nanostructures, such as single-, double- and multiwalled carbon nanotubes and graphitised carbon nanofibres, without detrimental effects on the catalytic activity of the metal centre, as demonstrated in styrene oxidation catalysed by [Cu(L)]. This approach shows promise for applications of salen-C60 complexes in heterogeneous catalysis.

Approaches to modelling irradiation-induced processes in transmission electron microscopy.

The recent progress in high-resolution transmission electron microscopy (HRTEM) has given rise to the possibility of in situ observations of nanostructure transformations and chemical reactions induced by electron irradiation. In this article we briefly summarise experimental observations and discuss in detail atomistic modelling of irradiation-induced processes in HRTEM, as well as mechanisms of such processes recognised due to modelling. Accurate molecular dynamics (MD) techniques based on first principles or tight-binding models are employed in the analysis of single irradiation-induced events, and classical MD simulations are combined with a kinetic Monte Carlo algorithm to simulate continuous irradiation of nanomaterials. It has been shown that sulphur-terminated graphene nanoribbons are formed inside carbon nanotubes as a result of an irradiation-selective chemical reaction. The process of fullerene formation in HRTEM during continuous electron irradiation of a small graphene flake has been simulated, and mechanisms driving this transformation analysed.

Coulomb fission in dielectric dication clusters: experiment and theory on steps that may underpin the electrospray mechanism.

A series of five molecular dication clusters, (H2O)n(2+), (NH3)n(2+), (CH3CN)n(2+), (C5H5N)n(2+), and (C6H6)n(2+), have been studied for the purpose of identifying patterns of behavior close to the Rayleigh instability limit where the clusters might be expected to exhibit Coulomb fission. Experiments show that the instability limit for each dication covers a range of sizes and that on a time scale of 10(-4) s ions close to the limit can undergo either Coulomb fission or neutral evaporation. The observed fission pathways exhibit considerable asymmetry in the sizes of the charged fragments, and are associated with kinetic (ejection) energies of ~0.9 eV. Coulomb fission has been modeled using a theory recently formulated to describe how charged particles of dielectric materials interact with one another (Bichoutskaia et al. J. Chem. Phys. 2010, 133, 024105). The calculated electrostatic interaction energy between separating fragments accounts for the observed asymmetric fragmentation and for the magnitudes of the measured ejection energies. The close match between theory and experiment suggests that a significant fraction of excess charge resides on the surfaces of the fragment ions. The experiments provided support for a fundamental step in the electrospray ionization (ESI) mechanism, namely the ejection from droplets of small solvated charge carriers. At the same time, the theory shows how water and acetonitrile may behave slightly differently as ESI solvents. However, the theory also reveals deficiencies in the point-charge image-charge model that has previously been used to quantify Coulomb fission in the electrospray process.

Electronic excitation in bulk and nanocrystalline alkali halides.

The lowest energy excitations in bulk alkali halides are investigated by considering five different excited state descriptions. It is concluded that excitation transfers one outermost halide electron in the fully ionic ground state to the lowest energy vacant s orbital of one closest cation neighbour to produce the excited state termed dipolar. The excitation energies of seven salts were computed using shell model description of the lattice polarization produced by the effective dipole moment of the excited state neutral halogen-neutral metal pair. Ab initio uncorrelated short-range inter-ionic interactions computed from anion wavefunctions adapted to the in-crystal environment were augmented by short-range electron correlation contributions derived from uniform electron-gas density functional theory. Dispersive attractions including wavefunction overlap damping were introduced using reliable semi-empirical dispersion coefficients. The good agreement between the predicted excitation energies and experiment provides strong evidence that the excited state is dipolar. In alkali halide nanocrystals in which each ionic plane contains only four ions, the Madelung energies are significantly reduced compared with the bulk. This predicts that the corresponding intra-crystal excitation energies in the nanocrystals, where there are two excited states depending on whether the halide electron is transferred to a cation in the same or in the neighbouring plane, will be reduced by almost 2 eV. For such an encapsulated KI crystal, it has been shown that the greater polarization in the excited state of the bulk crystal causes these reductions to be lowered to a 1.1 eV-1.5 eV range for the case of charge transfer to a neighbouring plane. For intra-plane charge transfer the magnitude of the polarization energy is further reduced thus causing the excitation in these encapsulated materials to be only 0.2 eV less than in the bulk crystal.

Controlling the regioselectivity of the hydrosilylation reaction in carbon nanoreactors.

Hollow graphitized carbon nanofibres (GNF) are employed as nanoscale reaction vessels for the hydrosilylation of alkynes. The effects of confinement in GNF on the regioselectivity of addition to triple carbon-carbon bonds are explored. A systematic comparison of the catalytic activities of Rh and RhPt nanoparticles embedded in a nanoreactor with free-standing and surface-adsorbed nanoparticles reveals key mechanisms governing the regioselectivity. Directions of reactions inside GNF are largely controlled by the non-covalent interactions between reactant molecules and the nanofibre channel. The specific π-π interactions increase the local concentration of the aromatic reactant and thus promote the formation of the E isomer of the ß-addition product. In contrast, the presence of aromatic groups on both reactants (silane and alkyne) reverses the effect of confinement and favours the formation of the Z isomer due to enhanced interactions between aromatic groups in the cis-orientation with the internal graphitic step-edges of GNF. The importance of π-π interactions is confirmed by studying transformations of aliphatic reactants that show no measurable changes in regioselectivity upon confinement in carbon nanoreactors.

A partially interpenetrated metal-organic framework for selective hysteretic sorption of carbon dioxide.

The selective capture of carbon dioxide in porous materials has potential for the storage and purification of fuel and flue gases. However, adsorption capacities under dynamic conditions are often insufficient for practical applications, and strategies to enhance CO(2)-host selectivity are required. The unique partially interpenetrated metal-organic framework NOTT-202 represents a new class of dynamic material that undergoes pronounced framework phase transition on desolvation. We report temperature-dependent adsorption/desorption hysteresis in desolvated NOTT-202a that responds selectively to CO(2). The CO(2) isotherm shows three steps in the adsorption profile at 195 K, and stepwise filling of pores generated within the observed partially interpenetrated structure has been modelled by grand canonical Monte Carlo simulations. Adsorption of N(2), CH(4), O(2), Ar and H(2) exhibits reversible isotherms without hysteresis under the same conditions, and this allows capture of gases at high pressure, but selectively leaves CO(2) trapped in the nanopores at low pressure.

Size, structure, and helical twist of graphene nanoribbons controlled by confinement in carbon nanotubes.

Carbon nanotubes (CNTs) act as efficient nanoreactors, templating the assembly of sulfur-terminated graphene nanoribbons (S-GNRs) with different sizes, structures, and conformations. Spontaneous formation of nanoribbons from small sulfur-containing molecules is efficiently triggered by heat treatment or by an 80 keV electron beam. S-GNRs form readily in CNTs with internal diameters between 1 and 2 nm. Outside of this optimum range, nanotubes narrower than 1 nm do not have sufficient space to accommodate the 2D structure of S-GNRs, while nanotubes wider than 2 nm do not provide efficient confinement for unidirectional S-GNR growth, thus neither can support nanoribbon formation. Theoretical calculations show that the thermodynamic stability of nanoribbons is dependent on the S-GNR edge structure and, to a lesser extent, the width of the nanoribbon. For nanoribbons of similar widths, the polythiaperipolycene-type edges of zigzag S-GNRs are more stable than the polythiophene-type edges of armchair S-GNRs. Both the edge structure and the width define the electronic properties of S-GNRs which can vary widely from metallic to semiconductor to insulator. The encapsulated S-GNRs exhibit diverse dynamic behavior, including rotation, translation, and helical twisting inside the nanotube, which offers a mechanism for control of the electronic properties of the graphene nanoribbon via confinement at the nanoscale.

High-precision imaging of an encapsulated Lindqvist ion and correlation of its structure and symmetry with quantum chemical calculations.

Low-voltage aberration-corrected transmission electron microscopy (AC-TEM) of discrete Lindqvist [W(6)O(19)](2-) polyoxometalate ions inserted from an ethanolic solution of [NBu(4)](2)[W(6)O(19)] into double walled carbon nanotubes (DWNTs) allows a higher precision structural study to be performed than previously reported. W atom column separations within the constituent W(6) tungsten cage can now be visualized with sufficient clarity that reliable correlation with structural predictions from density functional theory (DFT) can be achieved. Calculations performed on [W(6)O(19)](2-) anions encapsulated in carbon nanotubes show good agreement with measured separations between pairs of W(2) atom columns imaged within equatorial WO(6) polyhedral pairs and also single W atom positions located within individual axial WO(6) octahedra. Structural data from the tilted chiral encapsulating DWNT were also determined simultaneously with the anion structural measurements, allowing the influence of the conformation of the encapsulating tubule to be included in the DFT calculation and compared against that of other candidate encapsulating nanotubes. Additional DFT calculations performed using Li(+) cations as a model for the [NBu(4)](+) counterions indicate that the latter may help to induce charge transfer between the DWNT and the [W(6)O(19)](2-) ion and this may help to constrain the motion of the ion in situ.

Interactions and reactions of transition metal clusters with the interior of single-walled carbon nanotubes imaged at the atomic scale.

Clusters of transition metals, W, Re, and Os, upon encapsulation within a single-walled carbon nanotube (SWNT) exhibit marked differences in their affinity and reactivity with the SWNT, as revealed by low-voltage aberration-corrected high-resolution transmission electron microscopy (AC-HRTEM). Activated by an 80 keV electron beam, W reacts only weakly with the SWNT, Re creates localized defects on the sidewall, and Os reacts readily causing extensive defect formation and constriction of the SWNT sidewall followed by total rupture of the tubular structure. AC-HRTEM imaging at the atomic level of structural transformations caused by metal-carbon bonding of π- and σ-character demonstrates what a crucial role these types of bonds have in governing the interactions between the transition metal clusters and the SWNT. The observed order of reactivity W < Re < Os is independent of the metal cluster size, shape, or orientation, and is related to the metal to nanotube bonding energy and the amount of electronic density transferred between metal and SWNT, both of which increase along the triad W, Re, Os, as predicted by first-principles density functional theory calculations. By selecting the appropriate energy of the electron beam, the metal-nanotube interactions can be controlled (activated or precluded). At an electron energy as low as 20 keV, no visible transformations in the nanotube in the vicinity of Os-clusters are observed.

Reactions of the inner surface of carbon nanotubes and nanoprotrusion processes imaged at the atomic scale.

Although the outer surface of single-walled carbon nanotubes (atomically thin cylinders of carbon) can be involved in a wide range of chemical reactions, it is generally thought that the interior surface of nanotubes is unreactive. In this study, we show that in the presence of catalytically active atoms of rhenium inserted into nanotubes, the nanotube sidewall can be engaged in chemical reactions from the inside. Aberration-corrected high-resolution transmission electron microscopy operated at 80 keV allows visualization of the formation of nanometre-sized hollow protrusions on the nanotube sidewall at the atomic level in real time at ambient temperature. Our direct observations and theoretical modelling demonstrate that the nanoprotrusions are formed in three stages: (i) metal-assisted deformation and rupture of the nanotube sidewall, (ii) the fast formation of a metastable asymmetric nanoprotrusion with an open edge and (iii) a slow symmetrization process that leads to a stable closed nanoprotrusion.