Imaging the atomic structure of activated carbon

The precise atomic structure of activated carbon is unknown, despite its huge commercial importance in the purification of air and water. Diffraction methods have been extensively applied to the study of microporous carbons, but cannot provide an unequivocal identification of their structure. Here we show that the structure of a commercial activated carbon can be imaged directly using aberration-corrected transmission electron microscopy. Images are presented both of the as-produced carbon and of the carbon following heat treatment at 2000 degrees C. In the 2000 degrees C carbon clear evidence is found for the presence of pentagonal rings, suggesting that the carbons have a fullerene-related structure. Such a structure would help to explain the properties of activated carbon, and would also have important implications for the modelling of adsorption on microporous carbons.

The atomic structure of low-index surfaces of the intermetallic compound InPd

The intermetallic compound InPd (CsCl type of crystal structure with a broad compositional range) is considered as a candidate catalyst for the steam reforming of methanol. Single crystals of this phase have been grown to study the structure of its three low-index surfaces under ultra-high vacuum conditions, using low energy electron diffraction (LEED), X-ray photoemission spectroscopy (XPS), and scanning tunneling microscopy (STM). During surface preparation, preferential sputtering leads to a depletion of In within the top few layers for all three surfaces. The near-surface regions remain slightly Pd-rich until annealing to ∼580 K. A transition occurs between 580 and 660 K where In segregates towards the surface and the near-surface regions become slightly In-rich above ∼660 K. This transition is accompanied by a sharpening of LEED patterns and formation of flat step-terrace morphology, as observed by STM. Several superstructures have been identified for the different surfaces associated with this process. Annealing to higher temperatures (≥750 K) leads to faceting via thermal etching as shown for the (110) surface, with a bulk In composition close to the In-rich limit of the existence domain of the cubic phase. The Pd-rich InPd(111) is found to be consistent with a Pd-terminated bulk truncation model as shown by dynamical LEED analysis while, after annealing at higher temperature, the In-rich InPd(111) is consistent with an In-terminated bulk truncation, in agreement with density functional theory (DFT) calculations of the relative surface energies. More complex surface structures are observed for the (100) surface. Additionally, individual grains of a polycrystalline sample are characterized by micro-spot XPS and LEED as well as low-energy electron microscopy. Results from both individual grains and “global” measurements are interpreted based on comparison to our single crystals findings, DFT calculations and previous literature.

Imaging the structure of activated carbon using aberration corrected TEM

The precise atomic structure of activated carbon is unknown, despite its commercial importance. Here we show that the structure of a commercial activated carbon can be imaged directly using aberration corrected transmission electron microscopy. Images are presented both of the as-produced carbon and of the carbon following heat- treatment at 2000°C. In the 2000°C carbon clear evidence is found for the presence of pentagonal rings, suggesting that the carbons have a fullerene-related structure.

Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy

To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl–DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium.

Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution

Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 Angstrom. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)-C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson-Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7-N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration.

Surface structure of thin asymmetric PS-b-PMMA diblock copolymers investigated by atomic force microscopy

Asymmetric poly(styrene-b-methyl methacrylate) (PS-b-PMMA) diblock copolymers of molecular weight M-n = 29,700g mol(-1) (M-PS = 9300 g mol(-1) M-PMMA = 20,100 g mol(-1), PD = 1.15, chi(PS) = 0.323, chi(PMMA) = 0.677) and M-n = 63,900 g mol(-1) (M-PS = 50,500 g mol(-1), M-PMMA = 13,400 g mol(-1), PD = 1.18, chi(PS) = 0.790, chi(PMMA) = 0.210) were prepared via reversible addition-fragmentation chain transfer (RAFT) polymerization. Atomic force microscopy (AFM) was used to investigate the surface structure of thin films, prepared by spin-coating the diblock copolymers on a silicon substrate. We show that the nanostructure of the diblock copolymer depends on the molecular weight and volume fraction of the diblock copolymers. We observed a perpendicular lamellar structure for the high molar mass sample and a hexagonal-packed cylindrical patterning for the lower molar mass one. Small-angle X-ray scattering investigation of these samples without annealing did not reveal any ordered structure. Annealing of PS-b-PMMA samples at 160 degrees C for 24 h led to a change in surface structure.

Model catalyst studies of the strong metal-support interaction: Surface structure identified by STM on Pd nanoparticles on TiO2(110)

Model catalysts of Pd nanoparticles and films on TiO2 (I 10) were fabricated by metal vapour deposition (MVD). Molecular beam measurements show that the particles are active for CO adsorption, with a global sticking probability of 0.25, but that they are deactivated by annealing above 600 K, an effect indicative of SMSI. The Pd nanoparticles are single crystals oriented with their (I 11) plane parallel to the surface plane of the titania. Analysis of the surface by atomic resolution STM shows that new structures have formed at the surface of the Pd nanoparticles and films after annealing above 800 K. There are only two structures, a zigzag arrangement and a much more complex "pinwheel" structure. The former has a unit cell containing 7 atoms, and the latter is a bigger unit cell containing 25 atoms. These new structures are due to an overlayer of titania that has appeared on the surface of the Pd nanoparticles after annealing, and it is proposed that the surface layer that causes the SMSI effect is a mixed alloy of Pd and Ti, with only two discrete ratios of atoms: Pd/Ti of 1: 1 (pinwheel) and 1:2 (zigzag). We propose that it is these structures that cause the SMSI effect. (c) 2005 Elsevier Inc. All rights reserved.

The surface geometries of the medium and high coverage carbon monoxide structures c(2 × 4)–(2CO) and p(root7- x root7)R19°–(4CO) structure

The surface geometries of the p (root7- x root7)R19degrees-(4CO) and c(2 x 4)-(2CO) layers on Ni {111} and the clean Ni {111} surface were determined by low energy electron diffraction structure analysis. For the clean surface small but significant contractions of d(12) and d(23) (both 2.02 Angstrom) were found with respect to the bulk interlayer distance (2.03 Angstrom). In the c(2 x 4)-(2CO) structure these distances are expanded, with values of d(12) = 2.08 Angstrom and d(23) = 2.06 Angstrom and buckling of 0.08 and 0.02 Angstrom, respectively, in the first and second layer. CO resides near hcp and fcc hollow sites with relatively large lateral shifts away from the ideal positions leading to unequal C-Ni bond lengths between 1.76 and 1.99 Angstrom. For the p(root7- x root7-)R19'-(4CO) layer two best fit geometries were found, which agree in most of their atomic positions, except for one out of four CO molecules, which is either near atop or between bridge and atop. The remaining three molecules reside near hcp and fcc sites, again with large lateral deviations from their ideal positions. The average C Ni bond length for these molecules is, however, the same as for CO on hollow sites at low coverage. The average CNi bond length at hollow sites, the interlayer distances, and buckling in the first Ni layer are similar to the c(2 x 4)(2CO) geometry, only the buckling in the second layer (0.08 Angstrom) is significantly larger. Lateral and vertical shifts of the Ni atoms in the first layer lead to unsymmetric environments for the CO molecules, which can be regarded as an imprint of the chiral p(root7- x root7-)R19degrees lattice geometry onto the substrate.

Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand

We describe a crystal structure, at atomic resolution (1.1 Å, 100 K), of a ruthenium polypyridyl complex bound to duplex DNA, in which one ligand acts as a wedge in the minor groove, resulting in the 51° kinking of the double helix. The complex cation Λ-[Ru(1,4,5,8-tetraazaphenanthrene)2(dipyridophenazine)]2+ crystallizes in a 1∶1 ratio with the oligonucleotide d(TCGGCGCCGA) in the presence of barium ions. Each complex binds to one duplex by intercalation of the dipyridophenazine ligand and also by semiintercalation of one of the orthogonal tetraazaphenanthrene ligands into a second symmetrically equivalent duplex. The result is noncovalent cross-linking and marked kinking of DNA.

X‑ray crystal structure of rac-[Ru(phen)2dppz]2+ with d(ATGCAT)2 shows enantiomer orientations and water ordering

We report an atomic resolution X-ray crystal structure containing both enantiomers of rac-[Ru(phen)2dppz]2+ with the d-(ATGCAT)2 DNA duplex (phen = phenanthroline; dppz = dipyridophenazine). The first example of any enantiomeric pair crystallized with a DNA duplex shows different orientations of the Λ and Δ binding sites, separated by a clearly defined structured water monolayer. Job plots show that the same species is present in solution. Each enantiomer is bound at a TG/CA step and shows intercalation from the minor groove. One water molecule is directly located on one phenazine N atom in the Δ-enantiomer only.

On the difficulties of present theoretical models to predict the oxidation state of atomic Au adsorbed on regular sites of CeO2(111)

The electronic structure and oxidation state of atomic Au adsorbed on a perfect CeO2(111) surface have been investigated in detail by means of periodic density functional theory-based calculations, using the LDA+U and GGA+U potentials for a broad range of U values, complemented with calculations employing the HSE06 hybrid functional. In addition, the effects of the lattice parameter a0 and of the starting point for the geometry optimization have also been analyzed. From the present results we suggest that the oxidation state of single Au atoms on CeO2(111) predicted by LDA+U, GGA+U, and HSE06 density functional calculations is not conclusive and that the final picture strongly depends on the method chosen and on the construction of the surface model. In some cases we have been able to locate two well-defined states which are close in energy but with very different electronic structure and local geometries, one with Au fully oxidized and one with neutral Au. The energy difference between the two states is typically within the limits of the accuracy of the present exchange-correlation potentials, and therefore, a clear lowest-energy state cannot be identified. These results suggest the possibility of a dynamic distribution of Au0 and Au+ atomic species at the regular sites of the CeO2(111) surface.

Local and average structure in zinc cyanide: towards an understanding of the atomistic origin of negative thermal expansion

Neutron diffraction at 11.4 and 295 K and solid-state 67Zn NMR are used to determine both the local and average structures in the disordered, negative thermal expansion (NTE) material, Zn(CN)2. Solid-state NMR not only confirms that there is head-to-tail disorder of the C≡N groups present in the solid, but yields information about the relative abundances of the different Zn(CN)4-n(NC)n tetrahedral species, which do not follow a simple binomial distribution. The Zn(CN)4 and Zn(NC)4 species occur with much lower probabilities than are predicted by binomial theory, supporting the conclusion that they are of higher energy than the other local arrangements. The lowest energy arrangement is Zn(CN)2(NC)2. The use of total neutron diffraction at 11.4 K, with analysis of both the Bragg diffraction and the derived total correlation function, yields the first experimental determination of the individual Zn−N and Zn−C bond lengths as 1.969(2) and 2.030(2) Å, respectively. The very small difference in bond lengths, of ~0.06 Å, means that it is impossible to obtain these bond lengths using Bragg diffraction in isolation. Total neutron diffraction also provides information on both the average and local atomic displacements responsible for NTE in Zn(CN)2. The principal motions giving rise to NTE are shown to be those in which the carbon and nitrogen atoms within individual Zn−C≡N−Zn linkages are displaced to the same side of the Zn···Zn axis. Displacements of the carbon and nitrogen atoms to opposite sides of the Zn···Zn axis, suggested previously in X-ray studies as being responsible for NTE behavior, in fact make negligible contribution at temperatures up to 295 K.

Structure and stress of Re(11%21); chiral terraces at a racemic surface

The surface structure and morphology of the clean Re(11%21) surface has been investigated through combined low energy electron diffraction intensity analysis of data taken at multiple angles of incidence, scanning tunneling microscopy, and first-principles density functional calculations. The results show how this globally racemic surface terminates in two chirally distinct terraces, which show largescale out-of-plane atomic relaxations and in-plane lateral movement of the uppermost atoms. We further identify and discuss the initial stages of step bunching upon adsorption of oxygen that leads ultimately to the large-scale faceting of the surface. Finally, we present calculations of surface stress and the response to applied surface strain, which suggest routes to the exertion of control over the expression of chirality at the surface.