Atomic resolution of dielectric with low temperature coefficient

Ba(6-3x)Nd(8+2x)Ti(18)O(54) (BNTl14) is a high permittivity dielectric with low temperature coefficient (Tcf). Low coefficient of change of dielectric permittivity with temperature (Tcf) is an unusual materials property. The research is aimed at discovering how atomic structure relates to temperature coefficient. Sub-Ångström scanning transmission electron microscopy (STEM) is used to measure mixed occupancy of Nd and Ba in atomic columns. It was expected that phase separation would occur to accommodate mixing of dissimilar ions. However no evidence of phase separation was found. There is a good image match between experiment and high angle annular dark field (HAADF) simulation. Vacancies and excess Ba ions appear to be randomly arranged on the available sites which would result in distortion of TiO6 octahedra. The low Tcf may arise from TiO6 distortion.

Visualisation of a 2′-5′ parallel stranded double helix at atomic resolution: crystal structure of cytidylyl-2′,5′-adenosine

X-ray crystallographlc studies on 3′–5′ ollgomers have provided a great deal of information on the stereochemistry and conformational flexibility of nucleic acids and polynucleotides. In contrast, there is very little Information available on 2′–5′ polynucleotides. We have now obtained the crystal structure of Cytidylyl-2′,5′-Adenoslne (C2′p5′A) at atomic resolution to establish the conformational differences between these two classes of polymers. The dlnucleoside phosphate crystallises in the monocllnlc space group C2, with a = 33.912(4)Å, b =16.824(4)Å, c = 12.898(2)Å and 0 = 112.35(1) with two molecules in the asymmetric unit. Spectacularly, the two independent C2′p5′A molecules in the asymmetric unit form right handed miniature parallel stranded double helices with their respective crystallographic two fold (b axis) symmetry mates. Remarkably, the two mini duplexes are almost indistinguishable. The cytosines and adenines form self-pairs with three and two hydrogen bonds respectively. The conformation of the C and A residues about the glycosyl bond is anti same as in the 3′–5′ analog but contrasts the anti and syn geometry of C and A residues in A2′p5′C. The furanose ring conformation is C3′endo, C2′endo mixed puckering as in the C3′p5′A-proflavine complex. A comparison of the backbone torsion angles with other 2′–5′ dinucleoside structures reveals that the major deviations occur in the torsion angles about the C3′–C2′ and C4′-C3′ bonds. A right-handed 2′–5′ parallel stranded double helix having eight base pairs per turn and 45° turn angle between them has been constructed using this dinucleoside phosphate as repeat unit. A discussion on 2′–5′ parallel stranded double helix and its relevance to biological systems is presented.

Studying atomic-resolution by X-ray fluorescence holography

In this work, the results of numerical simulations of X-ray fluorescence holograms and the reconstructed atomic images for Fe single crystal are given. The influences of the recording angles ranges and the polarization effect on the reconstruction of the atomic images are discussed. The process for removing twin images by multiple energy fluorescence holography and expanding the energy range of the incident X-rays to improve the resolution of the reconstructed images is presented. (c) 2005 Elsevier B.V. All rights reserved.

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.

Electron microscopy of high pressure frozen samples: bridging the gap between cellular ultrastructure and atomic resolution

Transmission electron microscopy has provided most of what is known about the ultrastructural organization of tissues, cells, and organelles. Due to tremendous advances in crystallography and magnetic resonance imaging, almost any protein can now be modeled at atomic resolution. To fully understand the workings of biological "nanomachines" it is necessary to obtain images of intact macromolecular assemblies in situ. Although the resolution power of electron microscopes is on the atomic scale, in biological samples artifacts introduced by aldehyde fixation, dehydration and staining, but also section thickness reduces it to some nanometers. Cryofixation by high pressure freezing circumvents many of the artifacts since it allows vitrifying biological samples of about 200 mum in thickness and immobilizes complex macromolecular assemblies in their native state in situ. To exploit the perfect structural preservation of frozen hydrated sections, sophisticated instruments are needed, e.g., high voltage electron microscopes equipped with precise goniometers that work at low temperature and digital cameras of high sensitivity and pixel number. With them, it is possible to generate high resolution tomograms, i.e., 3D views of subcellular structures. This review describes theory and applications of the high pressure cryofixation methodology and compares its results with those of conventional procedures. Moreover, recent findings will be discussed showing that molecular models of proteins can be fitted into depicted organellar ultrastructure of images of frozen hydrated sections. High pressure freezing of tissue is the base which may lead to precise models of macromolecular assemblies in situ, and thus to a better understanding of the function of complex cellular structures.

Protein folding from a highly disordered denatured state: The folding pathway of chymotrypsin inhibitor 2 at atomic resolution

Previous experimental and theoretical studies have produced high-resolution descriptions of the native and folding transition states of chymotrypsin inhibitor 2 (CI2). In similar fashion, here we use a combination of NMR experiments and molecular dynamics simulations to examine the conformations populated by CI2 in the denatured state. The denatured state is highly unfolded, but there is some residual native helical structure along with hydrophobic clustering in the center of the chain. The lack of persistent nonnative structure in the denatured state reduces barriers that must be overcome, leading to fast folding through a nucleation–condensation mechanism. With the characterization of the denatured state, we have now completed our description of the folding/unfolding pathway of CI2 at atomic resolution.

Monitoring the GAP catalyzed H-Ras GTPase reaction at atomic resolution in real time

The molecular reaction mechanism of the GTPase-activating protein (GAP)-catalyzed GTP hydrolysis by Ras was investigated by time resolved Fourier transform infrared (FTIR) difference spectroscopy using caged GTP (P3-1-(2-nitro)phenylethyl guanosine 5′-O-triphosphate) as photolabile trigger. This approach provides the complete GTPase reaction pathway with time resolution of milliseconds at the atomic level. Up to now, one structural model of the GAP⋅Ras⋅GDP⋅AlFx transition state analog is known, which represents a “snap shot” along the reaction-pathway. As now revealed, binding of GAP to Ras⋅GTP shifts negative charge from the γ to β phosphate. Such a shift was already identified by FTIR in GTP because of Ras binding and is now shown to be enhanced by GAP binding. Because the charge distribution of the GAP⋅Ras⋅GTP complex thus resembles a more dissociative-like transition state and is more like that in GDP, the activation free energy is reduced. An intermediate is observed on the reaction pathway that appears when the bond between β and γ phosphate is cleaved. In the intermediate, the released Pi is strongly bound to the protein and surprisingly shows bands typical of those seen for phosphorylated enzyme intermediates. All these results provide a mechanistic picture that is different from the intrinsic GTPase reaction of Ras. FTIR analysis reveals the release of Pi from the protein complex as the rate-limiting step for the GAP-catalyzed reaction. The approach presented allows the study not only of single proteins but of protein–protein interactions without intrinsic chromophores, in the non-crystalline state, in real time at the atomic level.

Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein.

The Zn(Scys)4 unit is present in numerous proteins, where it assumes structural, regulatory, or catalytic roles. The same coordination is found naturally around iron in rubredoxins, several structures of which have been refined at resolutions of, or near to, 1 A. The fold of the small protein rubredoxin around its metal ion is an excellent model for many zinc finger proteins. Zn-substituted rubredoxin and its Fe-containing counterpart were both obtained as the products of the expression in Escherichia coli of the rubredoxin-encoding gene from Clostridium pasteurianum. The structures of both proteins have been refined with an anisotropic model at atomic resolution (1.1 A, R = 8.3% for Fe-rubredoxin, and 1.2 A, R = 9.6% for Zn-rubredoxin) and are very similar. The most significant differences are increased lengths of the M-S bonds in Zn-rubredoxin (average length, 2.345 A) as compared with Fe-rubredoxin (average length, 2.262 A). An increase of the CA-CB-SG-M dihedral angles involving Cys-6 and Cys-39, the first cysteines of each of the Cys-Xaa-Xaa-Cys metal binding motifs, has been observed. Another consequence of the replacement of iron by zinc is that the region around residues 36-46 undergoes larger displacements than the remainder of the polypeptide chain. Despite these changes, the main features of the FeS4 site, namely a local 2-fold symmetry and the characteristic network of N-H...S hydrogen bonds, are conserved in the ZnS4 site. The Zn-substituted rubredoxin provides the first precise structure of a Zn(Scys)4 unit in a protein. The nearly identical fold of rubredoxin around iron or zinc suggests that at least in some of the sites where the metal has mainly a structural role-e.g., zinc fingers-the choice of the relevant metal may be directed by its cellular availability and mobilization processes rather than by its chemical nature.

Atomic resolution studies of oxide superlattices and ultrathin films

The ability to grow ultrathin films layer-by-layer with well-defined epitaxial relationships has allowed research groups worldwide to grow a range of artificial films and superlattices, first for semiconductors, and now with oxides. In the oxides thin film research community, there have been concerted efforts recently to develop a number of epitaxial oxide systems grown on single crystal oxide substrates that display a wide variety of novel interfacial functionality, such as enhanced ferromagnetic ordering, increased charge carrier density, increased optical absorption, etc, at interfaces. The magnitude of these novel properties is dependent upon the structure of thin films, especially interface sharpness, intermixing, defects, and strain, layering sequence in the case of superlattices and the density of interfaces relative to the film thicknesses. To understand the relationship between the interfacial thin film oxide atomic structure and its properties, atomic scale characterization is required. Transmission electron microscopy (TEM) offers the ability to study interfaces of films at high resolution. Scanning transmission electron microscopy (STEM) allows for real space imaging of materials with directly interpretable atomic number contrast. Electron energy loss spectroscopy (EELS), together with STEM, can probe the local chemical composition as well as local electronic states of transition metals and oxygen. Both techniques have been significantly improved by aberration correctors, which reduce the probe size to 1 Å, or less. Aberration correctors have thus made it possible to resolve individual atomic columns, and possibly probe the electronic structure at atomic scales. Separately, using electron probe forming lenses, structural information such as the crystal structure, strain, lattice mismatches, and superlattice ordering can be measured by nanoarea electron diffraction (NED). The combination of STEM, EELS, and NED techniques allows us to gain a fundamental understanding of the properties of oxide superlattices and ultrathin films and their relationship with the corresponding atomic and electronic structure. In this dissertation, I use the aforementioned electron microscopy techniques to investigate several oxide superlattice and ultrathin film systems. The major findings are summarized below. These results were obtained with stringent specimen preparation methods that I developed for high resolution studies, which are described in Chapter 2. The essential materials background and description of electron microscopy techniques are given in Chapter 1 and 2. In a LaMnO3-SrMnO3 superlattice, we demonstrate the interface of LaMnO3-SrMnO3 is sharper than the SrMnO3-LaMnO3 interface. Extra spectral weights in EELS are confined to the sharp interface, whereas at the rougher interface, the extra states are either not present or are not confined to the interface. Both the structural and electronic asymmetries correspond to asymmetric magnetic ordering at low temperature. In a short period LaMnO3-SrTiO3 superlattice for optical applications, we discovered a modified band structure in SrTiO3 ultrathin films relative to thick films and a SrTiO3 substrate, due to charge leakage from LaMnO3 in SrTiO3. This was measured by chemical shifts of the Ti L and O K edges using atomic scale EELS. The interfacial sharpness of LaAlO3 films grown on SrTiO3 was investigated by the STEM/EELS technique together with electron diffraction. This interface, when prepared under specific conditions, is conductive with high carrier mobility. Several suggestions for the conductive interface have been proposed, including a polar catastrophe model, where a large built-in electric field in LaAlO3 films results in electron charge transfer into the SrTiO3 substrate. Other suggested possibilities include oxygen vacancies at the interface and/or oxygen vacancies in the substrate. The abruptness of the interface as well as extent of intermixing has not been thoroughly investigated at high resolution, even though this can strongly influence the electrical transport properties. We found clear evidence for cation intermixing through the LaAlO3-SrTiO3 interface with high spatial resolution EELS and STEM, which contributes to the conduction at the interface. We also found structural defects, such as misfit dislocations, which leads to increased intermixing over coherent interfaces.

Wrinkling of Atomic Planes in Ultrathin Au Nanowires

A detailed understanding of structure and stability of nanowires is critical for applications. Atomic resolution imaging of ultrathin single crystalline Au nanowires using aberration-corrected microscopy reveals an intriguing relaxation whereby the atoms in the close-packed atomic planes normal to the growth direction are displaced in the axial direction leading to wrinkling of the (111) atomic plane normal to the wire axis. First-principles calculations of the structure of such nanowires confirm this wrinkling phenomenon, whereby the close-packed planes relax to form saddle-like surfaces. Molecular dynamics studies of wires with varying diameters and different bounding surfaces point to the key role of surface stress on the relaxation process. Using continuum mechanics arguments, we show that the wrinkling arises due to anisotropy in the surface stresses and in the elastic response, along with the divergence of surface-induced bulk stress near the edges of a faceted structure. The observations provide new understanding on the equilibrium structure of nanoscale systems and could have important implications for applications in sensing and actuation.

Shifting atomic patterns: on the origin of the different atomic-scale patterns of graphite as observed using scanning tunnelling microscopy.

We present an in-depth study of the myriad atomically resolved patterns observed on graphite using the scanning tunnelling microscope (STM) over the past three decades. Through the use of highly resolved atomic resolution images, we demonstrate how the interactions between the different graphene layers comprising graphite affect the local surface atomic charge density and its resulting symmetry orientation, with particular emphasis on interactions that are thermodynamically unstable. Moreover, the interlayer graphene coupling is controlled experimentally by varying the tip-surface interaction, leading to associated changes in the atomic patterns. The images are corroborated by first-principles calculations, further validating our claim that surface graphene displacement, coming both from lateral and vertical displacement of the top graphene layer, forms the basis of the rich variety of atomic patterns observed in STM experiments on graphite.

Paving the way to nanoionics: atomic origin of barriers for ionic transport through interfaces

The blocking of ion transport at interfaces strongly limits the performance of electrochemical nanodevices for energy applications. The barrier is believed to arise from space-charge regions generated by mobile ions by analogy to semiconductor junctions. Here we show that something different is at play by studying ion transport in a bicrystal of yttria (9% mol) stabilized zirconia (YSZ), an emblematic oxide ion conductor. Aberration-corrected scanning transmission electron microscopy (STEM) provides structure and composition at atomic resolution, with the sensitivity to directly reveal the oxygen ion profile. We find that Y segregates to the grain boundary at Zr sites, together with a depletion of oxygen that is confined to a small length scale of around 0.5 nm. Contrary to the main thesis of the space-charge model, there exists no evidence of a long-range O vacancy depletion layer. Combining ion transport measurements across a single grain boundary by nanoscale electrochemical strain microscopy (ESM), broadband dielectric spectroscopy measurements, and density functional calculations, we show that grain-boundary-induced electronic states act as acceptors, resulting in a negatively charged core. Ultimately, it is this negative charge which gives rise to the barrier for ion transport at the grain boundary

Phase-Locked loops lock-in range in Frequency Modulated-Atomic Force Microscope nonlinear control system

Since the mid 1980s the Atomic Force Microscope is one the most powerful tools to perform surface investigation, and since 1995 Non-Contact AFM achieved true atomic resolution. The Frequency-Modulated Atomic Force Microscope (FM-AFM) operates in the dynamic mode, which means that the control system of the FM-AFM must force the micro-cantilever to oscillate with constant amplitude and frequency. However, tip-sample interaction forces cause modulations in the microcantilever motion. A Phase-Locked loop (PLL) is used to demodulate the tip-sample interaction forces from the microcantilever motion. The demodulated signal is used as the feedback signal to the control system, and to generate both topographic and dissipation images. As a consequence, a proper design of the PLL is vital to the FM-AFM performance. In this work, using bifurcation analysis, the lock-in range of the PLL is determined as a function of the frequency shift (Q) of the microcantilever and of the other design parameters, providing a technique to properly design the PLL in the FM-AFM system. (C) 2011 Elsevier B.V. All rights reserved.

Phase-Locked Loop design applied to frequency-modulated atomic force microscope

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Simulations of the Frequency Modulated Atomic Force Microscope (FM-AFM) nonlinear control system

The Frequency Modulated - Atomic Force Microscope (FM-AFM) is apowerful tool to perform surface investigation with true atomic resolution. The controlsystem of the FM-AFM must keep constant both the frequency and amplitude ofoscillation of the microcantilever during the scanning process of the sample. However,tip and sample interaction forces cause modulations in the microcantilever motion.A Phase-Locked Loop (PLL) is used as a demodulator and to generate feedback signalto the FM-AFM control system. The PLL performance is vital to the FM-AFMperformace since the image information is in the modulated microcantilever motion.Nevertheless, little attention is drawn to PLL performance in the FM-AFM literature.Here, the FM-AFM control system is simulated, comparing the performancefor di erent PLL designs.