Heavy Atom Clusters Research Articles

COHERENCE ASSEMBLY IN STRUCTURES WITH HEAVY METAL CLUSTERS

A crystallographic analysis of two structures, monoclinic Nа8[{Re4(PO)4}(CN)12]⋅18H2O⋅CH3OH (I) and orthorhombic [(C6H5)4P]4 [Ta6I12(CN6)] (II), in which clusters of heavy atoms are significantly rarefied in space, so that their mutual arrangement cannot be explained only in terms of chemical interaction, has been performed. In structure I the crystallographic planes with a high atomic density (“skeletal” planes) are located in the regions with dhkl = 10–5.5 Å and dhkl 3 Å. The planes in which atomic groups [Re4(PO)4] (playing the role of unified bulk objects) are concentrated are in fact selected in the first region. In the second region, ordering is implemented at the level of individual atoms. A crystallographic analysis showed that the structure basis is determined by the sites of heavy Re cations. A striking fact is that there are 1152 subcells and only 32 Re atoms per unit cell in this structure; i.e., only the fraction of 1/144 provides the basis of structure stability. In structure II “skeletal” planes are also absent in the range of dhkl from ∼7 to ∼4 Å. The planes in the range of large dhkl characterize cluster ordering, whereas the planes in the range of small dhkl characterize ordering of separate atoms. The geometry and local symmetry of the cluster group (Та6 octahedron) dictates the basis of translational symmetry—unified sublattice of sites, most of which are free of these atoms. The considered structures demonstrate the key role of heavy atoms in the formation of translational symmetry—the fundamental difference of the crystalline state from other condensed states. The newly formed structure retains partially local symmetry of cores (templates) of atomic groups, bound by strong chemical interactions, including the interactions between heavy and light atoms. The process of formation of a crystal structure from randomly oriented and randomly located templates—coherence assembly—is implemented according to the laws of dynamics of elastic media, where masses of atoms rather than their chemical characteristics are important.

The molecular mechanism of the ligand exchange reaction of an antibody against a glutathione-coated gold cluster

The labeling of proteins with heavy atom clusters is of paramount importance in biomedical research, but its detailed molecular mechanism remains unknown. Here we uncover it for the particular case of the anti-influenza N9 neuraminidase NC10 antibody against a glutathione-coated gold cluster by means of ab initio QM/MM calculations. We show that the labeling reaction follows an associative double SN2-like reaction mechanism, involving a proton transfer, with low activation barriers only if one of the two distinct peptide/peptidic ligands (the one that occupies the side position) is substituted. Positively charged residues in the vicinity of the incoming thiol result in strong interactions between the antibody and the AuMPC, favoring the ligand exchange reaction for suitable protein mutants. These results pave the way for future investigations aimed at engineering biomolecules to increase their reactivity towards a desired gold atom cluster.

Phasing and structure of bestrophin-1: a case study in the use of heavy-atom cluster compounds with multi-subunit transmembrane proteins.

The purification and three-dimensional crystallization of membrane proteins are commonly affected by a cumulation of pathologies that are less prevalent in their soluble counterparts. This may include severe anisotropy, poor spot shape, poor to moderate-resolution diffraction, crystal twinning, translational pseudo-symmetry and poor uptake of heavy atoms for derivatization. Such challenges must be circumvented by adaptations in the approach to crystallization and/or phasing. Here, an example of a protein that exhibited all of the above-mentioned complications is presented. Bestrophin-1 is a eukaryotic calcium-activated chloride channel, the structure of which was recently determined in complex with monoclonal antibody fragments using SAD phasing with tantalum bromide clusters (Ta6Br12·Br2). Some of the obstacles to obtaining improved diffraction and phasing for this particular channel are discussed, as well as the approach and adaptations that were key to determining the structure.

Can a relativistic differential equation be set up to treat the angularity of the valence electron density in heavy atom clusters?

This work provides an explicit relativistic non-linear differential equation to estimate the ground-state electron density, and especially its directionality dependence, for large clusters of heavy atoms, such as Pb, at their experimentally measured equilibrium geometry. The study embodies the early theory of Vallarta and Rosen, which seems to us to build a firm foundation on relativistic semi-classical many-electron theory. Assuming a finite nuclear radius for the heavy atoms would be advisable in subsequent numerical applications.

Diamonds in the rough: a strong case for the inclusion of weak-intensity X-ray diffraction data.

Overwhelming evidence exists to show that the inclusion of weak-intensity, high-resolution X-ray diffraction data helps improve the refinement of atomic models by imposing strong constraints on individual and overall temperature B factors and thus the quality of crystal structures. Some researchers consider these data to be of little value and opt to discard them during data processing, particularly at medium and low resolution, at which individual B factors of atomic models cannot be refined. Here, new evidence is provided to show that the inclusion of these data helps to improve the quality of experimental phases by imposing proper constraints on electron-density models during noncrystallographic symmetry (NCS) averaging. Using electron-density correlation coefficients as criteria, the resolution of data has successfully been extended from 3.1 to 2.5 Å resolution with redundancy-independent merging R factors from below 100% to about 310%. It is further demonstrated that phase information can be fully extracted from observed amplitudes through de novo NCS averaging. Averaging starts with uniform density inside double-shelled spherical masks and NCS matrices that are derived from bound heavy-atom clusters at the vertices of cuboctahedrally symmetric protein particles.

Comparison of the data of X-ray microtomography and fluorescence analysis in the study of bone-tissue structure

The possibility of localizing clusters of heavy atoms is substantiated by comparing the data of X-ray microtomography at different wavelengths, scanning electron microscopy, and X-ray fluorescence analysis. The proximal tail vertebrae of Turner’s thick-toed gecko (Chondrodactylus turneri) have been investigated for the first time by both histological and physical methods, including X-ray microtomography at different wavelengths and elemental analysis. This complex methodology of study made it possible to reveal the regions of accumulation of heavy elements in the aforementioned bones of Turner’s thick-toed gecko.

Special Issue: Advanced Electron Microscopy for Catalysis

Catalysis plays a key role for the sustainable development of our society. The characterization of morphology, chemical composition, surface, and internal structure of catalysts is of great importance for the synthesis of materials of high selectivity, high conversion rate, with long cycle times favored for their reduced environmental impact. Modern electron microscopy with its arsenal of imaging and spectroscopic techniques gives access to the collective and individual properties of such materials. From the very beginning of electron microscopy, its potential to reveal the microscopic details of catalysts has been explored. In 1940, M. von Ardenne and D. Beischer published in Angewandte Chemie possibly the first paper to describe the usefulness of transmission electron microscopy (TEM) for extracting morphological and structural information on supported and unsupported catalysts.1 J. Turkevich reported in 1945 the use of the electron microscope for the study of several important catalysts.2 Catalysis, together with the materials science of semiconductors, have been the driving force for the continuous improvement of electron optics and microscopic design for transmission electron microscopes. Not to forget, is Crewe’s pioneering development of the annular dark field scanning transmission electron microscopy (STEM) technique revealing single or small clusters of heavy atoms as bright features against the low intensity level of their supports.3 Advanced electron microscopes are not only marked by their high resolution, they are also defined by their high brightness field emission gun with its highly coherent electron beam. Aberration correction significantly improves the quality of high-resolution images by eliminating the Frensel fringes and delocalization effects, so that the surface structure of industrial catalysts can be determined (see the example in Figure 1).4, 5 The implementation of monochromators, and the development of high resolution electron-energy loss spectrometery (EELS), mark a new generation of analytical electron miscroscopy. Modern, advanced, analytical electron microscopes with aberration correctors provide genuine atomic and energy resolution and high sensitivity to heavy or light atoms.6 EELS, by using a monochromatized beam, is able to measure the core-Level near-edge structure in loss spectra with an energy resolution that is comparable to that measured with a synchrotron.7 Element mapping, a technique that provides a 2D image of inhomogeously distributed multi-components catalyst, is a well-established technique, used not only by catalytic researchers, but also other materials scientists, an example of which is illustrated in Figure 2. A newly developed windowless X-ray energy-dispersive spectrometer (XEDS) based on silicon drift detector technology8 allows a high speed recording of energy-dispersive spectrum and element mapping, down from hours to minutes, even at nanoscales. The combination of element mapping with electron tomography, a technique that is widely used by biologists, can give a truly 3D distribution of the active sites/phase of supported or mixed catalysts. In situ or environmental transmission electron microscopy allows for the first time the visualization of chemical/physical processes at atomic resolution. Advanced electron microscopy comes out from the shadow of being a “passive” characterization tool to become an active research method in materials and in catalysis. a) An experimental high-resolution image of the surface of an Ag catalyst used for the hydrogenation of acrolein. b) The structural model obtained from DFT calculations showing the position of α- and γ-oxygen on Ag. c) A simulated high-resolution image using the structure model in b. For more details, see Ref. [4]. Element mapping of an inhomogeously distributed multi-component catalyst. Advanced electron microscopy generates more realistic views of catalysts, allowing optimization of their structure to improve their performance. Presentations at the 1st International Symposium on Advanced Electron Microscopy for Catalysis and Energy Storage Materials at the Fritz-Haber Institute in Berlin provided a fascinating snapshot of the latest developments in catalyst microscopy. Aberration-corrected microscopes, cryo-tomography, and specialty heating stages are shedding new light on the nanoworld of catalysts and are beginning to facilitate improvements in catalyst design.9 This Special Issue contains selected papers presented at this symposium. Since then, other new developments in electron microscopy have emerged. By using photons as input rather than as an output signal, particularly in the form of femtosecond pulses, Zewail and colleagues developed ultrafast microscopy.10–12 The production of vortex electron beam in an electron microscope is exciting.13 The applications of direct relevance in catalysis are still to be identified, the potential could be tremendous.14 1

Recent advances and perspectives in four-component Dirac–Kohn–Sham calculations

We review recent theoretical and computational advances in the full relativistic four-component Dirac-Kohn-Sham (DKS) approach and its application to the calculation of the electronic structure of chemical systems containing many heavy atoms. We describe our implementation of an all-electron DKS approach based on the use of G-spinor basis sets, Hermite Gaussian functions, state-of-the-art density-fitting techniques and memory distributed parallelism. This approach has enormously extended the applicability of the DKS method, including for example large clusters of heavy atoms, and opens the way for future key developments. We examine the current limitations and future possible applications of the DKS approach, including the implementation of four-current density functionals and real-time propagation schemes. This would make possible to describe molecules in strong fields, accurately accounting for relativistic kinematic effects and spin-orbit coupling.

Time-dependent analysis of K2PtBr6binding to lysozyme studied by protein powder and single crystal X-ray analysis

Multi heavy atom cluster compounds like K2PtBr6 offer a way forward to solve, de novo, unknown protein structures by powder diffraction involving dispersive (measured at two X-ray wavelengths) and isomorphous intensity differences as a complement to micro-crystallography or by using both approaches in combination. Towards this end, using the ESRF high resolution synchrotron X-ray powder diffraction beamline ID31, we have recorded high quality protein powder diffractograms at the platinum LIII and bromine K absorption edges, as well as reference wavelengths, for K2PtBr6 bound to lysozyme. These experiments were conducted at 80K to protect the sample against X-radiation damage as much as possible and also to fix the K2PtBr6 bound state, which seemed to show instability at room temperature. With multiple powder pattern analysis we extracted intensities and showed the PtBr6 bound in lysozyme using ‘omit electron density maps’. In addition the wavelength dispersive Fourier around the Br K edge shows up the bromine signal at PtBr6 binding site 1 in one of the six samples tested. To better understand the chemical properties of this heavy atom compound we have elucidated the detailed binding behaviour using single crystal analyses with time-resolved freeze quenching after soak times of 10, 90 and 170 minutes. Whilst the quick soaking of 10 to 30 minutes, used at ESRF ID31 shows clear binding there is increasing binding strength with increasing soak time. Thus, these time-resolved analytical chemistry results show that further heavy atom signal optimizations are possible. Prospects for extending our approach to the yet larger isomorphous and wavelength dispersive signal case of Ta6Br12 bound to lysozyme are also described.

An Efficient Parallel All-Electron Four-Component Dirac-Kohn-Sham Program Using a Distributed Matrix Approach.

We show that all-electron relativistic four-component Dirac-Kohn-Sham (DKS) computations, using G-spinor basis sets and state-of-the-art density fitting algorithms, can be efficiently parallelized and applied to large molecular systems, including large clusters of heavy atoms. The performance of the parallel implementation of the DKS module of the program BERTHA is illustrated and analyzed by some test calculations on several gold clusters up to Au32, showing that calculations with more than 25 000 basis functions (i.e., DKS matrices on the order of 10 GB) are now feasible. As a first application of this novel implementation, we investigate the interaction of the atom Hg with the Au20 cluster.

Validation and generalization of a method for precise size measurements of metal nanoclusters on supports

We recently described a data analysis method for precise (∼0.1Å random error in the mean for a 200kV instrument with a 3Å FWHM probe size) size measurements of small clusters of heavy metal atoms on supports as imaged in a scanning transmission electron microscope, including an experimental demonstration using clusters that were primarily triosmium or decaosmium. The method is intended for low signal-to-noise ratio images of radiation-sensitive samples. We now present a detailed analysis, including a generalization to address issues of particle anisotropy and biased orientation distributions. In the future, this analysis should enable extraction of shape as well as size information, up to the noise-defined limit of information present in the image. We also present results from an extensive series of simulations designed to determine the method's range of applicability and expected performance in realistic situations. The simulations reproduce the experiments quite accurately, enabling a correction of systematic errors so that only the ∼0.1Å random error remains. The results are very stable over a wide range of parameters. We introduce a variation on the method with improved precision and stability relative to the original version, while also showing how simple diagnostics can test whether the results are reliable in any particular instance.

All-electron four-component Dirac-Kohn-Sham procedure for large molecules and clusters containing heavy elements

In exploiting state-of-the-art density fitting algorithms, we show that relativistic four-component Dirac-Kohn-Sham computations using G -spinor basis sets and Hermite Gaussian fitting functions can readily be applied to large molecular systems, including large clusters of heavy atoms. The inherent accuracy of the fitting procedure is discussed and the techniques to ensure high accuracy are mentioned. The power of the method, with its reduced scaling with respect to size and a prefactor shrunk by several orders of magnitude, is illustrated through some all-electron test calculations on gold clusters up to Au16. © 2008 The American Physical Society.

Reprint of “On the feasibility of visualizing ultrasmall gold labels in biological specimens by STEM tomography” [J. Struct. Biol. 159 (2007) 507–522

Labeling with heavy atom clusters attached to antibody fragments is an attractive technique for determining the 3D distribution of specific proteins in cells using electron tomography. However, the small size of the labels makes them very difficult to detect by conventional bright-field electron tomography. Here, we evaluate quantitative scanning transmission electron microscopy (STEM) at a beam voltage of 300kV for detecting 11-gold atom clusters (Undecagold) and 1.4nm-diameter nanoparticles (Nanogold) for a variety of specimens and imaging conditions. STEM images as well as tomographic tilt series are simulated by means of the NIST Elastic-Scattering Cross-Section Database for gold clusters embedded in carbon. The simulations indicate that the visibility in 2D of Undecagold clusters in a homogeneous matrix is maximized for low inner collection semi-angles of the STEM annular dark-field detector (15-20mrad). Furthermore, our calculations show that the visibility of Undecagold in 3D reconstructions is significantly higher than in 2D images for an inhomogeneous matrix corresponding to fluctuations in local density. The measurements demonstrate that it is possible to detect Nanogold particles in plastic sections of tissue freeze-substituted in the presence of osmium. STEM tomography has the potential to localize specific proteins in permeabilized cells using antibody fragments tagged with small heavy atom clusters. Our quantitative analysis provides a framework for determining the detection limits and optimal experimental conditions for localizing these small clusters.

Determination of quantitative distributions of heavy-metal stain in biological specimens by annular dark-field STEM

It is shown that dark-field images collected in the scanning transmission electron microscope (STEM) at two different camera lengths yield quantitative distributions of both the heavy and light atoms in a stained biological specimen. Quantitative analysis of the paired STEM images requires knowledge of the elastic scattering cross sections, which are calculated from the NIST elastic scattering cross section database. The results reveal quantitative information about the distribution of fixative and stain within the biological matrix, and provide a basis for assessing detection limits for heavy-metal clusters used to label intracellular proteins. In sectioned cells that have been stained only with osmium tetroxide, we find an average of 1.2+/-0.1 Os atom per nm(3), corresponding to an atomic ratio of Os:C atoms of approximately 0.02, which indicates that small heavy atom clusters of Undecagold and Nanogold can be detected in lightly stained specimens.

On the feasibility of visualizing ultrasmall gold labels in biological specimens by STEM tomography

Labeling with heavy atom clusters attached to antibody fragments is an attractive technique for determining the 3D distribution of specific proteins in cells using electron tomography. However, the small size of the labels makes them very difficult to detect by conventional bright-field electron tomography. Here, we evaluate quantitative scanning transmission electron microscopy (STEM) at a beam voltage of 300 kV for detecting 11-gold atom clusters (Undecagold) and 1.4 nm-diameter nanoparticles (Nanogold) for a variety of specimens and imaging conditions. STEM images as well as tomographic tilt series are simulated by means of the NIST Elastic-Scattering Cross-Section Database for gold clusters embedded in carbon. The simulations indicate that the visibility in 2D of Undecagold clusters in a homogeneous matrix is maximized for low inner collection semi-angles of the STEM annular dark-field detector (15–20 mrad). Furthermore, our calculations show that the visibility of Undecagold in 3D reconstructions is significantly higher than in 2D images for an inhomogeneous matrix corresponding to fluctuations in local density. The measurements demonstrate that it is possible to detect Nanogold particles in plastic sections of tissue freeze-substituted in the presence of osmium. STEM tomography has the potential to localize specific proteins in permeabilized cells using antibody fragments tagged with small heavy atom clusters. Our quantitative analysis provides a framework for determining the detection limits and optimal experimental conditions for localizing these small clusters.

Charging dynamics of metal clusters in intense laser fields

Clusters of heavy metal atoms in strong femtosecond laser-light fields undergo multi-ionization with the loss of hundreds of electrons. The cross section largely exceeds that of corresponding isolated atoms, which leads in the case of PbN to a complete ionization of the 4f shell with a light intensity of 1.2×1015 W/cm2. Experimental investigations on Pb and Pt clusters with variable pulse widths and, for the first time, with the pump&probe technique give insight into the dynamics of the coupling of electromagnetic radiation into the clusters. Both approaches support the picture according to which, after an initial charging, the clusters expand due to Coulomb forces. This expansion is accompanied by a reduction of the electron density and at the same time by an increase of the optical sensitivity. Once the plasmon energy of the diluted nanoplasma approaches the photon energy, the charging efficiency increases significantly. The experimental observations are confirmed by random-phase approximation (RPA) calculations of the optical response, including molecular-dynamics simulations of the expanding systems.

Electronic excitations in homopolyatomic bismuth cations: spectroscopic measurements in molten salts and an ab initio CI-singles study

The electronic excitations of the low-valence bismuth cluster cations Bi5(3+), Bi8(2+), and Bi9(5+) have been studied with experimental and theoretical techniques. The UV-visible spectra of the bismuth ions were measured in acidic chloroaluminate melts (mixture of 1-methyl-3-benzyl imidazolium chloride and AlCl3). The spectra of the Bi5(3+) and Bi8(2+) ions agree fairly well with previous reports, but also revealed additional low-energy absorptions. Ab initio methods were employed to assign the experimentally observed electronic transitions of these homopolyatomic bismuth cations. Structures were optimized at the RHF, MP2, and B3LYP levels of theory by using split-valence LANL2DZ basis sets that were augmented with one and two sets of pure d functions. The computed structures agree well with the results of neutron diffraction analyses of melts. Electronically excited states of the three clusters were treated by using the CI-Singles theory. The results of these calculations were used to explain the observed UV-visible spectra. The observed electronic excitations in the UV-visible range are all found to result from transitions involving the molecular orbitals formed by 6p-atomic-orbital overlap. This leads to the necessity of using basis sets that include d-type functions, which allow for an adequate description of the bonding that results from such p-orbital overlap. Spin-orbit coupling becomes increasingly important with increasing atomic number and its consideration is necessary when describing the electronic transitions in clusters of heavy atoms. The calculations show that singlet-triplet transitions, which are made accessible by strong spin-orbit coupling, are responsible for some of the observed absorptions.

Recollections of the Electron Crystallographic Heavy Atom Derivative Search of Purple Membrane: The Quest for EM Structure Determination

The use of multiple isomorphous replacement in protein electron crystallography for phase determination has been systematically studied only for purple membrane, even though the use of heavy atoms or heavy atom clusters has been used on many occasions in electron microscopy for locating domains or subunits in protein assemblies. The background behind the structure determination of bacteriorhodopsin, the protein component of purple membranes, is summarized and an evaluation of the strengths and weaknesses of using isomorphous replacement in electron crystallography is discussed.

From Lasers, Tabletop Nuclear Bursts

AMERICAN PHYSICAL SOCIETY MEETINGATLANTA-- At the American Physical Society meeting, held here from 20 to 26 March, physicists described a tabletop experiment that used laser light concentrated into unimaginably brilliant pulses to spark nuclear fusion in a chilled gas containing clusters of heavy hydrogen atoms. The new work could lead to compact sources of neutrons for testing materials that might be used in real fusion reactors.

Quantum-Chemical Study of the Structure and Properties of Hypothetical Superhard Materials Based on the Cubic Silicon−Carbon Nitrides

Density functional B3LYP/6-31G(d,p) calculations have been carried out to study the structural peculiarities and physical properties of the series of cubic (defect zinc-blende) silicon−carbon nitrides with composition SixC3-xN4 (x = 0, 1, 2, 3). As model systems, we have considered six clusters with the structure of the adamantane molecule (CH)4(CH2)6 (I), hexamethylenetetramine-like molecules N4(CH2)6-n(SiH2)n (II−V) (n = 0, 2, 4, 6), and silicon-substituted adamantane molecule (SiH)4(SiH2)6 (VI). These 10 heavy-atom clusters have been used to simulate the crystalline fragments of diamond (I), cubic (defect zinc-blende) silicon−carbon nitrides (II−V), and cubic (zinc-blende) silicon solid (VI). It was found that the full B3LYP/6-31G(d,p) geometry optimization of these clusters allow us to reproduce the structures, unit cell parameters, and bulk modulus (hardness) of real crystals (I and VI) quite well and to predict the structural and mechanical properties of the hypothetical crystalline compounds (II−V).