Relative Positions Of Atoms Research Articles

Effect of Equivalent Sites on the Dynamics of Bimetallic Nanoparticles

ABSTRACTUsing a Sutton and Chen interatomic potential, we study the molecular dynamics of Au-Pd nanoparticles with an initial icosahedral structure at different temperatures and concentrations, where each relative concentration of the 561-atom particles was made by placing atoms of the same species at equivalent sites, in order to identify under which conditions the melting transition temperature appears for each particle. In addition, we compute global order parameters in order to correlate the obtained results with the caloric curves of each particle. As a result, we observe that the melting transition temperature depends on the relative atomic positions of gold and palladium. The melting transition temperature of the Au-Pd alloy particles appears at higher temperature than that of the pure-gold particle. From the analysis of the structure of the particles, we found that the melting temperature increases with the proportion of gold atoms, and for those particles with a higher concentration of palladium on the surface, we observe an early migration of gold atoms before the melting transition temperature appears.

Interactive physically-based structural modeling of hydrocarbon systems

Hydrocarbon systems have been intensively studied via numerical methods, including electronic structure computations, molecular dynamics and Monte Carlo simulations. Typically, these methods require an initial structural model (atomic positions and types, topology, etc.) that may be produced using scripts and/or modeling tools. For many systems, however, these building methods may be ineffective, as the user may have to specify the positions of numerous atoms while maintaining structural plausibility. In this paper, we present an interactive physically-based modeling tool to construct structural models of hydrocarbon systems. As the user edits the geometry of the system, atomic positions are also influenced by the Brenner potential, a well-known bond-order reactive potential. In order to be able to interactively edit systems containing numerous atoms, we introduce a new adaptive simulation algorithm, as well as a novel algorithm to incrementally update the forces and the total potential energy based on the list of updated relative atomic positions. The computational cost of the adaptive simulation algorithm depends on user-defined error thresholds, and our potential update algorithm depends linearly with the number of updated bonds. This allows us to enable efficient physically-based editing, since the computational cost is decoupled from the number of atoms in the system. We show that our approach may be used to effectively build realistic models of hydrocarbon structures that would be difficult or impossible to produce using other tools.

Three‐dimensional structure and mimetic‐membrane association of consensus 11‐amino‐acid motif from soybean lea3 protein

The occurrence of a highly conserved 11-mer repeating motif in the primary sequence is a major characteristic of group 3 late embryogenesis abundant (LEA3) proteins, which are strongly associated with abiotic stress tolerance of the plants. In this study, the three-dimensional structure, mimetic membrane association, and salt effect for consensus 11-mer motif from soybean PM2 protein (LEA3) were investigated in sodium dodecyl sulfate (SDS) micelles by NMR techniques. It was shown that the 11-mer motif was disordered in aqueous solution, but adopted an α-helix in SDS micelles. NMR diffusion measurements demonstrated that the 11-mer motif was associated with SDS micelles. Paramagnetic quenching NMR experiments further revealed the orientation of the 11-mer motif with respect to the mimetic membrane: the ordered N-terminal segment was inserted into the mimetic membrane, and the disordered C-terminal segment was exposed to water. In addition, salt addition could not change the secondary structure of the 11-mer motif, but might slightly alter the relative spatial position of some N-terminal residue atoms. These results implied that the 11-mer motif would take an important role in structural plasticity and membrane stabilization for LEA3 proteins.

Off-lattice self-learning kinetic Monte Carlo: application to 2D cluster diffusion on thefcc(111) surface

We report developments of the kinetic Monte Carlo (KMC) method with improvedaccuracy and increased versatility for the description of atomic diffusivity on metalsurfaces. The on-lattice constraint built into our recently proposed self-learningKMC (SLKMC) (Trushin et al 2005 Phys. Rev. B 72 115401) is released, leavingatoms free to occupy ‘off-lattice’ positions to accommodate several processesresponsible for small-cluster diffusion, periphery atom motion and heteroepitaxialgrowth. This technique combines the ideas embedded in the SLKMC method with anew pattern-recognition scheme fitted to an off-lattice model in which relativeatomic positions are used to characterize and store configurations. Application of acombination of the ‘drag’ and the repulsive bias potential (RBP) methods forsaddle point searches allows the treatment of concerted cluster, and multiple-and single-atom, motions on an equal footing. This tandem approach has helpedreveal several new atomic mechanisms which contribute to cluster migration. Wepresent applications of this off-lattice SLKMC to the diffusion of 2D islands of Cu(containing 2–30 atoms) on Cu and Ag(111), using the interatomic potential from theembedded-atom method. For the hetero-system Cu/Ag(111), this technique hasuncovered mechanisms involving concerted motions such as shear, breathing andcommensurate–incommensurate occupancies. Although the technique introducescomplexities in storage and retrieval, it does not introduce noticeable extra computationalcost.

Surface structure analysis of metal adsorbed Si(1 1 1) surfaces by Patterson function with LEED I– V curves

Wu and Tong proposed the calculation method of Patterson function obtained directly from the LEED I– V curves which shows the relative position of surface atoms as an image. We have made the calculation program of Patterson function and applied to the structural analysis of the Si(1 1 1)1 × 1-Fe surface. Surface structure was able to be expressed almost correctly by the Patterson function obtained from the theoretical I– V curves for the model structure. In the Patterson function obtained from the experimental I– V curves, the locational relation between the atoms of subsurface layer was in agreement with the CsCl type structure. More over, because the faint peak, by which we can distinguish the model, can be seen, it seems that the model B8 is preferable to the model A8. This result is consistent with the model shown by Walter et al.

Structure and NMR assignment in calcined and as-synthesized forms of AlPO-14: a combined study by first-principles calculations and high-resolution 27Al–31P MAS NMR correlation

The high-resolution 27Al and 31P NMR spectra of two as-synthesized forms of the microporous aluminophosphate AlPO-14 and the corresponding calcined-dehydrated form were assigned using both "first-principles" calculations of NMR parameters (GIPAW, as implemented in NMR-CASTEP) and a 27Al-31P heteronuclear correlation NMR experiment (MQ-J-HETCOR) that exploits 27Al multiple-quantum coherences and J couplings to identify Al-O-P linkages. NMR parameters calculated from published AlPO-14 crystal structures, which are derived from powder X-ray diffraction (XRD) data, are in poor agreement with experiment and it was necessary to optimize the structure geometry using energy minimization before satisfactory agreement was obtained. Comparison of simulated powder XRD patterns from the experimental and the energy-minimized structures shows that the changes in relative atomic positions in the optimized structure are relatively small and yield only minor adjustments in the Bragg peak intensities. These results indicate that a combination of NMR spectroscopy and first-principles calculation of NMR parameters may soon be considered a generally useful step in the refinement of the structures of microporous materials derived from powder diffraction data.

Voids and Intermediate-Range Order in Network-Forming Liquids: Rb20Se80 and BiBr3

The RMC and Voronoi–Delaunay analyses were applied to study the void structure in the network-forming liquids: Rb 20 Se 80 and BiBr 3 . The distribution function of the relative positions of atoms and void centers in space, the coordination number of atoms and voids around a void and the size distribution of voids were examined using the previous experimental data for S ( Q ) to characterize the connectivity of the bonding network supporting voids and the intermediate-range correlation as manifested in the pre-peak of S ( Q ). The voids in l-Rb 20 Se 80 are formed by the 8-membered ring-like Se chains. A Rb cluster composed of 3–4 Rb atoms replaces one of five void sites and binds ∼4 Se rings involving voids around it through the interactions between Rb and Se and between Rb and Rb. In l-BiBr 3 the hexagonal cages involving voids are formed by the corner-sharing of the trigonal pyramidal BiBr 3 blocks. The strong preference of Bi ion for three-fold coordination helps to bind between the neighboring cages ...

Simulation of various possible cementite structures

The simulation of the cementite structure has been performed without resorting to any preliminary assumptions. The spheres simulating the Fe and C atoms are closely packed in accordance with the rules of pair interpenetration. The maximum depth of the interpenetration in the Fe-C pair was accepted to be intermediate between the maximum depths of the penetration in the Fe-Fe and C-C pairs in ferrite and diamond, respectively. Under such conditions, six iron atoms penetrate into a carbon atom. The carbon atom turns out to be located inside octahedra, which can be of various shapes, while the centers of iron atoms occupy the vertices of these octahedra. The translation of the octahedra leads to the formation of orthorhombic cementite structures with identical or close parameters, but with different relative positions of carbon and iron atoms.

On Updating Torsion Angles of Molecular Conformations

A conformation of a molecule is defined by the relative positions of atoms and by the chirality of asymmetric atoms in the molecule. The three main representations for conformations of molecules are Cartesian coordinates, a distance geometry descriptor (which consists of a distance matrix and the signs of the volumes of quadruples of atoms), and internal coordinates. In biochemistry, conformational changes of a molecule are usually described in terms of internal coordinates. However, for many applications, such as molecular docking, the Cartesian coordinates of atoms are needed for computation. Although, for each conformational change, the Cartesian coordinates of atoms can be updated in linear time (which is optimal asymptotically), the constant factor becomes significant if a large number of updates are needed. Zhang and Kavraki (J. Chem. Inf. Comput. Sci. 2002, 42, 64-70) examined three methods: the simple rotations, the Denavit-Hartenberg local frames, and the atom-group local frames. On the basis of their implementations, they showed that the atom-group local frames are more efficient than the other two. In this paper, by expressing the torsion-angle change as a composition of translations and rotations, we observe that the simple rotations can be implemented in an efficient way by taking advantage of consecutive operations. Both quantitative and experimental comparisons show that the improved simple rotations, in which rotations are expressed in unit quaternions, are as efficient as the atom-group local frames and, thus, have the advantage of avoiding the need of precomputations of a set of local frames and transformations between them.

Resolution Quality and Atom Positions in Sub-Ångström Electron Microscopy

Ability to determine whether an image peak represents one single atom or several depends on resolution of the HR-(S)TEM. Rayleigh's resolution criterion, an accepted standard in optics, was derived as a means for judging when two image intensity peaks from two sources of light (stars) are distinguishable from a single source. Atom spacings closer than the Rayleigh limit have been resolved in HR-TEM, suggesting that it may be useful to consider other limits, such as the Sparrow resolution criterion. From the viewpoint of the materials scientist, it is important to be able to use the image to deter-mine whether an image feature represents one or more atoms (resolution), and where the atoms (or atom columns) are positioned relative to one another (resolution quality). When atoms and the corresponding image peaks are separated by more than the Rayleigh limit of the HR-(S)TEM, it is possible to adjust imaging parameters so that relative peak positions in the image correspond to relative atom positions in the specimen. When atoms are closer than the Rayleigh limit, we must find the relationship of the peak position to the atom position by peak fitting or, if we have a suitable model, by image simulation. Our Rayleigh-Sparrow parameter QRS reveals the resolution quality of a microscope image. QRS values greater than 1 indicate a clearly resolved twin peak, while values between 1 and 0 mean a lower-quality resolution and an image with peaks displaced from the relative atom positions. The depth of the twin-peak minimum can be used to determine the value of QRS and the true separation of the atom peaks that sum to produce the twin peak in the image. The Rayleigh-Sparrow parameter can be used to refine relative atom positions in defect images where atoms are closer than the Rayleigh limit of the HR-(S)TEM, reducing the necessity for full image simulations from large defect models.

Interatomic voids in analysis of computer model structures of liquids and glasses

To analyze the structure of noncrystalline systems (liquids, glasses), it is suggested that the functions to be calculated should include not only the conventional atom-atom radial distribution function and structural factor, but also the same functions for a system of points representing the centers of interatomic voids. The points are located at the nodes of Voronoi polyhedra or, which is equivalent, at the centers of the spheres circumscribed around the Delaunay simplices. The system of points (system {D}) is unambiguously defined by the atomic coordinates and conveys additional information on the structure of the system because each interatomic void is determined by the relative positions of several atoms. Using a homogeneous noncrystalline packing model of atoms and inhomogeneous models derived from it as an example, we demonstrate that system {D} is sensitive to the structural features on medium scales and may be used along with the conventional atom-atom functions to study structural correlations other than short-range order correlations.

Collective effects in the dynamics of driven atoms in a high-Q resonator

We study the quantum dynamics of N coherently driven two-level atoms coupled to an optical resonator. In the strong coupling regime the cavity field generated by atomic scattering interferes destructively with the pump on the atoms. This suppresses atomic excitation and even for strong driving fields prevents atomic saturation, while the stationary intracavity field amplitude is almost independent of the atom number. The magnitude of the interference effect depends on the detuning between laser and cavity field and on the relative atomic positions and is strongest for a wavelength spaced lattice of atoms placed at the antinodes of the cavity mode. In this case three dimensional intensity minima are created in the vicinity of each atom. In this regime spontaneous emission is suppressed and the dominant loss channel is cavity decay. Even for a cavity linewidth larger than the atomic natural width, one regains strong interference through the cooperative action of a sufficiently large number of atoms. These results give a new key to understand recent experiments on collective cavity cooling and may allow to implement fast tailored atom-atom interactions as well as nonperturbative particle detection with very small energy transfer.

Forces and spatial ordering of driven atoms in a resonator in the regime of fluorescence suppression

An atom in a high-Q cavity, which is coherently driven at the frequency of a cavity mode, exhibits strong suppression of fluorescence when the atomic decay rate exceeds the cavity linewidth. This effect is due to destructive interference of cavity and pump field, such that at the atomic position the total field intensity has a local minimum. For atomic ensembles the magnitude of the interference effect grows with atom number and depends on the relative atomic positions. It is strongest for a wavelength spaced array of atoms placed at the antinodes of the cavity mode. This suppresses fluorescence and enhanced collective scattering into the cavity mode. We analyze the mechanical forces in the regime where the interference condition is fulfilled. We show that the atomic pattern is mechanically stable whenever the driving frequency is red detuned with respect to the cavity frequency, irrespective of the atomic transition frequency. Hence atomic selforganization, as predicted in [6] can also occur in the parameter regime where superradiant scattering is suppressed by collective interference.

Heterogeneity and Inaccuracy in Protein Structures Solved by X-Ray Crystallography

Proteins are dynamic molecules, exhibiting structural heterogeneity in the form of anisotropic motion and discrete conformational substates, often of functional importance. In protein structure determination by X-ray crystallography, the observed diffraction pattern results from the scattering of X-rays by an ensemble of heterogeneous molecules, ordered and oriented by packing in a crystal lattice. The majority of proteins diffract to resolutions where heterogeneity is difficult to identify and model, and are therefore approximated by a single, average conformation with isotropic variance. Here we show that disregarding structural heterogeneity introduces degeneracy into the structure determination process, as many single, isotropic models exist that explain the diffraction data equally well. The large differences among these models imply that the accuracy of crystallographic structures has been widely overestimated. Further, it suggests that analyses that depend on small differences in the relative positions of atoms may be flawed.

Interpreting the signal from a localized fluorescence sensor: a study by angle-resolved XPS and dynamic SIMS

Angle-resolved X-ray photoelectron spectroscopy (XPS) and dynamic secondary ion mass spectroscopy (DSIMS) experiments were conducted to assess the interactions between a diamine curing agent and a glycidoxysilane-modified glass substrate. This effort was motivated by earlier work, in which a fluorescent probe localized in dilute quantities in the silane layer was used to track the penetration of the resin into the silane layer, as well as the resin cure. XPS and DSIMS experiments were performed on the silane layers immersed only in the resin hardener, providing more detailed information about the concentration profile and structural reorganization within the silane layer due specifically to hardener penetration. Dynamic SIMS spectra reveal the presence of hardener in the layer, as indicated by the strong CN − signal throughout the silane layer thickness. The XPS results indicate the presence of an amine gradient within the top 10 nm of the silane coating, with less amine penetration deeper into the silane layer. The XPS data also suggest some level of anisotropy in the molecular structure of the diamine/glycidoxysilane coating, as revealed by the differences in the relative atomic concentrations and peak positions of the C1 s components at two different take-off angles.

High-resolution electron microscopy of individual metallofullerene molecules on the dipole orientations in peapods

Electron microscopy with atomic sensitivity enables us to obtain a direct image of the intra-molecular structure of metallofullerenes encapsulated inside single-walled carbon nanotubes. By a comparison of high-resolution images with a simulation to extract the relative atom positions for encaged metal atoms in each molecule, the distribution of the molecular orientations and interactions between adjacent molecules in metallofullerene peapods have been statistically analyzed. The results are suggestive of strong interactions between fullerene–fullerene and fullerene–tube in peapods at room temperature.

Molecular Mechanism of H + Conduction in the Single-File Water Chain of the Gramicidin Channel

The conduction of protons in the hydrogen-bonded chain of water molecules (or “proton wire”) embedded in the lumen of gramicidin A is studied with molecular dynamics free energy simulations. The process may be described as a “hop-and-turn” or Grotthuss mechanism involving the chemical exchange (hop) of hydrogen nuclei between hydrogen-bonded water molecules arranged in single file in the lumen of the pore, and the subsequent reorganization (turn) of the hydrogen-bonded network. Accordingly, the conduction cycle is modeled by two complementary steps corresponding respectively to the translocation 1) of an ionic defect (H +) and 2) of a bonding defect along the hydrogen-bonded chain of water molecules in the pore interior. The molecular mechanism and the potential of mean force are analyzed for each of these two translocation steps. It is found that the mobility of protons in gramicidin A is essentially determined by the fine structure and the dynamic fluctuations of the hydrogen-bonded network. The translocation of H + is mediated by spontaneous (thermal) fluctuations in the relative positions of oxygen atoms in the wire. In this diffusive mechanism, a shallow free-energy well slightly favors the presence of the excess proton near the middle of the channel. In the absence of H +, the water chain adopts either one of two polarized configurations, each of which corresponds to an oriented donor-acceptor hydrogen-bond pattern along the channel axis. Interconversion between these two conformations is an activated process that occurs through the sequential and directional reorientation of water molecules of the wire. The effect of hydrogen-bonding interactions between channel and water on proton translocation is analyzed from a comparison to the results obtained previously in a study of model nonpolar channels, in which such interactions were missing. Hydrogen-bond donation from water to the backbone carbonyl oxygen atoms lining the pore interior has a dual effect: it provides a coordination of water molecules well suited both to proton hydration and to high proton mobility, and it facilitates the slower reorientation or turn step of the Grotthuss mechanism by stabilizing intermediate configurations of the hydrogen-bonded network in which water molecules are in the process of flipping between their two preferred, polarized states. This mechanism offers a detailed molecular model for the rapid transport of protons in channels, in energy-transducing membrane proteins, and in enzymes.

電子顕微鏡法と電子分光法によるナノチューブ内一次元結晶「ピーポッド」の構造解析

Electron microscopy and spectroscopy with the single-atom sensitivity enables us to obtain a direct image of the intra-molecular structure and chemical identification of individual metallofullerenes encapsulated inside single-walled carbon nanotubes, so-called peapods. By a comparison of high resolution images with a simulation to extract the relative atom positions for encaged metal atom in each molecule, distribution of molecular orientation and its interaction between adjacent molecules in metallofullerene-peapods have been statistically analyzed. Moreover the techniques described here demonstrates the possibilities to observe individual chemical reaction inside carbon nanotubes.

Surface structures by direct transform of electron diffraction patterns

We find that electron diffraction patterns can be directly inverted to provide three-dimensional atomic structures for the system studied. Depending on the scattering process, either holography or a Patterson inversion scheme is used. For diffraction patterns which were generated from a localized emitter source or predominantly by an inelastic-scattering feature like low-energy Kikuchi electrons, holography inversion is needed. The information obtained from Kikuchi electron holography includes the building blocks on the surface and their relative position to the atoms below the surface layer. On the other hand, for diffraction patterns generated predominantly by an elastic-scattering feature like low-energy electron diffraction (LEED), a Patterson inversion is needed. The information obtained from the Patterson transform of the LEED I(E) curves is the relative positions of surface atoms to the atoms in underlying layers; no intra-layer information can be extracted with this method. High-fidelity and artifact-free three-dimensional atomic structures obtained by inversion of low-energy Kikuchi electron patterns and low-energy electron diffraction curves are presented. The results from the two inversion methods are complementary and can be used to construct or to discriminate the surface atomic structural models. The future of these direct methods by inverting diffraction patterns is discussed.

SLATE: a method for the superposition of flexible ligands.

A novel program for the superposition of flexible molecules, SLATE, is presented. It uses simulated annealing to minimise the difference between the distance matrices calculated from the hydrogen-bonding and aromaticring properties of two ligands. A method for generating a molecular stack using multiple pairwise matches is illustrated. These stacks are used by the program DOH to predict the relative positions of receptor atoms that could form hydrogen bonds to two or more ligands in the dataset. The methodology has been applied to ligands binding to dihydrofolate reductase, thermolysin. H3 histamine receptors, alpha2 adrenoceptors and 5-HT1D receptors. When there are sufficient numbers and diversity of molecules in the dataset, the prediction of receptor-atom positions is applicable to compound design.