Nearest-neighbor Bonds Research Articles

Control of Helix Formation in Vinylogous γ-Peptides by (E)- and (Z)-Double Bonds: A Way to Ion Channels and Monomolecular Nanotubes

[structure: see text] A complete overview on the alternative and competitive helices in vinylogous gamma-peptides is given, which was obtained on the basis of a systematic conformational analysis at various levels of ab initio MO theory (HF/6-31G*, DFT/B3LYP/6-31G*, PCM/HF/6-31G*). Contrary to the parent gamma-peptides, there is a strict control of helix formation by the configuration of the double bond between the C(alpha) and C(beta) atoms of the monomer constituents. (E)-Double bonds favor helices with larger pseudocycles beginning with 14- up to 27-membered hydrogen-bonded rings, whereas the (Z)-configuration of the double bonds supports a distinct preference of helices with smaller seven- and nine-membered pseudocycles showing interactions between nearest-neighbor peptide bonds. The rather stable helices of the (E)-vinylogous peptides with 22-, 24-, and 27-membered hydrogen-bonded pseudocycles have inner diameters large enough to let molecules or ions pass. Thus, they could be interesting model compounds for the design of membrane channels and monomolecular nanotubes. Since (E)- and (Z)-vinylogous gamma-amino acids and their oligomers are synthetically accessible, our study may stimulate structure research in this novel field of foldamers.

Dimer site-bond percolation on a square lattice

A generalization of the pure site and pure bond percolation problems in which pairs of nearest neighbor sites (site dimers) and linear pairs of nearest neighbor bonds (bond dimers) are independently occupied at random on a square lattice is studied. We called this model as dimer site-bond percolation. Motivated by considerations of cluster connectivity, we have used two distinct schemes (denoted as $S\cap B$ and $S\cup B$ ) for dimer site-bond percolation. In $S \cap B$ ( $S \cup B$ ), two points are said to be connected if a sequence of occupied sites and (or) bonds joins them. By using finite-size scaling theory, data from $S \cap B$ and $S \cup B$ are analyzed in order to determine i) the phase boundary between the percolating and non-percolating regions and ii) the numerical values of the critical exponents of the phase transition occurring in the system. The results obtained are discussed in comparison with the corresponding ones for classical monomer site-bond percolation.

Asymptotic expansions inn−1 for percolation critical values on then-Cube and ℤn

We use the lace expansion to prove that the critical values for nearest-neighbor bond percolation on the n-cube {0, 1}n and on the integer lattice Zn have asymptotic expansions, with rational coefficients, to all orders in powers of n-1.

Lattice-dependent anisotropy in the orientation of magnetic domain walls

We demonstrate theoretically that a large class of ultrathin ferromagnetic films shows anisotropy in the domain wall orientation in spite of the isotropy in the exchange interactions. The reason is an orientation-dependent density of nearest-neighbor atomic bonds due to the symmetry of an underlying atomic lattice.

Magnetic and Mössbauer spectral studies of R 3Fe 29− xMo x compounds (R = Y, Nd, Sm, Gd, Tb, and Dy)

The investigation of the structure, magnetic and Mössbauer properties for the series of R 3(Fe,Mo) 29 compounds has been performed, where R = Y, Nd, Sm, Gd, Tb, and Dy. The crystallographic structure of the ternary phase compounds has been investigated by Rietveld refinement of the X-ray diffraction patterns obtained at room temperature. The quality of the single-phase compounds was also checked by thermomagnetic measurements, from room temperature to above the Curie temperatures. From the magnetic isotherms for the free powder samples, measured at 4.2 K, the saturation magnetizations and the iron average magnetic moments have been derived. 57Fe Mössbauer spectra of the R 3(Fe,Mo) 29 compounds have been measured at 15 K. The analysis of spectra, in a model which takes into account both the Fe atom nearest neighbor numbers and the Fe Fe nearest neighbor bond lengths, indicates that the transferred contribution to the hyperfine field at the iron sites, due to rare earth moments, can be correlated with the rare earth effective spin.

Size effects in the Raman spectra of TiO 2 nanoparticles

To investigate the relationship between the particle size and the Raman bands of TiO 2 nanoparticles, two different size-selected samples of TiO 2 nanoparticles were investigated using transmission electron microscopy (TEM), X-ray absorption near edge structure (XANES), extended X-ray absorption fine structure (EXAFS), and Raman spectroscopy. Analysis of the XANES spectra showed that the nanoparticles in both sample A (particle size ∼30 nm) and sample B (particle size ∼12 nm) have an anatase structure, and that there is no difference between the electronic structure of titanium atoms in TiO 2 nanoparticles and that of titanium atoms in bulk TiO 2. The EXAFS results indicate that a contraction effect occurs in the anatase TiO 2 nanoparticles. In the Raman spectra, both broadening and shifts of the Raman bands with decreasing particle diameter were observed. In this paper, these Raman shifts are attributed to the effects of decreasing particle size on the force constants and vibrational amplitudes of the nearest neighbor bonds.

Diagonalization of replicated transfer matrices for disordered Ising spin systems

We present an alternative procedure for solving the eigenvalue problem of replicated transfer matrices describing disordered spin systems with (random) 1D nearest neighbor bonds and/or random fields, possibly in combination with (random) long range bonds. Our method is based on transforming the original eigenvalue problem for a $2^n\times 2^n$ matrix (where $n\to 0$) into an eigenvalue problem for integral operators. We first develop our formalism for the Ising chain with random bonds and fields, where we recover known results. We then apply our methods to models of spins which interact simultaneously via a one-dimensional ring and via more complex long-range connectivity structures, e.g. $1+\infty$ dimensional neural networks and `small world' magnets. Numerical simulations confirm our predictions satisfactorily.

First-principles study of binary bcc alloys using special quasirandom structures

We present three 16-atom special quasirandom structures (SQS's) for ${\mathrm{A}}_{1\ensuremath{-}x}{\mathrm{B}}_{x}$ bcc substitutional alloys at compositions $x=0.25$, 0.50 and 0.75, respectively. The structures possess local pair and multisite correlation functions that mimic those of the corresponding random bcc alloy. The introduction of these SQS's allows for the possibility of first-principles calculations of bcc solid solutions, even those with significant size-mismatch or atomic relaxation. We have tested our SQS's via first-principles calculations in the Mo--Nb, Ta--W and Cr--Fe systems, in which the bcc solid solution is observed to be stable over the whole composition range. Our first-principles SQS results provide formation enthalpies, equilibrium lattice parameters and magnetic moments of these bcc alloys which agree satisfactorily with most existing experimental data in the literature. In an effort to understand the atomic relaxation behavior in bcc solid solutions, we have also investigated the nearest neighbor bond length distributions in the random bcc alloys. The proposed bcc SQS's are quite general and can be applied to other binary bcc alloys.

Characterization of Raman Spectra of Size-Selected TiO2Nanoparticles by Two-Dimensional Correlation Spectroscopy

Nanometer-sized materials have intensively studied due to their unique physical and chemical properties as well as their great potential of technological applications. 1-5 Despite many studies on the structure-property relations of nanoparticles using the various characterization techniques, such an understanding is still to be answered. Therefore, we have recently explored the relationship between the size and structure of size-selected TiO 2 nanoparticles, which are prepared via a hydrolysis method with Ti[OCH(CH3)2]4 as the starting material, by X-ray absorption spectroscopy (XAS). 6 Analysis of the XAS of the samples with an average particle size of ~30 nm (sample A), ~12 nm (sample B), and ~7 nm (sample C) demonstrated that samples A and B have an anatase structure, whereas sample C has a structure very similar to that of the TiO 2 II phase. The TiO2 II phase generally arises only under high-pressure conditions. This difference can be attributed to size-induced radial pressure within the smaller nanoparticles, which plays an important role in the phase of TiO 2 nanoparticles in sample C. In addition, we have studied the relationship between the particle size and change of Raman bands of TiO 2 nanoparticles, sample A and sample B. 7 The obtained Raman spectra showed the broadening and shift of Raman bands with decreasing particle diameter. The origin of Raman shifts can be attributed to the effect of smaller particle size and it affects the force constant and vibrational amplitudes of the nearest neighbor bond. In this study, in order to analyze the vibrational modes of size-selected TiO2 nanoparticles and to the shift of Raman bands of TiO2 nanoparticles with particle size, we have applied two-dimensional (2D) correlation spectroscopy to the particle size-dependent Raman spectra of TiO 2 nanoparticles. Generalized 2D correlation spectroscopy has been applied extensively to the analysis of spectral data sets obtained during the observation of a system under some external perturbation. 8-10 Because of the wide range of applications of this technique, it has become one of the standard analytical techniques for interpreting various types of spectroscopic data. The details of this technique are described elsewhere, 8-10 so no further description is given here.

Geometric properties of two-dimensional critical and tricritical Potts models.

We investigate geometric properties of the general q-state Potts model in two dimensions, and define geometric clusters as sets of lattice sites in the same Potts state, connected by nearest-neighbor bonds with variable probability p. We find that, besides the random-cluster fixed point, both the critical and the tricritical Potts models have another fixed point in the p direction. For the critical model, the random-cluster fixed point p(r) is unstable and the other point p(g) > or =p(r) is stable; while p(r) is stable and p(g) < or =p(r) is unstable at tricriticality. Moreover, we show that the fixed point p(g) of a critical and tricritical q-state Potts models can be regarded to correspond to p(r) of a tricritical and critical q'-state Potts models, respectively. In terms of the coupling constant of the Coulomb gas g, these two models are related as gg'=16. By means of Monte Carlo simulations, we obtain p(g)=0.6227(2) and 0.6395(2) for the tricritical Blume-Capel and the q=3 Potts model, respectively, and confirm the predicted values of the magnetic and bond-dilution exponents near p(g).

Structural investigation of iron sulfides synthesized by mechanochemical reaction

In the current study, pure elemental powders of Fe and S were mixed to give the desired compositions of Fe 67 S 33 , Fe 50 S 50 and Fe 33 S 67 . A SPEX 8000D high-energy ball mill was used to synthesize iron sulfide powders under an Ar-filled atmosphere. The as-milled powders were examined by conventional X-ray diffraction (XRD) and synchrotron X-ray absorption spectroscopy (XAS). The experimental results showed that mechanochemical reactions occurred during the ball milling process for all the compositions investigated. The Fe 1− x S phase was observed at the end of milling. The formation time of the Fe 1− x S phase increased with increasing sulfur content. Extended X-ray absorption fine structure (EXAFS) results revealed that the nearest neighbor bond lengths of the radial distribution function for iron decreased when iron sulfides formed. X-ray absorption near-edge structure (XANES) of sulfar K-edge distinguished better the structural evolution of these iron sulfides.

Rock-scissors-paper game on regular small-world networks

The spatial rock-scissors-paper game (or cyclic Lotka-Volterra system) is extended to study how the spatiotemporal patterns are affected by the constructed backgrounds providing uniform number of neighbors (degree) at each site. On the square lattice this system exhibits a self-organizing pattern with equal concentration of the competing strategies (species). If the quenched background is constructed by substituting random links for the nearest neighbor bonds of a square lattice then a limit cycle occurs when the portion of random links exceeds a threshold value. This transition can also be observed if the standard link is replaced temporarily by a random one with a probability $P$ at each step of iteration. Above a second threshold value of $P$ the amplitude of global oscillation increases with time and finally the system reaches one of the homogeneous (absorbing) states. In this case the results of Monte Carlo simulations are compared with the predictions of the dynamical cluster technique evaluating all the configuration probabilities on one-, two-, four-, and six-site clusters.

Study of light-induced vector changes in the local atomic structure of As–Se glasses by EXAFS

We have observed light-induced vector changes in the local structure of As–Se glasses using extended X-ray absorption fine structure (EXAFS) experiments with in situ laser illumination. Local structure around As and Se atoms was determined for as-prepared as well as annealed a-As40Se60 films, which were exposed to bandgap light of polarization parallel and perpendicular to that of the X-rays. For the as-prepared film, the nearest neighbor bond distance around Se atoms increases, the magnitude of which varies with the polarization of light, thus confirming our previous observations on a-As50Se50 films. These results give an atomistic indication of a light-induced vector expansion in any material, and provide insight of the mechanisms of the light-induced atom displacements.

Molecular Dynamics Simulations of Glass Formation and Crystallization in Binary Liquid Metals

The glass formation of binary liquid metals are studied using molecular dynamics simulations, where the atomic interactions are modeled with a Sutton-Chen many-body potential. We use a model binary alloy system (Cu50Cu50) which differ in their atomic radii and/or cohesive energies between Cu* and Cu**. First, when we change the atomic size ratio λ (λ≤1.0) only, we find that there are three regimes defined by the magnitude of λ upon cooling. When λ is close to 1.0, crystallization occurs. Glass formation occurs at moderate λ values. When the λ is small, the alloy phase separates into pure phases. Second, when we vary λ and the cohesive energy ratio e (e ≤1.0) along the line in constant energy density space (e/λ=constant), glass formation occurs at moderate λ values but no phase separation is observed at any λ. Therefore, we find that the energy density is the dominant parameter in controlling the phase separation behavior of metallic alloys. From the studies of structural properties, we find that the fivefold symmetry becomes prominent in glasses and shows a maximum at λ=0.85 in both cases. Finally, when we vary e only while keeping λ constant, the system shows a very limited glass forming regime (e 0.95. To further investigate how the size ratios affect the properties of glasses, we analyze the structure of glasses as a function of λ. For glasses, we find that a very useful assessment of local structure is provided by Honeycutt and Andersen (HA) analysis [10]. In HA analysis, each type of bonding is classified by a sequence of four integers. The first integer is 1 if the atoms in the root pair are bonded, otherwise it is 2. The second integer is the number of near-neighbor atoms commonly shared by the root pair. The third integer is the number of nearest-neighbor bonds among the shared neighbors. The forth integer provides the information about nearest bond geometry. For example, the analysis of various structures in terms of HA pairs is given in Table I. The HA analysis results of the quenched binary Cu50Cu50 system is shown in Figure 2. At λ=1.0, the system becomes an FCC/HCP crystal, therefore it shows almost no 1551 pair character. As λ decreases, the system becomes a glass, and the 1551 and 2331 pairs dominate. The 1551 and 2331 pairs show a maximum at λ=0.85. The 1551 and 2331 pairs decrease abruptly while the 1421 and 1422 pairs start to increase at λ<0.60, implying the growth of crystallization tendency at small λ. Figure 1. Schematic diagram comparing the size ratio λ effect (topological disorder, scheme (a)), constant energy density effect (topological and chemical disorder, scheme (b)), and cohesive energy ratio e effect (chemical disorder, scheme (c)) of constituting elements (Cu* and Cu**). Figure 2. Honeycutt-Andersen pair fraction as a function of atomic size ratio (λ) at T=300K of cooling run. At λ=1.0, the system has many 1421 and 1422 pairs and almost no 1551 pairs indicating that it is composed of FCC and HCP phases. As λ decreases, the 1551 and 2331 pairs increase dramatically, showing a maximum at λ=0.85. Atomic size ratio λ 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 C oh es iv e en er gy r at io e 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 (a) Size effect only (b) Constant energy density line: e(λ)=λ (c) Bond character effect only λ 0.5 0.6 0.7 0.8 0.9 1.0 H A p ai r fra ct io n 0.0 0.2 0.4 0.6 0.8 1.0 1.2

Macroscopic entanglement jumps in model spin systems

In this paper, we consider some frustrated spin models for which the ground states are known exactly. The concurrence, a measure of the amount of entanglement can be calculated exactly for entangled spin pairs. Quantum phase transitions involving macroscopic magnetization changes at critical values of the magnetic field are accompanied by macroscopic jumps in the $T=0$ entanglement. A specific example is given in which magnetization plateaus give rise to a plateau structure in the amount of entanglement associated with nearest-neighbor bonds. We further show that macroscopic entanglement changes can occur in quantum phase transitions brought about by the tuning of exchange interaction strengths.

A new approach for studying nucleation phenomena using molecular simulations: Application to CO2 hydrate clathrates

We use an order-parameter formulation, in conjunction with non-Boltzmann sampling to study the nucleation of clathrate hydrates from water–CO2 mixtures, using computer simulations. A set of order parameters are defined: Φigg (i=1,2,…,n and gg for guest–guest), which characterize the spatial and orientational order of the CO2 molecules, and Φihh (hh for host–host), which govern the ordering of the water molecules. These are bond-orientational order parameters based on the average geometrical distribution of nearest-neighbor bonds. The free-energy hypersurface as a function of the order parameters is calculated using the Landau–Ginzburg approach. The critical cluster size that leads to the nucleation of the clathrate phase is determined accurately by analyzing the free energy surface. We find that the nucleation proceeds via “the local structuring mechanism,” i.e., a thermal fluctuation causing the local ordering of CO2 molecules leads to the nucleation of the clathrate, and not by the current conceptual picture, called “the labile cluster hypothesis.” The local ordering of the guest molecules induces ordering of the host molecules at the nearest- and next-to-nearest-neighbor shells, which are captured by a three-body host–host order parameter, ζhh; these thermodynamic fluctuations lead to the formation of the critical nucleus. Our results are significant in understanding the proposed sequestration of CO2 by direct ocean injection in order to mitigate the greenhouse effect.

Atomic structural environment of Y in the residual glass phase of silicon nitride and α-sialon

The atomic structural environments around Y ions in the residual glass phase of Si 3N 4 and α-sialon densified with Y 2O 3 and Al 2O 3 have been investigated using extended X-ray absorption fine structure (EXAFS). In the residual glass phase, on average, the Y–O/N nearest neighbor bond length is determined to be 2.30 Å, which corresponds to the Y–O bond length in cubic Y 2O 3, indicating that O is the dominant nearest neighbor of Y. The fitted apparent Y–O/N nearest neighbor coordination number is ~4, which is apparently lower than that when Y is dissolved in a bulk glass, indicating that Y occupies substitutional Si sites. It is also further suggested that the Y–O/N polyhedron in the residual glass phase in silicon nitride and α-sialon is more distorted in comparison with that when Y is dissolved in a bulk glass phase.

EFFECT OF THE ANNEALING TEMPERATURE ON THE ELECTRONIC AND ATOMIC STRUCTURES OF EXCHANGE-BIASED NiFe–FeMn BILAYERS

In this study we measured the Fe, Mn, and Ni L2,3-edge X-ray absorption near-edge structure (XANES) and K-edge extended X-ray absorption fine structure (EXAFS) of the ferromagnetic (FM) NiFe and antiferromagnetic (AFM) FeMn bilayer films prepared with various annealing temperatures. The branching ratios of the white-line intensities in the Fe, Mn, and Ni L2,3-edges XANES spectra and consequently the magnetic properties of these exchange-biased FM NiFe - AFM FeMn bilayers are found to depend strongly on the annealing temperature. We find that the first peak in the Fe, Mn, and Ni K-edge EXAFS Fourier transform spectra are very similar, which suggests that the nearest-neighbor bond lengths among Fe, Mn, and Ni atoms are essentially the same in the NiFe–FeMn bilayers. However, the peaks at distances greater than ~ 3 Å appear to be sensitive to the annealing temperature especially for the Fe and Mn K-edge spectra, which suggests that annealing alters the atomic structures of the next-nearest-neighbor and more distant shells surrounding the Fe and Mn atoms in the NiFe–FeMn bilayers.

Quantum phase transitions in spin-12frustrated molecular clusters: The numerical evidence

By exact diagonalization, we investigate several spin-$\frac{1}{2}$ ${J}_{1}\ensuremath{-}{J}_{2}$ real clusters of molecular scale with different shapes. Our calculations show that when the ratio $\ensuremath{\eta}$ of next-nearest-neighbor to nearest-neighbor bonds is equal to 1, even a cluster of only 25 sites exhibits bulk behaviors and has quantum phase transitions. Two effective critical points are around ${J}_{2}{/J}_{1}=0.3762$ and 0.612, respectively. They are very close to those of the infinite ${J}_{1}\ensuremath{-}{J}_{2}$ square lattice. But when $\ensuremath{\eta}&lt;~0.85,$ the quantum phase transition around ${J}_{2}{/J}_{1}=0.3762$ disappears. By calculating the distributions of the average values of ${S}_{i}^{z},$ the bulk behaviors are demonstrated graphically. In the intermediate phase, the sites on the corners have distinctly different character from the other sites. The distribution is obviously centralized on the corner sites.

Structure of clusters on embedded-atom-method metal fcc (111) surfaces

With a genetic algorithm, the structure of adatom clusters is optimized and studied systematically on different metal fcc (111) surfaces modeled by the embedded atom method. It is found that the various lowest-energy structures on the different surfaces can be explained in terms of the relative interaction range and the adatom-substrate interaction. The longer the relative interaction range becomes, the sharper or more extended the shape of the lowest-energy structure tends to be, in which the number of next-nearest-neighbor bonds decreases. When the compensation effect from the adatom-substrate interaction becomes strong, the configuration with the smaller number of nearest-neighbor bonds could be the lowest-energy structure; it also induces the shape of the lowest-energy structure as being sharp or extended. In this case, another interesting phenomenon is that the plane of the cluster is obviously bent.