A conformational analysis method for understanding the energy landscapes of clusters.

A newly developed unbiased structural optimization method, named dynamic lattice searching (DLS), is proposed as an approach for conformational analysis of atomic/molecular clusters and used in understanding the energy landscape of large clusters. The structures of clusters are described in terms of the number of basic tetrahedron (BT) units they contain. We found that the hit numbers of different structural motifs in DLS runs is proportional to the number of BTs. A parameter T(max) is defined to limit the maximal number of atoms moved in a structural transition. Results show that T(max) is a key parameter for modulating the efficiency of the DLS method and has a great influence on the hit number of different motifs in DLS runs. Finally, the effect of potential range on the conformational distribution of the (Morse)(98) cluster is also discussed with different potential-range parameters.     

Global minimum structures of morse clusters as a function of the range of the potential: 81<or=N<or=160

We have attempted to find the putative global minimum structures of Morse clusters for cluster size N=81-160 as a function of the range of the potential (with potential range rho0>or=3.0). Moreover, compared to the results for N相似文献   

MoDEL: an efficient strategy for ungapped local multiple alignment

We introduce a method for ungapped local multiple alignment (ULMA) in a given set of amino acid or nucleotide sequences. This method explores two search spaces using a linked optimization strategy. The first search space M consists of all possible words of a given length W, defined on the residue alphabet. An evolutionary algorithm searches this space globally. The second search space P consists of all possible ULMAs in the sequence set, each ULMA being represented by a position vector defining exactly one subsequence of length W per sequence. This search space is sampled with hill-climbing processes. The search of both spaces are coupled by projecting high scoring results from the global evolutionary search of M onto P. The hill-climbing processes then refine the optimization by local search, using the relative entropy between the ULMA and background residue frequencies as an objective function. We demonstrate some advantages of our strategy by analyzing difficult natural amino acid sequences and artificial datasets. A web interface is available at     

Dependence of computer model structure of an amorphous solid on hardness of the repulsive potential

In models of an amorphous solid with a potential U = ar_–n(n = 3–20), the main structural elements were found to be tetrahedron and quartoctahedron. At lower n there are more tetrahedra and less quartoctahedra. In addition to the fom and size of separate Delaunay simplices, their mutual arrangement has been studied by percolafion analysis. For that we used the coloring of the Voronoi network: according to tetrahedricity of simplices to identify dense atomic configurations, and according to the radii of mouths of cavities (passages between simplices) to identify the cavities. We have found percolative cavities in liquids and percolating dense configurations in all amorphous solid models.Institute of Chemical Kinetics and Combustion, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 34, No. 5, pp. 94–105, September–October, 1993.Translated by L. Smolina     

Syntheses and structures of two low-dimensional beryllium phosphate compounds: [C5H14N2]2[Be3(HPO4)5].H2O and [C6H18N2]0.5[Be2(PO4)(HPO4)OH].0.5H2O

The first two low-dimensional beryllium phosphates, [C5H14N2]2[Be3(HPO4)5].H2O (BePO-CJ29) and [C6H18N2]0.5[Be2(PO4)(HPO4)OH].0.5 H2O (BePO-CJ30), have been successfully synthesized under mild hydrothermal/solvothermal conditions. BePO-CJ29 is built up from strict alternation of BeO4 and HPO4 tetrahedra forming a unique one-dimensional double chains with 12-ring apertures. There are pseudo-10-ring apertures enclosed by two double chains through H-bonds. BePO-CJ29 can also be viewed as a pseudo 2-D layered structure stabilized by strong H-bonds. The diprotonated 2-methylpiperazium cations are located at three positions (i.e., inside the 12-ring aperture, inside the pseudo-10-ring aperture, and in the interlayer of the inorganic pseudo-layers. BePO-CJ30 is constructed by the alternation of Be-centered tetrahedra (including BeO4 and HBeO4) and P-centered tetrahedra (including PO4 and HPO4) resulting in a two-dimensional layered structure parallel to the (0 1 1) direction. The complex layer is composed of coupled 4.8 net sheets. The diprotonated 1,6-hexandiamine cations and water molecules reside in the interlayer regions and interact with the inorganic layers through H-bonds. Crystal data are as follows: [C5H14N2]2[Be3(HPO4)5].H2O (BePO-CJ29), triclinic, P1 (No. 2), a = 8.1000(9) A, b = 8.4841(14) A, c = 19.665(2) A, alpha = 89.683(10) degrees, beta = 78.182(8) degrees, gamma = 87.932(9) degrees, V = 1321.9(3) A3, Z = 2, R1 = 0.0523 (I > 2sigma(I)), and wR2 = 0.1643 (all data); [C6H18N2]0.5[Be2(PO4)(HPO4)OH].0.5 H2O (BePO-CJ30), orthorhombic, Pccn (No. 56), a = 26.01(4) A, b = 8.431(12) A, c = 9.598(13) A, V = 2105(5) A3, Z = 8, R1 = 0.0833 (I > 2sigma(I)), and wR2 = 0.2278 (all data).     

Investigation of complexes formed by interaction of cationic gemini surfactants with deoxyribonucleic acid

Cationic gemini surfactants, N,N-bis(dimethylalkyl)-alpha,omega-alkanediammonium dibromide [C(m)H(2m+1)(CH(3))(2)N(+)(CH(2))(s)N(+)(CH(3))(2)C(m)H(2m+1) x 2 Br(-), or m-s-m], have proven to be effective synthetic vectors for gene delivery (transfection). Complexes (lipoplexes) of gemini compounds, where m = 12, s = 3, 12 and m = 18 : 1(oleyl), s = 2, 3, 6, with DNA have been investigated using isothermal titration calorimetry (ITC), dynamic light scattering (DLS), zeta potential, atomic force microscopy (AFM) and circular dichroism (CD) techniques. The results show that lipoplex properties depend on the structural properties of the gemini surfactants, the presence of the helper lipid dioleoylphosphatidylethanolamine (DOPE), and the titration sequence. ITC data show that the interaction between DNA and gemini surfactants is endothermic and the observed enthalpy vs. charge ratio profile depends upon the titration sequence. Isoelectric points (IP) of lipoplex formation were estimated from the zeta potential measurements and show good agreement with the reaction endpoints (RP) obtained from ITC. DLS data indicate that DNA is condensed in the lipoplex. AFM images suggest that the lipoplex morphology changes from isolated globular-like aggregated particles to larger-size aggregates with great diversity in morphology. This change is further accentuated by the presence of DOPE in the lipoplexes. The results are interpreted in terms of some current models of lipoplex formation.     

A new ab initio potential energy surface for the NeCO complex with the vibrational coordinate dependence

A new high quality three-dimensional potential energy surface for the Ne-CO van der Waals complex is developed using the CCSD(T) method and avqz∕avqz+33221 basis set. The ab initio calculation is performed in a total of 1365 configurations with supermolecule method. There is a single global minimum located in a nearly T-shaped geometry. The global minimum energy is -49.4090 cm(-1) at R(e)=6.40a(0) and θ(e)=82.5(°) for V(00). Using the three-dimensional potential energy surface, we have calculated bound rovibrational energy levels up to J = 10 including the Coriolis coupling terms. Compared with the experimental transition frequencies, the theoretical results are in good agreement with the experimental results.     

Global optimization of bimetallic cluster structures. II. Size-matched Ag-Pd, Ag-Au, and Pd-Pt systems

Genetic algorithm global optimization of Ag-Pd, Ag-Au, and Pd-Pt clusters is performed. The 34- and 38-atom clusters are optimized for all compositions. The atom-atom interactions are modeled by a semiempirical potential. All three systems are characterized by a small size mismatch and a weak tendency of the larger atoms to segregate at the surface of the smaller ones. As a result, the global minimum structures exhibit a larger mixing than in Ag-Cu and Ag-Ni clusters. Polyicosahedral structures present generally favorable energetic configurations, even though they are less favorable than in the case of the size-mismatched systems. A comparison between all the systems studied here and in the previous paper (on size-mismatched systems) is presented.     

Ce4

The yellow-orange oxonitridosilicate oxide Ce4[Si4O4N6]O was obtained by the reaction of cerium metal with Si(NH)2 and SiO2 in a radiofrequency furnace at 1560 degrees C. The crystal structure was determined by single-crystal X-ray diffraction (a = 1033.67(6) pm, P2,3, Z = 4, R1 = 0.0412, wR2 = 0.0678) and powder neutron diffraction. In the solid there are complex cations [Ce4O]10+ that are enveloped by a hyperbolical layer structure [Si4O4N6]10-. The layer is built up by corner-sharing SiON3 tetrahedra of Q3 type. The oxygen atoms of the SiON3 tetrahedra are terminally bound to Si, while all nitrogen atoms bridge two neighboring Si centres. The crystallographic differentiation of O and N was unequivocally possible by a careful evaluation of the single-crystal X-ray diffraction data combined with lattice-energy calculations by using the MAPLE concept (Madelung part of lattice energy). Furthermore the results were confirmed by the chemical analyses. Subsequently, the determined N/O distribution and their crystallographic ordering was proved by neutron powder diffraction. In accordance with the molar ratio Si:(O,N) = 2:5 the [Si4O4N6]10- network may be classified as a layer silicate. In this specific case a hyperbolically corrugated topology of the layers is observed; this is correlated to periodic nodal surface (PNS) representatives.     

Structure and diffusion in amorphous aluminum silicate: a molecular dynamics computer simulation

The amorphous aluminum silicate (Al2O3)2(SiO2) [AS2] is investigated by means of large scale molecular dynamics computer simulations. We consider fully equilibrated melts in the temperature range 6100 K> or =T> or =2300 K as well as glass configurations that were obtained from cooling runs from T=2300 to 300 K with a cooling rate of about 10(12) K/s. Already at temperatures as high as 4000 K, most of the Al and Si atoms are fourfold coordinated by oxygen atoms. Thus, the structure of AS2 is that of a disordered tetrahedral network. The packing of AlO4 tetrahedra is very different from that of SiO4 tetrahedra in that Al is involved with a relatively high probability in small-membered rings and in triclusters in which an O atom is surrounded by four cations. We find as typical configurations two-membered rings with two Al atoms in which the shared O atoms form a tricluster. On larger length scales, the system shows a microphase separation in which the Al-rich network structure percolates through the SiO2 network. The latter structure gives rise to a prepeak in the static structure factor at a wave number q=0.5 A(-1). A comparison of experimental x-ray data with the results from the simulation shows good agreement for the structure function. The diffusion dynamics in AS2 is found to be much faster than in SiO2. We show that the self-diffusion constants for O and Al are very similar and that they are by a factor of 2-3 larger than the one for Si.     

Mixed metallic Ba(Co,Fe)X(0.2)O(3-δ) (X = F, Cl) hexagonal perovskites: drastic effect of Fe-incorporation on structural and electronic features

Starting from the parent 10H-Ba(5)Co(5)X(1-x)O(13-δ) (trimeric strings of face-sharing CoO(6) octahedra with terminal CoO(4) tetrahedra, stacking sequence (chhch')(2)) and 6H-Ba(6)Co(6)X(1-x)O(16-δ) (similar with tetrameric strings, stacking sequence chhhch') hexagonal perovskites forms (X = F, Cl; c, h = [BaO(3)] layers ; h' = [BaOX(1-y)] layers), we show here that the Fe incorporation leads to large domains of solid solutions for both X = F and Cl but exclusively stabilizes the 10H-form independently of the synthesis method. In this form, the lowest concentration of h-layers is stabilized by a sensitive metal reduction with increasing the Fe ratio. In a more general context of competition between several hexagonal perovskite polymorphs available for most of the transition metals, this redox change is most probably the key factor driving 1D (face-sharing chains) to 3D (corner-sharing) connectivities. Strikingly, ND data evidence the location of oxygen deficiencies in the tetrahedral (Co/Fe) coordination. This effect is exaggerated at high temperature, while (Co/Fe)O(4-δ) coordinations are completed by the displacement of X(-) anions toward the (Co/Fe) sphere of coordination following a "push-and-pull" mechanism within h'-[BaOX(1-y)] layers. The Fe-incorporation is also accompanied by increasing conduction gaps with predominant 1D variable range hopping. The full series show antiferromagnetic behavior with increasing T(N) as [Fe] increases. For Fe-rich compounds T(N) is estimated about 600 K, as rarely observed for hexagonal perovskite compounds. Finally, magnetic structures of all iron-doped compounds show a site-to-site AFM ordering, different of the magnetic structure of Co-only parent compounds. Here, DFT calculations predict low-spin octahedral Co configurations, but high-spin Fe species in the same sites.     

A dynamic lattice searching method for fast optimization of Lennard-Jones clusters

A highly efficient unbiased global optimization method called dynamic lattice searching (DLS) was proposed. The method starts with a randomly generated local minimum, and finds better solution by a circulation of construction and searching of the dynamic lattice (DL) until the better solution approaches the best solution. The DL is constructed adaptively based on the starting local minimum by searching the possible location sites for an added atom, and the DL searching is implemented by iteratively moving the atom located at the occupied lattice site with the highest energy to the vacant lattice site with the lowest energy. Because the DL can greatly reduce the searching space and the number of the time-consuming local minimization procedures, the proposed DLS method runs at a very high efficiency, especially for the clusters of larger size. The performance of the DLS is investigated in the optimization of Lennard-Jones (LJ) clusters up to 309 atoms, and the structure of the LJ(500) is also predicted. Furthermore, the idea of dynamic lattice can be easily adopted in the optimization of other molecular or atomic clusters. It may be a promising approach to be universally used for structural optimizations in the chemistry field.     

Characteristic sequences for DNA primary sequence

A DNA sequence can be identified with a word over an alphabet N = [A, C, G, T]. Characteristic sequences of a DNA sequence are given in term of classifications of bases of nucleic acids. Using the characteristic sequences, we construct a set of 2 x 2 matrices to represent DNA primary sequences, which are based on counting of the frequency of occurrence of all (0,1) triplets of characteristic sequences. Furthermore, the leading eigenvalues of these matrices are computed and considered as invariants for the DNA primary sequences. Similarity and dissimilarity analysis based on the characteristic sequences are given for eight exon-1 genes of beta-globin about eight species.     

Oxidation resistance of LnSiON powders (Ln=Y,Gd and La)

For application of LnSiON (Ln=Y, Gd and La) oxynitride materials, e.g. as host-lattices for lamp phosphors, oxidation resistance up to about 600 °C in air is a prerequisite. In this study we prepared LnSiON (Ln=Y, Gd and La) powders by solid state reaction and observed via TGA/DTA-experiments that most compounds are oxidation resistant up to 600 °C in air. The stability in air at high temperatures increases going from Ln₅(SiO₄)₃N, Ln₄Si₂O₇N₂, LnSiO₂N, Ln₂Si₃O₃N₄ to Ln₃Si₈O₄N₁₁. This is explained by an increasing cross-linking between the siliconoxygennitrogen tetrahedra in this sequence. For the lattices with less cross-linking between the siliconoxygennitrogen tetrahedra we observed that the oxidation resistance decreases slightly going from Y and Gd to La. For these lattices, also, an additional weight gain was observed during the oxidation reaction, which was higher than expected for complete oxidation. The additional weight gain was ascribed to an intermediate phase in which nitrogen retention takes place.     

Determination of structural transitions of atomic clusters from local and global bond orientational order parameters

Designing an effective order parameter for the identification of geometries in atomic clusters is an important step toward understanding the structural transitions occurring in these systems. We propose a method that simultaneously utilizes the local and global bond orientational order parameters for structural transitions. When applied to Lennard-Jones clusters at finite temperature over the size range 30< or =N< or =146, this method identified all the major geometries: icosahedra with Mackay overlayers, icosahedra with anti-Mackay overlayers, decahedra, octahedra, and tetrahedra. From the distributions of these geometries as a function of temperatures on clusters containing 38, 75, and 98 atoms, we are able to interpret all transition types without ambiguity.     

A dynamic lattice searching method with constructed core for optimization of large Lennard-Jones clusters

A variation of the previous dynamic lattice searching (DLS) method, named as DLS with constructed core (DLSc), was proposed for structural optimization of Lennard-Jones (LJ) clusters. In the new method, the starting random structure is generated with an icosahedron or a decahedron as a core. For a cluster with n shells, the atoms in the inner n - 2 shells are set as a fixed core, and the remaining atoms in the outer 2 shells are optimized by DLS. With applications of DLSc to optimization of LJ100-200 and LJ660-670, it was found that all the putative global minima can be obtained by using the DLSc method, and the method was proved to be high efficient compared with the previous DLS, because the searching space is reduced by the use of the fixed core. However, although DLSc is still an unbiased approach for smaller LJ clusters, it turned out to be biased for large ones. Further works are still needed to make it to be a more general method for cluster optimization problem.     

Size‐guided multi‐seed heuristic method for geometry optimization of clusters: Application to benzene clusters

Since searching for the global minimum on the potential energy surface of a cluster is very difficult, many geometry optimization methods have been proposed, in which initial geometries are randomly generated and subsequently improved with different algorithms. In this study, a size‐guided multi‐seed heuristic method is developed and applied to benzene clusters. It produces initial configurations of the cluster with n molecules from the lowest‐energy configurations of the cluster with n − 1 molecules (seeds). The initial geometries are further optimized with the geometrical perturbations previously used for molecular clusters. These steps are repeated until the size n satisfies a predefined one. The method locates putative global minima of benzene clusters with up to 65 molecules. The performance of the method is discussed using the computational cost, rates to locate the global minima, and energies of initial geometries. © 2018 Wiley Periodicals, Inc.     

Equilibrium spherically curved two-dimensional Lennard-Jones systems

To learn about the basic aspects of nanoscale spherical molecular shells during their formation, spherically curved two-dimensional N-particle Lennard-Jones systems are simulated, studying curvature evolution paths at zero temperature. For many N values (N<800) equilibrium configurations are traced as a function of the curvature radius R. Sharp jumps for tiny changes in R between trajectories with major differences in topological structure correspond to avalanche-like transitions. For a typical case, N=25, equilibrium configurations fall on smooth trajectories in state space which can be traced in the E-R plane. The trajectories show up with local energy minima, from which growth in N at steady curvature can develop.     

DNA closed nanostructures: a structural and Monte Carlo simulation study

DNA nanoconstructs are obtained in solution by using six unique 42-mer DNA oligonucleotides, whose sequences have been designed to form a pseudohexagonal structure. The required flexibility is provided by the insertion of two non-base-paired thymines in the middle of each sequence that work as flexible hinges and constitute the corners of the nanostructure when formed. We show that hexagonally shaped nanostructures of about 7 nm diameter and their corresponding linear open constructs are formed by self-assembly of the specifically designed linear oligonucleotides. The structural and dynamical characterization of the nanostructure is obtained in situ for the first time by using dynamic light scattering (DLS), a noninvasive method that provides a fast dynamic and structural analysis and allows the characterization of the different synthetic DNA nanoconstructs in solution. A validation of the LS results is obtained through Monte Carlo (MC) simulations and atomic force microscopy (AFM). In particular, a mesoscale molecular model for DNA, developed by Knotts et al., is exploited to perform MC simulations and to obtain information about the conformations as well as the conformational flexibilities of these nanostructures, while AFM provides a very detailed particle analysis that yields an estimation of the particle size and size distribution. The structural features obtained by MC and AFM are in good agreement with DLS, showing that DLS is a fast and reliable tool for characterization of DNA nanostructures in solution.