Charge patching method for electronic structure of organic systems

The development of the charge patching method for the calculation of the electronic structure of organic systems containing a large number of atoms was presented. The method was tested on a range of systems including alkane and alkene chains, polyacenes, polythiophenes, polypyrroles, polyfuranes, polyphenylene vinylene, and poly(amidoamine) dendrimers. The results obtained by the method are in very good agreement with direct calculations based on density functional theory, since the eigenstate errors are typically of the order of a few tens of meV.     

Overlapping fragments method for electronic structure calculation of large systems

We present a method for the calculation of the electronic structure of systems that contain tens of thousands of atoms. The method is based on the division of the system into mutually overlapping fragments and the representation of the single-particle Hamiltonian in the basis of eigenstates of these fragments. In practice, for the range of the system size that we studied (up to tens of thousands of atoms), the dominant part of the calculation scales linearly with the size of the system when all the states within a fixed energy interval are required. The method is highly suitable for making good use of parallel computing architectures. We illustrate the method by applying it to diagonalize the single-particle Hamiltonian obtained using the density functional theory based charge patching method in the case of amorphous alkane and polythiophene polymers.     

Structure of ultrathin polyethylene layers in multilayer films

The crystalline structures of “microlayer” and “nanolayer” polyethylene have been examined in coextruded films comprised of alternating layers of high-density polyethylene and polystyrene. Transmission electron microscopy (TEM), small-angle x-ray scattering (SAXS), and wide-angle x-ray scattering (WAXS) reveal that microlayer polyethylene, where the layer thickness is on the order of several microns, crystallizes with the normal unoriented lamellar morphology. In nanolayer films, where the film thickness of tens of nanometers is on the size scale of molecular dimensions, lamellae are oriented with the long axes perpendicular to the extrusion direction in a row-nucleated morphology similar to structures described in the literature. The lamellae are partially twisted about the long axes. The preferred twist angles of ±40° orient the lamellar surfaces normal to the layer surface. The row-nucleated morphology imparts highly anisotropic mechanical properties to the nanolayer polyethylene.     

Micro- and Nanoscale Heterogeneities in Zeolite Beta as Measured by Atom Probe Tomography and Confocal Fluorescence Microscopy

Micro- and nanoscale information on the activating and deactivating coking behaviour of zeolite catalyst materials increases our current understanding of many industrially applied processes, such as the methanol-to-hydrocarbon (MTH) reaction. Atom probe tomography (APT) was used to reveal the link between framework and coke elemental distributions in 3D with sub-nanometre resolution. APT revealed 10–20 nanometre-sized Al-rich regions and short-range ordering (within nanometres) between Al atoms. With confocal fluorescence microscopy, it was found that the morphology of the zeolite crystal as well as the secondary mesoporous structures have a great effect on the microscale coke distribution throughout individual zeolite crystals over time. Additionally, a nanoscale heterogeneous distribution of carbon as residue from the MTH reaction was determined with carbon-rich areas of tens of nanometres within the zeolite crystals. Lastly, a short length-scale affinity between C and Al atoms, as revealed by APT, indicates the formation of carbon-containing molecules next to the acidic sites in the zeolite.     

Why are buckyonions round?

Multi-layered round carbon particles (onions) containing tens to hundreds of thousands of atoms form during electron irradiation of graphite. However, theoretical models of large icosahedral fullerenes predict highly faceted shapes for molecules with more than a few hundred atoms. This discrepancy in shape may be explained by the presence of defects during the formation of carbon onions. Here, we use the semi-empirical tight-binding method for carbon to simulate the incorporation of pentagon-heptagon defects on to the surface of large icosahedral fullerenes. We show a simple mechanism that results in energetically competitive derivative structures and a global change in molecular shape from faceted to round. Our results provide a plausible explanation of the apparent discrepancy between experimental observations of round buckyonions and theoretical predictions of faceted icosahedral fullerenes. Received: 27 August 1997 / Accepted: 23 October 1997     

Theoretical Studies on Electronic Spectra and Second-order Nonlinear Optical Properties of Barbituric Acid Derivatives Substituted with Schiff Base

Barbituric acid (BA) is a very important kind of compound in biological chemistry and medicine. It can be applied in abirritative medicine and antioxidants.1 It is an important sort of raw material for organic synthe-sis.2 It predicts the important reactive mechanism for organic synthesis.3 Some investigations for NLO prop-erties of a series of BA derivatives have been reported by Feng and coworkers in the view of theory.4,5 The Schiff base has extensive application in the fields of organi…     

Crystal structure prediction using ab initio evolutionary techniques: principles and applications

We have developed an efficient and reliable methodology for crystal structure prediction, merging ab initio total-energy calculations and a specifically devised evolutionary algorithm. This method allows one to predict the most stable crystal structure and a number of low-energy metastable structures for a given compound at any P-T conditions without requiring any experimental input. Extremely high (nearly 100%) success rate has been observed in a few tens of tests done so far, including ionic, covalent, metallic, and molecular structures with up to 40 atoms in the unit cell. We have been able to resolve some important problems in high-pressure crystallography and report a number of new high-pressure crystal structures (stable phases: epsilon-oxygen, new phase of sulphur, new metastable phases of carbon, sulphur and nitrogen, stable and metastable phases of CaCO3). Physical reasons for the success of this methodology are discussed.     

Clusters as crystal fragments of silicon bulk

Silicon clusters of 13 to 43 atoms were studied with the semi-empirical method SINDO1. Crystalline structures of face-centered cubic (fcc), hexagonal close packed (hcp) and diamond type and noncrystalline structures of icosahedral type were compared. Noncrystalline structures are most stable for clusters up to 13 atoms. Clusters with 19 and more atoms of the fcc structure are preferable to the less dense diamond structure. With more than 35 Si atoms, the diamond structure is favored over the hcp structure. The binding energy of fcc and hcp structures decreases and that of the diamond structure increases with increasing cluster size. A similar trend is observed for the HOMO-LUMO energy gap which is taken as a measure of the band gap.     

2,4-二氟戊烷的构象与能量的理论研究

在MP2/6-311++G**和G3水平下,对2,4-二氟戊烷异构体的构象进行几何优化和能量计算.氟的强电负效应使构型发生偏转,同时导致了相隔超过3个键的原子间的电子相互作用.     

Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece

We report on the use of large-scale distributed computing simulation and novel analysis techniques for examining the dynamics of a small protein. Matters addressed include folding rate, very long time scale kinetics, ensemble properties, and interaction with water. The target system for the study, the villin headpiece, has been of great interest to experimentalists and theorists both. Sampling totaled nearly 500 mus-the most extensive published to date for a system of villin's size in explicit solvent with all atom detail-and was in the form of tens of thousands of independent molecular dynamics trajectories, each several tens of nanoseconds in length. We report on kinetics sensitivity analyses that, using a set of short simulations, probed the role of water in villin's folding and sensitivity to the simulation's electrostatics treatment. By constructing Markovian state models (MSMs) from the collected data, we were able to propagate dynamics to times far beyond those directly simulated and to rapidly compute mean first passage times, long time kinetics (tens of microseconds), and evolution of ensemble property distributions over long times, otherwise currently impossible. We also tested our MSM by using it to predict the structure of villin de novo.     

Quantitative study of filled rubber microstructure by optical and atomic force microscopy

A comprehensive approach is proposed for studying the microstructure of filled rubbers by optical and atomic force microscopy (AFM). The optical results are found to be dependent on the illumination angle. Algorithms based on the mathematical morphology are developed for the processing of optical images (removing scratches, identifying agglomerates). AFM-images are treated by a segmentation method which separates a continuous surface into segments that match filler. Parameters of secondary filler structures and the size of an area of homogeneous filler dispersion are obtained from the analysis of the segmented images. Seven carbon black filled rubbers with different mixing times are investigated. The combination of AFM with optical imaging techniques makes it possible to perform a quantitative structural analysis at scales from tens of nanometers to tens of microns, and to establish the relationship between the mixing time and the filler microstructure over the whole range of filler peculiarities.     

Sizes and properties of clusters of magnetic ferrite structures

The structures of the coordination spheres or orbits of hexagonal and cubic crystals and their sizes, coordination numbers, and coordinates of atoms and cavities have been studied. The orbits of atoms of all sublattices of octahedral and tetrahedral cavities have been calculated. The close-packed structures (FCC and HCP) of oxygen ions have been considered as basic structures. In both structures, the metal cations are distributed over octahedral and tetrahedral cavities. The developed method is used for calculating the orbits of clusters with the hexagonal crystal structure of magnetoplumbite, ilmenite, and corundum, as well as with the cubic structure of spinel and perovskite.     

Shell and subshell periodic structures of icosahedral nickel nanoclusters

Using the modified analytic embedded atom method and molecular dynamics, the binding energies and their second order finite differences (stability functions) of icosahedral Ni clusters with shell and subshell periodicity are studied in detail via atomic evolution. The results exhibit shell and subshell structures of the clusters with atoms from 147 to 250,000, and the atomic numbers corresponding to shell or subshell structures are in good agreement with the experimental magic numbers obtained in time-of-flight mass spectra of threshold photoionization, and Martin's theoretical proposition of progressive formation of atomic umbrellas. Clusters with size from 147 to 561 atoms are energetically investigated via one-by-one atomic evolution and their magic numbers are theoretically proved. For medium-size Ni clusters with 561 to 2057 atoms, the prediction of magic numbers with atomic numbers is performed on the basis of umbrella-like subshell growth in near face-edge-vertex order. The similarity of the energy curves makes it possible to extend the prediction to even larger Ni nanoclusters in hierarchical Mackay icosahedral configurations.     

Schwinger-Lanczos approach to solving scattering equations

The Lanczos method, well known in linear algebra, is applied to solving Lippmann-Schwinger equation describing scattering of non-relativistic particles with atoms and molecules. It is shown that a combination of the Lanczos technique with an appropriate contracting coordinate transformation and Romberg extrapolation generates a very efficient and accurate method for calculation of various scattering quantities with a very sparse grid. The method yields accurate results for a very low number of meshpoints (typically few tens in electron atom scattering calculation). Detailed test calculations were performed for scattering of electrons with hydrogen atoms and for dissociative attachment of electrons to diatomic molecules.     

Observation of two-step nucleation in methane hydrates

In this work we show that homogeneous nucleation of methane hydrate can, under appropriate conditions, be a very rapid process, achieved within tens of nanoseconds. In agreement with recent experimental results on different systems, we find that the nucleation of a gas hydrate crystal appears as a two-step process. It starts with the formation of disordered solid-like structures, which will then spontaneously evolve to more recognizable crystalline forms. This previously elusive first-stage state is confirmed to be post-critical in the nucleation process, and is characterized as processing reasonable short-range structure but essentially no long-range order. Its energy, molecular diffusion and local structure reflect a solid-like character, although it does exhibit mobility over longer (tens of ns) timescales. We provide insights into the controversial issue of memory effects in methane hydrates. We show that areas locally richer in methane will nucleate much more readily, and no 'memory' of the crystal is required for fast re-crystallization. We anticipate that much richer polycrystallinity and novel methane hydrate phases could be possible.     

Formation and oxidation mechanisms of Pd-Zn nanoparticles on a ZnO supported Pd catalyst studied by in situ time-resolved QXAFS and DXAFS

Formation and oxidation processes of PdZn nanoparticles on ZnO were successfully observed by means of in situ time-resolved X-ray absorption fine structure spectroscopy (XAFS), and the analysis of data on near-edge (XANES) and extended (EXAFS) structures revealed detailed changes in Pd during both processes. PdZn nanoparticles were formed on ZnO through a two-step scheme under a hydrogen atmosphere. The first process was the formation of metallic Pd nanoparticles, which was quickly finished within 1 s. The second process was the formation of PdZn nanoparticles, which took several tens of minutes. Oxidation of the PdZn nanoparticles also consisted of two processes. Zn atoms were oxidized prior to Pd atoms and the metallic Pd nanoparticles surrounded by ZnO were formed afterwards. Oxidation of the metallic Pd nanoparticles was scarce and very slow. According to the results of kinetic analyses, the metallic Pd surrounded by ZnO was a stable species under the oxidative atmosphere.     

Self-assembled templates for polypeptide synthesis

The chemical synthesis of polypeptide chains >50 amino acids with prescribed sequences is challenging. In one approach, native chemical ligation (NCL), short, unprotected peptides are connected through peptide bonds to render proteins in water. Here we combine chemical ligation with peptide self-assembly to deliver extremely long polypeptide chains with stipulated, repeated sequences. We use a self-assembling fiber (SAF) system to form structures tens of micrometers long. In these assemblies, tens of thousands of peptides align with their N- and C-termini abutting. This arrangement facilitates chemical ligation without the usual requirement for a catalytic cysteine residue at the reactive N-terminus. We introduced peptides with C-terminal thioester moieties into the SAFs. Subsequent ligation and disassembly of the noncovalent components produced extended chains > or =10 microm long and estimated at > or =3 MDa in mass. These extremely long molecules were characterized by a combination of biophysical, hydrodynamic, and microscopic measurements.     

Spectroscopic, morphological, and mechanistic investigation of the solvent-promoted aggregation of porphyrins modified in meso-positions by glucosylated steroids

Solvent-driven aggregation of a series of porphyrin derivatives was studied by UV/Vis and circular dichroism spectroscopy. The porphyrins are characterised by the presence in the meso positions of steroidal moieties further conjugated with glucosyl groups. The presence of these groups makes the investigated macrocycles amphiphilic and soluble in aqueous solvent, namely, dimethyl acetamide/water. Aggregation of the macrocycles is triggered by a change in bulk solvent composition leading to formation of large architectures that express supramolecular chirality, steered by the presence of the stereogenic centres on the periphery of the macrocycles. The aggregation behaviour and chiroptical features of the aggregates are strongly dependent on the number of moieties decorating the periphery of the porphyrin framework. In particular, experimental evidence indicates that the structure of the steroid linker dictates the overall chirality of the supramolecular architectures. Moreover, the porphyrin concentration strongly affects the aggregation mechanism and the CD intensities of the spectra. Notably, AFM investigations reveal strong differences in aggregate morphology that are dependent on the nature of the appended functional groups, and closely in line with the changes in aggregation mechanism. The suprastructures formed at lower concentration show a network of long fibrous structures spanning over tens of micrometres, whereas the aggregates formed at higher concentration have smaller rod-shaped structures that can be recognised as the result of coalescence of smaller globular structures. The fully steroid substituted derivative forms globular structures over the whole concentration range explored. Finally, a rationale for the aggregation phenomena was given by semiempirical calculations at the PM6 level.     

Halogen modified two-dimensional covalent triazine frameworks as visible-light driven photocatalysts for overall water splitting

The covalent triazine framework CTF-1 as a member of the two-dimensional covalent organic frameworks(COFs) is a category of novel metal-free photocatalysts for water splitting. The large band gap severely restricts its energy conversion efficiency. By means of the first-principles calculations, we proposed the decoration of CTF-1 by anchoring halogen atoms onto benzene moieties for improving the solar-to-hydrogen(STH) efficiency. The electronic structures reveal that the halogen substitution successfully decreases the band gap of CTF-1. Meanwhile, the calculated free energy changes along the reaction pathway indicate that all these COFs can spontaneously drive overall water splitting under light irradiation in a specific acid-base environment. The time-dependent ab initio non-adiabatic molecular dynamics simulations suggest that the electron-hole recombination periods of these COFs fall in a few to tens of nanoseconds. Excitingly, CTF-1 modified by linking six iodine atoms onto the benzene ring in the para-position(CTF-1-6I) shows a quite low band gap of 2.81 eV, indicating that it is a visible-light driven COF for overall photocatalytic water splitting. Correspondingly, CTF-1-6I also exhibits an extraordinarily promising STH efficiency of 3.70%, which is an order magnitude higher than that of the pristine CTF-1.     

Whiskers of poly(3-alkylthiophene)s

It is shown that poly(3-alkylthiophene)s may readily crystallize from poor solvents in the form of whiskers. The experimental conditions required for the formation of whiskers were found to depend upon the alkyl side-chain length, solvent quality, and temperature. In all cases studied for alkyl side-chain lengths of 3-12 carbon atoms, the widths of the whiskers were of the order of 15nm, while their lengths often exceeded tens of microns. The thickness of the whiskers formed under the experimental conditions employed was found to scale with side-chain length, and was approximately 2 or 3 times the a/2 lattice dimension of the polymer unit cell. Packing of the macromolecules within the whiskers was such that the polymer backbones were normal to the whisker length; that is, the b-axis was oriented parallel to the long axis of the whiskers. These results are thought to be relevant to known thermochromism phenomena associated with poly(3-alkylthiophene)s. © 1993 John Wiley & Sons, Inc.