Fluorination-induced magnetism in boron nitride nanotubes from ab initio calculations

Ab initio calculations were conducted to investigate the electronic structures and magnetic properties of fluorinated boron nitride nanotube (F-BNNT). It was found that the chemisorption of F atoms on the B atoms of BNNT can induce spontaneous magnetization, whereas no magnetism can be produced when the B and N atoms are equally fluorinated. This provides a different approach to tune the magnetic properties of BNNTs as well as a synthetic route toward metal-free magnetic materials.

Structure and phase stability of NiMnGa ferromagnetic shape memory alloys by experimental and ab-initio techniques

This paper summarizes some of our recent results on crystal structure, microstructure, orientation relationship between martensitic variants and crystallographic features of martensitic transformation in Ni-Mn-Ga FSMAs. It was shown that Ni53Mn25Ga22 has a tetragonal I4/mmm martensitic structure at room temperature. The neighboring martensitic variants in Ni53Mn25Ga22 have a compound twinning relationship with the twinning elements K1={112}, K2={11-2}, η1=<11-1>, η2=<111>, P={1-10} and s=0.379. The ratio of the relative amounts of twins within the same initial austenite grain is ~1.70. The main orientation relationship between austenite and martensite is Kurdjumov-Sachs (K-S) relationship. Based on the crystallographic phenomenological theory, the calculated habit plane is {0.690 -0.102 0.716}A (5.95° from {101}A), and the magnitude, direction and shear angle of the macroscopic transformation shear are 0.121, <-0.709 0.105 0.698>A (6.04° from <-101>A) and 6.88°, respectively.

Ab initio calculations, Raman and NMR investigation of the plastic crystal di-methyl pyrrolidinium iodide

Above 110 °C the symmetric di-methyl-pyrrolidinium iodide salt forms a plastic crystal phase of interest in the area of new electrolyte materials. In this study ab initio calculations of this material has been conducted in order to assign the vibrational spectra. Raman spectroscopy measurements on the solid salt as well as on the salt dissolved in different solvents has been performed and these have been compared to the theoretical spectra. Furthermore, Raman spectra as a function of temperature have been recorded to investigate possible changes in inter-ionic interaction and/or structure through the phase transition. 1H NMR linewidth measurements as a function of temperature showed a large decrease in linewidth above 100 °C, attributed here to an increase in mobility in agreement with a previously reported phase transition at ~110 °C.

C-BN single-walled nanotubes from hybrid connection of BN/C nanoribbons : prediction by ab initio density functional calculations

We demonstrated for the first time by ab initio density functional calculation and molecular dynamics simulation that C0.5(BN)0.5 armchair single-walled nanotubes (NT) are gapless semiconductors and can be spontaneously formed via the hybrid connection of graphene/BN Nanoribbons (GNR/BNNR) at room temperature. The direct synthesis of armchair C0.5(BN)0.5 via the hybrid connection of GNR/BNNR is predicted to be both thermodynamically and dynamically stable. Such novel armchair C0.5(BN)0.5 NTs possess enhanced conductance as that observed in GNRs. Additionally, the zigzag C0.5(BN)0.5 SWNTs are narrow band gap semiconductors, which may have potential application for light emission. In light of recent experimental progress and the enhanced degree of control in the synthesis of GNRs and BNNR, our results highlight an interesting avenue for synthesizing a novel specific type of C0.5(BN)0.5 nanotube (gapless or narrow direct gap semiconductor), with potentially important applications in BNC-based nanodevices.

Half metallicity in a zigzag double-walled nanotube nanodot : an ab initio prediction

Ab initio density functional calculations were performed to study finite-length zigzag (7, 0) @ (16, 0) double-walled carbon nanotubes (DWCNTs) with H-termination at the open ends. We find that such a DWCNT nanodot displays a very large magnetic moment at the zigzag edges and the ground state displays symmetric anti-ferromagnetic coupling. When an external electric field is applied along the direction of tube axis, a gap is opened for one spin channel, whereas another spin channel remains metallic, i.e. half metallicity occurs. Our results suggest an important new avenue for the development of CNT-based spintronic materials with enhanced properties. © 2008 Elsevier B.V. All rights reserved.

Estimating relative disulfide energies : an accurate ab initio potential energy surface

Disulfide torsional energy, a good predictor of disulfide redox potential in proteins, may be estimated by interpolation on a potential energy surface (PES) describing the twisting of diethyl disulfide through its three central dihedral angles. Here we update PES calculations at the M05-2X level of theory with the 6-31G(d) basis set. Although the surface shows no qualitative differences from an earlier MP2(full) PES, energy differences greater than 1 kJ mol^–1 were seen for conformations with χ₂ between –60° and 30°, or with χ₃ below 60° or above 130°. This is particularly significant for highly strained disulfides that are likely to be spontaneously reduced by mechanical means. In benchmarking against the high-level G3X method, M05-2X showed significantly reduced root mean squared deviation compared with MP2(full) (1.0 versus 2.0 kJ mol^–1 respectively). Results are incorporated into a web application that calculates relative torsional energies from disulfide dihedral angles (http://www.sbinf.org/applications/pes.html).

Electronic structure of the azide group in 3′-Azido-3′- deoxythymidine (AZT) compared to small azide compounds

Theoretical calculations for some structural and electronic properties of the azide moiety in the nucleoside reverse transcriptase (RT) inhibitor 3′-azido-3′- deoxythymidine (AZT) are reported. These properties, which include geometrical properties in three dimensional space, Hirshfeld charges, electrostatic potential (MEP), vibrational frequencies, and core and valence ionization spectra, are employed to study how the azide group is affected by the presence of a larger fragment. For this purpose, two small but important organic azides, hydrazoic acid and methyl azide, are also considered. The general features of trans Cs configuration for RNNN fragments[1] is distorted in the large AZT bio-molecule. Hirshfeld charge analysis shows charges are reallocated more evenly on azide when the donor group R is not a single atom. Infrared and photoelectron spectra reveal different aspects of the compounds. In conclusion, the electronic structural properties of the compounds depend on the specific property, the local structure and chemical environment of a species.

High-pressure structural transitions of Sc2O3 by X-ray diffraction, raman spectra, and ab initio calculations

The high-pressure behavior of scandium oxide (Sc₂O₃) has been investigated by angle-dispersive synchrotron powder X-ray diffraction and Raman spectroscopy techniques in a diamond anvil cell up to 46.2 and 42 GPa, respectively. An irreversible structural transformation of Sc₂O₃ from the cubic phase to a monoclinic high-pressure phase was observed at 36 GPa. Subsequent ab initio calculations for Sc₂O₃ predicted the phase transition from the cubic to monoclinic phase but at a much lower pressure. The same calculations predicted a second phase transition at 77 GPa from the monoclinic to hexagonal phase.

Inorganic-organic hybrids of the p,p'-diphenylmethylenediphosphinate, pcp2-. synthesis, characterization and XRPD structures of [Sn(pcp)] and [Cu(pcp)]

Two new inorganic-organic polymeric hybrids [Sn(pcp)] and [Cu(pcp)], pcp = CH₂(PhPO₂)₂^2-, have been synthesized and structurally chracterized. The tin derivative has been obtained by reaction of the p,p'-diphenylmethylenediphosphinic acid (H₂pcp) in water with SnCl₂·2H₂O, while the copper derivative has been synthesized through a hydrothermal reaction from the same H₂pcp acid and Cu(O₂CMe)₂·H₂O. The structures of these compounds have been solved "ab initio" by X-ray powder diffraction (XRPD) data. [Sn(pcp)] has a ladder-like polymeric structure, with tin(II) centers bridged by diphenylmethylenediphosphinate ligands, and alternating six- and eight-membered rings. The hemilectic coordination around the metal shows the tin(II) lone pair to be operative, resulting in significant interaction mainly with a C-C bond of one phenyl ring. The [Cu(pcp)] complex displays a polymeric columnar structure formed by two intersecting sinusoidal ribbons of copper(II) ions bridged by the bifunctional phosphinate ligands. The intersections of the ribbons are made of dimeric units of pentacoordinated copper ions. Crystal data for [Sn(pcp)]: monoclinic, space group P2₁Ic, a = 11.2851(1), b = 15.4495(6), c = 8.6830(1) Å, ^β= 107.546(1)°, V = 1443.44(9) Å, Z = 4. Crystal data for [Cu(pcp)]: triclinic, space group P, a = 10.7126(4), b = 13.0719(4), c = 4.9272(3) Å, α= 92.067(5), β= 95.902(7), γ= 87.847(4)°, V = 685.47(7), Z = 2. The tin compound has been characterized by ¹¹⁹Sn MAS NMR (magic-angle spinning NMR), revealing asymmetry in the valence electron cloud about tin. Low-temperature magnetic measurements of the copper compound have indicated the presence of weak antiferromagnetic interactions below 50 K.

On the components of the dielectric constants of ionic liquids : ionic polarization?

According to dielectric spectroscopy measurements, ionic liquids (ILs) have rather modest dielectric constants that reflect contributions from distortion and electronic polarization caused by the molecular polarizability as well as the orientation polarization caused by the permanent dipole moment of the ions. To understand the relative importance of these various contributions, the electronic polarizabilities of 27 routinely used ionic liquid ions of different symmetry and size were calculated using ab initio-based methods such as HF and MP2. Using the Clausius–Mossotti equation, these polarizabilities were then used to obtain the electronic polarization contribution (ε_op) to the dielectric constants of six ionic liquids, [C₂mim][BF₄], [C₂mpyr][N(CN)₂], [C₂mim][CF₃SO₃], [EtNH₃][NO₃], [C₂mim][NTf₂] and [C₂mim][EtSO₄]. Theoretical ε_op values were compared to experimental refractive indices of these ionic liquids as well as to those of traditional molecular solvents such as water, tetrahydrofuran (THF), dimethylsulfoxide (DMSO) and formamide. The dipole moments of the ions were also calculated, and from these it is shown that the molecular reorientation component of the dielectric constants of the ionic liquids consisting of ions with small or negligible dipole moments is quite small. Thus it is concluded that a contribution from a form of “ionic polarization” must be present.

Advanced graph mining methods for protein analysis

As one of the primary substances in a living organism, protein defines the character of each cell by interacting with the cellular environment to promote the cell’s growth and function [1]. Previous studies on proteomics indicate that the functions of different proteins could be assigned based upon protein structures [2,3]. The knowledge on protein structures gives us an overview of protein fold space and is helpful for the understanding of the evolutionary principles behind structure. By observing the architectures and topologies of the protein families, biological processes can be investigated more directly with much higher resolution and finer detail. For this reason, the analysis of protein, its structure and the interaction with the other materials is emerging as an important problem in bioinformatics. However, the determination of protein structures is experimentally expensive and time consuming, this makes scientists largely dependent on sequence rather than more general structure to infer the function of the protein at the present time. For this reason, data mining technology is introduced into this area to provide more efficient data processing and knowledge discovery approaches.

Unlike many data mining applications which lack available data, the protein structure determination problem and its interaction study, on the contrary, could utilize a vast amount of biologically relevant information on protein and its interaction, such as the protein data bank (PDB) [4], the structural classification of proteins (SCOP) databases [5], CATH databases [6], UniProt [7], and others. The difficulty of predicting protein structures, specially its 3D structures, and the interactions between proteins as shown in Figure 6.1, lies in the computational complexity of the data. Although a large number of approaches have been developed to determine the protein structures such as ab initio modelling [8], homology modelling [9] and threading [10], more efficient and reliable methods are still greatly needed.

In this chapter, we will introduce a state-of-the-art data mining technique, graph mining, which is good at defining and discovering interesting structural patterns in graphical data sets, and take advantage of its expressive power to study protein structures, including protein structure prediction and comparison, and protein-protein interaction (PPI). The current graph pattern mining methods will be described, and typical algorithms will be presented, together with their applications in the protein structure analysis.

The rest of the chapter is organized as follows: Section 6.2 will give a brief introduction of the fundamental knowledge of protein, the publicly accessible protein data resources and the current research status of protein analysis; in Section 6.3, we will pay attention to one of the state-of-the-art data mining methods, graph mining; then Section 6.4 surveys several existing work for protein structure analysis using advanced graph mining methods in the recent decade; finally, in Section 6.5, a conclusion with potential further work will be summarized.

Atom probe tomography investigation of heterogeneous short-range ordering in the 'komplex' phase state (K-state) of Fe-18Al (at.%)

We study an Fe-18Al (at.%) alloy after various thermal treatments at different times (24-336 h) and temperatures (250-1100 °C) to determine the nature of the so-called 'komplex' phase state (or "K-state"), which is common to other alloy systems having compositions at the boundaries of known order-disorder transitions and is characterised by heterogeneous short-range-ordering (SRO). This has been done by direct observation using atom probe tomography (APT), which reveals that nano-sized, ordered regions/particles do not exist. Also, by employing shell-based analysis of the three-dimensional atomic positions, we have determined chemically sensitive, generalised multicomponent short-range order (GM-SRO) parameters, which are compared with published pairwise SRO parameters derived from bulk, volume-averaged measurement techniques (e.g. X-ray and neutron scattering, Mössbauer spectroscopy) and combined ab-initio and Monte Carlo simulations. This analysis procedure has general relevance for other alloy systems where quantitative chemical-structure evaluation of local atomic environments is required to understand ordering and partial ordering phenomena that affect physical and mechanical properties.