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.

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.

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.

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.

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).

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.

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.

Comparison of the flexibility of eight-membered tetrasiloxane and stannasiloxane rings: a crystallographic and computational study

The syntheses and crystal structures of the eight-membered cyclo-stannasiloxanes cyclo-[t-Bu(OH)Si(OSnt-Bu₂O)₂Si(OH)t-Bu] (1) and cyclo-{t-Bu₂Si[OSn(CH₂SiMe₃)₂O]₂Sit-Bu₂} (2) as well as the synthesis of the six-membered cyclo-stannasiloxane cyclo-{t-Bu₂Si[OSn(CH₂SiMe₃)₂]₂O} (3) are reported. Compound 1 crystallizes as its trans isomer, but the cis isomer dominates in solution. In agreement with the experimentally obtained results, ab initio and DFT calculations on the model compounds cyclo-(H₂SiO)₄ (4), cyclo-[H₂Si(OSnH₂)OSiH₂] (5), cyclo-O(H₂SiOSnH₂)₂O (6), and cyclo-[H₂Si(OSiH₂)OSnH₂] (7) indicate that the energetic preference to adopt puckered structures increases and the ring flexibility decreases with an increasing number of tin atoms in the ring. The rich diversity of puckered conformations is attributed to the steric demand of the different organic substituents.

Ftir study of ion-pairing effects in plasticized polymer electrolytes

The effect of plasticizer on the ubiquitous ion-pairing observed in polymer electrolytes has been investigated using FTIR as a probe of the local environment of the triflate ion in sodium and lithium triflate based electrolytes. Plasticizers having a range of properties, such as, propylene carbonate, and dimethyl formamide (DMF), have been investigated in the pure state for comparison with the polymer (a random copolymer of ethylene oxide at propylene oxide (mol ratio 3: 1)). The different plasticizers exhibited strikingly different effects on the triflate ion bands normally observed in polyether salt systems. In particular, the cation associated triflate ion bands at 1288 and 1248 cm⁻¹ and the band at 1272 cm⁻¹ which has variously been assigned to the free ion and also to the strongly aggregated anion, are different. PC produces a rapid disappearance of the “free” ion band in favour of the monodentate ion pair. On the other hand, DMF strongly enhances the band near 1270 cm⁻¹ at salt concentrations higher than 0.7 mol kg⁻¹. These observations are discussed in terms of recent ab initio calculations of the triflate vibrational bands.

Analysis of genome-wide association study data using the protein knowledge base

Article 98

Candidate disease gene prediction using Gentrepid: application to a genome-wide association study on coronary artery disease

Current single-locus-based analyses and candidate disease gene prediction methodologies used in genome-wide association studies (GWAS) do not capitalize on the wealth of the underlying genetic data, nor functional data available from molecular biology. Here, we analyzed GWAS data from the Wellcome Trust Case Control Consortium (WTCCC) on coronary artery disease (CAD). Gentrepid uses a multiple-locus-based approach, drawing on protein pathway- or domain-based data to make predictions. Known disease genes may be used as additional information (seeded method) or predictions can be based entirely on GWAS single nucleotide polymorphisms (SNPs) (ab initio method). We looked in detail at specific predictions made by Gentrepid for CAD and compared these with known genetic data and the scientific literature. Gentrepid was able to extract known disease genes from the candidate search space and predict plausible novel disease genes from both known and novel WTCCC-implicated loci. The disease gene candidates are consistent with known biological information. The results demonstrate that this computational approach is feasible and a valuable discovery tool for geneticists.

Protic ionic liquids based on the dimeric and oligomeric anions: [(AcO)xHx−1]−

We describe a fluidity and conductivity study as a function of composition in N-methylpyrrolidine–acetic acid mixtures. The simple 1:1 acid–base mixture appears to form an ionic liquid, but its degree of ionicity is quite low and such liquids are better thought of as poorly dissociated mixtures of acid and base. The composition consisting of 3 moles acetic acid and 1 mole N-methylpyrrolidine is shown to form the highest ionicity mixture in this binary due to the presence of oligomeric anionic species [(AcO)_xH_x−1]− stabilised by hydrogen bonds. These oligomeric species, being weaker bases than the acetate anion, shift the proton transfer equilibrium towards formation of ionic species, thus generating a higher degree of ionicity than is present at the 1:1 composition. A Walden plot analysis, thermogravimetric behaviour and proton NMR data, as well as ab initio calculations of the oligomeric species, all support this conclusion.

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.