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).

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.

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.

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.

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.

Aluminium speciation in 1-Butyl-1-Methylpyrrolidinium Bis(trifluoromethylsulfonyl)amide/AlCl3 mixtures

Aluminium speciation: Aluminium speciation in NTf₂ ionic liquids has a strong influence on its electrodeposition from the liquid mixture. This work probed the nature of these species and proposes that the electroactive species involved are either [AlCl₃(NTf₂)]⁻ or [AlCl₂(NTf₂)₂]⁻ (e.g., see figure).


Electrodeposition of aluminium is possible from solutions of AlCl₃ dissolved in the 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)amide (C₄mpyrNTf₂) ionic liquid. However, electrodeposition is dependant on the AlCl₃ concentration as it only occurs at concentrations >1.6 mol L⁻¹. At these relatively high AlCl₃ concentrations the C₄mpyrNTf₂/AlCl₃ mixtures exhibit biphasic behaviour. Notably, at 1.6 mol L⁻¹ AlCl₃, aluminium can only be electrodeposited from the upper phase. Conversely, we found that at 3.3 mol L⁻¹ aluminium electrodeposition can only occur from the lower phase. The complex chemistry of the C₄mpyrNTf₂/AlCl₃ system is described and implications of aluminium speciation in several C₄mpyrNTf₂/AlCl₃ mixtures, as deduced from Raman and ²⁷Al NMR spectroscopic data, are discussed. The ²⁷Al NMR spectra of the C₄mpyrNTf₂/AlCl₃ mixtures revealed the presence of both tetrahedrally and octahedrally coordinated aluminium species. Raman spectroscopy revealed that the level of uncoordinated NTf₂⁻ anions decreased with increasing AlCl₃ concentration. Quantum chemical calculations using density functional and ab initio theory were employed to identify plausible aluminium-containing species and to calculate their vibrational frequencies, which in turn assisted the assignment of the observed Raman bands. The data indicate that the electroactive species involved are likely to be either [AlCl₃(NTf₂)]⁻ or [AlCl₂(NTf₂)₂]⁻.

Impact of nanodiffusion on the stacking fault energy in high-strength steels

A key requirement of modern steels – the combination of high strength and high deformability – can best be achieved by enabling a local adaptation of the microstructure during deformation. A local hardening is most efficiently obtained by a modification of the stacking sequence of atomic layers, resulting in the formation of twins or martensite. Combining ab initio calculations with in situ transmission electron microscopy, we show that the ability of a material to incorporate such stacking faults depends on its overall chemical composition and, importantly, the local composition near the defect, which is controlled by nanodiffusion. Specifically, the role of carbon for the stacking fault energy in high-Mn steels is investigated. Consequences for the long-term mechanical properties and the characterisation of these materials are discussed.

Studies on the mechanism of the peroxyoxalate chemiluminescence reaction Part 1. Confirmation of 1,2-dioxetanedione as an intermediate using 13C nuclear magnetic resonance spectroscopy

A simple model peroxyoxalate chemiluminescence system was monitored directly across a range of temperatures (from −80 to +20 °C) using ¹³C nuclear magnetic resonance spectroscopy. These experiments were made possible by the utilisation of ¹³C doubly labelled oxalyl chloride, which was reacted with anhydrous hydrogen peroxide in dry tetrahydrofuran. Ab initio quantum calculations were also performed to estimate the ¹³C nuclear magnetic resonance (NMR) shift of the most commonly postulated key intermediate 1,2-dioxetanedione and this data, in concert with the spectroscopic evidence, confirmed its presence during the reaction.

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.

Total synthesis of (±)-hyphodermins A and D

An efficient formal synthesis of (±)-hyphodermins A and D, metabolites of Hyphoderma radula, has been completed in 12 and 11 steps, respectively. The tricyclic carbon skeleton of enone 6 was rapidly assembled from diester 11 via an α brominationn−elimination sequence followed by anhydride formation. Regioselective reduction of the lactone group of enone 6 with LiAlH(t-BuO)3 gave lactol 15. Lactol 15 was converted in two steps to (±)-hyphodermin D, without the need for complex protection−deprotection strategies. Lactol 15 was converted in three steps to (±)-hyphodermin A, via the key step of epoxidation of an enone in the presence of a THP lactol. A combination of NMR and ab initio studies suggests that the structures of hyphodermin C and D should be interchanged.