Cr[Formula: see text]AlN and the search for the highest temperature superconductor in the M[Formula: see text]AX family.

We have developed a high-throughput computational method to predict the superconducting transition temperature in stable hexagonal M[Formula: see text]AX phases, and applied it to all the known possible choices for M (M: Sc, Ti, V, Cr, Mn, Fe, Y, Zr, Nb, Mo, Lu, Hf and Ta). We combine this with the best candidates for A (A: Al, Cu, Ge and Sn ) and X (X: C and N) from our previous work, and predict T[Formula: see text] for 60 M[Formula: see text]AX-phase materials, 53 of which have never been studied before. From all of these, we identify Cr[Formula: see text]AlN as the best candidate for the highest T[Formula: see text], and confirm its high T[Formula: see text] with more detailed density functional theory electron-phonon coupling calculations. Our detailed calculations predict [Formula: see text] = 14.8 K for Cr[Formula: see text]AlN, which is significantly higher than any [Formula: see text] value known or predicted for any material in the M[Formula: see text]AX family to date.

Advanced crystallisation methods for small organic molecules.

Molecular materials based on small organic molecules often require advanced structural analysis, beyond the capability of spectroscopic techniques, to fully characterise them. In such cases, diffraction methods such as single crystal X-ray diffraction (SCXRD), are one of the most powerful tools available to researchers, providing molecular and structural elucidation at atomic level resolution, including absolute stereochemistry. However SCXRD, and related diffraction methods, are heavily dependent on the availability of suitable, high-quality crystals, thus crystallisation often becomes the major bottleneck in preparing samples. Following a summary of classical methods for the crystallisation of small organic molecules, this review will focus on a number of recently developed advanced methods for crystalline material sample preparation for SCXRD. This review will cover two main areas of modern small organic molecule crystallisation, namely the inclusion of molecules within host complexes (e.g., "crystalline sponge" and tetraaryladamantane based inclusion chaperones) and the use of high-throughput crystallisation, employing "under-oil" approaches (e.g., microbatch under-oil and ENaCt). Representative examples have been included for each technique, together with a discussion of their relative advantages and limitations to aid the reader in selecting the most appropriate technique to overcome a specific analytical challenge.

Prediction of phonon-mediated superconductivity in new Ti-based M[Formula: see text]AX phases.

A high-throughput computational method is used to predict 39 new superconductors in the Ti-based M[Formula: see text]AX phases, and the best candidates are then studied in more detail using density functional theory electron-phonon coupling calculations. The detailed calculations agree with the simple predictions, and Ti[Formula: see text]AlX (X: B, C and N) materials are predicted to have higher values of [Formula: see text] than any currently known hexagonal M[Formula: see text]AX phases. The electronic states at the Fermi level are dominated by the Ti 3d states. The choice of X (X: B, C and N) has a significant impact on the electronic density of states but not on the phonon characteristics. The electron-phonon coupling parameter for Ti[Formula: see text]AlX (X: B, C and N) was determined to be 0.685, 0.743 and 0.775 with a predicted [Formula: see text] of 7.8 K, 10.8 K and 13.0 K, respectively.

Hydrogen peroxide assisted photorelease of an anthraquinone-based ligand from [Ru(2,2'-bipyridine)2(9,10-dioxo-9,10-dihydroanthracen-1-olate)]Cl in aqueous solution.

A new class of light-activated ruthenium(ii) complex was designed as a potential blocker of biological functioning, especially for targeting redox reactions within mitochondria under light activation. Based on our concepts the complex [Ru(bipy)2(1-hydroxyanthra-9,10 quinone)]Cl (RU1) was prepared and studied to understand the preliminary reaction mechanisms and its excited state behaviour through a series of stability tests, electrochemistry, UV-Visible kinetics and femtosecond transient absorption spectroscopy experiments. Under white light in the presence of H2O2 two different reactions (fast and slow) appear to take place. The complex loses the quinone-based ligand and a resulting Ru(iii) or Ru(v) species is produced. The complex RU1 shows potential to consume H2O2 from the one carbon metabolism in mitochondria, and hence may cut the energy cycle pathway of tumor cells.

Effective modelling of the Seebeck coefficient of Fe2VAl.

Previous first-principles calculations have failed to reproduce many of the key thermoelectric features of Fe2VAl, e.g. the maximum values of the Seebeck coefficient S and its asymmetry with respect to the chemical potential. Also, previous theoretical predictions suggested that the pseudo band gap of Fe2VAl switches from indirect to direct upon doping. In this work, we report first-principles calculations that correctly reproduce the experimentally measured thermoelectric properties of Fe2VAl. This is achieved by adding a larger Hubbard U term to V atoms than to Fe atoms and including a scissors operator afterwards. As a result, bulk Fe2VAl is modelled as a gapless semiconductor with maximum S values of 76 and -158 [Formula: see text]V K-1 for p - and n-type, respectively, which agree well with the experimental measurements.

A framework for analysing nitrification inhibition: A case study on 3,4-dimethylpyrazole phosphate (DMPP).

Nitrification inhibitors show great potential to reduce nitrogen losses from agricultural systems and to improve nitrogen use efficiency. The most recently developed nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) is gaining popularity due to its benefits relative to other compounds. However, the behaviour of DMPP and its effect on nitrification in soils has been characterised using inconsistent and confusing terminology. Many studies have used the term half-life to describe the persistence of DMPP but used different experimental methods to derive it leading to highly variable results. We assessed how different methodologies in experiments may have contributed to the variability in the results using a framework that describes the behaviour of DMPP and its effect on nitrification in terms of: persistence, bioactivity and longevity. We show that deriving the persistence of DMPP using 14C labelling techniques is challenging because it requires consideration of other 14C pools in the soil. We also describe the limitations of soil inorganic nitrogen measurements to characterise the bioactivity and longevity of the inhibitory effect on nitrification. We conclude by proposing experiments that can facilitate the evaluation of the benefits of DMPP across broader scales. While this study focused on DMPP, the concepts presented here are equally relevant to other nitrification inhibitors.

Quantum diffusion of H/D on Ni(111)-A partially adiabatic centroid MD study.

We present the results of a theoretical study of H/D diffusion on a Ni(111) surface at a range of temperatures, from 250 K to 75 K. The diffusion is studied using both classical molecular dynamics and the partially adiabatic centroid molecular dynamics method. The calculations are performed with the hydrogen (or deuterium) moving in 3D across a static nickel surface using a novel Fourier interpolated potential energy surface which has been parameterized to density functional theory calculations. The results of the classical simulations are that the calculated diffusion coefficients are far too small and with too large a variation with temperature compared with experiment. By contrast, the quantum simulations are in much better agreement with experiment and show that quantum effects in the diffusion of hydrogen are significant at all temperatures studied. There is also a crossover to a quantum-dominated diffusive regime for temperatures below ∼150 K for hydrogen and ∼85 K for deuterium. The quantum diffusion coefficients are found to accurately reproduce the spread in values with temperature, but with an absolute value that is a little high compared with experiment.

Theoretical study of core-loss electron energy-loss spectroscopy at graphene nanoribbon edges.

A systematic study of simulated atomic-resolution electronic energy-loss spectroscopy (EELS) for different graphene nanoribbons (GNRs) is presented. The results of ab initio studies of carbon [Formula: see text] core-loss EELS on GNRs with different ribbon edge structures and different hydrogen terminations show that theoretical core-loss EELS can distinguish key structural features at the atomic scale. In addition, the combination of polarized core-loss EELS with symmetry resolved electronic partial density of states calculations can be used to identify the origins of all the primary features in the spectra. For example, the nature of the GNR edge structure (armchair, zigzag, etc) can be identified, along with the degree of hydrogenation. Hence it is possible to use the combination of ab initio calculations with high resolution, high energy transmission core-loss EELS experiments to determine the local atomic arrangement and chemical bonding states (i.e. a structural fingerprint) in GNRs, which is essential for future practical applications of graphene.

Preparation and properties of a calcium(II)-based molecular chain decorated with manganese(II) butterfly-like complexes.

The room temperature reaction of [Mn2O2(bipy)4](ClO4)3 (bipy = 2,2'-bipyridine) with Ca(CHCl2COO)2 in methanol produced a yellow crystalline material. The X-ray determined structure comprises of a multiple calcium(II) carboxylate bridged chain-like structure which is decorated with [Mn(bipy)2(OH2)](2+) subunits. The redox behaviour for the complex in H2O and MeCN is reported. In the latter solvent the oxidation of the manganese ions appears to be facilitated by the presence of the calcium ions. Magnetic susceptibility and low temperature magnetization measurements show that the Mn moment is isotropic, with g = 1.99(1) and S = 5/2, confirming it is in the 2+ oxidation state. A very weak antiferromagnetic interaction is also detected. Frequency-dependent ac measurements evidence slow magnetic relaxation of the Mn(bipy)2 units. Two relaxation mechanisms are identified: a very slow direct process and a faster one caused by the Resonant Phonon Trapping mechanism. This is the first example of field-induced single ion magnet (SIM) behavior in a mononuclear Mn(II) complex.

Atomistic molecular dynamics simulations of shock compressed quartz.

Atomistic non-equilibrium molecular dynamics simulations of shock wave compression of quartz have been performed using the so-called BKS semi-empirical potential of van Beest, Kramer, and van Santen [Phys. Rev. B 43, 5068 (1991)] to construct the Hugoniot of quartz. Our scheme mimics the real world experimental set up by using a flyer-plate impactor to initiate the shock wave and is the first shock wave simulation that uses a geometry optimised system of a polar slab in a three-dimensional system employing periodic boundary conditions. Our scheme also includes the relaxation of the surface dipole in the polar quartz slab which is an essential pre-requisite to a stable simulation. The original BKS potential is unsuited to shock wave calculations and so we propose a simple modification. With this modification, we find that our calculated Hugoniot is in good agreement with experimental shock wave data up to 25 GPa, but significantly diverges beyond this point. We conclude that our modified BKS potential is suitable for quartz under representative pressure conditions of the Earth core, but unsuitable for high-pressure shock wave simulations. We also find that the BKS potential incorrectly prefers the ß-quartz phase over the α-quartz phase at zero-temperature, and that there is a ß â†’ α phase-transition at 6 GPa.

An ab initio study of xenon retention in α-quartz.

It has recently been suggested that a significant amount of Xe can be absorbed in α-quartz and that this might be a significant process in the recycling of Xe from the atmosphere to the interior of the Earth. This suggestion is tested by ab initio calculations of Xe in α-quartz using DFT. Three distinct candidate sites for Xe absorption are identified-substitutional at the silicon vacancy (Xe@V(Si)), at the oxygen vacancy (Xe@V(O)) and at an interstitial site (Xe@I)-and each is shown to be mechanically stable at both P=0 and 2 GPa. The energetics and electronic properties of these defect structures are analysed and it is shown that there is an energy barrier to the absorption at all sites at T=0. If the Xe absorption is a single-stage process in a perfect crystal then the lowest formation energy barrier (at both P=0 and 2 GPa) is for Xe@I at the interstitial site. If absorption is a two-stage process due to vacancies being already present at finite temperatures, then the subsequent barrier to Xe absorption is much lower and Xe@V(Si) has the lowest formation energy. However, it should be expected that there will be a much higher density of oxygen vacancies available for Xe absorption under realistic Earth core conditions and so in this scenario it is to be expected that all three candidate sites should be occupied.

Phase behavior of a three-dimensional core-softened model system.

The phase behavior of a three-dimensional model substance interacting via a continuous core-softened pair potential is studied. A combination of thermodynamic integration and free-energy augmented metadynamics is employed to identify the ground state structure as simple hexagonal. A transition to close packing is predicted at high pressure. The melting line is traced, which when combined with the liquid-vapor line, allows the liquid to be studied over its entire thermodynamically stable range. We find no liquid anomalies in the range of pressures for which the vaporization transition exists. Our results therefore support suggestions that the anomalous behavior of such fluids is unique to the two-dimensional case.

Progression of phase behavior for a sequence of model core-softened potentials.

A series of phase diagrams is obtained in three dimensions for a smooth pair potential with an outer well and a repulsive inner shoulder. Condensed phase boundaries are located using free energy calculations. Liquid-vapor equilibria are obtained with multicanonical methods. As the depth of the outer well is increased, a simple-hexagonal to close-packed transition appears in the solid, leading to a discontinuity in the slope of the melting curve. For deeper wells the simple hexagonal melting temperature exhibits a maximum with respect to pressure. The onset of the predicted metastable isostructural transition is also studied.

Langevin dynamics in constant pressure extended systems.

The advantages of performing Langevin dynamics in extended systems are discussed. A simple Langevin dynamics scheme for producing the canonical ensemble is reviewed, and is then extended to the Hoover ensemble. We show that the resulting equations of motion generate the isobaric-isothermal ensemble. The Parrinello-Rahman ensemble is then discussed and we show that despite the presence of intrinsic probability gradients in this system, a Langevin dynamics approach samples the extended phase space in the correct fashion. The implementation of these methods in the ab initio plane wave density functional theory code CASTEP [M. D. Segall, P. L. D. Lindan, M. J. Probert, C. J. Pickard, P. J. Hasnip, S. J. Clarke, and M. C. Payne, J. Phys.: Condens. Matter 14, 2717 (2003)] is demonstrated.

Comment on "Algorithm for normal random numbers".

We have performed some simple statistical tests on the recently proposed algorithm for generating normally distributed random numbers and we find that it has some serious flaws with regard to practical application. In particular, we find that there is a statistically significant difference between the sample mean and that expected when using the original authors' recommended parameters of the algorithm. Only by significantly increasing these parameters, at the cost of considerable extra computational effort, do we get satisfactory statistics.

New conformational constraints in isotopically (13C) enriched oligosaccharides.

Multidimensional heteronuclear NMR studies have been applied to the resonance assignment and conformational analysis of 13C-enriched Neu5Acalpha2-3Galbeta1-4Glc. It is demonstrated that three-dimensional ROESY-HSQC experiments provide through-space distance restraints which cannot be observed with conventional homonuclear 1H techniques due to resonance overlap. In particular, connectivities demonstrating the existence of the "anti" conformation about the Galbeta1-4Glc glycosidic linkage are unambiguously observed. It is shown that 13C isotopic enrichment of the trisaccharide at a level >95% enables straightforward measurement of trans-glycosidic 1H-13C and 13C-13C coupling constants and a Karplus-type relation is derived for the latter. In total 15 conformational restraints were obtained for the trisaccharide in aqueous solution, all of which were in excellent agreement with theoretical parameters computed from a 5 ns molecular dynamics simulation of the glycan.

Structure of a glycoconjugate in solution and in complex with an antibody Fv fragment.

By use of heteronuclear (13C, 1H) NMR methods, the three-dimensional structure and dynamics of the glycoconjugate estrone-3-glucuronide (E3G) uniformly 13C enriched in the glucuronic acid moiety has been probed both in free solution and in association with an anti-E3G antibody single-chain Fv fragment. The glycan is found to exist in multiple conformations in free solution, with particularly large torsional fluctuations about the glycosidic linkage psi. Resonance assignments and distance restraints for the glycoconjugate in the bound state were obtained from heteronuclear proton-carbon-carbon-proton-COSY and isotope-edited NOESY techniques, respectively. Quantitation of the NOE data with a full-relaxation matrix approach showed that the antibody selects a conformation from the solution repertoire which does not correspond with either of the two lowest energy conformations of the free glycan, and the internal energy of the glycan in the bound state is estimated to be at most approximately 15 kcal/mol higher than the global minimum energy conformation. The glucuronide moiety undergoes a stacking interaction with an aromatic ring in the binding site, and both ring-current shifts and nuclear Overhauser effects computed from the predicted bound-state conformation are in good agreement with experiment. The bound-state conformation is also in good agreement with preliminary x-ray data on a related complex.

Terminal beta-linked tyvelose creates unique epitopes in Trichinella spiralis glycan antigens.

Indirect evidence that the immunodominant N-glycans of the parasite, Trichinella spiralis are capped by novel beta-linked 3,6-dideoxy-D-arabinohexopyranosyl residues (tyvelose, Tyv) was obtained from immunochemical assays employing monoclonal antibodies and synthetic oligosaccharides. Three of four previously characterized monoclonal antibodies generated from the lymphocytes of T.spiralis infected rats bind BSA glycoconjugates bearing the synthetic epitope beta-D-Tyvp(1-->3)-beta-D-GalNAcp but not to the corresponding alpha-D-Tyvp(1-->3)-beta-D-GalNAcp-BSA glycoconjugate. Monosaccharide and disaccharide glycoside inhibition data mirrors the results of the direct binding experiments. The branched tetrasaccharide beta-D-Tyv(1-->3)-beta-D-GalNAcp(1-->4)[alpha-L-Fucp(1 -->3)] beta-D-GalNAcp is the most active synthetic oligosaccharide inhibitor for all four monoclonal antibodies studied, while the corresponding alpha-D-Tyv containing tetrasaccharide and the core trisaccharide beta-D-GalNAcp(1-->4)[alpha-L-Fucp(1-->3)]beta-D-GlcNAcp+ ++ are inactive. The exceptional inhibitory activity of the disaccharide beta-D-Tyvp(1-->3)-beta-D-GalNAcp with one mAb (18H) compared to that of the branched tetrasaccharide beta-D-Tyvp(1-->3)-beta-D-GalNAcp(1-->4)[alpha-L-Fucp( 1-->3)]-beta-D-GlcNAcp is indicative of the presence of linear, nonfucosylated glycan epitopes (beta-D-Tyvp(1-->3)-beta-D-GalNAcp(1-->4) beta-D-GlcNAcp) that lack a fucose residue in one arm of the antigenic, tetra-antennary N-glycan. This observation supports earlier FAB-mass spectrometry evidence for the existence of tetra-antennary, core fucosylated glycans that lack a fucose residue on one of their antennae.

Synthesis of alpha- and beta-linked tyvelose epitopes of the Trichinella spiralis glycan: 2-acetamido-2-deoxy-3-O-(3,6-dideoxy-D-arabino-hexopyranosyl)-beta -D-galactopyranosides.

The anomeric configuration of tyvelose, 3,6-dideoxy-D-arabino-hexopyranose, in the recently discovered glycan epitopes of the parasite Trichinella spiralis has not been established. Two 2-(trimethylsilyl)ethyl disaccharide glycosides, alpha- and beta-Tyv-(1-->3)-beta-D-GalNAc (4 and 5), have been synthesized to provide model compounds that, together with the methyl 3,6-dideoxy-alpha- and beta-D-arabino-hexopyranosides (2 and 3), aid the determination of the anomeric configuration of tyvelose residues in the parasite glycan, either indirectly by immunochemical inhibition data or directly by the technique of 1H NMR spectroscopy. Methyl 3,6-dideoxy-beta-D-arabino-hexopyranoside (3) was synthesized from methyl 2,3-anhydro-4,6-O-benzylidene-beta-D-mannopyranoside (9) by a method previously used for the alpha anomer 2. Benzylation of 2 provided a route to the glycosyl donor, 2,4-di-O-benzyl-3,6-dideoxy-alpha-D-arabino-hexopyranosyl chloride (30), that reacted with the selectively protected 2-acetamido-2-deoxy-D-galactopyranoside alcohol 18 in the presence of an insoluble silver zeolite catalyst to give the alpha- and beta-linked disaccharides 31 and 32. Glycosylation of the related 2-acetamido-2-deoxy-D-galactopyranoside alcohol 27 by 30 under similar conditions provided disaccharides 33 and 34 containing a tether. Deprotection of the saccharide and derivatization of the tether with 1,2-diaminoethane provided amide derivatives 35 and 36 suitable for the preparation of neoglycoconjugate antigens. Complete 1H and 13C NMR chemical shifts of the deprotected disaccharides and monosaccharides are reported.