Browsing by Author "Johnson, MR"
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- ItemAtomistic model of DNA: phonons and base-pair opening(American Physical Society, 2007-09) Merzel, F; Fontaine-Vive, F; Johnson, MR; Kearley, GJA fully atomistic model of B-DNA using the CHARMM (chemistry at Harvard molecular mechanics) force field is presented. Molecular dynamics simulations were used to prepare an equilibrium structure. The Hessian of interatomic forces obtained from CHARMM for the equilibrium structure was used as input to a large scale phonon calculation. The calculated dispersion relations at low frequency are compared with recently published experimental data, which shows the model to have good accuracy for the low frequency, vibrational modes of DNA. These are discussed in the context of base-pair opening. In addition to the widely reported modes at, or below, ~12.5 meV, a continuous band of modes with strong base-pair opening character is found up to 40 meV, which coincides with the typical denaturation temperature of DNA. © 2007, American Physical Society
- ItemBi1−xNbxO1.5+x (x=0.0625, 0.12) fast ion conductors: structures, stability and oxide ion migration pathways(Elsevier, 2015-05) Tate, ML; Hack, J; Kuang, X; McIntyre, GJ; Withers, RL; Johnson, MR; Evans, IRA combined experimental and computational study of Bi1−xNbxO1.5+x (x=0.0625 and 0.12) has been carried out using laboratory X-ray, neutron and electron diffraction, impedance measurements and ab-initio molecular dynamics. We demonstrate that Bi0.9375Nb0.0625O1.5625, previously reported to adopt a cubic fluorite-type superstructure, can form two different polymorphs depending on the synthetic method: a metastable cubic phase is produced by quenching; while slower cooling yields a stable material with a tetragonal √2×√2×1 superstructure, which undergoes a reversible phase transition into the cubic form at ~680 °C on subsequent reheating. Neutron diffraction reveals that the tetragonal superstructure arises mainly from ordering in the oxygen sublattice, with Bi and Nb remaining disordered, although structured diffuse scattering observed in the electron diffraction patterns suggests a degree of short-range ordering. Both materials are oxide ion conductors. On thermal cycling, Bi0.88Nb0.12O1.62 exhibits a decrease in conductivity of approximately an order of magnitude due to partial transformation into the tetragonal phase, but still exhibits conductivity comparable to yttria-stabilised zirconia (YSZ). Ab-initio molecular dynamics simulations performed on Bi0.9375Nb0.0625O1.5625 show that oxide ion diffusion occurs by O2− jumps between edge- and corner-sharing OM4 groups (M=Bi, Nb) via tetrahedral □M4 and octahedral □M6 vacancies. © 2015 Elsevier Inc.
- ItemCollagen and component polypeptides: low frequency and amide vibrations.(Elsevier, 2009-01-27) Fontaine-Vive, F; Merzel, F; Johnson, MR; Kearley, GJCollagen is a fibrous protein, which exists widely in the human body. The biomechanical properties of collagen depend on its triple helix structure and the corresponding low frequency vibrations. We use first-principles, density functional theory methods and analytical force fields to investigate the molecular vibrations of a model collagen compound, the results being validated by comparison with published, inelastic neutron scattering data. The results from these atomistic simulations are used at higher frequency to Study the Amide I and V vibrations and therefore the vibrational signature of secondary and tertiary structure formation. In addition to collagen, its component homopolymers, poly-glycine and poly-proline are also studied. The Amide V vibration of glycine is strongly modified in going from the single helix of poly-glycine II to the triple helix of collagen. The collagen models are hydrated and this work allows LIS to discuss the relative merits of density functional theory and force field methods when tackling complex, partially crystalline systems. © 2008, Elsevier Ltd.
- ItemCombined experimental and computational study of oxide ion conduction dynamics in Sr2Fe2O5 brownmillerite(American Chemical Society, 2013-08-13) Auckett, JE; Studer, AJ; Pellegrini, E; Ollivier, J; Johnson, MR; Schober, H; Miiller, W; Ling, CDWe report a detailed study of the dynamics of oxide ionic conduction in brownmillerite-type Sr2Fe2O5, including lattice anisotropy, based on neutron scattering studies of a large (partially twinned) single crystal in combination with ab initio molecular dynamics simulations. Single-crystal diffraction reveals supercell peaks due to long-range ordering among chains of corner-sharing FeO4 tetrahedra, which disappears on heating above 540 °C due to confined local rotations of tetrahedra. Our simulations show that these rotations are essentially isotropic, but are a precondition for the anisotropic motion that moves oxide ions into the tetrahedral layers from the octahedral layers, which we observe experimentally as a Lorentzian broadening of the quasielastic neutron scattering spectrum. This continual but incoherent movement of oxide ions in turn creates conduction pathways and activates long-range diffusion at the interface between layers, which appears to be largely isotropic in two dimensions, in contrast with previously proposed mechanisms that suggest diffusion occurs preferentially along the c axis.© 2013, American Chemical Society.
- ItemDensity functional calculations of potential energy surface and charge transfer integrals in molecular triphenylene derivative HAT(6)(Springer, 2010-03) Zbiri, M; Johnson, MR; Kearley, GJ; Mulder, FMWe investigate the effect of structural fluctuations on charge transfer integrals, overlap integrals, and site energies in a system of two stacked molecular 2,3,6,7,10,11-hexakishexyloxytriphenylene (HAT(6)), which is a model system for conducting devices in organic photocell applications. A density functional based computational study is reported. Accurate potential energy surface calculations are carried out using an improved meta-hybrid density functional to determine the most stable configuration of the two weakly bound HAT(6) molecules. The equilibrium parameters in terms of the twist angle and co-facial separation are calculated. Adopting the fragment approach within the Kohn-Sham density functional framework, these parameters are combined to a lateral slide, to mimic structural/conformational fluctuations and variations in the columnar phase. The charge transfer and spatial overlap integrals, and site energies, which form the matrix element of the Kohn-Sham Hamiltonian are derived. It is found that these quantities are strongly affected by the conformational variations. The spatial overlap between stacked molecules is found to be of considerable importance since charge transfer integrals obtained using the fragment approach differ significantly from those using the dimer approach. © 2010, Springer.
- ItemDirect view on nanoionic proton mobility(Wiley-Blackwell, 2011-04-22) Chan, WK; Haverkate, LA; Borghols, WJH; Wagemaker, M; Picken, SJ; van Eck, ERH; Kentgens, APM; Johnson, MR; Kearley, GJ; Mulder, FMThe field of nanoionics is of great importance for the development of superior materials for devices that rely on the transport of charged ions, like fuel cells, batteries, and sensors. Often nanostructuring leads to enhanced ionic mobilities due to the induced space-charge effects. Here these large space-charge effects occurring in composites of the proton-donating solid acid CsHSO4 and the proton-accepting TiO2 or SiO2 are studied. CsHSO4 is chosen for this study because it can operate effectively as a fuel-cell electrolyte at elevated temperature while its low-temperature conductivity is increased upon nanostructuring. The composites have a negative enthalpy of formation for defects involving the transfer of protons from the acid to the acceptor. Very high defect densities of up to 10% of the available sites are observed by neutron diffraction. The effect on the mobility of the protons is observed directly using quasielastic neutron scattering and nuclear magnetic resonance spectroscopy. Surprisingly large fractions of up to 25% of the hydrogen ions show orders-of-magnitude enhanced mobility in the nanostructured composites of TiO2 or SiO2, both in crystalline CsHSO4 and an amorphous fraction.© 2011, Wiley-Blackwell. The definitive version is available at www3.interscience.wiley.com
- ItemElectronic and vibronic properties of a discotic liquid-crystal and its charge transfer complex(AIP Publishing, 2014-01-06) Haverkate, LA; Zbiri, M; Johnson, MR; Carter, EA; Kotlewski, A; Picken, SJ; Mulder, FM; Kearley, GJDiscotic liquid crystalline (DLC) charge transfer (CT) complexes combine visible light absorption and rapid charge transfer characteristics, being favorable properties for photovoltaic (PV) applications. We present a detailed study of the electronic and vibrational properties of the prototypic 1:1 mixture of discotic 2,3,6,7,10,11-hexakishexyloxytriphenylene (HAT6) and 2,4,7-trinitro-9-fluorenone (TNF). It is shown that intermolecular charge transfer occurs in the ground state of the complex: a charge delocalization of about 10−2 electron from the HAT6 core to TNF is deduced from both Raman and our previous NMR measurements [L. A. Haverkate, M. Zbiri, M. R. Johnson, B. Deme, H. J. M. de Groot, F. Lefeber, A. Kotlewski, S. J. Picken, F. M. Mulder, and G. J. Kearley, J. Phys. Chem. B116, 13098 (2012)], implying the presence of permanent dipoles at the donor-acceptor interface. A combined analysis of density functional theory calculations, resonant Raman and UV-VIS absorption measurements indicate that fast relaxation occurs in the UV region due to intramolecular vibronic coupling of HAT6 quinoidal modes with lower lying electronic states. Relatively slower relaxation in the visible region the excited CT-band of the complex is also indicated, which likely involves motions of the TNF nitro groups. The fast quinoidal relaxation process in the hot UV band of HAT6 relates to pseudo-Jahn-Teller interactions in a single benzene unit, suggesting that the underlying vibronic coupling mechanism can be generic for polyaromatic hydrocarbons. Both the presence of ground state CT dipoles and relatively slow relaxation processes in the excited CT band can be relevant concerning the design of DLC based organic PV systems. © 2014 AIP Publishing LLC.
- ItemExperimental observation and computational study of the spin-gap excitation in Ba3BiRu2O9(American Physical Society, 2016-11-01) Ling, CD; Huang, Z; Kennedy, BJ; Rols, S; Johnson, MR; Zbiri, M; Kimber, SAJ; Hudspeth, J; Adroja, DT; Rule, KC; Avdeev, M; Blanchard, PERBa3BiRu2O9 is a 6H-type perovskite compound containing face-sharing octahedral M2O9 (M=Ir, Ru) dimers, which are magnetically frustrated at low temperatures. On cooling through T∗=176 K, it undergoes a pronounced magnetostructural transition, which is not accompanied by any change in space group symmetry, long-range magnetic ordering, or charge ordering. Here, we report the first direct evidence from inelastic neutron scattering that this transition is due to an opening of a gap in the excitation spectra of dimers of low-spin Ru4+ (S=1) ions. X-ray absorption spectroscopy reveals a change in Ru-Ru orbital overlap at T∗, linking the emergence of this spin-gap excitation to the magnetostructural transition. Ab initio calculations point to a geometrically frustrated magnetic ground state due to antiferromagnetic interdimer exchange on a triangular Ru2O9 dimer lattice. X-ray total-scattering data rule out long-range magnetic ordering at low temperatures, consistent with this geometrically frustrated model. ©2016 American Physical Society
- ItemLocal structure, dynamics, and the mechanisms of oxide ionic conduction in Bi26Mo10O69(American Chemical Society, 2012-12-11) Ling, CD; Miiller, W; Johnson, MR; Richard, D; Rols, S; Madge, J; Evans, IRWe report the results of a computational and experimental study into the stabilized fluorite-type delta-Bi(2)O(3)-related phase Bi(26)Mo(10)O(69) aimed at clarifying the local and average structure, for which two distinct models have previously been proposed, and the oxide ionic diffusion mechanism, for which three distinct models have previously been proposed. Concerning the structure, we propose a new model in which some molybdenum atoms have higher coordination numbers than 4; that is, some MoO(5) trigonal bipyramids coexist with MoO(4) tetrahedra. This accounts for the additional oxygen required to achieve the nominal composition (a tetrahedrononly model gives Bi(26)Mo(10)O(68)) without invoking a previously proposed unbonded interstitial site, which we found to be energetically unfavorable. All these MoO(x) units are rotationally disordered above a first-order transition at 310 degrees C, corresponding to a first-order increase in conductivity. Concerning oxide ionic diffusion above that transition temperature, we found excellent agreement between the results of ab initio molecular dynamics simulations and quasielastic neutron scattering experiments. Our results indicate a mechanism related to that proposed by Holmes et al. (Chem. Mater. 2008, 20, 3638), with the role previously assigned to partially occupied interstitial oxygen sites played instead by transient but stable MoO(5) trigonal bipyramids and with more relaxed requirements in terms of the orientation and timing of the diffusive jumps. © 2012, American Chemical Society.
- ItemMolecular modelling of ground- and excited-states vibrations in organic conducting devices: hexakis(n-hexyloxy)triphenylene (HAT(6)) as case study(CSIRO Publishing, 2010-03-26) Zbiri, M; Johnson, MR; Haverkate, LA; Mulder, FM; Kearley, GJIn order to gain insight into fundamental aspects of organic photocell materials, we have calculated ground and excited electronic-state structures and molecular vibrations for an isolated HAT6 molecule (hexakis(n-hexyloxy)triphenylene). Excited-state calculations are carried out using time-dependent density functional theory and frequencies are evaluated analytically using coupled perturbed Kohn–Sham equations. These model calculations have been validated against new infrared and ultraviolet data on HAT6 in solution. The main allowed valence excitation, having the largest oscillator strength, is chosen for the structural and vibrational investigations. Comparison with the ground-state vibrational dynamics reveals surprisingly large spectral differences. In addition, the alkoxy tails, which are usually considered to play only a structural role, are clearly involved in the molecular vibrations and the structural distortion of the excited electronic state compared with the ground state. The tails may play a more important role in charge separation, transport and excited-state relaxation than was previously thought. In this case, chemical modification of the tails would allow vibrational and related properties of organic photocell materials to be tailored. © 2010, CSIRO Publishing
- ItemA new n = 4 layered Ruddlesden–Popper phase K2.5Bi2.5Ti4O13 showing stoichiometric hydration(American Chemical Society, 2016-01-22) Liu, S; Avdeev, M; Liu, Y; Johnson, MR; Ling, CDA new bismuth-containing layered perovskite of the Ruddlesden–Popper type, K2.5Bi2.5Ti4O13, has been prepared by solid-state synthesis. It has been shown to hydrate to form stoichiometric K2.5Bi2.5Ti4O13·H2O. Diffraction data show that the structure consists of a quadruple-stacked (n = 4) perovskite layer, with potassium ions occupying the rock salt layer and its next-nearest A site. The hydrated sample was shown to remove the offset between stacked perovskite layers relative to the dehydrated sample. Computational methods show that the hydrated phase consists of intact H2O molecules in a vertical “pillared” arrangement bridging across the interlayer space. Rotations of H2O molecules about the c axis were evident in molecular dynamic calculations, which increased in rotation angle with increasing temperature. In situ diffraction data for the dehydrated phase point to a broad structural phase transition from orthorhombic to tetragonal at ∼600 °C. The relative bismuth-rich composition in the perovskite block results in a higher transition temperature compared to related perovskite structures. Water makes a significant contribution to the dielectric constant, which disappears after dehydration. © 2016 American Chemical Society
- ItemOn the morphology of a discotic liquid crystalline charge transfer complex(American Chemical Society, 2012-10-01) Haverkate, LA; Zbiri, M; Johnson, MR; Deme, B; de Groot, HJM; Lefeber, F; Kotlewski, A; Picken, SJ; Mulder, FM; Kearley, GJDiscotic liquid crystalline (DLC) charge transfer (CT) complexes, which combine visible light absorption with rapid charge transfer characteristics within the CT complex, can have a great potential for photovoltaic applications when they can be made to self-assemble in a bulk heterojunction arrangement with separate channels for electron and hole conduction. However, the morphology of some liquid crystalline CT complexes has been under debate for many years. In particular, the liquid crystalline CT complex built from the electron acceptor 2,4,7-trinitro-9-fluorenone (TNF) and discotic molecules has been reported to have the TNF "sandwiched" either between the discotic molecules within the same column or between the columns within the aliphatic tails of the discotic molecules. We present a detailed structural study of the prototypic 1:1 mixture of the discotic 2,3,6,7,10,11-hexakis(hexyloxy)triphenylene (HAT6) and TNF. Nuclear magnetic resonance (NMR) line widths and cross-polarization rates are consistent with the picosecond time scale anisotropic thermal motions of the HAT6 and TNF molecules previously observed. By computational integration of Rietveld refinement analyses of neutron diffraction patterns with density experiments and short-range structural constraints from heteronuclear 2D NMR, we determine that the TNF molecules are vertically oriented between HAT6 columns. The data provide the insight that a morphology of separate hole conducting channels of HAT6 molecules can be realized in the liquid crystalline CT complex. © 2012, American Chemical Society.
- ItemOxide ion and proton conductivity in highly oxygen-deficient cubic perovskite SrSc0.3Zn0.2Ga0.5O2.4(American Chemical Society, 2020-04-27) Fuller, CA; Berrod, Q; Frick, B; Johnson, MR; Avdeev, M; Evans, JSO; Evans, IRA series of Zn-substituted compounds, Sr2Sc1–xZnxGaO5–0.5x, based on the brownmillerite-type oxide ion conductor Sr2ScGaO5 have been synthesized, and a single-phase region has been identified at 0.4 ≤ x < 0.6. The structure and dynamics of Sr2Sc0.6Zn0.4GaO4.8 were investigated by X-ray and neutron diffraction, neutron total scattering and pair distribution function (PDF) analysis, impedance spectroscopy, and neutron spectroscopy. The material was found to be a highly disordered cubic perovskite with a remarkable level of oxygen deficiency across a large temperature range. These structural properties lead to an increase of oxide ion conductivity of about two orders of magnitude relative to the parent Sr2ScGaO5. The presence of proton conductivity and some water uptake was suggested by the impedance data and corroborated by thermogravimetric analysis (TGA), solid state nuclear magnetic resonance (NMR), variable temperature X-ray diffraction, and neutron spectroscopy. Both proton and oxide ion conductivity produced a measurable quasi-elastic neutron scattering (QENS) signal, and the onset of each dynamic process could be observed by monitoring the temperature dependence of the elastic and inelastic scattering intensities measured in fixed window scans. Neutron total scattering and PDF studies revealed a local structure that is markedly different from the perovskite average structure, and we propose that Sr2Sc0.6Zn0.4GaO4.8 contains a rare one-coordinate or terminal oxygen site. © 2020 American Chemical Society
- ItemPressure-induced intersite Bi--M (M=Ru, Ir) valence transitions in hexagonal perovskite(Wiley Online Library, 2014-02-24) Huang, Z; Auckett, JE; Blanchard, PER; Kennedy, BJ; Miller, W; Zhou, Q; Avdeev, M; Johnson, MR; Zbiri, M; Garbarino, G; Marshall, WG; Gu, QF; Ling, CDPressure-induced charge transfer from Bi to Ir/Ru is observed in the hexagonal perovskites Ba3+nBiM2+nO9+3n (n=0,1; M=Ir,Ru). These compounds show first-order, circa 1 % volume contractions at room temperature above 5 GPa, which are due to the large reduction in the effective ionic radius of Bi when the 6s shell is emptied on oxidation, compared to the relatively negligible effect of reduction on the radii of Ir or Ru. They are the first such transitions involving 4d and 5d compounds, and they double the total number of cases known. Ab initio calculations suggest that magnetic interactions through very short (ca. 2.6 Å) M[BOND]M bonds contribute to the finely balanced nature of their electronic states. © 2014 Wiley‐VCH.
- ItemStructural properties of the Nb-doped bismuth oxide materials, Bi1-xNbxO1.5+x(Australian Institute of Physics, 2015-02-03) Tate, ML; Hack, J; Kuang, XJ; McIntyre, GJ; Withers, RL; Johnson, MR; Evans, IRBismuth oxide (Bi2O3) exists in five polymorphs, and possesses excellent oxide ion conductivity when in the cubic fluorite structure type, due to its intrinsic oxide ion vacancies. However, this cubic structure is only stable over a small high-temperature range. Introducing niobium into the bismuth oxide structure stabilises the highly conductive cubic and tetragonal phases to room temperature, allowing for high oxide ion conductivity at lower temperatures. In addition to stabilising the high temperature structure types, doping with niobium also introduces interstitial oxygen atoms into the material in order to maintain a charge balance. Niobium-doped bismuth oxide samples, Bi1-xNbxO1.5+x (x = 0.0625, 0.12), were synthesised by a solid state synthetic method, before undergoing AC impedance spectroscopy experiments to study their electrical properties. Both samples showed excellent oxide ion conductivities, with the cubic sample (x = 0.12) possessing higher conductivity values than the tetragonal sample (x = 0.0625). The tetragonal sample does not exhibit a loss in conductivity on thermal cycling, unlike the cubic sample, where the conductivity decreases due to a phase transformation from the cubic to the tetragonal phase. Variable temperature X-ray powder diffraction elucidated the structural transformations which the tetragonal bismuth niobate undergoes; from being tetragonal at room temperature, to cubic above 680 °C, then returning to the tetragonal phase upon cooling. To locate the interstitial oxygen atom positions in the tetragonal phase, powder neutron diffraction has been undertaken.
- ItemStructure and dynamics studies of the short strong hydrogen bond in the 3,5-dinitrobenzoic acid-nicotinic acid molecular complex(Royal Society of Chemistry, 2013-01-01) Ford, SJ; McIntyre, GJ; Johnson, MR; Evans, IRThe molecular complex between 3,5-dinitrobenzoic acid and nicotinic acid (35DBNA) has been studied by variable temperature single crystal X-ray and neutron diffraction (30 to 300 K) and ab initio molecular dynamics, in order to investigate the dynamics and any proton migration in this system, which exhibits structural similarities with the well-known proton migration material 3,5-dicarboxylic acid. The refined structures clearly indicate a significant degree of proton transfer in the short NHO hydrogen bond, contrary to the previous description of 35DBNA as an organic adduct without proton transfer. This behaviour is consistent with the difference between the pKa values of 3,5-dinitrobenzoic acid and the ring nitrogen atom in nicotinic acid. Complementary ab initio MD simulations at 400 K show the key proton hopping across the NHO short hydrogen bond, spending short periods along the trajectory (8% of the simulation time) bonded to the O atom. Similar simulations performed on 3,5-dicarboxylic acid and 3,4-dicarboxylic acid show that the MD calculations correlate well with the experimental observations (or absence) of proton migration, and therefore suggest that they could be used as a predictive tool for investigating this phenomenon in short strong hydrogen bonds. © 2013, Royal Society of Chemistry.
- ItemThe structures, phase transitions and dynamics behind mixed ionic and electronic conduction in hydrated Ba4Nb2O9(Australian Institute of Physics, 2010-02-03) Ling, CD; Avdeev, M; Johnson, MRAlthough Ba4Nb2O9 was first synthesised in 1965,  its structure remained unsolved until a recent study  in which we showed that Ba4Nb2O9 has two basic polymorphs: a high temperature γ phase, which represents an entirely new structure type; and a low-temperature α phase, which has the rare Sr4Ru2O9 structure type. The phases are separated by a reconstructive transition at ~1370 K, the kinetics of which are sufficiently slow that the γ phase can easily be quenched to room temperature. Below ~950 K, both α and γ absorb significant amounts of water. In the γ phase, protons occupy ordered positions, giving rise to a stoichiometric phase γ -III-Ba4Nb2O9.1/3H2O at room temperature. γ-III-Ba4Nb2O9.1/3H2O partially dehydrates at ~760 K to γ-II-Ba4Nb2O9.1/6H2O, then completely dehydrates at ~950 K to γ-I-Ba4Nb2O9. The hydrated γ phases exhibit faster protonic and oxide ionic transport than the hydrated " phases, due to the presence in the gamma phases of 2D layers containing Nb5+ cations with unusually low oxygen coordination numbers (4 or 5) separated by discrete OH groups. In this paper, we will discuss the structures and mechanisms of hydration – and, therefore, of ionic conduction – in the various phases of Ba4Nb2O9 on the basis of neutron diffraction experiments and ab initio (density functional theory) dynamics simulations.
- ItemVibrational spectroscopy with neutrons - where are we now?(Elsevier, 2010-05-26) Kearley, GJ; Johnson, MRThis article reviews recent applications of inelastic neutron-scattering (INS) in the field of vibrational spectroscopy making the link between a broad range of current topics, modelling and instrumentation. We also show how this spectroscopy is positioned with respect the optical techniques, IR and Raman, how this has evolved over time and how it might develop in the future. Principle advantages of INS are described with appropriate examples whilst disadvantages and limitations are described towards the end. © 2009, Elsevier Ltd.