A first-principles density-functional calculation of the electronic and vibrational structure of the key melanin monomers

We report first-principles density-functional calculations for hydroquinone (HQ), indolequinone (IQ), and semiquinone (SQ). These molecules are believed to be the basic building blocks of the eumelanins, a class of biomacromolecules with important biological functions (including photoprotection) and with the potential for certain bioengineering applications. We have used the difference of self-consistent fields method to study the energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital, HL. We show that HL is similar in IQ and SQ, but approximately twice as large in HQ. This may have important implications for our understanding of the observed broadband optical absorption of the eumelanins. The possibility of using this difference in HL to molecularly engineer the electronic properties of eumelanins is discussed. We calculate the infrared and Raman spectra of the three redox forms from first principles. Each of the molecules have significantly different infrared and Raman signatures, and so these spectra could be used in situ to nondestructively identify the monomeric content of macromolecules. It is hoped that this may be a helpful analytical tool in determining the structure of eumelanin macromolecules and hence in helping to determine the structure-property-function relationships that control the behavior of the eumelanins.

Three-dimensional solution structure of alpha-conotoxin MII by NMR spectroscopy: Effects of solution environment on helicity

alpha-Conotoxin MII, a 16-residue polypeptide from the venom of the piscivorous cone snail Conus magus, is a potent and highly specific blocker of mammalian neuronal nicotinic acetylcholine receptors composed of alpha 3 beta 2 subunits. The role of this receptor type in the modulation of neurotransmitter release and its relevance to the problems of addiction and psychosis emphasize the importance of a structural understanding of the mode of interaction of MII with the alpha 3 beta 2 interface. Here we describe the three-dimensional solution structure of MIT determined using 2D H-1 NMR spectroscopy. Structural restraints consisting of 376 interproton distances inferred from NOEs and 12 dihedral restraints derived from spin-spin coupling constants were used as input for simulated annealing calculations and energy minimization in the program X-PLOR. The final set of 20 structures is exceptionally well-defined with mean pairwise rms differences over the whole molecule of 0.07 Angstrom for the backbone atoms and 0.34 Angstrom for all heavy atoms. MII adopts a compact structure incorporating a central segment of alpha-helix and beta-turns at the N- and C-termini. The molecule is stabilized by two disulfide bonds, which provide cross-links between the N-terminus and both the middle and C-terminus of the structure. The susceptibility of the structure to conformational change was examined using several different solvent conditions. While the global fold of MII remains the same, the structure is stabilized in a more hydrophobic environment provided by the addition of acetonitrile or trifluoroethanol to the aqueous solution. The distribution of amino acid side chains in MII creates distinct hydrophobic and polar patches on its surface that may be important for the specific interaction with the alpha 3 beta 2 neuronal nAChR. A comparison of the structure of MII with other neuronal-specific alpha-conotoxins provides insights into their mode of interaction with these receptors.

Community structure of Quaternary coral reefs compared with Recent life and death assemblages

This paper assesses the reliability with which fossil reefs record the diversity and community structure of adjacent Recent reefs. The diversity and taxonomic composition of Holocene raised fossil reefs was compared with those of modern reef coral life and death assemblages in adjacent moderate and low-energy shallow reef habitats Of Madang Lagoon, Papua New Guinea. Species richness per sample area and Shannon-Wiener diversity (H') were highest in the fossil reefs, intermediate in the life assemblages, and lowest in the death assemblages. The taxonomic composition of the fossil reefs was most similar to the combination of the life and death assemblages from the modern reefs adjacent to the two fossil reefs. Depth zonation was recorded accurately in the fossil reefs. The Madang fossil reefs represent time-averaged composites of the combined life and death assemblages as they existed at the time the reef was uplifted. Because fossil reefs include overlapping cohorts from the life and death assemblages, lagoonal facies of fossil reefs are dominated by the dominant sediment-producing taxa, which are not necessarily the most abundant in the life assemblage. Rare or slow-growing taxa accumulate more slowly than the encasing sediments and are underrepresented in fossil reef lagoons. Time-averaging dilutes the contribution of rare taxa, rather than concentrating their contribution. Consequently, fidelity indices developed for mollusks in sediments yield low values in coral reef death and fossil assemblages. Branching corals dominate lagoonal facies of fossil reefs because they are abundant, they grow and produce sediment rapidly, and most of the sediment they produce is not exported. Fossil reefs distinguished kilometer-scale variations in community structure more clearly than did the modern life assemblages. This difference implies that fossil,reefs may provide a better long-term record of community structure than modern reefs. This difference also suggests that modern kilometer-scale variation in coral reef community structure may have been reduced by anthropogenic degradation, even in the relatively unimpacted reefs of Madang Lagoon. Holocene and Pleistocene fossil reefs provide a time-integrated historical record of community composition and may be used as long-term benchmarks for comparison with modern, degraded, nearshore reefs. Comparisons between fossil reefs and degraded modern reefs display gross changes in community structure more effectively than they demonstrate local extinction of rare taxa.

Pore structure characterisation of pillared clays using a modified MP method

The data of nitrogen adsorption on pillared clays (PILC) are converted to comparison plots (t-plots) to derive their pore size distribution (PSD). As in the MP method, the surface area of a group of pores having similar pore sizes is calculated from the slopes of tangent lines at two succeeding points on a comparison plot. By the modified MP method in this work, the tangent line is extrapolated to the adsorption axis on the t-plot, and the difference between intercepts is used to obtain the volume of the group of pores. From the information of surface area and pore volume, the average width of the pore group can be calculated and hence the PSDs of PILCs are obtained by carrying out such calculation procedures from high to low t. With this method, PSDs of several pillared clays are calculated over a wide pore size range, from micropores to mesopores. It is found that the modified MP method could result in the underestimation of the width of ultramicropores due to the enhancement in adsorption energy in these pores. Nevertheless, the method can be very useful in calculating the surface area and pore volume, as well as a mean width of these pores. For super-micropores and mesopores, pore size can also be underestimated, due to deviation of the pore shape from a slit. The principles of the improved MP method, as well as problems associated with it are thoroughly discussed in this paper. In general, this modified method provides practically meaningful results which are consistent with the pore dimension obtained from powder X-ray diffraction measurements, but involves no complicated theoretical treatment or assumptions.

Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics

Smoothing the potential energy surface for structure optimization is a general and commonly applied strategy. We propose a combination of soft-core potential energy functions and a variation of the diffusion equation method to smooth potential energy surfaces, which is applicable to complex systems such as protein structures; The performance of the method was demonstrated by comparison with simulated annealing using the refinement of the undecapeptide Cyclosporin A as a test case. Simulations were repeated many times using different initial conditions and structures since the methods are heuristic and results are only meaningful in a statistical sense.

Photoinduced electron transfer and electronic energy transfer in naphthyl-appended cyclams

A series of novel macrocyclic tetraaza ligands that incorporate a naphthalene moiety as a photoactive chromophore have been prepared and structurally characterized as their Cu(II) complexes. Variable-temperature photophysical studies have concluded that the luminescence quenching evident in the Cu(H) complexes is due to intramolecular electronic energy transfer (EET). In their free-base forms, these ligands undergo reductive luminescence quenching via photoinduced electron transfer (PET) reactions, with proximate amine lone pairs acting as electron donors. Consequently, the emission behavior can be modulated by variations in pH and/or the presence of other Lewis acids such as Zn(H).

Hydraulic Performances of Minimum Energy Loss Culverts in Australia

Culverts are among the most common hydraulic structures. Modern designs do not differ from ancient structures and are often characterised by significant afflux at design flows. A significant advance was the development of the Minimum Energy Loss (MEL) culverts in the late 1950s. The design technique allows a drastic reduction in upstream flooding associated with lower costs. The development and operational performances of this type of structure is presented. The successful operation of MEL culverts for more than 40 years is documented with first-hand records during and after floods. The experiences demonstrate the design soundness while highlighting the importance of the hydraulic expertise of the design engineers.

A generalised dynamic model for char particle gasification with structure evolution and peripheral fragmentation

A generalised model for the prediction of single char particle gasification dynamics, accounting for multi-component mass transfer with chemical reaction, heat transfer, as well as structure evolution and peripheral fragmentation is developed in this paper. Maxwell-Stefan analysis is uniquely applied to both micro and macropores within the framework of the dusty-gas model to account for the bidisperse nature of the char, which differs significantly from the conventional models that are based on a single pore type. The peripheral fragmentation and random-pore correlation incorporated into the model enable prediction of structure/reactivity relationships. The occurrence of chemical reaction within the boundary layer reported by Biggs and Agarwal (Chem. Eng. Sci. 52 (1997) 941) has been confirmed through an analysis of CO/CO2 product ratio obtained from model simulations. However, it is also quantitatively observed that the significance of boundary layer reaction reduces notably with the reduction of oxygen concentration in the flue gas, operational pressure and film thickness. Computations have also shown that in the presence of diffusional gradients peripheral fragmentation occurs in the early stages on the surface, after which conversion quickens significantly due to small particle size. Results of the early commencement of peripheral fragmentation at relatively low overall conversion obtained from a large number of simulations agree well with experimental observations reported by Feng and Bhatia (Energy & Fuels 14 (2000) 297). Comprehensive analysis of simulation results is carried out based on well accepted physical principles to rationalise model prediction. (C) 2001 Elsevier Science Ltd. AH rights reserved.

Characterisation of pore structure of carbon adsorbents using regularisation procedure

The constrained regularisation procedure was applied to compute the pore size distributions (PSDs, f(x)) for a variety of activated carbons using overall adsorption equation based on the combination of the Kelvin equation and the statistical adsorbed film thickness. The impact of the boundary values of relative nitrogen pressure p/p(0) was analysed on the basis of the corresponding alterations in the PSDs. Changes in microporosity and mesoporosity of activated carbons can be described adequately only when the range of p/p(0) is as wide as possible, as at a high initial p/p(0) value, the f(x) curves can be broadened with shifted maxima especially for micropores and narrow mesopores. Comparative analysis of the PSDs and the adsorption potential, adsorption energy and fractal dimension distributions gives useful information on the complete description of the adsorbent characteristics. (C) 2001 Elsevier Science B.V. All rights reserved.

Intramolecular electronic energy transfer in bichromophoric macrocyclic complexes

Efficient intramolecular electronic energy transfer (EET) has been demonstrated for three novel bichromophoric compounds utilizing a macrocyclic spacer as the bridge between the electronic energy donor and acceptor fragments. As their free base forms, emission from the electronically excited donor is absent and the acceptor emission is reductively quenched via photoinduced oxidation of proximate amine lone pairs. As their Zn(II) complexes, excitation of the donor results in sensitization of the electronic acceptor emission.

Microscopic structure of opalescent and nonopalescent pecans

The ultrastructure of pecans was investigated using light microscopy, environmental scanning electron microscopy, scanning electron microscopy, and transmission electron microscopy. Specific methodology for the sample preparation of pecans for electron microscopy investigations was developed. Electron microscopy of the ultrastructure of opalescent (discoloration of the interior) and nonopalescent kernels revealed that cellular damage was occurring in opalescent kernels. The damage was due to cell wall and membrane rupture, which accounted for the release of oil throughout the kernel. This rupture is due to the lower level of calcium in the cell membranes of opalescent pecans, as shown by energy dispersive X-ray spectrometry, making them more susceptible to damage.

Phase equilibria and surface tension of pure fluids using a molecular layer structure theory (MLST) model

This paper presents a new model based on thermodynamic and molecular interaction between molecules to describe the vapour-liquid phase equilibria and surface tension of pure component. The model assumes that the bulk fluid can be characterised as set of parallel layers. Because of this molecular structure, we coin the model as the molecular layer structure theory (MLST). Each layer has two energetic components. One is the interaction energy of one molecule of that layer with all surrounding layers. The other component is the intra-layer Helmholtz free energy, which accounts for the internal energy and the entropy of that layer. The equilibrium between two separating phases is derived from the minimum of the grand potential, and the surface tension is calculated as the excess of the Helmholtz energy of the system. We test this model with a number of components, argon, krypton, ethane, n-butane, iso-butane, ethylene and sulphur hexafluoride, and the results are very satisfactory. (C) 2002 Elsevier Science B.V. All rights reserved.

Variation of the crystalline structure of coal char during gasification

The variation of the crystallite structure of several coal chars during gasification in air and carbon dioxide was studied by high-resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD) techniques. The XRD analysis of the partially gasified coal chars, based on two approaches, Scherrer's equation and Alexander and Sommer's method, shows a contradictory trend of the variation of the crystallite height with carbon conversion, despite giving a similar trend for the crystallite width change. The HRTEM fringe images of the partially gasified coal chars indicate that large and highly ordered crystallites exist at conversion levels as high as 86%. It is also demonstrated that the crystalline structure of chars can be very different although their pore structures are similar, suggesting a combination of crystalline structure analysis with pore structure analysis in studies of carbon gasification.

Shoemaker impact structure, Western Australia

The Shoemaker impact structure, on the southern margin of the Palaeoproterozoic Earaheedy Basin, with an outer diameter of similar to30 km, consists of two well-defined concentric ring structures surrounding a granitoid basement uplift. The concentric structures, including a ring syncline and a ring anticline, formed in sedimentary rocks of the Earaheedy Group. In addition, aeromagnetic and geological field observations suggest that Shoemaker is a deeply eroded structure. The central 12 km-diameter uplift consists of fractured Archaean basement granitoids of syenitic composition (Teague Granite). Shock-metamorphic features include shatter cones in sedimentary rocks and planar deformation features in quartz crystals of the Teague Granite. Universal-stage analysis of 51 sets of planar deformation features in 18 quartz grains indicate dominance of sets parallel to omega (10 (1) over bar3}, but absence of sets parallel to pi (10 (1) over bar2}, implying peak shock pressures in the range of 10-20 GPa for the analysed sample. Geophysical characteristics of the structure include a -100 mus(-2) gravity anomaly coincident with the central uplift and positive circular trends in both magnetic and gravity correlating with the inner ring syncline and outer ring anticline. The Teague Granite is dominated by albite-quartz-K-feldspar with subordinate amounts of alkali pyroxene. The alkali-rich syenitic composition suggests it could either represent a member of the Late Archaean plutonic suite or the product of alkali metasomatism related to impact-generated hydrothermal activity. In places, the Teague Granite exhibits partial to pervasive silicification and contains hydrothermal minerals, including amphibole, garnet, sericite and prehnite. Recent isotopic age studies of the Teague Granite suggest an older age limit of ca 1300 Ma (Ar-Ar on K-feldspar) and a younger age limit of ca 568 Ma (K-Ar on illite-smectite). The significance of the K-Ar age of 568 Ma is not clear, and it might represent either hydrothermal activity triggered by impact-related energy or a possible resetting by tectonothermal events in the region.