Size dependence of biomass spectra and abundance spectra: the optimal distributions

Based on the hypothesis of self-optimization, we derive four models of biomass spectra and abundance spectra in communities with size-dependent metabolic rates. In Models 1 and 2, the maximum diversity of population abundance in different size classes subject to the constraints of constant mean body mass and constant mean respiration rate is assumed to be the strategy for ecosystems to organize their size structure. In Models 3 and 4, the organizing strategy is defined as the maximum diversity of biomass in different size classes without constraints on mean body mass and subject to the constant mean specific respiration rate of all individuals, i.e. the average specific respiration rate over all individuals of a community or group, which characterizes the mean rate of energy consumption in a community. Models 1 and 2 generate peaked distributions of biomass spectral density whereas Model 3 generates a fiat distribution. In Model 4, the distributions of biomass spectral density and of abundance spectral density depend on the Lagrangian multipler (lambda (2)). When lambda (2) tends to zero or equals zero, the distributions of biomass spectral density and of abundance spectral density correspond to those from Model 3. When lambda (2) has a large negative value, the biomass spectrum is similar to the empirical fiat biomass spectrum organized in logarithmic size intervals. When lambda (2) > 0, the biomass spectral density increases with body mass and the distribution of abundance spectral density is an unimodal curve. (C) 2001 Elsevier Science B.V. All rights reserved.

DFT calculations of the structures and vibrational spectra of the [Fe(bpy)(3)](2+) and [Ru(bpy)(3)](2+) complexes

Structures of the [M(bpy)(3)](2+) complexes (M = Fe and Ru) have been calculated at the B3-LYP/DZVP level. IR and Raman spectra were calculated using the optimised geometries, employing a scaled quantum chemical force field, and compared with an earlier normal coordinate analysis of [Ru(bpy)(3) ](2+) which was based upon experimental data alone, and the use of a simplified model. The results of the calculations provide a highly satisfactory fit to the experimental data and the normal coordinate analyses, in terms of potential energy distributions, allow a detailed understanding of the vibrational spectra of both complexes. Evidence is presented for Jahn-Teller distortion in the E-1 MLCT excited state. (C) 2008 Elsevier B.V. All rights reserved.

Vibrational spectra of α-amino acids in the zwitterionic state in aqueous solution and the solid state: DFT calculations and the influence of hydrogen bonding

The zwitterionic forms of the two simplest alpha-amino acids, glycine and l-alanine, in aqueous solution and the solid state have been modeled by DFT calculations. Calculations of the structures in the solid state, using PW91 or PBE functionals, are in good agreement with the reported crystal structures, and the vibrational spectra computed at the optimized geometries provide a good fit to the observed IR and Raman spectra in the solid state. DFT calculations of the structures and vibrational spectra of the zwitterions in aqueous solution at the B3-LYP/cc-pVDZ level were found to require both explicit and implicit solvation models. Explicit solvation was modeled by inclusion of five hydrogen-bonded water molecules attached to each of the five possible hydrogen-bonding sites in the zwitterion and the integration equation formalism polarizable continuum model (IEF-PCM) was employed, providing a satisfactory fit to observed IR and Raman spectra. Band assignments are reported in terms of potential-energy distributions, which differ in some respects to those previously reported for glycine and l-alanine.

Effect of relaxation on the oxygen K-edge electron energy-loss near-edge structure in yttria-stabilized zirconia

The electron energy-loss near-edge structure (ELNES) at the oxygen K-edge has been investigated in a range of yttria-stabilized zirconia (YSZ) materials. The electronic structure of the three polymorphs of pure ZrO2 and of the doped YSZ structure close to the 33 mol %Y2O3 composition have been calculated using a full-potential linear muffin-tin orbital method (NFP-LMTO) as well as a pseudopotential based technique. Calculations of the ELNES dipole transition matrix elements in the framework of the NFP-LMTO scheme and inclusion of core hole screening within Slater's transition state theory enable the ELNES to be computed. Good agreement between the experimental and calculated ELNES is obtained for pure monoclinic ZrO2. The agreement is less good with the ideal tetragonal and cubic structures. This is because the inclusion of defects is essential in the calculation of the YSZ ELNES. If the model used contains ordered defects such as vacancies and metal Y planes, agreement between the calculated and experimental O K-edges is significantly improved. The calculations show how the five different O environments of Zr,Y,O, are connected with the features observed in the experimental spectra and demonstrate clearly the power of using ELNES to probe the stabilization mechanism in doped metal oxides.

The near-edge structure in energy-loss spectroscopy: many-electron and magnetic effects in transition metal nitrides and carbides

We investigate the ability of the local density approximation (LDA) in density functional theory to predict the near-edge structure in electron energy-loss spectroscopy in the dipole approximation. We include screening of the core hole within the LDA using Slater's transition state theory. We find that anion K-edge threshold energies are systematically overestimated by 4.22 +/- 0.44 eV in twelve transition metal carbides and nitrides in the rock-salt (B1) structure. When we apply this 'universal' many-electron correction to energy-loss spectra calculated within the transition state approximation to LDA, we find quantitative agreement with experiment to within one or two eV for TiC, TiN and VN. We compare our calculations to a simpler approach using a projected Mulliken density which honours the dipole selection rule, in place of the dipole matrix element itself. We find remarkably close agreement between these two approaches. Finally, we show an anomaly in the near-edge structure in CrN to be due to magnetic structure. In particular, we find that the N K edge in fact probes the magnetic moments and alignments of ther sublattice.

DFT studies of long-chain FAMEs: theoretical justification for determining chain length and unsaturation from experimental Raman spectra

Density functional calculations, using B3LPY/6-31G(d) methods, have been used to investigate the conformations and vibrational (Raman) spectra of a series of long-chain, saturated fatty acid methyl esters (FAMEs) with the formula CH2nO2 (n = 5-21) and two series of unsaturated FAMEs. The calculations showed that the lowest energy conformer within the saturated FAMEs is the simple (all-trans) structure and, in general, it was possible to reproduce experimental data using calculations on only the all-trans conformer. The only exception was C6H12O2, where a second low-lying conformer had to be included in order to correctly simulate the experimental Raman spectrum. The objective of the work was to provide theoretical justification for the methods that are commonly used to determine the properties of the fats and oils, such as chain length and degree of unsaturation, from experimental Raman data. Here it is shown that the calculations reproduce the trends and calibration curves that are found experimentally and also allow the reasons for the failure of what would appear to be rational measurements to be understood. This work shows that although the assumption that each FAME can simply be treated as a collection of functional groups can be justified in some cases, many of the vibrational modes are complex motions of large sections of the molecules and thus would not be expected to show simple linear trends with changes in structure, such as increasing chain length and/or unsaturation. Simple linear trends obtained from experimental data may thus arise from cancellation of opposing effects, rather than reflecting an underlying simplicity.

Dissociation of H2+ from a short, intense, infrared laser pulse: proton emission spectra and pulse calibration

The proton energy spectrum from photodissociation of the hydrogen molecular ion by short intense pulses of infrared light is calculated. The time-dependent Schrödinger equation is discretized and integrated. For few-cycle pulses one can resolve vibrational structure, arising from the experimental preparation of the molecular ion. We calculate the corresponding energy spectrum and analyse the dependence on the pulse time delay, pulse length and intensity of the laser for ? ~ 790 nm. We conclude that the proton spectrum is a sensitive probe of both the vibrational populations and phases, and allows us to distinguish between adiabatic and nonadiabatic dissociation. Furthermore, the sensitivity of the proton spectrum from H2+ is a practical means of calibrating the pulse. Our results are compared with recent measurements of the proton spectrum for 65 fs pulses using a Ti:Sapphire laser (? ~ 790 nm) including molecular orientation and focal-volume averaging. Integrating over the laser focal volume, for the intensity I ~ 3 × 1015 W cm-2, we find our results are in excellent agreement with these experiments.

An investigation of Fe XVI emission lines in solar and stellar extreme-ultraviolet and soft X-ray spectra

New fully relativistic calculations of radiative rates and electron impact excitation cross-sections for Fe XVI are used to determine theoretical emission-line ratios applicable to the 251-361 and 32-77 angstrom portions of the extreme-ultraviolet (EUV) and soft X-ray spectral regions, respectively. A comparison of the EUV results with observations from the Solar Extreme-Ultraviolet Research Telescope and Spectrograph (SERTS) reveals excellent agreement between theory and experiment. However, for emission lines in the 32-49 angstrom portion of the soft X-ray spectral region, there are large discrepancies between theory and measurement for both a solar flare spectrum obtained with the X-Ray Spectrometer/Spectrograph Telescope (XSST) and for observations of Capella from the Low- Energy Transmission Grating Spectrometer (LETGS) on the Chandra X-ray Observatory. These are probably due to blending in the solar flare and Capella data from both first-order lines and from shorter wavelength transitions detected in second and third order. By contrast, there is very good agreement between our theoretical results and the XSST and LETGS observations in the 50-77 angstrom wavelength range, contrary to previous results. In particular, there is no evidence that the Fe XVI emission from the XSST flare arises from plasma at a much higher temperature than that expected for Fe XVI in ionization equilibrium, as suggested by earlier work.

Nebular and Auroral Emission Lines of [Ar IV] in the Optical Spectra of Planetary Nebulae

Recent R-matrix calculations of electron impact excitation rates in Ar IV are used to calculate the emission-line ratio: ratio diagrams (R₁, R₂), (R_1, R₃), and (R_1, R₄), where K₁ = I(4711 Å)/I(4740 Å), R₂ = I(7238 Å)/I(4711 + 4740 Å), R₃ = I(7263 Å)/I(4711 + 4740 Å), and R₄ = I(7171 Å)/I(4711 + 4740 Å), for a range of electron temperatures (T_e = 5000-20,000 K) and electron densities (N_e = 10-10⁶ cm^-3) appropriate to gaseous nebulae. These diagrams should, in principle, allow the simultaneous determination of T_e and N_e from measurements of the [Ar IV] lines in a spectrum. Plasma parameters deduced for a sample of planetary nebulae from (R_1, R₃) and (R_1, R₄), using observational date obtained with the Hamilton echelle spectrograph on the 3 m Shane Telescope at the Lick Observatory, are found to show excellent internal consistency and to be in generally good agreement with the values of T_e and N_e estimated from other line ratios in the echelle spectra. These results provide observational support for the accuracy of the theoretical ratios and, hence, the atomic data adopted in their derivation. In addition, they imply that the 7171 Å line is not as seriously affected by telluric absorption as previously thought. However, the observed values of R₂ are mostly larger than the theoretical high-temperature and density limit, which is due to blending of the Ar IV 7237.54 Å line with the strong C II transition at 7236 Å. 

Electron shell contributions to gamma-ray spectra of positron annihilation in noble gases

Gamma-ray positron annihilation spectra of the noble gases are simulated using computational chemistry tools for the bound electron wavefunctions and plane-wave approximation for the low-energy positron. The present annihilation line shapes, i.e. the full width at half maximum, Delta epsilon, of the gamma-ray annihilation spectra for He and Ar (valence) agree well with available independent atomic calculations using a different algorithm. For other noble gases they achieve moderate agreement with the experimental measurements. It is found that the contributions of various atomic electron shells to the spectra depend significantly on their principal quantum number n and orbital angular momentum quantum number l. The present study further reveals that the outermost ns electrons of the noble gases exhibit spectral line shapes in close agreement with those measured, indicating (as expected) that the measurements are not due to a simple sum over the momentum densities for all atomic electrons. The robust nature of the present approach makes it possible for us to proceed to more complex molecular systems using the tools of modern computational chemistry.

TIME-RESOLVED ABSORPTION, INFRARED, AND RESONANCE RAMAN-SPECTRA OF THE COMPLEXES [RU(X)(R)(CO)(2)(ALPHA-DIIMINE)] (X=HALIDE R=ALKYL) - INFLUENCE OF X ON THE CHARGE-TRANSFER CHARACTER OF THE LOWEST EXCITED-STATE

Nanosecond time-resolved absorption (TA), resonance Raman (TR(3)), and infrared (TRIR) spectra are reported for several complexes [Ru(X)(R)(CO)(2)(alpha-diimine)] (X = Cl, Br, I; R = Me, Et; alpha-diimine = N,N'-diisopropyl-1,4-diaza-1,3-butadiene (iPr-DAB), pyridine-2-carbaldehyde-N-isopropylimine (iPr-PyCa), 2,2'-bipyridine (bpy)). This is the first instance in which the TA, TR(3), and TRIR techniques have been used to probe excited states in the same series of complexes. The TA spectra of the iodide complexes show a transient absorption between 550 and 700 nm, which does not depend on the solvent but shifts to lower energy in the order iPr-DAB > bpy > iPr-PyCa. This band is assigned to an intraligand transition. For the corresponding chloride and bromide complexes this band occurs at higher energy, most probably because of a change of character of the lowest excited state from XLCT to MLCT. The TRIR spectra show an increase in v(CO) (and k(CO)) on promotion to the excited state; however, the shifts Delta v(CO) show a decrease in the order Cl- > Br- > I-. The TR(3) spectra of the excited complexes [Ru(X)(R)(Co)(2)(iPr-DAB)] show v(s)(CN) of the iPr-DAB ligand 50-80 cm(-1) lower in frequency than for the complexes in their ground state. This frequency shift decreases in the order Cl- > Br- > I-, indicating a decrease of CT character of the lowest excited state in this order. However, going from X = Br to I, the effect on Delta v(CO) is much larger than the decrease of Delta v(s)(CN). This different effect on the CO- and CN-stretching frequencies is assigned to a gradual change in character of the lowest excited state from MLCT to XLCT when Cl- is replaced by Br- and I-. This result confirms a similar conclusion derived from previous resonance Raman and emission experiments on these complexes.

RESONANCE RAMAN-SPECTRA OF THE TRIPLET-STATE OF FREE-BASE TETRAPHENYLPORPHYRIN AND 6 OF ITS ISOTOPOMERS

The resonance Raman spectra of the ground state and the lowest excited tripler state of free-base tetraphenylporphyrin and six of its isotopomers have been obtained using two-color time-resolved techniques. Ground-state spectra were recorded using low-energy 447 nm probe laser pulses, and triplet-state spectra were probed, with similar pulses, 30 ns after high-energy excitation with 532 nm pump pulses. Polarization data on both the ground and triplet states are also reported. The resonance Raman spectrum of the triplet is very different from that of the ground state but the combination of extensive isotope substitution with polarization data allows bands in the ground state to be assigned and corresponding bands in the tripler state to be located. Isotope shifts of the same bands in the S-0 and T-1 states are similar, implying that the compositions of the vibrational modes do not change significantly on excitation. Two of the strongest bands in the T-1 spectra are associated with phenyl ring substituents; these are shifted less than 5 cm(-1) between the S-0 and T-1 states so that bonding in the phenyl substituents is barely affected by excitation to the T-1 state. The changes in position of the porphyrin ring bands are larger, but still only tens of cm(-1) or less, the main changes in the spectra being due to differences in relative band intensities in the two states. The relatively small shifts in the porphyrin ring band positions which are observed show that the excitation energy is not localized on a single small region of the molecule but is delocalized over the entire porphyrin skeleton. This picture of an excited species with high chemical reactivity, but with individual bonds only slightly perturbed from the ground state, is contrasted with molecules, such as benzophenone, where excitation causes a large perturbation in the bonding within a single functional group.

Role of low-energy electrons in Ar emission from low-pressure radio frequency discharge plasma

Optical emission spectra from a low-pressure Ar plasma were studied with high spatial resolution. It has been shown that the intensity ratios of Ar lines excited through metastable levels to those excited directly from the ground state are sensitive to the shape of electron energy distribution function. From these measurements, important information on the spatial variation of plasma parameters can be obtained. (C) 1999 American Institute of Physics. [S0003-6951(99)01629-0].

Energy distributions of copper ions and atoms sputtered by atomic and molecular ions

Non-resonant multiphoton ionization combined with quadrupole and time-of-flight analysis has been used to study sputtering by both atomic and molecular ion beams. The mass spectra and energy distributions of both sputtered atoms and secondary ions produced by 3.6 keV Ar+, N+, N-2(+), CF2+ and CF3+ ion bombardment at 45 degrees to a polycrystalline copper target have been measured. The energy distributions of the copper ions and atoms are found to be different and quite complex. The ion distributions can generally be described by a linear collision cascade model, with possible evidence for a knock-on contribution. The sputtered atom distributions are partially described by a combination of linear collision cascade and dense cascade (thermal spike) models. This is interpreted as support for a time-evolving sputtering mechanism.

Effect of positron-atom interactions on the annihilation gamma spectra of molecules

Calculations of ?-spectra for positron annihilation on a selection of molecules, including methane and its fluoro-substitutes, ethane, propane, butane and benzene are presented. The annihilation ?-spectra characterise the momentum distribution of the electron-positron pair at the instant of annihilation. The contribution to the ?-spectra from individual molecular orbitals is obtained from electron momentum densities calculated using modern computational quantum chemistry density functional theory tools. The calculation, in its simplest form, effectively treats the low-energy (thermalised, room-temperature) positron as a plane wave and gives annihilation ?-spectra that are about 40% broader than experiment, although the main chemical trends are reproduced. We show that this effective 'narrowing' of the experimental spectra is due to the action of the molecular potential on the positron, chiefly, due to the positron repulsion from the nuclei. It leads to a suppression of the contribution of small positron-nuclear separations where the electron momentum is large. To investigate the effect of the nuclear repulsion, as well as that of short-range electron-positron and positron-molecule correlations, a linear combination of atomic orbital description of the molecular orbitals is employed. It facilitates the incorporation of correction factors which can be calculated from atomic many-body theory and account for the repulsion and correlations. Their inclusion in the calculation gives -spectrum linewidths that are in much better agreement with experiment. Furthermore, it is shown that the effective distortion of the electron momentum density, when it is observed through positron annihilation -spectra, can be approximated by a relatively simple scaling factor. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.