Notations and conventions in molecular spectroscopy: part 2. Symmetry notation

The field of Molecular Spectroscopy was surveyed in order to determine a set of conventions and symbols which are in common use in the spectroscopic literature. This document, which is Part 2 in a series, establishes the notations and conventions used for the description of symmetry in rigid molecules, using the Schoenflies notation. It deals firstly with the symmetry operators of the molecular point groups (also drawing attention to the difference between symmetry operators and elements). The conventions and notations of the molecular point groups are then established, followed by those of the representations of these groups as used in molecular spectroscopy. Further parts will follow, dealing inter alia with permutation and permutation-inversion symmetry notation, vibration-rotation spectroscopy and electronic spectroscopy.

Microwave spectrum of 2-aminopyridine

The microwave spectra of 2-aminopyridine-NH2, -ND2, and of both of the two possible -NHD molecules have been observed and assigned in the 0+ vibrational state of the amino group inversion vibration; the assignment for three of the molecules in the 0− state is also made. From intensity measurements the 0+-0− splitting is estimated to be 135 ± 25 cm−1 for the -NH2 molecule and 95 ± 30 cm−1 for the -ND2 molecule. The rotational constants are interpreted in terms of a structure in which the amino group is bent about 32° out of the molecular plane, the c coordinates of the two amino H atoms being 0.21 and 0.28 Å. Stark effect measurements give a dipole moment of about 0.9 D which is almost entirely in the b axis, and which changes quite significantly between the 0+ and 0− states.

The ν2, 2ν2, 3ν2, ν4 and ν2+ν4 bands of 15NH3

The ir absorption of gaseous 15NH3 between 510 and 3040 cm−1 was recorded with a resolution of 0.06 cm−1. The ν2, 2ν2, 3ν2, ν4, and ν2 + ν4 bands were measured and analyzed on the basis of the vibration-rotation Hamiltonian developed by V. Špirko, J. M. R. Stone, and D. Papoušek (J. Mol. Spectrosc. 60, 159–178 (1976)). A set of effective molecular parameters for the ν2 = 1, 2, 3 states was derived, which reproduced the transition frequencies within the accuracy of the experimental measurements. For ν4 and ν2 + ν4 bands the standard deviation of the calculated spectrum is about four times larger than the measurements accuracy: a similar result was found for ν4 in 14NH3 by Š. Urban et al. (J. Mol. Spectrosc. 79, 455–495 (1980)). This result suggests that the present treatment takes into account only the most significant part of the rovibration interaction in the doubly degenerate vibrational states of ammonia.

Two-dimensional anharmonic oscillator: application to 2,5-dihydrofuran

A program has been developed to calculate the energy levels and corresponding wavefunctions for a two‐dimensional anharmonic potential surface of at least C2v symmetry. This program has been employed to explain the high resolution splittings observed in the far infrared spectrum of 2,5‐dihydrofuran. The magnitude of the cross term connecting the ring‐twisting and ring‐puckering modes of 2,5‐dihydrofuran is sufficiently large to be significant. The potential surface determined also suggests that the ring‐twisting mode may be slightly anharmonic.

The assignment of ν2 and ν4 of SO3

Three experiments have been performed to resolve an uncertainty in the assignment of ν2 and ν4 for SO3: (i) the gas phase Raman spectrum has been measured; (ii) the infrared active combination band ν3 + ν4 has been measured; (iii) a band contour calculation has been performed taking account of the ℓ-type resonance in ν4 and a strong Coriolis resonance between ν2 and ν4. These experiments establish beyond any doubt that ν2 lies at about 497.5 cm−1 and ν4 lies at about 530.2 cm−1. The contour calculation also shows that the Coriolis resonance gives rise to a positive intensity perturbation.

The microwave spectrum of thietan-2,2,4,4-d4

The microwave spectrum for thietan-2,2,4,4-d4 is analysed in six of its lowest puckering states and up to J = 25. The close lying pairs of states of vp = 0/1, 2/3 and 4/5 are treated with a vibration-rotation hamiltonian which includes an off-diagonal coupling term in vp. Additional corrections to this coupling term in higher powers of the angular momentum operator are derived and their importance for improving the fit of calculated to observed data is tested. The variation of the centrifugal distortion constants with vp follows the model of Creswell and Mills (1974, J. molec. Spectrosc., 52, 392). A value is determined for the derivative with respect to the puckering coordinate of the ac-component of the inverse moment of inertia tensor.

The infrared spectrum of the ν2 and ν3 bands of H16OF, H18OF, and D16OF

Fourier transform IR spectra in the ν2 and ν3 regions between 800 and 1500 cm−1 have been measured of H16OF with a resolution of 0.007 cm−1 and of H18OF and DOF with a resolution of 0.040 cm−1. Ground state constants have been improved for H16OF and have been obtained for the first time for H18OF. Parameters of the v2 = 1 and v3 = 1 excited states have been determined from rovibrational analyses of ca. 1000 ν2/ν3 lines which were fitted with σ 0.36, 4.5, and 7.6 × 10−3 cm−1 for H16OF, H18OF, and D16OF, respectively. Band centers of ν2/ν3 are 1353.40466(5)/889.07974(6), 1350.3976(5)/862.2967(7), and 1002.0083(9)/891.0014(15) cm−1, respectively, for the three isotopic species. While ν2 and ν3 are sufficiently separated in HOF to be treated independently, a Coriolis resonance is evident in DOF, the interaction constant ξ23c = 0.19073(16) cm−1 being in agreement with the prediction from the harmonic force field.

Multi-model assessment of stratospheric ozone return dates and ozone recovery in CCMVal-2 models

Projections of stratospheric ozone from a suite of chemistry-climate models (CCMs) have been analyzed. In addition to a reference simulation where anthropogenic halogenated ozone depleting substances (ODSs) and greenhouse gases (GHGs) vary with time, sensitivity simulations with either ODS or GHG concentrations fixed at 1960 levels were performed to disaggregate the drivers of projected ozone changes. These simulations were also used to assess the two distinct milestones of ozone returning to historical values (ozone return dates) and ozone no longer being influenced by ODSs (full ozone recovery). The date of ozone returning to historical values does not indicate complete recovery from ODSs in most cases, because GHG-induced changes accelerate or decelerate ozone changes in many regions. In the upper stratosphere where CO2-induced stratospheric cooling increases ozone, full ozone recovery is projected to not likely have occurred by 2100 even though ozone returns to its 1980 or even 1960 levels well before (~2025 and 2040, respectively). In contrast, in the tropical lower stratosphere ozone decreases continuously from 1960 to 2100 due to projected increases in tropical upwelling, while by around 2040 it is already very likely that full recovery from the effects of ODSs has occurred, although ODS concentrations are still elevated by this date. In the midlatitude lower stratosphere the evolution differs from that in the tropics, and rather than a steady decrease in ozone, first a decrease in ozone is simulated from 1960 to 2000, which is then followed by a steady increase through the 21st century. Ozone in the midlatitude lower stratosphere returns to 1980 levels by ~2045 in the Northern Hemisphere (NH) and by ~2055 in the Southern Hemisphere (SH), and full ozone recovery is likely reached by 2100 in both hemispheres. Overall, in all regions except the tropical lower stratosphere, full ozone recovery from ODSs occurs significantly later than the return of total column ozone to its 1980 level. The latest return of total column ozone is projected to occur over Antarctica (~2045–2060) whereas it is not likely that full ozone recovery is reached by the end of the 21st century in this region. Arctic total column ozone is projected to return to 1980 levels well before polar stratospheric halogen loading does so (~2025–2030 for total column ozone, cf. 2050–2070 for Cly+60×Bry) and it is likely that full recovery of total column ozone from the effects of ODSs has occurred by ~2035. In contrast to the Antarctic, by 2100 Arctic total column ozone is projected to be above 1960 levels, but not in the fixed GHG simulation, indicating that climate change plays a significant role.

CD27 mediates interleukin-2-independent clonal expansion of the CD8+ T cell without effector differentiation

The clonal expansion of antigen-specific CD8+ T cells in response to microbial infections is essential for adaptive immunity. Although IL-2 has been considered to be primarily responsible for this process, quantitatively normal expansion occurs in the absence of IL-2 receptor signaling. Here, we show that ligating CD27 on CD8+ T cells that have been stimulated through the T cell receptor causes their expansion in the absence of IL-2 by mediating two distinct cellular processes: enhancing cell cycling and promoting cell survival by maintaining the expression of IL-7 receptor alpha. This pathway for clonal expansion of the CD8+ T cell is not associated with the development of a capacity either for production of IFN-gamma or for cytotoxic T lymphocyte function and, therefore, is uncoupled from differentiation. Furthermore, ligating CD27 increases the threshold concentration at which IL-2 induces IFN-gamma-producing capability by the CD8+ T cell, suggesting that CD27 signaling may suppress effector differentiation. Finally, CD8+ T cells that have been stimulated by the TCR/CD27 pathway maintain their capacity for subsequent expansion and effector differentiation in response to a viral challenge in vivo. Thus, the TCR/CD27 pathway enables the CD8+ T cell to replicate by a process of self-renewal, which may contribute to the continuous generation of new effector CD8+ T cells in persistent viral infections.

The two Caenorhabditis elegans metallothioneins (CeMT-1 and CeMT-2) discriminate between essential zinc and toxic cadmium

The nematode Caenorhabditis elegans expresses two metallothioneins (MTs), CeMT-1 and CeMT-2, that are believed to be key players in the protection against metal toxicity. In this study, both isoforms were expressed in vitro in the presence of either Zn(II) or Cd(II). Metal binding stoichiometries and affinities were determined by ESI-MS and NMR, respectively. Both isoforms had equal zinc binding ability, but differed in their cadmium binding behaviour, with higher affinity found for CeMT-2. In addition, wild-type C. elegans, single MT knockouts and a double MT knockout allele were exposed to zinc (340 μm) or cadmium (25 μm) to investigate effects in vivo. Zinc levels were significantly increased in all knockout strains, but were most pronounced in the CeMT-1 knockout, mtl-1 (tm1770), while cadmium accumulation was highest in the CeMT-2 knockout, mtl-2 (gk125) and the double knockout mtl-1;mtl-2 (zs1). In addition, metal speciation was assessed by X-ray absorption fine-structure spectroscopy. This showed that O-donating, probably phosphate-rich, ligands play a dominant role in maintaining the physiological concentration of zinc, independently of metallothionein status. In contrast, cadmium was shown to coordinate with thiol groups, and the cadmium speciation of the wild-type and the CeMT-2 knockout strain was distinctly different to the CeMT-1 and double knockouts. Taken together, and supported by a simple model calculation, these findings show for the first time that the two MT isoforms have differential affinities towards Cd(II) and Zn(II) at a cellular level, and this is reflected at the protein level. This suggests that the two MT isoforms have distinct in vivo roles.

Initial results from Phase 2 of the international urban energy balance model comparison

Urban land surface schemes have been developed to model the distinct features of the urban surface and the associated energy exchange processes. These models have been developed for a range of purposes and make different assumptions related to the inclusion and representation of the relevant processes. Here, the first results of Phase 2 from an international comparison project to evaluate 32 urban land surface schemes are presented. This is the first large-scale systematic evaluation of these models. In four stages, participants were given increasingly detailed information about an urban site for which urban fluxes were directly observed. At each stage, each group returned their models' calculated surface energy balance fluxes. Wide variations are evident in the performance of the models for individual fluxes. No individual model performs best for all fluxes. Providing additional information about the surface generally results in better performance. However, there is clear evidence that poor choice of parameter values can cause a large drop in performance for models that otherwise perform well. As many models do not perform well across all fluxes, there is need for caution in their application, and users should be aware of the implications for applications and decision making.

Whole crop cereals 2. Prediction of apparent digestibility and energy value from in vitro digestion techniques and near infrared reflectance spectroscopy and of chemical composition by near infrared reflectance spectroscopy

Samples of whole crop wheat (WCW, n = 134) and whole crop barley (WCB, n = 16) were collected from commercial farms in the UK over a 2-year period (2003/2004 and 2004/2005). Near infrared reflectance spectroscopy (NIRS) was compared with laboratory and in vitro digestibility measures to predict digestible organic matter in the dry matter (DOMD) and metabolisable energy (ME) contents measured in vivo using sheep. Spectral models using the mean spectra of two scans were compared with those using individual spectra (duplicate spectra). Overall NIRS accurately predicted the concentration of chemical components in whole crop cereals apart from crude protein. ammonia-nitrogen, water-soluble carbohydrates, fermentation acids and solubility values. In addition. the spectral models had higher prediction power for in vivo DOMD and ME than chemical components or in vitro digestion methods. Overall there Was a benefit from the use of duplicate spectra rather than mean spectra and this was especially so for predicting in vivo DOMD and ME where the sample population size was smaller. The spectral models derived deal equally well with WCW and WCB and Would he of considerable practical value allowing rapid determination of nutritive value of these forages before their use in diets of productive animals. (C) 2008 Elsevier B.V. All rights reserved.

Pea-barley intercropping for efficient symbiotic N-2-fixation, soil N acquisition and use of other nutrients in European organic cropping systems

Complementarity in acquisition of nitrogen (N) from soil and N-2-fixation within pea and barley intercrops was studied in organic field experiments across Western Europe (Denmark, United Kingdom, France, Germany and Italy). Spring pea and barley were sown either as sole crops, at the recommended plant density (P100 and B100, respectively) or in replacement (P50B50) or additive (P100B50) intercropping designs, in each of three cropping seasons (2003-2005). Irrespective of site and intercrop design, Land Equivalent Ratios (LER) between 1.4 at flowering and 1.3 at maturity showed that total N recovery was greater in the pea-barley intercrops than in the sole Crops Suggesting a high degree of complementarity over a wide range of growing conditions. Complementarity was partly attributed to greater soil mineral N acquisition by barley, forcing pea to rely more on N-2-fixation. At all sites the proportion of total aboveground pea N that was derived from N-2-fixation was greater when intercropped with barley than when grown as a sole crop. No consistent differences were found between the two intercropping designs. Simultaneously, the accumulation Of Phosphorous (P), potassium (K) and sulphur (S) in Danish and German experiments was 20% higher in the intercrop (P50B50) than in the respective sole crops, possibly influencing general crop yields and thereby competitive ability for other resources. Comparing all sites and seasons, the benefits of organic pea-barley intercropping for N acquisition were highly resilient. It is concluded that pea-barley intercropping is a relevant cropping strategy to adopt when trying to optimize N-2-fixation inputs to the cropping system. (C) 2009 Elsevier B.V. All rights reserved.