Cis-retinoids and the chemistry of vision

We discuss here principal biochemical transformations of retinoid molecules in the visual cycle. We focus our analysis on the accumulating evidence of alternate pathways and functional redundancies in the cycle. The efficiency of the visual cycle depends, on one hand, on fast regeneration of the photo-bleached chromophores. On the other hand, it is crucial that the cyclic process should be highly selective to avoid accumulation of byproducts. The state-of-the-art knowledge indicates that single enzymatically active components of the cycle are not strictly selective and may require chaperones to enhance their rates. It appears that protein–protein interactions significantly improve the biological stability of the visual cycle. In particular, synthesis of thermodynamically less stable 11-cis-retinoid conformers is favored by physical interactions of the isomerases present in the retina with cellular retinaldehyde binding protein

Crystal chemistry and hydrogen bonding of rustumite Ca10(Si2O7)2(SiO4)(OH)2Cl2 with variable OH, Cl, F

Three samples of the skarn mineral rustumite Ca10(Si2O7)2(SiO4)(OH)2Cl2, space group C2/c, a ≈7.6, b ≈ 18.5, c ≈ 15.5 Å, β ≈ 104°, with variable OH, Cl, F content were investigated by electron microprobe, single-crystal X-ray structure refinements, and Raman spectroscopy. “Rust1LCl” is a low chlorine rustumite Ca10(Si2O7)2(SiO4)(OH1.88F0.12)(Cl1.28,OH0.72) from skarns associated with the Rize batholith near Ikizedere, Turkey. “Rust2F” is a F-bearing rustumite Ca10(Si2O7)2(SiO4)(OH1.13F0.87) (Cl1 96OH0.04) from xenoliths in ignimbrites of the Upper Chegem Caldera, Northern Caucasus, Russia. “Rust3LClF” represents a low-Cl, F-bearing rustumite Ca10(Si2O7)2(SiO4)0.87(H4O4)0.13(OH1.01F0.99) (Cl1.00 OH1.00) from altered merwinite skarns of the Birkhin massif, Baikal Lake area, Eastern Siberia, Russia. Rustumite from Birkhin massif is characterized by a significant hydrogarnet-like or fluorine substitution at the apices of the orthosilicate group, leading to specific atomic displacements. The crystal structures including hydrogen positions have been refined from single-crystal X-ray data to R1 = 0.0205 (Rust1_LCl), R1 = 0.0295 (Rust2_F), and R1 = 0.0243 (Rust3_LCl_F), respectively. Depletion in Cl and replacement by OH is associated with smaller unit-cell dimensions. The substitution of OH by F leads to shorter hydrogen bonds O-H⋯F instead of O-H⋯OH. Raman spectra for all samples have been measured and confirm slight strengthening of the hydrogen bonds with uptake of F.This study discusses the complex crystal chemistry of the skarn mineral rustumite and may provide a wider understanding of the chemical reactions related to contact metamorphism of limestones.

First foot prints of chemistry on the shore of the Island of Superheavy Elements

Chemistry has arrived on the shore of the Island of Stability with the first chemical investigation of the superheavy elements Cn, 113, and 114. The results of three experimental series leading to first measured thermodynamic data and qualitatively evaluated chemical properties for these elements are described. An interesting volatile compound class has been observed in the on-line experiments for the elements Bi and Po. Hence, an exciting chemical study of their heavier transactinide homologues, elements 115 and 116 is suggested.

The Crystal Chemistry of Holtite

Holtite, approximately (Al,Ta,square)Al(6)(BO(3))(Si,Sb(3+),As(3+))(Sigma 3)O(12)(O,OH,square)(Sigma 3), is a member of the dumortierite group that has been found in pegmatite, or alluvial deposits derived from pegmatite, at three localities: Greenbushes, Western Australia; Voron'i Tundry, Kola Peninsula, Russia; and Szklary, Lower Silesia, Poland. Holtite can contain >30 wt.% Sb(2)O(3), As(2)O(3), Ta(2)O(5), Nb(2)O(5), and TiO(2) (taken together), but none of these constituents is dominant at a crystallographic site, which raises the question whether this mineral is distinct from dumortierite. The crystal structures of four samples from the three localities have been refined to R(1) = 0.02-0.05. The results show dominantly: Al, Ta, and vacancies at the Al(1) position; Al and vacancies at the Al(2), (3) and (4) sites; Si and vacancies at the Si positions; and Sb, As and vacancies at the Sb sites for both Sb-poor (holtite I) and Sb-rich (holtite II) specimens. Although charge-balance calculations based on our single-crystal structure refinements suggest that essentially no water is present, Fourier transform infrared spectra confirm that some OH is present in the three samples that could be measured. By analogy with dumortierite, the largest peak at 3505-3490 cm(-1) is identified with OH at the O(2) and O(7) positions. The single-crystal X-ray refinements and FTIR results suggest the following general formula for holtite: Al(7-[5x+y+z]/3)(Ta,Nb)(x)square([2x+y+z]/3)BSi(3-y)(Sb,As)(y)O(18-y-z)(OH)(z), where x is the total number of pentavalent cations, y is the total amount of Sb + As, and z <= y is the total amount of OH. Comparison with the electron microprobe compositions suggests the following approximate general formulae Al(5.83)(Ta,Nb)(0.50)square(0.67)BSi(2.50)(Sb,As)(0.50)O(17.00)(OH)(0.50) and Al(5.92)(Ta,Nb)(0.25)square(0.83)BSi(2.00)(Sb,As)(1.00) O(16.00)(OH)(1.00) for holtite I and holtite II respectively. However, the crystal structure refinements do not indicate a fundamental difference in cation ordering that might serve as a criterion for recognizing the two holtites as distinct species, and anion compositions are also not sufficiently different. Moreover, available analyses suggest the possibility of a continuum in the Si/(Sb + As) ratio between holtite I and dumortierite, and at least a partial continuum between holtite I and holtite II. We recommend that use of the terms holtite I and holtite II be discontinued.

The Effects of Flowline Length Evolution on Chemistry-Delta O-18 Profiles from Penny Ice Cap, Baffin Island, Canada

The isotopic and chemical signatures for ice-age and Holocene ice from Summit, Greenland and Penny Ice Cap, Baffin Island, Canada, arc compared. The usual pattern of low delta(18)O, high Ca2+ and high Cl- is presented in the Summit records, but Penny Ice Cap has lower than present Cl- in its ice-age ice. A simple extension of the Hansson model (Hansson, 1994) is developed and used to simulate these signatures. The low ice-age Cl- from Penny Ice Cap is explained by having the ice-age ice originating many thousands of km inland near the centre of the Laurentide ice sheet and much further from the marine sources. Summit's flowlines all start close to the present site. The Penny Ice Cap early-Holocene delta(18)O's had to be corrected to offset the Laurentide meltwater distortion. The analysis suggests that presently the Summit and Penny Ice Cap marine impurity originates about,500 km away, and that presently Penny Ice Cap receives a significant amount of local continental impurity.

Modeling Englacial Radar Attenuation at Siple Dome, West Antarctica, Using Ice Chemistry and Temperature Data

The radar reflectivity of an ice-sheet bed is a primary measurement for discriminating between thawed and frozen beds. Uncertainty in englacial radar attenuation and its spatial variation introduces corresponding uncertainty in estimates of basal reflectivity. Radar attenuation is proportional to ice conductivity, which depends on the concentrations of acid and sea-salt chloride and the temperature of the ice. We synthesize published conductivity measurements to specify an ice-conductivity model and find that some of the dielectric properties of ice at radar frequencies are not yet well constrained. Using depth profiles of ice-core chemistry and borehole temperature and an average of the experimental values for the dielectric properties, we calculate an attenuation rate profile for Siple Dome, West Antarctica. The depth-averaged modeled attenuation rate at Siple Dome (20.0 +/- 5.7 dB km(-1)) is somewhat lower than the value derived from radar profiles (25.3 +/- 1.1 dB km(-1)). Pending more experimental data on the dielectric properties of ice, we can match the modeled and radar-derived attenuation rates by an adjustment to the value for the pure ice conductivity that is within the range of reported values. Alternatively, using the pure ice dielectric properties derived from the most extensive single data set, the modeled depth-averaged attenuation rate is 24.0 +/- 2.2 dB km(-1). This work shows how to calculate englacial radar attenuation using ice chemistry and temperature data and establishes a basis for mapping spatial variations in radar attenuation across an ice sheet.

Experimental Determination of Salinity, Temperature, Growth, and Metabolic Effects on Shell Isotope Chemistry of Mytilus edulis Collected from Maine and Greenland

To study the effects of temperature, salinity, and life processes (growth rates, size, metabolic effects, and physiological/ genetic effects) on newly precipitated bivalve carbonate, we quantified shell isotopic chemistry of adult and juvenile animals of the intertidal bivalve Mytilus edulis (Blue mussel) collected alive from western Greenland and the central Gulf of Maine and cultured them under controlled conditions. Data for juvenile and adult M. edulis bivalves cultured in this study, and previously by Wanamaker et al. (2006), yielded statistically identical paleotemperature relationships. On the basis of these experiments we have developed a species-specific paleotemperature equation for the bivalve M. edulis [T degrees C = 16.28 (+/- 0.10) -4.57 (+/- 0.15) {delta(18)O(c) VPBD - delta(18)O(w) VSMOW} + 0.06 (+/- 0.06) {delta(18)O(c) VPBD - delta(18)O(w) VSMOW}(2); r(2) = 0.99; N = 323; p < 0.0001]. Compared to the Kim and O'Neil (1997) inorganic calcite equation, M. edulis deposits its shell in isotope equilibrium (delta(18)O(calcite)) with ambient water. Carbon isotopes (delta(13)C(calcite)) from sampled shells were substantially more negative than predicted values, indicating an uptake of metabolic carbon into shell carbonate, and delta(13)C(calcite) disequilibrium increased with increasing salinity. Sampled shells of M. edulis showed no significant trends in delta(18)O(calcite) based on size, cultured growth rates, or geographic collection location, suggesting that vital effects do not affect delta(18)O(calcite) in M. edulis. The broad modern and paleogeographic distribution of this bivalve, its abundance during the Holocene, and the lack of an intraspecies physiologic isotope effect demonstrated here make it an ideal nearshore paleoceanographic proxy throughout much of the North Atlantic Ocean.

A High-Altitude Snow Chemistry Record from Amundsenisen, Dronning Maud Land, Antarctica

In this paper a detailed record of major ions from a 20 in deep firn core from Amundsenisen, western Dronning Maud Land, Antarctica, is presented. The core was drilled at 75degreesS, 2degrees E (2900 m.a.s.l.) during austral summer 1991/92. The following ions were measured at 3 cm resolution: Na+, Mg2+, Ca2+, Cl-, NO3-, SO42- and CH3SO3H (MSA). The core was dated back to 1865 using a combination of chemical records and volcanic reference horizons. The volcanic eruptions identified in this core are Mount Ngauruhoe, New Zealand (1974-75), Mount Agung, Indonesia (1963), Azul, Argentina (1932). and a broad peak that corresponds in time to Tarawera, New Zealand (1886), Falcon Island, South Shetlands, Southern Ocean (1885), and Krakatau, Indonesia (1883). There are no trends in any of the ion records, but the annual to decadal changes are large. The mean concentrations of the measured ions are in agreement with those from other high-altitude cores from the Antarctic plateau. At this core site there may be a correspondence between peaks in the MSA record and major El Nino-Southern Oscillation events.

Monsoonal Circulation of the McMurdo Dry Valleys, Ross Sea Region, Antarctica: Signal from the Snow Chemistry

McMurdo Dry Valleys (MDV, Ross Sea region, Antarctica) precipitation exhibits extreme seasonality in ion concentration, 3-5 orders of magnitude between summer and winter precipitation. To identify aerosol sources and investigate causes for the observed amplitude in concentration variability, four snow pits were sampled along a coast-Polar Plateau transect across the MDV. The elevation of the sites ranges from 50 to 2400 m and the distance from the coast from 8 to 93 km. Average chemistry gradients along the transect indicate that most species have either a predominant marine or terrestrial source in the MDV. Empirical orthogonal function analysis on the snow-chemistry time series shows that at least 57% of aerosol deposition occurs concurrently. A conceptual climate model, based on meteorological observations, is used to explain the strong seasonality in the MDV. Our results suggest that radiative forcing of the ice-free valleys creates a surface low-pressure cell during summer which promotes air-mass flow from the Ross Sea. The associated precipitating air mass is relatively warm, humid and contains a high concentration of aerosols. During winter, the MDV are dominated by air masses draining off the East Antarctic ice sheet, that are characterized by cold, dry and low concentrations of aerosols. The strong differences between these two air-mass sources create in the MDV a polar version of the monsoonal flow, with humid, warm summers and dry, cold winters.

Experimental Determination of Salinity, Temperature, Growth, and Metabolic Effects on Shell Isotope Chemistry of Mytilus Edulis Collected from Maine and Greenland

To study the effects of temperature, salinity, and life processes (growth rates, size, metabolic effects, and physiological/ genetic effects) on newly precipitated bivalve carbonate, we quantified shell isotopic chemistry of adult and juvenile animals of the intertidal bivalve Mytilus edulis (Blue mussel) collected alive from western Greenland and the central Gulf of Maine and cultured them under controlled conditions. Data for juvenile and adult M. edulis bivalves cultured in this study, and previously by Wanamaker et al. (2006), yielded statistically identical paleotemperature relationships. On the basis of these experiments we have developed a species-specific paleotemperature equation for the bivalve M. edulis [T degrees C = 16.28 (+/- 0.10) -4.57 (+/- 0.15) {delta(18)O(c) VPBD - delta(18)O(w) VSMOW} + 0.06 (+/- 0.06) {delta(18)O(c) VPBD - delta(18)O(w) VSMOW}(2); r(2) = 0.99; N = 323; p < 0.0001]. Compared to the Kim and O'Neil (1997) inorganic calcite equation, M. edulis deposits its shell in isotope equilibrium (delta(18)O(calcite)) with ambient water. Carbon isotopes (delta(13)C(calcite)) from sampled shells were substantially more negative than predicted values, indicating an uptake of metabolic carbon into shell carbonate, and delta(13)C(calcite) disequilibrium increased with increasing salinity. Sampled shells of M. edulis showed no significant trends in delta(18)O(calcite) based on size, cultured growth rates, or geographic collection location, suggesting that vital effects do not affect delta(18)O(calcite) in M. edulis. The broad modern and paleogeographic distribution of this bivalve, its abundance during the Holocene, and the lack of an intraspecies physiologic isotope effect demonstrated here make it an ideal nearshore paleoceanographic proxy throughout much of the North Atlantic Ocean.

Impact of geomagnetic excursions on atmospheric chemistry and dynamics

Geomagnetic excursions, i.e. short periods in time with much weaker geomagnetic fields and substantial changes in the position of the geomagnetic pole, occurred repeatedly in the Earth's history, e.g. the Laschamp event about 41 kyr ago. Although the next such excursion is certain to come, little is known about the timing and possible consequences for the state of the atmosphere and the ecosystems. Here we use the global chemistry climate model SOCOL-MPIOM to simulate the effects of geomagnetic excursions on atmospheric ionization, chemistry and dynamics. Our simulations show significantly increased concentrations of nitrogen oxides (NOx) in the entire stratosphere, especially over Antarctica (+15%), due to enhanced ionization by galactic cosmic rays. Hydrogen oxides (HOx) are also produced in greater amounts (up to +40%) in the tropical and subtropical lower stratosphere, while their destruction by reactions with enhanced NOx prevails over the poles and in high altitudes (by −5%). Stratospheric ozone concentrations decrease globally above 20 km by 1–2% and at the northern hemispheric tropopause by up to 5% owing to the accelerated NOx-induced destruction. A 5% increase is found in the southern lower stratosphere and troposphere. In response to these changes in ozone and the concomitant changes in atmospheric heating rates, the Arctic vortex intensifies in boreal winter, while the Antarctic vortex weakens in austral winter and spring. Surface wind anomalies show significant intensification of the southern westerlies at their poleward edge during austral winter and a pronounced northward shift in spring. Major impacts on the global climate seem unlikely.

Does fog chemistry in Switzerland change with altitude?

During two extended summer seasons in 2006 and 2007 we operated two battery driven versions of the Caltech active strand cloud water collector (MiniCASCC) at the Niesen mountain (2362 m a.s.l.) in the northern part of the Swiss Alps, and two devices at the Lägeren research tower (690 m a.s.l.) at the northern boundary of the Swiss Plateau. During these two field operation phases we gained weekly samples of fog water, where we analyzed the major anions and cations, and the isotope ratios of fog water (in form of δ2H and δ18O). Dominant ions in fog water at all sites were NH4+, NO3−, and SO42 −. Compared to precipitation, the enrichment factors in fog water were in the range 5–9 at the highest site, Niesen Kulm. We found considerably lower summertime ion loadings in fog water at the two Alpine sites than at lower elevations above the Swiss Plateau. The lowest ion concentrations were found at the Niesen Kulm site at 2300 m a.s.l., whereas the highest concentrations (a factor 7 compared to Niesen Kulm) were found in fog water at the Lägeren site. Occult nitrogen deposition was estimated from fog frequency and typical fog water flux rates. This pathway contributes 0.3–3.9 kg N ha− 1 yr− 1 to the total N deposition at the highest site on Niesen mountain, and 0.1–2.2 kg N ha− 1 yr− 1 at the lower site. These inputs are the reverse of ion concentrations measured in fog due to the 2.5 times higher frequency of fog occurrence at the mountain top (overall fog occurrence was 25% of the time) as compared to the lower Niesen Schwandegg site. Although fog water concentrations were on the lower range reported in earlier studies, fog water is likely to be an important N source for Northern Alpine ecosystems and might reach values up to 16% of the total N deposition and up to 75% of wet N deposition by precipitation.