Solvated helical backbones: X-ray diffraction study of Boc-Ala-Leu-Aib-Ala-Leu-Aib-OMe &#183; H<SUB>2</SUB>O

A second example of insertion of a water molecule into the helical backbone of an apolar peptide is presented here and compared to a similar occurrence in a longer peptide with the same type of sequence of residues, i.e., Boc-Aib-(Ala-Leu-Aib)3-OMe. The backbone of the title compound assumes an approximate 310-helical form with three 4 &#8594; 1 hydrogen bonds. In the place of a fourth 4 &#8594;1 hydrogen bond, a water molecule is inserted between O(1) and N(4), and acts as a bridge by forming hydrogen bonds N(4) W(1) (2.95 &#197;) and W(1) O(1) (2.81&#197;). The water molecule participates in a third hydrogen bond with a neighboring peptide molecule, W(1) O(4) (2.91 &#197;). The insertion of the water molecule causes the apolar peptide to mimic an amphiphilic helix. Crystals grown from ethyl acetate/petroleum ether (reported here) or from methanol/water solution are in space group P212121 with a = 12.024(4) &#197;, b = 15.714(6) &#197;, c = 21.411(7) &#197;, Z = 4 and dcalc = 1.124 g/cm3 for C32H58N6O9 &#183; H2O. The overall agreement factor R is 6.3% for 2707 reflections observed with intensities &gt; 3&#963;(F) and the resolution is 0.90 &#197;

Aqueous channels within apolar peptide aggregates: solvated helix of the &#945;-aminoisobutyric acid (Aib)-containing peptide Boc-(Aib-Ala-Leu)<SUB>3</SUB>-Aib-OMe.2H<SUB>2</SUB>O.CH<SUB>3</SUB>OH in crystals

Although the peptide Boc-Aibl-Ala2-Leu3- Aib4-Ala5-Leu6-Aib7-Ala8-Leu9-Aib10-OMe [with a t-butoxycarbonyl (Boc) blocking group at the amino terminus, a methyl ester (OMe) at the carboxyl terminus, and four &#945;-aminoisobutyric (Aib) residues] has a 3-fold repeat of residues, the helix formed by the peptide backbone is irregular. The carboxyl-terminal half assumes an &#945;-helical form with torsion angles ) and &#968; of approximately -60&#176; and -45&#176;, respectively, whereas the amino-terminal half is distorted by an insertion of a water molecule between the amide nitrogen of Ala5 [N(5)] and the carbonyl oxygen of Ala2 [0(2)]. The water molecule W(1) acts as a bridge by forming hydrogen bonds N(5).W(1) (2.93 A) and W(1)---0(2) (2.86 A). The distortion of the helix exposes the carbonyl oxygens of Aib1 and Aib4 to the outside environment, with the consequence that the helix assumes an amphiphilic character despite having all apolar residues. Neighboring helices in the crystal run in antiparallel directions. On one side of a helix there are only hydrophobic contacts with efficient interdigitation of leucine side chains with those from the neighboring helix. On the other side of the helix there are hydrogen bonds between protruding carbonyl oxygens and four water molecules that separate two neighboring helices. Along the helix axis the helices bind head-to-tail with a direct hydrogen bond N(2)-0(9) (3.00 A). Crystals grown from methanol/water solution are in space group P21, with a = 15.778 &#177; 0.004 A, b = 11.228 &#177; 0.002 A, c = 18.415 &#177; 0.003 A, &#946; = 102.10 &#177; 0.02&#176; and two formula units per cell for C49H88N1003. 2H2O.CH3OH. The overall agreement factor R is 7.5% for 3394 reflections observed with intensities &gt; 3&#963;(F), and the resolution is 0.90 A

Optimizing H1 cavities for the generation of entangled photon pairs

We report on the theoretical investigation of photonic crystal cavities etched on a suspended membrane for the generation of polarization entangled photon pairs using the biexciton cascade in a single quantum dot. The implementation of spontaneous emission enhancement effect increases the entanglement visibility, while the concomitant preferential funneling of the emission in the cavity mode increases the collection of both entangled photons. We demonstrate and quantify that standard cavity designs present a polarization dependent emission diagram, detrimental to entanglement. The optimization of H1 cavities allows to obtain both high collection efficiencies and polarization independent emission, while keeping high Purcell factors necessary for high quality entangled photon sources

Helix construction using &#945;-aminoisobutyryl residues in a modular approach to synthetic protein design. Conformational properties of an apolar decapeptide in two different crystal forms and in solution

A modular strategy for the assembly of synthetic protein mimics is outlined. This approach is based on the ability of α -aminoisobutyric acid (Aib) to promote helical folding in peptides. The design of apolar, peptide helices with a high solubility in organic solvents facilitates structural design based on stereochemical constraints imposed by chosen non-protein residues. The design of individual helices is illustrated by the analysis of the decapeptide Boc-Aib-Ala-Leu-A!a-Aib-Aib-Leu-~Ala-Leu-Aib-OMe. Crystal structures of two polymorphic forms reveal an almost completely α-helical backbone. These high-resolution structures permit detailed characterization of the helix. H NMR and CD studies demonstrate maintenance of the helical conformation in solution, a feature that is a consequence of the limited flexibility of Aib residues in φ, ψ space

Heterogeneous integration and precise alignment of InP-based photonic crystal lasers to complementary metal-oxide semiconductor fabricated silicon-on-insulator wire waveguides

The integration of two-dimensional III-V InP-based photonic crystal and silicon wire waveguides is achieved through an accurate alignment of the two optical levels using mix-and-match deep ultraviolet (DUV)/electron beam lithography. The adhesively bonded structures exhibit an enhancement of light emission at frequencies where low group velocity modes of the photonic crystal line defect waveguides occur. Pulsed laser operation is obtained from these modes at room temperature under optical pumping. The laser light is coupled out of the Si waveguide via grating couplers directly to single mode fiber

Factors influencing organic carbon recycling and burial in Skagerrak sediments

Different factors influencing recycling and burial rates of organic carbon (OC) were investigated in the continental margin sediments of the Skagerrak (NE North Sea). Two different areas, one in the southern and one in the northeastern part of the Skagerrak were visited shortly after a spring bloom (March 1999) and in late summer (August 2000). Results suggested that: (1) Organic carbon oxidation rates (Cox) (2.2–18 mmol C m-2d-11) were generally larger than the O2 uptake rates (1.9 –25 mmol m-2d-1). Both rates were measured in situ using a benthic lander. A mean apparent respiration ratio (Cox:O2corr) of 1.3±0.5 was found, indicating some long-term burial of reduced inorganic substances in these sediments. Measured O2 fluxes increased linearly with increasing Cox rates during the late summer cruise but not on the early spring cruise, indicating a temporal uncoupling of anaerobic mineralization and reoxidation of reduced substances. (2) Dissolved organic carbon (DOC) fluxes (0.2–1.0 mmol C m-2d-1) constituted 3–10% of the Cox rates and were positively correlated with the latter, implying that net DOC production rates were proportional to the overall sediment OC remineralization rates. (3) Chlorophyll a (Chl-a) concentrations in the sediment were significantly higher in early spring compared to late summer. The measured Cox rates, but not O2 fluxes, showed a strong positive correlation with the Chl-a inventories in the top 3 cm of the sediment. (4) Although no relationship was found between the benthic fluxes and the macrofaunal biomass in the chambers, total in situ measured dissolved inorganic carbon (CT) fluxes were 1–5.4 times higher than diffusive mediated CT fluxes, indicating that macrofauna have a significant impact on benthic exchange rates of OC remineralization products in Skagerrak sediments. (5) OC burial fluxes were generally higher in northeastern Skagerrak than in the southern part. The same pattern was observed for burial efficiencies, with annual means of ~62% and ~43% for the two areas respectively. (6) On a basin-wide scale, there was a significant positive linear correlation between the burial efficiencies and sediment accumulation rates. (7) The calculated particulate organic carbon (POC) deposition, from benthic flux and burial measurements, was only 24 –78% of the sediment trap measured POC deposition, indicating a strong near-bottom lateral transport and resuspension of POC. (8) A larger fraction of the laterally advected material of lower quality seemed to settle in the northeastern Skagerrak rather than in the southern Skagerrak. (9) Skagerrak sediments, especially in the northeastern part, act as an efficient net sink for organic carbon, even in a global continental margin context

Optical Properties of Deep Ice at the South Pole - Absorption

We discuss recent measurements of the wavelength-dependent absorption coefficients in deep South Pole ice. The method uses transit time distributions of pulses from a variable-frequency laser sent between emitters and receivers embedded in the ice. At depths of 800 to 1000 m scattering is dominated by residual air bubbles, whereas absorption occurs both in ice itself and in insoluble impurities. The absorption coefficient increases approximately exponentially with wavelength in the measured interval 410 to 610 nm. At the shortest wavelength our value is about a factor 20 below previous values obtained for laboratory ice and lake ice; with increasing wavelength the discrepancy with previous measurements decreases. At around 415 to 500 nm the experimental uncertainties are small enough for us to resolve an extrinsic contribution to absorption in ice: submicron dust particles contribute by an amount that increases with depth and corresponds well with the expected increase seen near the Last Glacial Maximum in Vostok and Dome C ice cores. The laser pulse method allows remote mapping of gross structure in dust concentration as a function of depth in glacial ice.Comment: 26 pages, LaTex, Accepted for publication in Applied Optics. 9 figures, not included, available on request from [email protected]

Statistical Mechanics of Glass Formation in Molecular Liquids with OTP as an Example

We extend our statistical mechanical theory of the glass transition from examples consisting of point particles to molecular liquids with internal degrees of freedom. As before, the fundamental assertion is that super-cooled liquids are ergodic, although becoming very viscous at lower temperatures, and are therefore describable in principle by statistical mechanics. The theory is based on analyzing the local neighborhoods of each molecule, and a statistical mechanical weight is assigned to every possible local organization. This results in an approximate theory that is in very good agreement with simulations regarding both thermodynamical and dynamical properties