Rotational CARS N2 thermometry: validation experiments for the influence of nitrogen spectral line broadening by hydrogen

Rotational coherent anti‐Stokes Raman spectroscopy (CARS) in fuel‐rich hydrocarbon flames, with a large content of hydrogen in the product gases (∼20%), has in previous work shown that evaluated temperatures are raised several tens of Kelvin by taking newly derived N₂ H₂ Raman line widths into account. To validate these results, in this work calibrated temperature measurements at around 300, 500 and 700 K were performed in a cell with binary gas mixtures of nitrogen and hydrogen. The temperature evaluation was made with respect to Raman line widths either from self‐broadened nitrogen only, N₂ N₂ [energy‐corrected‐sudden (ECS)], or by also taking nitrogen broadened by hydrogen, N₂ H₂ [Robert–Bonamy (RB)], Raman line widths into account. With increased amount of hydrogen in the cell at constant temperature, the evaluated CARS temperatures were clearly lowered with the use of Raman line widths from self‐broadened nitrogen only, and the case with inclusion of N₂ H₂ Raman line widths was more successful. The difference in evaluated temperatures between the two different sets increases approximately linearly, reaching 20 K (at T ∼ 300 K), 43 K (at T = 500 K) and 61 K (at T = 700 K) at the highest hydrogen concentration (90%). The results from this work further emphasize the importance of using adequate Raman line widths for accurate rotational CARS thermometry. Copyright © 2010 John Wiley & Sons, Ltd.     

A Protein‐Based Encapsulation System with Calcium‐Controlled Cargo Loading and Detachment

Protein‐based encapsulation systems have a wide spectrum of applications in targeted delivery of cargo molecules and for chemical transformations in confined spaces. By engineering affinity between cargo and container proteins it has been possible to enable the efficient and specific encapsulation of target molecules. Missing in current approaches is the ability to turn off the interaction after encapsulation to enable the cargo to freely diffuse in the lumen of the container. Separation between cargo and container is desirable in drug delivery applications and in the use of capsids as catalytic nanoparticles. We describe an encapsulation system based on the hepatitis B virus capsid in which an engineered high‐affinity interaction between cargo and capsid proteins can be modulated by Ca²⁺. Cargo proteins are loaded into capsids in the presence of Ca²⁺, while ligand removal triggers unbinding inside the container. We observe that confinement leads to hindered rotation of cargo inside the capsid. Application of the designed container for catalysis was also demonstrated by encapsulation of an enzyme with β‐glucosidase activity.     

Residue-specific pKa determination of lysine and arginine side chains by indirect 15N and 13C NMR spectroscopy: application to apo calmodulin

Electrostatic interactions in proteins can be probed experimentally through determination of residue-specific acidity constants. We describe here triple-resonance NMR techniques for direct determination of lysine and arginine side-chain protonation states in proteins. The experiments are based on detection of nonexchangeable protons over the full range of pH and temperature and therefore are well suited for pKa determination of individual amino acid side chains. The experiments follow the side-chain 15Nzeta (lysine) and 15Nepsilon or 13Czeta (arginine) chemical shift, which changes due to sizable changes in the heteronuclear electron distribution upon (de)protonation. Since heteronuclear chemical shifts are overwhelmed by the charge state of the amino acid side chain itself, these methods supersede 1H-based NMR in terms of accuracy, sensitivity, and selectivity. Moreover, the 15Nzeta and 15Nepsilon nuclei may be used to probe changes in the local electrostatic environment. Applications to three proteins are described: apo calmodulin, calbindin D9k, and FKBP12. For apo calmodulin, residue-specific pKa values of lysine side chains were determined to fall between 10.7 and 11.2 as a result of the high net negative charge on the protein surface. Ideal two-state titration behavior observed for all lysines indicates the absence of significant direct charge interactions between the basic residues. These results are compared with earlier studies based on chemical modification.     

Temperature and concentration measurements in acetylene-nitrogen mixtures in the range 300–600 K using dual-broadband rotational CARS

Pure rotational coherent anti-Stokes Raman scattering (CARS) experiments have been performed in acetylene for temperatures ranging from 294 to 582 K, and in mixtures of acetylene and nitrogen in the mole fraction range of 0.06–0.32 for acetylene at room temperature. The experimental spectra are evaluated by a least-square fitting to libraries of theoretically calculated spectra using two different Raman linewidth models, one with and one without dependence on the rotational quantum number J. It is found that a J-dependent model is favourable, both regarding temperature measurements in pure acetylene, and simultaneous acetylene concentration and temperature measurements in different mixtures of acetylene and nitrogen. For the temperature measurements performed in pure acetylene the temperature inaccuracy is generally less than 2% when the J-dependent model for the Raman linewidths is used. It is found that fitting the value of the non-resonant susceptibility significantly improves the quality of the spectral fits and is a requirement for high temperature accuracy with the present model. The evaluated concentrations show a maximum error of 13% on a relative scale. Potential sources of systematical errors both regarding measured temperatures and acetylene concentrations are discussed. Received: 8 June 1999 / Revised version: 3 Spetember 1999 / Published online: 3 November 1999     

Three-level phase modulator based on orthoconic antiferroelectric liquid crystals

Surface-stabilized orthoconic antiferroelectric liquid crystals (OAFLCs) have a director tilt of theta = 45 degrees and are, with no field applied, negatively uniaxial with the optic axis perpendicular to the cell substrates. We demonstrate that OAFLCs can be utilized to achieve lossless phase modulation with three almost equidistant phase levels. This turns out to be true also for polymer-stabilized OAFLCs, where the polymer network increases the switching speed of the device without affecting the phase modulation appreciably.     

B-norsteroids from Hymenoscyphus pseudoalbidus

Two viridin-related B-norsteroids, B-norviridiol lactone (1) and B-norviridin enol (2), both possessing distinct unprecedented carbon skeletons, were isolated from a liquid culture of the ash dieback-causing fungus Hymenoscyphus pseudoalbidus. Compound 2 was found to degrade to a third B-norsteroidal compound, 1β-hydroxy-2α-hydro-asterogynin A (3), which was later detected in the original culture. The proposed structure of 1 is, regarding connectivity, identical to the original erroneous structure for TAEMC161, which was later reassigned as viridiol. Compound 2 showed an unprecedented 1H-13C HMBC correlation through an intramolecular hydrogen bond. The five-membered B-ring of compounds 1-3 was proposed to be formed by a benzilic acid rearrangement. The known compound asterogynin A was found to be formed from 3 by a β-elimination of water. All compounds were characterized by NMR spectroscopy, LC-HRMS and polarimetry.     

Composite multi-parameter ranking of real and virtual compounds for design of MC4R agonists: Renaissance of the Free-Wilson methodology

Drug design is a multi-parameter task present in the analysis of experimental data for synthesized compounds and in the prediction of new compounds with desired properties. This article describes the implementation of a binned scoring and composite ranking scheme for 11 experimental parameters that were identified as key drivers in the MC4R project. The composite ranking scheme was implemented in an AstraZeneca tool for analysis of project data, thereby providing an immediate re-ranking as new experimental data was added. The automated ranking also highlighted compounds overlooked by the project team. The successful implementation of a composite ranking on experimental data led to the development of an equivalent virtual score, which was based on Free-Wilson models of the parameters from the experimental ranking. The individual Free-Wilson models showed good to high predictive power with a correlation coefficient between 0.45 and 0.97 based on the external test set. The virtual ranking adds value to the selection of compounds for synthesis but error propagation must be controlled. The experimental ranking approach adds significant value, is parameter independent and can be tuned and applied to any drug discovery project.     

Energy Fluctuations Shape Free Energy of Nonspecific Biomolecular Interactions

Understanding design principles of biomolecular recognition is a key question of molecular biology. Yet the enormous complexity and diversity of biological molecules hamper the efforts to gain a predictive ability for the free energy of protein-protein, protein-DNA, and protein-RNA binding. Here, using a variant of the Derrida model, we predict that for a large class of biomolecular interactions, it is possible to accurately estimate the relative free energy of binding based on the fluctuation properties of their energy spectra, even if a finite number of the energy levels is known. We show that the free energy of the system possessing a wider binding energy spectrum is almost surely lower compared with the system possessing a narrower energy spectrum. Our predictions imply that low-affinity binding scores, usually wasted in protein-protein and protein-DNA docking algorithms, can be efficiently utilized to compute the free energy. Using the results of Rosetta docking simulations of protein-protein interactions from Andre et al. (Proc. Natl. Acad. Sci. USA 105:16148, 2008), we demonstrate the power of our predictions.     

Leakage current and capacitance characteristics of Si/SiO2/Si single-barrier varactor

We investigate, both experimentally and theoretically, current and capacitance (I–V/C–V) characteristics and the device performance of Si/SiO₂/Si single-barrier varactor diodes (SBVs). Two diodes were fabricated with different SiO₂ layer thicknesses using the state-of-the-art wafer bonding technique. The devices have very low leakage currents (about 5×10^-2 and 1.8×10^-2 mA/mm²) and intrinsic capacitance levels of typically 1.5 and 50 nF/mm² for diodes with 5-nm and 20-nm oxide layers, respectively. With the present device physical parameters (25-mm² device area, 760-μm modulation layer thickness and ≈10¹⁵-cm^-3 doping level), the estimated cut-off frequency is about 5×10⁷ Hz. With the physical parameters of the present existing III–V triplers, the cut-off frequency of our Si-based SBV can be as high as 0.5 THz. Received: 9 February 2001 / Accepted: 9 February 2001 / Published online: 23 March 2001