Atmospheric chemistry of diazomethane – an experimental and theoretical study

The kinetics of the O₃, OH and NO₃ radical reactions with diazomethane were studied in smog chamber experiments employing long-path FTIR and PTR-ToF-MS detection. The rate coefficients were determined to be k _CH2NN+O3?=?(3.2?±?0.4)?×?10^?17 and k _CH2NN+OH?=?(1.68?±?0.12)?×?10^?10 cm³ molecule^?1 s^?1 at 295?±?3?K and 1013?±?30 hPa, whereas the CH₂NN?+?NO₃ reaction was too fast to be determined in the static smog chamber experiments. Formaldehyde was the sole product observed in all the reactions. The experimental results are supported by CCSD(T*)-F12a/aug-cc-pVTZ//M062X/aug-cc-pVTZ calculations showing the reactions to proceed exclusively via addition to the carbon atom. The atmospheric fate of diazomethane is discussed.     

Visible-Light Photoswitching by Azobenzazoles

Three visible-light responsive photoswitches are reported, azobis(1-methyl-benzimidazole) ( 1 ), azobis(benzoxazole) ( 2 ) and azobis(benzothiazole) ( 3 ). Photostationary distributions are obtained upon irradiation with visible light comprising approximately 80 % of the thermally unstable isomer, with thermal half-lives up to 8 min and are mostly invariant to solvent. On protonation, compound 1 H⁺ has absorption extending beyond 600 nm, allowing switching with yellow light, and a thermal half-life just under 5 minutes. The two isomers have significantly different pK_a values, offering potential as a pH switch. The absorption spectra of 2 and 3 are insensitive to acid, although changes in the thermal half-life of 3 indicate more basic intermediates that significantly influence the thermal barrier to isomerization. These findings are supported by high-level ab initio calculations, which validate that protonation occurs on the ring nitrogen and that the Z isomer is more basic in all cases.     

Stability Enhancement of a Dimeric HER2-Specific Affibody Molecule through Sortase A-Catalyzed Head-to-Tail Cyclization

Natural backbone-cyclized proteins have an increased thermostability and resistance towards proteases, characteristics that have sparked interest in head-to-tail cyclization as a method to stability-enhance proteins used in diagnostics and therapeutic applications, for example. In this proof-of principle study, we have produced and investigated a head-to-tail cyclized and HER2-specific Z_HER2:342 Affibody dimer. The sortase A-mediated cyclization reaction is highly efficient (>95%) under optimized conditions, and renders a cyclic Z_HER3:342-dimer with an apparent melting temperature, T_m, of 68 °C, which is 3 °C higher than that of its linear counterpart. Circular dichroism spectra of the linear and cyclic dimers looked very similar in the far-UV range, both before and after thermal unfolding to 90 °C, which suggests that cyclization does not negatively impact the helicity or folding of the cyclic protein. The cyclic dimer had an apparent sub-nanomolar affinity (K_d ~750 pM) to the HER2-receptor, which is a ~150-fold reduction in affinity relative to the linear dimer (K_d ~5 pM), but the anti-HER2 Affibody dimer remained a high-affinity binder even after cyclization. No apparent difference in proteolytic stability was detected in an endopeptidase degradation assay for the cyclic and linear dimers. In contrast, in an exopeptidase degradation assay, the linear dimer was shown to be completely degraded after 5 min, while the cyclic dimer showed no detectable degradation even after 60 min. We further demonstrate that a site-specifically DyLight 594-labeled cyclic dimer shows specific binding to HER2-overexpressing cells. Taken together, the results presented here demonstrate that head-to-tail cyclization can be an effective strategy to increase the stability of an Affibody dimer.     

Topology optimization of fluids in Stokes flow

We consider topology optimization of fluids in Stokes flow. The design objective is to minimize a power function, which for the absence of body fluid forces is the dissipated power in the fluid, subject to a fluid volume constraint. A generalized Stokes problem is derived that is used as a base for introducing the design parameterization. Mathematical proofs of existence of optimal solutions and convergence of discretized solutions are given and it is concluded that no regularization of the optimization problem is needed. The discretized state problem is a mixed finite element problem that is solved by a preconditioned conjugate gradient method and the design optimization problem is solved using sequential separable and convex programming. Several numerical examples are presented that illustrate this new methodology and the results are compared to results obtained in the context of shape optimization of fluids. Copyright © 2003 John Wiley & Sons, Ltd.     

Improved Synthesis of 1-Bromo-3-buten-2-one

A convenient procedure for the synthesis of 1-bromo-3-buten-2-one, 4, from commercially available 2-ethyl-2-methyl-1,3-dioxolane, 1, is described. The procedure involves three reaction steps: (1) The acetal 1 is converted to 2-(1-bromoethyl)-2-bromomethyl-1,3-dioxolane, 2, by reacting 1 with elemental bromine in dichloromethane to yield 98% of 2. (2) Dehydrobromination of 2 with potassium tert-butoxide in tetrahydrofuran gives 2-bromomethyl-2-vinyl-1,3-dioxolane, 3, in 84–93% yield. (3) Removal of the acetal protection from 3 by formolysis for 6–10 h afforded 1-bromo-3-buten-2-one, 4, in 85–94% yield. A more rapid method is acid hydrolysis of 3 under microwave activation (100 °C, 8–10 min), by which 4 was obtained in 75% yield. Full experimental details are given.

The effect of sample salt additives on capillary electrophoresis analysis of intact proteins using surface modified capillaries

The effect of adding alkali salts to protein samples for capillary electrophoretic (CE) analysis of intact proteins was studied. A high degree of peak stacking, even for large proteins, was found to occur when alkali salts were added to the sample. The addition of salt to the protein sample promotes a strong improvement in the peak efficiency of individual proteins giving up to 2.1 × 10⁶ apparent plates/m. The concentration of salt required in the sample to reach optimal peak efficiency show dependency on both the molecular weight and molar concentration of the protein. However, adding salt will, at a sufficiently high concentration, cause a mixture of proteins to co-migrate to one very sharp peak. The observed sample stacking effect was obtained with a number of different surface modified silica capillaries indicating a general phenomenon and not surface coating specific.     

Some transformation techniques with applications in global optimization

In this paper some transformation techniques, based on power transformations, are discussed. The techniques can be applied to solve optimization problems including signomial functions to global optimality. Signomial terms can always be convexified and underestimated using power transformations on the individual variables in the terms. However, often not all variables need to be transformed. A method for minimizing the number of original variables involved in the transformations is, therefore, presented. In order to illustrate how the given method can be integrated into the transformation framework, some mixed integer optimization problems including signomial functions are finally solved to global optimality using the given techniques.     

Computer generated phase holograms (kinoforms) for millimeter and submillimeter wavelengths

Computer generated Fourier transform phase holograms, known as kinoforms, have been synthesized, manufactured and their performance evaluated at a wavelength of 3 mm (100 GHz). The kinoforms were synthesized to give a prescribed far-field intensity distribution and manufactured by milling the computed kinoform surface relief into a Teflon plate, using a numerically controlled milling machine. The measured diffraction efficiencies exceed 50 percent. Millimeter-wave kinoforms can be used in various quasi-optical applications,e.g. distributing a local oscillator signal to an array of detector elements in heterodyne receivers.