Investigating a Boronate-Affinity-Guided Acylation Reaction for Labelling Native Antibodies

The excellent molecular recognition capabilities of monoclonal antibodies (mAbs) have opened up exciting opportunities for biotherapeutic discovery. Taking advantage of the full potential of this tool necessitates affinity ligands capable of conjugating directly with small molecules to a defined degree of biorthogonality, especially when modifying natural Abs. Herein, a bioorthogonal boronate-affinity-based Ab ligand featuring a 4-(dimethylamino)pyridine and an S-aryl thioester to label full-length Abs is reported. The photoactivatable linker in the acyl donor facilitated purification of azide-labelled Ab (N₃-Ab) was quantitatively cleaved upon brief exposure to UV light while retaining the original Ab activity. Click reactions enabled the precise addition of biotin, a fluorophore, and a pharmacological agent to the purified N₃-Abs. The resulting immunoconjugate showed selectivity against targeted cells. Bioorthogonal traceless design and reagentless purification allow this strategy to be a powerful tool to engineer native antibodies amenable to therapeutic intervention.     

Coupled solution of the species conservation equations using unstructured finite‐volume method

A coupled solver was developed to solve the species conservation equations on an unstructured mesh with implicit spatial as well as species‐to‐species coupling. First, the computational domain was decomposed into sub‐domains comprised of geometrically contiguous cells—a process similar to additive Schwarz decomposition. This was done using the binary spatial partitioning algorithm. Following this step, for each sub‐domain, the discretized equations were developed using the finite‐volume method, and solved using an iterative solver based on Krylov sub‐space iterations, that is, the pre‐conditioned generalized minimum residual solver. Overall (outer) iterations were then performed to treat explicitness at sub‐domain interfaces and nonlinearities in the governing equations. The solver is demonstrated for both two‐dimensional and three‐dimensional geometries for laminar methane–air flame calculations with 6 species and 2 reaction steps, and for catalytic methane–air combustion with 19 species and 24 reaction steps. It was found that the best performance is manifested for sub‐domain size of 2000 cells or more, the exact number depending on the problem at hand. The overall gain in computational efficiency was found to be a factor of 2–5 over the block (coupled) Gauss–Seidel procedure. All calculations were performed on a single processor machine. The largest calculations were performed for about 355 000 cells (4.6 million unknowns) and required 900 MB of peak runtime memory and 19 h of CPU on a single processor. Copyright © 2009 John Wiley & Sons, Ltd.     

Putative One‐Pot Prebiotic Polypeptides with Ribonucleolytic Activity

KIA7, a peptide with a highly restricted set of amino acids (Lys, Ile, Ala, Gly and Tyr), adopts a specifically folded structure. Some amino acids, including Lys, Ile, Ala, Gly and His, form under the same putative prebiotic conditions, whereas different conditions are needed for producing Tyr, Phe and Trp. Herein, we report the 3D structure and conformational stability of the peptide KIA7H, which is composed of only Lys, Ile, Ala, Gly and His. When the imidazole group is neutral, this 20‐mer peptide adopts a four‐helix bundle with a specifically packed hydrophobic core. Therefore, one‐pot prebiotic proteins with well‐defined structures might have arisen early in chemical evolution. The Trp variant, KIA7W, was also studied. It adopts a 3D structure similar to that of KIA7H and its previously studied Tyr and Phe variants, but is remarkably more stable. When tested for ribonucleolytic activity, KIA7H, KIA7W and even short, unstructured peptides rich in His and Lys, in combination with Mg⁺⁺, Mn⁺⁺ or Ni⁺⁺ (but not Cu⁺⁺, Zn⁺⁺ or EDTA) specifically cleave the single‐stranded region in an RNA stem–loop. This suggests that prebiotic peptide–divalent cation complexes with ribonucleolytic activity might have co‐inhabited the RNA world.     

Generalized thermo-visco-elastic problem of a spherical shell with three-phase-lag effect

This problem deals with the thermo-visco-elastic interaction due to step input of temperature on the stress free boundaries of a homogeneous visco-elastic isotropic spherical shell in the context of generalized theories of thermo-elasticity. Using the Laplace transformation the fundamental equations have been expressed in the form of vector–matrix differential equation which is then solved by eigen value approach. The inverse of the transformed solution is carried out by applying a method of Bellman et al. [R. Bellman, R.E. Kolaba, J.A. Lockette, Numerical Inversion of the Laplace Transform, American Elsevier Publishing Company, New York, 1966]. The stresses are computed numerically and presented graphically in a number of figures for copper material. A comparison of the results for different theories (TEWED (GN-III), three-phase-lag method) is presented. When the body is elastic and the outer radius of the shell tends to infinity, the corresponding results agree with the result of existing literature.     

Colorimetric sensor arrays for molecular recognition

The development of colorimetric sensor arrays for the detection of volatile organic compounds is reported. Using an array of chemo-responsive dyes, enormous discriminatory power is created in a simple device that can imaged easily with an ordinary flat-bed scanner. High sensitivities (ppb) have been demonstrated for the detection of biologically important analytes, including amines, carboxylic acids, and thiols. By the proper choice of dyes and substrate, the array can be made essentially non-responsive to changes in humidity.     

Acyclic diaminocarbene-based Thiele,Chichibabin, and Müller hydrocarbons

Thiele, Chichibabin and Müller hydrocarbons are considered as classical Kekulé diradicaloids. Herein we report the synthesis and characterization of acyclic diaminocarbene (ADC)-based Thiele, Chichibabin, and Müller hydrocarbons. The calculated singlet–triplet energy gaps are ΔE_S–T = −27.96, −3.70, −0.37 kcal mol⁻¹, respectively, and gradually decrease with the increasing length of the π-conjugated spacer (p-phenylene vs. p,p′-biphenylene vs. p,p′′-terphenylene) between the two ADC-scaffolds. In agreement with the calculations, we also experimentally observed the enhancement of paramagnetic diradical character as a function of the length of the π-conjugated spacer. ADC-based Thiele''s hydrocarbon is EPR silent and exhibits very well resolved NMR spectra, whereas ADC-based Müller''s hydrocarbon displays EPR signals and featureless NMR spectra at room temperature. The spacer also has a strong influence on the UV-Vis-NIR spectra of these compounds. Considering that our methodology is modular, these results provide a convenient platform for the synthesis of an electronically modified new class of carbon-centered Kekulé diradicaloids.

We report the synthesis of acyclic diaminocarbene (ADC)-scaffold based Thiele, Chichibabin, and Müller hydrocarbons. Studies support that the singlet-triplet energy gap depends on the π-conjugated spacer between the ADC scaffolds.     

Molecular, supramolecular structure and catalytic activity of transition metal complexes of phenoxy acetic acid derivatives

Six mononuclear complexes [M(L₁)₂(H₂O)₄] (M = Co(II), 1a and M = Mn(II), 1b), [Cu(L₁)₂(H₂O)₂] (1c), [Cu(L₁)₂(H₂O)(Py)₂] (1d), [Cu(L₃)(H₂O)Cl] · H₂O (3a) and [Co(Sal)(H₂O)(Py)₃] · 2ClO₄ · H₂O (3b) of phenoxyacetic acid derivatives and Schiff base were determined by single crystal X-ray diffraction. The Co(II) (1a) and Mn(II) (1b) complexes are isomorphous. X-ray crystal structural analyses reveal that these coordination complexes form polymeric structure via formation of different types of hydrogen bonding and π-stacking interactions in solid. Thermal analysis along with the powder X-ray diffraction data of these complexes shows the importance of the coordinated and/or crystal water molecules in stabilizing the MOF structure. Complexes 1a, 1c, 3a show marginal catalytic activity in the oxidation of olefins to epoxides in the presence of i-butyraldehyde and molecular oxygen.     

Fabrication of microfluidic mixers and artificial vasculatures using a high-brightness diode-pumped Nd:YAG laser direct write method

This paper describes a direct write laser technology, which is fast and flexible, for fabricating multiple-level microfluidic channels. A high brightness diode-pumped Nd-YAG laser with slab geometry was used for its excellent beam quality. Channels with flat walls and staggered herringbone ridges on the floor have been successfully fabricated and their ability to perform passive mixing of liquid is discussed. Also, a multi-width multi-depth microchannel has been fabricated to generate biomimetic vasculatures whose channel diameters change according to Murray's law, which states that the cube of the radius of a parent vessel equals the sum of the cubes of the radii of the daughters. The multi-depth architecture allows for flow patterns to resemble physiological vascular systems with lower overall resistance and more uniform flow velocities throughout the network compared to planar patterning techniques which generate uniformly thin channels. The ability to directly fabricate multiple level structures using relatively straightforward laser technology enhances our ability to rapidly prototype complex lab-on-a-chip systems and to develop physiological microfluidic structures for tissue engineering and investigations in biomedical fluidics problems.