Light-directed radial combinatorial chemistry: orthogonal safety-catch protecting groups for the synthesis of small molecule microarrays

We describe the development of photolabile protecting groups based on the 3,4,5-trimethoxyphenacyl group (TMP). Orthogonal safety-catches were created by introducing an acid-activatible dimethyl ketal (AA-TMP) and an oxidatively activatible 1,3-dithiane (OA-TMP) into the photolabile TMP group. We demonstrate the application of these protecting groups in light-directed synthesis of small molecule microarrays with diversity elements radially attached to a hydroxyproline scaffold.     

Polymerization of vinylcarbazole on copper(II)-13X molecular sieves: Role of copper(II) salts

Copper(II)-exchanged-13X molecular sieves, prepared from four copper(II) salts, namely, sulfate, nitrate, chloride, and acetate, and their activities in the polymerization of N-vinylcarbazole at a fixed copper ion exchange level were studied. From the kinetic characteristics of polymerization it was established that the variation in activities of the Cu-exchanged sieves is due primarily to the difference in the pH of the original salt solution, which is responsible for the varying degree of proton exchange with the zeolite during copper ion exchange. A first-order dependence of the rate of polymerization was observed with respect to H⁺ ion concentration of the original copper-salt solution. It was further established that the rate of polymerization of exchanged copper ion, at a hypothetical zero proton concentration, is low. A mechanism of polymerization of NVC on copper-exchanged-13X zeolite was suggested on the basis of the results obtained.     

Mechanism of N-vinylcarbazole polymerization on Co(II)–13X molecular sieve

Kinetics of polymerization of N-vinylcarbazole over Co(II)-13X molecular sieves in toluene have been studied. The rate of polymerization (R_p) has been found to be second order with respect to percent exchange level of Co(II) and also to the NVC concentration at all the reaction temperatures of 40, 50 and 60°C. The rate increases with decreasing pH of the original exchanging salt solution up to a pH of about 3.5, beyond which it falls. The overall activation energy of polymerization has been found to decrease with increase in monomer concentration, exchange level of Co(II), and the hydrogen ion concentration of the original exchange solution. Average degree of polymerization also follows a similar trend. A mechanism of polymerization involving simultaneous propagation on both metal ion Co(II) and proton on a zeolite surface has been suggested. The two propagation routes are characterized by an average activation energy of 10.36 kcal/mol and 5.40 kcal/mol on the metal ion and proton centers, respectively.     

Stereopositional Outcome in the Packing of Dissimilar Aromatics in Designed β‐Hairpins

A popular strategy in the de novo design of stable β‐sheet structures for various biomedical applications is the incorporation of aromatic pairs at the non‐hydrogen‐bonding (NHB) position. However, it is important to explicitly understand how aryl pair packing at the NHB region is coordinated with backbone structural rearrangements, and to delineate the benefits and drawbacks associated with stereopositional choice of dissimilar aromatic pairs. Here, we probe the consequences of flipped Trp/Tyr pairs by using engineered permutants at the NHB position of dodecapeptide β‐hairpins, proximal and distal to the turn. Extensive conformational analysis of these peptides using NMR and CD spectroscopy reveal that a classic Edge‐to‐Face and Face‐to‐Edge geometry at the proximal and distal aromatic pairs, respectively, in YW‐WY, is the most stabilizing. Such a preferred packing geometry in YW‐WY results in a highly twisted β‐sheet backbone, with Trp always providing a ‘Face’ orientation to its dissimilar aromatic partner Tyr. Flipping the proximal and/or distal aromatic pair distorts the ideal T‐shaped geometry, and results in alternate aryl arrangements that can adversely affect strand twist and β‐sheet stability. Our study reveals the existence of a strong stereopositional influence on the packing of dissimilar aromatic pairs. Our findings highlight the importance of modeling physical interaction forces while designing protein and peptide structures for functional applications.     

Synthesis and Characterization of Some New Benzimidazole Derivatives

Synthesis of nine new benzimidazole derivatives was reported. The products were identified by ¹H NMR, mass spectroscopy, and infrared spectroscopy.     

A Surrogate for Debye-Waller Factors from Dynamic Stokes Shifts

We show that the short-time behavior of time-resolved fluorescence Stokes shifts (TRSS) are similar to that of the intermediate scattering function obtained from neutron scattering at q near the peak in the static structure factor for glycerol. This allows us to extract a Debye-Waller (DW) factor analog from TRSS data at times as short as 1 ps in a relatively simple way. Using the time-domain relaxation data obtained by this method we show that DW factors evaluated at times ≥ 40 ps can be directly influenced by α relaxation and thus should be used with caution when evaluating relationships between fast and slow dynamics in glassforming systems.     

Post-buckling of cantilever columns having variable cross-section under a combined load

Post-buckling of a cantilever column is examined under a combined load consisting of a tip-concentrated load and a distributed axial load, through dynamic formulation. The formulation of the problem is based on the moment–curvature relationship. The two-point boundary value problem described by the governing equations is dependent on the frequency parameter and the two load parameters. The buckling loads are those loads at which the eigencurve, namely, the load versus frequency curve of the column meets the load axis. A simple and reliable iterative procedure to convert the two-point boundary value problem into an initial value problem is followed and solved the non-linear differential equations utilizing a fourth-order Runge–Kutta integration scheme. To demonstrate the potentiality of the adopted numerical scheme, linear vibration frequencies of truncated, tapered cantilever wedges and cones are determined and compared with the published analytical and test results. Buckling and post-buckling loads of a simply supported stepped column are obtained and compared with the published test results. The loads and deflections of non-uniform cantilever columns are obtained for various slopes at the tip. The interaction of load parameters for a free–free truncated conical column has also been examined. The numerical results indicate that the path represented by the two load parameters turns out to be nearly a straight line.     

On the nature of the phase transition in the KDP systems

Using the Landau theory of phase transitions it has been shown that for a second order phase transition Ω/k_BT_c ? 0.01. and its isomorphs 4Ω/J¹ ? 1 and for a first order transition Ω/k_BT_c ? 0.01.     

Effect of metal cationization on the tandem mass spectra of glycosyl dithioacetals

The effect of metal cationization on the tandem mass spectra of glycosyl dithioacetals of glucose, mannose, galactose, rhamnose, arabinose and xylose was studied by electrospray ionization mass spectrometry under ammonium and metal (Li, Na, Ag and Cu) ion cationization conditions. The ammonium-cationized glycosyl dithioacetals fragment by loss of ammonia followed by either two molecules of EtSH or one molecule of EtSH and one molecule of H2O. Lithium cationization leads to additional eliminations such as EtSEt and EtSSEt and C-C cleavages. Elimination of EtSH is not observed under sodium cationization. Silver cationization, on the other hand, leads to additional fragmentations involving the elimination of silver as AgOH and AgSEt. Copper cationization results in adducts where copper has undergone a change of oxidation state from II to I. Li+, Ag+ and Cu+ cationization seem to favour cyclization resulting in elimination of EtSH. However, the mechanisms seem to be differently affected by different metal ions. Li+ and Ag+ cationization appear to be non-specific and favour cyclization involving C2-, C4- and C5-hydroxyl hydrogens, whereas Cu+ cationization seems to favour cyclization involving C4-hydroxyl hydrogen.     

Spatial photorelease of oligonucleotides, using a safety-catch photolabile linker

[reaction: see text] We report the development of a safety-catch photolabile linker that allows the light-directed synthesis and spatially selective photorelease of oligonucleotides from microarrays. The linker remains stable to light during DNA synthesis, and is activated for photorelease after acidic hydrolysis. We demonstrate that the photoreleased oligonucleotides can be amplified by PCR to produce double stranded DNA. The advantages offered by this linker could aid the development of an automated gene synthesis platform.