A new tri-orthogonal strategy for peptide cyclization

A solid phase tri-orthogonal protection/cleavage strategy that uses acidic, basic, and neutral conditions is described. Strategically protected alpha-azido-gamma-9-fluorenylmethyl-L-glutamate (1) and alpha-azido-epsilon-N-Fmoc-L-lysine (2) were incorporated into growing peptides on Wang resin using a novel azide protection strategy. These residues, separated by 1-3 monomers, were deprotected at the side chains and cyclized via lactam formation. The N-terminus was further functionalized to extend the chain. This method represents a straightforward protocol for peptide cyclization on solid support.     

Uses and analyses of curtin-hammett/winstein-holness systems involving second order reactions

The Curtin-Hammett (C-H) principle and the Winstein-Holness (W-H) equation approximate the product ratio and overall rate constant of reaction for systems involving a starting material which exists in two forms, each of which reacts via first-order kinetics to give a different product. The C-H/W-H approximations are valid when the rates of isomer interconversion are significantly faster than the rates of product formation. The present treatment encompasses non-first-order reactions to product. A numerical predictor-corrector technique is used to show (1) that relative reagent concentration can affect both the product ratio and the observed rates of product formation; (2) that the absolute concentration of reagent and substrate can affect the kinetics; and (3) that factors (1) and (2) above can affect the validity of the C-H/W-H approximations for non-first-order C-H/W-H schemes.     

Theoretical and Practical Reasoning in Chemistry

Traditional philosophy of science regards theoretical reasoning, based on the example of Euclidian geometry, as the hallmark of a mature science. There is, however, a parallel tradition of practical reasoning based on specific cases that goes back to Aristotle. In this paper I argue that practical reasoning is an essential part of the practice of chemistry and should be understood and appreciated on its own merits rather than regarded as a symbol of the immaturity and inferiority of chemistry as a science. This revised version was published online in July 2006 with corrections to the Cover Date.     

Active site reactant center geometry in the Co(II)-product radical pair state of coenzyme B12-dependent ethanolamine deaminase determined by using orientation-selection electron spin-echo envelope modulation spectroscopy

The distances and orientations among reactant centers in the active site of coenzyme B12-dependent ethanolamine deaminase from Salmonella typhimurium have been characterized in the Co(II)-product radical pair state by using X-band electron paramagnetic resonance (EPR) and two-pulse electron spin-echo envelope modulation (ESEEM) spectroscopies in the disordered solid state. The unpaired electron spin in the product radical is localized on C2. Our approach is based on the orientation-selection created in the EPR spectrum of the biradical by the axial electron-electron dipolar interaction. Simulation of the EPR line shape yielded a best-fit Co(II)-C2 distance of 9.3 A. ESEEM spectroscopy performed at four magnetic field values addressed the hyperfine coupling of the unpaired electron spin on C2 with 2H in the C5' methyl group of 5'-deoxyadenosine and in the beta-2H position at C1 of the radical. Global ESEEM simulations (over the four magnetic fields) were weighted by the orientation dependence of the EPR line shape. A Nelder-Mead direct search fitting algorithm was used to optimize the simulations. The results lead to a partial model of the active site, in which C5' is located a perpendicular distance of 1.6 A from the Co(II)-C2 axis, at distances of 6.3 and 3.5 A from Co(II) and C2, respectively. The van der Waals contact of the C5'-methyl group and C2 indicates that C5' remains close to the radical species during the rearrangement step. The C2-Hs-C5' angle including the strongly coupled hydrogen, Hs, and the C5'-Hs orientation relative to the C1-C2 axis are consistent with a linear hydrogen atom transfer coordinate and an in-line acceptor p-orbital orientation. The trigonal plane of the C2 atom defines sub-spaces within the active site for C5' radical migration and hydrogen atom transfers (side of the plane facing Co(II)) and amine migration (side of the plane facing away from Co(II)).     

Cumulative indices for Spectrochima Acta, Part A and Spectrochimica Acta, Part B

This article is an electronic publication in Spectrochimica Acta Electronica (SAE), a section of Spectrochimica Acta, Part B (SAB). The hardcopy text is accompanied by an electronic archive, stored on the SAE homepage at http://www.elsevier.nl/locate/sabe. The archive contains data, index and program files. The main article discusses the bibliographical purpose of the program and data files. A collective index for Spectrochimica Acta for volumes since it was split into Parts A and B, and continuing through 1991 for SAA and 1997 for SAB, is presented in DBF format, along with rudimentary data entry and access software.     

MECHANISM OF OXYGEN DETOXIFICATION IN NEONATAL RAT LUNG TISSUE

Abstract— Pulmonary macrophages obtained from neonatal rats contain approximately four times the activity of cyanide resistant superoxide dismutase and catalase compared with the cells from adult animals. The activity is highest immediately after birth and diminishes with age until the minimum level is reached at approximately 3 weeks of age. Superimposed upon this change in basal activity is the capability of neonatal cells to synthesize additional cyanide resistant superoxide dismutase and catalase when either the animals or isolated pulmonary macrophages are exposed to 95–100% oxygen. The inductive effect begins at 2–3 days after birth, peaks at 10 days, and disappears at approximately 15 days after birth. In contrast to adult rats, neonatal rats are extremely resistant to the toxic effects of oxygen. If, however, the oxygen mediated increase in both enzymes is prevented or the maximum effective pulmonary macrophage number is diminished in test animals, these animals become vulnerable to toxic effects of oxygen exposure, observed by gross and histologic examination of lung tissue, in a manner similar to adult animals. These data indicate that both cyanide-resistant superoxide dismutase and catalase may be part of the endogenous defense mechanisms which provide neonatal rats with an exceptional resistance to oxygen toxicity.     

Preparation of 4-aryl-1,2,3,4-tetrahydro-3,3-dimethylisoquinolines and 1,2,3,4-tetrahydro-3,3-dimethyl-4-phenylbenz[h]isoquinolines

Synthetic procedures to prepare a number of 4-aryl-1,2,3,4-tetrahydro-3,3-dimethylisoquinolines and their benzo-homogues 3 through a series of intermediates are described. The condensation of α-(1-amino-1-methylethyl)arylmethanols 5 with arylaldehydes 6 gave imino derivatives 7 which on reduction with borohydride gave secondary amines 8 . The treatment of 8 with mineral acids gave the target compounds 3 . Biological activities of 3 are briefly discussed.     

A simultaneous TG–DTA study of the thermal decomposition of 2-hydroxybenzoic acid, 2-carboxyphenyl ester (salsalate)

Simultaneous thermogravimetry–differential thermal analysis (TG–DTA) and gas and liquid chromatography with mass spectrometry detection have been used to study the kinetics and decomposition of 2-hydroxybenzoic acid, 2-carboxyphenyl ester, commercially known as salsalate. Samples of salsalate were heated in the TG–DTA apparatus in an inert atmosphere (100 ml min⁻¹ nitrogen) in the temperature range 30–500 °C. The data indicated that the decomposition of salsalate is a two-stage process. The first decomposition stage (150–250 °C) had a best fit with second-order kinetics with E_a=191–198 kJ/mol. The second decomposition stage (300–400 °C) is described as a zero-order process with E_a=72–80 kJ/mol. The products of the decomposition were investigated in two ways:

(a)Salsalate was heated in a gas chromatograph at various isothermal temperatures in the range 150–280 °C, and the exit gas stream analyzed by mass spectrometry (GC–MS). This approach suggested that salsalate decomposes with the formation of salicylic acid, phenol, phenyl salicylate, and cyclic oligomers of salicylic acid di- and tri-salicylides.

(b)One gram samples of salsalate were heated in a vessel under nitrogen to 150 °C, and the residues were analyzed by liquid chromatography–mass spectrometry (LC–MS). The major compound detected was a linear tetrameric salicylate ester.

     

Application of NMR SHAPES screening to an RNA target

Several NMR screening techniques have been developed in recent years to aid in the identification of lead drug compounds. These NMR methods have traditionally been used for protein targets, and here we examine their applicability for an RNA target. We used the SHAPES compound library to test three different NMR screening methodologies: the saturation transfer difference (STD), the 2D trNOESY, and the WaterLOGSY experiments. We found that the WaterLOGSY experiment was the most sensitive method for our RNA target, the P4P6 domain of the Tetrahymena thermophila Group I intron. Using the WaterLOGSY experiment, we found that 23 of the 112 SHAPES compounds interact with P4P6. To identify which of these 23 hits bind through nonspecific interactions, we counterscreened with a linear duplex RNA control and identified one of the SHAPES compounds as interacting with P4P6 specifically. We thus demonstrated that the WaterLOGSY experiment in combination with the SHAPES compound library can be used to efficiently find RNA binding lead compounds.