Photolithographic synthesis of peptoids

We describe a novel photolithographic approach to the synthesis of peptoids (oligo-N-substituted glycines). This strategy enables the construction of a spatially addressable peptoid microarray, thus providing a potentially powerful tool for the discovery of protein ligands.     

Carbamoylimidazolium and thiocarbamoylimidazolium salts: novel reagents for the synthesis of ureas, thioureas, carbamates, thiocarbamates and amides

Carbamoylimidazolium salts act as efficient N,N-disubstituted carbamoylating reagents. These salts are readily prepared by the sequential treatment of secondary amines with N,N′-carbonyldiimidazole (CDI) and iodomethane. The carbamoylimidazolium salts are more efficient carbamoyl transfer reagents than the intermediate carbamoylimidazoles, as a result of the ‘imidazolium’ effect. Kinetic studies on the base promoted hydrolysis of both carbamoylimidazoles and carbamoylimidazolium salts reveal over a hundred-fold rate acceleration. The salts react with amines, thiols, phenols/alcohols, and carboxylic acids in high yields, without the need for subsequent chromatographic purification of the products, producing ureas, thiocarbamates, carbamates, and amides, respectively. Analogous thiocarbamoylimidazolium salts were also synthesized from secondary amines and N,N′-thiocarbonyldiimidazole (TCDI), followed by methylation with iodomethane.     

Investigation of cytolysin variants by peptide mapping: enhanced protein characterization using complementary ionization and mass spectrometric techniques

Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) have been used in conjunction with time-of-flight (TOF) and quadrupole ion trap (IT) mass spectrometry, respectively, to analyze various cytolysin proteins isolated from the sea anemone Stichodactyla helianthus and digested by the protease trypsin. By employing different ionization methods, the subsequent changes in ionization selectivity for the peptides in the digested protein samples resulted in ion abundance variation reflected in the mass spectra. Upon investigation of this variation generated by the two ionization processes, it has been shown in this study that enhanced protein coverage (e.g., >95% for cytolysin III) can be achieved. Additionally, capillary and microbore reversed-phase high-performance liquid chromatography (RP-HPLC) coupled with ESI mass spectrometry (MS) as well as flow injection analysis by nanoflow ESI-MS afforded the necessary limit of detection (LOD) for detailed structural information of the cytolysin proteins by tandem mass spectrometry (MS/MS) methods. It can be concluded that cytolysins II and III correspond to sticholysins I and II, that "cytolysin I" is a mixture of modified forms of cytolysins II and III, and that "cytolysin IV" is an incompletely processed precursor of cytolysin III.     

Oxidatively truncated docosahexaenoate phospholipids: total synthesis,generation, and Peptide adduction chemistry

The recent immunological detection of extraordinarily high levels of carboxyethylpyrrole (CEP) modifications of proteins from the retinas of individuals with age-related macular degeneration provided presumptive evidence for the involvement of docosahexaenoate-derived oxidatively truncated phospholipids in retinal pathology. To facilitate the in vivo detection and characterization of the chemistry and biological activities of these postulated naturally occurring molecules, a family of oxidatively truncated phospholipids was prepared by total syntheses. Their formation in oxidation reactions of a docosahexaenoate ester of 2-lysophosphatidylcholine (DHA-PC) was also demonstrated. Free radical-induced oxidative cleavage of DHA-PC promoted by myeloperoxidase or copper ions generates similar mixtures of these phospholipids. The most abundant products were 1-palmitoyl-2-succinoyl-sn-glycero-3-phosphatidylcholine (4.7%) and 2-(6-carboxy-4-oxohex-5-enoyl)-1-palmitoyl-sn-glycero-3-phosphatidylcholine (1.7%). Both of these oxidatively truncated phospholipids are homologues of biologically active arachidonate-derived phospholipids. A minor product from DHA-PC, 2-(4-hydroxy-7-oxohept-5-enoyl)-1-palmitoyl-sn-glycero-3-phosphatidylcholine (0.4% yield), reacted with the epsilon-amino group of a peptide lysyl residue to produce a CEP derivative in 0.7% yield. These observations support the previous conclusion, based on immunological evidence, that CEPs are generated by the reaction of an oxidatively truncated phospholipid with proteins in the retina and further indicate that CEP protein modifications probably represent only a tiny fraction of the products generated upon oxidative damage of DHA-PC in photoreceptor disk membranes.     

Benzannelated analogs of phenanthro[1,2-b]- and [2,1-b]thiophene: Synthesis and structural characterization by two-dimensional NMR and X-ray techniques

Syntheses of benzo[3,4]phenanthro[1,2-b]thiophene, benzo[3,4]phenanthro[2,1-b]thiophene and their 1-methyl analogs are reported as potential constituents of solvent refined coal liquids and for mutagenicity testing. The attempted synthesis of the 13-methyl analogs which gave the 11-methyl isomers is also described. Total assignments of the ¹H- and ¹³C-nmr spectra based on long range optimized heteronuclear protoncarbon two-dimensional chemical shift correlation are reported. Carbon assignments obtained for benzo[3,4]-phenanthro[1,2-b]thiophene using this approach were confirmed with a 125 MHz ¹³C–¹³C INADEQUATE spectrum. X-Ray crystal structures were determined for benzo[3,4]phenanthro[1,2-b]thiophene and 1-methyl-benzo[3,4]phenanthro[2,1-b]thiophene. Both molecules were helically distorted from planarity. Close intramolecular contacts between the bay region H1–H13 and ClMe-H13 of 2.03 and 2.28 Å, respectively, were responsible for the distortions. There were no close intermolecular contacts of <3.5Å. both molecules refined to an R value of <0.05.     

The chemistry of 2'' ,3''-seconucleosides II. Reactions and biological properties of 2'',3''-secopyrimidine ribonucleosides

Reaction of 2',3'-secouridine with acetone gave the 3',5'-$\text{O}$-isopropylidene derivative (1) which upon treatment with mesylchloride gave the 2'-$\text{O}$-mesyl compound (2). Replacement of the mesyl group of 2 with halide could be effected by reaction with a metal halide in DMF. The 3',5'-$\text{O}$-isopropylidene group was removed simultaneously to give a 2'-halogeno-2'-deoxy-2',3'-secouridine. 2',3'-Dichloro-2',3'-dideoxy-2',3'-secouridine upon treatment with base gave 6($\text{R}$)-chloromethyl-2($\text{R}$)-(uracil-1-yl)-1,4-dioxane in addition to O²,2'-anhydro-3'-chloro-3'-deoxy-2',3'-secouridine, as previously reported. 2',3'-Dichloro-2',3'-dideoxy-5'-0-trityl-2',3'-secouridine was converted to 2',3'-dichloro-2',3'-dideoxy-2',3'-secocytidine (16) $\text{via}$ a triazole derivative. Compound 16 was unstable and appeared to form O²,2'-anhydro-3'-chloro-3'-deoxy-2,3'-secocytidine upon standing at room temperature. 5-Vinyl- and 5-($\text{E}$) (2-bromovinyl) uridine dialdehydes have been made, as well as a number of other 5-substituted 2',3'-secouridine derivatives. None of the compounds obtained showed significant activity against a number of virus strains or tumor cell lines, except for 5-($\text{E}$)(2-bromovinyl) uridine dialdehyde, which was inhibitory to the growth of human lymphoblast (Raji, Namalva) cells at a concentration of 28 μ/ml.     

Synthesis of some heterocyclic skeletons via organoiron complexes. Crystal and molecular structure of (5a,6,7,8,9,9a-η6-1,4-benzoxathiino[3,2-b]pyridine)(η5-cyclopentadienyl)iron hexafluorophosphate

Synthesis of the heterocyclic skeletons of some biologically active compounds from (η⁶-o-dichlorobenzene)(η⁵-cyclopentadienyrl)iron hexafluorophosphate in a two step procedure is described. Cyclopentadienyliron hexafluorophosphate complexes of 1,4-benzodioxino[2,3-b]pyridine, 1,4-benzoxathiino[3,2-b]pyridine, 10H-pyrido[3,2-b]benzoxazine, benzo[b]naphtho[2,3-e][1,4]dioxin, 4-methylbenzo[b]benzopyran-2-one[7,6-e][1,4]dioxin and benzo[b]anthracen-9,10-diono[1,2-e][1,4]dioxin were isolated and characterized. Upon pyrolytic sublimation of these complexes the free heterocycles were obtained and characterized. (η⁶-1,4-Benzoxathiino[3,2-b]pyridine)(η⁵-cyclopentadienyl)iron hexafluorophosphate crystalizes in the orthothombic system, space group Pbca; the dihedral angle between the planes of outer rings was found to be 176.8 (1).     

Resonance-enhanced multiphoton ionization (2+1) of the\tilde B and\tilde C' states of ammonia

Resonance-enhanced multiphoton ionization (REMPI) of the \(\tilde B\) and \(\tilde C'\) states of NH₃ in a pulsed supersonic molecular beam was observed at 304–340 nm, using the multiphoton-ionization mass-spectrometer system described herein. The observed features are the result of a 2+1 MPI process and correspond quite well with the reported 3+1 MPI of NH₃ in the literature from the ground state of opposite parity.     

Determination of fluid--solid transitions in model protein solutions using the histogram reweighting method and expanded ensemble simulations

Protein crystallization conditions are usually identified by empirical screening methods because of the complexity of the process, such as the existence of nonequilibrium phases and the different crystal forms that may result from changes in solution conditions. Here the crystallization of a model protein is studied using computer simulation. The model consists of spheres that have both an isotropic interaction of short range and anisotropic interactions between patch-antipatch pairs. The free energy of a protein crystal is calculated using expanded ensemble simulations of the Einstein crystal, and NpT-Monte Carlo simulations with histogram reweighting are used to determine the fluid-solid coexistence. The histogram reweighting method is also used to trace out the complete coexistence curve, including multiple crystal phases, with varying reduced temperature, which corresponds to changing solution conditions. At a patch-antipatch interaction strength five times that of the isotropic interaction, the protein molecules form a stable simple cubic structure near room temperature, whereas an orientationally disordered face-centered-cubic structure is favored at higher temperatures. The anisotropic attractions also lead to a weak first-order transition between orientationally disordered and ordered face-centered-cubic structures at low temperature, although this transition is metastable. A complete phase diagram, including a fluid phase, three solid phases, and two triple points, is found for the six-patch protein model. A 12-patch protein model, consistent with the face-centered-cubic structure, leads to greater thermodynamic stability of the ordered phase. Metastable liquid-liquid phase equilibria for isotropic models with varying attraction tails are also predicted from Gibbs ensemble simulations.     

Enthalpies of aqueous solution of noble gases at 25°C

The standard enthalpies of solution of rare gases (helium, neon, argon, krypton, and xenon) in water at 25°C have been measured by a high precision steady-state calorimetric method. The aqueous solvation process is energetically favorable at 25°C for the gases studied. Values of the standard free energy, enthalpy, and entropy changes are found to be well correlated with cavity surface areas and the number of water molecules in the first solvation shell. Also, the values of the standard enthalpy and entropy of solution for the rare gases are found to have the same dependence on the number of solvation shell water molecules as inorganic and hydrocarbon gases. These results imply that the dominant source of enthalpy and entropy change resides in the first solvation shell.