Computational study of conformational preferences of thioamide-containing azaglycine peptides

The effect of thioamide substitution on the conformational stability of an azaglycine-containing peptide, For-AzaGly-NH2 (1), was investigated for the sake of finding possible applications by using ab initio and DFT methods. As model compounds, For-[psiCSNH]-AzaGly-NH2 (2), For-AzaGly-[psiCSNH]-NH2 (3), and For-[psiCSNH]-AzaGly-[psiCSNH]-NH2 (4) were used. Two-dimensional phi-psi potential energy surfaces (PESs) for 2-4 were calculated at the B3LYP/6-31G*//HF/6-31G* level in gas (epsilon = 1.0) and in water (epsilon = 78.4) by applying the isodensity polarizable continuum model (IPCM) method. On the basis of these PESs, the minimum energy conformations for 2-4 were characterized at the B3LYP level with 6-31G*, 6-311G**, and 6-31+G** basis sets. The remarkable structural effect of thioamide substitution for 2-4 is that beta-strand structure is observed as a global or local minimum. The minima of 2-4 are also compared with those for glycine and thioamide-containing glycine peptides. Our theoretical results demonstrate that compounds 2-4 would be used to design controllable secondary structures.     

Construction of a 2,6-difunctionalized 2-methyl-2H-1-benzopyran library by using a solid-phase synthesis protocol

[reaction: see text] A library containing 1200 analogues of 2,6-difunctionalized 2-methyl-2H-1-benzopyran was constructed by using a solid-phase synthesis protocol. Polymer-bound 6-amido-, 6-sulfonamido-, and 6-uredo-functionalized 2-hydroxymethyl-2-methylbenzopyrans 10 were prepared as part of a first-generation diversification step by employing reactions of respective acid halides, sulfonyl chlorides, and isocyanates with the amine precursor 7. Transformations of the resin-bound intermediates 10 by reactions with alkyl and acid halides were then used to produce a diverse series of 2,6-difunctionalized 2-methyl-2H-1-benzopyran analogues 12 and 14.     

Stereoselective synthesis of (+)-SCH 351448: a unique ligand system for sodium, calcium, and other cations

(+)-SCH 351448 (Na+ salt A) was synthesized employing ring-closing olefin metathesis reaction of an open diene diester intermediate for construction of the 28-membered macrodiolide structure. The open diene diester was prepared from the monomeric hydroxy carboxylic acid and two different olefin fragments. The monomeric hydroxy acid was synthesized via Julia-Julia coupling reaction of intermediates derived from the same olefinic fragments. Oxane units in these fragments were prepared by radical cyclization reactions of beta-alkoxyacrylates. Analogous SCH 351448 salts incorporating other mono- and divalent cations may be prepared. Under acidic conditions, SCH 351448 (Na+ salt A) was the most stable complex, but SCH 351448 (Ca2+ salt) and (Na+ salt B) appear to be physiologically important species.     

Lifetime of living polymers in cationic polymerization. II. Living polymerization of isobutyl vinyl ether initiated by the hydrogen iodide/zinc halide systems

In the living cationic polymerization of isobutyl vinyl ether (IBVE) initiated by the hydrogen iodide/zinc halide (HI/ZnX₂; X = I, Br, Cl) systems, the concentration ([P^*]) of the living propagating species was determined by quenching with sodiomalonic ester ( 1 ). The quenching reaction was shown to be clean, instantaneous, and quantitative to give poly (IBVE) with a terminal malonate group from which [P^*] was obtained by ¹H-NMR spectroscopy. In the polymerizations in toluene below +25°C, [P^*] was constant and equal to the initial concentration ([HI]₀) of hydrogen iodide, independent of the type and concentrations of ZnX₂ as well as monomer conversion. At 0 and +25°C, however, the living species started decaying immediately after the complete consumption of monomer. In contrast, such a decay process was absent at ?15°C even in the absence of monomer until about an hour (depending on the conditions) after the end of polymerization. The deactivation reaction was first order in [P^*], and the lifetime (half-life) of the living species was longer at lower temperature and at lower ZnX₂ concentration. On the basis of these [P^*] and lifetime measurements, the HI/ZnX₂ systems were also compared with the HI/I₂ counterpart.     

Pattern generation of biological ligands on a biodegradable poly(glycolic acid) film

The micropatterns of biological ligands (biotin and RGD peptides) were generated on a flat surface of biodegradable polymer, poly(glycolic acid) (PGA). The immobilization of biological ligands onto the surface of biodegradable polymers (especially aliphatic polyesters) is usually hampered by the absence of functionalizable groups on the polymer backbone. We demonstrate herein that PGA polymer films were modified by surface hydrolysis to introduce carboxylic acid groups on the film surfaces, which were subsequently used for patterning amine-terminated ligands by microcontact printing. Fluorescence microscopy was used to verify the pattern of biotin on the surface of the PGA films after complexation with fluorescein-conjugated streptavidin. In addition, the cellular micropatterns were obtained from micropatterns of RGD peptides on the surface-hydrolyzed PGA films.     

Surface-initiated growth of poly d(A-T) by Taq DNA polymerase

In this paper, we report surface-initiated d(A-T) polymerization by Taq DNA polymerase as a method for constructing DNA-tethered surfaces using an enzyme. The enzymatic polymerization was conducted successfully via two steps: tethering of oligo d(A-T)s onto the surface presenting carboxylic acids by amide coupling and surface-initiated polymerization using Taq DNA polymerase. In this enzymatic polymerization process, the design and construction of carboxylic acid-presenting surfaces were found to be an important factor: DNA growth did not occur on the gold surface coated only with the self-assembled monolayer (SAM) of 16-mercaptohexadecanoic acid (MHDA), but effectively proceeded on the surfaces presenting mixed SAMs of MHDA and 1-pentadecanethiol. The coupling of oligo d(A-T)s and the subsequent DNA polymerization reaction were characterized by polarized infrared external reflectance spectroscopy, ellipsometry, X-ray photoelectron spectroscopy, and atomic force microscopy.     

Kinetic and thermodynamic characterization of the cobalt and manganese oxyhydroxide cores formed in horse spleen ferritin

Horse spleen ferritin (HoSF) containing 800-1500 cobalt or 250-1200 manganese atoms as Co(O)OH and Mn(O)OH mineral cores within the HoSF interior (Co-HoSF and Mn-HoSF) was synthesized, and the chemical reactivity, kinetics of reduction, and the reduction potentials were measured. Microcoulometric and chemical reduction of HoSF containing the M(O)OH mineral core (M = Co or Mn) was rapid and quantitative with a reduction stoichiometry of 1.05 +/- 0.10 e/M forming a stable M(OH)(2) mineral core. At pH 9.0, ascorbic acid (AH(2)), a two-electron reductant, effectively reduced the mineral cores; however, the reaction was incomplete and rapidly reached equilibrium. The addition of excess AH(2) shifted the reaction to completion with a M(3+)/AH(2) stoichiometry of 1.9-2.1, consistent with a single electron per metal atom reduction. The rate of reaction between M(O)OH and excess AH(2) was measured by monitoring the decrease in mineral core absorbance with time. The reaction was first order in each reactant with second-order rate constants of 0.53 and 4.74 M(-1) min(-1), respectively, for Co- and Mn-HoSF at pH 9.0. From the variation of absorbance with increasing AH(2) concentration, equilibrium constants at pH 9.0 of 5.0 +/- 1.9 for Co-HoSF and 2.9 +/- 0.9 for Mn-HoSF were calculated for 2M(O)OH + AH(2) = 2M(OH)(2) + D, where AH(2) and D are ascorbic acid and dehydroascorbic acid, respectively. Consistent with these equilibrium constants, the standard potential for the reduction of Co(III)-HoSF is 42 mV more positive than that of the ascorbic acid reaction, while the standard potential of Mn(III)-HoSF is 27 mV positive relative to AH(2). Fe(2+) in solution with Co- and Mn-HoSF under anaerobic conditions was oxidized to form Fe(O)OH within the HoSF interior, resulting in partial displacement of the Co or Mn by iron.     

Ring-opening polymerization of 2-azabicyclo-[2,2,1]-hept-5-en-3-one using metathesis catalysts

The ring-opening polymerization of an unsaturated bicyclic lactam, 2-azabicyclo-[2,2,1]-hept-5-en-3-one (ABHEO), was carried out using metathesis catalysts under various reaction conditions. It is observed that the best results (34% conversion and η_inh: 0.18 dL/g) were obtained when the mole ratios of ABHEO to WCl₆ as a catalyst and WCl₆ to AlEt₃ as a cocatalyst were 200 and 4, respectively. The infrared (IR) and nuclear magnetic resonance (¹H- and ¹³C-NMR) spectra of the polymer obtained indicated that the ABHEO was transformed to the ring-opened polymer, poly(2-pyrrolidone-3,5-diylvinylene) [poly(ABHEO)]. The resulting polymer was amorphous as determined by DSC analysis, which showed only secondary transition at 100°C.     

Computer-assisted optimization of reversed-phase HPLC isocratic separation of neutral compounds

An appropriate optimization strategy should be used to find a desired resolution or selectivity with a minimum number of experiments in a limited time, which could assure the baseline separation of all target compounds. It was usually realized by means of a specialized computer program. In this paper, mapping optimization method and overlapping resolution mapping were compared for the optimization of a reversed-phase high-performance liquid chromatography (HPLC) isocratic separation of neutral compounds. The calculated resolutions and separation time of 7 to 10 experiments are fitted by different equations, which were used to build a contour plot with a minimum effective resolution and maximum retention time as a function of a mobile phase composition. The balance between resolution and analysis time could be easily realized by the overlapping of the final overlapping resolution mapping and analysis time mapping. The validity of the two methods was confirmed by some typical experiments. The models are simple, visual, and common without theoretical arithmetic.