Improvement of in-gel digestion protocol for peptide mass fingerprinting by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

High-sensitivity, high-throughput analysis of proteins for proteomics studies is usually performed by polyacrylamide gel electrophoresis in combination with mass spectrometry. However, the quality of the data obtained depends on the in-gel digestion procedure employed. This work describes an improvement in the in-gel digestion efficiency for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) analysis. A dramatic improvement in the coverage of tryptic peptides was observed when n-octyl glucoside was added to the buffer. Whole cell extracted proteins from S. cerevisiae were separated by two-dimensional gel electrophoresis and stained with silver. Protein spots were identified using our improved in-gel digestion method and MALDI-TOFMS. In addition, the mass spectra obtained by using the matrix alpha-cyano-4-hydroxycinnamic acid (CHCA) were compared with those obtained using 2,5-dihydroxybenzoic acid (DHB). The DHB matrix usually gave more peaks, which led to higher sequence coverage and, consequently, to higher confidence in protein identification. This improved in-gel digestion protocol is simple and useful for protein identification by MALDI-TOFMS.     

Photochemical study of [3(3)](1,3,5)cyclophane and emission spectral properties of [3n]cyclophanes (n = 2-6)

Thephotochemical reaction of [3(3)](1,3,5)cyclophane 2, which is a photoprecursor for the formation of propella[3(3)]prismane 18, was studied using a sterilizing lamp (254 nm). Upon photolysis in dry and wet CH2Cl2 or MeOH in the presence of 2 mol/L aqueous HCl solution, the cyclophane 2 afforded novel cage compounds comprised of new skeletons, tetracyclo[6.3.1.0.(2,7)0(4,11)]dodeca-5,9-diene 43, hexacyclo[6.4.0.0.(2,6)0.(4,11)0.(5,10)0(9,12)]dodecane 44, and pentacyclo[6.4.0.0.(2,6)0.(4,11)0(5,10)]dodecane 45. All of these products were confirmed by the X-ray structural analyses. A possible mechanism for the formation of these photoproducts via the hexaprismane derivative 18 is proposed. The photophysical properties in the excited state of the [3n]cyclophanes ([3n]CP, n = 2-6) were investigated by measuring the emission spectra and determining the quantum yields and lifetimes of the fluorescence. All [3n]CPs show excimeric fluorescence without a monomeric one. The lifetime of the excimer fluorescence becomes gradually longer with the increasing number of the trimethylene bridges. The [3n]CPs also shows excimeric phosphorescence spectra without vibrational structures for n = 2, 4, and 5, while phosphorescence is absent for n = 3 and 6. With an increase in symmetry of the benzene skeleton in the [3(3)]- and [3(6)]CPs, the probability of the radiation (phosphorescence) process from the lowest triplet state may drastically decrease.     

Diastereoselective Iodocarbocyclization Reaction of 2- or 3-Oxy-4-pentenylmalonate Derivatives

1,2- Or 1,3-asymmetric induction in the iodocarbocyclization reaction of 4-pentenylmalonate derivatives having a stereogenic center at an allylic or a homoallylic position has been investigated. The iodocarbocyclization reactions of 3-oxy-4-pentenylmalonate derivatives proceeded with high cis-selectivity through stereoelectronic control of the oxygenated substituent at an allylic position. In the reaction of (S)-2-siloxy-4-pentenylmalonate, an excellent diastereoselectivity was achieved through the utilization of double stereodifferentiation with a chiral titanium catalyst. Furthermore, as an application of the present reaction, the asymmetric syntheses of cyclosarkomycin and a synthetic intermediate of brefeldin A from optically pure 2- and 3-oxy-4-pentenylmalonate derivatives are also described.     

Synthesis and applications of [1-(15)N]-labeled 4,6-dimethyl-4H-[1,2,5]oxadiazolo[3,4-d]pyrimidine-5,7-dione 1-oxide as a useful tool for mechanistic investigations

[1-(15)N]-Labeled 4,6-dimethyl-4H-[1,2,5]oxadiazolo[3,4-d]pyrimidine-5,7-dione 1-oxide (1-(15)N1) was easily prepared by nitration of commercially available 6-amino-1,3-dimethyl-1H-pyrimidine-2,4-dione using 15N-enriched nitric acid followed by an intramolecular oxidative cyclization with iodosylbenzene diacetate under mild conditions. On the basis of the experimental results using 1-(15)N1, the formation of 8-phenyltheophylline (3), the 1,3-dimethylalloxazines (4: n = 0, 1), and 1,3,7,9-tetramethyl-1H,9H-pyrimido[5,4-g]pteridine-2,4,6,8-tetraone++ + (5) in the thermal reaction of the N-oxide 1 with benzylamine, aniline, or piperidine, and the generation of NO or NO-related species in the reaction with N-acetylcysteamine were reasonably explained by considering the initial attack of the employed nucleophiles on the 3a-position of 1.     

Application of AMS <Superscript>14</Superscript>C measurements to criminal investigations

¹⁴C variations of atmospheric CO₂ as well as carbonaceous fraction of living materials, such as collagen from tooth and bone, tissue, skin, hair, nail, etc., of modern humans are influenced by ¹⁴C produced artificially by nuclear bomb tests in the atmosphere from late 1950s to early 1960s. By careful investigation of ¹⁴C concentration of tree rings and human body samples formed in this time intervals, we can establish a relationship of their ¹⁴C concentrations with calendar year. By applying this relation to a sample whose ¹⁴C concentration can be measured, we can estimate the formation age of the sample. In addition, sources of the chemicals that were used in some criminal cases can be possibly identified, by their carbon isotope ratios (¹³C/¹²C and ¹⁴C/¹²C). This method of age determination has been applied to a forensic study, i.e., two criminal cases of murder. For each case, by comparing the measured ¹⁴C abundances of several pieces of hair and one tooth (the third molar) from the body with the annual change on concentrations of bomb-produced ¹⁴C, the time of death of the body and the age of the victim were estimated. The estimated values were consistent with the real ones that were revealed by the confession of the real murderers.     

Synthesis of thermally-induced phase separating polymer with well-defined polymer structure by living cationic polymerization. I. Synthesis of poly(vinyl ether)s with oxyethylene units in the pendant and its phase separation behavior in aqueous solution

Living cationic polymerization of alkoxyethyl vinyl ether [CH₂?CHOCH₂CH₂OR; R: CH₃ (MOVE), C₂H₅ (EOVE)] and related vinyl ethers with oxyethylene units in the pendant was achieved by 1-(isobutoxy)ethyl acetate ( 1 )/Et_1.5AlCl_1.5 initiating system in the presence of an added base (ethyl acetate or THF) in toluene at 0°C. The polymers had a very narrow molecular weight distribution (M?_w/M?_n = 1.1–1.2) and the M?_n proportionally increased with the progress of the polymerization reaction. On the other hand, the polymerization by 1 /EtAlCl₂ initiating system in the presence of ethyl acetate, which produces living polymer of isobutyl vinyl ether, yielded the nonliving polymer. When an aqueous solution of the polymers thus obtained was heated, the phase separation phenomenon was clearly observed in each polymer at a definite critical temperature (T_ps). For example, T_ps was 70°C for poly(MOVE), and 20°C for poly(EOVE) (1 wt % aqueous solution, M?_n ～ 2 × 10⁴). The phase separation for each case was quite sensitive (ΔT_ps = 0.3–0.5°C) and reversible on heating and cooling. The T_ps or ΔT_ps was clearly dependent not only on the structure of polymer side chains (oxyethylene chain length and ω-alkyl group), but also on the molecular weight (M?_n = 5 × 10³-7 × 10⁴) and its distribution. © 1992 John Wiley & Sons, Inc.     

Synthesis,Properties, and Redox Behavior of 1,1,4,4‐Tetracyano‐2‐ferrocenyl‐1,3‐butadienes Connected by Aryl,Biaryl, and Teraryl Spacers

Aryl‐substituted 1,1,4,4‐tetracyano‐1,3‐butadienes (FcTCBDs) and bis(1,1,4,4‐tetracyanobutadiene)s (bis‐FcTCBDs), possessing a ferrocenyl group on each terminal, were prepared by the reaction of a variety of alkynes with tetracyanoethylene (TCNE) in a [2+2] cycloaddition reaction, followed by retro‐electrocyclization of the initially formed [2+2] cycloadducts (i.e., cyclobutene derivatives). The characteristic intramolecular charge transfer (ICT) between the donor (ferrocene) and acceptor (TCBD) moieties were investigated by using UV/Vis spectroscopy. The redox behaviors of FcTCBDs and bis‐FcTCBDs were examined by cyclic voltammetry (CV) and differential pulse voltammetry (DPV), which revealed their properties of multi‐electron transfer depending on the number of ferrocene and TCBD moieties. Moreover, significant color changes were observed by visible spectroscopy under the electrochemical reduction conditions.