Dynamic identification of phosphopeptides using immobilized metal ion affinity chromatography enrichment, subsequent partial beta-elimination/chemical tagging and matrix-assisted laser desorption/ionization mass spectrometric analysis

The enrichment of phosphopeptides using immobilized metal ion affinity chromatography (IMAC) and subsequent mass spectrometric analysis is a powerful protocol for detecting phosphopeptides and analyzing their phosphorylation state. However, nonspecific binding peptides, such as acidic, nonphosphorylated peptides, often coelute and make analyses of mass spectra difficult. This study used a partial chemical tagging reaction of a phosphopeptide mixture, enriched by IMAC and contaminated with nonspecific binding peptides, following a modified beta-elimination/Michael addition method, and dynamic mass analysis of the resulting peptide pool. Mercaptoethanol was used as a chemical tag and nitrilotriacetic acid (NTA) immobilized on Sepharose beads was used for IMAC enrichment. The time-dependent dynamic mass analysis of the partially tagged reaction mixture detected intact phosphopeptides and their mercaptoethanol-tagged derivatives simultaneously by their mass difference (-20 Da for each phosphorylation site). The number of new peaks appearing with the mass shift gave the number of multiply phosphorylated sites in a phosphopeptide. Therefore, this partial chemical tagging/dynamic mass analysis method can be a powerful tool for rapid and efficient phosphopeptide identification and analysis of the phosphorylation state concurrently using only MS analysis data.     

Efficient excitation energy transfer in long meso-meso linked Zn(II) porphyrin arrays bearing a 5,15-bisphenylethynylated Zn(II) porphyrin acceptor

Electronically coupled porphyrin arrays are suitable for artificial light harvesting antenna in light of a large absorption cross-section and fast excitation energy transfer (EET). Along this line, an artificial energy transfer model system has been synthesized, comprising of an energy donating meso-meso linked Zn(II) porphyrin array and an energy accepting 5,15-bisphenylethynylated Zn(II) porphyrin linked via a 1,4-phenylene spacer. This includes an increasing number of porphyrins in the meso-meso linked Zn(II) porphyrin array, 1, 2, 3, 6, 12, and 24 (Z1A, Z2A, Z3A, Z6A, Z12A, and Z24A). The intramolecular singlet-singlet EET processes have been examined by means of the steady-state and time-resolved spectroscopic techniques. The steady-state fluorescence comes only from the acceptor moiety in Z1A-Z12A, indicating nearly the quantitative EET. In Z24A that has a molecular length of ca. 217 A, the fluorescence comes largely from the acceptor moiety but partly from the long donor array, indicating that the intramolecular EET is not quantitative. The transient absorption spectroscopy has provided the EET rates in real time scale: (2.5 ps)(-1) for Z1A, (3.3 ps)(-1) for Z2A, (5.5 ps)(-1) for Z3A, (21 ps)(-1) for Z6A, (63 ps)(-1) for Z12A, and (108 ps)(-1) for Z24A. These results have been well explained by a revised F?rster equation (Sumi formula), which takes into account an exciton extending coherently over several porphyrin pigments in the donor array, whose length is not much shorter than the average donor-acceptor distance. Advantages of such strongly coupled porphyrin arrays in light harvesting and transmission are emphasized in terms of fast EET and a large absorption cross-section for incident light.     

X-ray spectroscopy of enzyme active site analogues and related molecules: bis(dithiolene)molybdenum(IV) and -tungsten(IV,VI) complexes with variant terminal ligands

The X-ray absorption spectra at the molybdenum and selenium K-edges and the tungsten L2,3-edges are acquired for a set of 14 Mo(IV) and W(IV,VI) bis(dithiolene) complexes related to the active sites of molybdo- and tungstoenzymes. The set includes square pyramidal [MoIVL(S2C2Me2)2]- (L = O2-, R3SiO-, RO-, RS-, RSe-) and [WIV(OR)(S2C2Me2)2]-, distorted trigonal prismatic [MoIV(CO)(SeR)(S2C2Me2)2]- and [WIV(CO)L(S2C2Me2)2]- (L = RS-, RSe-), and distorted octahedral [WVIO(OR)(S2C2Me2)2]-. The dithiolene simulates the pterin-dithiolene cofactor ligand, and L represents a protein ligand. Bond lengths are determined by EXAFS analysis using the GNXAS protocol. Normalized edge spectra, non-phase-shift-corrected Fourier transforms, and EXAFS data and fits are presented. Bond lengths determined by EXAFS and X-ray crystallography agree to < or = 0.02 A as do the M-Se distances determined by both metal and selenium EXAFS. The complexes [MoIV(QR)(S2C2Me2)2]- simulate protein ligation by the DMSO reductase family of enzymes, including DMSO reductase itself (Q = O), dissimilatory nitrate reductase (Q = S), and formate dehydrogenase (Q = Se). Edge shifts of these complexes correlate with the ligand electronegativities. Terminal ligand binding is clearly distinguished in the presence of four Mo-S(dithiolene) interactions. Similarly, five-coordinate [ML(S2C2Me2)2]- and six-coordinate [M(CO)L(S2C2Me2)2]- are distinguishable by edge and EXAFS spectra. This study expands a previous XAS investigation of bis(dithiolene)metal(IV,V,VI) complexes (Musgrave, K. B.; Donahue, J. P.; Lorber, C.; Holm, R. H.; Hedman, B.; Hodgson, K. O. J. Am. Chem. Soc. 1999, 121, 10297) by including a larger inventory of molecules with variant physiologically relevant terminal ligation. The previous and present XAS results should prove useful in characterizing and refining metric features and structures of enzyme sites.     

Metal-oxygen-metal arrays in lamellar hybrid materials: cobalt and manganese 4-cyclohexene-1,2-dicarboxylates

We have obtained three layered hybrid materials from the hydrothermal reaction of 4-cyclohexene-1,2-dicarboxylic acid with Co and Mn salts: Co(C(8)H(8)O(4))[1], Mn(H(2)O)(C(8)H(8)O(4))[2], and Mn(4)(H(2)O)(C(8)H(8)O(4))(4).0.3(H(2)O)[3]. The structures for all materials were solved by single-crystal XRD ([1]P1, a=4.805(2) A, b=6.650(3) A, c=12.960(6) A, alpha=98.285(7) degrees, beta=98.986(7) degrees, gamma=95.689(7) degrees, V= 401.6(3) A(3), R(1)= 0.0438; [2] P2(1)/c, a=11.151(2) A, b=11.330(2) A, c=7.6560(15) A, beta=108.813(3) degrees , V=915.6(3) A(3), R(1)=0.0412; [3] P1, a= 11.412(3) A, b=12.136(4) A, c=13.809(4) A, alpha=104.703(6) degrees, beta=103.207(6) degrees, gamma=92.468(5) degrees, V=1790.6(9) A(3), R(1)=0.1056). While all three structures are two-dimensional overall, the metal-oxygen-metal dimensionality within the layers varies from isolated metal atoms in the case of [1] to 1D ribbons of vertex sharing MnO(6) octahedra [2] and 2D arrays of edge- and vertex-sharing polyhedra in [3].     

Integral equation theory for two-dimensional polymer melts

The polymer reference interaction site model theory is investigated for two-dimensional polymer melts composed of freely-jointed hard disk chains and tangent-disk rods. Exact results for the intramolecular pair correlation functions are input into the theory, and predictions of the theory for the intermolecular pair correlation functions are tested via comparison with simulation. The theory is not as accurate for this system as it is for three-dimensional polymer melts, and the quantitative predictions are not good except at the highest area fractions. Possible reasons for the deficiency in the theory are discussed.     

Chlorinated briarane-type diterpenoids from the gorgonian coral Ellisella robusta (Ellisellidae)

Four chlorinated metabolites featuring briarane carbon skeletons have been isolated from the gorgonian coral Ellisella robusta, which was collected off the coast of southern Taiwan: two new natural products, robustolides D (1) and E (2), and two known metabolites, robustolides F (3) and G (4). The structures of metabolites 1–4 were determined by spectroscopic methods, using 1D and 2D NMR in particular. The structures and absolute stereochemistry of robustolides D (1), F (3), and G (4) were directly established by X-ray diffraction analysis. Robustolide D (1) is the first metabolite of briarane-related natural products found to possess two halogen atoms.     

Integral equation theory of random copolymer melts: self-consistent treatment of intramolecular and intermolecular correlations

A self-consistent integral equation theory is presented for the conformational properties and spinodal lines of random copolymer melts. The theory combines field-theoretic methods with the polymer reference interaction site model (PRISM) theory. The many-chain problem is replaced by a single chain where the sites interact via a bare plus a self-consistently determined medium-induced potential, and the conformational properties are obtained using a variational method. The theoretical prediction for the spinodal line is qualitatively similar to that of non-self-consistent PRISM theory. The theory predicts macroscopic phase separation for all values of the monomer correlation strength, lambda. The inverse spinodal temperature is a nonmonotonic function of lambda with a maximum at lambda(max). For large values of lambda( approximately 1), the values of spinodal temperatures are almost identical to those of non-self-consistent PRISM theory. For low values of lambda, however, the theory predicts higher values for spinodal temperatures than non-self-consistent PRISM theory. The theory predicts significant changes in the mean-square end-to-end distance as the temperature is decreased.     

Photophysical properties of porphyrin tapes

The novel fused Zn(II)porphyrin arrays (Tn, porphyrin tapes) in which the porphyrin macrocycles are triply linked at meso-meso, beta-beta, beta-beta positions have been investigated by steady-state and time-resolved spectroscopic measurements along with theoretical MO calculations. The absorption spectra of the porphyrin tapes show a systematic downshift to the IR region as the number of porphyrin pigments increases in the arrays. The fused porphyrin arrays exhibit a rapid formation of the lowest excited states (for T2, approximately 500 fs) via fast internal conversion processes upon photoexcitation at 400 nm (Soret bands), which is much faster than the internal conversion process of approximately 1.2 ps observed for a monomeric Zn(II)porphyrin. The relaxation dynamics of the lowest excited states of the porphyrin tapes were accelerated from approximately 4.5 ps for the T2 dimer to approximately 0.3 ps for the T6 hexamer as the number of porphyrin units increases, being explained well by the energy gap law. The overall photophysical properties of the porphyrin tapes were observed to be in a sharp contrast to those of the orthogonal porphyrin arrays. The PPP-SCI calculated charge-transfer probability indicates that the lowest excited state of the porphyrin tapes (Tn) resembles a Wannier-type exciton closely, whereas the lowest excited state of the directly linked porphyrin arrays can be considered as a Frenkel-type exciton. Conclusively, these unique photophysical properties of the porphyrin tapes have aroused much interest in the fundamental photophysics of large flat organic molecules as well as in the possible applications as electric wires, IR sensors, and nonlinear optical materials.     

New tetradentate Schiff-base polymers: preparation of poly[2,5-(didodecyloxy)phenylene-1,4-diyl-alt-N,N-(o-phenylene)-bis(salicylideneiminato-4,4-diyl)] and poly[2,5-(didodecyloxy)phenylene-1,4-diyl-alt-N,N-(alkylidene)-bis(salicylideneiminato-4,4-diyl)]s

New tetradentate Schiff-base polymers, in which phenylene units alternate with salicylideneiminato units, have been prepared by condensation of 2,5-(didodecyloxy)-1,4-bis(3-formyl-4-hydroxyphenyl)benzene (DFHB) with appropriate diamines in a mixed solution of CHCl₃/toluene/acetic acid with 31-79% yields. DFHB as the key building block was prepared by the Suzuki reaction of 2,5-(didodecyloxy)benzene-1,4-diboronic acid with 5-bromosalicylaldehyde in a two-phase solution of tetrahydrofuran/water in the presence of NaHCO₃/Pd(PPh₃)₄ in 45% yield. The molecular structures of the prepared compounds were identified by spectroscopy. Their absorption spectroscopic profiles have been analyzed.