Gas-phase chemistry of the negative ions of fully-protected peptides by high-resolution electrospray ionization tandem mass spectrometry

Fully-protected C-terminal free peptides can be conveniently analyzed by high-resolution electrospray tandem mass spectrometry (ESI-MS/MS) in a quadrupole quadrupole time-of-flight tandem hybrid mass spectrometer, operated in the negative (-) ionizaionization mode. The unusual choice of negative ions in mass spectrometry applications to peptide analysis was needed to obtain exhaustive sequence and structural data. The low-energy collision-induced dissociation (CID) experiments provided, in fact, tandem mass spectra displaying highly diagnostic fragments with a good signal-to-noise ratio. The method is applied to segments of porcine calcitonin (Cal), Cal (1016, 1), Cal (1724, 2) and Cal (2528, 3) whose [M H]- deprotonated molecular ions provided low-energy CID mass spectra which allow the evaluation either of the primary structure of the peptide and of the location of the side-chain protective groups. ESI (+) MS can be conveniently used, in the high resolution mode, to achieve precise information on the elemental composition of the examined peptides.     

Decarboxylative aldol reactions of allyl beta-keto esters via heterobimetallic catalysis

Mild and selective heterobimetallic-catalyzed decarboxylative aldol reactions involving allyl beta-keto esters have been developed. The reaction is promoted by Pd(0)- and Yb(III)-DIOP complexes at room temperature and involves the in situ formation of a ketone enolate from allyl beta-keto esters followed by addition of the enolate to aldehydes. The reaction is a new example of heterobimetallic catalysis in which the optimized reaction conditions require the addition of both metals.     

Theoretical modeling of vibroelectronic quantum states in complex molecular systems: solvated carbon monoxide, a test case

In this paper we extend the perturbed matrix method by explicitly including the nuclear degrees of freedom, in order to treat quantum vibrational states in a perturbed molecule. In a previous paper we showed how to include, in a simple way, nuclear degrees of freedom for the calculation of molecular polarizability. In the present work we extend and generalize this approach to model vibroelectronic transitions, requiring a more sophisticated treatment.     

Optical properties of nanocrystalline Y2O3:Eu depending on its odd structure

The structure of nanocrystalline Y2O3:Eu prepared by a combustion reaction was analyzed by XRD and high-resolution electron microscopy. Compared with a large-scale particles, 5-nm Y2O3:Eu particles presented as distorted crystallite and rough surfaces. Luminescent and absorption properties of nano-Y2O3:Eu showed remarkably particle size effects. At Y2O3:Eu particle sizes smaller than 10 nm some new results were observed: (a) a red shift of the charge-transfer-state absorption; (b) new emission bands of Eu3+ in the 5D0 --> 7F2 region; (c) luminescent decay of energy level 5D0 of Eu3+ turning to a two-step exponential; and (d) a pronounced increase in quenching concentration and much lower phonon density compared with those of the bulk material. All these phenomena can be attributed to the effect of the softened lattice and surface state of the nanomaterial. The latter was confirmed by stronger excitation by the host absorption after the surface modification.     

Average peptide score: a useful parameter for identification of proteins derived from database searches of liquid chromatography/tandem mass spectrometry data

The quantity and variable quality of data that can be generated from liquid chromatography (LC)/mass spectrometry (MS)-based proteomics analyses creates many challenges in interpreting the spectra in terms of the actual proteins in a complex sample. In spite of improvements in algorithms that match putative peptide sequences to MS/MS spectra, the assembly of these lists of possible or probable peptides into a 'correct' set of proteins is still problematic. We have observed a trend in a simple relationship, derived from standard database search outputs, which can be useful in assessing the quality of a MS/MS-based protein identification. Specifically, the ratio of the protein score and number of non-redundant peptides, or average peptide score (APS), can facilitate initial filtering of database search results in addition to providing a useful measure of confidence for the proteins identified. This parameter has been applied to results from the analysis of multi-protein complexes derived from pull-down experiments analyzed using a two-dimensional LC/MS/MS workflow. In particular, the complex list of protein identifications derived from a drug affinity pull-down with immobilized ampicillin and an E. coli lysate was greatly simplified by applying the APS as a filter, allowing for facile identification of the penicillin-binding proteins known to interact with ampicillin. Furthermore, an APS threshold can be used for any data sets derived from electrospray ionization (ESI)- or matrix-assisted laser desorption/ionization (MALDI)-MS/MS experiments and is also not specific to any database search program.     

Synthesis of functionalized polyhedral oligomeric silsesquioxane (POSS) macromers by microwave assisted 1,3-dipolar cycloaddition

In this paper we report the first synthesis of isoxazolidine and isoxazoline-POSS macromers by 1,3-dipolar cycloaddition reactions of vinyl- and styryl-POSS with N-methyl-C-ethoxycarbonylnitrone and ethoxycarbonyl nitrile oxide, promoted by microwave irradiation. The nature of the resulting cycloadducts has been determined by NOE experiments and supported by computational studies at PM3 and DFT B3LYP/6-31G* levels.     

Long‐range π‐type hydrogen bond in dimers CH2?HF,CH2O?H2O,and CH2O?NH3

Using four basis bets, (6‐311G(d,p), 6‐31+G(d,p), 6‐31++G(2d,2p), and 6‐311++G(3df,3pd), the optimized structures with all real frequencies were obtained at the MP2 level for the dimers CH₂O? HF, CH₂O? H₂O, CH₂O? NH₃, and CH₂O? CH₄. The structures of CH₂O? HF, CH₂O? H₂O, and CH₂O? NH₃ are cycle‐shaped, which result from the larger bend of σ‐type hydrogen bonds. The bend of σ‐type H‐bond O…H? Y (Y?F, O, N) is illustrated and interpreted by an attractive interaction of a chemically intuitive π‐type hydrogen bond. The π‐type hydrogen bond is the interaction between one of the H atoms of CH₂O and lone pair(s) on the F atom in HF, the O atom in H₂O, or the N atom in NH₃. In contrast with the above three dimers, for CH₂O? CH₄, because there is not a π‐type hydrogen bond to bend its linear hydrogen bond, the structure of CH₂O? CH₄ is noncyclic shaped. The interaction energy of hydrogen bonds and the π‐type H‐bond are calculated and discussed at the CCSD (T)/6‐311++G(3df,3pd) level. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Poly(butylene terephthalate)/poly(ε-caprolactone) blends: Influence of PCL molecular mass on PBT melting and crystallization behavior

The isothermal crystallization kinetics and melting behavior of poly(butylene terephthalate) (PBT) in binary blends with poly(ε-caprolactone) (PCL) was investigated as a function of PCL molecular mass by differential scanning calorimetry and optical microscopy. The components are miscible in the melt when oligomeric PCL (M_w = 1250) is blended with PBT, whereas only partial miscibility was found in mixtures with higher molecular mass (M_w = 10,000 and 50,000). The equilibrium melting point of PBT in the homopolymer and in blends with PCL was determined through a non-linear extrapolation of the T_m = f(T_c) curve. The PBT spherulitic growth rate and bulk crystallization rate were found to increase with respect to plain PBT in blends with PCL1250 and PCL10000, whereas addition of PCL50000 causes a reduction of PBT solidification rate. The crystallization induction times were determined by differential scanning calorimetry for all the mixtures through a blank subtraction procedure that allows precise estimation of the crystallization kinetics of fast crystallizing polymers. The results have been discussed on the basis of the Hoffman-Lauritzen crystallization theory and considerations on both the transport of chains towards the crystalline growth front and the energy barrier for the formation of critical nuclei in miscible and partially miscible PBT/PCL mixtures are widely debated.     

Intercalation of α,ω-alkyldiamines in layered α-zirconium phosphate and the inclusion behaviour of some of the intercalates obtained

The paper reports a study on the intercalation mechanism of NH₂(CH₂) _n NH₂ (withn=2, 4, 6, 8, 10) diamines in layered Zr(HOPO₃)₂·H₂O, performed by titrating the host with aqueous solutions of amines at 80°C. The intercalation reactions occur stepwise according to the ‘moving boundary’ model, with the formation of a number of intermediate intercalation compounds of formula Zr(HOPO₃)₂·xNH₂(CH₂) _n NH₂ (0<x<1) before obtaining the fully intercalated ones (x=1). For each diamine the batch titration curve and a diagram of the phases involved in the interaclation reaction are reported. Twenty-two intercalation compounds have been isolated and characterized by their composition, XRD patterns and thermal behaviour, and information on the disposition of the guests within the interlayer region have been derived. At full intercalation the diamines form a monolayer of extended molecules with their axis inclined at 58° to the plane of the sheet. The terminal amino groups are protonated by the —POH groups of the host, thus each diamine binds adjacent layers and, in a sense, transforms a layered structure into a framework structure that may have an accessible or potentially accessible porosity. The intercalation compound Zr(HOPO₃)₂·0.5NH₂(CH₂)₈NH₂ is indeed able to include polar molecules such as water and short chain alkanols.     

NO Release from trans-[Ru(NH3)4L(NO)]3+ Complexes Upon Reduction (L = 1-Methylimidazole or Benzoimidazole)

The synthesis, characterization and reactivity of trans-[Ru(NH₃)₄(L)NO](PF₆)₃(L = benzoimidazole or 1-methylimidazole in trans position to NO) are presented. ¹H-n.m.r. spectroscopy data indicate that the benzoimidazole and 1-methylimidazole ligands are coordinated to Ru^II through carbon and nitrogen, respectively. The nitrosyl stretching frequencies [(NO) > 1900 cm^–1] suggest that the coordinated nitrosyl has substantial NO⁺ character. The complexes undergo a single-electron reduction (E ⁰–0.245 versus NHE), which involves the coordinated nitrosyl. Dissociation of NO in the reduced species is facilitated by the 1-methylimidazole ligand, which is not observed for the benzoimidazole species. The complex with 1-methylimidazole does not suffer hydroxide attack on the NO⁺, at least at pH values lower than 11.