Calculation of Franck-Condon factors including anharmonicity: simulation of the C2H4+X2B3u<--C2H4X1A(g) band in the photoelectron spectrum of ethylene

Our new simple method for calculating accurate Franck-Condon factors including nondiagonal (i.e., mode-mode) anharmonic coupling is used to simulate the C2H4+X2B3u<--C2H4X1A(g) band in the photoelectron spectrum. An improved vibrational basis set truncation algorithm, which permits very efficient computations, is employed. Because the torsional mode is highly anharmonic it is separated from the other modes and treated exactly. All other modes are treated through the second-order perturbation theory. The perturbation-theory corrections are significant and lead to a good agreement with experiment, although the separability assumption for torsion causes the C2D4 results to be not as good as those for C2H4. A variational formulation to overcome this circumstance, and deal with large anharmonicities in general, is suggested.     

Determination of ageing time of spirits in oak barrels using a headspace–mass spectrometry (HS-MS) electronic nose system and multivariate calibration

The aromatic composition of sugar cane spirits and, in general, of alcoholic beverages, is mainly influenced by the ageing process in wood barrels. There are several factors that affect the quality of the final aged product, but the time of the storage in the barrel is perhaps the most important one. Ageing time must therefore be controlled in order to detect counterfeits; however, this parameter is very difficult to control and, at present, there is no analytical method available to determine it. We propose a quantitative method for determining the ageing time of sugar cane spirits in oak barrels by using an electronic nose based on coupling directly a headspace sampler to a mass spectrometer (HS-MS), and multivariate calibration. The method developed is simple and provides, in 5 min, the ageing time of spirits with an accuracy of about 1 month.     

Wavelength-dependent properties of photodynamic therapy using hypericin in vitro and in an animal model

Wavelength effects in photodynamic therapy (PDT) with hypericin (HY) were examined in a C26 colon carcinoma model both in vitro and in vivo. Irradiation of HY-sensitized cells in vitro with either 550 or 590 nm caused the loss of cell viability in a drug- and light-dose-dependent manner. The calculated ratio of HY-based PDT (HY-PDT) efficiencies at these two wavelengths was found to correlate with the numerical ratio of absorbed photons at each wavelength. In vivo irradiation of C26-derived tumors, 6 h after intraperitoneal administration of HY (5 mg/kg), caused extensive vascular damage and tumor necrosis. The depth of tumor necrosis (d) was more pronounced at 590 than at 550 nm and increased when the light dose was raised from 60 to 120 J/cm2. The maximal depths of tumor necrosis (at 120 J/cm2) were 7.5+/-1.5 mm at 550 nm and 9.9+/-0.8 mm at 590 nm. Both values are rather high in view of the limited penetration of green-yellow light into the tissue. Moreover, the depth ratio, d590/d550 = 1.3 (P < 0.001), is smaller than expected considering the 2.2-fold lower HY absorbance and the 1.7-fold lower tissue penetration of radiation at 550 than at 590 nm. This finding indicates that in vivo the depth at which HY-PDT elicits tumor necrosis is not only determined by photophysical considerations (light penetration, number of absorbed photons) but is also influenced significantly by other mechanisms such as vascular effects. Therefore, despite the relatively short-wavelength peaks of absorption, our observations suggest that HY is an effective photodynamic agent that can be useful in the treatment of tumors with depths in the range of 1 cm.     

Comparison of liquid chromatography-mass spectrometry interfaces for the analysis of polar metabolites of benz[a]pyrene

 The performance of two liquid chromatography-mass spectrometry (LC/MS) interfacing techniques, thermospray (TSP) and atmospheric pressure chemical ionization (APCI), for the analysis of benzo[a]pyrene (BaP) metabolites (hydroxy, epoxy and quinone derivatives) was compared. Interface and detection parameters such as source temperature, eluent composition or flow rate were optimized using negative ion mode. In TSP, the main ions are mostly [M]^-, [M−H₂O]^- or [M+CH₃COO]^-, whereas APCI gives mainly the [M]^- and [M−H]^- ions. Quantification was carried out by flow injection. Calibration graphs were linear in the range of 10 ng to 1000 ng in TSP and 0.1 ng to 10 ng in APCI. Detection limits were in the range of 1 ng to 20 ng in TSP and 0.002 ng to 0.2 ng in APCI. The presence of BaP-1,6-dione, BaP-3,6-dione, and BaP-6,12-dione was confirmed in environmental samples of air particulate matter. Received: 6 January 1997/Accepted: 18 April 1997     

A molecular dynamics study of the pentacyclo-undecane cage amino acid tripeptide

In this paper, we report on the conformational profile of the pentacyclo-undecane (PCU) cage tripeptide carried out by molecular dynamics (MD) simulation using water as an explicit solvent. The MD solution phase studies carried on the model peptide analogues (A)=Ac–Ala–Ala–Ala–NHMe; (B)=Ac–Cage–Cage–Cage–NHMe; (C)=Ac–Ala–Cage–Ala–NHMe and (D)=Ac–Ala–Pro–Ala–NHMe, are used as a complimentary technique to the corresponding gas phase simulated annealing (SA) study previously carried out in our laboratory. No significant structural changes were observed over the MD trajectories. However, the results reported here provide further evidence that the (PCU) cage amino acid exhibits C_7eq, C_7aq, _R and _L conformations, and the theoretical results suggest that the PCU cage amino acid is a strong β-turn inducer. These results support the prediction that when the PCU cage residues are in the (i) and (i+2) positions, the β-turn can be extended in either direction to form anti-parallel β-pleated sheets, thereby forming the basis of the mechanism for the folding back of the chain in a cross-β-turn structure.     

Reduced Hamiltonians. II: The size-consistency of reduced Hamiltonians defined in model spaces

The link between the Absar-Coleman and the Valdemoro reduced Hamiltonian has been established. Further, a study of the size-consistency of approximations based on these Hamiltonians has been carried out. It is found that the energies obtained with reduced Hamiltonians that are defined in the full configuration interaction model spaces are not size consistent.     

Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In the post-genomic era, several projects focused on the massive experimental resolution of the three-dimensional structures of all the proteins of different organisms have been initiated. Simultaneously, significant progress has been made in the ab initio prediction of protein three-dimensional structure. One of the keys to the success of such a prediction is the use of local information (i.e. secondary structure). Here we describe a new limited proteolysis methodology, based on the use of unspecific exoproteases coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), to map quickly secondary structure elements of a protein from both ends, the N- and C-termini. We show that the proteolytic patterns (mass spectra series) obtained can be interpreted in the light of the conformation and local stability of the analyzed proteins, a direct correlation being observed between the predicted and the experimentally derived protein secondary structure. Further, this methodology can be easily applied to check rapidly the folding state of a protein and characterize mutational effects on protein conformation and stability. Moreover, given global stability information, this methodology allows one to locate the protein regions of increased or decreased conformational stability. All of this can be done with a small fraction of the amount of protein required by most of the other methods for conformational analysis. Thus limited exoproteolysis, together with MALDI-TOF MS, can be a useful tool to achieve quickly the elucidation of protein structure and stability.     

Reactivity of pyrrole pigments,part 15: On the oxidation of bilirubins and biliverdins

Summary Characteristic oxidation reactions of bilin-1,19-diones (biliverdins) and biladien-ac-1,19-diones (bilirubins) were reinvestigated. These include bromine and iodine oxidation of biliverdin IX, bilirubin IX and their Zn(II) complexes, the reaction described by Siedel (1941) of mesobilirubin XIII dimethyl ester with nitric acid (Gmelin reaction) and Smith's oxidation (1977) of etiobiliverdin IV using Tl triacetate and Pb tetra-acetate. For some of these reaction products new structures were assigned on the basis of their spectrometric data. These structures agreed with the expected reactivity pattern of biliverdins and bilirubins.

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Reaktivität von Pyrrolpigmenten, 15 Mitt.: Über die Oxidation von Bilirubinen und Biliverdinen

Zusammenfassung Einige bekannte Oxydationen von Bilin-1,19-dionen (Biliverdinen) und Biladien-ac-dionen (Bilirubinen) wurden neuerlich untersucht, und zwar die Brom- und Jodoxydation von Biliverdin IX und Bilirubin IX sowie der entsprechenden Zn(II)-Komplexe, die Reaktion des Dimethylesters von Mesobilirubin XIII mit HNO₃ (Gmelinreaktion; Siedel 1941) und Smith's Oxydation von Etiobiliverdin IV mit Thaliumtriacetat und Bleitetraacetat. Für einige Reaktionsprodukte wurden aufgrund spektroskopischer Daten neue Strukturen-konsistent mit dem bekannten Reaktionsverhalten von Biliverdinen und Bilirubinen-formuliert.

     

Oxidative addition of the ethane C-C bond to Pd. An ab initio benchmark and DFT validation study

We have computed a state-of-the-art benchmark potential energy surface (PES) for the archetypal oxidative addition of the ethane C-C bond to the palladium atom and have used this to evaluate the performance of 24 popular density functionals, covering LDA, GGA, meta-GGA, and hybrid density functionals, for describing this reaction. The ab initio benchmark is obtained by exploring the PES using a hierarchical series of ab initio methods [HF, MP2, CCSD, CCSD(T)] in combination with a hierarchical series of five Gaussian-type basis sets, up to g polarization. Relativistic effects are taken into account either through a relativistic effective core potential for palladium or through a full four-component all-electron approach. Our best estimate of kinetic and thermodynamic parameters is -10.8 (-11.3) kcal/mol for the formation of the reactant complex, 19.4 (17.1) kcal/mol for the activation energy relative to the separate reactants, and -4.5 (-6.8) kcal/mol for the reaction energy (zero-point vibrational energy-corrected values in parentheses). Our work highlights the importance of sufficient higher angular momentum polarization functions for correctly describing metal-d-electron correlation. Best overall agreement with our ab initio benchmark is obtained by functionals from all three categories, GGA, meta-GGA, and hybrid DFT, with mean absolute errors of 1.5 to 2.5 kcal/mol and errors in activation energies ranging from -0.2 to -3.2 kcal/mol. Interestingly, the well-known BLYP functional compares very reasonably with a slight underestimation of the overall barrier by -0.9 kcal/mol. For comparison, with B3LYP we arrive at an overestimation of the overall barrier by 5.8 kcal/mol. On the other hand, B3LYP performs excellently for the central barrier (i.e., relative to the reactant complex) which it underestimates by only -0.1 kcal/mol.