Use of decomposition of ion charge-state distributions for the interpretation of electrospray ionization mass spectra of bioorganic compound

The application of our method of the decomposition of mass spectral peak series due to independent unique modifications at a number of molecular sites to the analysis of electrospray ionization mass spectra containing multiply charged ions peaks of biopolymer solutions is considered. The capabilities and limitations of this approach are discussed. Data on the results mass spectrum decomposition of the chicken eggs lysozyme and pepsin at different acquisition conditions are presented. Based on these data, at least partial unfolding of the initially native lisozyme biomolecule in solution in the electrospray ion source can be supposed. The presence of pepsin positive ions with the number of charges significantly exceeding five basic amino acid residues can be explained by the localization of two positive solvent ions close to some initially negatively charged groups of acidic amino acid residues in the ion source.     

An approach to the structure and spectra of copper barbiturate trihydrate

In the neutral title complex [Cu(C₄N₂H₃)₂(H₂O)₃] or [Cu(BBR)₂(H₂O)₃] (BBR^– = Barbiturate), the Cu^II ion, in the slightly distorted square-pyramidal geometry, is coordinated by two O atoms of the two monodentate barbiturates and three O atoms of three water ligands. The average bond length of Cu—O (BBR^–) is 1.981(5) Å and the average bond length of Cu—O (H₂O) at the basal sites is 1.94(5) Å, i.e. much shorter than that of Cu—O (H₂O) [2.175(11) Å]. The crystal structure is characterized by an extensive network of hydrogen bonds in which each [Cu(BBR)₂(H₂O)₃] entity links to six adjacent [Cu(BBR)₂(H₂O)₃] by O(C=O) ··· H—O(H₂O) bonds. Tautomerism in the coordination process for BBR^– was found from the crystal structure and i.r. spectral analysis. The interaction of Cu^II and BBR^– in aqueous solution was also investigated by electronic spectra and electrochemical method. It was observed that the copper ion could not only form the [Cu(BBR)₂(H₂O)₃] complex in aqueous but also catalyze the decomposition of BBR^– at pH 1.1.     

Applications of molecular orbital theory to the interpretation of mass spectra. Prediction of primary fragmentation sites in organic molecules

Semi-empirical molecular orbital calculations have been carried out on the steroidal hormone estrone, both as a neutral molecule and the corresponding positively charge molecular ion. These calculations provide estimates of bond densities and net atomic charges, factors deemed important in past correlations of observed mass spectra with molecular structure. Calculated net charges appear to be unrelated to fragmentation processes. Calculated bond densities of the ground state molecular ion of estrone allow prediction of gross features of fragmentation. Bond densities of excited electronic states of the molecular ion may provide a basis for finer distinction among sites of initial bond cleavage, which is information crucial to rationalization of subsequent fragmentation of the molecular ion.     

Relationships observed in the structure and spectra of uracil and its 5-substituted derivatives

The effects on the geometry structure, atomic charges and vibrational wavenumbers of the main different substituents in the 5th position of the uracil ring were analysed, and relationships were established. The 5-monosubstituted derivatives studied were 5-XU (X = F, Cl, Br, I, CH₃, NH₂, NO₂). The geometry and vibrational wavenumbers were determined in these molecules. The FT-IR and Raman spectra were studied with the support of B3LYP calculations using several basis sets. Several general conclusions were underlined.     

The computer processing and interpretation of mass spectral information. I—The reduction of raw mass spectra to monoisotopic form

An algorithm of the AELITA program (Atomic-Element Identification) is described which enables both low and high resulution mass spectra to be processed to give the elemental composition and ion abundances of the mass spectra in monoisotopic form. The program has no limitations in respect of the elemental composition and spectrum complexity. The criterion for the choice of the most probable solution is based either on the accuracy of measurement of the peak abundances and/or the masses. The program is written in ALGOL, run on a BESM-6 computer, and occupies about 19K core memory.     

Applications of artificial intelligence for chemical inference—X : Intsum. A data interpretation and summary program applied to the collected mass spectra of estrogenic steroids

A method for systematic interpretation and summary of evidence found for all possible mass spectral fragmentations of a molecule or set of related molecules is described. The method is embodied in a computer program (INTSUM) which interprets, in terms of fragmentation processes, mass spectral data collected on known compounds. Utilizing high resolution mass spectra from 47 estrogenic steroids, the method is verified and new findings are discussed. Finally, the method is used to explore the fragmentations of equilenins and several acetate and benzoate ester derivatives.     

An empirical approach to the bond additivity model in quantitative interpretation of sum frequency generation vibrational spectra

Knowledge of the ratios between different polarizability betai'j'k' tensor elements of a chemical group in a molecule is crucial for quantitative interpretation and polarization analysis of its sum frequency generation vibrational spectroscopy (SFG-VS) spectrum at interface. The bond additivity model (BAM) or the hyperpolarizability derivative model along with experimentally obtained Raman depolarization ratios has been widely used to obtain such tensor ratios for the CH3, CH2, and CH groups. Successfully, such treatment can quantitatively reproduce the intensity polarization dependence in SFG-VS spectra for the symmetric (SS) and asymmetric (AS) stretching modes of CH3 and CH2 groups, respectively. However, the relative intensities between the SS and AS modes usually do not agree with each other within this model even for some of the simplest molecular systems, such as the air/methanol interface. This fact certainly has cast uncertainties on the effectiveness and conclusions based on the BAM. One of such examples is that the AS mode of CH3 group has never been observed in SFG-VS spectra from the air/methanol interface, while this AS mode is usually very strong for SFG-VS spectra from the air/ethanol interface, other short chain alcohol, as well as long chain surfactants. In order to answer these questions, an empirical approach from known Raman and IR spectra is used to make corrections to the BAM. With the corrected ratios between the betai'j'k' tensor elements of the SS and AS modes, all features in the SFG-VS spectra of the air/methanol and air/ethanol interfaces can be quantitatively interpreted. This empirical approach not only provides new understandings of the effectiveness and limitations of the bond additivity model but also provides a practical way for its application in SFG-VS studies of molecular interfaces.     

Emulsion polymerizations. I. A novel approach to the evaluation of the molecular weight distributions

A simple, probabilistic approach describing the number distribution of the molecular weight (MWD) of polymers formed by emulsion polymerization is presented. The radical populations of the reacting system are formally split into infinite, quickly convergent series of particularly tagged radical populations. These populations are characterized by the nature and the number of the state transitions of the associated latex particles. For each kind of single radical or radical pairs a distribution function is then defined. These functions can be specified on the basis of α_i and Q_i, the growth probabilities, within a latex particle in state i, of a single radical and a radical pair respectively. The overall MWDs are then given by summation over all the distributions of the radical populations and over all the allowed states. Only one set of ordinary differential equations (the Smith–Ewart equations) are involved in the mathematical formulation, single distribution functions being obtained by solving simple exponential-type integrals. In this paper, analytic solutions are presented for the zero-one, zero-one-two and general systems. Analogies and differences between our approach and previously reported treatments are critically discussed.     

A novel derivatization method for peptides to increase sensitivity and backbone fragmentation in liquid secondary-ion mass spectra.

Derivatization is used to increase both negative-ion sensitivity and positive-ion sequence information in the liquid secondary-ion mass spectra (LSIMS) of a series of peptides. The derivatization method involves acylation with pentafluorobenzoyl fluoride in a single-step reaction, and the reaction mixture is applied directly to the probe tip for analysis. Acylation takes place at the unprotected N-terminus, tyrosine, and lysine. The derivatives exhibit increased signal-to-noise ratio for [M-H]- ions, especially where there is not already an acidic amino acid residue in the peptide. In positive-ion LSIMS, the N-terminal group acts to retain the charge at the N-terminus, simplifying the fragmentation by producing N-terminal fragment ions. It also increases positive-ion fragmentation, sometimes very dramatically, making sequence determination more straightforward. The simplicity of the process, together with the enhancements it provides, make this a generally useful method for obtaining peptide structural information.     

Proximity effects in the electron impact mass spectra of aurones and related compounds

The principal ions in the electron impact mass spectra of a series of 6-methoxyaurones have been shown to be due to four separate reactions associated with proximity effects involving the phenyl group and the coumaran-one residue. A detailed study with labelled derivatives has been supplemented by a study of the vinylogue 2-cinnamylidene-6-methoxycoumaran-3-one and compounds in which the aurone phenyl group has been replaced by α-naphthyl, β-naphthyl and 9-anthryl.     

A study of the ortho effects and rearrangement processes in the mass spectra of 2-arylaminothiazine and -thiazoline derivatives

The behaviour of the title compounds under electron impact has been investigated using low and high resolution mass spectrometry and partial ¹⁵N and D labelling. A number of ions produced by rearrangement were observed. Abundant ions are formed by intramolecular ortho substitution reactions (cyclizations), as demonstrated by energetic and kinetic considerations and by studying the decomposition pathways of these ions. The ortho substitution processes involve loss or rearrangement of an ortho group of the aromatic ring.     

Approximate methods for the fast computation of EPR and ST-EPR spectra. I. A perturbation approach

The electron paramagnetic resonance (EPR) and saturation transfer electron paramagnetic resonance (ST-EPR) spectra of nitroxide spin labels are theoret     

A systematic approach for the generation and verification of structural hypotheses

During the process of molecular structure elucidation the selection of the most probable structural hypothesis may be based on chemical shift prediction. The prediction is carried out using either empirical or quantum‐mechanical (QM) methods. When QM methods are used, NMR prediction commonly utilizes the GIAO option of the DFT approximation. In this approach the structural hypotheses are expected to be investigated by scientist. In this article we hope to show that the most rational manner by which to create structural hypotheses is actually by the application of an expert system capable of deducing all potential structures consistent with the experimental spectral data and specifically using 2D NMR data. When an expert system is used the best structure(s) can be distinguished using chemical shift prediction, which is best performed either by an incremental or neural net algorithm. The time‐consuming QM calculations can then be applied, if necessary, to one or more of the ‘best’ structures to confirm the suggested solution. Copyright © 2009 John Wiley & Sons, Ltd.     

Photodegradation of poly(vinyl esters)—II. Volatile product formation and changes in the absorption spectra and molecular mass distributions

The vacuum photodegradation of poly(vinyl acetate) (PVAC) has been re-examined and the investigation extended to include poly(vinyl propanoate) (PVPR) and poly(ethylene-co-vinyl acetate) (PEVAC). Acid, aldehyde and carbon dioxide were the major products in the vacuum photodegradations of all three polymers. Comparison of the proportions of acetic acid formed from PEVAC and PVAC indicated that the photo-elimination of acid in the latter occurred as random independent events. Support for this conclusion has been obtained from a quantitative study of the ultraviolet spectrum of photodegraded PVAC. Changes in the molecular mass distributions of the soluble fractions and in the gel content on photolysis indicate that a balance exists between crosslinking and chain scission in PVAC while chain scission dominates in PEVAC.