Towards SiC surface functionalization: an ab initio study

We present a microscopic model of the interaction and adsorption mechanism of simple organic molecules on SiC surfaces as obtained from ab initio molecular-dynamics simulations. Our results open the way to functionalization of silicon carbide, a leading candidate material for biocompatible devices.     

The kinetics of addition and fragmentation in reversible addition fragmentation chain transfer polymerization: An ab initio study

High-level ab initio calculations of the forward and reverse rate coefficients have been performed for a series of prototypical reversible addition fragmentation chain transfer (RAFT) reactions: R* + S=C(Z)SCH3 --> R-SC*(Z)SCH3, for R = CH3, with Z = CH3, Ph, and CH2Ph; and Z = CH3, with R = (CH3), CH2COOCH3, CH2Ph, and C(CH3)2CN. The addition reactions are fast (ca. 10(6)-10(8) L mol(-1) s(-1)), typically around three orders of magnitude faster than addition to the C=C bonds of alkenes. The fragmentation rate coefficients are much more sensitive to the nature of the substituents and vary from 10(-4) to 10(7) s(-1). In both directions, the qualitative effects of substituents on the rate coefficients largely follow those on the equilibrium constants of the reactions, with fragmentation being favored by bulky and radical-stabilizing R-groups and addition being favored by bulky and radical-stabilizing Z-groups. However, there is evidence for additional polar and hydrogen-bonding interactions in the transition structures of some of the reactions. Ab initio calculations were performed at the G3(MP2)-RAD//B3-LYP/6-31G(d) level of theory, and rates were obtained via variational transition state theory in conjunction with a hindered-rotor treatment of the low-frequency torsional modes. Various simplifications to this methodology were investigated with a view to identifying reliable procedures for the study of larger polymer-related systems. It appears that reasonable results may be achievable using standard transition state theory, in conjunction with ab initio calculations at the RMP2/6-311+G(3df,2p) level, provided the results for delocalized systems are corrected to the G3(MP2)-RAD level using an ONIOM-based procedure. The harmonic oscillator (HO) model may be suitable for qualitative "order-of-magnitude" studies of the kinetics of the individual reactions, but the hindered-rotor (HR) model is advisable for quantitative studies.     

Possible oxidative polymerization mechanism of 5,6-dihydroxyindole from ab initio calculations

The reactivity of 5,6-dihydroxyindole and its major dimers has been studied with the use of a recently proposed general-purpose reactive indicator (Anderson et al. J. Chem. Theory Comput. 2007, 3, 358-374) from ab initio density-functional theory calculations. Theoretical prediction has reasonably explained previously isolated oligomers up to tetramers. The oxidative polymerization is governed by the electron-transfer-controlled reaction. The electrostatic interaction plays a regioselective role in the reactant complex and/or intermediates. A monomer-dimer coupling is able to form trimers, while a part of it is prevented by the exchange repulsion, i.e., steric hindrance. Therefore, a dimer-dimer coupling is also able to form tetramers.     

A combined ab initio and photoionization mass spectrometric study of polyynes in fuel-rich flames

Polyynic structures in fuel-rich low-pressure flames are observed using VUV photoionization molecular-beam mass spectrometry. High-level ab initio calculations of ionization energies for C2nH2 (n=1-5) and partially hydrogenated CnH4 (n=7-8) polyynes are compared with photoionization efficiency measurements in flames fuelled by allene, propyne, and cyclopentene. C2nH2 (n=1-5) intermediates are unambiguously identified, while HC[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-CH=C=CH2, HC[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-CH=CH2 (vinyltriacetylene) and HC[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-CH[double bond, length as m-dash]CH-C[triple bond, length as m-dash]CH are likely to contribute to the C7H4 and C8H4 signals. Mole fraction profiles as a function of distance from the burner are presented. C7H4 and C8H4 isomers are likely to be formed by reactions of C2H and C4H radicals but other plausible formation pathways are also discussed. Heats of formation and ionization energies of several combustion intermediates have been determined for the first time.     

The effect of different catalytic chain transfer agents on particle nucleation and the course of the polymerization in ab initio batch emulsion polymerization of methyl methacrylate

The effect a Co(II) based catalytic chain transfer agent (CCTA) has on the course of the polymerization and the product properties of an emulsion polymerization is governed by the intrinsic activity and the partitioning behavior of the catalyst. The effect on the conversion time history, the molecular weight distribution and the particle size distribution is evaluated in batch emulsion polymerization of methyl methacrylate for three different CCTAs, which cover a range of intrinsic activities and partitioning behaviors. It was demonstrated that radical desorption from the particle phase to the aqueous phase preceded by chain transfer is the main kinetic event controlling the course of the polymerization and the product properties in terms of the particle size distribution. The experimental results show that the aqueous phase solubility of the CCTA is the key parameter controlling the course of the polymerization and the particle size distribution. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 1038–1048, 2010     

Empirical force-field and ab initio calculations on delocalized open chain cations

Force-field calculations are reported for large delocalized cations. The results for the geometries, heats of formation, and π-electron densities agree well with MP2(full)/6–31G^* ab initio calculations. Both methods give similar results for the distortion of the carbon skeletons of unsubstituted cations by hyperconjugating methyl groups. Because of the SCF treatment of π-interactions, the MMP2 force-field technique enables calculations of resonance energies in delocalized cations. The additional resonance stabilization produced by extending conjugation is directly related to the π-charge on the carbon at which a vinyl group is substituted. The good agreement of MMP2 results for nonbonded resonance effects in large delocalized cationic π-systems with ab initio data suggests that MMP2 can be used to study the influence of these interactions in cationic π-systems too large to be calculated by correlated ab initio methods. © 1997 by John Wiley & Sons, Inc.     

Mass spectrometric analysis of halogenated polymers

Controlled pyrolysis—electron impact mass spectrometry is a general method for the identification of polymers. It is shown here to be useful for the diagnosis of commercial halogen-containing polymers. The application of the technique both in a purely fingerprinting role, and by rationalising spectra in terms of structure and generalised thermal degradation pathways, is demonstrated. Inorganic oxides can have a secondary effect on degradative behaviour and spectral form.     

Mass spectrometric analysis of hydroxyproline glycans

Mass spectrometric techniques are presented which allow one to analyze the sugar part bound to hydroxyproline in hydroxyproline-rich glycoproteins. The hydroxyproline (Hyp) glycans obtained by alkaline hydrolysis give abundant [M + Na](+) ions by electrospray ionization which after collision-induced dissociation (CID) yield inter alia [Hyp - H + Na](+). In mixtures a parent ion scan of this species will indicate the various molecular species which can then be analyzed by MS(n) after CID in an ion trap, where successive losses of the sugar units are observed. Methylation techniques allow one to distinguish between linear and branched isomeric structures.     

Mass spectrometric analysis of protein phosphorylation

Phosphorylation is one of the most common posttranslational modifications of proteins in eukaryotic cells; it plays an important role in a wide spectrum of biological processes. This makes its study an important task for understanding cell functioning mechanisms. The aim of phosphoproteomics is a global mass spectral analysis of the phosphoprotein composition of cells, i.e., phosphoproteome. Nowadays, new effective methods are actively developed, which succeed not only in the detection of phosphorylated proteins but also in the determination of phosphorylated amino acid residues (phosphorylation sites) and in the quantitative comparison of phosphorylation among several specimens. Despite the analysis of protein phosphorylation remains a complicated problem, the available methods nowadays allow the detection of thousands of phosphorylation sites in the very same experiment. The present review covers the main methods utilized in contemporary phosphoproteomics: phosphoprotein and phosphopeptides enrichment as well as the mass spectrometric analysis of protein phosphorylation.     

Mass spectrometric analysis of porcine rhodopsin

Rhodopsin is the dim light photosensitive pigment of animals. In this work, we undertook to study the structure of rhodopsin from swine and compare it with bovine and rat rhodopsin. Porcine rhodopsin was analyzed using methodology developed previously for mass spectrometric analysis of integral membrane proteins. Combining efficient protein cleavage and high performance liquid chromatography separation with the sensitivity of mass spectrometry (MS), this technique allows the observation of the full protein map and the posttranslational modifications of the protein in a single experiment. The rhodopsin protein from a single porcine eye was sequenced completely, with the exception of two single-amino acid fragments and one two-amino acid fragment, and the gene sequence reported previously was confirmed. The posttranslational modifications, similar to the ones reported previously for bovine and rat rhodopsin, were also identified. Although porcine rhodopsin has a high degree of homology to bovine and rat rhodopsins and most of their posttranslational modifications are identical, the glycosylation and phosphorylation patterns observed were different. These results show that rhodopsin from a single porcine eye can be characterized completely by MS. This technology opens the possibility of rhodopsin structural and functional studies aided by powerful mass spectrometric analysis, using the fellow eye as an internal control.     

Dominant folding pathways of a peptide chain from ab initio quantum-mechanical simulations

Using the dominant reaction pathways method, we perform an ab initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of these systems, without resorting to an empirical representation of the molecular force field. It also allows to study rare transitions involving rearrangements in the electronic structure. By comparing the results of the ab initio simulation with those obtained by employing a standard force field, we discuss its capability to describe the nonequilibrium dynamics of conformational transitions.     

Mass spectrometric analysis of high-purity carbon dioxide

A high-vacuum, low-temperature, continuous separation technique has been used in conjunction with a mass spectrometer for the analysis of carbon dioxide containing vpm amounts of H(2), He, CH(4), Ne, N(2), CO, O(2) and Ar. The method relies on the condensation of carbon dioxide on the walls of a glass U-tube, cooled in liquid nitrogen, connected between an inlet and the ion source. A high-pressure carbon dioxide sample thus enters the inlet leak but only the impurities pass through the U-tube and reach the ion source, resulting in considerable gain in sensitivity and elimination of interference from carbon dioxide. The sensitivity of the method is several orders of magnitude better than the normal mass spectrometric method.     

Mass spectrometric analysis of carbon monoxide-nitrogen mixtures

A method for the analysis of gas mixtures containing both carbon monoxide and nitrogen, by using a single-focussing mass spectrometer, is described. It involves measurement of the mass spectrum of a gas sample before and after conversion of the carbon monoxide present into carbon dioxide by means of the Schütze catalyst.     

Mass spectrometric analysis of mixtures without separation

Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 6, p. 1450, June, 1989.