Showing papers in "Canadian Journal of Chemistry in 2004"

New applications of the genetic algorithm for the interpretation of high-resolution spectra

Abstract: Rotationally resolved electronic spectroscopy yields a wealth of information on molecular structures in different electronic states. Unfortunately, for large molecules the spectra get rapidly very congested owing to close-lying vibronic bands, other isotopomers with similar zero-point energy shifts, or large-amplitude internal motions. A straightforward assignment of single rovibronic lines and, therefore, line position assigned fits are impossible. An alternative approach is unassigned fits of the spectra using genetic algorithms (GAs) with special cost functions for evaluation of the quality of the fit. This paper decribes the improvements we established on the GA method discussed before (J.A. Hageman, R. Wehrens, R. de Gelder, W.L. Meerts, and L.M.C. Buydens. J. Chem. Phys. 113, 7955 (2000)). In particular, we succeeded in obtaining a dramatic reduction in computing time that made it possible to apply the GA process in a large number of cases. A completely automated fit of a rotationally resolved laser-induced fluorescence spectrum without any prior knowledge of the molecular parameters can now be performed in less than 1 h. We demonstrate the power of the method on a number of typical examples such as very dense rovibronic spectra of van der Waals clusters and overlapping spectra due to different isotopomers. The discussed results demonstrate the extreme power of the GA in automated fitting and assigning of complex spectra. It opens the road to the analysis of complex spectra of biomolecules and their building blocks.

The synthesis of some mechanistic probes for sialic acid processing enzymes and the labeling of a sialidase from Trypanosoma rangeli

Abstract: Sialyl hydrolases, trans-sialidases, and sialyl transferases are biologically important enzymes that are responsible for the incorporation and removal of sialic acid residues, which decorate many c

An intercomparison of measured pressure-broadening and pressure-shifting parameters of water vapor

Abstract: The present work is an intercomparison of experimental results on the pressure broadening and pressure shifting of water vapor absorption lines. The work focuses on application to the Earth's atmosphere; hence measurements of nitrogen, oxygen, air, and H2O as the buffer, or perturbing gas, were considered. The literature was searched and over 100 papers found. The data, measured half-widths, their temperature dependence, and the line shifts, were taken and databases created for each perturbing gas. The databases were reordered, grouping data for rovibrational transitions, and intercomparisons of the measurements made. Trends in the data, relationships between the data sets, and dependences on temperature and quantum numbers were investigated. The data were averaged and an estimated uncertainty determined. The averaged data sets are evaluated with respect to the need of the spectroscopic and remote sensing communities. Based on these studies, recommendations for new measurements are made.Key words: water v...

Photogeneration of 1,5-naphthoquinone methides via excited-state (formal) intramolecular proton transfer (ESIPT) and photodehydration of 1-naphthol derivatives in aqueous solution

Abstract: The photochemistry of naphthols 1, 2, 4, 5 and 9, and phenol 10 has been studied in aqueous solution with the primary aim of exploring the viability of such compounds for naphthoquinone and quinone...

Concerning the mechanism of the Friedländer quinoline synthesis

Abstract: Detailed experiments regarding the mechanism of the Friedlander synthesis of quinolines from o-aminobenzaldehydes and simple aldehydes or ketones are described. Under the basic or acidic conditions...

Azabenzenes (azines) The nitrogen derivatives of benzene with one to six N atoms: Stability, homodesmotic stabilization energy, electron distribution, and magnetic ring current; a computational study

Abstract: The twelve azabenzenes — the species formed by replacing CH groups of benzene by N — were examined computationally (with emphasis on the six contiguous-nitrogen species). MP2(fc)/6-31G*, B3LYP/6-31G*, CCSD(T)/6-31G*//MP2(fc)/6-31G*, and G3(MP2) calculations were used to probe kinetic and thermodynamic stabilities, homodesmotic ring-opening energies, electron distribution (bond orders and lengths, Bird index), and NICS values, primarily to discern where the transition occurs from reasonably stable to highly fragile species. Some azabenzenes with three and those with four or more nitrogens are thermodynamically unstable, but kinetic stabilities indicated that, with the possible exception of hexaazabenzene, all the azabenzenes should be isolable, although some with four nitrogens might decompose at room temperature, and pentaazabenzene would require matrix isolation techniques. Although homodesmotic ring-opening reactions showed an almost monotonic decrease in the stability of the cyclic relative to the open...

Molecular tectonics Use of urethanes and ureas derived from tetraphenylmethane and tetraphenylsilane to build porous chiral hydrogen-bonded networks

Abstract: Tetraphenylmethane, tetraphenylsilane, and simple derivatives with substituents that do not engage in hydrogen bonding typically crystallize as close-packed structures with essentially no space ava...

Distribution of oxides on iron materials used for remediation of organic groundwater contaminants Implications for hydrogen evolution reactions

Abstract: The distribution of oxides on commercial iron materials used for remediation of organic groundwater contaminants was studied using confocal Raman microspectroscopy. Raman microprobe mapping experim...

Highly accurate transition frequencies in the H2 Lyman and Werner absorption bands

Abstract: The transition frequencies of low-J excitation lines in the B1Σu+– X1Σg+,(ν′,0) Lyman bands have been measured for ν′ = 2–18 and in the C1Πu–X1Σg+,(ν′,0) Werner bands for ν′ = 0–4, using a narrow-b...

Identification of glycerophospholipids in rapeseed, olive, almond, and sunflower oils by LC-MS and LC-MS-MS

Abstract: HPLC employing a thermostatted Lichrospher 100 diol column was used to separate mixtures of glycerophospholipids of rapeseed, olive, almond, and sunflower oils. Elution was performed with a binary ...

Biobleaching chemistry of laccase-mediator systems on high-lignin-content kraft pulps

Abstract: A high-lignin-content softwood kraft pulp was reacted with laccase in the presence of 1-hydroxybenzotriazole (HBT), N-acetyl-N-phenylhydroxylamine (NHA), and violuric acid (VA). The biodelignification response with violuric acid was superior to both 1-hydroxybenzotriazole and N-acetyl-N-phenylhydroxylamine. NMR analysis of residual lignins isolated before and after the biobleaching treatments revealed that the latter material was highly oxidized and that the magnitude of structural changes was most pronounced with the laccase – violuric acid biobleaching system. An increase in the content of carboxylic acid groups and a decrease in methoxyl groups were noted with all three laccase-mediator systems. The oxidation biobleaching pathway is directed primarily towards noncondensed C5 phenolic lignin functional structures for all three laccase-mediated systems. The laccase – violuric acid system was also reactive towards C5-condensed phenolic lignin structures.Key words: laccase, mediator, lignin, pulp, biobleac...

Total synthesis of ()-xyloketal D and its enantiomer Confirmation of absolute stereochemistry

Abstract: The total synthesis of (–)-xyloketal D and its enantiomer have been achieved by the reaction of an ortho-quinone methide with (4R)- and (4S)-4,5-dihydro-2,4-dimethylfuran via a diastereoselective i...

A new family of monocyclopentadienyl organoscandium bis-alkyls supported by a bulky trialkylphosphine oxide ancillary

Abstract: Treatment of the oligomeric compound [Cp*ScCl2]n (Cp* = C5Me5) with tri-tert-butylphosphine oxide in THF leads to the monocyclopentadienyl scandium dichloride [Cp*(t-Bu3P=O)ScCl2] as a monomeric, T...

A study of the A2Π/B2Σ+ X2Σ+ band systems of calcium monohydride (CaH) using a supersonic molecular beam source and laser-induced fluorescence detection

Abstract: The high-resolution laser-induced fluorescence spectrum of a molecular beam sample of calcium monohydride (CaH) in the region of the strongly overlapped (1,0) A2Π – X2Σ+ and (0,0) B2Σ+ – X2Σ+ band...

Solubility of crystalline nonelectrolyte solutes in organic solvents Mathematical correlation of 2-methoxybenzoic acid and 4-methoxybenzoic acid solubilities with the Abraham solvation parameter model

Abstract: The Abraham solvation parameter model is used to calculate the numerical values of the solute descriptors for 2-methoxybenzoic acid and 4-methoxybenzoic acid from experimental solubilities in organic solvents. The mathematical correlations take the form of log(CS/CW) = c + eE + sS + aA + bB + vV log(CS/CG) = c + eE + sS + aA + bB + lL where CS and CW refer to the solute solubility in the organic solvent and water, respectively, CG is a gas phase concentration, E is the solute excess molar refraction, V is the McGowan volume of the solute, A and B are measures of the solute hydrogen-bond acidity and hydrogen-bond basicity, S denotes the solute dipolarity–polarizability descriptor, and L is the logarithm of the solute gas phase dimensionless Ostwald partition coefficient into hexadecane at 298 K. The remaining symbols in the above expressions are known solvent coefficients, which have been determined previously for a large number of gas–solvent and water–solvent systems. The Abraham solvation parameter mode...

Infrared photodissociation spectroscopy of Si+(CO2)n and Si+(CO2)nAr complexes Evidence for unanticipated intracluster reactions

Abstract: Si+(CO2)n and Si+(CO2)nAr ion–molecule complexes were produced by laser vaporization in a pulsed supersonic expansion. The ions were mass-selected in a reflectron time-of-flight spectrometer and st...

Is acyl migration to the aglycon avoidable in 2-acyl assisted glycosylation reactions?

Abstract: This report unequivocally separates orthoester formation from acyl transfer for the first time and indicates possible routes to eliminate 2-O-acyl transfer during glycosylation reactions. Experimental evidence is shown that acyl transfer from 2-O-acyl-3,4,6-tri-O-benzyl-D-galactopyranose-derived glycosyl donors decreases in the order formyl > acetyl > pivaloyl. The 2-O-benzoyl derivatives are more variable, in some cases transferring easily, and in others not at all. Density functional theory (DFT) calculations of the structure and energetics of dioxolenium ion and related intermediates suggest that a proton transfer pathway from the nucleophile to O-2 provides an explanation for the observed trends. These DFT calculations of the proton transfer pathway support a mechanism in which a relay molecule is involved. Further DFT calculations used a constraint based on linear combinations of six bond lengths to establish the sequence of bond breaking and bond forming. The calculated anomeric carbon to former car...

Chemical adsorption of salicylate on silver - A systematic approach to the interpretation of surface-enhanced vibrational spectra

Abstract: In this work, surface-enhanced vibrational spectroscopy and normal vibrational spectroscopy as well as density functional theory (DFT) computational methods have been employed to investigate the na...

Green preparation of quinoline derivatives through FeCl3.6H2O catalyzed friedlander reaction in ionic liquids

Abstract: The preparation of substituted quinoline derivatives through a Friedlander condensation reaction utilizing the ionic liquid [bmim][BF4] as the reaction medium and iron chloride hexahydrate (FeCl3·6...

Surface-enhanced Raman spectroscopy with a laser pointer light source and miniature spectrometer

Abstract: The initial steps toward a miniature, field portable sensor based on surface-enhanced Raman spectroscopy (SERS) are presented. It is demonstrated that a low-cost miniaturized Raman system can be us...

Investigation of thermochromism in a series of side-chain, liquid-crystalline, azobenzene-containing polymers

Abstract: The thermochromic properties of a series of liquid crystalline polymethacrylates, containing azobenzene side-chains with variable spacer lengths, were investigated. Annealing the amorphous polymer thin films above the glass transition temperature results in a rearrangement of the azobenzene moieties, causing a hypsochromic shift in the electronic absorption spectra. A detailed investigation of the spectral shift was performed by in situ UV–vis spectroscopy and indicated the formation of H-type aggregates by the side-chain chromophores above the glass transition temperature. The rate at which the hypsochromic shift occurs is faster for polymers with shorter spacers since their high glass transition temperature results in a higher thermal energy during the thermochromic effect. Experimentally determined activation energies show that the aggregation occurs primarily due to side-chain relaxation (β-relaxation) and main-chain relaxation (α-relaxation). Further annealing above the isotropization temperature res...

Comparison of the free radical scavenger activities of quercetin and rutin An experimental and theoretical study

Abstract: Natural radical scavengers have recently received considerable interest owing to the role of free radicals in causing oxidative stress in living organisms. Flavonoids constitute one of the most important families of molecules with antioxidant activities, a characteristic associated with the presence in their structure of hydroxyl groups bound to aromatic rings. Quercetin is a potent antioxidant whose high reactivity could be associated with the presence of the OH group in the C ring. To address the role of this group in quercetin's free radical scavenging capacity, we have carried out experimental determinations and theoretical calculations regarding the reactivity of quercetin and rutin. The reactivity of both compounds towards free radicals was assessed employing the radical anion 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonate) and peroxyl radicals. These measurements indicate that quercetin is more reactive and has more reactive centers than rutin, suggesting that the extra OH group located in the C ...

In situ ATR-SEIRAS study of adsorption and phase formation of trimesic acid on Au(111-25 nm) film electrodes

Abstract: The adsorption and phase formation of 3 mmol L–1 trimesic acid (TMA) on Au(111-25 nm) film electrodes in contact with aq. 0.1 mol L–1 HClO4 electrolyte have been investigated by in situ ATR-SEIRAS, cyclic voltammetry, chronoamperometry, and STM measurements. Depending on the applied electrode potential, TMA molecules assemble in three distinctly different 2D ordered adlayers. In the range 0.10 < E < 0.50 V, planar-oriented molecules form an open ring honeycomb pattern (phase I) stabilized by directional hydrogen bonds. Interfacial water molecules are being replaced. A close-packed, physisorbed adlayer II forms at higher potentials in the range 0.58 < E < 0.75 V. Further increase of the electrode potential causes an orientation change. An initially disordered phase transforms into an ordered, stripe-like chemisorbed adlayer III of perpendicularly oriented TMA molecules (0.90 < E < 1.20 V). One carboxylate group per molecule is bound to the electrode surface, while the two other protonated carboxyl groups a...

Fermi resonance and conformation in glycolaldehyde particles

Abstract: The infrared spectra of gas-phase glycolaldehyde and small glycolaldehyde particles both exhibit a split carbonyl band around 1730 cm–1. Ab initio calculations show that this splitting can be traced back to a Fermi resonance involving the C=O-stretching band and the first overtone of the C–C-stretching band. The analysis of this resonance leads to detailed information about the conformation of glycolaldehyde in the particles. The results can be summarized as follows. (i) In the particles, monomers with OCCO dihedral angles of 0° and CCOH dihedral angles around 50° are strongly preferred. (ii) The intramolecular hydrogen bond observed in the gas phase is partly replaced by intermolecular hydrogen bonds. (iii) The calculated infrared spectrum and the results from the Fermi resonance analysis are in good agreement with the formation of long chains of monomeric glycolaldehyde. This is in contrast to the solid bulk, which consists of chemically bound dimers. Key words: Fermi resonance, conformation, glycolalde...

2004 Bader Award LectureMetal-ion-catalyzed acyl and phosphoryl transfer reactions to alcohols: La3+-promoted alcoholysis of activated amides, carboxylate esters, and neutral organophosphorus esters

Abstract: Unlike metal-ion-catalyzed hydrolysis processes, metal-ion-catalyzed methanolysis processes have received scant attention in the literature particularly from the standpoint of mechanistic studies. ...

The titanocene-catalyzed reduction of acetamides to tertiary amines by PhMeSiH2

Abstract: A variety of acetamide derivatives are reduced in excellent yields to tertiary amines by PhMeSiH2 in the presence of Cp2TiX2 (X = F or Me) catalysts. The reactions are very clean at 80 °C. At room ...

Taxol interaction with DNA and RNA: Stability and structural features

Abstract: Taxol (paclitaxel) is an anticancer drug that interacts with microtubule proteins in a manner that catalyzes their formation from tubulin and stabilizes the resulting structures. However, in the hu...

Total synthesis of ()-pateamine A, a novel immunosuppressive agent from Mycale sp

Abstract: A convergent synthesis of the unique thiazole-containing polyene bis-lactone pateamine A (1) isolated from the marine sponge Mycale sp is described. The synthesis features the ubiquitous Stille sp2...

Identification of complexes involving toxic heavy metals with amino acid ligands by electrospray ionization mass spectrometry

Abstract: Electrospray ionization mass spectra (ESI-MS) of reaction mixtures containing ions of the heavy metals, cadmium, mercury, thallium, lead, and bismuth with each of the naturally occurring amino acids allows for definitive identification of monocationic complexes in the gas phase Prominent m/z peaks are assigned to ions of the type [E(Am) – xH]+ (x = 0, 1, 2), [E(Am)2 – xH]+ (x = 0, 1, 2), [E2(Am) – xH]+ (x = 1, 2, 3), and (or) [E2(Am)2 – xH]+ (x = 1, 3, 5) for all amino acids studied (Am) with all metals studied (E = Cd, Hg, Tl, Pb) except bismuth, which shows complexes with only seven amino acids (Am = His, Thr, Met, Cys, Hcys, Asn, Gln) The results demonstrate the potential application of ESI-MS as a versatile and efficient approach to study toxic heavy metals in biological systemsKey words: heavy metals, amino acids, electrospray ionization mass spectrometry

Methods for Calculating Vibrational Energy Levels

Abstract: This article reviews new methods for computing vibrational energy levels of small polyatomic molecules. The principal impediment to the calculation of energy levels is the size of the required basi...