The hydrogen bonding properties of cytosine: a computational study of cytosine complexed with hydrogen fluoride, water, and ammonia

Density functional theory is used to study the hydrogen bonding pattern in cytosine, which does not contain alternating proton donor and acceptor sites and therefore is unique compared with the other pyrimidines. Complexes between various small molecules (HF, H(2)O, and NH(3)) and four main binding sites in (neutral and (N1) anionic) cytosine are considered. Two complexes (O2(N1) and N3(N4)) involve neighboring cytosine proton acceptor and donor sites, which leads to cooperative interactions and bidendate hydrogen bonds. The third (less stable) complex (N4) involves a single cytosine donor. The final (O2-N3) complex involves two cytosine proton acceptors, which leads to an anticooperative hydrogen bonding pattern for H(2)O and NH(3). On the neutral surface, the anticooperative O2-N3 complex is less stable than those involving bidentate hydrogen bonds, and the H(2)O complex cannot be characterized when diffuse functions are included in the (6-31G(d,p)) basis set. On the contrary, the anionic O2-N3 structure is the most stable complex, while the HF and H(2)O N3(N4) complexes cannot be characterized with diffuse functions. B3LYP and MP2 potential energy surface scans are used to consider the relationship between the water N3(N4) and O2-N3 complexes. These calculations reveal that diffuse functions reduce the conversion barrier between the two complexes on both the neutral and anionic surfaces, where the reduction leads to a (O2-N3) energy plateau on the neutral surface and complete (N3(N4)) complex destabilization on the anionic surface. From these complexes, the effects of hydrogen bonds on the (N1) acidity of cytosine are determined, and it is found that the trends in the effects of hydrogen bonds on the (N1) acidity are similar for all pyrimidines.     

Synthesis,structures and mass spectrometry of lanthanide nitrate complexes with tricyclohexylphosphine oxide

The complexes Ln(NO₃)₃(OPCy₃)₃(EtOH)_x (Cy = cyclohexyl, C₆H₁₁x = 0 for Ln = Eu, Er, x = 0.5 for Ln = La, Nd and x = 1 for Ln = Tm, Yb) have been prepared by reaction of lanthanide nitrates with Cy₃PO in ethanol. The single crystal X-ray structures for Ln = La, Nd, Eu, Er, Tm and Yb are reported. The structures for Ln = La–Eu have two molecules in the unit cell in which the nitrates are all bound as bidentate ligands. The unit cell for Ln = Er contains two distinct molecules; one with three bidentate nitrates and one with two bidentate and one monodentate nitrate. The Tm and Yb complexes have one molecule in the unit cell with two bidentate and one monodentate nitrate ligands. The monodentate nitrates are hydrogen bonded to ethanol in the Tm and Yb structures but not in the Er complex. The infrared spectra of the three classes of complex do not readily permit identification of the monodentate nitrate groups. Electrospray mass spectrometry indicates that redistribution/ionisation reactions occur in solution. Ions formed by solvolysis reactions are attributed to gas phase processes associated with the electrospray technique. Tandem mass spectrometry for the La, Ho and Yb complexes shows that in the gas phase loss of Cy₃PO is the sole fragmentation pathway for all but the Yb complex where the higher energy required for initial fragmentation leads to a more complex fragmentation pattern.     

Multi-residue method for rapid screening and confirmation of pesticides in crude extracts of fruits and vegetables using isocratic liquid chromatography with electrospray tandem mass spectrometry

A LC-MS-MS method capable of the quantitative determination of a range of pesticide residues present in crude extracts from a variety of fruit and vegetables has been developed. Isocratic LC conditions have been used in conjunction with electrospray ionisation tandem mass spectrometry to detect and identify up to 38 pesticides presented as various mixtures in different matrices. The utility of the method is demonstrated by the analysis of crude extracts, with no sample clean up, from grape, kiwi fruit, strawberry, spinach, lemon, peach and nectarine. Mean recoveries ranging from 63 to 96% with relative standard deviations < 20% were obtained for 30 of the 38 pesticides following analysis of organic produce fortified at concentrations between 0.01 and 0.8 mg/kg. Detected residues were quantified from interpolation against calibration data generated using matrix-matched standards that covered analyte concentration ranges between 0.005 and 0.8 microg/ml. Conditions suitable for the qualitative and quantitative confirmation of residues detected in samples are specified.     

SITE-DIRECTED MUTAGENESIS OF THE LH2 LIGHT-HARVESTING COMPLEX OF Rhodobacter sphaeroides: CHANGING βLys23 TO Gin RESULTS IN A SHIFT IN THE 850 nm ABSORPTION PEAK

The present study describes the construction of a Rhodobacter sphaeroides light-harvesting (LH2) mutant in which the charged residue βSLys23 is changed by site-directed mutagenesis to a Gin residue, and the characterization of the resulting mutant complex by a range of spectroscopic techniques. In the 77 K absorption spectrum of the mutant, the peak equivalent to the 850 nm peak in the wild-type membrane is blue-shifted by approximately 18 nm to 837 nm; except for this blue-shift, the 77 K. fluorescence excitation and emission spectra and the circular dichroism spectrum of the mutant are very similar to the equivalent spectra from the wild-type membranes, suggesting that the mutation βLys23 → Gin probably does not cause any major changes in the conformation or aggregation state of these membranes. Possible causes of the 18 nm blue-shift in the absorption spectrum are discussed.     

High-performance liquid chromatographic strategies for the determination and confirmation of anticoagulant rodenticide residues in animal tissues

A comprehensive approach to the analysis of anticoagulant rodenticide residues in animal tissues based on high-performance liquid chromatography (HPLC) has been developed. Residues of warfarin, coumatetralyl, difenacoum, brodifacoum, bromadiolone, diphacinone and chlorophacinone were extracted with chloroformacetone (1:1, v/v). Extracts were cleaned-up by an integrated gel permeation and adsorption chromatographic procedure which divided the rodenticides into two groups. Residues were then determined and confirmed using normal-phase, ion-pair and weak ion-exchange HPLC techniques. Ion-pair gradient separation resolved all seven rodenticides in a single chromatographic analysis. UV detection methods were employed for all seven rodenticides. Use of a diode array detection system permitted additional confirmation of residues down to 0.1 mg kg-1 by matching UV spectra and derivatives of spectra. Sensitive fluorescence detection was possible for the coumarin-based rodenticides but not for diphacinone and chlorophacinone. Post-column pH-switching fluorescence detection methods were shown to be superior to other methods of fluorescence detection of coumarin-based rodenticides. Recoveries from spiked liver tissue were around 90% at levels from 0.05 to 1 mg kg-1. Detection limits of around 0.002 mg kg-1 for most rodenticides and of 0.01 mg kg-1 for warfarin could be achieved with animal tissue extracts.     

Mapping the binding site topology of amyloid protein aggregates using multivalent ligands

A key process in the development of neurodegenerative diseases such as Alzheimer''s and Parkinson''s diseases is the aggregation of proteins to produce fibrillary aggregates with a cross β-sheet structure, amyloid. The development of reagents that can bind these aggregates with high affinity and selectivity has potential for early disease diagnosis. By linking two benzothiazole aniline (BTA) head groups with different length polyethylene glycol (PEG) spacers, fluorescent probes that bind amyloid fibrils with low nanomolar affinity have been obtained. Dissociation constants measured for interaction with Aβ, α-synuclein and tau fibrils show that the length of the linker determines binding affinity and selectivity. These compounds were successfully used to image α-synuclein aggregates in vitro and in the post-mortem brain tissue of patients with Parkinson''s disease. The results demonstrate that multivalent ligands offer a powerful approach to obtain high affinity, selective reagents to bind the fibrillary aggregates that form in neurodegenerative disease.

Multivalent ligands offer a powerful approach to obtain high affinity reagents to bind the aggregates that form in neurodegenerative disease. Selectivity for different proteins was achieved by using different linkers to connect the head groups.     

The relationship between the Ritz variational method and Frobenius's method of solving Schrödinger's equation

The solution of a linear homogeneous differential equation (in particular the Schrödinger equation) by expansion of the solutions (wave functions) in a discrete complete set of function is considered. The coefficients of the expansion are determinable by either the Ritz variational (integral) method, or by a generalisation of Frobenius's (non-integral) method. Each method leads to an infinite matrix eigenvalue equation. It is shown that the integral and non-integral matrix equations are related by the overlap matrix of the set of basis functions. The effects of truncating the infinite matrices to finite order are described. A hybrid method of transformation to a matrix representation is proposed, which employs some techniques from each of the original methods.

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Zusammenfassung Die Lösung einer linearen homogenen Differentialgleichung (besonders der Schrödinger-Gleichung) durch Entwicklung der Lösungen (Wellenfunktionen) nach einem diskreten vollständigen Satz von Funktionen wird untersucht. Die Entwicklungskoeffizienten sind entweder durch die Variations-Methode (Integral-Methode) oder durch Verallgemeinerung der Methode von Frobenius (Methode ohne Integrale) bestimmbar. Beide Methoden führen zur einer unendlichen Matrix-Eigenwert-Gleichung. Es wird gezeigt, daß die Matrizengleichungen der beiden Verfahren durch die Überlappungsmatrix des Satzes von Basisfunktionen in Beziehung stehen. Es werden die Effekte beschrieben, die sich ergeben, wenn die Matrizen von unendlicher auf endliche Ordnung reduziert werden. Eine Hybridmethode zur Transformation in eine Matrixdarstellung wird vorgeschlagen, die einige Rechenoperationen aus jeder der Originalmethoden anwendet.

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Résumé On considère la résolution d'une équation différentielle linéaire homogène (en particulier l'équation Schrödinger) en développant les solutions (fonctions d'ondes) dans un groupe discret complet de fonctions. Les coefficients du développement peuvent être déterminés par la méthode de la variation de Ritz (intégral) ou par une généralisation de la méthode de Frobenius (non-intégral). Chaque méthode mène à une équation infinie matrice eigenvalue. On montre que les équations matrice, intégrales et non-intégrales, sont reliées par la matrice à recouvrement du groupe des fonctions fondamentales. On décrit les effects de tronquer les matrices infinies en ordre limité. On présente une méthode hybride de transformation à une représentation de matrice, qui utilise des techniques de chacune des méthodes originales.

     

An NMR study of some substituted 1,5-benzodiazepines and 1,5-benzothiazepines

The ¹H NMR spectra of a series of substituted 1,5-benzodiazepines and thiazepines are analysed by the LAOCN3 fitting program. The saturated molecules appear to exist in puckered chair conformations. The effect of increasing methyl substitution is a reduction in the amount of puckering with a flattening of the chair. Symmetrical substitution of the heterocyclic rings allows a ready inversion at room temperature whereas asymmetrical substitution stabilises the least hindered conformation. Variable temperature measurements are reported.     

Convergence rates of a global optimization algorithm

Second order conditions for the (pseudo-) convexity of a function restricted to an affine subspace are obtained by extending those already known for functions on ⁿ . These results are then used to analyse the (pseudo-) convexity of potential functions of the type introduced by Karmarkar.This research was completed while the first author was on sabbatical leave at the Département d'Informatiques et de Recherche Opérationelle, Université de Montréal, and supported by NSERC (grant Q015807). This research was also supported by NSERC (grants A8312 and A5408) and la Coopération franco-québécoise (project 20-02-13).     

A note on the numerical evaluation of finite integrals of oscillatory functions

A method is described for the numerical evaluation of integrals of the form ∫ _?1 ¹ f(x)K(m,x)dx, wheref(x) is smooth in [?1,1], whileK(m,x) is highly oscillatory for large values ofm.