Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields

An intramolecular NEMO potential is presented for the N-formylglycinamide molecule together with an intermolecular potential for the N-formylglycinamide-water system. The intramolecular N-formylglycinamide potential can be used as a building block for the backbone of polypeptides and proteins. Two intramolecular minima have been obtained. One, denoted as C5, is stabilized by a hydrogen bonded five member ring, and the other, denoted as C7, corresponds to a seven membered ring. The interaction between one water molecule and the N-formylglycinamide system is also studied and compared with Hartree-Fock SCF calculations and with the results obtained for some of the more commonly used force fields. The agreement between the NEMO and SCF energies for the complexes is in general superior to that of the other force fields. In the C7 region the surfaces obtained from the intramolecular part of the commonly used force fields are too flat compared to the NEMO potential and the ab initio calculations. We further analyze the possibility of using a charge distribution obtained from one conformation to describe the charge distribution of other conformations. We have found that the use of polarizabilities and generic dipoles can model most of the changes in charge density due to the different geometry of the new conformations, but that one can expect additional errors in the interaction energies that are of the order of 1 kcal/mol.     

The cyano nitronyl nitroxide radical: experimental and theoretical evidence for the fourth case of the McConnell-I mechanism

The nitronyl nitroxide 2-cyano-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (1) crystallises in the tetragonal P42(1)m space group with a=7.4050(7), c=8.649(1) A. In the crystal the molecules form layers parallel to the ab plane in which they are orthogonal to each other. In the layers there are close contacts, 2.953(2) A, between the NO groups and the bridging carbon atoms of the O-N-C-N-O fragment of neighbouring radicals. The calculated spin density shows a positive population mainly and equally localised on the NO groups and small but significant negative spin densities on the bridging carbon atom and the cyano nitrogen. Absorption spectra show temperature-dependent transitions related to the magnetic behaviour. The temperature dependence of the magnetic susceptibility in the range 2-300 K reveals that couplings between the radicals are antiferromagnetic, and is interpreted by considering a two-dimensional square array of spin S=1/2 antiferromagnetically coupled (J=-10 cm(-1) and g=2.01). This is interpreted as an exchange coupling through close contact between positive and negative spin densities in orthogonal orbitals on oxygen and carbon atoms, respectively.     

On describing the steady absorption of brownian particles by a restricted random walk

This paper is concerned with idealizing brownian motion as a random walk, using the diffusion equation, and finding the boundary condition at an absorbing surface - all with an eye towards chemical kinetics. Three models of random walk (due to Smoluchowski, Fermi, and Lorentz) are considered, and it is concluded that the lorentzian model is the most appropriate.     

Topographical properties of polymer films deposited in capillaries for electrophoretic separations of large organic molecules

Topography and thickness of hydrophilic polymer coatings of fused-silica capillaries for capillary electrophoresis (CE) were investigated using atomic force microscopy (AFM), scanning electron microscopy (SEM), and profilometry. Three hydrogels, poly(2-hydroxyethyl methacrylate) [poly(HEMA)], poly(diethylene glycol monomethacrylate) [poly(DEGMA)], and poly(triethylene glycol monomethacrylate) [poly(TEGMA)], were deposited using two procedures, either by simple physical sorption of the polymers, or by derivatization of the capillary wall surface with glycidyl methacrylate (EPMA) followed by polymerization of the appropriate monomers. The performance of the modified capillaries was tested under CE conditions (decrease in the electroosmotic flow, EOF dependence on pH, separation of milk and standard proteins). It has been found that the most important property of the polymer coating is its thickness, whereas its topography and the degree of its hydrophobicity are less significant. Film deposition by physical adsorption is preferable to polymerization on the derivatized surface.     

Photoinitiated carbonylation with [(11)C]carbon monoxide using amines and alkyl iodides

Photoinitiated radical carbonylation with [(11)C]carbon monoxide at low concentration was employed in syntheses of carbonyl-(11)C-labeled amides using alkyl iodides and amines as precursors. Eleven (11)C-amides were synthesized in up to 74% decay-corrected radiochemical yields with reaction times of 400 s and with up to 95% conversion of carbon monoxide. Starting with 26.3 GBq of [(11)C]carbon monoxide, 10.6 GBq of 1-cyclohexane [(11)C]carbonyl-4-phenyl-piperazine (15) was obtained within 35 min from the end of bombardment (33 microA) and with a specific radioactivity of 192 GBq/micromol at the same time point. The influence of solvents was investigated. The described procedure extends the range of accessible labeling methods. The method may also be useful for preparation of (13)C- and (14)C-substituted compounds.     

Hyperfine structure of Mn II by fast ion beam-laser spectroscopy

We report the first measurements of the hyperfine splitting of the fine structure levels 3d ⁵'4s a ⁵ S ₂ and 3d ⁵ 4p z ⁵ P _1,2,3 ⁰ in singly ionised manganese in a collinear fast ion beam-laser experiment. The ions are excited by the intracavity frequency doubled output of a ring dye laser. The observed linewidth is sufficiently narrow to identify all hyperfine components of each fine structure level.     

Di-2-pyridylmethylamine-based palladium complexes as new catalysts for Heck,Suzuki, and Sonogashira reactions in organic and aqueous solvents

A new palladium-dipyridylmethylamine complex is an excellent catalyst for C-C bond-forming processes such as the Heck, Suzuki, and Sonogashira reactions in organic and aqueous solvents under homogeneous conditions. [reaction: see text]     

Determination of dopamine and its metabolites in small volumes of rat brain dialysates using small-bore liquid chromatography with electrochemical detection

A miniaturized liquid chromatographic system with electrochemical detection (LC-ED) was developed and applied to the analysis of dopamine and its metabolites in dialysate samples collected from the rat brain in vivo. An existing LC-ED system was down-scaled using a 1 mm I.D. small-bore column operated at a reduced flow-rate and with an injection volume of 1 microliter. With the small-bore system the limit of detection for dopamine of ca. 0.06 pg was almost 50 times less than with the conventional system, which represents a two-fold improvement in concentration sensitivity. Miniaturization was accomplished with negligible loss in resolution by using a conventional commercial amperometric detector with minor modifications. The results indicate that a number of useful advantages could be realized by the combination of this small-bore LC-ED system and the in vivo brain dialysis method.     

Mass spectrometric analysis of androstan-17β-ol-3-one and androstadiene-17β-ol-3-one isomers

Mass spectrometric identification and characterization of steroids using electrospray ionization and tandem mass spectrometry has advantages in drug testing and doping control analysis attributable to limitations of gas chromatography followed by electron ionization mass spectrometry. Steroids with an androstadiene-17beta-ol-3-one nucleus and double bonds located either at C-1 and C-4, C-4 and C-9, or C-4 and C-6 were used to determine characteristic fragmentation pathways. Diagnostic dissociation routes are proposed using deuterium labeling, MS3 experiments, and analyses of structurally closely related compounds. Steroids such as boldenone (androst-1,4-diene-17beta-ol-3-one) produced characteristic product ions at m/z 121, 135, and 147. Compounds with double bonds at C-4 and C-9 generated abundant product ions at m/z 145 and 147. Conjugated double bonds at C-4 and C-6 gave rise to an intense and characteristic signal at m/z 133. Stereochemical differentiation between 5alpha- and 5beta-isomers of androstan-17beta-ol-3-ones was possible because of significant differences in relative abundance of product ions generated by elimination of acetone from alpha,beta-saturated 3-keto steroids.     

Protein identification platform utilizing micro dispensing technology interfaced to matrix-assisted laser desorption ionization time-of-flight mass spectrometry

An integrated protein microcharacterization/identification platform has been developed. The system has been designed to allow a high flexibility in order to tackle challenging analytical problems. The platform comprises a cooled microautosampler, an integrated system for microcolumn HPLC, and a capillary reversed-phase column that is interfaced to matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) system via a low internal volume flow-through microdispenser. The chromatographic separation is continuously transferred onto a MALDI target plate as discrete spots as the dispenser ejects bursts of droplets of the column effluent in a precise array pattern. A refrigerated microfraction collector was coupled to the outlet of the flow-through microdispenser enabling enrichment and re-analysis of interesting fractions. The use of target plates pre-coated with matrix simplified and increased the robustness of the system. By including a separation step prior to the MALDI-TOF-MS analysis and hereby minimizing suppression effects allowed us to obtain higher sequence coverage of proteins compared to conventional MALDI sample preparation methodology. Additionally, synthetic peptides corresponding to autophosphorylated forms of the tryptic fragment 485-496 (ALGADDSYYTAR) of tyrosine kinase ZAP-70 were identified at sensitivities reaching 150 amol.