The synthesis and conformational analysis of tetrahydro-1,2,4-oxadiazines

The synthesis and variable temperature ¹H and ¹³C NMR spectra of three tetrahydro-1,2,4-oxadiazines are reported. The N(4)-Me inversion barriers are 6.8–7.0 (ax→ts) and 7.4–7.9 kcal mol^?1 (eq→ts) with ΔG° 0.6–0.9 kcal mol^?1. The N(2)-Me inversion barriers are 10.4–11.4 (ax→ts) and 11.6–13.1 kcal mol^?1 (eq→ts) with ΔGδ 1.2–1.7 kcal mol^?1. The barrier to ring inversion is ca. 12.7 kcal mol^?1. “R value” analysis shows the ring to have a 56.5±2δ dihedral angle about the C(5)-(6) bond, indicative of the expected chair conformation.     

Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors

We present a computational protocol which uses the known three-dimensional structure of a target enzyme to identify possible ligands from databases of compounds with low molecular weight. This is accomplished by first mapping the essential interactions in the binding site with the program GRID. The resulting regions of favorable interaction between target and ligand are translated into a database query, and with UNITY a flexible 3D database search is performed. The feasibility of this approach is calibrated with thrombin as the target. Our results show that the resulting hit lists are enriched with thrombin inhibitors compared to the total database.     

Donor-stabilized cations and imine transfer from N-silylphosphoranimines

A series of donor-stabilized N-silylphosphoranimine salts [DMAP.PCl2=NSiMe3]+X- (DMAP = 4-(dimethylamino)pyridine) were prepared by the reaction of Cl3P=NSiMe3 with DMAP in the presence of silver salts AgX (X = OSO2CF3, BF4, and SbF6). Repeating the reaction in the absence of AgX gave the chloride salt [DMAP.PCl2=NSiMe3]Cl which has been shown to be in equilibrium with free DMAP and Cl3P=NSiMe3. Attempts to stabilize a N-silylphosphoranimine cation with phosphine donors led to unexpected imine transfer chemistry. For example, Cl3P=NSiMe3 reacts with phosphines, R3P (R = nBu and Ph), to produce the metathesis products PCl3 and R3P=NSiMe3 which subsequently react together to afford the N-phosphinophosphoranimines R3P=N-PCl2 and ClSiMe3 as a byproduct.     

Application of NMR SHAPES screening to an RNA target

Several NMR screening techniques have been developed in recent years to aid in the identification of lead drug compounds. These NMR methods have traditionally been used for protein targets, and here we examine their applicability for an RNA target. We used the SHAPES compound library to test three different NMR screening methodologies: the saturation transfer difference (STD), the 2D trNOESY, and the WaterLOGSY experiments. We found that the WaterLOGSY experiment was the most sensitive method for our RNA target, the P4P6 domain of the Tetrahymena thermophila Group I intron. Using the WaterLOGSY experiment, we found that 23 of the 112 SHAPES compounds interact with P4P6. To identify which of these 23 hits bind through nonspecific interactions, we counterscreened with a linear duplex RNA control and identified one of the SHAPES compounds as interacting with P4P6 specifically. We thus demonstrated that the WaterLOGSY experiment in combination with the SHAPES compound library can be used to efficiently find RNA binding lead compounds.     

Level decay and orientational kinetics of the rhodamine B monomer and dimer

The population kinetics and the rotational diffusion of the rhodamine B monomer and dimer were measured by using picosecond pulses from a mode-locked Nd : YAG laser to induce and time resolve the concentration-dependent transient absorption saturation of various aqueous solutions of this organic dye.     

Restricted diffusion in silica particles measured by pulsed field gradient NMR

The restricted diffusion coefficient of water through porous silica is measured by pulsed field gradient (PFG) NMR as a function of loading in order to develop a model for self-diffusion at full pore filling in sol-gel-made porous silica particles. This model describes the pore or intraparticle diffusion coefficient as a function of particle porosity, tortuosity, and the steric hindrance applied on the molecules by the pore space. The particle morphology is characterized by nitrogen adsorption and an appropriate tortuosity model is chosen in comparison with literature data. To characterize the material, NMR relaxation and diffusion studies at different degrees of pore filling were carried out in relation to the silica/water adsorption isotherm.     

CoI- and Co0-bipyridine complexes obtained by reduction of CoBr2bpy: electrochemical behaviour and investigation of their reactions with aromatic halides and vinylic acetates

The electrochemical behaviour of CoBr(2)bpy (bpy=2,2'-bipyridine) catalyst precursor in acetonitrile has been studied, revealing its possible reduction into the corresponding Co(I) and Co(0) complexes. These low-valent cobalt species appear to be stable on the time scale of cyclic voltammetry. In the presence of aromatic halides, both complexes undergo oxidative addition, the latter Co(0) species allowing the activation of poorly reactive aromatic chlorides. The arylcobalt(III) and arylcobalt(II) obtained are reduced at the same potential as the original Co(II) and Co(I) complexes, respectively, resulting in the observation of overall ECE mechanisms in both cases. The electrochemical study shows that vinylic acetates competitively react with electrogenerated Co(0) species, leading to a labile complex. Preparative scale electrolyses carried out from solutions containing aromatic halides (ArX), vinyl acetate (vinylOAc) and a catalytic amount of CoBr(2)bpy lead to a mixture of biaryl (Ar-Ar) and arene (ArH) as long as the potential is set on the plateau of the Co(II) right arrow over left arrow Co(I) reduction wave. The coupling product (Ar-vinyl) is formed only if the electrolysis is performed on the plateau of the Co(I)/Co(0) reduction wave. A mechanism is proposed for the overall cobalt-catalyzed coupling reaction between aromatic halides and allylic acetates.     

Chiral capillary electrophoretic determination of the enantiomeric purity of tetrahydronaphthalenic derivatives, melatoninergic ligands, using highly sulfated beta-cyclodextrins

Using cyclodextrin capillary zone electrophoresis (CD-CZE), baseline separation of synthetic tetrahydronaphthalenic derivatives, potential melatoninergic compounds, was achieved. A method for the enantioresolution of these tetralins and determination of their enantiomeric purity was developed using anionic CDs (highly sulfated-CD or highly S-CD) as chiral selectors and capillaries dynamically coated with polyethylene oxide (PEO). Operational parameters such as the nature and concentration of the chiral selectors, buffer pH, organic modifiers, temperature and applied voltage were investigated. The use of charged CDs provides a driving force for our neutral compounds in the running buffer and enantiomeric resolution by inclusion of compounds in the CD cavity. The highly S-beta-CD was found to be the most effective complexing agent, allowing good enantiomeric resolution. The complete resolution of three tetralin compounds was obtained using 25 mM phosphate buffer at pH 2.5 containing 2.5% w/v of highly S-beta-CD at 25 degrees C with an applied field of 0.25 kV/cm. The apparent association constants of the inclusion complexes were calculated. This optimized method was validated in terms of linearity, sensitivity, accuracy and recovery. The enantiomeric purity for the three molecules was determined and the detection limit of enantiomer impurities is about 0.3-0.6%.     

Application of simultaneous excitation/detection to generate real-time excitation profiles in Fourier transform ion cyclotron resonance mass spectrometry

Simultaneous excitation/detection (SED), which permits observation of ion motion during an excitation event, is used to generate real-time Fourier transform ion cyclotron resonance (FTICR) excitation profiles that track the radial extent of ion motion in a trapped-ion cell. The conventional FTICR excitation profile is collected in a series of individual experiments in which peak magnitude is monitored as excitation voltage is increased. In contrast, SED permits the single-scan detection of ion cyclotron motion within the trapped-ion cell and consequently yields the data that produces a real-time excitation profile. Data analysis techniques are presented that facilitate conversion of a time domain SED profile into an excitation profile. An order of magnitude decrease in the amount of time is required to acquire an excitation profile, while the precision of the measurement is improved. To demonstrate the utility of the technique, it is applied to the study of axial and radial ion loss mechanisms for argon, benzene, and acetophenone ions under different conditions. SED excitation profiles are also used to illustrate the facility of quadrupolar excitation for minimizing radial ion loss.     

Remarkable stereocontrol in the synthesis of 1,2,3,5-tetrasubstituted tetrahydropyrans via an asymmetric heterocycloaddition of a ketone-derived enol ether

The synthesis of chiral 1,2,3,5-substituted tetrahydropyrans has been realized via an asymmetric hetero Diels-Alder (HDA) reaction. The key step that involved a trisubstituted chiral enol ether derived from (R)-mandelic acid as the dienophile promoted the creation of three stereogenic centers with a remarkable and unprecedented endo and facial stereocontrol. The hydrogenation of the heteroadduct 2 was optimized by using Pd on charcoal and diisopropylethylamine, leading to a unique isomer. The chiral inductor was cleanly and stereoselectively removed via an acetal reduction, which demonstrated the potential of this methodology for the efficient construction of key intermediate of biologically active molecules.