Gas-phase reactivity of the O=P(OCH3)2+ phosphonium ion with aliphatic esters in a quadrupole ion trap. Spontaneous elimination of ketenes

Ion-molecule reactions between the O=P(OCH(3))(2) (+) phosphonium ions and five aliphatic esters (methyl acetate, methyl propionate, methyl 2-methylpropionate, methyl butyrate and ethyl acetate) were performed in a quadrupole ion trap mass spectrometer. The O=P(OCH(3))(2) (+) phosphonium ions, formed by electron ionization from neutral trimethyl phosphite, were found to react with aliphatic esters to give an adduct ion [RR'CHCOOR", O=P(OCH(3))(2)](+), which loses spontaneously a molecule of ketene CH(2)=CO or substituted ketenes RR'C=CO. Isotope-labeled methyl acetate was used to elucidate fragmentation mechanisms. The potential energy surface obtained from B3LYP/6-31G(d,p) calculations for the reaction between O=P(OCH(3))(2) (+) and methyl acetate is described.     

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.     

Solid-state vibrational spectroscopy: Part VI. An infrared and raman spectroscopic study of transition metal(II)4-methylpyridine complexes

Infrared (4000–200 cm^?1) and Raman (3500–300 cm^?1 ) spectra are reported for metal(II) halide and thiocyanate 4-methylpyridine complexes of the following stoichiometries: (MX₂(4-Mepy)₂) {M = Mn, Co, Cu or Zn, X = Cl or Br; M = Mn, Ni or Zn, X = NCS}; (MX₂(4-Mepy)₄) {M = Mn, Fe, Co or Ni, X = Cl or Br; M = Mn, Fe, Co, W or Cu, X = NCS}. For a given series of isomorphous complexes there is a correlation between the sum of the differences between the liquid and ligand values of the ν₁, ν₂, ν₃, ν₄, ν₅, ν₆, ν₇, ν₈, ν₉, ν₁₀, ν₁₂, ν₁₃ and ν₁₄ modes of 4-methylpyridine and the strength of the metal-nitrogen bond. Comparison of the shift values of pyridine and 4-methylpyridine complexes supports the suggestion that, unlike the situation in the pyridine complexes, back-donation from the metal to the ligand is unimportant in the 4-methylpyridine complexes.     

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.     

Monomeric, tetrameric, and polymeric copper di-tert-butyl phosphate complexes containing pyridine ancillary ligands

The reaction of di-tert-butyl phosphate (((t)BuO)(2)P(O)(OH), dtbp-H) with copper acetate in the presence of pyridine (py) and 2,4,6-trimethylpyridine (collidine) has been investigated. Copper acetate reacts with dtbp-H in a reaction medium containing pyridine, DMSO, THF, and CH(3)OH to yield a one-dimensional polymeric complex [Cu(dtbp)(2)(py)(2)(mu-OH(2))](n) (1) as blue hollow crystalline tubes. The copper atoms in 1 are octahedral and are surrounded by two terminal phosphate ligands, two pyridine molecules, and two bridging water molecules. The mu-OH(2) ligands that are present along the elongated Jahn-Teller axis are responsible for the formation of the one-dimensional polymeric structure. Recrystallization of 1 in a DMSO/THF/CH(3)OH mixture results in the reorganization of the polymer and its conversion to a more stable tetranuclear copper cluster [Cu(4)(mu(3)-OH)(2)(dtbp)(6)(py)(2)] (2) in about 60% yield. The molecular structure of 2 is made up of a tetranuclear core [Cu(4)(mu(3)-OH)(2)] which is surrounded by six bidentate bridging dtbp ligands. While two of the copper atoms are pentacoordinate with a tbp geometry, the other two copper atoms exhibit a pseudooctahedral geometry with five normal Cu-O bonds and an elongated Cu-O linkage. The pentacoordinate copper centers bear an axial pyridine ligand. The short Cu.Cu nonbonded distances in the tetranuclear core of 2 lead to magnetic ordering at low temperature with an antiferromagnetic coupling at approximately 20 K (J(P) = -44 cm(-1), J(c) = -66 cm(-1), g = 2.25, and rho = 0.8%). When the reaction between di-tert-butyl phosphate (dtbp-H) and copper acetate was carried out in the presence of collidine, large dark-blue crystals of monomeric copper complex [Cu(dtbp)(2)(collidine)(2)] (3) formed as the only product. A single-crystal X-ray diffraction study of 3 reveals a slightly distorted square-planar geometry around the copper atom. Thermogravimetric analysis of 1-3 revealed a facile decomposition of the coordinated ligands and dtbp to produce a copper phosphate material around 500 degrees C. An independent solid-state thermolysis of all the three complexes in bulk at 500-510 degrees C for 2 days produced copper pyrophosphate Cu(2)P(2)O(7) along with small quantities of Cu(PO(3))(2) as revealed by DR-UV spectroscopic and PXRD studies.     

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.     

Electrophoresis of concentrated mercury drops

The electrophoretic behavior of concentrated monodispersed, positively charged mercury drops is investigated theoretically. The present study extends previous analyses by considering arbitrary surface potentials, double-layer polarization, and the interaction between adjacent double layers. The coupled equations describing the spatial variations in the flow field, the electric field, and the concentration field are solved by a pseudo-spectral method. For a low surface potential phi(r), the mobility increases monotonically with kappaalpha; kappa and alpha are respectively the reciprocal Debye length and the radius of a mercury drop. For medium and high phi(r), the mobility curve has a reflection point, which arises from the interaction of adjacent double layers, for kappaalpha. Also, if phi(r) is high, the mobility curve may exhibit a local minimum as kappaalpha varies. This phenomenon is pronounced if the concentration of the dispersed phase is high. If the double layer is thick, the mobility increases with phi(r), and the reverse is true if it is thin. We show that the higher the concentration of the dispersed phase the smaller the mobility, and as kappaalpha becomes large the mobility approaches a constant value, which is independent of the concentration of the dispersed phase. The mobility of mercury drops is larger than that of the corresponding rigid particles.     

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.