Gas-phase electron diffraction studies on two 11-vertex Dicarbaboranes, closo-2,3-C2B9H11 and nido-2,9-C2B9H13

The molecular structures of two carbaboranes, closo-2,3-C(2)B(9)H(11) and nido-2,9-C(2)B(9)H(13), were determined experimentally for the first time using gas-phase electron diffraction (GED). For closo-2,3-C(2)B(9)H(11), a model with C(2)(v)() symmetry was refined to give C-B bond distances ranging 158.3-167.0 pm and B-B distances ranging 177.4-200.0 pm. The structure of nido-2,9-C(2)B(9)H(13) was refined using a model with C(s)() symmetry to give C-B bond lengths ranging 160.3-171.9 pm and B-B lengths ranging 173.0-196.1 pm. Ab initio computations (up to MP2/6-311+G) were also carried out on these and the related nido-7,8-C(2)B(9)H(13), which was not sufficiently stable to allow determination of its molecular structure by GED.     

Asymmetric synthesis of alpha-amino allyl,benzyl, and propargyl silanes by metalation and rearrangement

[reaction: see text] Metalation of a Boc-protected N-silylamine alpha to nitrogen results in migration of the silicon from nitrogen to carbon (reverse aza-Brook rearrangement), yielding an alpha-amino silane. The Boc group acts initially as a metalation-directing group and then to stabilize the nitrogen anion, providing a driving force for the rearrangement. In the presence of (-)-sparteine, the new chiral center is formed in >90% ee from allyl, benzyl, and propargylamines.     

Enhanced stability to decomposition of a cobalt-dioxygen adduct supported in a copolymer matrix

Summary The decomposition of the Co^II complex of a macrocyclic cyclidene ligand is reported both in solution and when bound to a copolymer support. E.s.r. studies show that the decomposition of the complex in pyridine solution, under an atmosphere of O₂, has an estimated half-life of ca. 36 h at 295 K. This suggests that decomposition of the O₂ adduct is the second step observed in earlier electronic spectroscopic studies, and infers that the cyclidene O₂ adducts are much longer lived than originally thought. The Co^II cyclidene complex forms a coordinate bond to the pyridine group of n-butyl methacrylate/4-vinyl pyridine copolymers and the resulting five-coordinate complexes undergo reversible oxygenation. The polymer-supported O₂ adducts are much more stable to decomposition than those in the solution phase and have an estimated half-life of ca. 30 days at 295 K. The enhanced stability to decomposition of the complexes in the polymer matrix is attributed to the low mobility of the complexes in the glassy polymer.     

Development of polyphosphate parameters for use with the AMBER force field

Accurate force fields are essential for reproducing the conformational and dynamic behavior of condensed-phase systems. The popular AMBER force field has parameters for monophosphates, but they do not extend well to polyphorylated molecules such as ADP and ATP. This work presents parameters for the partial charges, atom types, bond angles, and torsions in simple polyphosphorylated compounds. The parameters are based on molecular orbital calculations of methyldiphosphate and methyltriphosphate at the RHF/6-31+G* level. The new parameters were fit to the entire potential energy surface (not just minima) with an RMSD of 0.62 kcal/mol. This is exceptional agreement and a significant improvement over the current parameters that produce a potential surface with an RMSD of 7.8 kcal/mol to that of the ab initio calculations. Testing has shown that the parameters are transferable and capable of reproducing the gas-phase conformations of inorganic diphosphate and triphosphate. Also, the parameters are an improvement over existing parameters in the condensed phase as shown by minimizations of ATP bound in several proteins. These parameters are intended for use with the existing AMBER 94/99 force field, and they will permit users to apply AMBER to a wider variety of important enzymatic systems.     

Synthesis and characterization of a new family of square-planar nickel(II) carbonyl derivatives

The reaction of [NBu(4)](2)[Ni(C(6)F(5))(4)] (1) with solutions of dry HCl(g) in Et(2)O results in the protonolysis of two Nibond;C(6)F(5) bonds giving [NBu(4)](2)[[Ni(C(6)F(5))(2)](2)(mu-Cl)(2)] (2 a) together with the stoichiometrically required amount of C(6)F(5)H. Compound 2 a reacts with AgClO(4) in THF to give cis-[Ni(C(6)F(5))(2)(thf)(2)] (3). Reacting 3 with phosphonium halides, [PPh(3)Me]X, gives dinuclear compounds [PPh(3)Me](2)[[Ni(C(6)F(5))(2)](2)(mu-X)(2)] (X=Br (2 b) or I (2 c)). Solutions of compounds 2 in CH(2)Cl(2) at 0 degrees C do not react with excess CNtBu, but do react with CO (1 atm) to split the bridges and form a series of terminal Ni(II) carbonyl derivatives with general formula Qcis-[Ni(C(6)F(5))(2)X(CO)] (4). The nu(CO) stretching frequencies of 4 in CH(2)Cl(2) solution decrease in the order Cl (2090 cm(-1))>Br (2084 cm(-1))>I (2073 cm(-1)). Compounds 4 revert to the parent dinuclear species 2 on increasing the temperature or under reduced CO pressure. [NBu(4)]cis-[Ni(C(6)F(5))(2)Cl(CO)] (4 a) reacts with AgC(6)F(5) to give [NBu(4)][Ni(C(6)F(5))(3)(CO)] (5, nu(CO)(CH(2)Cl(2))=2070 cm(-1)). Compound 5 is also quantitatively formed ((19)F NMR spectroscopy) by 1:1 reaction of 1 with HCl(Et(2)O) in CO atmosphere. Complex 3 reacts with CO at -78 degrees C to give cis-[Ni(C(6)F(5))(2)(CO)(2)] (6, nu(CO)(CH(2)Cl(2))=2156, 2130 cm(-1)), which easily decomposes by reductive elimination of C(6)F(5)bond;C(6)F(5). Compounds 3 and 6 both react with CNtBu to give trans-[Ni(C(6)F(5))(2)(CNtBu)(2)] (7). The solid-state structures of compounds 3, 4 b, 6, and 7 have been established by X-ray diffraction methods. Complexes 4-6 are rare examples of square-planar Ni(II) carbonyl derivatives.     

Reductive amination of carbohydrates using NaBH(OAc)<Subscript>3</Subscript>

An improved protocol for reductive amination of carbohydrates is developed. This derivatization facilitates the detection of oligosaccharides in HPLC-UV and mass spectrometric applications by enhancing the signal of the carbohydrates. In this study, reductive amination was achieved using NaBH(OAc)₃.This reducing agent is an attractive alternative to the toxic, but extensively used reducing agent, NaBH₃CN. Several types of carbohydrates were successfully derivatized using NaBH(OAc)₃, and the results obtained from this protocol were compared with those obtained with NaBH₃CN. Both reducing agents were equally effective in side-by-side analysis. Two purification strategies (purification by zip-tip and HPLC) were implemented and the instrumental limit of detection of each method was compared. The detection limit was ~1,000 times lower when the purification was done using HPLC, compared to using the zip-tip. Since the derivatization by-products in this protocol are not toxic, MS analysis also could also be performed directly, without purification. The MS/MS data of derivatized and underivatized oligosaccharides were acquired as well. The derivatized oligosaccharides produce more easily interpretable product ions than underivatized oligosaccharides.     

Examining the out-of-center distortion in the [NbOF5]2- anion

Out-of-center "primary" electronic distortions are inherent to the oxide fluoride anions of the early d0 transition metals. In the [NbOF5]2- anion, the Nb5+ moves from the center of the octahedron toward the oxide ligand to form a short Nb=O bond and long trans Nb-F bond. The combined results of single-crystal X-ray diffraction and electronic structure calculations indicate that the primary distortion of the [NbOF5]2- anion is affected by the coordination environment that is created by the three-dimensional extended structure. The formation of bonds between an M(L)4(2+) (M = Cd2+, Cu2+; L = 3-aminopyridine, 4-aminopyridine) cation and the oxide and/or trans-fluoride ligands of the [NbOF5]2- anion weakens the pi component of the Nb=O bond. At the same time, hydrogen bond interactions between the equatorial fluorides and the aminopyridine groups both lengthen the equatorial Nb-F bonds and can further reduce the symmetry of the [NbOF5]2- anion. These combined three-dimensional bond network interactions that serve to lengthen the Nb=O bond and thereby decrease the primary distortion of the [NbOF5]2- anion are illustrated in the structures of three new niobium oxide fluoride phases, [4-apyH]2[Cu(4-apy)4(NbOF5)2] (4-apy = 4-aminopyridine), Cd(3-apy)4NbOF5 (3-apy = 3-aminopyridine), and Cu(3-apy)4NbOF5, that were synthesized and characterized using X-ray diffraction. Crystal data for [4-apyH]2[Cu(4-apy)4(NbOF5)2]: tetragonal, space group /4(1)/ acd (No. 142), with a = 20.8745(8) A, c = 17.2929(9) A, and Z= 8. Cd(3-apy)4NbOF5: tetragonal, space group P4(3) (No. 78), with a = 8.4034(4) A, c = 34.933(3) A, and Z = 4. Cu(3-apy)4NbOF5: monoclinic, space group P2(1)/n (No. 14), with a = 8.822(1) A, b = 16.385(3) A, c = 8.902(1) A, beta = 109.270(3) degrees, and Z = 2.     

Conservation of mus-ms enzyme motions in the apo- and substrate-mimicked state

Solution NMR spin-relaxation experiments were used to compare mus-ms dynamics in RNase A in the apo form and as complexed to the substrate-mimic, pTppAp. The crystal structure of the RNase A/pTppAp complex was determined and demonstrates that this ligand binds at the active site and utilizes established substrate binding sites in its interaction with RNase A. Relaxation-compensated CPMG experiments identify flexible residues in and around the active site in both the apo and pTppAp-bound enzyme. Quantitative analysis of the NMR spin-relaxation dispersion curves show that the time scale of motion in RNase A is unchanged when pTppAp binds and is similar to the time scale for the rate-determining step of the catalytic reaction. Temperature-dependent measurements provide an activation barrier for motion of 5.2 +/- 1.0 kcal/mol and 4.5 +/- 1.2 kcal/mol for the apo and pTppAp forms of RNase A, respectively. These data indicate very similar motion exists in the free and bound enzyme. Additionally, chemical shift data suggests that the magnitude of motion is also similar for these two forms and that it is likely that apo enzyme interconverts to a structure that resembles a ligand-bound form. Likewise, it appears that the bound conformation samples the apo enzyme form even when ligand is present. Taken together the data imply that RNase A is in a preexisting dynamic equilibrium between two conformations that represent the open and closed enzyme forms. These data suggest that ligand binding stabilizes the bound conformer but does not induce it.     

Highly asymmetric coordination in alkenes: gas-phase structures of trans-1,2-dichloro-1,2-disilylethene and 1-bromo-1-silylethene

The molecular structures of trans-1,2-dichloro-1,2-disilylethene and 1-bromo-1-silylethene have been determined by gas-phase electron diffraction (GED) and ab initio molecular orbital calculations (MP2/6-311G). Both compounds were found to have highly asymmetric coordination around the carbon atoms with [ab initio (r(e))/GED (r(a))] C=C-Cl [117.0/117.0(2) degrees] and C=C-Si [126.2/128.1(1) degrees] in the C(2)(h) structure of trans-1,2-dichloro-1,2-disilylethene and C=C-Br [119.2/120.7(4) degrees] and C=C-Si [125.0/125.0(4) degrees] in the C(s) structure of 1-bromo-1-silylethene. Other important structural parameters for trans-1,2-dichloro-1,2-disilylethene are C=C [135.2/134.5(3) pm], C-Si [189.4/187.9(2) pm], and C-Cl [175.1/174.9(1) pm], and C=C [134.2/133.4(2) pm], C-Si [187.8/187.2(3) pm], and C-Br [191.3/191.0(3) pm] for 1-bromo-1-silylethene. Further ab initio calculations were carried out on CH(2)CRX and trans-(CRX)(2) (R = SiH(3), CH(3), or H; X = H, F, Cl, or Br) to gauge the effects of electron-withdrawing and electron-donating groups on the structures. They reveal some even more distorted structures. The asymmetric appearance of these molecules can largely be accounted for by valence shell electron pair repulsion theory.     

DNA hybridization assays using temperature gradient focusing and peptide nucleic acids

Two types of DNA hybridization assays are demonstrated with temperature gradient focusing (TGF) and peptide nucleic acids (PNAs). In TGF, the application of a controlled temperature gradient along the length of a microchannel filled with an appropriate temperature-dependent buffer results in the formation of a gradient in both the electric field and electrophoretic velocity. Ionic species move in this gradient and concentrate at a unique point where the total velocity sums to zero. The first assay is a mixing assay in which PNA is allowed to flow through spatially focused DNA targets within a capillary. The second assay detects single base pair mutations (SBPM) by monitoring the fluorescence intensity of PNA/DNA duplexes as a function of temperature within the capillary. The SBPM analysis can be performed in less than 5 min with 100-fold more dilute analyte compared to conventional UV melting measurements.