Triisopropyltriazacyclononane copper(II): an efficient phosphodiester hydrolysis catalyst and DNA cleavage agent

A 6000-fold rate enhancement has been observed for the hydrolysis of bis(p-nitrophenyl)phosphate (BNPP) in the presence of 0.2 mM Cu(i-Pr(3)[9]aneN(3))(2+) at pH 9.2 and 50 degrees C. In a direct comparison, the rate of hydrolysis of BNPP is accelerated at least 60-fold over the previously reported catalyst Cu([9]aneN(3))(2+). As observed for Cu([9]aneN(3))(2+), hydrolysis is selective for diesters over monoesters. Hydrolysis of BNPP by Cu(i-Pr(3)[9]aneN(3))(2+) is catalytic, exhibiting both rate enhancement and turnover. The reaction is inhibited by both p-nitrophenyl phosphate and inorganic phosphate. The reaction is first-order in substrate and half-order in metal complex, with a k(1.5) of 0.060 +/- 0.004 M(-1/2) s(-1) at 50 degrees C. The temperature dependence of the rate constant results in a calculated activation enthalpy (Delta H(++) of 51 +/- 2 kJ mol(-1) and activation entropy (Delta S(++)) of -110 +/- 6 J mol(-1) K(-1). The kinetic pK(a) of 7.8 +/- 0.2 is close to the thermodynamic pK(a) of 7.9 +/- 0.2, consistent with deprotonation of a coordinated water molecule in the active form of the catalyst. The active catalyst [Cu(i-Pr(3)[9]aneN(3))(OH)(OH(2))](+) is in equilibrium with an inactive dimer, and the formation constant for this dimer is between 216 and 1394 M(-1) at pH 9.2 and 50 degrees C. Temperature dependence of the dimer formation constant K(f) indicates an endothermic enthalpy of formation for the dimer of 27 +/- 3 kJ mol(-1). The time course of anaerobic DNA cleavage by Cu(i-Pr(3)[9]aneN(3))(2+) is presented over a wide range of concentrations at pH 7.8 at 50 degrees C. The concentration dependence of DNA cleavage by Cu([9]aneN(3))(2+) and Cu(i-Pr(3)[9]aneN(3))(2+) reveals a maximum cleavage efficiency at sub-micromolar concentrations of cleavage agent. DNA cleavage by Cu(i-Pr(3)[9]aneN(3))(2+) is twice as efficient at pH 7.8 as at pH 7.2.     

Effects of DNA secondary structure on oligonucleotide probe binding efficiency

Secondary structure motifs in nucleic acid probes generally impair intended hybridization reactions and so efforts to predict and avoid such structures are commonly employed in probe design schemes. Another key facet of probe design that has received much less attention, however, is that secondary structure at targeted probe binding site regions may also impair hybridization. Thus, evaluation of both probe and target site secondary structures together should improve hybridization prediction and design effectiveness. Several challenges confound this goal, including imperfect empirical rules and parameters underlying predictions and the fact that folding algorithms scale poorly with respect to sequence length. Here, we attempt to quantify the consequences of target site structure on predicted hybridization using sequences sampled from the human genome. We also provide a methodology for choosing a reasonable “window size” around target sites that is as small as possible without compromising folding algorithm prediction accuracy.     

Electrochemical and spectroscopic characterization of the novel charge-transfer ground state in diimine complexes of ytterbocene

The novel charge-transfer ground state found in alpha,alpha'-diimine adducts of ytterbocene (C(5)Me(5))(2)Yb(L) [L = 2,2'-bipyridine (bpy) and 1,10-phenanthroline (phen)] in which an electron is spontaneously transferred from the f(14) metal center into the lowest unoccupied (pi*) molecular orbital (LUMO) of the diimine ligand to give an f(13)-L(*)(-) ground-state electronic configuration has been characterized by cyclic voltammetry, UV-vis-near-IR electronic absorption, and resonance Raman spectroscopies. The voltammetric data demonstrate that the diimine ligand LUMO is stabilized and the metal f orbital is destabilized by approximately 1.0 V each upon complexation for both bpy and phen adducts. The separation between the ligand-based oxidation wave (L(0/-)) and the metal-based reduction wave (Yb(3+/2+)) in the ytterbocene adducts is 0.79 V for both bpy and phen complexes. The UV-vis-near-IR absorption spectroscopic data for both the neutral adducts and the one-electron-oxidized complexes are consistent with those reported recently, but previously unreported bands in the near-IR have been recorded and assigned to ligand (pi*)-to-metal (f orbital) charge-transfer (LMCT) transitions. These optical electronic excited states are the converse of the ground-state charge-transfer process (e.g., f(13)-L(*-) <--> f(14)-L(0)). These new bands occur at approximately 5000 cm(-1) in both adducts, consistent with predictions from electrochemical data, and the spacings of the resolved vibronic bands in these transitions are consistent with the removal of an electron from the ligand pi* orbital. The unusually large intensity observed in the f --> f intraconfiguration transitions for the neutral phenanthroline adduct is discussed in terms of an intensity-borrowing mechanism involving the low-energy LMCT states. Raman vibrational data clearly reveal resonance enhancement for excitation into the low-lying pi* --> pi* ligand-localized excited states, and comparison of the vibrational energies with those reported for alkali-metal-reduced diimine ligands confirms that the ligands in the adducts are reduced radical anions. Differences in the resonance enhancement pattern for the modes in the bipyridine adduct with excitation into different pi* --> pi* levels illustrate the different nodal structures that exist in the various low-lying pi* orbitals.     

Analysis of methoxypyrazines in wine using headspace solid phase microextraction with isotope dilution and comprehensive two-dimensional gas chromatography

This study reports an optimized headspace-solid phase microextraction (HS-SPME) method for the determination of methoxypyrazines in wine. Analysis was performed by using comprehensive two-dimensional gas chromatography with novel detection capabilities, including nitrogen phosphorus detection (GC x GC-NPD) and time-of-flight mass spectrometry (GC x GC-TOFMS). In the latter, stable isotope dilution was performed for the quantitation of 2-methoxy-3-(2-methylpropyl) pyrazine (IBMP), using labelled 2-(2H3)methoxy-3-(2-methylpropyl)pyrazine (d3-IBMP) as the internal standard, and resolution of the two analogues was facilitated using the deconvolution capabilities of the TOFMS. This research represents the first report of HS-SPME with isotope dilution and GC x GC-TOFMS (GC x GC-IDTOFMS). Analysis by GC x GC-NPD enabled detection limits of 0.5 ng/L for the quantitation of IBMP, which was superior to that obtained using GC x GC-IDTOFMS (1.95 ng/L). Nevertheless, both methods were adequately sensitive for real wine analysis, yielding highly comparable IBMP concentrations of 26.1 and 27.8 ng/L, respectively, from a Sauvignon blanc wine. The complexity of the real wine headspace was simplified as a result of selective detection using GC x GC-NPD and, in the case of GC x GC-IDTOFMS, the use of extracted ion chromatograms (EICs).     

Siloxyaluminate and Siloxygallate Complexes as Models for Framework and Partially Hydrolyzed Framework Sites in Zeolites and Zeotypes

Anionic molecular models for nonhydrolyzed and partially hydrolyzed aluminum and gallium framework sites on silica, M[OSi(OtBu)₃]₄⁻ and HOM[OSi(OtBu)₃]₃⁻ (where M=Al or Ga), were synthesized from anionic chlorides Li{M[OSi(OtBu)₃]₃Cl} in salt metathesis reactions. Sequestration of lithium cations with [12]crown-4 afforded charge-separated ion pairs composed of monomeric anions M[OSi(OtBu)₃]₄⁻ with outer-sphere [([12]crown-4)₂Li]⁺ cations, and hydroxides {HOM[OSi(OtBu)₃]₃} with pendant [([12]crown-4)Li]⁺ cations. These molecular models were characterized by single-crystal X-ray diffraction, vibrational spectroscopy, mass spectrometry and NMR spectroscopy. Upon treatment of monomeric [([12]crown-4)Li]{HOM[OSi(OtBu)₃]₃} complexes with benzyl alcohol, benzyloxide complexes were formed, modeling a possible pathway for the formation of active sites for Meerwin–Ponndorf–Verley (MPV) transfer hydrogenations with Al/Ga-doped silica catalysts.     

Photoswitchable Composite Polymer Electrolytes Using Spiropyran-Immobilized Nanoporous Templates

Composite polymer electrolytes (CPEs) with smart, stimuli-responsive characteristics have gained considerable attention owing to their noninvasive manipulation and applications in future technologies. To address this potential, in this work, we demonstrate photoresponsive composite polymer electrolytes, consisting of gel polymer electrolyte (GPE) and spiropyran-immobilized nanoporous anodic aluminum oxide (SP-AAO) templates. Under UV irradiation, the close SP form isomerizes to the open merocyanine (MC) form, creating extremely polarized AAO surfaces; whereas, under visible light irradiation, the MC form reverts to the SP form, creating neutral surface conditions. The electrostatic interactions between ions and AAO surfaces are investigated by attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. Moreover, the behavior of ionic conductivity of the GPE@SP-AAO is found to be consistent with the kinetics of isomerization tracked by UV-Vis spectroscopy. This work provides a promising platform for developing next-generation photoelectronic smart devices.     

Convex Entire Noncommutative Functions are Polynomials of Degree Two or Less

We establish several new relations between the discrete transition operator, the continuous Laplacian and the averaging operator associated with combinatorial and metric graphs. It is shown that these operators can be expressed through each other in a very explicit way. In particular, the averaging operator appears to be closely related to the solutions of the associated wave equation. The machinery used allows one to study a class of infinite graphs without assumption on the local finiteness.     

Concurrent combined verification: reducing false positives in automated NMR structure verification through the evaluation of multiple challenge control structures

Automated structure verification using ¹H NMR data or a combination of ¹H and heteronuclear single‐quantum correlation (HSQC) data is gaining more interest as a routine application for qualitative evaluation of large compound libraries produced by synthetic chemistry. The goal of this automated software method is to identify a manageable subset of compounds and data that require human review. In practice, the automated method will flag structure and data combinations that exhibit some inconsistency (i.e. strange chemical shifts, conflicts in multiplicity, or overestimated and underestimated integration values) and validate those that appear consistent. One drawback of this approach is that no automated system can guarantee that all passing structures are indeed correct structures. The major reason for this is that approaches using only ¹H or even ¹H and HSQC spectra often do not provide sufficient information to properly distinguish between similar structures. Therefore, current implementations of automated structure verification systems allow, in principle, false positive results. Presented in this work is a method that greatly reduces the probability of an automated validation system passing incorrect structures (i.e. false positives). This novel method was applied to automatically validate 127 non‐proprietary compounds from several commercial sources. Presented also is the impact of this approach on false positive and false negative results. Copyright © 2012 John Wiley & Sons, Ltd.