Addition of p-azido-L-phenylalanine to the genetic code of Escherichia coli

We report the selection of a new orthogonal aminoacyl tRNA synthetase/tRNA pair for the in vivo incorporation of a photocrosslinker, p-azido-l-phenylalanine, into proteins in response to the amber codon, TAG. The amino acid is incorporated in good yield with high fidelity and can be used to crosslink interacting proteins.     

Diastereoselective formation of glycoluril dimers: isomerization mechanism and implications for cucurbit[n]uril synthesis

Cucurbit[6]uril (CB[6]) is a macrocyclic compound, prepared in one pot from glycoluril and formaldehyde, whose molecular recognition properties have made it the object of intense study. Studies of the mechanism of CB[n] formation, which might provide insights that allow the tailor-made synthesis of CB[n] homologues and derivatives, have been hampered by the complex structure of CB[n]. By reducing the complexity of the reaction to the formation of S-shaped (12S-18S) and C-shaped (12C-18C) methylene bridged glycoluril dimers, we have been able to probe the fundamental steps of the mechanism of CB[n] synthesis to a level that has not been possible previously. For example, we present strong evidence that the mechanism of CB[n] synthesis proceeds via the intermediacy of both S-shaped and C-shaped dimers. The first experimental determination of the relative free energies of the S-shaped and C-shaped dimers indicates a thermodynamic preference (1.55-3.25 kcal mol(-)(1)) for the C-shaped diastereomer. This thermodynamic preference is not because of self-association, solvation, or template effects. Furthermore, labeling experiments have allowed us to elucidate the mechanism of this acid-catalyzed equilibrium between the S-shaped and C-shaped diastereomers. The equilibration is an intramolecular process that proceeds with high diastereoselectivity and retention of configuration. On the basis of the broad implications of these results for CB[n] synthesis, we suggest new synthetic strategies that may allow for the improved preparation of CB[n] (n > 8) and CB[n] derivatives from functionalized glycolurils.     

Characterization of a new qQq-FTICR mass spectrometer for post-translational modification analysis and top-down tandem mass spectrometry of whole proteins

The use of a new electrospray qQq Fourier transform ion cyclotron mass spectrometer (qQq-FTICR MS) instrument for biologic applications is described. This qQq-FTICR mass spectrometer was designed for the study of post-translationally modified proteins and for top-down analysis of biologically relevant protein samples. The utility of the instrument for the analysis of phosphorylation, a common and important post-translational modification, was investigated. Phosphorylation was chosen as an example because it is ubiquitous and challenging to analyze. In addition, the use of the instrument for top-down sequencing of proteins was explored since this instrument offers particular advantages to this approach. Top-down sequencing was performed on different proteins, including commercially available proteins and biologically derived samples such as the human E2 ubiquitin conjugating enzyme, UbCH10. A good sequence tag was obtained for the human UbCH10, allowing the unambiguous identification of the protein. The instrument was built with a commercially produced front end: a focusing rf-only quadrupole (Q0), followed by a resolving quadrupole (Q1), and a LINAC quadrupole collision cell (Q2), in combination with an FTICR mass analyzer. It has utility in the analysis of samples found in substoichiometric concentrations, as ions can be isolated in the mass resolving Q1 and accumulated in Q2 before analysis in the ICR cell. The speed and efficacy of the Q2 cooling and fragmentation was demonstrated on an LCMS-compatible time scale, and detection limits for phosphopeptides in the 10 amol/muL range (pM) were demonstrated. The instrument was designed to make several fragmentation methods available, including nozzle-skimmer fragmentation, Q2 collisionally activated dissociation (Q2 CAD), multipole storage assisted dissociation (MSAD), electron capture dissociation (ECD), infrared multiphoton induced dissociation (IRMPD), and sustained off resonance irradiation (SORI) CAD, thus allowing a variety of MS(n) experiments. A particularly useful aspect of the system was the use of Q1 to isolate ions from complex mixtures with narrow windows of isolation less than 1 m/z. These features enable top-down protein analysis experiments as well structural characterization of minor components of complex mixtures.     

Kinetics of CO oxidation on high-concentration phases of atomic oxygen on Pt(111)

Temperature-programmed reaction spectroscopy (TPRS) and direct, isothermal reaction-rate measurements were employed to investigate the oxidation of CO on Pt(111) covered with high concentrations of atomic oxygen. The TPRS results show that oxygen atoms chemisorbed on Pt(111) at coverages just above 0.25 ML (monolayers) are reactive toward coadsorbed CO, producing CO(2) at about 295 K. The uptake of CO on Pt(111) is found to decrease with increasing oxygen coverage beyond 0.25 ML and becomes immeasurable at a surface temperature of 100 K when Pt(111) is partially covered with Pt oxide domains at oxygen coverages above 1.5 ML. The rate of CO oxidation measured as a function of CO beam exposure to the surface exhibits a nearly linear increase toward a maximum for initial oxygen coverages between 0.25 and 0.50 ML and constant surface temperatures between 300 and 500 K. At a fixed CO incident flux, the time required to reach the maximum reaction rate increases as the initial oxygen coverage is increased to 0.50 ML. A time lag prior to the reaction-rate maximum is also observed when Pt oxide domains are present on the surface, but the reaction rate increases more slowly with CO exposure and much longer time lags are observed, indicating that the oxide phase is less reactive toward CO than are chemisorbed oxygen atoms on Pt(111). On the partially oxidized surface, the CO exposure needed to reach the rate maximum increases significantly with increases in both the initial oxygen coverage and the surface temperature. A kinetic model is developed that reproduces the qualitative dependence of the CO oxidation rate on the atomic oxygen coverage and the surface temperature. The model assumes that CO chemisorption and reaction occur only on regions of the surface covered by chemisorbed oxygen atoms and describes the CO chemisorption probability as a decreasing function of the atomic oxygen coverage in the chemisorbed phase. The model also takes into account the migration of oxygen atoms from oxide domains to domains with chemisorbed oxygen atoms. According to the model, the reaction rate initially increases with the CO exposure because the rate of CO chemisorption is enhanced as the coverage of chemisorbed oxygen atoms decreases during reaction. Longer rate delays are predicted for the partially oxidized surface because oxygen migration from the oxide phase maintains high oxygen coverages in the coexisting chemisorbed oxygen phase that hinder CO chemisorption. It is shown that the time evolution of the CO oxidation rate is determined by the relative rates of CO chemisorption and oxygen migration, R(ad) and R(m), respectively, with an increase in the relative rate of oxygen migration acting to inhibit the reaction. We find that the time lag in the reaction rate increases nearly exponentially with the initial oxygen coverage [O](i) (tot) when [O](i) (tot) exceeds a critical value, which is defined as the coverage above which R(ad)R(m) is less than unity at fixed CO incident flux and surface temperature. These results demonstrate that the kinetics for CO oxidation on oxidized Pt(111) is governed by the sensitivity of CO binding and chemisorption on the atomic oxygen coverage and the distribution of surface oxygen phases.     

Metal ion scrambling in hexanuclear M(6)(Et(2)NCO(2))(12) complexes (M = Co,Mg). Synthesis,solid state structure,and solution dynamics of heteronuclear Co(n)Mg(6-n)(Et(2)NCO(2))(12) complexes

Heteronuclear diethylcarbamato complexes of the form Co(n)()Mg(6)(-)(n)()(Et(2)NCO(2))(12) were prepared from the isostructural homonuclear precursors Mg(6)(Et(2)NCO(2))(12), 1, and Co(6)(Et(2)NCO(2))(12), 2, via a solvothermal methodology. Two materials were selected for single-crystal X-ray diffraction analysis: Co(1.6)Mg(4.4)(Et(2)NCO(2))(12) and Co(2.7)Mg(3.3)(Et(2)NCO(2))(12). Both compounds crystallize in the orthorhombic space group Ccca, as do 1 and 2. The molecular structure is best described as two trinuclear M(3) units cross-linked by diethylcarbamate ligands and twisted about one another, so that the complex has overall D(2) symmetry and is chiral. Each trinuclear unit consists of two terminal pentacoordinate metal ions and one central hexacoordinate metal ion. The X-ray diffraction data were unambiguous that the Co(2+) ions migrate exclusively to the pentacoordinate sites in the heteronuclear complexes, thus demonstrating that metal ion scrambling at the molecular level must occur. The composition of individual crystals can be continuously varied for Co(2+) mole fractions chi(Co) < 0.5, and the a and c unit cell distances are linearly related to chi(Co). This indicates that the compounds behave as solid solutions. There appears to be either a chemical or crystallographic phenomenon inherent in the synthetic methodology that prevents isolation of heteronuclear materials having chi(Co) > 0.5. Solution electronic spectroscopy and molecular weight measurements show that 2 can dissociate in chloroform and cyclohexane solution to give a dimeric complex 2'. This behavior contrasts with the stability of 1 in solution, as shown by NMR. The kinetic rate profile for formation of Co(n)Mg(6-n)(Et(2)NCO(2))(12) reveals saturation kinetics and is consistent with direct attack by 2' on 1 to give the heteronuclear complex via a higher nuclearity intermediate. This study illustrates a general method for the preparation of solids based on heteronuclear Werner-type complexes of the M(6)(Et(2)NCO(2))(12) structure type, and the mechanism by which such compounds can be formed from isostructural homonuclear precursors.     

Direct coupling of polymer-based microchip electrophoresis to online MALDI-MS using a rotating ball inlet

We report on the coupling of a polymer-based microfluidic chip to a MALDI-TOF MS using a rotating ball interface. The microfluidic chips were fabricated by micromilling a mold insert into a brass plate, which was then used for replicating polymer microparts via hot embossing. Assembly of the chip was accomplished by thermally annealing a cover slip to the embossed substrate to enclose the channels. The linear separation channel was 50 microm wide, 100 microm deep, and possessed an 8 cm effective length separation channel with a double-T injector (V(inj) = 10 nL). The exit of the separation channel was machined to allow direct contact deposition of effluent onto a specially constructed rotating ball inlet to the mass spectrometer. Matrix addition was accomplished in-line on the surface of the ball. The coupling utilized the ball as the cathode transfer electrode to transport sample into the vacuum for desorption with a 355 nm Nd:YAG laser and analyzed on a TOF mass spectrometer. The ball was cleaned online after every rotation. The ability to couple poly(methylmethacrylate) microchip electrophoresis devices for the separation of peptides and peptide fragments produced from a protein digest with subsequent online MALDI MS detection was demonstrated.     

Carbohydrate-based DNA ligands: sugar-oligoamides as a tool to study carbohydrate-nucleic acid interactions

Sugar-oligoamides have been designed and synthesized as structurally simple carbohydrate-based ligands to study carbohydrate-DNA interactions. The general design of the ligands 1-3 has been done as to favor the bound conformation of Distamycin-type gamma-linked covalent dimers which is a hairpin conformation. Indeed, NMR analysis of the sugar-oligoamides in the free state has indicated the presence of a percentage of a hairpin conformation in aqueous solution. The DNA binding activity of compounds 1-3 was confirmed by calf thymus DNA (ct-DNA) NMR titration. Interestingly, the binding of the different sugar-oligoamides seems to be modulated by the sugar configuration. Semiquantitative structural information about the DNA ligand complexes has been derived from NMR data. A competition experiment with Netropsin suggested that the sugar-oligoamide 3 bind to DNA in the minor groove. The NMR titrations of 1-3 with poly(dA-dT) and poly(dG-dC) suggested preferential binding to the ATAT sequence. TR-NOE NMR experiments for the sugar-oligoamide 3-ct-DNA complex both in D(2)O and H(2)O have confirmed the complex formation and given information on the conformation of the ligand in the bound state. The data confirmed that the sugar-oligoamide ligand is a hairpin in the bound state. Even more relevant to our goal, structural information on the conformation around the N-glycosidic linkage has been accessed. Thus, the sugar asymmetric centers pointing to the NH-amide and N-methyl rims of the molecule have been characterized.     

Use of Ag(II) as a removable template in porphyrin chemistry: diol cleavage products of [meso-tetraphenyl-2,3-cis-diolchlorinato]silver(II)

The use of Ag^II as a removable template in synthetic porphyrin chemistry is described. Mild procedures for the insertion of Ag^II into chlorins and the demetallation of the [chlorinato]Ag^II complexes are delineated. The UV-vis spectra of the novel [chlorinato]Ag^II complexes are discussed. The diol cleavage products of [meso-tetraphenyl-2,3-diolchlorinato]silver(II) under a number of conditions are characterized and compared to those resulting from the cleavage of the corresponding free base diol chlorin or its Ni^II complex, highlighting the unique templating effect of Ag^II. The scopes and limits of electrospray ionization mass spectrometry (ESI-MS) for the analysis of Ag^II chlorins is described. The use of Ag^II as a templating metal is superior over Ni^II or Zn^II for the preparation of free base pyrrole-modified porphyrins along metal templated pathways.     

Recent advances toward sustainable flow photochemistry

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Substrate oxidation by copper-dioxygen adducts: mechanistic considerations

A series of copper-dioxygen adducts [{Cu(II)(MePY2)(R)}(2)(O(2))](B(C(6)F(5))(4))(2) (1(R)()), systematically varying in their electronic properties via ligand pyridyl donor substituents (R = H, MeO, and Me(2)N), oxidize a variety of substrates with varying C-H or O-H bond dissociation enthalpies. Detailed mechanistic studies have been carried out, including investigation of 1(R)() thermodynamic redox properties, 1(R)() tetrahydrofuran (THF) and N,N'-dimethylaniline (DMA) oxidation kinetics (including analyses of substrate dicopper binding equilibria), and application of mechanistic probes (N-cyclopropyl-N-methylaniline (CMA) and (p-methoxyphenyl)-2,2-dimethylpropanol (MDP)), which can distinguish if proton-coupled electron-transfer (PCET) processes proceed through concerted electron-transfer proton-transfer (ETPT) or consecutive electron-transfer proton-transfer (ET/PT) pathways. The results are consistent with those of previous complementary studies; at low thermodynamic driving force for substrate oxidation, an ET/PT is operable, but once ET (i.e., substrate one-electron oxidation) becomes prohibitively uphill, the ETPT pathway occurs. Possible differences in coordination structures about 1(Me)()()2(N)()/1(MeO)() compared to those of 1(H)() are also used to rationalize some of the observations.