Toward a small molecule, biomimetic carbonic anhydrase model: theoretical and experimental investigations of a panel of zinc(II) aza-macrocyclic catalysts

A panel of five zinc-chelated aza-macrocycle ligands and their ability to catalyze the hydration of carbon dioxide to bicarbonate, H(2)O + CO(2) → H(+) + HCO(3)(–), was investigated using quantum-mechanical methods and stopped-flow experiments. The key intermediates in the reaction coordinate were optimized using the M06-2X density functional with aug-cc-pVTZ basis set. Activation energies for the first step in the catalytic cycle, nucleophilic CO(2) addition, were calculated from gas-phase optimized transition-state geometries. The computationally derived trend in activation energies was found to not correspond with the experimentally observed rates. However, activation energies for the second, bicarbonate release step, which were estimated using calculated bond dissociation energies, provided good agreement with the observed trend in rate constants. Thus, the joint theoretical and experimental results provide evidence that bicarbonate release, not CO(2) addition, may be the rate-limiting step in CO(2) hydration by zinc complexes of aza-macrocyclic ligands. pH-independent rate constants were found to increase with decreasing Lewis acidity of the ligand-Zn complex, and the trend in rate constants was correlated with molecular properties of the ligands. It is suggested that tuning catalytic efficiency through the first coordination shell of Zn(2+) ligands is predominantly a balance between increasing charge-donating character of the ligand and maintaining the catalytically relevant pK(a) below the operating pH.     

Major groove substituents and polymerase recognition of a class of predominantly hydrophobic unnatural base pairs

Expansion of the genetic alphabet with an unnatural base pair is a long‐standing goal of synthetic biology. We have developed a class of unnatural base pairs, formed between d 5SICS and analogues of d MMO2 that are efficiently and selectively replicated by the Klenow fragment (Kf) DNA polymerase. In an effort to further characterize and optimize replication, we report the synthesis of five new d MMO2 analogues bearing different substituents designed to be oriented into the developing major groove and an analysis of their insertion opposite d 5SICS by Kf and Thermus aquaticus DNA polymerase I (Taq). We also expand the analysis of the previously optimized pair, d NaM –d 5SICS , to include replication by Taq. Finally, the efficiency and fidelity of PCR amplification of the base pairs by Taq or Deep Vent polymerases was examined. The resulting structure–activity relationship data suggest that the major determinants of efficient replication are the minimization of desolvation effects and the introduction of favorable hydrophobic packing, and that Taq is more sensitive than Kf to structural changes. In addition, we identify an analogue (d NMO1 ) that is a better partner for d 5SICS than any of the previously identified d MMO2 analogues with the exception of d NaM . We also found that d NaM –d 5SICS is replicated by both Kf and Taq with rates approaching those of a natural base pair.     

Efforts toward developing direct probes of protein dynamics

We report the first IR characterization of a single C-D bond within a protein, methyl-d1 Met80 of horse heart cytochrome c. A comparison was made to methyl-d1/d3 methionine as well as methyl-d3 Met80. We found that for methyl-d1 and the asymmetric stretches of methyl-d3, line widths/line shapes are dominated by inhomogeneous broadening, whereas the symmetric stretch of methyl-d3 has a significant homogeneous component. Vibrational energy relaxation calculations found that a significantly stronger Fermi resonance exists for the symmetric stretch than for the asymmetric stretches, thereby suggesting that a difference in intramolecular vibrational relaxation (IVR) causes the observed line width/line shape difference between the symmetric and asymmetric stretches.     

Peculiarities of thermo-optic coefficient under different temperature regimes in optical fibers containing fiber Bragg gratings

Direct experimental measurements of the thermo-optic for fixed temperature intervals (20–200 °C, 200–500 °C, 500–660 °C, 660–780 °C) in fused silica fiber containing fiber Bragg gratings (FBGs) were conducted. The diffraction efficiency of a FBG fluctuated with temperature between 2.01 × 10^? 4 and 0.17 × 10^? 4 while the temperature shift of the Bragg's peak was monitored between 1300 and 1311 nm with sub-Angstrom precision. Numerical simulations were focused on FBG's diffraction efficiency calculations accounting for the temperature drift of the gratings, and found to be in excellent agreement with obtained experimental data.It was found that the first-order thermo-optic coefficient changes between 1.29 and 1.85 × 10^? 5 K^? 1 for the linear fit and at T = 0 °C its value was found to be close to 2.37 × 10^? 5 K^? 1 for the polynomial fit of experimental data. The average thermo-optic coefficient undergoes a minimum in the vicinity of 440 °C. Additional observation indicates a negative sign of the second-order thermo-optic coefficient. The value of thermal expansion coefficient was much less (0.5 × 10^? 6 K^? 1) than that for the average thermo-optic coefficient. Based on the energy dispersive spectroscopy it was determined that thermal erasing of the FBGs at a temperature around 780 °C corresponds to germanium monoxide diffusion out of core in silica-based fibers.     

A Synthesis of 2-(6′-Carboxy-2′-cis-Hexenyl)-4-Hydroxycyclopent-2-EN-1-ONE,a Prostagiandin Intermediate1

Several recent publications² report the synthesis of prostaglandin E₁ (PGE₁, 2) and some of its derivatives by conjugate addition reactions to ether-ester forms of hydroxycyclopentenone acid 1.³ The simplicity of this approach makes its application to the preparation of prostaglandins of the PG₂- and PG₃ - series (cis-Δ⁵)⁴ an attractive alternative to the existing elegant methods.⁵ We now wish to report a five-step synthesis of the requisite hydroxycyclopentenone precursor 3 from the readily available⁶ lactone 4.