The synthesis,structural characterization and biocidal properties of some triorganotin(IV) esters of N-arylidene-ω-amino acids.

The methods of synthesis, elemental analysis, IR and NMR spectroscopic data and fungicidal activity against Ceratocystis ulmi are reported for a series of triorganotin esters of N-arylidene-ω-amino acids of general formula R₃SnOCO(CH₂)_nN = CHAr (R = Ph, n-Bu; Ar = 2-HOC₆H₄, 2-HOC₁₀H₆; n = 1, 2, 3 and 5). The crystal structures for two of the compounds, tributyltin N-2-hydroxynaphthalidene glycinate ( 1 ) and tributyltin N-2-hydroxynaphthalidene-β-alaninate ( 2 ), have been determined. Although both of these compounds have a trans-R₃SnO₂ structure, in compound 1 the carboxylate group is monodentate and the fifth coordination position around the tin atom is taken up by a coordinated phenolic group, whereas in 2 the carboxylate group is bridging. These two examples thus correspond to the two different structures reported for trans-R₃SnO₂ complexes. Both compounds were found to be active against Ceratocystis ulmi, but there was no significant difference in their levels of biological activity against this particular fungus. Apart from compound 1 , the other tributyltin compounds reported are believed to adopt the carboxylate bridging mode shown by compound ( 2 ). Crystal data: for 1 , crystals monoclinic, space group P 2₁/ c , a = 12.9435(11) Å, b = 13.5769(10) Å, c = 15.7715(12) Å, β = 108.919(6)°, Z = 4, R _f = 0.046 and R _w = 0.058 for 1448 significant reflections; for 2 , crystals monoclinic, space group C 2/ c , a = 24.588(14) Å, b = 9.733(3) Å, c = 27.611(12) Å, β = 113.49(4)°, Z = 8, R _f = 0.053 and R _w = 0.069 for 3822 significant reflections. © 1998 John Wiley & Sons, Ltd.     

Multiple time scales in solvation dynamics of DNA in aqueous solution: the role of water, counterions, and cross-correlations

Recent time domain experiments have explored solvation dynamics of a probe located inside a DNA duplex, in an effort to gain information, e.g., on the dynamics of water molecules in the DNA major and minor grooves and their environment. Multiple time constants in the range of a few picoseconds to several nanoseconds were obtained. We have carried out 15 ns long atomistic molecular dynamics simulations to study the solvation dynamics of bases of a 38 base-pair long DNA duplex in an aqueous solution containing counterions. We have computed the energy-energy time correlation function (TCF) of the four individual bases (A, T, G, and C) to characterize the solvation dynamics. All the TCFs display highly nonexponential decay with time. When the trajectories are analyzed with 100 fs time resolution, the TCF of each base shows initial ultrafast decay (with tau1 approximately equal 60-80 fs) followed by two intermediate components (tau2 approximately equal 1 ps, tau3 approximately equal 20-30 ps), in near complete agreement with a recent time domain experiment on DNA solvation. Interestingly, the solvation dynamics of each of the four different nucleotide bases exhibit rather similar time scales. To explore the existence of slow relaxation at longer times reported recently in a series of experiments, we also analyzed the solvation TCFs calculated with longer time trajectories and with a larger time resolution of 1 ps. In this case, an additional slow component with a time constant of the order of 250 ps is observed. Through an analysis of partial solvation TCFs, we find that the slow decay originates mainly from the interaction of the nucleotides with the dipolar water molecules and the counterions. An interesting negative cross-correlation between water and counterions is observed, which makes an important contribution to relaxation at intermediate to longer times.     

Entropy of water in the hydration layer of major and minor grooves of DNA

Transport properties (translational and rotational) of water in the two grooves of the B-DNA duplex are known to be different from those in the bulk. Here, we use a recently developed theoretical scheme to compute the entropies of water molecules in both of the grooves of DNA and compare them with that in the bulk. The scheme requires as input both translational and rotational velocity autocorrelation function (C(V)(t) and C(omega)(t), respectively) data. These velocity autocorrelation functions were computed from an atomistic MD simulation of a B-DNA duplex (36 base pairs long) in explicit water (TIP3P). The average values of the entropy of water at 300 K in both of the grooves of DNA (the TS value in the major groove is 6.71 kcal/mol and that in the minor groove is 6.41 kcal/mol) are found to be significantly lower than that in bulk water (the TS value is 7.27 kcal/mol). Thus, the entropic contribution to the free energy change (TDeltaS) of transferring a minor groove water molecule to the bulk is 0.86 kcal/mol and of transferring a major groove water to the bulk is 0.56 kcal/mol at 300 K, which is to be compared with 1.44 kcal/mol for melting of ice at 273 K. We also calculate the energy of interaction of each water molecule with the rest of the atoms in the system and hence calculate the chemical potential (Helmholtz free energy per water molecule, A = E - TS) in the different domains. The identical free energy value of water molecules in the different domains proves the robustness of the scheme. We propose that the configurational entropy of water in the grooves can be used as a measure of the mobility (or microviscosity) of water molecules in a given domain.     

Water reorientation dynamics in the first hydration shells of F- and I-

Molecular dynamics and analytic theory results are presented for the reorientation dynamics of first hydration shell water molecules around fluoride and iodide anions. These ions represent the extremes of the (normal) halide series in terms of their size and conventional structure-making and -breaking categorizations. The simulated reorientation times are consistent with NMR and ultrafast IR experimental results. They are also in good agreement with the theoretical predictions of the analytic Extended Jump Model. Analysis through this model shows that while sudden, large amplitude jumps (in which the reorienting water exchanges hydrogen-bond partners) are the dominant reorientation pathway for the I(-) case, they are comparatively less important for the F(-) case. In particular, the diffusive reorientation of an intact F(-)···H(2)O hydrogen-bonded pair is found to be most important for the reorientation time, a feature related to the greater hydrogen-bond strength for the F(-)···H(2)O pair. The dominance of this effect for e.g. multiply charged ions is suggested.     

Differentiating allylic and vinylic leaving groups for Pd catalysis. The use of vinyl iodide to facilitate room temperature activation of a vinyl CX bond in the presence of allyl carbonate

Ionization of allylic, stabilized leaving groups by Pd catalysis is a very facile process at or below room temperature, whereas oxidative addition of many vinyl or aryl CX bonds requires heating. There are only a handful of examples in the literature where a vinyl leaving group can be activated in a competitive fashion in the presence of a suitable allylic one. In this report a series of polyfunctional olefin building blocks have been constructed that allow vinyl halides to be selectively and routinely activated in the presence of highly active allylic leaving groups. This differentiation is dependent solely on the bond strengths of the leaving groups involved and shows no temperature dependence to differentiate the two processes.     

Organocatalytic diastereo- and enantioselective Michael addition reactions of 5-aryl-1,3-dioxolan-4-ones

5-Aryl-1,3-dioxolan-4-one heterocycles derived from mandelic acid derivatives and hexafluoroacetone have been identified as new and effective pro-nucleophiles in highly diastereo- and enantioselective Michael addition reactions to nitro olefins catalyzed by bifunctional epi-9-amino-9-deoxy cinchona alkaloid derivatives. Diastereoselectivities up to 98% and enantioselectivities up to 89% for a range of nitro olefins and 5-aryl-1,3-dioxolan-4-ones under mild reaction conditions are reported.     

Radical quantum yields from formaldehyde photolysis in the 30,400-32,890 cm(-1) (304-329 nm) spectral region: detection of radical photoproducts using pulsed laser photolysis-pulsed laser induced fluorescence

The relative quantum yield for the production of radical products, H + HCO, from the UV photolysis of formaldehyde (HCHO) has been measured using a pulsed laser photolysis–pulsed laser induced fluorescence (PLP–PLIF) technique across the 30,400–32,890 cm(–1) (304–329 nm) spectral region of the ?(1)A2–X?(1)A1 electronic transition. The photolysis laser had a bandwidth of 0.09 cm(–1), which is slightly broader than the Doppler width of a rotational line of formaldehyde at 300 K (0.07 cm(–1)), and the yield spectrum shows detailed rotational structure. The H and HCO photofragments were monitored using LIF of the OH radical as a spectroscopic marker. The OH radicals were produced by rapid reaction of the H and HCO photofragments with NO2. This technique produced an “action” spectrum that at any photolysis wavelength is the product of the H + HCO radical quantum yield and HCHO absorption cross section at the photolysis wavelength and is a relative measurement. Using the HCHO absorption cross section previously obtained in this laboratory, the relative quantum yield was determined two different ways. One produced band specific yields, and the other produced yields averaged over each 100 cm(–1). Yields were normalized to a value of 0.69 at 31,750 cm(–1) based on the current recommendation of Sander et al. (Sander, S. P.; Abbatt, J.; Barker, J. R.; Burkholder, J. B.; Friedl, R. R.; Golden, D. M.; Huie, R. E.; Kolb, C. E.; Kurylo, M. J.; Moortgat, G. K.; et al. Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 17; Jet Propulsion Laboratory: Pasadena, CA, USA, 2011). The resulting radical quantum yields agree well with previous experimental studies and the current JPL recommendation but show greater wavelength dependent structure. A significant decrease in the quantum yield was observed for the 5(0)(1) + 1(0)(1)4(0)(1) combination band centered at 31,125 cm(–1). This band has a low absorption cross section and has little impact on the calculated atmospheric photodissociation rate but is a further indication of the complexity of HCHO photodissociation dynamics.