Binding sites of nitrogenase: kinetic and theoretical studies of cyanide binding to extracted FeMo-cofactor derivatives

The first kinetic study of a substrate (CN(-)) binding to the isolated active site (extracted FeMo-cofactor) of nitrogenase is described. The kinetics of the reactions between CN(-) and various derivatives of extracted FeMo-cofactor [FeMoco-L; where L is bound to Mo, and is NMF, Bu(t)NC, or imidazole (ImH)] have been followed using a stopped-flow, sequential-mix method in which the course of the reaction is followed indirectly, by monitoring the change in the rate of the reaction of the cofactor with PhS(-). The kinetic results, together with DFT calculations, indicate that the initial site of CN(-) binding to FeMoco-L is controlled by a combination of the electron-richness of the cluster core and lability of the Mo-L bond. Ultimately, the reactions between FeMoco-L and CN(-) involve displacement of L and binding of CN(-) to Mo. These reactions occur with a variety of rates and rate laws dependent on the nature of L. For FeMoco-NMF, the reaction with CN(-) is complete within the dead-time of the apparatus (ca. 4 ms), while with FeMoco-CNBu(t) the reaction is much slower and exhibits first order dependences on the concentrations of both FeMoco-CNBu(t) and CN(-) (k = 2.5 +/- 0.5 x 10(4) dm(3) mol(-1) s(-1)). The reaction of FeMoco-ImH with CN(-) occurs at a rate which exhibits a first order dependence on FeMoco-ImH but is independent of the concentration of CN(-) (k = 50 +/- 10 s(-1)). The results are interpreted in terms of CN(-) binding directly to the Mo site for FeMoco-NMF and FeMoco-ImH, but with FeMoco-CNBu(t) initial binding at an Fe site is followed by movement of CN(-) to Mo. Complementary DFT calculations are consistent with this interpretation, indicating that, in FeMoco-L, the Mo-L bond is stronger for L = ImH than for L = CNBu(t) and the binding of CN(-) to Mo is stronger than to any Fe atom in the cofactor.     

PHOTOINHIBITION OF PHOTOSYNTHESIS IN NATURAL WATERS*

Abstract— A quantitative analysis of the wavelength-dependent influence of solar irradiance on natural phytoplankton photosynthesis has been made. The effect on productivity due to several different UV radiation regimes has been measured. In the course of this analysis, it has been shown that the biological weighting function for photoinhibition of chloroplasts (Jones and Kok, 1966) allows the calculation of a biologically effective dose which is consistent with the measured photoinhibition in natural phytoplankton populations. The ecological implications of a change in available UV radiation, possibly due to anthropogenic altering of the ozone layer, are explored and it is found that the present static bottle ^l4C technique of measuring in situ phytoplankton productivity does not lend itself to assessing accurately the potential ecological consequences of possible increased MUV (middle ultraviolet radiation in the 280–340 nm region) on phytoplankton populations. A small change in MUV has a relatively minor effect on photoinhibition dose rates whereas it has a large potential effect on DNA dose rates.     

Effect of ethanol on the interaction between poly(vinylpyrrolidone) and sodium dodecyl sulfate

The effect of ethanol on the interaction between the anionic surfactant sodium dodecyl sulfate (SDS) and the nonionic polymer poly(vinylpyrrolidone) (PVP) has been investigated using a range of techniques including surface tension, fluorescence, electron paramagnetic resonance (EPR), small-angle neutron scattering (SANS), and viscosity. Surface tension and fluorescence studies show that the critical micelle concentration (cmc) of the surfactant decreases to a minimum value around 15 wt % ethanol; that is, it follows the cosurfactant effect. However, in the presence of PVP, the onset of the interaction, denoted cmc(1), between the surfactant and the polymer is considerably less dependent on ethanol concentration. The saturation point, cmc(2), however, reflects the behavior of the cmc in that it decreases upon addition of ethanol. This results in a decrease in the amount of surfactant bound to the polymer [C(bound) = cmc(2) - cmc] at saturation. The viscosity of simple PVP solutions depends on ethanol concentration, but since SANS studies show that ethanol has no effect on the polymer conformation, the changes observed in the viscosity reflect the viscosity of the background solvent. There are significant increases in bulk viscosity when the surfactant is added, and these have been correlated with the polymer conformation extracted from an analysis of the SANS data and with the amount of polymer adsorbed at the micelle surface. Competition between ethanol and PVP to occupy the surfactant headgroup region exists; at low ethanol concentration, the PVP displaces the ethanol and the PVP/SDS complex resembles that formed in the absence of the ethanol. At higher ethanol contents, the polymer does not bind to the ethanol-rich micelle surface.     

Hydrogen Atoms Are Produced When Tryptophan within a Protein Is Irradiated with Ultraviolet Light

Abstract— The UV photolysis of the aromatic amino acid, tryptophan (Trp), in the Ca²⁺-binding protein, cod paralbumin, type III, was studied using electron paramagnetic resonance (EPR) spectroscopy in the temperature range 4–80 K. For the Ca²⁺-bound protein, irradiation with UV light (250–400 nm) resulted in the generation of atomic hydrogen with a hyperfine splitting of 50.9 mT, whereas in the Ca²⁺-free form, where the Trp is exposed to solvent, the trapped atomic hydrogen was not in evidence. In the same spectra, the radical signal in the g = 2.00 region could be detected. The line shape of the Ca²⁺-bound form is similar to the EPR line shape obtained for Trp in micellar systems. In contrast, the EPR line shape for the Ca²⁺-free form is essentially featureless up to 80 K. The EPR spectra of the photoproducts of Trp and the nature of the photoreactions are therefore sensitive to the environment of Trp within the protein.     

Calculation of enthalpies of hydrogenation of hydrocarbons

Sets of hydrogen molecule equivalents have been developed which permit the calculation of hydrogenation of different types of carbon-carbon bonds from ab initio total energies (3-21G and 6-31G* basis sets, and, to a more limited extent, for MP2/6-31G* data) of reactants and products. The calculated enthalpies of hydrogenation are in good agreement with experiment for unstrained molecules, with average errors on the order of 2 kcal/mol. The 6-31G* equivalents allow the enthalpies for strained molecules to be calculated accurately, but the 3-21G equivalents do not. The equivalents for both basis sets have been tested by calculating the enthalpies of hydrogenation of carbon-carbon bonds in nitrogen- and oxygen-containing organic molecules, free radicals, and classical carbocations. The results are in good agreement with experiment in most cases.     

The Remarkable Structure of Lithium Cyanide/Isocyanide

Electron correlation corrections have a considerable influence on the relative stabilities of lithium isocyanide ( 1 ), lithium cyanide ( 2 ), and the bridged form, 3 . While Hartree-Fock theory finds 1 to be most stable and 3 not to be a minimum, MP2/6-31G* optimization indicates 3 to be the global minimum. At higher levels employing full fourth-order Møller-Plesset theory and a quadruply split valence and polarized basis set (MP4STDQ/6-311+G*), 2 is only about 2 kcal/mol less stable than 1 and 3 , which are indicated to have nearly the same energy. LiNC thus is similar to C(Na)N and C(K)N, both of which are known to prefer T-shaped (bridged) structures in the gas phase. However, to an even greater extent than formerly realized, rotation of the lithium cation around the cyanide anion nucleus should be practically free. ΔH (LiCN) = 32.8 kcal/mol is estimated from the calculated lithium cation affinity of 151.2 kcal/mol. In addition, we find at the MP4SDTQ/6-31+G*//MP2/6-31G* level that the bridged form of NaCN is favored by 2–3 kcal/mol over the corresponding linear forms, which have nearly the same energy.     

An example where orbital relaxation is an important contribution to the Fukui function

Density-functional electronic structure calculations are performed on the molecules Cr2(hpp)4, Mo2(hpp)4, and W2(hpp)4, where the bridging ligand, hpp, is the anion of 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine. The calculated electronic densities are used to determine the Fukui functions. These molecules are unique not only in their ability as electron donors but also because orbital relaxation plays a decisive role in their reactivity. Unlike other examples in the literature, the reactivity of these compounds cannot be expressed solely in terms of the highest occupied and lowest unoccupied Kohn-Sham orbitals but only using the Fukui function, which includes the effects of orbital relaxation.     

Physicochemical characterization of degradable thermosensitive polymeric micelles

Amphiphilic AB block copolymers consisting of thermosensitive poly(N-(2-hydroxypropyl) methacrylamide lactate) and poly(ethylene glycol), pHPMAmDL-b-PEG, were synthesized via a macroinitiator route. Dynamic light scattering measurements showed that these block copolymers form polymeric micelles in water with a size of around 50 nm by heating of an aqueous polymer solution from below to above the critical micelle temperature (cmt). The critical micelle concentration as well as the cmt decreased with increasing pHPMAmDL block lengths, which can be attributed to the greater hydrophobicity of the thermosensitive block with increasing molecular weight. Cryogenic transmission electron microscopy analysis revealed that the micelles have a spherical shape with a narrow size distribution. 1H NMR measurements in D2O showed that the intensity of the peaks of the protons from the pHPMAmDL block significantly decreased above the cmt, indicating that the thermosensitive blocks indeed form the solidlike core of the micelles. Static light scattering measurements demonstrated that pHPMAmDL-b-PEG micelles with relatively large pHPMAmDL blocks possess a highly packed core that is stabilized by a dense layer of swollen PEG chains. FT-IR analysis indicated that dehydration of amide bonds in the pHPMAmDL block occurs when the polymer dissolved in water is heated from below to above its cmt. The micelles were stable when an aqueous solution of micelles was incubated at 37 degrees C and at pH 5.0, where the hydrolysis rate of lactate side groups is minimized. On the other hand, at pH 9.0, where hydrolysis of the lactic acid side groups occurs, the micelles started to swell after 1.5 h of incubation and complete dissolution of micelles was observed after 4 h as a result of hydrophilization of the thermosensitive block. Fluorescence spectroscopy measurements with pyrene loaded in the hydrophobic core of the micelles showed that when these micelles were incubated at pH 8.6 and at 37 degrees C the microenvironment of pyrene became increasingly hydrated in time during this swelling phase. The results demonstrate the potential applicability of pHPMAmDL-b-PEG block copolymer micelles for the controlled delivery of hydrophobic drugs.     

Nitrile-functionalized pyridinium ionic liquids: synthesis, characterization, and their application in carbon-carbon coupling reactions

A series of relatively low-cost ionic liquids, based on the N-butyronitrile pyridinium cation [C(3)CNpy](+), designed to improve catalyst retention, have been prepared and evaluated in Suzuki and Stille coupling reactions. Depending on the nature of the anion, these salts react with palladium chloride to form [C(3)CNpy](2)[PdCl(4)] when the anion is Cl(-) and complexes of the formula [PdCl(2)(C(3)CNpy)(2)][anion](2) when the anion is PF(6)(-), BF(4)(-), or N(SO(2)CF(3))(2)(-). The solid-state structures of [C(3)CNpy]Cl and [C(3)CNpy](2)[PdCl(4)] have been established by single-crystal X-ray diffraction. The catalytic activity of these palladium complexes following immobilization in both N-butylpyridinium and nitrile-functionalized ionic liquids has been evaluated in Suzuki and Stille coupling reactions. All of the palladium complexes show good catalytic activity, but recycling and reuse is considerably superior in the nitrile-functionalized ionic liquid. Inductive coupled plasma spectroscopy reveals that the presence of the coordinating nitrile moiety in the ionic liquid leads to a significant decrease in palladium leaching relative to simple N-alkylpyridinium ionic liquids. Palladium nanoparticles have been identified as the active catalyst in the Stille reaction and were characterized using transmission electron microscopy.