High-frequency (140-GHz) time domain EPR and ENDOR spectroscopy: the tyrosyl radical-diiron cofactor in ribonucleotide reductase from yeast

High-frequency pulsed EPR and ENDOR have been employed to characterize the tyrosyl radical (Y*)-diiron cofactor in the Y2-containing R2 subunit of ribonucleotide reductase (RNR) from yeast. The present work represents the first use of 140-GHz time domain EPR and ENDOR to examine this system and demonstrates the capabilities of the method to elucidate the electronic structure and the chemical environment of protein radicals. Low-temperature spin-echo-detected EPR spectra of yeast Y* reveal an EPR line shape typical of a tyrosyl radical; however, when compared with the EPR spectra of Y* from E. coli RNR, a substantial upfield shift of the g(1)-value is observed. The origin of the shift in g(1) was investigated by 140-GHz (1)H and (2)H pulsed ENDOR experiments of the Y2-containing subunit in protonated and D(2)O-exchanged buffer. (2)H ENDOR spectra and simulations provide unambiguous evidence for one strongly coupled (2)H arising from a bond between the radical and an exchangeable proton of an adjacent residue or a water molecule. Orientation-selective 140-GHz ENDOR spectra indicate the direction of the hydrogen bond with respect to the molecular symmetry axes and the bond length (1.81 A). Finally, we have performed saturation recovery experiments and observed enhanced spin lattice relaxation rates of the Y* above 10 K. At temperatures higher than 20 K, the relaxation rates are isotropic across the EPR line, a phenomenon that we attribute to isotropic exchange interaction between Y* and the first excited paramagnetic state of the diiron cluster adjacent to it. From the activation energy of the rates, we determine the exchange interaction between the two irons of the cluster, J(exc) = -85 cm(-)(1). The relaxation mechanism and the presence of the hydrogen bond are discussed in terms of the differences in the structure of the Y*-diiron cofactor in yeast Y2 and other class I R2s.     

Synthesis of Novel Nucleic Acid Mimics via the Stereoselective Intermolecular Radical Coupling of 3'-Iodo Nucleosides and Formaldoximes(1)

A highly convergent free radical coupling of alkyl iodides and oximes, mediated by bis(trimethylstannyl) benzopinacolate (8), has been utilized to prepare a series of dimeric nucleosides as mimics of natural nucleic acids. The systematic optimization of the reaction conditions allowed for the single-step conversion of the appropriate iodides and oximes into the 2'-deoxy dimers 9 in moderate to excellent yields. For example, the reaction of 3'-deoxy-3'-iodo-5'-(triphenylmethyl)thymidine (6a) with 3'-O-(tert-butyldiphenylsilyl)-5'-O-(methyleneimino)thymidine (7a) in the presence of 8 in degassed benzene gave an 81% yield of 3'-de(oxyphosphinico)-3'-(methyleneimino)-5'-O-(triphenylmethyl)thymidylyl-(3'-->5')-3'-O-(tert-butyldiphenylsilyl)thymidine (9a). Similarly prepared were dimers containing both pyrimidine (thymine, 5-methylcytosine) and purine (adenine, guanine) bases. The reaction was highly stereoselective, giving only a single dimeric species having the ribo-configuration of the newly introduced C-3'-branched methylene moiety. Also prepared were dimers 16, incorporating 2'-O-methyl ribonucleosides in both halves of the dimer. This required the synthesis of 3'-deoxy-3'-iodo-2'-O-methyl nucleosides 12 as well as 2'-O-methyl-5'-O-methyleneimino nucleosides 15. For example, 5'-O-(tert-butyldiphenylsilyl)-3'-deoxy-3'-iodo-2'-O-methyl-5-methyluridine (12e) was prepared in 80% yield by displacement of the corresponding triflate with Bu(4)NI. Also prepared were the suitably protected 3'-deoxy-3'-iodo adenosine and guanosine derivatives. Compounds 15 were prepared in high yield by a regioselective Mitsunobu reaction to give the corresponding 5'-O-phthalimido nucleosides 13, which were subsequently converted to the requisite oximes 15. In the 2'-O-methyl series, the pinacolate coupling reaction proceeded with efficiency equal to that observed for the 2'-deoxy series 9, but with slightly less stereoselectivity, giving predominantly the C-3'ribo products 16, contaminated with 5-25% of the epimeric material. Mixed base dimers containing both pyrimidine and purine bases at all possible positions, including purine-purine dimers were prepared. The hydroxylamine or methyleneimino (MI) backbone of several representative dimers so prepared was converted via methylation to give the corresponding methylenemethylimino (MMI)-linked compounds, which are novel phosphate surrogates for use in antisense oligonucleotides.     

Chemical modification of fluorinated self-assembled monolayer surfaces by low energy reactive ion bombardment

Reactive collisions of low energy (<100-eV) mass-selected ions are used to chemically modify fluorinated self-assembled monolayer surfaces comprised of alkanethiolate chains CF₃(CF₂)₁₁(CH₂)₂S— bound to Au. Typical experiments were done by using 1-nA/cm² beams and submonolayer doses of reactant ions. Characterization of the modified surface was achieved by in situ chemical sputtering (60-eV Xe^+·) and by independent high mass resolution time-of-flight-secondary ionization mass spectrometry (TOF-SIMS) (15–25-keV, Ga⁺) experiments. Treatment with Si³⁵C1 ₄ ^+· produced a surface from which Xe⁺ sputtering liberated CF₂ ³⁵C1⁺ ions, which suggested Cl-for-F halogen exchange at the surface. Isotopic labeling studies that used Si³⁵Cl₂ ³⁷Cl ₂ ^+· ; and experiments with bromine-containing and iodine-containing projectiles, confirmed this reaction. High mass resolution TOF-SIMS spectra, as well as high spatial resolution images, provided further evidence as to the existence of halogen-exchanged species at the bombarded surface. Analogous Cl-for-F halogen substitution was observed in a model gas-phase reaction. The ion-surface reaction is suggested to proceed through an intermediate fluoronium ion in which the projectile is bonded to the target molecule. The most significant conclusion of the study is that selective chemical modification of monolayer surfaces can be achieved by using reactive ion beams, which lead to new covalent bonds at the surface and in the scattered ions.     

Tetronic acids and derivatives. Part XI . Structure of coupling products of tetronic acids with benzenediazonium sulfate

¹³C Nmr, ¹H nmr and ir parameters of coupling products of tetronic acids (4-hydroxy-5H-furan-2-ones) with benzene diazonium sulfate are only consistent with a phenylhydrazone formulation with an almost equal ratio of the syn and anti configurations. These results contrast with those of coupling products of acyclic 3-ketoesters, existing mainly as anti tautomers, and more sharply with the 3-parabromophenylhydrazone of L-dehydro ascorbic acid, which is exclusively syn.     

Fine characterization of the ethylene and ethane sorption in poly(amide 12-block-tetramethylenoxide) copolymer/AgBF4 membranes

Ethylene/ethane sorption characteristics were determined for dry Pebax™ (poly(amide 12-block-tetramethylenoxide) copolymer)/AgBF₄ membranes by using an electronic microbalance. The membranes containing 0.7 and 22 wt.% AgBF₄ showed a dual-mode sorption isotherm. The ethane isotherms for all the membranes were of the Henry-type, which is the normal sorption for gases in rubbery polymers. The abnormal presence of Langmuir sorption sites only for ethylene in the rubbery copolymer, never reported sofar, is attributed to the silver-based specific complexation sites. The silver salt which dissolved in limited amounts in the rubbery copolymer had a much smaller Langmuir sorption capacity than the salt that crystallized in the copolymer. The sorption kinetics indicate that the crystallized salt did adsorb slowly ethylene according to a zeroth-order kinetics, but not ethane. The gas uptake kinetics resulting from a step of the pressure surrounding the copolymer exhibited one stage for ethane but two stages for ethylene. For the latter, there was first a fast Fickian sorption stage, then a drift of the zeroth-order sorption of ethylene on salt crystals, which contributes for a large part to the total uptake. The zeroth-order sorption suggests that the sorbed ethylene amount in the second-stage is independent of the crystal-surface coverage. The value of the Fickian diffusion coefficient calculated by fitting the kinetics with a solution of the second Fick’s law was 5 × 10⁻¹² m²/s for both ethylene (the first stage) and ethane, and is typical for small organic compounds in a rubbery material.     

Kinetics evidence for a complex between peroxynitrous acid and titanium(IV)

The reaction between TiO(2+) and ONOOH in 0.9 M H(2)SO(4) provides evidence for direct formation, previously unobserved, of a HOONO-metal complex. The reaction proceeds via formation of an end-on complex (k = 3.0 x 10(2) M(-1) s(-1)) that rearranges to form a side-on complex (k approximately equal to 20 s(-1)). With ONOOH in excess, this rearrangement proceeds more slowly (k approximately equal to 0.1 s(-1)), probably because multiple hydrogen oxoperoxonitrate molecules form end-on complexes with oxotitanium(IV) and hinder rearrangement to the side-on complex. The absorption spectrum of the final product is that of TiO(2)(2+). Presumably, during the rearrangement or later, NO+ is lost.     

Selective alterations of the antibody response to HIV-1

HIV infection leads to progressive alterations of humoral immune functions, including B-cell hyperplasia, hypergammaglobulinemia, elevated autoantibody titers, a poor response to neoantigens and mitogens, polyclonal B-cell activation, monoclonal gammopathies, and a significant deterioration of the antigen-specific humoral response. There is also an important isotypic imbalance of the antibody (Ab) response in the systemic compartment and a profound modification of mucosal immune functions. These abnormalities may contribute to disease progression and development of opportunistic infections, despite the presence of serum-neutralizing anti-HIV Abs. Equally important are the abnormal selection mechanisms of the Ab repertoire that seem to be responsible for B-cell clonal deletions. The V_H3 gene family, which encodes for approx 50% of immunoglobulins expressed by peripheral B-cells from normal adults, is underrepresented in human monoclonal antibodies to HIV-1 and in the peripheral B-cells of AIDS patients. These abnormalities, together with features of germinal center alteration, could be responsible for the clonal elimination of a subset of B-cells, and could contribute to HIV pathogenesis.     

Gas-phase derivatization of [C3H5]+ ions using tandem mass spectrometry methods A13C labelling study

The study of specifically ¹³C-labelled precursors sheds further light on the gas-phase chemistry of allyl and 2-propenyl cations. It is demonstrated that both species are formed from allyl and 2-propenyl bromide upon 70 eV electron impact ionization without skeletal reorganization. Gas-phase derivatization of the [C₃ H₅]⁺ ions with benzene facilitates, as suggested and observed earlier, the distinction of the two isomers using collision-induced dissociation of the Wheland complexes (or isomers thereof). The ¹³C labelling data clearly demonstrate that 64% of allyl cations survive the derivatization while 36% isomerize to 2-phenylpropyl cations; the latter are also formed via the reaction of 2-propenyl cation with benzene, protonation of α-methylstyrene and water loss from protonated 2-phenyl-2-propanol, respectively. Unimolecular loss of C₂H₄ from protonated allylbenzene proceeds via two competing reaction channels: one involves heterolysis of 1-phenylpropyl cations (～30%); the major pathway (～70%), however, involves decomposition via propylene benzenium ions.     

Structure, bonding, and reactivity of Ti and Zr amidate complexes: DFT and X-ray crystallographic studies

Easily prepared and highly modular organic amide proligands have been used to synthesize a series of new bis(amidate)-bis(amido) Ti and Zr complexes via protonolysis. These complexes have been structurally characterized by NMR spectroscopy and X-ray crystallography. The solid-state molecular structures of these complexes indicate that the amidate ligands bind to the metal centers in an exclusively bidentate fashion, resulting in discrete monomeric species. Geometric isomerism in these species is highly dependent upon the steric characteristics of the proligands utilized in the synthesis. In solution, these complexes are observed to isomerize on the NMR time scale, with one isomer being predominant. Bonding in the bis(amidate)-bis(amido) complexes was investigated by DFT calculations. The geometric isomers predicted by theory matched the experimentally observed results, within experimental error. The orbitals associated with amidate-metal bonding are energetically well below the frontier orbitals. The HOMO in these complexes is a pi orbital associated with amido ligand-to-metal bonding character, while the LUMO in all cases is a vacant d orbital on the metal center.     

Theoretical and experimental reevaluation of the basicity of lambda3-phosphinine

We have investigated the basicity of phosphinine (C5H5P, phosphabenzene) in reevaluating its proton affinity (PA) and gas-phase basicity (GB) and the pK(a) value of its protonated form. As a necessary step, we have first determined its gas-phase proton affinity. Using both mass spectrometric and quantum chemical methods, we have obtained the values PA(C5H5P) = 195.8 +/- 1.0 kcal mol(-1) and GB(298)(C5H5P) = 188.1 +/- 1.0 kcal mol(-1), in good agreement with previous results. We then derived a value of pK(a)(C5H6P+) = -16.1 +/- 1.0 in aqueous solution using three different approaches: the latter markedly differs from the currently available value of -10. The reason for such a discrepancy in the pK(a) of protonated phosphinine in solution is discussed. In the theoretical determination of PAs, evaluation of the basis set superposition error (BSSE) showed that this effect is quite small, being 0.1-0.2 kcal mol(-1) for phosphinine, when a density functional theory (DFT) method in conjunction with a large basis set were used.