Measurement of Very Fast Exchange Rates of Individual Amide Protons in Proteins by NMR Spectroscopy

NMR spectroscopy is a pivotal technique to measure hydrogen exchange rates in proteins. However, currently available NMR methods to measure backbone exchange are limited to rates of up to a few per second. To raise this limit, we have developed an approach that is capable of measuring proton exchange rates up to approximately 10⁴ s⁻¹. Our method relies on the detection of signal loss due to the decorrelation of antiphase operators 2N_xH_z by exchange events that occur during a series of pi pulses on the ¹⁵N channel. In practice, signal attenuation was monitored in a series of 2D H(CACO)N spectra, recorded with varying pi-pulse spacing, and the exchange rate was obtained by numerical fitting to the evolution of the density matrix. The method was applied to the small calcium-binding protein Calbindin D_9k, where exchange rates up to 600 s⁻¹ were measured for amides, where no signal was detectable in ¹⁵N−¹H HSQC spectra. A temperature variation study allowed us to determine apparent activation energies in the range 47–69 kJ mol⁻¹ for these fast exchanging amide protons, consistent with hydroxide-catalyzed exchange.     

Unraveling the dynamics of the C(3P,1D) + C2H2 reactions by the crossed molecular beam scattering technique

A detailed investigation of the dynamics of the reactions of ground- and excited-state carbon atoms, C(3P) and C(1D), with acetylene is reported over a wide collision energy range (3.6-49.1 kJ mol-1) using the crossed molecular beam (CMB) scattering technique with electron ionization mass spectrometric detection and time-of-flight (TOF) analysis. We have exploited the capability of (a) generating continuous intense supersonic beams of C(3P, 1D), (b) crossing the two reactant beams at different intersection angles (45, 90, and 135 degrees ) to attain a wide range of collision energies, and (c) tuning the energy of the ionizing electrons to low values (soft ionization) to suppress interferences from dissociative ionization processes. From angular and TOF distribution measurements of products at m/z=37 and 36, the primary reaction products of the C(3P) and C(1D) reactions with C2H2 have been identified to be cyclic (c)-C3H + H, linear (l)-C3H + H, and C3 + H2. From the data analysis, product angular and translational energy distributions in the center-of-mass (CM) system for both the linear and cyclic C3H isomers as well as the C3 product from C(3P) and for l/c-C3H and C3 from C(1D) have been derived as a function of collision energy from 3.6 to 49.1 kJ mol-1. The cyclic/linear C3H ratio and the C3/(C3 + c/l-C3H) branching ratios for the C(3P) reaction have been determined as a function of collision energy. The present findings have been compared with those from previous CMB studies using pulsed beams; here, a marked contrast is noted in the CM angular distributions for both C3H- and C3-forming channels from C(3P) and their trend with collision energy. Consequently, the interpretation of the reaction dynamics derived in the present work contradicts that previously proposed from the pulsed CMB studies. The results have been discussed in the light of the available theoretical information on the relevant triplet and singlet C3H2 ab initio potential energy surfaces (PESs). In particular, the branching ratios for the C(3P) + C2H2 reaction have been compared with the available theoretical predictions (approximate quantum scattering calculations and quasiclassical trajectory calculations on ab initio triplet PESs and, very recent, statistical calculations on ab initio triplet PESs as well as on ab initio triplet/singlet PESs including nonadiabatic effects, that is, intersystem crossing). While the experimental branching ratios have been corroborated by the statistical predictions, strong disagreement has been found with the results of the dynamical calculations. The astrophysical implications of the present results have been noted.     

Allylation of exocyclic N-Acyliminium ions generated from chiral N-[1-(phenylsulfonyl)alkyl]oxazolidin-2-ones

N-[1-(Phenylsulfonyl)alkyl]oxazolidin-2-ones are successfully prepared by condensation of the corresponding optically active oxazolidin-2-ones with aldehydes and benzenesulfinic acid. At low temperature, in the presence of titanium tetrachloride, these sulfones are converted into N-acyliminium ions, which react with allyltrimethylsilane with a variable degree of stereoselectivity. The best results are obtained with (R)-5,5-dimethyl-4-phenyloxazolidin-2-one as a chiral auxiliary. Cleavage of the oxazolidin-2-one ring with lithium/ammonia affords the corresponding homoallylamines, which reveal an absolute configuration opposite that expected on the basis of the usual steric effects. A complexation of the Lewis acid with the N-acyliminium ion may be responsible of this rather unusual stereochemical outcome.     

Thermodynamic study of (heptane + amine) mixtures. III: Excess and partial molar volumes in mixtures with secondary,tertiary, and cyclic amines at 298.15 K

Excess molar volumes V^E at 298.15 K were determined by means of a vibrating tube densimeter for binary mixtures of {heptane + open chain secondary (diethyl to dibutyl) and tertiary (triethyl to tripentyl) amines} as well as for cyclic imines (C₂, C₃, C₄, C₆, and C₇) and primary cycloalkylamines (C₅, C₆, C₇, and C₁₂). The V^E values were found positive for mixtures involving small size amines, with V^E decreasing as the size increases. Negative V^E’s were found for tributyl- and tripentylamine, heptamethylenimine, and cyclododecylamine. Mixtures of heptane with cycloheptylamine showed an s-shaped curve.Partial molar volumes $V^{°}$ of amines at infinite dilution in heptane were obtained from V^E and compared with $V^{°}$ of hydrocarbons and other classes of organic compounds taken from literature. An additivity scheme, based on the intrinsic volume approach, was applied to estimate group (CH₃, CH₂, CH, C, NH₂, NH, N, OH, O, CO, and COO) contributions to $V^{°}$. These contributions, the effect of cyclization on $V^{°}$, and the limiting slope of the apparent excess molar volumes were discussed in terms of solute–solvent and solute–solute interactions.     

Models for biological trinuclear copper clusters. Characterization and enantioselective catalytic oxidation of catechols by the copper(II) complexes of a chiral ligand derived from (S)-(-)-1,1'-binaphthyl-2,2'-diamine

The dinuclear and trinuclear Cu(II) complexes of an octadentate ligand derived from (S)-1,1'-binaphthyl-2,2'-diamine have been prepared and characterized by UV/Vis, CD, EPR and NMR spectroscopy. The ligand contains two tridentate aminobis(benzimidazole) donor arms connected to a central bidentate diaminobinaphthyl linker, which hosts the chiral unit. In the dinuclear Cu complex the ligation occurs essentially within the tridentate arms of the ligand. The two Cu centers are EPR nonequivalent and noninteracting. The EPR data suggests that one of the Cu ions additionally interacts with one of the tertiary aminonaphthyl donors. In the trinuclear complex the two aminonaphthyl donors bind the third Cu ion. The EPR spectrum of this complex shows the signal for a mononuclear Cu(II) center bound to a tridentate arm, while the remaining two Cu(II) centers are coupled through hydroxo groups. The CD spectrum shows that in the free ligand a severe reduction of the dihedral angle between the naphthyl groups from the strain free range occurs. This conformation is stabilized by ring stacking interactions with the benzimidazole groups. On complex formation this interaction is removed because the benzimidazole groups are involved in metal binding. In the dinuclear Cu complex the conformation of the binaphthyl chromophore probably approaches the strain free range, while in the trinuclear Cu complex a marked flattening of the dihedral angle between the two naphthyl rings occurs. Both complexes are active catalysts in the oxidation of L-/D-Dopa derivatives to quinones. High enantioselectivity is observed in the oxidation of L-/D-Dopa methyl ester catalyzed by the dinuclear Cu complex, which exhibits strong preference for the d enantiomer. The enantioselectivity is largely lost for the trinuclear Cu complex.     

Nitrite increases the enantioselectivity of sulfoxidation catalyzed by myoglobin derivatives in the presence of hydrogen peroxide

The effect of nitrite in the sulfoxidation of organic sulfides catalyzed by myoglobin (Mb) in the presence of hydrogen peroxide has been investigated. A general improvement in enantioselectivity was found for the reaction catalyzed by horse heart metMb and a series of sperm whale metMb derivatives including the wild type protein, the active site mutants T67K Mb, T67R Mb, T67R/S92D Mb, and the T67K Mb derivative reconstituted with the modified prosthetic group protohemin-l- histidine methyl ester.     

Thermodynamic study of heptane + secondary, tertiary and cyclic amines mixtures. Part IV. Excess and solvation enthalpies at 298.15 K

Partial molar enthalpies and excess enthalpies H^E of binary mixtures of heptane + secondary and tertiary n-alkyl, primary cycloalkyl, and secondary (hetero)cyclic amines have been determined at 298.15 K by isothermal titration calorimetry in the whole composition range. All mixtures showed positive H^E values which decrease with increasing amine size in each category, and decrease in the order cyclic primary > cyclic secondary > linear primary [1] > secondary > tertiary when comparing amines of similar size in different categories. From partial molar enthalpies at infinite dilution and known enthalpies of vaporization, the solvation enthalpies have been calculated either for heptane in amines and for amines in heptane. These quantities, together with their cavitational and interactional terms obtained applying the scaled particle theory, are discussed to get insight into the types and relative strength of solute-solvent interactions and into their effects on molecular structure features such as branching and cyclization.     

Structural flexibility and role of vicinal 2-thienyl rings in 2,3-dicyano-5,6-di(2-thienyl)-1,4-pyrazine, [(CN)2Th2Pyz], its palladium(II) complex [(CN)2Th2Pyz(PdCl2)2], and the related pentametallic pyrazinoporphyrazines [(PdCl2)4Th8TPyzPzM] (M = Mg(II)(H2O), Zn(II))

The solid state and solution structure of 2,3-dicyano-5,6-di(2-thienyl)-1,4-pyrazine, [(CN)(2)Th(2)Pyz], and its Pd(II) derivative, [(CN)(2)Th(2)Pyz(PdCl(2))(2)]·H(2)O, formed by reaction of [(CN)(2)Th(2)Pyz] with [(C(6)H(5)CN)(2)PdCl(2)] were characterized by X-ray, UV-visible, (1)H and (13)C NMR, and extended X-ray absorption fine structure (EXAFS) spectral measurements. The X-ray crystal structure of [(CN)(2)Th(2)Pyz] shows the presence of one thienyl ring positioned orthogonal to the rest of the molecule, with the two vicinal thienyl rings lying orthogonal to each other in a rare arrangement. NMR studies of [(CN)(2)Th(2)Pyz] in the solid state and in solutions of dimethylformamide or dimethyl sulfoxide confirm a nonequivalence of the thienyl rings in the solid state and also in solution. EXAFS results indicate that two distinct Pd(II) coordination sites are formed at the di(2-thienyl)pyrazino moiety of [(CN)(2)Th(2)Pyz(PdCl(2))(2)]·H(2)O, with identical Pd-N(pyz) (2.03(3) ?) and Pd-Cl (2.36(3) ?) bond lengths but with different Pd-S1 (2.25(4) ?) and Pd-S2 (3.21(5) ?) bond distances in an overall asymmetric molecular framework. Density functional theory (DFT) and time-dependent DFT (TDDFT) theoretical studies also provide information about the structure and spectral behavior of the precursor and its metalated Pd(II) derivative. (1)H/(13)C NMR and UV-visible spectral measurements were also carried out on two heteropentametallic porphyrazine macrocycles which were prepared by a reaction of PdCl(2) with [Th(8)TPyzPzM] where Th(8)TPyzPz = tetrakis-2,3-[5,6-di-(2-thienyl)-pyrazino]porphyrazinato dianion and M = Mg(II)(H(2)O) or Zn(II). Spectroscopic data on the newly synthesized [(PdCl(2))(4)Th(8)TPyzPzM] compounds suggest that the binding of PdCl(2) involves coordination sites of the type S(2(th))PdCl(2) with the two thienyl rings of each di(2-thienyl)pyrazino fragment bound to Pd(II) in an equivalent manner ("th-th" coordination). This is similar to what was found for the corresponding octapyridinated analogues ("py-py" coordination).     

Tuning the excitonic and plasmonic properties of copper chalcogenide nanocrystals

The optical properties of stoichiometric copper chalcogenide nanocrystals (NCs) are characterized by strong interband transitions in the blue part of the spectral range and a weaker absorption onset up to ~1000 nm, with negligible absorption in the near-infrared (NIR). Oxygen exposure leads to a gradual transformation of stoichiometric copper chalcogenide NCs (namely, Cu(2-x)S and Cu(2-x)Se, x = 0) into their nonstoichiometric counterparts (Cu(2-x)S and Cu(2-x)Se, x > 0), entailing the appearance and evolution of an intense localized surface plasmon (LSP) band in the NIR. We also show that well-defined copper telluride NCs (Cu(2-x)Te, x > 0) display a NIR LSP, in analogy to nonstoichiometric copper sulfide and selenide NCs. The LSP band in copper chalcogenide NCs can be tuned by actively controlling their degree of copper deficiency via oxidation and reduction experiments. We show that this controlled LSP tuning affects the excitonic transitions in the NCs, resulting in photoluminescence (PL) quenching upon oxidation and PL recovery upon subsequent reduction. Time-resolved PL spectroscopy reveals a decrease in exciton lifetime correlated to the PL quenching upon LSP evolution. Finally, we report on the dynamics of LSPs in nonstoichiometric copper chalcogenide NCs. Through pump-probe experiments, we determined the time constants for carrier-phonon scattering involved in LSP cooling. Our results demonstrate that copper chalcogenide NCs offer the unique property of holding excitons and highly tunable LSPs on demand, and hence they are envisaged as a unique platform for the evaluation of exciton/LSP interactions.