Hydration free energies of monovalent ions in transferable intermolecular potential four point fluctuating charge water: an assessment of simulation methodology and force field performance and transferability

Hydration free energies of nonpolarizable monovalent atomic ions in transferable intermolecular potential four point fluctuating charge (TIP4P-FQ) are computed using several commonly employed ion-water force fields including two complete model sets recently developed for use with the simple water model with four sites and Drude polarizability and TIP4P water models. A simulation methodology is presented which incorporates a number of finite-system free energy corrections within the context of constant pressure molecular dynamics simulations employing the Ewald method and periodic boundary conditions. The agreement of the computed free energies and solvation structures with previously reported results for these models in finite droplet systems indicates good transferability of ion force fields from these water models to TIP4Q-FQ even when ion polarizability is neglected. To assess the performance of the ion models in TIP4P-FQ, we compare with consensus values for single-ion hydration free energies arising from recently improved cluster-pair estimates and a reevaluation of commonly cited, experimentally derived single-ion hydration free energies; we couple the observed consistency of these energies with a justification of the cluster-pair approximation in assigning single-ion hydration free energies to advocate the use of these consensus energies as a benchmark set in the parametrization of future ion force fields.     

High-temperature ultra-performance liquid chromatography coupled to hybrid quadrupole time-of-flight mass spectrometry applied to ibuprofen metabolites in human urine

The application of sub-2 microm porous particle liquid chromatography (LC) operated at elevated temperatures, coupled with time-of-flight mass spectrometry (MS), to the separation and identification of metabolites of ibuprofen present in human urine following oral administrations is illustrated. The LC/MS system generated a high-resolution analytical separation that, with an analysis time of 20 min, provided a peak capacity in the order of ca. 350. Using this system a total of nine glucuronides of the drug and its metabolites were detected, including a number of isomeric acyl glucuronides of ibuprofen itself, a side-chain-oxidized carboxylic acid acyl glucuronide and a number of acyl glucuronides of various hydroxylated metabolites. The identities of the metabolites were confirmed by their accurate mass values and the presence of the common fragment ions from ibuprofen.     

Direct observation of a 14-electron ruthenacyclobutane relevant to olefin metathesis

The 14-electron ruthenium phosphonium alkylidene complex [(IH2Mes)Cl2Ru=CH(PCy3)][B(C6F5)4], 1b, a highly active olefin metathesis catalyst, reacts with stoichiometric quantities of ethylene at -50 degrees C in CD2Cl2 to generate the ruthenacyclobutane complex [(IH2Mes)Cl2RuCH2CH2CH2], 2, and [CH2=CH(PCy3)][B(C6F5)4] in quantitative yield by NMR spectroscopy. 1H and 13C NMR spectroscopies on 2 and 2-13C3 are consistent with a symmetrical C2v structure, providing the first experimental information concerning this crucial intermediate in ruthenium-mediated olefin metathesis. At -50 degrees C, exchange with free ethylene takes place on the chemical time scale. Complex 2 decomposes in solution upon warming to room temperature, generating propene and unknown ruthenium product(s).     

Synthesis and characterisation of tungsten(VI) oxo-salicylate complexes for use in the chemical vapour deposition of self-cleaning films

Tungsten(VI) oxo-salicylate complexes were prepared in moderate yield (47 to 63%) by the reactions of WOCl4 and two equivalents of either 3-methylsalicylic acid (MesaliH2) or 3,5-di-isopropylsalicylic acid (di-i-PrsaliH2). Performing the reaction in refluxing toluene afforded the two analogous ditungsten complexes 1, [{WO(Mesali)(MesaliH)}2(mu-O)], and 2, [{WO(di-i-Prsali)(di-i-PrsaliH)}2(mu-O)], however in refluxing hexane the mononuclear tungsten complex , [WO(di-i-Prsali)(di-i-PrsaliH)Cl], was isolated. The single crystal X-ray study of revealed a pseudo-octahedral geometry around the tungsten centres. Aerosol assisted chemical vapour deposition of or afforded brown tungsten trioxide thin films. These films were converted to yellow fully oxidised WO3 on annealing in air at 550 degrees C for 30 minutes. The yellow WO3 films demonstrate preferred orientation on the substrate and show interesting functional properties-photo induced hydrophilicity and photocatalytic activity.     

Synthesis and Characterization of Water-Soluble 1,2-Bis(bis(hydroxyalkyl)phosphino)ethane Ligands and Their Nickel(II), Ruthenium(III), and Rhodium(I) Complexes

The syntheses of the water-soluble, chelating phosphines 1,2-bis(bis(hydroxybutyl)phosphino)ethane (1, n = 3; DHBuPE) and 1,2-bis(bis(hydroxypentyl)phosphino)ethane (1, n = 4; DHPePE) are reported. These ligands (and, in general, other 1,2-bis(bis(hydroxyalkyl)phosphino)ethane ligands) can be used to impart water solubility to metal complexes. As examples of this, the [Ni(DHPrPE)(2)Cl]Cl (2), [Rh(DHPrPE)(2)][Cl] (3), and [Ru(DHBuPE)(2)Cl(2)][Cl] (4) complexes were synthesized; they are indeed soluble in water (>0.5 M). Crystals of DHPrPE (1, n = 2) are monoclinic, space group P2(1)/c, with a = 9.5935(8) ?, b = 9.353(2) ?, c = 10.655(2) ?, alpha = 90 degrees, beta = 100.03(1) degrees, gamma = 90, V = 941.5(5) ?(3), R = 0.051, and Z = 2. Crystals of [Ni(DHPrPE)(2)Cl]Cl (2) are monoclinic, space group I2, with a = 15.951(3) ?, b = 11.454(2) ?, c = 20.843(3) ?, alpha = 90 degrees, beta = 91.24(2) degrees, gamma = 90 degrees, V = 3807(2) ?(3), R = 0.062, and Z = 4. Crystals of [Rh(DHPrPE)(2)][Cl] (3) are triclinic, space group P&onemacr;, with a = 13.900(2) ?, b = 15.378(2) ?, c = 18.058(2) ?, alpha = 87.71(1) degrees, beta = 75.03(1) degrees, gamma = 85.24(1), V = 3715(2) ?(3), R = 0.044, and Z = 4. Crystals of [Ru(DHBuPE)(2)Cl(2)][Cl] (4) are monoclinic, space group C2/c, with a = 14.310(2) ?, b = 21.630(2) ?, c = 15.459(3) ?, alpha = 90 degrees, beta = 99.83(1) degrees, gamma = 90, V = 4715(1) ?(3), R = 0.056, and Z = 4.     

Surface heterogeneity of polystyrene latex particles determined by dynamic force microscopy

Atomic force microscopy (AFM) was employed to characterize the surface chemistry distribution on individual polystyrene latex particles. The particles were obtained by surfactant-free emulsion polymerization and contained hydrophilic quaternary ammonium chloride, sodium sulfonate, or hydroxyethyl groups. The phase shift in dynamic force mode AFM is sensitive to charge/chemical interactions between an oscillating atomic force microscope tip and a sample surface. In this work, the phase imaging technique distinguished phase domains of 50-100 nm on the surfaces of dried latex particles in ambient air. The domains are attributed to the separation of ion-rich and ion-poor components of the polymer on the particle surface.     

Electrospray ionization tandem mass spectrometry of model peptides reveals diagnostic fragment ions for protein ubiquitination

In this work, synthetic peptides were used to determine the fragmentation behavior of ubiquitinated peptides and to find ions diagnostic for peptide ubiquitination. The ubiquitin-calmodulin peptide1 was chosen as the model peptide for naturally occurring ubiquitinated proteins cleaved with endoproteinase gluC. In addition, the fragmentation behavior of model ubiquitinated peptides produced by tryptic digestion was also of great interest since the standard protocols for proteomics-based protein identification use trypsin as the protease. Attachment of ubiquitin to a target protein results in a branched structure, but only ions from the ubiquitin side chain (and the lysine to which it is attached) can be used as diagnostic ions, since fragment ions that contain other amino acids from the parent protein will vary in mass. Characteristic b-type fragment ions from the gluC cleavage of the ubiquitin side chain (designated as b ions) were found which involve only the ubiquitin tail (b2, b3, b4, b5 and b6 ions at m/z 189.06, 302.12, 439.18, 552.30 and 651.30, respectively). Maximum production of these ions occurred at a collision energy of 45 eV in a Q-TOF instrument. Although a non-ubiquitinated peptide may produce isobaric fragment ions, it is unlikely that it can produce these ions in combination. With liquid chromatography/tandem mass spectrometry (LC/MS/MS) experiments, ubiquitinated peptides can readily be determined by surveying the reconstructed or extracted ion chromatograms of the diagnostic fragment ions for common peaks. Characteristic ions resulting from tryptic cleavage of the side chain were found in cleavage products with a missed cleavage, resulting in a LRGG- tag instead of a GG- tag. For the LRGG-tagged peptide, diagnostic MS/MS fragment ions (at m/z 270.17 and 384.21) from the ubiquitin tail (b2 and b4, respectively) were found, along with an internal fragment ion (LRGGK-28) at m/z 484.30. These ions should prove useful in precursor-ion scanning experiments for identifying peptides modified by attachment of ubiquitin, and for locating the site of ubiquitin attachment.     

The Hydrogenobyric Acid Structure Reveals the Corrin Ligand as an Entatic State Module Empowering B12 Cofactors for Catalysis

The B₁₂ cofactors instill a natural curiosity regarding the primordial selection and evolution of their corrin ligand. Surprisingly, this important natural macrocycle has evaded molecular scrutiny, and its specific role in predisposing the incarcerated cobalt ion for organometallic catalysis has remained obscure. Herein, we report the biosynthesis of the cobalt‐free B₁₂ corrin moiety, hydrogenobyric acid ( Hby ), a compound crafted through pathway redesign. Detailed insights from single‐crystal X‐ray and solution structures of Hby have revealed a distorted helical cavity, redefining the pattern for binding cobalt ions. Consequently, the corrin ligand coordinates cobalt ions in desymmetrized “entatic” states, thereby promoting the activation of B₁₂‐cofactors for their challenging chemical transitions. The availability of Hby also provides a route to the synthesis of transition metal analogues of B₁₂.