Chemical markup,XML, and the World Wide Web. 4. CML schema

A revision to Chemical Markup Language (CML) is presented as a XML Schema compliant form, modularized into nonchemical and chemical components. STMML contains generic concepts for numeric data and scientific units, while CMLCore retains most of the chemical functionality of the original CML 1.0 and extends it by adding handlers for chemical substances, extended bonding models and names. We propose extension via new namespaced components for chemical queries, reactions, spectra, and computational chemistry. The conformance with XML schemas allows much greater control over datatyping, document validation, and structure.     

Ground states of molecules. 53.MNDO calculations for molecules containing chlorine

MNDO calculations of heats of formation, dipole moments, ionization potentials, and structures are reported for a wide range of compounds containing chlorine in its characteristic valence state (Cl^I) and one or more of the elements H, B, Be, C, N, O, and F. The calculated errors in the heats of formation and the dipole moments are not significantly greater than those previously reported for compounds containing no chlorine. First vertical ionization potentials were on average 0.95 eV too high. The ordering of higher cationic states was found to be correct, even for species such as Cl₂O, Cl₂, and HOCl, where ab initio–Koopmans' theorem calculations predict the incorrect ordering. The calculated energies and geometries of compounds such as CIF₃ are qualitatively incorrect, probably because of the lack of 3d atomic orbitals in the orbital basis set.     

Approaching the Hartree-Fock limit for organotransition metal complexes

In theoretical studies of the electronic structure of organometallic complexes, the choice of basis set is critical, much more so than for analogous studies of molecules containing only H, C, N, and O. This problem is discussed in the light of structural predictions for the transition metal hydrides MH, MH₂, and MH₄, for the fluorides MF₂ and MF₃, and for Ni(CO)₄, Ni(C₂H₄)₃, (CO)₃NiCH₂, and Ni(C₄H₄)₂.     

MIL-50, an open-framework GaPO with a periodic pattern of small water ponds and dry rubidium atoms: a combined XRD,NMR, and computational study

A new fluorinated gallium phosphate, MIL-50, has been synthesized under mild hydrothermal conditions using 1,6-diaminohexane. The chemical formula of MIL-50 is Rb(2)Ga(9)(PO(4))(8)(HPO(4))(OH)F(6).2N(2)C(6)H(18).7H(2)O. The structure is a network of hexameric units of Ga(3)(PO(4))(3)F(2) and Ga(3)(PO(4))(2)(HPO(4))F(3) via corner sharing. It creates a three-dimensional open-framework delimiting 6- and 18-ring channels running along the c axis. The diprotonated 1,6-diaminohexane and water molecules are trapped within the 18-ring pores, whereas the rubidium cations reside in the 6-ring ones. A double quantum (31)P NMR experiment and partial charge calculations indicate that water molecules are present under the form of periodic small clusters, lowering the multiplicity of one phosphorus site, P3. Though water hops within the clusters, the motion leaves the water pattern periodic. Rubidium is so tightly embedded into the framework that water moving in the large 18-ring channels does not reach it, leaving it therefore dry. The crystal framework may be ascribed to the orthorhombic space group Cmc2(1) (n degrees 36), a = 32.1510(2), b = 17.2290(3), c = 10.2120(1) A. The periodic water pattern has a different symmetry than that of the framework. A method has been devised to superpose the two sublattices that coexist in the same unit cell in order to have full occupancy of each site and to perform Madelung summations. This original method is of general interest for most zeolitic materials exhibiting a different symmetry for the framework and the template sublattices.     

Diethyl benzoylphosphonate as a ligand

Summary Complexes (2 : 1) of diethyl benzoylphosphonate (debp) with 3d metal perchlorates were synthesized and characterized by means of i.r. and electronic spectral, magnetic susceptibility and conductance measurements. In new complexes of the types [M(debp)₂(OClO₃)(OH₂)](ClO₄) (M = Fe, Co, Zn) and [Fe(debp)₂(OClO₃)(OH₂)](ClO₄)₂, both debp ligands function as bidentate chelating agents, coordinating through the P=O and C=O oxygens. In contrast, in the manganese(II) and nickel(II) complexes, which are of the [M(debp)₂(OClO₃)(OH₂)₂](ClO₄) type, one debp acts as a bidentate chelating ligand, while the second debp is unidentate, coordinating only through the P=O oxygen. Hexacoordination in the new cationic complexes is completed by coordination of aqua and unidentate perchlorato ligands, which are in competition for sites in the inner coordination sphere of the central metal ion with the weak debp ligand. On the other hand, debp, owing to its bulkiness, and especially the presence of the benzoyl substituent, introduces sufficiently severe steric hindrance during coordination. As a result of this, the formation of [M(debp)₃]ⁿ⁺ tris-chelate cationic complexes with the 3 d metal ions under study does not seem to be possible.     

The first example of a nitrile hydratase model complex that reversibly binds nitriles

Nitrile hydratase (NHase) is an iron-containing metalloenzyme that converts nitriles to amides. The mechanism by which this biochemical reaction occurs is unknown. One mechanism that has been proposed involves nucleophilic attack of an Fe-bound nitrile by water (or hydroxide). Reported herein is a five-coordinate model compound ([Fe(III)(S(2)(Me2)N(3)(Et,Pr))](+)) containing Fe(III) in an environment resembling that of NHase, which reversibly binds a variety of nitriles, alcohols, amines, and thiocyanate. XAS shows that five-coordinate [Fe(III)(S(2)(Me2)N(3)(Et,Pr))](+) reacts with both methanol and acetonitrile to afford a six-coordinate solvent-bound complex. Competitive binding studies demonstrate that MeCN preferentially binds over ROH, suggesting that nitriles would be capable of displacing the H(2)O coordinated to the iron site of NHase. Thermodynamic parameters were determined for acetonitrile (DeltaH = -6.2(+/-0.2) kcal/mol, DeltaS = -29.4(+/-0.8) eu), benzonitrile (-4.2(+/-0.6) kcal/mol, DeltaS = -18(+/-3) eu), and pyridine (DeltaH = -8(+/-1) kcal/mol, DeltaS = -41(+/-6) eu) binding to [Fe(III)(S(2)(Me2)N(3)(Et,Pr))](+) using variable-temperature electronic absorption spectroscopy. Ligand exchange kinetics were examined for acetonitrile, iso-propylnitrile, benzonitrile, and 4-tert-butylpyridine using (13)C NMR line-broadening analysis, at a variety of temperatures. Activation parameters for ligand exchange were determined to be DeltaH(+ +) = 7.1(+/-0.8) kcal/mol, DeltaS(+ +) = -10(+/-1) eu (acetonitrile), DeltaH(+ +) = 5.4(+/-0.6) kcal/mol, DeltaS(+ +) = -17(+/-2) eu (iso-propionitrile), DeltaH(+ +) = 4.9(+/-0.8) kcal/mol, DeltaS(+ +) = -20(+/-3) eu (benzonitrile), and DeltaH(+ +) = 4.7(+/-1.4) kcal/mol DeltaS(+ +) = -18(+/-2) eu (4-tert-butylpyridine). The thermodynamic parameters for pyridine binding to a related complex, [Fe(III)(S(2)(Me2)N(3)(Pr,Pr))](+) (DeltaH = -5.9(+/-0.8) kcal/mol, DeltaS = -24(+/-3) eu), are also reported, as well as kinetic parameters for 4-tert-butylpyridine exchange (DeltaH(+ +) = 3.1(+/-0.8) kcal/mol, DeltaS(+ +) = -25(+/-3) eu). These data show for the first time that, when it is contained in a ligand environment similar to that of NHase, Fe(III) is capable of forming a stable complex with nitriles. Also, the rates of ligand exchange demonstrate that low-spin Fe(III) in this ligand environment is more labile than expected. Furthermore, comparison of [Fe(III)(S(2)(Me2)N(3)(Et,Pr))](+) and [Fe(III)(S(2)(Me2)N(3)(Pr,Pr))](+) demonstrates how minor distortions induced by ligand constraints can dramatically alter the reactivity of a metal complex.     

1,3,4-oxadiazolin-2-ones from carbo-t-butoxyhydrazones

5-Substituted-1,3,4-oxadiazolin-2-ones 2 were synthesized by the oxidation of carbo-t-butoxyhydrazones 1 of aromatic aldehydes with lead tetraacetate or, preferably, iodosobenzene diacetate. In some instances 5-acetoxy-1,3,4-oxadiazoles 3 were obtained along with 2 . The oxidation of carboethoxyhydrazones 4 gave 2-ethoxy-1,3,4-oxadiazoles 5 .     

Simplified current decoupler for microchip capillary electrophoresis with electrochemical and pulsed amperometric detection

There is a need to develop broadly applicable, highly sensitive detection methods for microchip CE that do not require analyte derivatization. LIF is highly sensitive but typically requires analyte derivatization. Electrochemistry provides an alternative method for direct analyte detection; however, in its most common form, direct current (DC) amperometry, it is limited to a small number of easily oxidizable or reducible analytes. Pulsed amperometric detection (PAD) is an alternative waveform that can increase the number of electrochemically detectable analytes. Increasing sensitivity for electrochemical detection (EC) and PAD requires the isolation of detection current (nA) from the separation current (muA) in a process generally referred to as current decoupling. Here, we present the development of a simple integrated decoupler to improve sensitivity and its coupling with PAD. A Pd microwire is used as the cathode for decoupling and a second Au or Pt wire is used as the working electrode for either EC or PAD. The electrode system is easy to make, requiring no clean-room facilities or specialized metallization systems. Sensitive detection of a wide range of analytes is shown to be possible using this system. Using this system we were able to achieve detection limits as low as 5 nM for dopamine, 74 nM for glutathione, and 100 nM for glucose.