First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations

The role of the second shell in the process of metal binding and selectivity in metalloproteins has been elucidated by combining Protein Data Bank (PDB) surveys of Mg, Mn, Ca, and Zn binding sites with density functional theory/continuum dielectric methods (DFT/CDM). Peptide backbone groups were found to be the most common second-shell ligand in Mg, Mn, Ca, and Zn binding sites, followed (in decreasing order) by Asp/Glu, Lys/Arg, Asn/Gln, and Ser/Thr side chains. Aromatic oxygen- or nitrogen-containing side chains (Tyr, His, and Trp) and sulfur-containing side chains (Cys and Met) are seldom found in the second coordination layer. The backbone and Asn/Gln side chain are ubiquitous in the metal second coordination layer as their carbonyl oxygen and amide hydrogen can act as a hydrogen-bond acceptor and donor, respectively, and can therefore partner practically every first-shell ligand. The second most common outer-shell ligand, Asp/Glu, predominantly hydrogen bonds to a metal-bound water or Zn-bound histidine and polarizes the H-O or H-N bond. In certain cases, a second-shell Asp/Glu could affect the protonation state of the metal ligand. It could also energetically stabilize a positively charged metal complex more than a neutral ligand such as the backbone and Asn/Gln side chain. As for the first shell, the second shell is predicted to contribute to the metal selectivity of the binding site by discriminating between metal cations of different ionic radii and coordination geometries. The first-shell-second-shell interaction energies decay rapidly with increasing solvent exposure of the metal binding site. They are less favorable but are of the same order of magnitude as compared to the respective metal-first-shell interaction energies. Altogether, the results indicate that the structure and properties of the second shell are dictated by those of the first layer. The outer shell is apparently designed to stabilize/protect the inner-shell and complement/enhance its properties.     

Synthesis of 1-alkoxy-5-alkyluracils

1-Alkoxy-5-alkyluracils 2a-f have been prepared by the reaction of 2-alkyl-3-methoxyacryloyl isocyanates 8a-b with alkoxyamines 9a-c followed by cyclization of the resulting N-alkoxy-N'-(2-alkyl-3-methoxyacryloyl)ureas 10a-f. The isocyanates 8a-b were prepared from ethyl 2-alkylacrylates 3a-b in 5 steps.     

Thermodynamics of electrolyte solutions. The system HCl + CaCl2 + H2O at 298.15°K

Activity coefficients of hydrochloric acid have been determined from electromotive-force measurements of cells containing mixtures of hydrochloric acid and calcium chloride at constant total ionic strengthsI=0.1, 0.5, 1.0, 2.0, and 3.0 mole-kg^–1 at 298.15°K. Interpretations based on Scatchard's and Pitzer's equations indicate that Pitzer's equations probably provide a more convenient guide to the thermodynamic properties of the mixed-electrolyte solutions. Activity coefficients for calcium chloride were derived from these equations.     

Determination of trace elements in human serum by inductively coupled plasma atomic emission spectrometry with flow injection

An analytical method for the simultaneous determination of some trace elements (Au, Fe, Mg, Li, Sr, Zn) in human serum by inductively coupled plasma atomic emission spectrometry (ICP-AES) with flow injection is described. Physical interference caused by the change of sample viscosity is discussed. When 100 μl of serum was injected, the relevant recoveries of > 99% for Li, > 98% for Cu and Mg, > 95% for Fe were obtained for an NIST SRM with R.S.D. > 1.3% using optimized flow injection parameters. The prepared lyophilized control serum for routine analysis in clinical laboratories was analyzed and verified for the validity of the technique employed in this experiment using NIST SRM 909 as a primary reference material.     

Steric Stabilization of Colloids by Poly(dimethylsiloxane) in Carbon Dioxide: Effect of Cosolvents

Steric stabilization and flocculation of colloids with surface-grafted poly(dimethylsiloxane) (PDMS) chains are examined in liquid and supercritical carbon dioxide with and without hexane as a cosolvent. Neither poly(methyl methacrylate) (PMMA) nor silica particles with grafted 10,000 g/mol PDMS could be stabilized in pure CO(2) at pressures up to 345 bar at 25 degrees C and 517 bar at 65 degrees C without stirring. The addition of 15 wt% hexane to CO(2) led to stable dispersions with sedimentation velocities of 0.2 mm/min for 1-2 μm PMMA particles. The critical flocculation pressure of the colloids in the hexane/CO(2) mixture, determined from turbidity versus time measurements, was found to be the same for silica and PMMA particles and was well above the upper critical solution pressure for the PDMS-CO(2) system. The addition of a nonreactive cosolvent, hexane, eliminates flocculation of PMMA particles synthesized through dispersion polymerization in CO(2) with PDMS-based surfactants. Copyright 2000 Academic Press.     

Non self-consistent field theory — A new approach in quantum mechanical calculations

An R ^o-independent electronic repulsion matrix is constructed, replacing the R ^o-dependent Hamiltonian matrix (R ^o is the density matrix). A non-SCF theory is developed to solve the eigenequation without using an iterative procedure. Three methods are proposed to solve for the eigenvectors and eigenvalues. Illustrative calculations are reported comparing the non-SCF and SCF theories. The calculated results are as expected: the ground state energies are nearly unchanged while the orbital energies are nearer to the experimental results. Other physical properties and spectral quantities are also compared. It is found that the ZDO assumption is applicable in the non-SCF theory if it is applicable in SCF theory.

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Zusammenfassung Eine R ^o-unabhängige Elektronenabstoßungsmatrix wird eingeführt, die die R ^o-abhängige Hamiltonmatrix ersetzt (R ^o ist die Dichtematrix). Zur Lösung der Eigenwertgleichung ohne iterative Prozeduren wird eine sog. Nicht-SCF-Theorie aufgestellt. An Beispielen werden die Ergebnisse von SCF- und Nicht-SCF-Rechnungen verglichen; dabei erweisen sich die Energien des Grundzustandes als nahezu unverändert, während die Energien der Orbitale näher bei den experimentellen Werten liegen. Die zero-differential-overlap-Näherung ist immer dann in der neuen Theorie anwendbar, wenn sie in der SCF-Theorie anwendbar ist.

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Résumé Une matrice de répulsion électronique indépendante de R ^o est construite, remplaçant la matrice hamiltonienne dépendant de R ^o (R ^o matrice de densité). Une théorie non SCF est développée afin de résoudre l'équation aux valeurs propres sans itérations. Trois méthodes de résolution du problème aux valeurs propres sont proposées. Des calculs illustrent la comparaison entre les théories SCF et non SCF. Les résultats des calculs sont comme prévus: l'énergie de l'état fondamental varie peu alors que les énergies orbitales sont plus proches des résultats expérimentaux. D'autres propriétés physiques ainsi que des grandeurs spectrales sont comparées. On trouve que l'approximation du recouvrement différentiel nul est applicable dans la théorie non SCF si elle est applicable dans la théorie SCF.

     

Regioselective hydroborations of methylvinylchlorosilanes

The regioselectivity of the hydroboration of the methylchlorovinylsilanes, Cl_nMe_3?nSiCHCH₂ (n= 0 ? 3), has been investigated using BH₃←THF, 9-BBN, disiamyl- and dicyclohexylborane. Methylation of the adducts with methylmagnesium bromide is complicated by formation of tetraalkylboronates. Alkaline hydrogen peroxide oxidation of the boronates gives reasonable yields of the corresponding α- and β-trimethylsilylethanols forn= 0 and 1. Forn= 2 and 3, conversion of the adducts to the corresponding α- and β- deuteroethylsilanes by treatment with excess sodium methoxide in methanol-0-d provides a more effective means of derivatization. Addition of the alkenes,n= 2 or 3, to excess BH₃←THF givesca. 90% of the α-boro-organo-chlorosilanes. For all of the alkenes, the dialkylboranes giveca. 80% of the β-boron adducts.     

Size-based analysis of incinerator fly ash using gravitational SPLITT fractionation, sedimentation field-flow fractionation, and inductively coupled plasma-atomic emission spectroscopy

Fly ash has been regarded as hazardous because of its high adsorption of toxic organic and/or inorganic pollutants. Fly ash is also known to have broad distributions of different chemical and physical properties, such as size and density. In this study, fly ash emitted from a solid waste incinerator was pre-fractionated into six sub-populations by use of gravitational SPLITT fractionation (GSF). The GSF fractions were then analyzed by sedimentation field-flow fractionation (SdFFF) and ICP–AES. SdFFF analysis showed the fly ash has a broad size distribution ranging from a few nanometers up to about 50 µm. SdFFF results were confirmed by electron microscopy. Inductively coupled plasma–atomic emission spectroscopy (ICP–AES) analysis of the GSF fractions showed the fly-ash particles contain a variety of inorganic elements including Ca, Si, Mg, Fe, and Pb. The most abundant in fly ash was Ca, followed by Si then Mg. No correlations were found between trace element concentration and particle size.     

Chemical and thermal stability of alkanethiol and sulfur passivated InP(100)

InP(100) surfaces treated with Na2Sx9H20 and CnH(2n+1)SH are examined by contact angle measurement, X-ray photoelectron spectroscopy, and atomic force microscopy to determine the chemical and thermal behavior of these passivated surfaces. The surfaces coated by octadecanethiol (n = 18) self-assembled monolayers (SAMs) are found to be more stable toward oxidation than the S-passivated surface. The chemical stability of octadecanethiol SAMs in various environments is examined. The thiol monolayer is found to be stable in 0.1 M HCl but degrades in 0.1 M NaOH, boiling chloroform, and water. The behavior of these surfaces at elevated temperatures under a vacuum is also investigated. The octadecanethiol-coated InP(100) is stable up to 473 K, above which the films begin to degrade. Unlike other substrates on which the entire molecule including the sulfur headgroup desorbs together, on InP, the sulfur headgroup remains on the surface even after annealing to 673 K. These observations suggest that the desorption occurs by S-C bond cleavage as well as In-S bond cleavage. The sulfur of S-passivated InP is found to be more thermally stable than that of the octadecanethiol monolayer, perhaps due to their different bonding geometries and hence energies.     

Arbophylline, a novel heptacyclic indole with a cage skeleton incorporating an acetal moiety

A new indole alkaloid, arbophylline, possessing a novel heptacyclic cage skeleton, and incorporating an acetal function, was obtained from the Malayan Kopsia arborea. The structure was established by spectroscopic analysis and a possible biogenetic pathway from an akuammiline-type precursor is presented.