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.     

Metal Ions versus Protons: Tracking of Charge-Carrier Insertion into a Cathode Oxide in Aqueous Rechargeable Batteries

Protons in aqueous electrolytes can perform as an additional type of charge carrier for insertion/extraction in addition to the primary carrier cations in aqueous rechargeable batteries. Despite many diverse claims regarding the effect of protons, mutually conflicting experimental results and their interpretations without direct evidence have been reported over the last decade. Systematic examinations and analyses are thus imperative to clarify the conditions of proton insertion in aqueous rechargeable batteries. Utilizing V₂O₅ as a model cathode and beaker-type cells with a sufficient amount of ZnSO₄ aqueous electrolytes in this work, it is demonstrated that protons are inserted into the cathode prior to Zn-ions in low-pH conditions (pH ≤ 3.0). In stark contrast, the influence of protons on the discharge voltage and capacity is insignificant, when either the pH becomes higher (pH ≥ 4.0) or the electrolyte volume is considerably low in coin-type cells. Similar behavior of pH-dependent proton insertion is also verified in Na–, Mg–, and Al-ion electrolytes. Providing a resolution to the controversy regarding proton insertion, the present study emphasizes that the influence of protons substantially varies depending on the pH and relative volume of electrolytes in aqueous batteries.     

Skin-like Omnidirectional Stretchable Platform with Negative Poisson's Ratio for Wearable Strain–Pressure Simultaneous Sensor

Conventional elastomeric polymers used as substrates for wearable platforms have large positive Poisson's ratios (≈0.5) that cause a deformation mismatch with human skin that is multidirectionally elongated under bending of joints. This causes practical problems in elastomer-based wearable devices, such as delamination and detachment, leading to poorly reliable functionality. To overcome this issue, auxetic-structured mechanical reinforcement with glass fibers is applied to the elastomeric film, resulting in a negative Poisson's ratio (NPR), which is a skin-like stretchable substrate (SLSS). Several parameters for determining the materials and geometrical dimensions of the auxetic-structured reinforcing fillers are considered to maximize the NPR. Based on numerical simulation and digital image correlation analysis, the deformation tendencies and strain distribution of the SLSS are investigated and compared with those of the pristine elastomeric substrate. Owing to the strain-localization characteristics, an independent strain-pressure sensing system is fabricated using SLSS with a Ag-based elastomeric ink and a carbon nanotube-based force-sensitive resistor. Finally, it is demonstrated that the SLSS-based sensor platform can be applied as a wearable device to monitor the physical burden on the wrist in real time.     

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.