Energy decompositions according to physical space partitioning schemes: treatments of the density cumulant

This article is a continuation of our previous paper on schemes of energy decompositions of molecular systems in the real space [D. R. Alcoba et al., J. Chem. Phys. 122, 074102 (2005)] now using correlated state functions. We study, according to physical arguments, the appropriate management of the density cumulant arising from the second-order reduced density matrix at correlated level, whose contributions can be assigned to one-center or to two-center terms in the energy partitioning. Our treatments are applied within two physical space partitioning schemes: the Bader partitioning into atomic basins and the fuzzy atom procedure. The results obtained in selected molecules are analyzed and discussed in detail.     

Ferrocenyl-substituted α,β-unsaturated ketones in synthesis of tetrahydropyrimidinones

Ferrocenyltetrahydropyrimidin-2-ones were prepared by reactions of linear and cyclic ,-unsaturated ketones of the ferrocene series with urea in i-PrOH in the presence of t-BuOK. The structures of the compounds prepared were studied by ¹H and ¹³C NMR and IR spectroscopy, and also by single crystal X-ray diffraction.Translated from Zhurnal Obshchei Khimii, Vol. 74, No. 11, 2004, pp. 1887–1893.Original Russian Text Copyright © 2004 by E. Klimova, Lorez, T. Klimova, Garcia, Hernandez, Ramirez.This revised version was published online in April 2005 with a corrected cover date.     

Synthesis of ynones by palladium-catalyzed acylation of terminal alkynes with acid chlorides

Phosphane-free oxime-derived palladacycle 2 is an efficient precatalyst for the copper-free acylation of terminal alkynes with different carboxylic acid chlorides in toluene in the presence of 3 equiv of TEA as base, giving the corresponding ynones in good yields. The coupling reaction can normally be performed under air or under inert atmosphere when very low catalyst loadings (10(-3) mol % Pd) (turnover numbers (TONs) up to 23,000, turnover frequencies (TOFs) up to 958 h(-1)) or sensitive carboxylic acid chlorides are used. In addition, Pd(OAc)(2) has been shown as an efficient catalyst for the ligandless process, although usually working under higher loading conditions. This new protocol allows one to perform the synthesis of ynones at 110 degrees C, at room temperature, or under microwave irradiation conditions.     

Rapid and sensitive method for determining free amino acids in honey by gas chromatography with flame ionization or mass spectrometric detection

This paper describes a rapid, sensitive and specific method for determination of free amino acids in honey involving a new reaction of derivatization and gas chromatography (GC) with flame ionization (FID) and mass spectrometric (MS) detection. The method allows the determination of 22 free amino acids in honey samples in a short time: 8 and 5 min for GC-FID and GC-MS, respectively. Quantitation was performed using Norvaline as internal standard, with detection limits ranging between 0.112 and 1.795 mg/L by GC-FID and between 0.001 and 0.291 mg/L by GC-MS in the selected-ion monitoring mode. The method was validated and applied to a set of 74 honey samples belonging to four different botanical origins: eucaliptus, rosemary, orange and heather. The statistical treatment of data shows a correct classification of different origins over 90%.     

L-arginine binding to human inducible nitric oxide synthase: an antisymmetric funnel route toward isoform-specific inhibitors?

Nitric oxide (NO) is an important signaling molecule produced by a family of enzymes called nitric oxide synthases (NOS). Because NO is involved in various pathological conditions, the development of potent and isoform-selective NOS inhibitors is an important challenge. In the present study, the dimer of oxygenase domain of human iNOS (iNOSoxy) complexed to its natural substrate L-arginine (L-Arg) and both heme and tetrahydro-L-biopterin (BH4) cofactors was studied through multiple molecular dynamics simulations. Starting from the X-ray structure available for that complex (PDB: 1NSI ), a 16 ns equilibration trajectory was first obtained. Twelve dynamics of slow extraction of L-Arg out from the iNOSoxy active site were then performed. The steered molecular dynamics (SMD) approach was used starting from three different points of the reference trajectory for a total simulation time of 35 ns. A probable unbinding/binding pathway of L-Arg was characterized. It was suggested that a driving force directed the substrate toward the heme pocket. Key intermediate steps/residues along the access route to the active site were identified along this "funnel shape" pathway and compared to existing data. A quasi-normal mode analysis performed on the SMD data suggested that large collective motions of the protein may be involved in L-Arg binding and that opening the route to the active site in one monomer promoted an inverse, closing motion in the second monomer. Finally, our findings might help to rationalize the design of human iNOS isoform competitive inhibitors.     

A metal-complex-tolerant CuAAC 'click' protocol exemplified through the preparation of homo- and mixed-metal-coordinated [2]rotaxanes

A series of mono- and bis-metallated [2]rotaxanes has been prepared using a CuAAC 'click' protocol that is compatible with metal-coordinated building blocks and ligands; the methodology provides a general means for appending a metal ion or complex to an organic scaffold via Cu(I)-catalysed 'click' chemistry, even when the molecule contains redox-active or kinetically labile metals or vacant ligand sites.     

STRUCTURAL ORIGIN OF GLASS FORMATION IN GROUP IV DISELENIDES

Abstract

SiSe₂, GeSe₂ and SnSe₂ crystallize in a quasi 1-d, quasi 2-d and a quasi 2-d structure with the cations possessing a coordination number (CN) of 4,4 and 6, respectively. SiSe₂ and GeSe₂ melts readily yield bulk glasses upon water quenching, while non-crystalline SnSe₂ can only be prepared by vapor deposition onto room temperature substrates as amorphous thin-films. In the non-crystalline state, a cation CN of 4 is preferred largely because tetrahedral Si(Se_1/2)₄, Ge(Se_1/2)₄ and Sn(Se_1/2)₄ units form the principal building blocks of these networks. Furthermore, tetrahedra share predominantly edges in SiSe₂ glass, a combination of both corners and edges in GeSe₂ glass and corners in amorphous SnSe2 films. The intermediate range order of these non-crystalline materials has emerged from Raman scattering, Mossbauer spectroscopy and neutron structure-factor measurements.     

Interfacial energy exchange and reaction dynamics in collisions of gases on model organic surfaces

Molecular beam scattering experiments and molecular dynamics simulations have been combined to develop an atomic-level understanding of energy transfer, accommodation, and reactions during collisions between gases and model organic surfaces. The work highlighted in this progress report has been motivated by the scientific importance of understanding fundamental interfacial chemical reactions and the relevance of reactions on organic surfaces to many areas of environmental chemistry. The experimental investigations have been accomplished by molecular beam scattering from ω-functionalized self-assembled monolayers (SAMs) on gold. Molecular beams provide a source of reactant molecules with precisely characterized collision energy and flux; SAMs afford control over the order, structure, and chemical nature of the surface. The details of molecular motion that affect energy exchange and scattering have been elucidated through classical-trajectory simulations of the experimental data using potential energy surfaces derived from ab initio calculations. Our investigations began by employing rare-gas scattering to explore how alkanethiol chain length and packing density, terminal group relative mass, orientation, and chemical functionality influence energy transfer and accommodation at organic surfaces. Subsequent studies of small molecule scattering dynamics provided insight into the influence of internal energy, molecular orientation, and gas–surface attractive forces in interfacial energy exchange. Building on the understanding of scattering dynamics in non-reactive systems, our work has recently explored the reaction probabilities and mechanisms for O₃ and atomic fluorine in collisions with a variety of functionalized SAM surfaces. Together, this body of work has helped construct a more comprehensive understanding of reaction dynamics at organic surfaces.     

Reversible Clustering of Gold Nanoparticles under Confinement

A limiting factor of solvent‐induced nanoparticle self‐assembly is the need for constant sample dilution in assembly/disassembly cycles. Changes in the nanoparticle concentration alter the kinetics of the subsequent assembly process, limiting optical signal recovery. Herein, we show that upon confining hydrophobic nanoparticles in permeable silica nanocapsules, the number of nanoparticles participating in cyclic aggregation remains constant despite bulk changes in solution, leading to highly reproducible plasmon band shifts at different solvent compositions.