A note on heuristics for the traveling salesman problem

We introduce subclasses of the traveling salesman problem (TSP) and analyze the behaviour of heuristics on them. We derive bounds for the performance of the algorithms.     

The vilsmeier-haack formylation of 1,2,3-trimethylindole

The title reaction yields mainly a side-chain monosubstituted formyl derivative, namely 2-(1,3-dimethylindolyl)acetaldehyde.     

Study of the reaction of bis- and tris-pyrylium and -thiopyrylium cations with methoxide ion. Electronic effects of the heterocyclic rings as substituents

The bis- and tris-pyrylium and thiopyrylium cations 1-4 were prepared in gram scale by heterocyclization of the corresponding bis- and tris-1,5-pentanediones 6 and 8. Their reaction with CD3ONa in CD3OD was studied by 1H NMR at -40 degrees C and at +25 degrees C. At low temperature, kinetically controlled mixtures of 2H and/or 4H adducts were detected, whereas at room temperature the mixtures equilibrated to yield, in all of the cases, the more stable 2H adducts exclusively. A spectrophotometric study of the reactions with sodium methoxide in methanol was carried out at 25.0 degrees C with the aim of determining the stepwise equilibrium constants for the addition of MeO- at the alpha position of the heteroaromatic rings. The obtained equilibrium constants allowed the evaluation of the electronic effects of chalcogenopyrylium and 2H-chalcogenopyran subunits as substituents. Despite the different sensitivity to electronic effects, pyrylium and thiopyrylium rings have a similar electron-withdrawing effect with a sigma(+)p approximately 0.8 and a sigma(+)m approximately 0.5. Apart from the expected importance of the inductive effect due to the positive charge, the difference between these two values remarks the importance of the resonance contribution. In contrast both the neutral 2H-pyranyl and thiopyranyl rings have a negligible effect as substituents, independently of the position, para or meta, they occupy.     

Dynamical Aspects of TEM-1 β-Lactamase Probed by Molecular Dynamics

The dynamical aspects of the fully hydrated TEM-1 β-lactamase have been determined by a 5 ns Molecular Dynamics simulation. Starting from the crystallographic coordinates, the protein shows a relaxation in water with an overall root mean square deviation from the crystal structure increasing up to 0.17 nm, within the first nanosecond. Then a plateau is reached and the molecule fluctuates around an equilibrium conformation. The results obtained in the first nanosecond are in agreement with those of a previous simulation (Diaz et al., J. Am. Chem. Soc., (2003) 125, 672–684). The successive equilibrium conformation in solution shows an increased mobility characterized by the following aspects. A flap-like translational motion anchores the Ω-loop to the body of the enzyme. A relevant part of the backbone dynamics implies a rotational motion of one domain relative to the other. The water molecules in the active site can exchange with different residence times. The H-bonding networks formed by the catalytic residues are frequently interrupted by water molecules that could favour proton transfer reactions. An additional simulation, where the aspartyl dyad D214–D233 was considered fully deprotonated, shows that the active site is destabilized.     

Nature of the chemical bond between metal atoms and oxide surfaces: new evidences from spin density studies of K atoms on alkaline earth oxides

We have studied the interaction of K atoms with the surface of polycrystalline alkaline-earth metal oxides (MgO, CaO, SrO) by means of CW- and Pulsed-EPR, UV-Vis-NIR spectroscopies and DFT cluster model calculations. The K adsorption site is proposed to be an anionic reverse corner formed at the intersection of two steps, where K binds by more than 1 eV, resulting in thermally stable species up to about 400 K. The bonding has small covalent and large polarization contributions, and the K atom remains neutral, with one unpaired electron in the valence shell. The interaction results in strong modifications of the K electronic wave function which are directly reflected by the hyperfine coupling constant, (K)a(iso). This is found to be a very efficient "probe" to measure the degree of metal-oxide interaction which directly depends on the substrate basicity. These results provide an original and general model of the early stages of the metal-support interaction in the case of ionic oxides.     

Aggregation tendency and reactivity toward AgX of cationic half-sandwich ruthenium(II) complexes bearing neutral N,O-ligands

The aggregation tendency of complexes [Ru(eta6-cymene)(N,O)Cl]X [N,O = 2-benzoylpyridine (2-bzpy), 1, and 2-acetylpyridine (2-acpy), 2, X- = BPh4- or PF6-] has been studied by means of PGSE NMR experiments. It was found that complexes with PF6- as counterion are mainly present in CD2Cl2 as ion pairs at low concentration, as a mixture of ion triples and free anions at medium concentration and as ion quadruples at elevated concentration. 19F, 1H-HOESY NMR experiments revealed that in ion triples and ion quadruples two cationic Ru-units pair up. Consistently, in the solid-state structure of 1PF6, determined through X-ray single-crystal investigation, two cationic Ru-units are held together by an intermolecular pi-pi stacking interaction between the pyridyl rings. Complexes having BPh4- as counterion are only present in solution as even aggregates, namely ion pairs at low concentration and ion quadruples at elevated concentration. In such a case a counteranion bridges two cationic Ru-units as observed in the solid-state structure of 1BPh4. The reactivity of complexes 1-2 toward AgX salts has been investigated in different solvents. Bicationic [Ru(eta6-cymene)(N,O)(MeCN)]X2 (N,O = 2-bzpy, 3, and 2-acpy, 4) and [Ru(MeCN)4(N,O)]X2 (N,O = 2-bzpy, 5, and 2-acpy, 6) complexes were obtained by the reaction of 1 and 2 with AgX in the presence of three equivalents of acetonitrile or in acetonitrile, respectively. The reaction of 1 with AgPF6 in acetone afforded complex [Ru(eta6-cymene)(N,O,O)]PF6 (7, where N,O,O = 4-alcoxide-4-phenyl-4-(pyridin-2-yl)butan-2-one) from the C-C coupling of a deprotonated methyl group of the coordinated acetone and the C=O moiety of 2-bzpy ligand.     

Nature of point defects on SiO2/Mo(112) thin films and their interaction with Au atoms

We have studied by means of periodic DFT calculations the structure and properties of point defects at the surface of ultrathin silica films epitaxially grown on Mo(112) and their interaction with adsorbed Au atoms. For comparison, the same defects have been generated on an unsupported silica film with the same structure. Four defects have been considered: nonbridging oxygen (NBO, [triple bond]Si-O(*)), Si dangling bond (E' center, [triple bond]Si(*)), oxygen vacancy (V(O), [triple bond]Si-Si[triple bond]), and peroxo group ([triple bond]Si-O-O-Si[triple bond]), but only the NBO and the V(O) centers are likely to form on the SiO(2)/Mo(112) films under normal experimental conditions. The [triple bond]Si-O(*) center captures one electron from Mo forming a silanolate group, [triple bond]Si-O(-), sign of a direct interaction with the metal substrate. Apart from the peroxo group, which is unreactive, the other defects bind strongly the Au atom forming stable surface complexes, but their behavior may differ from that of the same centers generated on an unsupported silica film. This is true in particular for the two most likely defects considered, the nonbridging oxygen, [triple bond]Si-O(*), and the oxygen vacancy, [triple bond]Si-Si[triple bond].     

Charge transfers at metal/oxide interfaces: a DFT study of formation of K delta+ and Au delta- species on MgO/Ag(100) ultra-thin films from deposition of neutral atoms

Ultra-thin oxide films grown on a metal substrate and of thickness smaller than 1 nm may exhibit unusual properties with respect to thicker films or single crystal oxide surfaces. In a previous study [G. Pacchioni, L. Giordano and M. Baistrocchi, Phys. Rev. Lett., 2005, 94, 226104] we have suggested that a Au atom adsorbed on a MgO/Mo(100) thin film becomes negatively charged by direct electron tunneling from the Mo metal and that this is related to the low MgO/Mo(100) work function. Here we show, based on periodic DFT supercell calculations, that charge transfer can occur also in the opposite direction by adsorption of electropositive K atoms on MgO/Ag(100) films. We predict the occurrence of a charge transfer also for Au on MgO/Ag(100) films despite the fact that here the work function is 1 eV larger than in MgO/Mo(100). The formation of a layer of adsorbed negative (Au delta-/MgO/Ag) or positive (K delta+/MgO/Ag) adsorbates results in an increase or decrease, respectively, of the MgO/Ag(100) work function as predicted by the classical Gurney model for ionic adsorbates on metal surfaces.     

A finite-element-based coarse-grained model for global protein vibration

Meccanica - Protein mechanical vibrations play a pivotal role in biological activity. In particular, low-frequency (terahertz) modes are related to protein conformational changes, which represent...