Structural and chiroptical properties of the two coordination isomers of YbDOTA-type complexes

Studies of the structural, physical, and chemical properties of the lanthanide(III) complexes of DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) and related ligands are often complicated by the presence of two coordination isomers in solution. Since these coordination isomers are in exchange and cannot be separated, many techniques offer information only on the weighted average of the two isomers. Lanthanide ion complexes formed with the ligands S(RRRR)NO2BnDOTMA and S(SSSS)NO2BnDOTMA preferentially adopt only one of the two common coordination isomers in solution, so the ytterbium complexes of these ligands offer a unique opportunity to study the near-infrared circular dichroism (NIR-CD) characteristics of each coordination geometry in isolation. The spectra acquired support many of the conclusions and assumptions of previous studies and demonstrate that this spectroscopy is particularly sensitive to the distortion of the coordination polyhedron. This will have particularly relevant consequences when studying achiral YbDOTA-like systems forming labile adducts with (chiral) hosts and receptors.     

Rosenbluth-sampled nonequilibrium work method for calculation of free energies in molecular simulation

We present methods that introduce concepts from Rosenbluth sampling [M. N. Rosenbluth and A. W. Rosenbluth, J. Chem. Phys. 23, 356 (1955)] into the Jarzynski nonequilibrium work (NEW) free-energy calculation technique [C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)]. The proposed hybrid modifies the way steps are taken in the NEW process. With it, each step is selected from a range of alternatives, with bias given to steps that contribute the least work. The definition of the work average is modified to account for the bias. We introduce two variants of this method, lambda-bias sampling and configuration-bias sampling, respectively; a combined lambda- and configuration-bias method is also considered. By reducing the likelihood that large nonequilibrated work values enter the ensemble average, the Rosenbluth sampling aids in remedying problems of inaccuracy of the calculation. We demonstrate the performance of the proposed methods through a model system of N independent harmonic oscillators. This model captures the difficulties involved in calculating free energies in real systems while retaining many tractable features that are helpful to the study. We examine four variants of this model that differ qualitatively in the nature of their phase-space overlap. Results indicate that the lambda-bias sampling method is most useful for systems with entropic sampling barriers, while the configuration-bias methods are best for systems with energetic sampling barriers. The Rosenbluth-sampling schemes yield much more accurate results than the unbiased nonequilibrium work method. Typically the accuracy can be improved by about an order of magnitude for a given amount of sampling; this improvement translates into two or more orders of magnitude less sampling required to obtain a given level of accuracy, owing to the generally slow convergence of the NEW calculation when the inaccuracy is large.     

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.     

Hybrid Siloxane-Based Nano Building Blocks for Optical Applications: Optimization of the Synthetic Procedures by Spectroscopic Analysis

Diphenylsilanediol (DPDO) reacts with triethoxysilane (TREOS) in anhydrous conditions and in the presence of pyridine, to form complex mixtures of linear and cyclic condensation products which were identified by ²⁹Si NMR and ATR/FTIR spectroscopies. The distribution of products can be varied by modifying the reaction conditions. Spectroscopic analysis allowed to identify the optimal reagents ratio and concentration for the production of hetero-condensation products minimizing the number of residual –OH groups whose presence would affect the performance of optical waveguides based on the synthesised nano building blocks.     

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.     

On the Characterization of the Dynamic Performances of Planar Manipulators

The characterization of the dynamic performances of a manipulator is important both to compare different manipulators and to improve the dynamic performances of a manipulator during the design stage. In a previous paper the concepts of swiftness and of dynamic isotropy were used to characterize some dynamic performances of 3-dof manipulators. This paper analyzes the usefulness of these concepts for three-dof planar manipulators and shows that the concept of swiftness is still significant, whereas the concept of dynamic isotropy has no practical interest. Moreover, it introduces three new dynamic properties that are useful in the design of a 3-dof planar manipulator. Finally, it proposes some indices that measure both the swiftness and the three new dynamic properties and shows how to use them, both for evaluating the dynamic performances of a given 3-dof planar manipulator and for improving the dynamic performances during its design.     

Preliminary evidence for UA(1) breaking in QCD from lattice calculations

We suggest a simple definition of the topological charge density Q(x) in the lattice Yang-Mills theory and evaluate A≡∝d⁴x〈Q(x)Q(0)〉 in SU(2) by Monte Carlo simulation. The “data” interpolate well between the strong and weak coupling expansions, which we compute to order g^?12 and g⁶, respectively. After subtraction of the perturbative tail, our points exhibit the expected asymptotic freedom behaviour giving $\text{A}{}^{\mathrm{<mtext>1</mtext><mtext>4</mtext>}}\text{≌(0.11±0.02)K}{}^{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}$, K being the SU(2) quarkless string tension. Although a larger value for $\text{A}{}^{\mathrm{<mtext>1</mtext><mtext>4</mtext>}}\text{K}{}^{\mathrm{<mtext>?</mtext><mtext>1</mtext><mtext>2</mtext>}}$ would be preferable, we are led to conclude (at least tentatively) that the U_A(1) problem of QCD is indeed solved perturbatively in the quark loop expansion.     

Infrared spectrum and vibrational potential function of thionylimide (HNSO)

The ir absorption of gaseous HNSO, DNSO and H¹⁵NSO is recorded in the range 300–4100 cm^?1 at medium resolution. Besides the fundamental vibrations, overtones and combination bands are measured and assigned. From these data, combined with the ir absorptions of four more isotopic species of thionylimide, and with the centrifugal distortion constants of HNSO and DNSO, a harmonic force field, with 11 constants was derived.