Vibrational analysis of x-ray absorption fine structure thermal factors by ab initio molecular dynamics: the Zn(II) ion in aqueous solution as a case study

In this work, we consider a new combination of vibrational analysis and normal-like mode decomposition of Debye-Waller factors of solvated ions entirely based on molecular dynamics data. Such a novel time-dependent analysis procedure provides a direct link between x-ray absorption fine structure parameters and normal mode contributions for an ion-solvent system. The potentialities of such a methodology rely on two fundamental aspects which distinguish it from already available tools. First, a general vibrational analysis that does not require any Gaussian or harmonic model for describing atomic fluctuations in liquids. Second, a very accurate sampling of the short range motions around the structural probe via the recently developed atom centered density matrix propagation/general liquid optimized boundary method. This novel molecular dynamics methodology is based on an integrated ab initio/classical potential using localized basis functions and nonperiodic boundary conditions. As a case study we have chosen the Zn(II) ion in aqueous solution. The consistency of our results and the observed good agreement with experiments show how the key support to advanced structural techniques from molecular dynamics can be further expanded and investigated.     

Absorption and emission spectra of fluorescent silica nanoparticles from TD-DFT/MM/PCM calculations

A multi-scale computational protocol, which combines Quantum Mechanics and Molecular Mechanics (QM/MM) calculations with the polarisable continuum model (PCM), has been used to study the tetramethylrhodamine isothiocyanate (TRITC) fluorophore, embedded in three different environments, namely in water, on an amorphous silica surface and covalently encapsulated in a silica nanoparticle (C dot). Absorption and emission spectra have been simulated by using TD-B3LYP/PCM calculations, performed on the TRITC ground and excited state geometries, optimized at the QM/MM level. The results are in good agreement with experimental data confirming the caging effect played by the silica shell on the mobility of the TRITC molecule when covalently encapsulated in silica nanoparticles. This could result in a decrease of the nonradiative decay rate and thus an increase of the quantum yield of the molecule.     

Fluorescence spectra of organic dyes in solution: a time dependent multilevel approach

Classical all-atom molecular dynamics (MD) simulations and quantum mechanical (QM) time-dependent density functional theory (TD-DFT) calculations are employed to study the conformational and photophysical properties of the first emitter excited state of tetramethyl-rhodamine iso-thiocyanate fluorophore in aqueous solution. For this purpose, a specific and accurate force field has been parameterised from QM data to model the fluorophore's first bright excited state. During the MD simulations, the consequences of the π→π* electronic transition on the structure and microsolvation sphere of the dye has been analysed in some detail and compared to the ground state behaviour. Thereafter, fluorescence has been calculated at the TD-DFT level on configurations sampled from the simulated MD trajectories, allowing us to include time dependent solvent effects in the computed emission spectrum. The latter, when compared with the absorption spectrum, reproduces well the experimental Stokes shift, further validating the proposed multilevel computational procedure.     

The strange-quark distribution

We discuss the latest CCFR determination of the strange sea density of the proton. We comment on the differences with a previous, leading-order, result and point out the relevance of quark mass effects and current non-conservation effects. By taking them into account it is possible to solve the residual discrepancy with another determination of the strange-quark distribution. Two important sources of uncertainties are also analysed.     

Tin–DNA complexes investigated by nuclear inelastic scattering of synchrotron radiation

Nuclear inelastic scattering (NIS) of synchrotron radiation has been used to investigate the dynamics of tin ions chelated by DNA. Theoretical NIS spectra have been simulated with the help of density functional theory (DFT) calculations using 12 models for different binding sites of the tin ion in (CH₃)Sn(DNA_Phosphate)₂. The simulated spectra are compared with the measured spectrum of the tin–DNA complex.     

Pyrazolo[3,4-d][1,2,3]triazolo[1,5-a]pyrimidine: a new ring system through Dimroth rearrangement

Derivatives of the new ring system pyrazolo[3,4-d][1,2,3]triazolo[1,5-a]pyrimidine were synthesized from the corresponding angular isomers, through a Dimroth rearrangement, in quantitative yields. Preliminary computational studies demonstrated that this class of compounds could be a good candidate as DNA intercalating agents.     

A search for neutrino oscillations

We present here the final results of experiments searching for neutrino oscillations, carried out by the CHARM Collaboration. The data — taking took place in 1983. The first experiment was performed by exposing two detectors simultaneously to the CERN PS low energyv _µ beam. In the second experiment the full CHARM detector was exposed to the wide-band horn-focusedv _µ beam of the CERN SPS. Complete details of the experiments and data reduction are presented. No statistically significant signals for neutrino oscillations were observed. Our 90% CL limits in the appearance experiment (v _µ→v _e ) exclude Δm ²≧0.19 eV² for complete mixing (sin²2θ=1), and sin²2θ≧0.008 for the region Δm ²≧30 eV². These results, and the limits observed for (v _µ→v _x ) (disappearance of (v _µ), are in agreement with those of most other experiments but exclude part of the region previously reported as a possible indication ofv _µ→v _e oscillations.     

A theoretical characterization of the structure formation enthalpy,and fluzional behaviour of B2H6 and AlBH6

Summary A comprehensive study of the binary association complexes B₂H₆ and AlBH₆ has been performed by ab initio molecular orbital theory. Reliable formation enthalpies can be computed only be extended basis sets and a reasonably complete account of correlation. The greater stability towards neutral dissociation of AlBH₆ with respect to B₂H₆ obtained at the Hartree-Fock level employing the 6-21G^* basis set ( 10 kcal/mol) is reduced to only 2 kcal/mol when the basis set is sufficiently saturated and correlation energy properly included. The value of the activation energy for hydrogen scrambling in AlBH₆ is much less sensitive to the method used, although correlation still plays a significant rôle reducing the potential energy barrier from 11.4 to 7.7 kcal/mol.