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.     

Carbonic anhydrase inhibitors: X-ray crystallographic studies for the binding of N-substituted benzenesulfonamides to human isoform II

N-substituted benzenesulfonamides, incorporating the N-amino-, N-hydroxy- and N-methoxy-moieties at the sulfonamide zinc binding group, have been investigated as CAIs by means of inhibition and structural studies, unraveling interesting aspects related to their inhibition mechanism.     

Raman and computational study of solvation and chemisorption of thiazole in silver hydrosol

A SERS investigation combined with ab initio computational analysis involving Car-Parrinello molecular dynamics simulations and Density Functional Theory approach allows fundamental information to be obtained on the behaviour of thiazole in silver aqueous suspension where solvation and chemisorption processes competitively occur.     

Exploring the accuracy level of new potential energy surfaces for the F + HD reactions: from exact quantum rate constants to the state-to-state reaction dynamics

Exact quantum reactive scattering calculations in the collision energy range 1-250 meV have been carried out for both the isotopic product channels of the title system. The dynamical studies compares an ab initio potential energy surface (PES) recently appeared in the literature (J. Chem. Phys., 2008, 129, 011103) with other phenomenological PESs. Vibrational branching ratios, cross sections and rate constants are presented and compared with molecular beam scattering experiments as well as with chemical kinetics data. In particular, the agreement of the vibrational branching ratios with experimental measurements is improved with respect to previous studies on other PESs, mainly because of the presence of a broad peak in the HF(v' = 3) integral cross section completely absent in the previous simulations. This feature, observed by molecular beam experiments, is the fingerprint of a new reaction mechanism operative in the dynamics described by the new PES. A conjecture for its origin, able to explain many of its characteristic aspects, is analyzed and discussed.     

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.     

A molecular dynamics study of structure, stability and fragmentation patterns of sodium bis(2-ethylhexyl)sulfosuccinate positively charged aggregates in vacuo

Positively charged supramolecular aggregates formed in vacuo by n AOTNa (sodium bis(2-ethylhexyl)sulfosuccinate) molecules and n(c) additional sodium ions, i.e. [AOT(n)Na(n+n(c))](n(c)), have been investigated by molecular dynamics (MD) simulations for n = 1-20 and n(c) = 0-5. Statistical analysis of physical quantities like gyration radii, atomic B-factors and moment of inertia tensors provides detailed information on their structural and dynamical properties. Even for n(c) = 5, all stable aggregates show a reverse micelle-like structure with an internal solid-like core including sodium counterions and surfactant polar heads surrounded by an external layer consisting of the surfactant alkyl chains. Moreover, the aggregate shapes may be approximated by rather flat and elongated ellipsoids whose longer axis increases with n and n(c). The fragmentation patterns of a number of these aggregates have also been examined and have been found to markedly depend on the aggregate charge state. In one particular case, for which experimental findings are available in the literature, a good agreement is found with the present fragmentation data.     

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.     

Chemical composition and possible in vitro antigermination activity of three Hypericum essential oils

The essential oils of Hypericum perforatum, H. perfoliatum and H. hircinum, growing in Southern Italy, were analyzed by GC and GC/MS. In the three oils, 111 compounds in all were identified: 53 for the oil of H. hircinum (93.7% of the total oil), 55 for H. perforatum (96.5% of the total oil) and 63 for H. perfoliatum (98.7% of the total oil). The major fraction of the essential oils of H. perforatum and H. hircinum was represented by sesquiterpene hydrocarbons, while the monoterpene alpha-pinene, and the phenol thymol were the most abundant compounds in the essential oil of H. perfoliatum. The oils were evaluated for their potential in vitro phytotoxic activity against germination and early radicle elongation of Raphanus sativus and Lepidium sativum. The germination of this latter was significantly inhibited by the essential oil of H. hircinum, at the highest doses tested, whereas radicle elongation of garden cress was significantly inhibited by the essential oils of H. perfoliatum and H. hircinum. The radicle elongation of radish was inhibited by the essential oil of H. hircinum to a major extent and by H. perforatum and perfoliatum in a minor measure.     

The Spectrum of the Cubic Oscillator

We prove the simplicity and analyticity of the eigenvalues of the cubic oscillator Hamiltonian, $$\begin{array}{ll}H(\beta)=-\frac{d^2}{dx^2}+x^2+i\sqrt{\beta}x^3\end{array}$$ , for β in the cut plane ${\mathcal{C}_c:=\mathcal{C}\backslash \mathcal{R}_-}$ . Moreover, we prove that the spectrum consists of the perturbative eigenvalues {E _n (β)} _{n ≥ 0} labeled by the constant number n of nodes of the corresponding eigenfunctions. In addition, for all ${\beta \in \mathcal{C}_c, E_n(\beta)}$ can be computed as the Stieltjes-Padé sum of its perturbation series at β = 0. This also gives an alternative proof of the fact that the spectrum of H(β) is real when β is a positive number. This way, the main results on the repulsive PT-symmetric and on the attractive quartic oscillators are extended to the cubic case.