Does Fe(2+) in olivine-based interstellar grains play any role in the formation of H2? Atomistic insights from DFT periodic simulations.

Using periodic DFT-D2 methods, atomistic simulations of interstellar H adsorption and H2 formation on a (010) Fe-containing olivine surface are presented. At variance with the (010) Mg2SiO4 surface and key to these processes are the large Fe/H interaction energies, suggesting that olivine surfaces are good reservoirs of H atoms for subsequent recombination to form H2.

Performance of six functionals (LDA, PBE, PBESOL, B3LYP, PBE0, and WC1LYP) in the simulation of vibrational and dielectric properties of crystalline compounds. The case of forsterite Mg2SiO4.

The performance of six different density functionals (LDA, PBE, PBESOL, B3LYP, PBE0, and WC1LYP) in describing the infrared spectrum of forsterite, a crystalline periodic system with orthorhombic unit cell (28 atoms in the primitive cell, Pbmn space group), is investigated by using the periodic ab initio CRYSTAL09 code and an all-electron Gaussian-type basis set. The transverse optical (TO) branches of the 35 IR active modes are evaluated at the equilibrium geometry together with the oscillator strengths and the high-frequency dielectric tensor ϵ(∞) . These quantities are essential to compute the dielectric function ϵ(ν), and then the reflectance spectrum R(ν), which is compared with experiment. It turns out that hybrid functionals perform better than LDA and GGA, in general; that B3LYP overperforms WC1LYP and, in turn, PBE0; that PBESOL is better than PBE; that LDA is the worst performing functional among the six under study.

Is the peptide bond formation activated by Cu(2+) interactions? Insights from density functional calculations.

The catalytic role that Cu(2+) cations play in the peptide bond formation has been addressed by means of density functional calculations. First, the Cu(2+)-(glycine)2 --> Cu(2+)-(glycylglycine) + H2O reaction was investigated since mass spectrometry low collision activated dissociation (CAD) spectra of Cu(2+)-(glycine)2 led to the elimination of a water molecule, which suggested that an intracomplex peptide bond formation might have occurred. Results show that this intracomplex condensation is associated to a very high free energy barrier (97 kcal mol(-1)) and reaction free energy (66 kcal mol(-1)) because of the loss of metal coordination during the reaction. Second, on the basis of the salt-induced peptide formation theory, the condensation reaction between two glycines was studied in aqueous solution using discrete water molecules and the conductor polarized continuum model (CPCM) continuous method. It is found that the synergy between the interaction of glycines with Cu(2+) and the presence of water molecules acting as proton-transfer helpers significantly lower the activation barrier (from 55 kcal/mol for the uncatalyzed system to 20 kcal/mol for the Cu(2+) solvated system) which largely favors the formation of the peptide bond.

An ab initio periodic study of acidic chabazite as a candidate for dihydrogen storage.

A theoretical B3LYP study, adopting a polarized double-zeta quality Gaussian basis set, was performed to characterize acidic chabazite by using the periodic CRYSTAL03 program. Different Si/Al loadings (1/1, 3/1, 5/1, and 11/1) were considered, and for each of them the most stable aluminum distribution and location of the acidic proton, needed as charge balancer, were identified. With the optimal structures, the energy of formation and the anharmonic O-H stretching frequency were calculated with the latter being in good agreement with the experimental data. The B3LYP optimal position of H2 physisorbed at the acidic Brönsted sites of chabazite (Si/Al = 11/1 and 5/1) brings about an interaction energy definitely smaller than that derived from infrared spectroscopy, because of the known deficiencies of this functional to cope with dispersive interactions. The latter was included by means of an ONIOM-like procedure that combines periodic B3LYP energy with results at the MP2 level on selected clusters cut out of the chabazite framework. Adsorption of two H2 molecules for Si/Al = 5/1 chabazite showed a complete independence of each Brönsted site, and neither through-space nor intrastructure polarization effects are present. Within the periodic B3LYP approach shifts in both O-H and H-H anharmonic frequencies were also computed and compared with unperturbed values and with the available experimental results.

Vibrational spectrum of katoite Ca3Al2[(OH)4]3: a periodic ab initio study.

The vibrational spectrum of the Si-free katoite hydrogarnet (116 atoms in the unit cell) has been calculated at the periodic ab initio quantum mechanical level with the CRYSTAL program, by using a Gaussian type basis set and the hybrid B3LYP Hamiltonian. The harmonic frequencies at the Gamma point have been obtained by diagonalizing the mass-weighted Hessian matrix, that is evaluated by numerical differentiation of the analytical first derivatives of the energy with respect to the atomic Cartesian coordinates. The parameters controlling the numerical differentiation, as well as the numerical integration of the exchange-correlation functional for the self-consistent field (SCF) calculation, are shown to affect the obtained frequencies by less than 3 cm-1. Before diagonalization, the dynamical matrix is transformed to a block diagonal form according to the irreducible representations of the point group, so that the 345 vibrational modes are automatically classified by symmetry. Various tools are adopted (graphical representation, isotopic substitution, "freezing" part of the unit cell) that permit a complete classification of normal modes and, in particular, an analysis of the modes in terms of simple models (octahedra modes, Ca modes, H stretching, bending, rotations). The harmonic OH stretching band (48 modes) is quite narrow (20 cm-1), indicating that the interaction among OH groups is very weak. As the OH stretching modes are known to be totally separable from the other modes and strongly anharmonic, the one-dimensional Schroedinger equation for the anharmonic oscillator is solved numerically for the two extreme situations, corresponding to the vibration of one decoupled OH and of all 48 OH groups moving in phase. The anharmonic frequencies are 3682 and 3673 cm-1, respectively, in good agreement with IR experiments (a single band at 3661 cm-1 with a width at half band height of 33 cm-1) and confirming that the interaction between OH groups is extremely weak.

The katoite hydrogarnet Si-free Ca3Al2([OH]4)3: a periodic Hartree-Fock and B3-LYP study.

The structure of the Si-free katoite hydrogarnet (116 atoms in the unit cell) has been investigated at the periodic ab initio quantum mechanical level with the CRYSTAL program, by using a Gaussian type basis set and both the HF and the hybrid B3-LYP Hamiltonians. The structure has been fully optimized at various pressures in the 0-46 GPa range; the modifications of the structure, and in particular of the (OH)4 group, as a function of pressure are analyzed. At the B3-LYP level and P greater than 15 GPa, a O-H...O interaction of increasing strength appears, with important modifications in the local geometry of the tetrahedral site. The calculated omega01(O-H) fundamental vibrational frequency at zero pressure is in excellent agreement with experiment (3674 and 3663 cm(-1), respectively); the omega01(O-H) stretching frequency remains essentially constant in the 0-15 GPa interval, whereas it dramatically decreases at higher pressures with a corresponding anharmonicity increase, as a consequence of the formation of a strong hydrogen bond. The hydration energy of grossular and the formation energy of Si-free katoite have also been computed, and the B3-LYP results are in quite good agreement with experiment.

Entrapping molecules in zeolites nanocavities: a thermodynamic and ab-initio study.

Adsorption enthalpies of Ar, N2, CO, H2O, CH3CN and NH3 on H-BEA and H-MFI zeolites and on Silicalite, have been measured calorimetrically at 303K in order to assess the energetic features of dispersive forces interactions (confinement effects), H-bonding interactions with surface silanols and specific interactions with Lewis and Brønsted acidic sites. The adsorption of the molecular probes with model clusters mimicking surface silanols, Lewis and Brønsted sites has been simulated at ab-initio level. The combined use of the two different approaches allowed to discriminate among the different processes contributing to the measured (-deltaadsH). Whereas CO and N2 single out contributions from Lewis and Brønsted acidic sites, Ar is only sensitive to confinement effects. For H2O, CH3CN and NH3 the adsorption on Brønsted sites is competitive with the adsorption on Lewis sites. The energy of interaction of H2O with all considered zeolites is surprisingly higher than expected on the basis of -deltaadsH vs PA correlation.

Ab initio conformational study of the phenylisoserine side chain of paclitaxel.

Paclitaxel (Taxol) and related compounds are important antitumor drugs, currently used for the treatment of several types of cancer. The flexible amino acidic C13 side chain is a key element of the taxoid pharmacophore, and the identification of the bioactive conformation is a top priority for a better understanding of the mode of action of these anticancer agents. The conformational features of the side chain have been investigated by Hartree-Fock ab initio and semiempirical PM3 calculations. To gain a better understanding of solvent effects, different molecular models of paclitaxel were used in the calculations. The gas-phase calculations confirm that only one conformation, named ch1 (very similar to the one found in the crystal structure of docetaxel), is present in apolar environments. The preference for this conformer has been rationalized in terms of its L shape, which minimizes steric and Coulombic interactions, and of a favorable arrangement of the glycolate moiety. When a polar solvent was simulated by different methods, a greater conformational variability was found, with different conformations differing by less than 1.5 kcal/mol. Among these conformations, only one (ch5', similar to molecule B of the crystal structure of paclitaxel) is particularly apt to interact with solvent molecules. In light of these data, it seems reasonable to assume that, when the drug is bound to the lipophilic pocket of the tubuline receptor, the C13 amino acidic side chain assumes a conformation close to ch1.