Geometries and properties of excited states in the gas phase and in solution: theory and application of a time-dependent density functional theory polarizable continuum model

In this paper we present the theory and implementation of analytic derivatives of time-dependent density functional theory (TDDFT) excited states energies, both in vacuo and including solvent effects by means of the polarizable continuum model. The method is applied to two case studies: p-nitroaniline and 4-(dimethyl)aminobenzonitrile. For both molecules PCM-TDDFT is shown to be successful in supporting the analysis of experimental data with useful insights for a better understanding of photophysical and photochemical pathways in solution.     

Surface enhanced second harmonic generation from macrocycle, catenane, and rotaxane thin films: experiments and theory

Surface enhanced second harmonic generation (SE SHG) experiments on molecular structures, macrocycles, catenanes, and rotaxanes, deposited as monolayers and multilayers by vacuum sublimation on silver, are reported. The measurements show that the molecules form ordered thin films, where the highest degree of order is observed in the case of macrocycle monolayers and the lowest in the case of rotaxane multilayers. The second harmonic generation activity is interpreted in terms of electric field induced second harmonic (EFISH) generation where the electric field is created by the substrate silver atoms. The measured second order nonlinear optical susceptibility for a rotaxane thin film is compared with that obtained by considering only EFISH contribution to SHG intensity. The electric field on the surface of a silver layer is calculated by using the Delphi4 program for structures obtained with TINKER molecular mechanics/dynamics simulations. An excellent agreement is observed between the calculated and the measured SHG susceptibilities.     

Solid-phase synthesis of cyclic PNA and PNA-DNA chimeras

[structure: see text] A new and versatile on-line automated solid-phase approach to obtain cyclic PNA (I and III) and cyclic PNA-DNA chimeras (II) in highly pure form has been developed. Starting from a Tentagel matrix functionalized with a 3-chloro-4-hydroxyphenylacetic linker, the synthesis of representative, new cyclic molecules by standard peptide and phosphoramidite-based chemistry has been achieved.     

Differentiability properties for a class of non-convex functions

Closed sets K ⊂ satisfying an external sphere condition with uniform radius (called ϕ-convexity or proximal smoothness) are considered. It is shown that for -a.e. x ∊ ∂K the proximal normal cone to K at x has dimension one. Moreover if K is the closure of an open set satisfying a (sharp) nondegeneracy condition, then the De Giorgi reduced boundary is equivalent to ∂ K and the unit proximal normal equals -a.e. the (De Giorgi) external normal. Then lower semicontinuous functions f : with ϕ-convex epigraph are shown, among other results, to be locally BV and twice -a.e. differentiable; furthermore, the lower dimensional rectifiability of the singular set where f is not differentiable is studied. Finally we show that for -a.e. x there exists δ (x) > 0 such that f is semiconvex on B(x,δ(x)). We remark that such functions are neither convex nor locally Lipschitz, in general. Methods of nonsmooth analysis and of geometric measure theory are used. Work partially supported by M.I.U.R., project “Viscosity, metric, and control theoretic methods for nonlinear partial differential equations.”     

Behavior of disordered boron carbide under stress

Gibbs free-energy calculations based on density functional theory have been used to determine the possible source of failure of boron carbide just above the Hugoniot elastic limit (HEL). A range of B4C polytypes is found to be stable at room pressure. The energetic barrier for shock amorphization of boron carbide is by far the lowest for the B12(CCC) polytype, requiring only 6 GPa approximately = P(HEL) for collapse under hydrostatic conditions. The results clearly demonstrate that the collapse of the B12(CCC) phase leads to segregation of B12 and amorphous carbon in the form of 2-3 nm bands along the (113) lattice direction, in excellent agreement with recent transmission electron microscopy results.     

Gold-catalyzed regiospecific intermolecular hydrothiolation of allenes

AuBr₃-catalyzed regiospecific intermolecular hydrothiolation of aromatic allenes and aromatic thiols afforded the corresponding dithioacetals in good yields at 0 °C in 5 min.     

Thiazolo[5,4-d]thiazole-2,5-dicarboxylic acid,C6H2N2O4S2, and its coordination polymers

Thiazolo[5,4-d]thiazole-2,5-dicarboxylic acid, C₆H₂N₂O₄S₂, was isolated as a polycrystalline material, and its crystal structure was determined by ab-initio X-ray powder diffraction (XRPD) methods. This species, upon deprotonation, was subsequently used in preparing the new coordination polymers Ag₂(C₆N₂O₄S₂), Mn(C₆N₂O₄S₂)(H₂O)₂, Co(C₆N₂O₄S₂)(H₂O)₂, Cu(C₆N₂O₄S₂)(H₂O) and Zn(C₆N₂O₄S₂)(H₂O)₂, fully characterized by analytical, thermal and XRPD structural methods – including in situ thermodiffractometry and simultaneous TGA and DSC. In the first-row transition metal derivatives, the [C₆N₂O₄S₂]^2? anion systematically prefers the N,O-chelating, vs. the expected O,O′-bridging, coordination mode, not allowing the formation of porous 3D frameworks. Indeed, these species are dense 1D coordination polymers. At variance, the silver derivative possesses a complex, dense 3D framework, due to the presence of μ₆-[C₆N₂O₄S₂]^2? ligands showing two μ₂-bridging carboxylates and two monohapto N-donor sites. When dehydration is viable, materials of E_n(C₆N₂O₄S₂) formulation are irreversibly recovered (n = 1 for E = Mn, Co, Zn, Cu; n = 2, for E = H).     

Rotational invariance and double frustration in the structures of gold clusters growing around the F(s)-defected MgO (100) surface

The interaction of small gold clusters (Au(n), n = 1-4, 20) and a gold monolayer with the MgO (100) surface surrounding a neutral oxygen vacancy (F(s) center) is investigated using density-functional (DF) calculations. It is found that the presence of the defect modifies the interaction of gold not only with the vacancy itself, but also with the oxygen and magnesium atoms around it by increasing both the adhesion energy and the equilibrium bond distances. This is at variance with the interaction of metal atoms with the regular MgO (100) surface or the F(s) defect itself, in which an increase of the adhesion energy is associated with a shortening of the metal-surface distance. The resulting double frustration and cylindrical invariance of the metal-surface interaction cause small gold clusters growing around an F(s) nucleation center to be highly fluxional in terms both of rotational freedom and of multiple competing structural motifs. Fragmentation energies of the gold clusters are also discussed, finding that the lowest-energy pathway corresponds to the detachment of a dimer.     

Theoretical investigation of hydrogen atom transfer in the hydrated C–G base pair

Hydrogen atom transfer and the related electronic rearrangement in the hydrated C–G base pair have been studied in order to understand the role of the hydrogen bonds between the bases and those with the water molecules in these processes. The modification of hydrogen transfer due to the first shell and bulk hydration has been analysed. The different structures, when the hydrogen atom moves in a H-bond or in another bond, have been studied. Two naïve schemes, where the water molecules are only indirectly or directly involved in the hydrogen atom transfer, have been considered. The results support the idea that the actual mechanisms are more complex than these schemes. Hydration modifies the potential energy curves of both tautomers and zwitterionic structures, but does not generate new stable structures (minimum PES) of these types. We find a new stable structure due to both a reorganization of the two down water molecules and other global changes of the system. This new system is generated from a zwitterionic structure. The charges, during hydrogen transfer, of the hydrogen donor and of the hydrogen acceptor part of the base pair and of the hydrogen atoms between the bases have been determined and their modifications, due to the first shell and bulk hydration, have been analysed. The qualitative and quantitative behavior has been studied.