Modelling vibrational coupling in DNA oligomers: a computational strategy combining QM and continuum solvation models

In this paper, a computational strategy, based on DFT calculations at the M06-2X level, combined with the polarizable continuum model, the Hessian matrix reconstruction method and the Partial hessian vibrational approach is applied to evaluate inter- and intra-layer vibrational couplings between hydrogen bonded and stacked DNA base pairs. The present work demonstrates that this computational scheme can effectively predict and interpret the vibrational couplings of nucleic acids in solution. The effect of the environment described in a cluster or in a continuum manner is necessary in order to improve the agreement with the experimental values.     

Synthesis and characterization of functional polyesters tailored for biomedical applications

This work aimed at the development of bioactive polymeric materials to be used for targeted drug delivery and tissue engineering applications. The proposed strategy was based on the design of macromolecular systems whose functionality can be easily modified. Polyesters containing side‐chain end capped by primary hydroxyl groups were synthesized by polyaddition of oxetanes and carboxylic anhydrides catalyzed by quaternary onium salts. The polyaddition of bis(oxetane) with different dicarboxylic acids was also investigated. In all cases, oxetane monomers contained one hydroxyl group either free or protected by a benzyl group. The polymer yield and molecular weight were relatively high when aromatic anhydrides were used. In all other cases, low conversions or no polymerization at all were obtained. In a parallel research line, several alkanols were successfully employed to synthesize different α,β′,β‐trisubstituted‐β‐lactones. These monomers were prepared in five steps starting from diethyl oxalpropionate according to established synthetic routes. Final yields depended on both preparation method and side‐chain structure. By using quaternary ammonium salts as catalysts, the synthesized functional lactones underwent anionic ring opening polymerization leading to the corresponding homopolymers and copolymers in fairly good yields. The prepared polymeric materials were extensively characterized by spectroscopic techniques, size exclusion chromatography, and thermal analysis. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2459–2476, 2008     

Acid-base properties of the N3 ruthenium(ii) solar cell sensitizer: a combined experimental and computational analysis

We report a combined spectro-photometric and computational investigation of the acid-base equilibria of the N3 solar cell sensitizer [Ru(dcbpyH(2))(2)(NCS)(2)] (dcbpyH(2) = 4,4'-dicarboxyl-2,2' bipyridine) in aqueous/ethanol solutions. The absorption spectra of N3 recorded at various pH values were analyzed by Single Value Decomposition techniques, followed by Global Fitting procedures, allowing us to identify four separate acid-base equilibria and their corresponding ground state pK(a) values. DFT/TDDFT calculations were performed for the N3 dye in solution, investigating the possible relevant species obtained by sequential deprotonation of the four dye carboxylic groups. TDDFT excited state calculations provided UV-vis absorption spectra which nicely agree with the experimental spectral shapes at various pH values. The calculated pK(a) values are also in good agreement with experimental data, within <1 pK(a) unit. Based on the calculated energy differences a tentative assignment of the N3 deprotonation pathway is reported.     

Increasing radial solutions for Neumann problems without growth restrictions

We study the existence of positive increasing radial solutions for superlinear Neumann problems in the ball. We do not impose any growth condition on the nonlinearity at infinity and our assumptions allow for interactions with the spectrum. In our approach we use both topological and variational arguments, and we overcome the lack of compactness by considering the cone of nonnegative, nondecreasing radial functions of H¹(B)$H^1(B)$.     

Comprehensive Photophysical Behaviour of Ethynyl Fluorenes and Ethynyl Anthracenes Investigated by Fast and Ultrafast Time‐Resolved Spectroscopy

Detailed investigations by time‐resolved transient absorption and fluorescence spectroscopies with nano‐ and femtosecond time resolutions are carried out with the aim of characterising the lowest excited singlet and triplet states of three ethynyl fluorenes ( 1 – 3 ) and three ethynyl anthracenes ( 4 – 6 ) in solvents of different polarity. The solvent is found to modify the deactivation pathways of the lowest excited singlet state of compounds 1 – 4 , thus changing their fluorescence, intersystem crossing and internal conversion efficiencies. The fluorescence and triplet yields gradually decrease, while the internal conversion quantum yield increases upon increasing the solvent dielectric constant. These experimental results, coupled with the marked fluorosolvatochromic effect, point to the involvement of an emitting state with a charge‐transfer (CT) character, strongly stabilised by polar solvents. This is proved by ultrafast spectroscopic studies in which two transients, distinguished by characteristic spectral shapes assigned to locally excited (LE) and CT states, are detected, the CT state being the longer lived and fluorescent one in highly polar solvents. The intramolecular LE→CT process, operative in highly polar media, becomes particularly fast (up to ≈300 fs) in the case of the NO₂ derivative 1 . No push–pull character is found for 5 and 6 , which exhibit different photophysical behaviour; indeed, the solvent polarity does not modify significantly the dynamics of the lowest excited singlet states. Quantum mechanical calculations at the TDDFT level are also used to determine the state order and nature of the lowest excited singlet and triplet states and to rationalise the different photophysical behaviour of fluorine and anthracene derivatives, particularly concerning the intersystem crossing process.     

Formation and relaxation of excited states in solution: a new time dependent polarizable continuum model based on time dependent density functional theory

In this paper a novel approach to study the formation and relaxation of excited states in solution is presented within the integral equation formalism version of the polarizable continuum model. Such an approach uses the excited state relaxed density matrix to correct the time dependent density functional theory excitation energies and it introduces a state-specific solvent response, which can be further generalized within a time dependent formalism. This generalization is based on the use of a complex dielectric permittivity as a function of the frequency, epsilonomega. The approach is here presented in its theoretical formulation and applied to the various steps involved in the formation and relaxation of electronic excited states in solvated molecules. In particular, vertical excitations (and emissions), as well as time dependent Stokes shift and complete relaxation from vertical excited states back to ground state, can be obtained as different applications of the same theory. Numerical results on two molecular systems are reported to better illustrate the features of the model.     

Solvation of coumarin 153 in supercritical fluoroform

We present a study of local density augmentation around an attractive solute (i.e., giving rise to more attractive interaction with the solvent than solvent-solvent interactions) in supercritical fluoroform. This work is based on molecular dynamics simulations of coumarin 153 in supercritical fluoroform at densities both above and below the critical density, ranging from dilute gas-like to liquid-like, at a reduced temperature (T/T(c)) of 1.03. We focused on studying the structure of the solvation shell and the variation of the solute electronic absorption and emission shifts with density. Quantum calculations at the density functional theory (DFT) level were run on the solute in the ground state, and time-dependent DFT calculations were performed in the solute excited state in order to determine the solute-solvent potential parameters. The results obtained for the Stokes shift are in agreement with the experimental measurements. To evaluate local density augmentation from simulations, we used two different definitions, one based on the solvation number and the other derived from solvatochromic shifts. In the former case, the agreement with experimental results is good, while, in the latter case, better agreement is achieved by perturbatively including the induced-dipole contribution to the solvation energy.     

Halforders and automorphisms of chain structures

The concepts of halfordered set, halfordered permutation set and halfordered chain structure will be presented and their interplay investigated. For this purpose the automorphism groups of these structures will be studied. Received 20 October 1999.     

Cationic dye dimers: a theoretical study

In this work we present a quantum-mechanical study on the structure and electronic spectra of three cationic dyes monomers and dimers: acridine orange (AO), proflavine (PF) and methylene blue (MB). The geometries were obtained from crystallographic data, the electronic properties were calculated with DFT (B3LYP functional) and the theoretical spectra were obtained with ZINDO. The solvation methodology adopted was the Integral Equation Formalism (IEF) version of the Polarizable Continuum Model (PCM). This study shows that the differences, even small, between optimized and crystal geometries are responsible for important spectral characteristics. Also, it indicates possible structures for interacting dimers.