Using molecular dynamics and quantum mechanics calculations to model fluorescence observables

We provide a critical examination of two different methods for generating a donor-acceptor electronic coupling trajectory from a molecular dynamics (MD) trajectory and three methods for sampling that coupling trajectory, allowing the modeling of experimental observables directly from the MD simulation. In the first coupling method we perform a single quantum-mechanical (QM) calculation to characterize the excited state behavior, specifically the transition dipole moment, of the fluorescent probe, which is then mapped onto the configuration space sampled by MD. We then utilize these transition dipoles within the ideal dipole approximation (IDA) to determine the electronic coupling between the probes that mediates the transfer of energy. In the second method we perform a QM calculation on each snapshot and use the complete transition densities to calculate the electronic coupling without need for the IDA. The resulting coupling trajectories are then sampled using three methods ranging from an independent sampling of each trajectory point (the independent snapshot method) to a Markov chain treatment that accounts for the dynamics of the coupling in determining effective rates. The results show that the IDA significantly overestimates the energy transfer rate (by a factor of 2.6) during the portions of the trajectory in which the probes are close to each other. Comparison of the sampling methods shows that the Markov chain approach yields more realistic observables at both high and low FRET efficiencies. Differences between the three sampling methods are discussed in terms of the different mechanisms for averaging over structural dynamics in the system. Convergence of the Markov chain method is carefully examined. Together, the methods for estimating coupling and for sampling the coupling provide a mechanism for directly connecting the structural dynamics modeled by MD with fluorescence observables determined through FRET experiments.     

Time resolved spectroscopy of 2-(dimethylamine)fluorene. Solvent effects and photophysical behavior

The effect of different solvents on the fluorescent properties of 2-(dimethylamine)fluorene (DAF) were studied. In aprotic solvents we detected a strongly emissive intramolecular charge transfer (ICT) state that decayed by intersystem crossing to triplet. In proton-accepting solvents DAF exhibits in the excited state an intramolecular proton transfer. An ionized species is postulated, which simultaneously twists to a rotated conformation in the excited state. Thus, the specific solvent interactions supplement but do not replace the twist mechanism and accompany the charge transfer accepted as the prerequisite for twisted intramolecular charged transfer (TICT) state formation.     

Structure prediction, disorder and dynamics in a DMSO solvate of carbamazepine

We have applied crystal structure prediction methods to understand and predict the formation of a DMSO solvate of the anti-convulsant drug carbamazepine (CBZ), in which the DMSO molecules are disordered. Crystal structure prediction calculations on the 1:1 CBZ:DMSO solvate revealed the generation of two similar low energy structures which differ only in the orientation of the DMSO molecules. Analysis of crystal energy landscapes generated at 0 K suggests the possibility of solvent disorder. A combined computational and experimental study of the changes in the orientation of the DMSO within the crystal structure revealed that the nature of the disorder changes with temperature. At low temperature, the DMSO disorder is static whilst at high temperature the DMSO configurations can interconvert by a 180° rotation of the DMSO molecules within the lattice. This 180° rotation of the DMSO molecules drives a phase change from a high temperature dynamically disordered phase to a low temperature phase with static disorder. Crystallisation of a DMSO solvate of the related molecule epoxycarbamazepine resulted in a different degree of DMSO disorder in the crystal structure, despite the similarity of the carbamazepine and epoxycarbamazepine molecules. We believe consideration of disorder and its contribution to entropy and crystal free energies at temperature other than 0 K is fundamental for the accuracy of future energy rankings in crystal structure prediction calculations of similar solvated structures.     

O-Alkylation of 3-hydroxy-1-phenyl-2-pyrazolin-5-one

3-Hydroxy-1-phenyl-2-pyrazolin-5-one 1 reacts with primary, secondary and allylic alcohols under catalytic acidic conditions and in the presence of 3 Å molecular sieves, to afford 3-alkoxy-1-phenyl-2-pyrazolin-5-ones 3 .     

A Model for Community Nursing in a Rural County

A model for the working day of the community nurse is proposed. This takes into account the attachment of the nurse to the patients registered with assigned general practices and the effect that this will have on her travelling time, visiting time and administrative duties. It also leads to a method of dividing the country into nursing team regions, assessing the level of nursing service thereby provided.     

Characterization of foxing stains in early twentieth century photographic and paper materials

Abstract

The subject of this present work is a group of nine historical pictures shot in Palermo by the Sicilian photographer E. Interguglielmi in 1912. They are nine matte-collodion prints mounted on the original cardboard supports and all of them show foxing stains affecting the paper surface. In order to characterise the chemical composition of the supports and investigate foxing spots, non-destructive and micro-destructive analysis were carried out. X-rays fluorescence (XRF) analysis was used to characterise the elemental composition of all the mounting boards, allowing a comparison between the foxing spots and non-affected areas. Laser-Induced Breakdown Spectroscopy was used to investigate the presence of lower atomic number elements, not detectable by XRF, while SEM imaging allowed the investigation of surface appearance and nature of original paper samples from the cardboards.     

Sustainable self-assembly strategies for emerging nanomaterials

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Pd-catalysed asymmetric mono- and bis-alkoxycarbonylation of vinylarenes

The asymmetric alkoxycarbonylation of vinylarenes catalysed by palladium complexes bearing chiral phosphine ligands has attracted much attention over the last decades. The products of both mono- and bis(alkoxycarbonylation) reactions are important intermediates in the syntheses of pharmaceuticals such as 2-arylpropionic acids, the most important class of non-steroidal anti-inflammatory drugs. In this article, a general overview of the topics will be presented and the recent advances in this field will be particularly detailed. Besides the term alkoxycarbonylation, hydroesterification and hydroalkoxycarbonylation are also used in the literature to describe this reaction. Furthermore, more specific terms such as methoxycarbonylation can be found. In this report, the term alkoxycarbonylation will be used as the general term, and specific terms will be used to unambiguously define which reaction is meant.     

Towards prediction of stoichiometry in crystalline multicomponent complexes

We report on the crystal structure of urea (U) with acetic acid (A), its physical stability and its predictability using computational methods. The crystal structure of urea:acetic acid (U:A) shows hydrogen-bond ribbons and a 1:2 stoichiometry. Crystal structure prediction calculations are presented for two sets of U:A stoichiometries: 1:1 and 1:2. A 1:3 stoichiometry is also partially explored by means of a synthon approach. The calculated lattice energies, along with hydrogen-bond patterns, of crystal structures predicted with the three stoichiometries are presented and analysed to provide a rationalisation for the stoichiometry observed. Exploring stoichiometric diversity using computational methods provides a tool for the rationalisation of stoichiometry preferences in crystalline multicomponent systems and a first step towards their prediction.     

Hydration properties of aqueous Pb(II) ion

Using density functional theory and polarized continuum models, we have determined the most probable coordination number and structure of the first hydration shell of aqueous Pb(II). The geometries and hydration free energies of Pb(H2O)(1-9)(2+) were examined and benchmarked against experimental values. The free energies of hydration of Pb(H2O)(6-8)(2+) were found to match the experimental value within 10 kcal/mol. Moreover, based upon our thermochemical results for single water addition, primary hydration numbers of 6, 7, and 8 are all thermally accessible at STP. Use of a small-core 60 electron effective core potential (ECP) with the aug-cc-pvdz-PP basis on Pb resulted in structures that are significantly less hemidirected than predicted when using the large-core 78 electron ECP and the lanl2DZ basis on the metal. Our results imply that the hemi- to holo-directed transition in Pb(II)-water complexes is driven by coordination number and not hybridization of the 6s lone-pair orbital or enhanced covalent bonding in the Pb-OH2 bond. In addition to basis set effects, the influence of different solvation models on hydration reactions has further been examined so as to determine the relative accuracy of the calculated hydration thermochemistry.