Density functional theory study of the trans-trans-cis (TTC)-->trans-trans-trans (TTT) isomerization of a photochromic spiropyran merocyanine

Density Functional Theory (DFT) calculations have been performed on the TTC-->TTT isomerization reaction of the open forms of the 1',3'-dihydro-8-bromo-6-nitro-1',3',3'-trimethylspiro[2H-1-benzopyran-2,2'-(2H)indole (8-Br-6-nitro-BIPS) system. The calculations were carried out in vacuo and in methylene chloride solution at different temperatures. Results are compared with the available experimental values of free energy difference and activation energy in solution.     

Preparative three-dimensional GC and nuclear magnetic resonance for the isolation and identification of two sesquiterpene ethers from Dictyota Dichotoma

Separation science plays a crucial role in the isolation of novel compounds contained in complex matrices. Yet their rationale employment needs preliminary structure elucidation, which usually requires sufficient aliquots of grade substances to characterize the molecule by nuclear magnetic resonance experiments. In this study, two peculiar oxa-tricycloundecane ethers were isolated by means of preparative multidimensional gas chromatography from the brown alga species Dictyota dichotoma (Huds.) Lam., aiming to assign their 3D structures. Density functional theory simulations were carried out to select the correct configurational species matching the experimental NMR data (in terms of enantiomeric couples). In this case, the theoretical approach was crucial as the protonic signal overlap and spectral overcrowding were preventing any other unambiguous structural information. Just after the identification through the density functional theory data matching of the correct relative configuration it was possible to verify an enhanced self-consistency with the experimental data, confirming the stereochemistry. The results obtained further pave the way toward structure elucidation of highly asymmetric molecules, whose configuration cannot be inferred by other means or strategies.     

The unusual reaction of semiquinone radicals with molecular oxygen

Hydroquinones (benzene-1,4-diols) are naturally occurring chain-breaking antioxidants, whose reactions with peroxyl radicals yield 1,4-semiquinone radicals. Unlike the 1,2-semiquinone radicals derived from catechols (benzene-1,2-diols), the 1,4-semiquinone radicals do not always trap another peroxyl radical, and instead the stoichiometric factor of hydroquinones varies widely between 0 and 2 as a function of ring-substitution and reaction conditions. This variable antioxidant behavior has been attributed to the competing reaction of the 1,4-semiquinone radical with molecular oxygen. Herein we report the results of experiments and theoretical calculations focused on understanding this key reaction. Our experiments, which include detailed kinetic and mechanistic investigations by laser flash photolysis and inhibited autoxidation studies, and our theoretical calculations, which include detailed studies of the reactions of both 1,4-semiquinones and 1,2-semiquinones with O2, provide many important insights. They show that the reaction of O2 with 2,5-di-tert-butyl-1,4-semiquinone radical (used as model compound) has a rate constant of 2.4 +/- 0.9 x 10(5) M-1 s-1 in acetonitrile and as high as 2.0 +/- 0.9 x 10(6) M-1 s-1 in chlorobenzene, i.e., similar to that previously reported in water at pH approximately 7. These results, considered alongside our theoretical calculations, suggest that the reaction occurs by an unusual hydrogen atom abstraction mechanism, taking place in a two-step process consisting first of addition of O2 to the semiquinone radical and second an intramolecular H-atom transfer concerted with elimination of hydroperoxyl to yield the quinone. This reaction appears to be much more facile for 1,4-semiquinones than for their 1,2-isomers.     

The Synthesis of Organic Molecules of Intrinsic Microporosity Designed to Frustrate Efficient Molecular Packing

Efficient reactions between fluorine‐functionalised biphenyl and terphenyl derivatives with catechol‐functionalised terminal groups provide a route to large, discrete organic molecules of intrinsic microporosity (OMIMs) that provide porous solids solely by their inefficient packing. By altering the size and substituent bulk of the terminal groups, a number of soluble compounds with apparent BET surface areas in excess of 600 m² g^?1 are produced. The efficiency of OMIM structural units for generating microporosity is in the order: propellane>triptycene>hexaphenylbenzene>spirobifluorene>naphthyl=phenyl. The introduction of bulky hydrocarbon substituents significantly enhances microporosity by further reducing packing efficiency. These results are consistent with findings from previously reported packing simulation studies. The introduction of methyl groups at the bridgehead position of triptycene units reduces intrinsic microporosity. This is presumably due to their internal position within the OMIM structure so that they occupy space, but unlike peripheral substituents they do not contribute to the generation of free volume by inefficient packing.     

Reading of Protein Surfaces in the Native State at Micromolar Concentrations by a Chirogenetic Porphyrin Probe

The recognition of some globular proteins was carried out in aqueous solution, at micromolar concentrations, by using an uncharged symmetrical cobalt–porphyrin (Co–P). By means of UV/Vis, induced circular dichroism, and fluorescence spectroscopy techniques, it was ascertained that the interactions between specific amino acid residues and Co–P occurred on the protein surface. In particular, spectroscopic evidence showed the formation of supramolecular complexes without disruption of the native structure of the proteins and, furthermore, that signal changes were characteristic of each Co–P/protein system, so that they could be used as a highly sensitive analytical tool for protein recognition. The relative association constants were proportional to the protein molecular masses (and then to the number of amino acid residues).     

Polymeric membranes conditioning for sensors applications: mechanism and influence on analytes detection

In this work, we studied an ion-exchange membrane based on an inert polymer skeleton in which it is dispersed and anchored a molecule with charged groups able to discriminate and bind positive or negatively charged ions present in a sample. In order to be ready to work, electromembranes need a complex procedure called activation or conditioning. Although most of the known literature looks at the subject from an electrochemical point of view, we put forward a structural approach. Membrane conditioning, in fact, is considered a required step to improve sensor performances and to allow the collection of reproducible data. Even if this operation is carefully followed by all the operators working with sensors equipped with a membrane, it looks like that a thoroughly explanation of the working mechanism and a detailed balance of cost and gains has still not been carried out. As a consequence, we suggest a bulk or membrane approach, where the landscape is mainly characterized by the long-range structure of the membrane itself. Our findings suggest that membrane conditioning has to be carried out carefully and the advantages of this pre-treatment can be appreciated especially for very low concentration measurements. The need for the conditioning mainly results from the necessity of a complete permeation of all the different tortuous channels constituting the membrane itself.     

Determination of cylindrospermopsin in freshwaters and fish tissue by liquid chromatography coupled to electrospray ion trap mass spectrometry

Cylindrospermopsin (CYN) is a toxic alkaloid‐like compound produced by some strains of cyanobacteria, procariotic organisms occurring in water blooms, observed worldwide in eutrophic lakes and drinking water reservoirs. Methods for determination of CYN in freshwater and fish muscle by liquid chromatography coupled to electrospray ion trap mass spectrometry are herein described. The performances of both methods are reported; ion trap LC/ESI‐MS/MS resulted highly selective and reliable in unambiguous identification of CYN, based on monitoring the precursor ion and three product ions. The methods developed showed satisfactory mean recoveries (higher than 63.6%) and relative standard deviations, ranging from 5.8 to 9.8%. The limits of quantification at 0.10 ng/mL in freshwaters and 1.0 ng/g in fish muscle, respectively, allow for determination of CYN also in early contamination stages. Ion trap LC/ESI‐MS/MS was successfully applied to the identification and quantification of CYN in water and cyanobacteria extracts from Lake Averno, near Naples, representing the first case of contamination described in southern Italy. Copyright © 2009 John Wiley & Sons, Ltd.     

The directed profitable location Rural Postman Problem

In this paper we introduce an extension of the well known Rural Postman Problem, which combines arc routing with profits and facility location. Profitable arcs must be selected, facilities located at both end-points of the selected arcs, and a tour identified so as to maximize the difference between the profit collected along the arcs and the cost of traversing the arcs and installing the facilities. We analyze properties of the problem, present a mathematical programming formulation and a branch-and-cut algorithm. In an extensive computational experience the algorithm could solve instances with up to 140 vertices and 190 arcs and up to 50 vertices and 203 arcs.     

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.