Where are embarrassingly parallel problems? The atom-diatom quasiclassical reactivity

Summary The apparently embarrassingly parallel problem of calculating a batch of quasiclassical trajectories to evaluate cross sections or rate constants has been analyzed. The study shows that only an accurate evaluation of the performance parameters and a consequent appropriate restructuring of the computer code allows the achievement of high speedup and efficiency especially when large calculations are implemented on massively parallel systems.     

Electron transfer rates and Franck–Condon factors: an application to the early electron transfer steps in photosynthetic reaction centers

Mechanistic aspects of some of the early electron transfer steps occurring in photosynthetic reaction centers are discussed. Starting from the normal modes of the redox cofactors involved in the electron transfer processes, we show how a series of quantities which regulate electron transfer rates, such as (i) the electron transfer active modes, (ii) the intramolecular reorganization energy, and (iii) the mutual couplings between the vibronic states of the donor and the acceptor, can be obtained and used to draw qualitative conclusions on ET rates.     

Structure and spectroscopic characterization of the quaternary system: Copper(II), pyridine-2,6-dicarboxylate, 2,2′-bipyridyl and pyridine

Conclusion The x-ray structural results confirm what has been ascertained by thermodynamic and spectroscopic data in aqueous solution(7). It is evident that the addition of pyridine to the solution containing the mixed species [Cu(bipy)(pydca)(H₂O)] leads to the substitution of a water molecule directly bound to copper(II) ion by a pyridine molecule. This experiment also demonstrated the presence of a water molecule in the equatorial plane of the complex.The subsequent diffractometric study on single crystals derived from the copper(II)/bipy/pydca system revealed the existence in the solid state of [Cu₂(bipy)₂(pydca)₂] · 4H₂O. Thus the pydca dianion, instead of forming the statistically favoured mixed complex [Cu(bipy)(pydca)], gives rise to crystals containing two different copper(II) environments: [Cu(pydca)₂]^2– and [Cu(bipy)₂]²⁺, linked by O-carboxylate bridges. The facility with which [Cu(bipy)(pydca)(py)] can be obtained shows that the addition of pyridine prevents the formation of polynuclear species.     

The influence of the solvent on the conformational energy differences due to the anomeric effect

The solvation free energy ΔG^sol of molecules exhibiting the anomeric effect is computed in an approach that considers a continuous distribution for the solvent. A partition of ΔG^sol into separately evaluated contributions confirms that changes in the energy of the systems due to changes in conformation of the solute are ruled by the electrostatic contribution. A comparison with the “exact” values indicates that the approximate expression for the electrostatic contribution to ΔG^sol are not accurate enough to permit a proper modeling of the solvent influence on the anomeric effect. The systems are composed of methanediol, methoxymethanol, dimethoxymethane, and 2-methoxytetrahydropyran in carbon tetrachloride, chloroform, acetone, and water. The calculations have been performed at the SCF level with the STO -3G and 4–31G basis sets.     

A novel oxidative side-chain transformation of α-amino acids and peptides by methyltrioxorhenium/H2O2 system

N-Boc derivatives of Met, Cys, and Trp, the properties of which resemble those of the respective amino acid residues present in proteins, are efficiently oxidized by methyltrioxorhenium and H₂O₂. A high regioselectivity for the oxidation of these residues when embedded into peptides was also found.     

A novel chemo-multienzymatic synthesis of bioactive cyclophellitol and epi-cyclophellitol in both enantiopure forms

A new route to synthesize cyclophellitol and epi-cyclophellitol from racemic starting materials in enantiopure forms has been developed. The synthesis involves a multi-enzymatic biotransformation pathway of the novel cyano-cyclitol (1R,4S,5R,6R)/(1S,4R,5S,6S)-4,5,6-trihydroxycyclohex-2-enecarbonitrile by a cooperative use of lipase, nitrile hydratase, and amidase.     

Thermo-chemical manifold reduction for tabulated chemistry modeling. Temperature and dilution constraints for smooth combustion reactors

New scenarios for energy systems pointed out the importance of designing innovative combustion systems. In this context, high levels of internal dilution and preheating show interesting features related to low emissions, smooth temperature gradients, absence of visible flame and large fuel and load flexibility. Those characteristics are very difficult to obtain simultaneously with conventional combustion processes in the same device.The large-scale utilization of such novel concepts relies on the developments of proper modeling tools that should consider the multiple physical phenomena involved under distributed ignition. A challenging modeling aspect is related to the strong coupling between fluid-dynamics and kinetic time scales that implies the use of detailed mechanisms. Moreover, the heat transfer mechanisms and the heat loss at walls play key roles.In this context, tabulated chemistry methods are viable solutions to represent the thermo-chemical pattern in combustion systems with internal recirculation. However, the identification of adequate controlling variables for these systems is not trivial. In fact, in addition to mixture fraction and progress variable, an internal dilution and a heat loss parameter must be considered, leading to a 4-dimensional thermo-chemical manifold, with an inherent increase of computational costs.In this work a novel tabulation procedure is proposed in order to represent such comprehensive manifold taking into account the primary role of the internal recirculation on system reactivity.Moreover, a reduction of the thermo-chemical manifold was carried out by exploiting active interconnections between experiments and computations and embedding physical and process constraints based on measurable quantities obtained from experiments. These constrains are related to minimum ignition and maximum attainable process temperatures, heat loss through the surroundings and recirculation rate. The reliability of the proposed approach was assessed by comparing the reduced manifolds to the measured data for a cyclonic burner operating under massive internal dilution levels.     

The occurrence of electron transfer in aromatic nitration: dynamical aspects

Electron transfer (ET) from toluene to the nitronium ion in the region of van der Waals intermolecular distances has been investigated by a quantum dynamical analysis performed on potential-energy surfaces computed at the ab initio multireference configuration interaction level. The results show that ET is very fast, occurring on a timescale of a few picoseconds. This has important implications for the mechanism of aromatic nitration: the ET path can compete efficiently with the direct attack of the nitronium ion to the aromatic substrate to yield the Wheland intermediate and that could explain some unsettled points in the mechanism of aromatic nitration. Received: 16 September 1999 / Accepted: 3 February 2000 / Published online: 12 May 2000     

Stimuli‐Responsive Lipidic Cubic Phase: Triggered Release and Sequestration of Guest Molecules

New stimuli‐responsive nanomaterials, made up of host–guest lipidic cubic phases (LCPs) are presented. These biocompatible, stable, transparent and water‐insoluble LCPs are composed of monoolein (MO) as a neutral host, and small amounts of one of three judiciously designed and synthesized designer lipids as guest that preserve the structure and stability of LCPs, but render them specific functionalities. Efficient pH‐ and light‐induced binding, release and sequestration of hydrophilic dyes are demonstrated. Significantly, these processes can be performed sequentially, thereby achieving both temporal and dosage control, opening up the possibility of using such LCPs as effective carriers to be used in drug delivery applications. Specifically, because of the inherent optical transparency and molecular isotropy of LCPs they can be envisaged as light‐induced drug carriers in ophthalmology. The results presented here demonstrate the potential of molecular design in creating new functional materials with predicted operating mode.