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.     

Integrated NMR and computational study of push-pull NLO probes: interplay of solvent and structural effects

In this study we combined QM calculations and NMR measurements to understand at a detailed level the complex interplay of structural/electronic properties with the effects of the solvent in the NLO activity of push-pull systems, quantified in terms of variations of the static hyperpolarizability. Different parameters (bond lengths and bond length alternation, vibrational frequencies, electronic charge distribution) are introduced and tested to rationalize both the solvent sensitivity of three molecular systems (namely, p-nitroaniline, ethyl 4-ammino benzoate, and 5-nitro-1H-indole) and the differences among them. This analysis has finally allowed us to establish a clear correlation between the charge transfer behavior of the systems, their NLO properties, and NMR parameters also validating simplified but effective chemical analyses based on resonance limit forms.     

Thiazole orange (TO) as a light-switch probe: a combined quantum-mechanical and spectroscopic study

A Density Functional Theory (DFT) study of the absorbance and fluorescence emission characteristics of the cyanine thiazole orange (TO) in solution and when intercalated in DNA was carried out in combination with spectrophotometric and spectrofluorometric experiments under different conditions (temperature, concentration, solvent viscosity). T-jump relaxation kinetics of the TO monomer-dimer conversion enabled the thermodynamic parameters of this process to be evaluated. The overall data collected provided information on the features of the "light-switch" by the fluorescent TO and the comparison between experimental and calculated photo-physical properties allowed us to explain and rationalize both shifts and quenching/enhancing effects on fluorescence due to solvation, dimerisation and intercalation in the DNA.     

Steady-state and time-resolved investigations of a crown thioether conjugated with methylacridinium and its complexes with metal ions

The crown thioether 9-[4-(4,7,10,13-tetrathia-1-azacyclopentadecyl]phenyl-N-methylacridinium perchlorate (TCMA) was synthesized and characterized with the aim to verify its ability to interact selectively with metal ions and substantiate the possibility to detect easily the presence of heavy metals in fluid samples. The spectroscopic properties of TCMA, alone and in the presence of metal ions, were therefore studied in polar solvents (MeCN and H(2)O); in particular, steady-state UV-Vis spectrophotometric and fluorimetric techniques were used together with transient absorption spectroscopy with fs time resolution to investigate the spectral and dynamic properties of the lowest excited singlet state of TCMA and of TCMA/metal ion complexes. The absorption in the Vis region is characterized by a charge-transfer nature with the methylacridinium moiety acting as the electron-acceptor and the anilic group as the electron-donor. No emission from the S(1) was detected both in MeCN and H(2)O, while a small S(2)→ S(0) fluorescence emission (λ(max) = 485 nm and ?(F) = 0.0011) was detected in water. Time-resolved measurements with fs resolution of TCMA in MeCN have shown that the relaxed S(1) state is reached ～0.6 ps after the laser pulse, while the S(1)→ S(0) time constant is 3.7 ps. Among the investigated metal ions, only Fe(3+) (in MeCN) and Hg(2+) (in MeCN and H(2)O) were able to form stable complexes (association constant, K(ass) = 1-11 × 10(4) M(-1)) with TCMA. The S(1) state of the TCMA/M(n+) complexes emits with low quantum yield (?(F) = 0.0023-0.014) and decays with time constants much longer than TCMA itself, at least in the case of TCMA/Hg(2+) in MeCN. This study showed that TCMA is a good candidate for colorimetric/fluorimetric sensing of Hg(2+) in aqueous media owing to its high selectivity towards metal ions.     

Some Novel Cobalt Diphenylphosphine Complexes: Synthesis,Characterization, and Behavior in the Polymerization of 1,3-Butadiene

Some novel cobalt diphenylphosphine complexes were synthesized by reacting cobalt(II) chloride with (2-methoxyethyl)diphenylphosphine, (2-methoxyphenyl)diphenylphosphine, and 2-(1,1-dimethylpropyl)-6-(diphenylphosphino)pyridine. Single crystals suitable for X-ray diffraction studies were obtained for the first two complexes, and their crystal structure was determined. The novel compounds were then used in association with methylaluminoxane (MAO) for the polymerization of 1,3-butadiene, and their behavior was compared with that exhibited in the polymerization of the same monomer by the systems CoCl₂(PⁿPrPh₂)₂/MAO and CoCl₂(PPh₃)₂/MAO. Some significant differences were observed depending on the MAO/Co ratio used, and a plausible interpretation for such a different behavior is proposed.     

Resolution of (R,S)-flurbiprofen catalysed by dry mycelia in organic solvent

Mycelia of Aspergillus oryzae display high enantioselectivity towards (R)-flurbiprofen and can be efficiently used in pure organic solvent for the resolution of (R,S)-flurbiprofen through esterification. The use of the lyophilized mycelia facilitates the separation process so that in one step the two enantiomers of flurbiprofen, which are both valuable for pharmaceutical applications, can be easily separated. The biotransformation can be carried out in different apolar solvents using different primary alcohols as nucleophiles under very mild conditions.     

Synthesis of new [[(3-substituted-5-isoxazolyl)-alkyliden]iminooxy]aminopropanol derivatives

The preparation of new [[(3-substituted-5-isoxazolyl)alkyliden]iminooxy]aminopropanol compounds is reported starting from the corresponding 1-isoxazolylalkanones. The ¹H- and ¹³C-nmr studies, carried out to establish the Z- and E-configuration of new derivatives, are also described.     

Statistical estimates and physics of close binary systems (CBS) of neutron stars

After some statistical considerations about the number of CBSs with one neutron star in our galaxy, we study the possible kinds of emission of CBSs with two neutron stars. Section 2 contains considerations on the dimension of such a system at the moment of its formation. From the comparison of different kinds of power emitted we deduce that the orbital gravitational emissionP _go dominates. The dynamical evolution of the orbital elementsa ande is determined byP _go and by tidal friction, which produce opposite effects. The quantitative comparison betweenP _goandP _tf (work made per unit time by tidal torque) says thatP _go>P _tf. Therefore we conclude that it isa<0 ande<0; that is the evolution of the systems is towards the collapse.