The decay from the dark npi* excited state in uracil: an integrated CASPT2/CASSCF and PCM/TD-DFT study in the gas phase and in water

By integrating the results of MS-CASPT2/CASSCF and TD-PBE0 calculations, we propose a mechanism for the decay of the excited dark state in pyrimidine, fully consistent with all the available experimental results. An effective conical intersection (CI-npi) exists between the spectroscopic pi/pi* excited state (Spi) and a dark n/pi* state (Sn), and a fraction of the population decays to the minimum of Sn (Sn-min). The conical intersection between Sn and the ground-state is not involved in the decay mechanism, because of its high energy gap with respect to Sn-min. On the other hand, especially in hydrogen bonding solvents, the energy gap between Sn-min and CI-npi is rather small. After thermalization in Sn-min, the system can thus recross CI-npi and then quickly proceed on the Spi barrierless path toward the conical intersection with the ground state.     

Can TD‐DFT calculations accurately describe the excited states behavior of stacked nucleobases? The cytosine dimer as a test case

By using calculations rooted in the time dependent density functional theory (TD-DFT) we have investigated how the lowest energy excited states of a face-to-face pi-stacked cytosine dimer vary with the intermonomer distance (R). The perfomances of different density functionals have been compared, focussing mainly on the lowest energy single excited state of the dimer (S(1))(2). TD-PBE0, TD-LC-omegaPBE, and TD-M05-2X provide a picture very similar to that obtained at the CASPT2 level by Merchan et al. (J Chem Phys 2006, 125, 231102), predicting that (S(1))(2) has a minimum for R approximately 3 A, with a binding energy of approximately 0.5 eV, whereas TD-B3LYP, TD-CAM-B3LYP, and TD-PBE understimate the binding energy. However, independently of the functional employed, no low-energy spurious charge transfer transitions are predicted by TD-DFT calculations, also when a nonsymmetric dimer is investigated, providing encouraging indications for the use of TD-DFT for studying the excited state of pi-stacked nucleobases.     

Heptagon-Containing Nanographene Embedded into [10]Cycloparaphenylene

We report the synthesis and characterization of a novel type of nanohoop, consisting of a cycloparaphenylene derivative incorporating a curved heptagon-containing π-extended polycyclic aromatic hydrocarbon (PAH) unit. We demonstrate that this new macrocycle behaves as a supramolecular receptor of curved π-systems such as fullerenes C₆₀ and C₇₀, with remarkably large binding constants (ca. 10⁷ M⁻¹), as estimated by fluorescence measurements. Nanosecond and femtosecond spectroscopic analysis show that these host-guest complexes are capable of quasi-instantaneous charge separation upon photoexcitation, due to the ultrafast charge transfer from the macrocycle to the complexed fullerene. These results demonstrate saddle-shaped PAHs with dibenzocycloheptatrienone motifs as structural components for new macrocycles displaying molecular receptor abilities and versatile photochemical responses with promising electron-donor properties in host-guest complexes.     

Catalytic Alkyne Semihydrogenation with Polyhydride Ni/Ga Clusters

The bimetallic, decanuclear Ni₃Ga₇-cluster of the formula [Ni₃(GaTMP)₃(μ²-GaTMP)₃(μ³-GaTMP)] ( 1 , TMP=2,2,6,6-tetramethylpiperidinyl) reacts reversibly with dihydrogen under the formation of a series of (poly-)hydride clusters 2 . Low-temperature 2D NMR experiments at −80 °C show that 2 consist of a mixture of a di- ( 2_Di ), tetra- ( 2_Tetra ) and hexahydride species ( 2_Hexa ). The structures of 2_Di and 2_Tetra are assessed by a combination of 2D NMR spectroscopy and DFT calculations. The cooperation of both metals is essential for the high hydrogen uptake of the cluster. Polyhydrides 2 are catalytically active in the semihydrogenation of 4-octyne to 4-octene with good selectivity. The example is the first of its kind and conceptually relates properties of molecular, atom-precise transition metal/main group metal clusters to the respective solid-state phase in catalysis.     

Vibronically resolved electronic circular dichroism spectra of (R)-(+)-3-methylcyclopentanone: a theoretical study

The vibrationally resolved electronic circular dichroism (ECD) spectra of the two dominant conformers of (R)-(+)-3-methylcyclopentanone in gas phase are computed by density functional response theory, with a full account of Franck-Condon and Herzberg-Teller vibrational contributions at the harmonic level. Proper inclusion of the latter contributions was made possible by the recent implementation of effective-scaling computations of vibrational overlaps and of analytical gradients of time dependent DFT. The Coulomb-attenuated Becke three parameters Lee-Yang-Parr (CAM-B3LYP) functional reproduces both the position and the intensity of the experimental peaks, providing a remarkable improvement over the spectra obtained with the popular hybrid B3LYP functional, and allowing a confident assignment of the CD fine vibrational structure. Franck-Condon and Herzberg-Teller contributions are discussed in detail. The computed decrease of the CD intensity in the gas phase upon increase of the temperature of the sample follows the trend observed experimentally in different solvents.     

A study of the reactive intermediate IF and I atoms with photoelectron spectroscopy

Angle-resolved photoelectron (PE) spectra were recorded for IF and I. These were prepared as primary and secondary products of the F + CH2I2 reaction. PE spectra were recorded with different IF-to-I ratios to evaluate the relative intensities of IF and I photoelectron bands where their bands were overlapped. Improved values were obtained for the vertical and adiabatic ionization energies of the IF(+)(X(2)Pi(3/2)) <-- IF(X(1)sigma(+)) and IF(+)((2)Pi(1/2)) <-- IF(X(1)sigma(+)) ionizations and for the spectroscopic constants omega(e) and omega(e)ex(e) for the two IF ionic states X(2)Pi(3/2) and (2)Pi(1/2). Equilibrium bond lengths r(e) of these IF ionic states were derived from the experimental relative intensities of the vibrational components and calculated Franck-Condon factors. Threshold photoelectron (TPE) spectra were also recorded under the same reaction conditions. On comparing the TPE and PE spectra, the contributions from atomic iodine were much more intense in the TPE spectra. No difference was seen between the vibrational envelopes of the two observed IF bands, and no extra structure was seen associated with the TPE bands of IF as has been observed in TPE spectra of other diatomic halogens. The extra features that were observed in the TPE spectra can be assigned to contributions from autoionization of known I Rydberg states.     

Synthesis of 4,5-dihydroisoxazoles by condensation of primary nitro compounds with alkenes by using a copper/base catalytic system

A new procedure for the synthesis of 4.5-dihydroisoxazoles by condensation of primary nitro compounds with olefins by using a copper/base catalytic system is described. The catalytic effect of copper(II) salts is evidenced by comparison of the reaction rates. Thus, activated nitro compounds react faster than with organic catalysis by tertiary amines, whereas nitroalkanes, unable to condense with dipolarophiles in the presence of the base alone, undergo the reaction on addition of a copper(II) catalyst. The observed occurrence of induction periods in most reactions is ascribed to an equilibrium preceding the rate-determining step, and gives a hint as to the proposed reaction mechanism. The results indicate that this method might be of practical and general utility for synthetic practice.     

Water-soluble gold nanoparticles protected by fluorinated amphiphilic thiolates

The preparation and the properties of gold nanoparticles (Au NPs) protected by perfluorinated amphiphiles are described. The thiols were devised to form a perfluorinated region close to the gold surface and to have a hydrophilic portion in contact with the bulk solvent to impart solubility in water. The monolayer protected clusters were prepared, in an homogeneous phase using sodium thiolates because of the low nucleophilicity of the alpha-perfluorinated thiols, and fully characterized with (1)H, (19)F NMR spectrometry, IR and UV-vis absorption spectroscopies, transmission electron microscopy (TEM), thermogravimetric analysis (TGA), and X-ray photoelectron spectroscopy (XPS). Au NPs with core diameters ranging from 1.6 to 2.9 nm, depending on the reaction conditions, were obtained. Water-soluble NPs (MPC-F8-PEGs) were obtained with the thiol HS-F8-PEG ending with a short poly(ethylene glycol) unit (PEG-OMe 550), whereas thiols with shorter PEG chains give rise to NPs insoluble in water. MPC-F8-PEGs undergo an exchange reaction with amphiphilic alkyl thiols. ESR investigations, using a hydrophobic radical probe, indicate that the MPC-F8-PEG monolayer shows a greater hydrophobicity compared to the analogous hydrogenated monolayer.     

Structure and dynamics of a partially folded protein are decoupled from its mechanism of aggregation

A common strategy to study the mechanism of amyloid formation is the characterization of the structure and dynamics of the precursor state, which is in most cases a partially folded protein. Here we investigated the highly dynamic conformational state formed by the protein domain HypF-N at low pH, before aggregation, using fluorescence, circular dichroism, and NMR spectroscopies. The NMR analysis allowed us, in particular, to identify the regions of the sequence that form hydrophobic interactions and adopt an alpha-helical secondary structure in the pH-denatured ensemble. To understand the role that this residual structure plays in the aggregation of this protein, we probed the mechanism of aggregation using protein engineering experiments and thus identified the regions of the sequence of HypF-N that play a critical role in the conversion of this dynamic state into thioflavin T-binding and beta-sheet containing protofibrils. The combination of these two complementary approaches revealed that the aggregation of pH-denatured HypF-N is not structure-dependent, meaning that it is not driven by the regions of the protein that are either less or more protected in the initial partially folded state. It is, by contrast, promoted by discrete protein regions that have the highest intrinsic propensity to aggregate because of their physicochemical properties.