Toward Quantum-dot Cellular Automata units: thiolated-carbazole linked bisferrocenes.

Quantum-dot Cellular Automata (QCA) exploit quantum confinement, tunneling and electrostatic interaction for transistorless digital computing. Implementation at the molecular scale requires carefully tailored units which must obey several structural and functional constraints, ranging from the capability to confine charge efficiently on different 'quantum-dot centers'-in order to sharply encode the Boolean states-up to the possibility of having their state blanked out upon application of an external signal. In addition, the molecular units must preserve their geometry in the solid state, to interact electrostatically in a controlled way. Here, we present a novel class of organometallic molecules, 6-3,6-bis(1-ethylferrocen)-9H-carbazol-9-yl-6-hexan-1-thiols, which are engineered to satisfy all such crucial requirements at once, as confirmed by electrochemistry and scanning tunneling microscopy measurements, and first principles density functional calculations.

Observation and control of coherent torsional dynamics in a quinquethiophene molecule.

By applying femtosecond pump-probe spectroscopy to a substituted quinquethiophene molecule in solution, we observe in the time domain the coherent torsional dynamics that drives planarization of the excited state. Our interpretation is based on numerical modeling of the ground and excited state potential energy surfaces and simulation of wavepacket dynamics, which reveals two symmetric excited state deactivation pathways per oscillation period. We use the acquired knowledge on torsional dynamics to coherently control the excited state population with a pump-dump scheme, exploiting the non-stationary Franck-Condon overlap between ground and excited states.

Electrostatic spin crossover effect in polar magnetic molecules.

The magnetic configuration of a nanostructure can be altered by an external magnetic field, by spin-transfer torque or by its magnetoelastic response. Here, we explore an alternative route, namely the possibility of switching the sign of the exchange coupling between two magnetic centres by means of an electric potential. This general effect, which we name electrostatic spin crossover, occurs in insulating molecules with super-exchange magnetic interaction and inversion symmetry breaking. As an example we present the case of a family of di-cobaltocene-based molecules. The critical fields for switching, calculated from first principles, are of the order of 1 V nm(-1) and can be achieved in two-terminal devices. More crucially, such critical fields can be engineered with an appropriate choice of substituents to add to the basic di-cobaltocene unit. This suggests that an easy chemical strategy for achieving the synthesis of suitable molecules is possible.

Rectification in supramolecular zinc porphyrin/fulleropyrrolidine dyads self-organized on gold(111).

Self-assembled donor/acceptor dyads are of current interest as they are biomimetic to the natural photosynthetic conversion system. Herein, we present an ultrahigh-vacuum scanning tunneling microscopy and scanning tunneling spectroscopy (UHV-STM/STS) study of ex situ self-assembled supramolecular dyads consisting of fulleropyrrolidines (PyC(2)C(60)) axially ligated to zinc(II) tetraphenylporphyrin (ZnTPP), self organized on a 4-aminothiophenol (4-ATP) self-assembled monolayer on gold(111). These dyads show both bias-polarity-dependent apparent height in STM images and highly rectifying behavior in tunneling spectroscopy. First-principles density functional theory calculations clarify the conformational and electronic properties of the 4-ATP/ZnTPP/PyC(2)C(60) system. Interestingly, we find easier tunneling for electrons moving from the acceptor side of the dyads to the donor side, in the inverse-rectifying sense with respect to previously reported molecular rectifiers. Such behavior cannot be explained as an elastic resonant tunneling process, but it can by using a model based on the Aviram-Ratner mechanism.

Microwave-assisted synthesis of thiophene fluorophores, labeling and multilabeling of monoclonal antibodies, and long lasting staining of fixed cells.

We report the expedient microwave-assisted synthesis of thiophene based 4-sulfo-2,3,5,6,-tetrafluorophenyl esters whose molecular structure was engineered to achieve blue to red bright fluorescence. The reactivity toward monoclonal antibodies of the newly synthesized fluorophores was analyzed in comparison with that of the corresponding N-succinimidyl esters. Single-fluorophore and multiple-fluorophore labeled antibodies were easily prepared with both types of esters. Multiple-fluorophore labeling with blue and orange emitting fluorophores resulted in white fluorescent antibodies. Thiophene based fluorophores displayed unprecedented fluorescence stability in immunostaining experiments. First-principles TD-DFT theoretical calculations helped us to interpret the behavior of fluorescence emission in different environments.

Raman spectra of poly(p-phenylenevinylene)s with fluorinated vinylene units: evidence of inter-ring distortion.

Ring the changes: Experimental Raman spectra of fluorinated and non-fluorinated polyphenylenevinylenes are assigned according to quantum chemical calculations for oligomer model systems [picture: see text]. Characteristic differences in the spectra can be traced back to strong inter-ring distortion of the fluorinated compounds.The Raman spectrum of poly{2-methoxy-5-[(2-ethylhexyl)oxy]-1,4-phenylenedifluorovinylene} (MEH-PPDFV) is reported and compared with that of a well-known non-fluorinated reference polymer, namely poly{2-methoxy-5-[(2-ethylhexyl)oxy]-1,4-phenylenevinylene} (MEH-PPV). The Raman spectra of both polymers are assigned on the basis of density functional theory calculations of the corresponding oligomers. The main differences between vinylene fluorinated and non-fluorinated structures deal with the intensity, frequency shift and broadening of C--C vinylene stretching. Additional differences concern the relative intensities of C-C phenylene and vinylene stretching as well as the deformation modes in the range 1250-1350 cm(-1). It is shown that these effects are due to the larger distortion from planarity of the fluorinated polymer, compared with the non-fluorinated counterpart, induced by repulsive interactions between the fluorine atoms on the vinylene units and the oxygen atoms of the alkoxy groups on the aromatic rings.

Absorption and fluorescence properties of oligothiophene biomarkers from long-range-corrected time-dependent density functional theory.

The absorption and fluorescence properties in a class of oligothiophene push-pull biomarkers are investigated with a long-range-corrected (LC) density functional method. Using linear-response time-dependent density functional theory (TDDFT), we calculate excitation energies, fluorescence energies, oscillator strengths, and excited-state dipole moments. To benchmark and assess the quality of the LC-TDDFT formalism, an extensive comparison is made between LC-BLYP excitation energies and approximate coupled cluster singles and doubles (CC2) calculations. When using a properly-optimized value of the range parameter, mu, we find that the LC technique provides an accurate description of charge-transfer excitations as a function of biomarker size and chemical functionalization. In contrast, we find that re-optimizing the fraction of Hartree Fock exchange in conventional hybrid functionals still yields an inconsistent description of excitation energies and oscillator strengths for the two lowest excited states in our series of biomarkers. The results of the present study emphasize the importance of a distance-dependent contribution of exchange in TDDFT for investigating excited-state properties.

Large blue-shift in the optical spectra of fluorinated polyphenylenevinylenes. A combined theoretical and experimental study.

Modifications of the optical properties of poly[2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] induced by fluorination of the vinylene units are investigated by means of time dependent density functional theory (TD-DFT) calculations and spectroscopic measurements in solution. The energy of the main absorption peak is blue-shifted by more than 0.8 eV in the fluorinated polymers. TD-DFT excitation energies for non-fluorinated and fluorinated oligomer structures of increasing number of monomers, employing fully relaxed geometries, are compared to the experimental absorption energies of the polymers. We found that the measured large blue-shift induced by the fluorination of the vinylene units is not caused by the electron-withdrawing effect of the fluorine substituents but it is related to a steric effect. The inter-monomer torsional angle of the fluorinated structures increases above 50 degrees , while in the non-fluorinated systems it is below 20 degrees . Further insight into the origin of the large blue-shift of the excitation energies is gained by a detailed analysis of the torsional potentials of non-fluorinated and fluorinated dihydroxystilbene. While for planar geometries the energy gap increases due to fluorination, it decreases for highly distorted geometries. In addition, we found that the torsional potential of dihydroxystilbene is rather flat, meaning that different isomers might, e.g., in the solid state, coexist.

Direct influence of hydrogen-bonding on the reduction potential of a CuII center.

Two hydrogen-bonds from geometrically constrained OH groups to coordinated oxygen donors shift the reduction potential of a Cu(II) complex by +270 mV as compared to the structurally analogous reference complex missing the OH groups.

Van der Waals complexes of polar aromatic molecules: unexpected structures for dimers of azulene.

Full geometry optimizations at the dispersion corrected DFT-BLYP/TZV2P level of theory have been performed for dimers of azulene that may serve as a model system for the van der Waals complexes of polar pi systems. The structures and binding energies for 11 dimers are investigated in detail. The DFT-D interaction energies have been successfully checked against results from the accurate SCS-MP2/aug-cc-pVTZ approach. Out of the nine investigated stacked complexes, eight have binding energies larger than 7.4 kcal/mol (SCS-MP2) that exceed the value of 7.1 kcal/mol for the best naphthalene dimer. T-shaped arrangements (CH...pi) are significantly less stable. Two out of the three best structures have an antiparallel alignment of the monomer dipole moments in the complex, although the best ones with a parallel orientation are only about 0.5 kcal/mol less strongly bound which points to a minor importance of dipole-dipole interactions to binding. Quite surprisingly, the energetically lowest structure (DeltaE = -9.2 kcal/mol) corresponds to a situation where the two seven-membered rings are located almost on top of each other (7-7) and the long molecular axes are rotated against each other by 130 degrees. The 7-7 structural motif is found also in other energetically low-lying structures, and the expected 5-7 (two-side) arrangement is less strongly bound by about 2 kcal/mol. This can be explained by the electrostatic potential of azulene that only partially reflects the charge separation according to the common 4n + 2 pi electron rule. General rules for predicting stable van der Waals complexes of polar pi systems are discussed.

Van der Waals interactions in aromatic systems: structure and energetics of dimers and trimers of pyridine.

Full geometry optimizations at the dispersion-corrected DFT-BLYP level of theory were carried out for dimers and trimers of pyridine. The DFT-D interaction energies were checked against results from single-point SCS-MP2/aug-cc-pVTZ calculations. Three stacked structures and a planar H-bonded dimer were found to be very close in energy (interaction energies in the range from -3.4 to -4.0 kcal mol(-1)). Two T-shaped geometries are higher lying, by about 1 kcal mol(-1), which is explained by the more favorable electrostatic interactions in the stacked and H-bonded arrangements. The DFT-D approach has proved to be a reliable and efficient tool to explore the conformational space of aromatic van der Waals complexes and furthermore provides interaction energies with errors of less than 10-20 % of DeltaE. Comparisons with previous results obtained by using only partially optimized model geometries strongly indicate that unconstrained optimizations are mandatory in such weakly bonded low-symmetry systems.

Less symmetrical dicopper(II) complexes as catechol oxidase models--an adjacent thioether group increases catecholase activity.

Three new unsymmetrical compartmental dinucleating ligands, 4-bromo-2-(4-methylpiperazin-1-ylmethyl)-6-[{2-(1-piperidyl)ethyl}aminomethyl]phenol (HL1), 4-bromo-2-(4-methylpiperazin-1-ylmethyl)-6-[{2-(morpholin-4-yl)ethyl}aminomethyl]phenol (HL2), and 4-bromo-2-(4-methylpiperazin-1-ylmethyl)-6-[{2-(thiomorpholin-4-yl)ethyl}aminomethyl]phenol (HL3), have been synthesized in order to model the active site of type 3 copper proteins. The dicopper(II) complexes of these ligands give first hints about the influence of a thioether group close to the metal site. The bromophenol-based ligands have one piperazine arm and one other bidentate arm in positions 2 and 6 of the phenolic ring, respectively. With each ligand a dinuclear copper(II) complex was prepared and structurally characterized. The copper ions were found to have square pyramidal environments and a mixture of endogenous phenoxo and exogenous acetate bridging. The influence of a heteroatom in one arm of the ligand on catecholase activity and speciation in solution was studied by UV/Vis spectroscopy, ESI-MS experiments and, DFT calculations.

Orthoesters versus 2-O-acyl glycosides as glycosyl donors: theorectical and experimental studies.

n-Pentenyl orthoesters (NPOEs) undergo routine acid catalyzed rearrangement into 2-O-acyl n-pentenyl glycosides (NPGs). The reactant and product can both function as glycosyl donors affording 1,2-trans linked glycosides predominantly. However, both donors differ in their rates of reactions, the yields they produce, and the nature of their byproducts, indicating that the NPOE/NPG pair may not be reacting through the same intermediates. We have therefore applied quantum chemical calculations using DFT methods and MP second order perturbation theory to learn more about orthoesters and their 2-O-acyl glycosidic counterparts. The calculations show that in the case of a manno NPG and NPOE pair, each donor goes initially to a different cationic intermediate. Thus, the former goes to a high-energy oxocarbenium ion before descending to a trioxolenium ion in which the charge is distributed over the pyrano ring oxygen, as well as the carbonyl and ether oxygen atoms of the putative C2 ester. On the other hand, ionization of the NPOE produces a dioxolenium ion lying slightly above the more stable trioxolenium counterpart. For the gluco pair, the NPG also goes to a very high-energy oxocarbenium ion, which also descends to a trioxolenium ion. However, unlike the manno analogue, the gluco NPOE does not give a dioxolenium ion; indeed, the dioxolenium is not energetically distinguishable from the trioxolenium counterpart. The theoretical observations have been tested experimentally. Thus, it was found that with manno derivatives, the orthoester is a more reactive donor than the corresponding NPG donor, whereas, for gluco derivatives, there is no advantage to using one over the other, unless one resorts to carefully selected promoters.

Epoxidation of C-branched glycals: unexpected stereochemical results and their theoretical rationale.

This paper describes the synthesis of C-3 methyl-branched glycosides by epoxidation of partially unblocked L-configured glycals. The stereochemical result depends on the orientation of the allylic hydroxyl group. A theoretical explanation is presented, based on the conformational preferences of the respective glycal half-chair conformations that were estimated by applying the BP density functional and a valence triple-zeta basis set.