Aminorhodamine (ARh): A Bichromophore with Three Emission Bands in Low Temperature Glasses.

At first glance, aminorhodamine (ARh) is a typical pH responsive fluorescent, rhodamine-type dye. However, hidden under the typical rhodamine absorption band, ARh has another electronic transition of similar energy, but polarized orthogonal to that of the rhodamine chromophore. This transition-assigned to an arylpyrylium type chromophore contained in the system-is responsible for the sensor action of the dye. ARh is non-fluorescent, while protonation of a donor amino group turn on a strong rhodamine-type emission. At low temperature in frozen solution emission from both electronic subsystems of ARh are observed. In order to achieve more complete understanding of the photophysical mechanisms in this type of fluorescent probes, ARh and its protonated counterpart HARh were studied by absorption and fluorescence spectroscopy, computational chemistry, and at low temperatures in solid solution. Results from fluorescence anisotropy and time-resolved fluorescence spectra establish a bichromophore model and suggest that a remarkable weak coupling between the two nearly isoenergetic excited states in ARh enables the dual emission. All the complicated properties observed for ARh was accounted for by a bichromophore model describing the electronic system of ARh as a bichromophore constituted by a rhodamine and an arylpyrylium subsystem.

A fluorescence study of isofagomine protonation in ß-glucosidase.

N-(10-Chloro-9-anthracenemethyl)isofagomine 5 and N-(10-chloro-9-anthracenemethyl)-1-deoxynojirimycin 6 were prepared, and their inhibition of almond ß-glucosidase was measured. The isofagomine derivative 5 was found to be a potent inhibitor, while the 1-deoxynojirimycin derivative 6 displayed no inhibition at the concentrations investigated. Fluorescence spectroscopy of 5 with almond ß-glucosidase at different pH values showed that the inhibitor nitrogen is not protonated when bound to the enzyme. Analysis of pH inhibition data confirmed that 5 binds as the amine to the enzyme's unprotonated dicarboxylate form. This is a radically different binding mode than has been observed with isofagomine and other iminosugars in the literature.

FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids.

Förster resonance energy transfer (FRET) is a technique commonly used to unravel the structure and conformational changes of biomolecules being vital for all living organisms. Typically, FRET is performed using dyes attached externally to nucleic acids through a linker that complicates quantitative interpretation of experiments because of dye diffusion and reorientation. Here, we report a versatile, general methodology for the simulation and analysis of FRET in nucleic acids, and demonstrate its particular power for modelling FRET between probes possessing limited diffusional and rotational freedom, such as our recently developed nucleobase analogue FRET pairs (base-base FRET). These probes are positioned inside the DNA/RNA structures as a replacement for one of the natural bases, thus, providing unique control of their position and orientation and the advantage of reporting from inside sites of interest. In demonstration studies, not requiring molecular dynamics modelling, we obtain previously inaccessible insight into the orientation and nanosecond dynamics of the bases inside double-stranded DNA, and we reconstruct high resolution 3D structures of kinked DNA. The reported methodology is accompanied by a freely available software package, FRETmatrix, for the design and analysis of FRET in nucleic acid containing systems.

A triptycene-based approach to solubilising carbon nanotubes and C60.

We describe herein the synthesis of a triptycene-based surfactant designed with the ability to solubilise single-walled carbon nanotubes (SWNTs) and C(60) in water through non-covalent interactions. Furthermore, an amphiphilic naphthalene-based surfactant with the same ability to solubilise SWNTs and C(60) has also been prepared. The compounds synthesised were designed with either two ionic or non-ionic tails to ensure a large number of supramolecular interactions with the solvent, thereby promoting strong solubilisation. The surfactants produced stable suspensions in which the SWNTs are dispersed and the surfactant/SWNT complexes formed are stable for more than one year. UV/Vis/NIR absorption spectroscopy, TEM and AFM were employed to probe the solubilisation properties of the dispersion of surfactants and SWNTs in water.

Exploration of the π-electronic structure of singlet, triplet, and quintet states of fulvenes and fulvalenes using the electron localization function.

The singlet ground states and lowest triplet states of penta- and heptafulvene, their benzannulated derivatives, as well as the lowest quintet states of pentaheptafulvalenes, either the parent compound or compounds in which the two rings are intercepted by either an alkynyl or a phenyl segment, were investigated at the (U)OLYP/6-311G(d,p) density functional theory level. The influence of (anti)aromaticity was analyzed by the structure-based aromaticity index HOMA, the harmonic oscillator model of aromaticity. The extent of (anti)aromatic character was also evaluated in terms of the π-electron (de)localization as measured by the π component of the electron localization function (ELF(π)). The natural atomic orbital (NAO) occupancies were calculated in order to evaluate the degree of π-electron shift caused by the opposing electron-counting rules for aromaticity in the electronic ground state (S(0); Hückel's rule) and the first ππ* excited triplet state (T(1); Baird's rule). Pentaheptafulvalene (5) shows a shift of 0.5 π electrons from the 5-ring to the 7-ring when going from the S(0) state to the lowest quintet state (Qu(1)). The pentaheptafulvalene 5 and [5.6.7]quinarene 7 were also investigated in their 90° twisted conformations. From our study it is apparent that excitation localization in fulvalenes, but not in fulvenes, to a substantial degree is determined by aromaticity localization to triplet biradical 4n π-electron cycles. Isolated benzene rings in these compounds tend to remain as closed-shell 6π-electron cycles.

Fulleropyrrolidine end-capped molecular wires for molecular electronics--synthesis, spectroscopic, electrochemical, and theoretical characterization.

In continuation of previous studies showing promising metal-molecule contact properties a variety of C(60) end-capped "molecular wires" for molecular electronics were prepared by variants of the Prato 1,3-dipolar cycloaddition reaction. Either benzene or fluorene was chosen as the central wire, and synthetic protocols for derivatives terminated with one or two fullero[c]pyrrolidine "electrode anchoring" groups were developed. An aryl-substituted aziridine could in some cases be employed directly as the azomethine ylide precursor for the Prato reaction without the need of having an electron-withdrawing ester group present. The effect of extending the π-system of the central wire from 1,4-phenylenediamine to 2,7-fluorenediamine was investigated by absorption, fluorescence, and electrochemical methods. The central wire and the C(60) end-groups were found not to electronically communicate in the ground state. However, the fluorescence of C(60) was quenched by charge transfer from the wire to C(60). Quantum chemical calculations predict and explain the collapse of coherent electronic transmission through one of the fulleropyrrolidine-terminated molecular wires.

Influence of excited state aromaticity in the lowest excited singlet states of fulvene derivatives.

The absorption spectra and excited state dipole moments of four differently substituted fulvenes have been investigated both experimentally and computationally. The results reveal that the excited state dipole moment of fulvenes reverses in the first excited singlet state when compared to the ground state. The oppositely polarized electron density distributions, which dominate the ground state and the first excited singlet state of fulvenes, respectively, reflect the reversed π-electron counting rules for aromaticity in the two states (4n + 2 vs. 4n, respectively). The results show that substituents indeed influence the polarity of fulvenes in the two states, however, cooperative interactions between the substituents and the fulvene moiety are most pronounced in the ground state.

A statistical approach to inelastic electron tunneling spectroscopy on fullerene-terminated molecules.

We report on the vibrational fingerprint of single C(60) terminated molecules in a mechanically controlled break junction (MCBJ) setup using a novel statistical approach manipulating the junction mechanically to address different molecular configurations and to monitor the corresponding vibrational modes. In the IETS spectra, the vibrations of the anchoring C(60) dominate the spectra; thus information on the unit anchored with C(60) to the electrodes is masked by the modes arising from the anchoring groups. However, we have identified the additional modes from the fluorene backbone optically.

Arylethynyl derivatives of the dihydroazulene/vinylheptafulvene photo/thermoswitch: tuning the switching event.

A selection of dihydroazulene (DHA) photoswitches incorporating an arylethynyl-substituent in the seven-membered ring was prepared by palladium-catalyzed Sonogashira cross-coupling reactions employing a suitable bromo-functionalized DHA. Shielding of the alkyne bridge and separating the aryl and DHA units, by sterically demanding groups, was required to obtain stable compounds. The DHAs underwent a light-induced ring-opening to vinylheptafulvenes (VHFs) which were thermally converted to a mixture of two DHA regioisomers, one of which was the original one. The influence of the aryl groups on the DHA and VHF absorptions and on their interconversion was investigated in detail. The rates of the switching events were finely tuned by the donor or acceptor strength of the aryl group. The thermal ring closure was found to proceed most readily in the presence of an electron-donating group on the seven-membered ring. The rate constant was found to follow a Hammett linear free energy correlation, which signals that stabilization of a positive charge in the seven-membered ring plays a crucial role in the ring-closure reaction. In view of these findings, it was possible to control the switching event by protonation/deprotonation of an anilino-substituted DHA. Also, the light-induced ring opening reaction was strongly controlled by acid/base. In addition to the mesomeric effects exerted by an arylethynyl group, the inductive effects exerted by different groups on the thermal ring closure were elucidated. Although the alkyne bridge transmits the electronic character of the aryl group, the ring-closure is retarded for all the ethynylated compounds relative to the parent unsubstituted compound. Along with our synthesis of suitable arylalkynes, we discovered an interesting byproduct in a Sonogashira cross-coupling reaction involving a nitrophenyl group, namely a diaryl azoxy compound. Its structure was confirmed by X-ray crystallographic analysis.

Proton and hydride affinities in excited states: magnitude reversals in proton and hydride affinities between the lowest singlet and triplet states of annulenyl and benzannulenyl anions and cations.

Aromaticity has importance for proton and hydride affinities in the singlet ground state (S(0)) of annulenyl anions and cations so that, e.g., cyclopentadiene is an acidic hydrocarbon. For the lowest pipi* excited triplet state (T(1)), Baird's rule concludes that annulenes with 4n pi-electrons are aromatic and those with 4n+2 pi-electrons are antiaromatic, opposite to Huckel's rule for aromaticity in S(0). Our hypothesis is now that the relative magnitudes of proton and hydride affinities of annulenyl anions and cations reverts systematically as one goes from S(0) to T(1) as a result of the opposite electron counting rules for aromaticity in the two states. Using quantum chemical calculations at the G3(MP2)//(U)B3LYP/6-311+G(d,p) level we have examined the validity of this hypothesis for eight proton and eight hydride addition reactions of anions and cations, respectively, of annulenyl and benzannulenyl type. We categorize the (4n+2)pi-electron systems in S(0) and the 4npi-electron systems in T(1) to be of A-character and 4npi-electron systems in S(0) and (4n+2)pi-electron systems in T(1) to be of AA-character (A, aromatic; AA, anti/nonaromatic). The average proton affinities of anions of A- and AA-characters in S(0) are 1447 and 1521 kJ/mol, respectively, and in T(1) they are 1365 and 1493 kJ/mol. The average hydride affinities of A- and AA-character cations in S(0) are 826 and 996 kJ/mol, and in T(1) they are 790 and 879 kJ/mol, respectively. Thus, the calculated proton and hydride affinities are in general lower for anions and cations of A-character than for those of AA-character, in good support of our hypothesis. The findings could likely be applied in synthetic organic photochemistry and other areas where excited state acid-base chemistry plays a role.

Substituent effects on the electron affinities and ionization energies of tria-, penta-, and heptafulvenes: a computational investigation.

The extent of substituent influence on the vertical electron affinities (EAs) and ionization energies (IEs) of 43 substituted tria-, penta-, and heptafulvenes was examined computationally at the OVGF/6-311G(d)//B3LYP/6-311G(d) level of theory and compared with those of tetracyanoquinodimethane (TCNQ) and tetrathiafulvalene (TTF) as representing strong electron-acceptor and -donor compounds, respectively. The substituents X at the exocyclic positions of the fulvenes were either NH(2), H, or CN, while the substituents Y at the ring positions were H, Cl, F, CN, or NH(2). The variations of the EAs and IEs were rationalized by qualitative arguments based on frontier orbital symmetries for the different fulvene classes with either X or Y being constant. The minimum and maximum values found for the calculated EAs of the tria-, penta-, and heptafulvenes were 0.51-2.05, 0.24-3.63, and 0.53-3.14 eV, respectively, and for the IEs 5.27-9.96, 7.07-10.31, and 6.35-10.59 eV, respectively. Two of the investigated fulvenes outperform TCNQ (calcd EA = 2.63 eV) and one outperforms TTF (calcd IE = 6.25 eV) with regard to acceptor and donor abilities, respectively. We also evaluated the properties of bis(fulvene)s, i.e., compounds composed of a donor-type heptafulvene fused with an acceptor-type pentafulvene, and it was revealed that these bis(fulvene)s can be designed so that the IE and EA of the two separate fulvene segments are retained, potentially allowing for the design of compact donor-acceptor dyads.

Photophysical and structural properties of the fluorescent nucleobase analogues of the tricyclic cytosine (tC) family.

Fundamental insight into the unique fluorescence and nucleobase-mimicking properties of the fluorescent nucleobase analogues of the tC family is not only vital in explaining the behaviour of these probes in nucleic acid environments, but will also be profitable in the development of new and improved fluorescent base analogues. Here, temperature-dependent fluorescence quantum yield measurements are used to successfully separate and quantify the temperature-dependent and temperature-independent non-radiative excited-state decay processes of the three nucleobase analogues tC, tC(O) and tC(nitro); all of which are derivatives of a phenothiazine or phenoxazine tricyclic framework. These results strongly suggest that the non-radiative decay process dominating the fast deactivation of tC(nitro) is an internal conversion of a different origin than the decay pathways of tC and tC(O). tC(nitro) is reported to be fluorescent only in less dipolar solvents at room temperature, which is explained by an increase in excited-state dipole moment along the main non-radiative decay pathway, a suggestion that applies in the photophysical discussion of large polycyclic nitroaromatics in general. New insight into the ground and excited-state potential energy surfaces of the isolated tC bases is obtained by means of high level DFT and TDDFT calculations. The S(0) potential energy surfaces of tC and tC(nitro) possess two global minima corresponding to geometries folded along the middle sulfur-nitrogen axis separated by an energy barrier of 0.05 eV as calculated at the B3LYP/6-311+G(2d,p) level. The ground-state potential energy surface of tC(O) is also predicted to be shallow along the bending coordinate but with an equilibrium geometry corresponding to the planar conformation of the tricyclic framework, which may explain some of the dissimilar properties of tC and tC(O) in various confined (biological) environments. The S(1) equilibrium geometries of all three base analogues are predicted to be planar. These results are discussed in the context of the tC bases positioned in double-stranded DNA scenarios.

Synthesis and characterization of tetrathiafulvalene-substituted di- and tetraethynylethenes with p-nitrophenyl acceptors.

Novel di- and tetraethynylethene (DEE and TEE) compounds functionalized with tetrathiafulvalene (TTF) donor groups and p-nitrophenyl acceptor groups were synthesized by palladium-catalyzed cross-coupling reactions under various conditions. The molecules are strong chromophores and were investigated for their optical properties. Placement of two TTFs and two p-nitrophenyls about a central TEE core provides a molecule with a high third-order optical nonlinearity. The molecules experience reversible oxidations of the TTF units, and the optical properties of the oxidized species were elucidated by spectroelectrochemistry. The degree of quinoid character of the p-nitrophenyl in the molecules was determined by X-ray crystallography.

Size- and solvent-dependent kinetics for cis-trans isomerization in donor-acceptor systems.

We have investigated, using time-resolved and steady-state optical spectroscopy, the cis-trans isomerization dynamics in a series of charge transfer, donor-acceptor compounds. The number of donor (dithiafulvene) and acceptor (p-nitrophenyl) moieties as well as their spatial arrangement around a central ethynylethene core has been varied in a systematic way. All compounds in the series are weakly fluorescent. We show that the fluorescence spectrum red-shifts within a few picoseconds, a shift which occurs concurrently with a blue-shift of the transient absorption spectrum. The kinetics following the initial relaxation are in all cases multi-exponential, and the time constants correlate with molecular size and solvent viscosity. We interpret the data as a result of conformational change where the conjugation through the central double bond is broken upon excitation into the charge-transfer transition, and the time for rotation around this bond is dependent on the molecular interactions between solute and solvent.

Perylenediimide--metal ion dyads for photo-induced electron transfer.

A novel perylene diimide incorporating a tetradentate ligand was synthesized and the photophysical properties of its Cu(+), Cu(2+), and Fe(3+) complexes were investigated by fluorescence experiments.

Synthesis of oligo(phenyleneethynylene)-tetrathiafulvalene cruciforms for molecular electronics.

[reaction: see text] Novel oligo(phenyleneethynylene) (OPE)-tetrathiafulvalene (TTF) cruciform molecules containing thiol end-groups have been prepared and characterized. These redox-active molecules are interesting for future applications as molecular wires/transistors for molecular electronics.

Cyclometalated iridium(III)-sensitized titanium dioxide solar cells.

Ir(III) dyes used as sensitizers in dye-sensitized solar cells produced quantum yields approaching unity for conversion of absorbed photons to current under simulated air mass 1.0 sunlight, with current production resulting from ligand-to-ligand charge-transfer states, rather than the typical metal-to-ligand charge-transfer states in ruthenium-based cells.

Lewis acid enhanced switching of the 1,1-dicyanodihydroazulene/vinylheptafulvene photo/thermoswitch.

Mild Lewis acids enhance the rate of the thermal conversion of vinylheptafulvene (VHF) to dihydroazulene (DHA). In the absence of light, stronger Lewis acids promote the otherwise photoinduced DHA to VHF conversion.

On the intrinsic optical absorptions by tetrathiafulvalene radical cations and isomers.

Gas-phase action spectroscopy shows unambiguously that the low-energy absorptions by tetramethylthiotetrathiafulvalene and tetrathianaphthalene cations in solution phase are due to monomers and not π-dimers.