A fluorescence study of isofagomine protonation in β-glucosidase

N-(10-Chloro-9-anthracenemethyl)isofagomine 5 inhibits β-glucosidase strongly yet the nitrogen atom plays little role in binding.

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.

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.

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.

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.

Characterization of nucleobase analogue FRET acceptor tCnitro

The fluorescent nucleobase analogues of the tricyclic cytosine (tC) family, tC and tC(O), possess high fluorescence quantum yields and single fluorescence lifetimes, even after incorporation into double-stranded DNA, which make these base analogues particularly useful as fluorescence resonance energy transfer (FRET) probes. Recently, we reported the first all-nucleobase FRET pair consisting of tC(O) as the donor and the novel tC(nitro) as the acceptor. The rigid and well-defined position of this FRET pair inside the DNA double helix, and consequently excellent control of the orientation factor in the FRET efficiency, are very promising features for future studies of nucleic acid structures. Here, we provide the necessary spectroscopic and photophysical characterization of tC(nitro) needed in order to utilize this probe as a FRET acceptor in nucleic acids. The lowest energy absorption band from 375 to 525 nm is shown to be the result of a single in-plane polarized electronic transition oriented approximately 27 degrees from the molecular long axis. This band overlaps the emission bands of both tC and tC(O), and the Forster characteristics of these donor-acceptor pairs are calculated for double-stranded DNA scenarios. In addition, the UV-vis absorption of tC(nitro) is monitored in a broad pH range and the neutral form is found to be totally predominant under physiological conditions with a pK(a) of 11.1. The structure and electronic spectrum of tC(nitro) is further characterized by density functional theory calculations.

A class of fluorescent heterocyclic dyes revisited: photophysics, structure, and solvent effects

The photophysical behavior of a series of 2-methylthio-5-(Z-carbonyl)thieno-[3,4-e]-3,4-dihydro-1,2,3-triazine-4-ones was investigated by absorption and emission spectroscopy in a range of solvents representing a systematic variation in polarity, polarizability, as well as hydrogen bond donating and accepting capabilities. In all the investigated compounds, the heterocyclic 6-membered ring of the chromophore is involved in interactions between electron donor and acceptor substituents on the thiophene ring. Throughout the series, the charge-donating methylthio group is kept constant, while the acceptor (Z-carbonyl) is varied between amide, ester, and ketone functionalities. The fluorescent first electronically excited state is primarily of intramolecular HOMO-LUMO charge transfer character. All members of the series exhibit solvent-dependent photophysics, although the magnitude of the dependence varies with the nature of the acceptor group. In addition to the solvent-sensitive photophysics, the investigated class of compounds shows high thermal and chemical stability. Among this class of heterocyclic dyes, the amide-substituted compound is superior with respect to high quantum yield and lifetime, and also shows the largest change in emission lifetimes and fluorescence quantum yields upon solvent variation (about 5-fold).

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 and characterization of cruciform-conjugated molecules based on tetrathiafulvalene

Stepwise acetylenic scaffolding provides cruciform-conjugated molecules with vertically disposed pi-systems, one being an extended tetrathiafulvene (TTF) unit. Two synthetic routes for a cruciform dimer incorporating a total of two extended TTFs was developed, employing either an oxidative Hay coupling reaction as the final dimerization step or as one of the initial steps. Both routes take advantage of ready access to new mono- and diethynylbenzene building blocks incorporating a variety of other functionalitites. The redox and optical properties of the cruciform molecules were investigated by cyclic and differential pulse voltammetries and UV-vis absorption spectroscopy. The access to multiple redox states renders the molecules attractive candidates as wires, or possibly transistors, for molecular electronics. Generation of a quinoid structure by oxidation is supported by density functional theory calculations.

Dianions of 7,7,8,8-tetracyano-p-quinodimethane and perfluorinated tetracyanoquinodimethane: Information on excited states from lifetime measurements in an electrostatic storage ring and optical absorption spectroscopy

We have developed an experimental technique that allows us to study the physics of short lived molecular dianions in the gas phase. It is based on the formation of monoanions via electrospray ionization, acceleration of these ions to keV energies, and subsequent electron capture in a sodium vapor cell. The dianions are stored in an electrostatic ion storage ring in which they circulate with revolution times on the order of 100 micros. This enables lifetime studies in a time regime covering five orders of magnitude, 10(-5)-1 s. We have produced dianions of 7,7,8,8-tetracyano-p-quinodimethane and 2,3,5,6-tetrafluoro-7,7,8,8-tetracyano-p-quinodimethane (TCNQ-F(4)) and measured their lifetimes with respect to electron autodetachment. Our data indicate that most of the dianions were initially formed in electronically excited states in the electron transfer process. Two levels of excitation were identified by spectroscopy on the dianion of TCNQ-F(4), and the absorption spectrum was compared with spectra obtained from spectroelectrochemistry of TCNQ-F(4) in acetonitrile solution.

Scope and Limitations of Baird's Theory on Triplet State Aromaticity: Application to the Tuning of Singlet–Triplet Energy Gaps in Fulvenes

Utilizing Baird's theory on triplet state aromaticity, we show that the singlet-triplet energy gaps (DeltaE(ST)) of pentafulvenes are easily varied through substitution by as much as 36 kcal mol(-1). This exploits the fact that fulvenes act as aromatic chameleons in which the dipoles reverse on going from the singlet ground state (S(0)) to the lowest pipi* triplet state (T1); thus, their electron distributions are adapted so as to achieve some aromaticity in both states. The results are based on quantum chemical calculations with the OLYP density functional theory method and the CASPT2 ab initio method, as well as spectroscopic determination of DeltaE(ST) by triplet sensitization. The findings can also be generalized to fulvenes other than the pentafulvenes, even though the effect is attenuated as the size of the fulvene increases. Our studies thus reveal that triplet-state aromaticity can greatly influence the properties of conjugated compounds in the T1 state.

Synthesis and Characteristics of a Nonaggregating Tris(tetrathiafulvaleno)dodecadehydro[18]annulene

A new tris(tetrathiafulvaleno)dodecadehydro[18]annulene with six peripheral n-hexyl substituents was prepared by oxidative Glaser-Hay cyclization of a corresponding diethynylated tetrathiafulvalene (TTF) precursor. The electronic properties of the neutral and oxidized species were studied by both UV/Vis absorption spectroscopy and electrochemistry. From these studies, it transpires that the strongly violet-colored macrocycle does not aggregate in solution to any significant degree, which was confirmed by (1)H NMR spectroscopy. This reluctance towards aggregation contrasts that observed for related TTF-annulenes containing other peripheral substitutents. Oxidation of the TTF-annulene occurs in two three-electron steps as inferred from both the peak amplitudes and the spectroelectrochemical study. We find that the tris(TTF)-fused dehydro[18]annulene is more difficult to oxidize (by +0.20 V) than the silyl-protected diethynylated mono-TTF precursor. In contrast, the first vertical ionization energy calculated at the B3 LYP/6-311+G(2d,p) level for the parent tris(TTF)-fused dehydro[18]annulene devoid of peripheral hexyl substituents is in fact lower (by 0.44 eV). Moreover, the surface morphology of 1 d drop-cast on a mica substrate was investigated by atomic force microscopy (AFM). Crystalline domains with slightly different orientations were observed. The thickness of individual layers seen in the crystalline domains and the thickness of a monolayer obtained from a very dilute solution were determined to 1.8-1.9 nm. This thickness corresponds to the diameter of the macrocycle and the layers seen in the film are apparently formed when the molecules stack in the horizontal direction relative to the substrate.

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.

Intersystem Crossing versus Electron Transfer in Porphyrin-Based Donor−Bridge−Acceptor Systems: Influence of a Paramagnetic Species

We have investigated how the spin state of an acceptor influences the photophysical processes in a donor-bridge-acceptor (D-B-A) system. The system of choice has zinc porphyrin as the electron donor and high- or low-spin iron(III) porphyrin as the acceptor. The spin state of the acceptor porphyrin is switched simply by coordinating imidazole ligands to the metal center. The D-A center-center distance is 26 A, and the bridging chromophore varies from pi-conjugated to a sigma-bonded system. The presence of a high-spin iron(III) porphyrin in such systems has previously been shown to significantly enhance intersystem crossing in the remote zinc porphyrin donor, whereas no significant electron transfer to the iron porphyrin acceptor was observed, even though the thermodynamics would allow for photoinduced electron transfer. Here, we demonstrate that by switching the acceptor to a low-spin state, the dominating photophysical process is drastically changed; the low-spin system shows long-range electron transfer on the picosecond time-scale, and intersystem crossing occurs at its "normal" rate.

Control of electron transfer in supramolecular systems

The fluorescence quantum yield of zinc porphyrin (ZnP) covalently linked to 9,10-bis(phenylethynyl)anthracene (AB) is strongly dependent upon the solvent properties. The bichromophoric system ZnP-AB exhibits 'normal' zinc porphyrin fluorescence in solvents that cannot coordinate to the central zinc atom. In contrast, if a Lewis base, such as pyridine, is added to a sufficiently polar solvent, the fluorescence is significantly quenched. Picosecond transient absorption measurements, in conjunction with fluorescence quenching and cyclic voltammetric measurements, suggest that the quenching mechanism is intramolecular electron transfer from ZnP to AB. The charge separated state. ZnP*+-AB*-, has a lifetime of not more than 220 ps before recombining. If a secondary electron acceptor, iron(III) porphyrin (FeP), is covalently connected to the AB unit, a second electron transfer from AB*- to FeP occurs and the charge separated state, ZnP*+-AB-FeP*-, has a lifetime of at least 5 ns. This demonstrates that electron transfer might be sensitively tuned (switched on) by specific solvent effects.

Enhanced intersystem crossing in donor/acceptor systems based on zinc/iron or free-base/iron porphyrins

The deactivation pathways of the singlet excited state of a series of zinc or free-base donor porphyrins covalently linked by a bridge to a paramagnetic iron(III) chloride porphyrin acceptor have been studied. These donor-bridge-acceptor systems all share a similar geometry (25 A donor-acceptor center-to-center distance), but the bridges vary in electronic structure. In previously reported investigations of zinc/iron porphyrin systems, the fluorescence quenching of the donor has predominantly been assigned to electron transfer. However, for the porphyrin systems studied in this paper, we show that the dominant deactivation channels are enhanced intersystem crossing and singlet energy transfer. In both series, the intersystem crossing rate (S1-->T1) of the donor moiety is almost doubled in the presence of a paramagnetic high-spin metal-porphyrin acceptor. The significant spectral overlap of the donor fluorescence and acceptor absorption in both series allows for efficient singlet energy transfer (Forster mechanism). Furthermore, the bridging chromophores mediate energy transfer and the enhancement is inversely dependent upon the energy gap between the donor and bridge excited states. Although Marcus theory predicts thermodynamically favorable electron transfer to occur in the systems investigated, the quenching rate constants were found to be independent of solvent polarity, and no charge-separated state could be detected, indicating very small electronic coupling for electron transfer.

Bridge-dependent electron transfer in porphyrin-based donor-bridge-acceptor systems

Photoinduced electron transfer in donor-bridge-acceptor systems with zinc porphyrin (or its pyridine complex) as the donor and gold(III) porphyrin as the acceptor has been studied. The porphyrin moieties were covalently linked with geometrically similar bridging chromophores which vary only in electronic structure. Three of the bridges are fully conjugated pi-systems and in a fourth, the conjugation is broken. For systems with this bridge, the quenching rate of the singlet excited state of the donor was independent of solvent and corresponded to the rate of singlet energy transfer expected for a Förster mechanism. In contrast, systems with a pi-conjugated bridging chromophore show a solvent-dependent quenching rate that suggests electron transfer in the Marcus normal region. This is supported by picosecond transient absorption measurements, which showed formation of the zinc porphyrin radical cation only in systems with pi-conjugated bridging chromophores. On the basis of the Marcus and Rehm-Weller equations, an electronic coupling of 5-20 cm(-)(1) between the donor and acceptor is estimated for these systems. The largest coupling is found for the systems with the smallest energy gap between the donor and bridge singlet excited states. This is in good agreement with the coupling calculated with quantum mechanical methods, as is the prediction of an almost zero coupling in the systems with a nonconjugated bridging chromophore.