Through-bond and through-space interactions : The electronic spectrum of barrelene

The first theoretical calculations that reproduce the observed UV spectrum of bairelene are reported. Absorptions above 200 nm are assigned as π →σ^* while the first excitation that is essentially π → π^* is predicted at ca 180 nm. These results are interpreted in terms of through-space π - π interaction, which splits the π-levels, and through-bond interaction, which mixes σ into the π, and fills in the gap between the antibonding π-orbitals. The latter interaction is such that the σ-framework, in each of the three bridges, couples the ethylenic moieties that are based on the other two.     

Protein-induced excited-state dynamics of protochlorophyllide

The light-driven NADPH:protochlorophyllide oxidoreductase (POR) is a key enzyme of chlorophyll biosynthesis in angiosperms. POR's unique requirement for light to become catalytically active makes the enzyme an attractive model to study the dynamics of enzymatic reactions in real time. Here, we use picosecond time-resolved fluorescence and femtosecond pump-probe spectroscopy to examine the influence of the protein environment on the excited-state dynamics of the substrate, protochlorophyllide (PChlide), in the enzyme/substrate (PChlide/POR) and pseudoternary complex including the nucleotide cofactor NADP(+) (PChlide/NADP(+)/ POR). In comparison with the excited-state processes of unbound PChlide, the lifetime of the thermally equilibrated S(1) excited state is lengthened from 3.4 to 4.4 and 5.4 ns in the PChlide/POR and PChlide/NADP(+)/POR complex, whereas the nonradiative rates are decreased by ～30 and 40%, respectively. This effect is most likely due to the reduced probability of nonradiative decay into the triplet excited state, thus keeping the risk of photosensitized side reactions in the enzyme low. Further, the initial reaction path involves the formation of an intramolecular charge-transfer state (S(ICT)) as an intermediate product. From a strong blue shift in the excited-state absorption, it is concluded that the S(ICT) state is stabilized by local interactions with specific protein sites in the catalytic pocket. The possible relevance of this result for the catalytic reaction in the enzyme POR is discussed.     

Through-bond and through-space interactions of substituents and the nonlinearity of X-C≡Y Linkages

Ab initio SCF calculations using the split valence basis sets 3–21G, 4–21G, 4–31G, 5–31G, and 3–321G, which were augmented by a set of polarization functions on the nonhydrogen atoms, were performed on a series of propynes, nitriles, isonitriles, and geminal dinitriles. Substituent effects on the structures of these molecules have been interpreted via appropriate concepts. In contrast to widespread opinion, the CC triple bond may be highly sensitive to effects of substituents, particularly when these effects are associated with -bonding interaction. This is reflected, for instance, by the appreciable contraction of the CC bond length in 1 -fluoropropyne (1 -FP) of 1.173 Å in comparison to the same bond in cyanopropyne, 1.183 Å. One of the interesting results of the present work is the markedly short C-F bond distance of 1.275 Å in 1-FP. The most acceptable rationale for this bonding behavior is provided by electrostatic arguments. The geometric results of both F₂C(CN)₂ and CF₃NC, particularly the short C-F bond distance of 1.323 Å and 1.306 Å, respectively, indicate the presence of fluorine negative hyperconjugation (anomeric effect). The characteristic nonlinearity of the C-CN chain in several geminally substituted dinitriles, YC(CN)₂, has been discussed. It appears that a relationship exists between the direction of bending of the C-CN moieties and the electronegativity of Y.     

On the nature of sigma-coupled transitions : Through-bond interactions in 1-aza-adamantane derivatives

1-Aza-adamant-4-one and a number of its derivatives, in which the CO function is modified, show absorption in the near UV region which is attributed to a sigma-coupled transition. From absorption and emission spectroscopic data it is shown that this transition has to be charge transfer in character and that it derives its intensity mainly from a local π-π* transition in the (modified) CO group. From the relative basicities, the IR spectra and the ¹³C NMR spectra it is concluded that the amount of charge transfer in the electronic ground-state is very small for the compounds studied.     

Microsolvation effects on the excited-state dynamics of protonated tryptophan

To better understand the complex photophysics of the amino acid tryptophan, which is widely used as a probe of protein structure and dynamics, we have measured electronic spectra of protonated, gas-phase tryptophan solvated with a controlled number of water molecules and cooled to approximately 10 K. We observe that, even at this temperature, the bare molecule exhibits a broad electronic spectrum, implying ultrafast, nonradiative decay of the excited state. Surprisingly, the addition of two water molecules sufficiently lengthens the excited-state lifetime that we obtain a fully vibrationally resolved electronic spectrum. Quantum chemical calculations at the RI-CC2/aug-cc-pVDZ level, together with TDDFT/pw based first-principles MD simulations of the excited-state dynamics, clearly demonstrate how interactions with water destabilize the photodissociative states and increase the excited-state lifetime.     

Emission spectroscopy and excited-state dynamics of chromyl-chloride vapor

A tunable dye laser has been used to excite single vibronic features in the low-pressure vapor of CrO₂Cl₂. The fluorescence spectrum, fluorescence excitation spectrum and time-resolved fluorescence decay are discussed. It is shown that the active ν′₄ and ν″₄ modes are the same frequency in the gas phase, thus collapsing the sequence congestion normally observed in gas-phase spectra. This degeneracy makes impossible the excitation of single vibronic levels. It is shown that the fluorescence lifetime of the excited state in all except the vibrationally cold level is severely shortened by unimolecular radiationless decay. This radiationless rate is strongly dependent upon the partitioning of energy into various excited-state modes. The radiative lifetime of the vibrationally cold excited state is (1.34 ± 0.08) μs and the apparent bimolecular quenching rate is (5.9 ± 0.2) × 10^?10 cm³/molecules. No evidence of emission from the lowest-energy excited electronic state recently reported by Spoliti [J. Mol. Spectrosc. 52 (1973) 146] is observed.     

Singlet excited-state interactions in naphthalene-thymine dyads.

Two thymidine-derived nucleosides 1 and 2 were prepared by attaching a chiral naphthalene to the positions 5' and 3' of the sugar. The resulting dyads, which contain key substructures present in drugs and nucleic acids, exhibit different spatial arrangements (transoid or cisoid) of the fluorophore relative to the thymine unit. Emission measurements on these compounds in the presence of ROH molecules revealed a remarkable intramolecular prescence quenching for dyad 1. The obtained results are consistent with quenching of the singlet excited state of 1 by hydrogen-bond donor solvents. Thus, a physical deactivation process (vibronically induced internal conversion) would be the pathway responsible for the accelerated decay of 1*, favorably competing with fluorescence and intersystem crossing to the triplet. This effect appears to be strongly dependent on the relative spatial arrangement between the naphthalene and thymine units, together with the hydrogen-bonding ability of the employed ROH.     

Ultrafast excited-state dynamics of RNA and DNA C tracts

The excited-state dynamics of the RNA homopolymer of cytosine and of the 18-mer (dC)₁₈ were studied by steady-state and time-resolved absorption and emission spectroscopy. At pH 6.8, excitation of poly(rC) by a femtosecond UV pump pulse produces excited states that decay up to one order of magnitude more slowly than the excited states formed in the mononucleotide cytidine 5′-monophosphate under the same conditions. Even slower relaxation is observed for the hemiprotonated, self-associated form of poly(rC), which is stable at acidic pH. Transient absorption and time-resolved fluorescence signals for (dC)₁₈ at pH 6.8 are similar to ones observed for poly(rC) near pH 4, indicating that hemiprotonated structures are found in DNA C tracts at neutral pH. In both systems, there is evidence for two kinds of emitting states with lifetimes of 100 ps and slightly more than 1 ns. The former states are responsible for the bulk of emission from the hemiprotonated structures. Evidence suggests that slow electronic relaxation in these self-complexes is the result of vertical base stacking. The similar signals from RNA and DNA C tracts suggest a common base-stacked structure, which may be identical with that of i-motif DNA.     

Initial excited-state structural dynamics of thymine are coincident with the expected photochemical dynamics

To explore the excited-state structural dynamics of thymine, a DNA nucleobase, we measured the resonance Raman spectra of thymine in aqueous solution at wavelengths throughout the lowest-energy absorption band. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism yielded the excited-state structural dynamics. The photochemically relevant C=C stretching and C-H deformation vibrational modes were found to exhibit maximum resonance Raman intensity and structural change upon photoexcitation for thymine, suggesting that the initial dynamics of thymine lie along the photochemical reaction coordinate.     

Disentangling intrinsic ultrafast excited-state dynamics of cytosine tautomers

Gas-phase ultrafast excited-state dynamics of cytosine, 1-methylcytosine, and 5-fluorocytosine were investigated in molecular beams using femtosecond pump-probe photoionization spectroscopy to identify the intrinsic dynamics of the major cytosine tautomers. The results indicate that, upon photoexcitation in the first absorption band, the cytosine enol tautomer exhibits a significantly longer excited-state lifetime than its keto and imino counterparts. The initially excited states of the cytosine keto and imino tautomers decay with sub-picosecond dynamics for excitation wavelengths shorter than 300 nm, whereas that of the cytosine enol tautomer decays with time constants ranging from 3 to 45 ps for excitation between 260 and 285 nm.     

Ultrafast excited-state dynamics of nanoscale near-infrared emissive polymersomes

Formed through cooperative self-assembly of amphiphilic diblock copolymers and electronically conjugated porphyrinic near-infrared (NIR) fluorophores (NIRFs), NIR-emissive polymersomes (50 nm to 50 microm diameter polymer vesicles) define a family of organic-based, soft-matter structures that are ideally suited for deep-tissue optical imaging and sensitive diagnostic applications. Here, we describe magic angle and polarized pump-probe spectroscopic experiments that: (i) probe polymersome structure and NIRF organization and (ii) connect emitter structural properties and NIRF loading with vesicle emissive output at the nanoscale. Within polymersome membrane environments, long polymer chains constrain ethyne-bridged oligo(porphinato)zinc(II) based supermolecular fluorophore (PZn n ) conformeric populations and disperse these PZn n species within the hydrophobic bilayer. Ultrafast excited-state transient absorption and anisotropy dynamical studies of NIR-emissive polymersomes, in which the PZn n fluorophore loading per nanoscale vesicle is varied between 0.1-10 mol %, enable the exploration of concentration-dependent mechanisms for nonradiative excited-state decay. These experiments correlate fluorophore structure with its gross spatial arrangement within specific nanodomains of these nanoparticles and reveal how compartmentalization of fluorophores within reduced effective dispersion volumes impacts bulk photophysical properties. As these factors play key roles in determining the energy transfer dynamics between dispersed fluorophores, this work underscores that strategies that modulate fluorophore and polymer structure to optimize dispersion volume in bilayered nanoscale vesicular environments will further enhance the emissive properties of these sensitive nanoscale probes.     

Ab initio excited-state dynamics of the photoactive yellow protein chromophore

The photoisomerization mechanism of the neutral form of the photoactive yellow protein (PYP) chromophore is investigated using ab initio quantum chemistry and first-principles nonadiabatic molecular dynamics (ab initio multiple spawning or AIMS). We identify the nature of the two lowest-lying excited states, characterize the short-time behavior of molecules excited directly to S2, and explain the origin of the experimentally observed wavelength-dependent photoisomerization quantum yield.     

Through-bond versus through-space coupling in mixed-valence molecules: observation of electron localization at the single-molecule scale

Scanning tunneling microscopy (STM) is used to study two dinuclear organometallic molecules, meta-Fe2 and para-Fe2, which have identical molecular formulas but differ in the geometry in which the metal centers are linked through a central phenyl ring. Both molecules show symmetric electron density when imaged with STM under ultrahigh-vacuum conditions at 77 K. Chemical oxidation of these molecules results in mixed-valence species, and STM images of mixed-valence meta-Fe2 show pronounced asymmetry in electronic state density, despite the structural symmetry of the molecule. In contrast, images of mixed-valence para-Fe2 show that the electronic state density remains symmetric. Images are compared to constrained density functional (CDFT) calculations and are consistent with full localization of charge for meta-Fe2 on to a single metal center, as compared with charge delocalization over both metal centers for para-Fe2. The conclusion is that electronic coupling between the two metal centers occurs through the bonds of the organic linker, and through-space coupling is less important. In addition, the observation that mixed-valence para-Fe2 is delocalized shows that electron localization in meta-Fe2 is not determined by interactions with the Au(111) substrate or the position of neighboring solvent molecules or counterion species.     

Ultrafast excited-state dynamics of oxazole yellow DNA intercalators

The excited-state dynamics of the DNA intercalator YO-PRO-1 and of three derivatives has been investigated in water and in DNA using ultrafast fluorescence spectroscopy. In the free form, the singly charged dyes exist both as monomers and as H-dimers, while the doubly charged dyes exist predominantly as monomers. Both forms are very weakly fluorescent: the monomers because of ultrafast nonradiative deactivation, with a time constant on the order of 3-4 ps, associated with large amplitude motion around the methine bridge, and the H-dimers because of excitonic interaction. Upon intercalation into DNA, large amplitude motion is inhibited, H-dimers are disrupted, and the molecules become highly fluorescent. The early fluorescence dynamics of these dyes in DNA exhibits substantial differences compared with that measured with their homodimeric YOYO analogues, which are ascribed to dissimilarities in their local environment. Finally, the decay of the fluorescence polarization anisotropy reveals ultrafast hopping of the excitation energy between the intercalated dyes. In one case, a marked change of the depolarization dynamics upon increasing the dye concentration is observed and explained in terms of a different binding mode.     

Ultrafast excited-state dynamics of tetraphenylethylene studied by semiclassical simulation

Detailed simulation study is reported for the excited-state dynamics of photoisomerization of cis-tetraphenylethylene (TPE) following excitation by a femtosecond laser pulse. The technique for this investigation is semiclassical dynamics simulation, which is described briefly in the paper. Upon photoexcitation by a femtosecond laser pulse, the stretching motion of the ethylenic bond of TPE is initially excited, leading to a significant lengthening of ethylenic bond in 300 fs. Twisting motion about the ethylenic bond is activated by the energy released from the relaxation of the stretching mode. The 90 degrees twisting about the ethylenic bond from an approximately planar geometry to nearly a perpendicular conformation in the electronically excited state is completed in 600 fs. The torsional dynamics of phenyl rings which is temporally lagging behind occurs at about 5 ps. Finally, the twisted TPE reverts to the initial conformation along the twisting coordinate through nonadiabatic transitions. The simulation results provide a basis for understanding several spectroscopic observations at molecular levels, including ultrafast dynamic Stokes shift, multicomponent fluorescence, viscosity dependence of the fluorescence lifetime, and radiationless decay from electronically excited state to the ground state along the isomerization coordinate.     

Singlet and triplet excited-state interactions and photochemical reactivity of phenyleneethynylene oligomers

The rigid rodlike character of phenyleneethynylenes and their ability to communicate charge/excitation energy over long distances have made them useful as molecular linkers in the light energy harvesting assemblies and molecular electronics devices. These linker molecules themselves possess rich photochemistry as evident from the relatively large yields of the excited singlet (0.5-0.66) and triplet (0.4-0.5) states of two model oligomers, 1,4-bis(phenylethynyl)-2,5-bis(hexyloxy)benzene (OPE-1) and 1,4-bis((4-phenylethynyl)phenylethynyl)-2,5-bis(hexyloxy)benzene (OPE-2). In particular, the long-lived triplet excited state is capable of undergoing deactivation by self-quenching processes such as ground-state quenching and triplet-triplet (T-T) annihilation. The T-T annihilation occurs with a nearly diffusion-controlled rate (approximately 2 x 10(9) M(-1) s(-1)), and ground-state quenching occurs with a rate constant of approximately 6 x 10(7) M(-1) s(-1). The electron transfer from the excited OPE-1 and OPE-2 to benzoquinone as characterized from the transient absorption spectroscopy illustrates the ability of these molecules to shuttle the electrons to acceptor moieties. In addition, pulse radiolysis experiments confirm the spectroscopic fingerprint of the cation radical (or "trapped hole") with absorption bands in the 500-600 nm region.     

Nonadiabatic excited-state molecular dynamics: numerical tests of convergence and parameters

Nonadiabatic molecular dynamics simulations, involving multiple Born-Oppenheimer potential energy surfaces, often require a large number of independent trajectories in order to achieve the desired convergence of the results, and simulation relies on different parameters that should be tested and compared. In addition to influencing the speed of the simulation, the chosen parameters combined with the frequently reduced number of trajectories can sometimes lead to unanticipated changes in the accuracy of the simulated dynamics. We have previously developed a nonadiabatic excited state molecular dynamics methodology employing Tully's fewest switches surface hopping algorithm. In this study, we seek to investigate the impact of the number of trajectories and the various parameters on the simulation of the photoinduced dynamics of distyrylbenzene (a small oligomer of polyphenylene vinylene) within our developed framework. Various user-defined parameters are analyzed: classical and quantum integration time steps, the value of the friction coefficient for Langevin dynamics, and the initial seed used for stochastic thermostat and hopping algorithms. Common approximations such as reduced number of nonadiabatic coupling terms and the classical path approximation are also investigated. Our analysis shows that, at least for the considered molecular system, a minimum of ~400 independent trajectories should be calculated in order to achieve statistical averaging necessary for convergence of the calculated relaxation timescales.     

A fluorescence study of the excited-state dynamics of boron dipyrrin molecular rotors

Noticeable viscosity dependence has been revealed for fluorescence spectra of three phenyl derivatives of boron dipyrrin in aqueous glycerol solutions. This dependence is less pronounced for the fluorescence lifetimes. Such behavior is characteristic of molecular rotors used as media microviscosity sensors. A significant growth of the radiative deactivation constant is observed in the range 298-150 K. Quantumchemical calculation of the model fluorophore support the assumption on barrier-free relaxation of the excited state from the pretwisted to the flattened conformation. The spectral-kinetic parameters of fluorophores have been determined, and viscosity graduation curves are presented.