Folding and unfolding of chromophoric foldamers show unusual colorful single molecule spectral dynamics

A series of well-defined linear multichromophoric foldamers with a specific sequence of alternating rigid perylene chromophores and flexible ethylene glycol chains were studied by single molecule fluorescence spectroscopy. Monomer showed minor spectral fluctuations compared to trimer and hexamer, which showed unusual and colorful spectral dynamics attributed to a stochastic photoinduced unfolding/folding phenomenon. The range of spectral shapes observed indicates varying degrees of pi-pi interaction between adjacent chromophores, with vibronically resolved green emission indicating completely unfolded structures and broad red emission indicating highly coupled and extensively folded pi-stacks. The rate of switching between different spectral shapes in the spectral trajectories suggests the existence of multiple pathways between the folded and unfolded states.     

Synthesis and properties of a series of well-defined and polydisperse benzo[1,2-b:4,3-b']dithiophene oligomers

Monodisperse and polydisperse oligomers of benzo[1,2-b:4,3-b']dithiophene (BDT) (1-14), including three types of oligomers with different spacers combining BDT units (direct linkage, vinylene spacers, and ethynylene spacers), were synthesized, and their thermal, optical, and electrochemical properties were investigated. The oligomers were synthesized using Suzuki, Stille, Wittig, and Sonogashira coupling reactions. All of the monodisperse oligomers showed high melting points and 5% weight loss temperatures (T(d) > 400 degrees C). The fluorescence maxima of all oligomers were red-shifted, and the emission colors varied from blue to yellow as the chain lengths-and thus the conjugation lengths-increased. The vinylene-bridged oligomers emitted at longer wavelengths than the direct-linked and ethynylene-bridged oligomers. UV-vis absorption spectra in toluene solution indicated an effective conjugation length of about six BDT units for polydisperse oligomer 5. Cyclic voltammetry measurement indicated that tetramer 3 had high electrochemical stability. Although tetramer 3 and vinylene-bridged tetramer 8 exhibited reversible oxidation waves, ethynylene-bridged tetramer 13 showed an irreversible oxidation process. Each type of monodisperse oligomer exhibited higher HOMO levels with increasing chain length.     

Ultrafast exciton transfers in DNA and its nonlinear optical spectroscopy

We have calculated the nonlinear response function of a DNA duplex helix including the contributions from the exciton population and coherence transfers by developing an appropriate exciton theory as well as by utilizing a projector operator technique. As a representative example of DNA double helices, the B-form (dA)10-(dT)10 is considered in detail. The Green functions of the exciton population and coherence transfer processes were obtained by developing the DNA exciton Hamiltonian. This enables us to study the dynamic properties of the solvent relaxation and exciton transfers. The spectral density describing the DNA base-solvent interactions was obtained by adjusting the solvent reorganization energy to reproduce the absorption and steady-state fluorescence spectra. The time-dependent fluorescence shift of the model DNA system is found to be ultrafast and it is largely determined by the exciton population transfer processes. It is further shown that the nonlinear optical spectroscopic techniques such as photon echo peak shift and two-dimensional photon echo can provide important information on the exciton dynamics of the DNA double helix. We have found that the exciton-exciton coherence transfer plays critical roles in the peculiar energy transfer and ultrafast memory loss of the initially created excitonic state in the DNA duplex helix.     

Oligodeoxyfluorosides: Strong Sequence Dependence of Fluorescence Emission

We describe the properties of a series of oligomeric polyfluorophores assembled on the DNA backbone. The 11 oligomers (oligodeoxyfluorosides, ODFs), 4-7 monomers in length, were composed of only two fluorescent monomers and a spacer in varied sequences, and were designed to test how fluorescent nucleobases can interact electronically to yield complexity in fluorescence emission. The monomer fluorophores were deoxyribosides of pyrene and perylene, which emit light in violet and blue wavelengths, respectively. The experiments show that simple variation in sequence and spacing can dramatically change fluorescence, yielding emission maxima ranging from 380 to 557 nm and visible colors from violet to orange-red. Fluorescence lifetime data, excitation spectra, and absorption data point to a number of multi-fluorophore electronic interactions, including pyrene-pyrene and perylene-perylene excimers, pyrene-perylene exciplexes, as well as monomer dye emissions, contributing to the final spectral outcomes. Thus, two simple fluorophores can be readily combined to give emissions over much of the visible spectrum, all requiring only a single excitation. The results demonstrate that fluorescent nucleobases in oligomeric form can act cooperatively as electronic units, and that fluorophore sequence in such oligomers is as important as fluorophore composition in determining fluorescence properties.     

Oligomeric cholates: amphiphilic foldamers with nanometer-sized hydrophilic cavities

The hydroxyl at the C-3 of cholic acid was converted to an amino group, and the resulting amino-functionalized cholic acid was used as a monomer to prepare amide-linked oligomeric cholates. These cholate oligomers fold into helical structures with nanometer-sized hydrophilic internal cavities in solvent mixtures consisting of mostly nonpolar solvents such as carbon tetrachloride or ethyl acetate/hexane and 2-5% of a polar solvent such as methanol or DMSO. The conformations of the foldamers were studied by UV, fluorescence, fluorescence quenching, and fluorescence resonance energy transfer. The nature of the polar/nonpolar solvents and their miscibility strongly influenced the folding reaction. Folding was cooperative, as evidenced by the sigmoidal curves in solvent denaturation experiments. The folded conformers became more stable with an increase in the chain length. The folding/unfolding equilibrium was highly sensitive toward the amount of polar solvent. One percent variation in the solvent composition could change the folding free energies by 0.5-1.4 kcal/mol.     

Beyond exciton theory: a time-dependent DFT and Franck-Condon study of perylene diimide and its chromophoric dimer

The diimide perylene motif exhibits a dramatic intensity reversal between the 0 --> 0 and 0 --> 1 vibronic bands upon pi-pi stacking; this distinct spectral property has previously been used to measure folding dynamics in covalently bound oligomers and synthetic biological hybrid foldamers. It is also used as a tool to assess organization of the pi-stacking, indicating the presence of H- or J-aggregation. The zeroth-order exciton model, often used to describe the optical properties of chromophoric aggregates, is solely a transition dipole coupling scheme, which ignores the explicit electronic structure of the system as well as vibrational coupling to the electronic transition. We have therefore examined the optical properties of gas-phase perylene tetracarboxylic diimide (PTCDI) and its chromophoric dimer as a function of conformation to relate the excited-state distributions predicted by exciton theory with that of time-dependent density functional theory (TDDFT). Using ground- and excited-state geometries, the Franck-Condon (FC) factors for the lowest energy molecular nature electronic transition have been calculated and the origin of the intensity reversal of 0 --> 0 and 0 --> 1 vibronic bands has been proposed.     

Protein unfolding and subsequent refolding: a spectroscopic investigation

The mechanism by which the protein Bovine Serum Albumin (BSA) undergoes unfolding induced by Guanidine Hydrochloride (GdHCl) and then the subsequent refolding brought in by many-fold dilution was studied by steady-state fluorescence, anisotropy, time resolved measurements and Circular Dichroism (CD) spectroscopy. CD data reveal that the protein attains a degree of extra rigidity at low concentrations of the denaturant, GdHCl, and this observation was correlated with other techniques used in this present work. The unfolding and refolding of BSA appear to proceed through intermediates and both the processes are sequential in nature. The intrinsic fluorescence from the tryptophan amino acid residue of BSA and another external fluorophore Nile Red was made use of in order to investigate the mechanisms of unfolding and refolding and we have conclusively proved that both these processes follow a reversible mechanism.     

Singlet-triplet and triplet-triplet interactions in conjugated polymer single molecules

Single molecule fluorescence correlation spectroscopy has been used to investigate the photodynamics of isolated single multichromophoric polymer chains of the conjugated polymers MEH-PPV and F8BT on the microsecond to millisecond time scale. The experimental results (and associated kinetic modeling) demonstrate that (i) triplet exciton pairs undergo efficient triplet-triplet annihilation on the <30 micros time scale, (ii) triplet-triplet annihilation is the dominant mechanism for triplet decay at incident excitation powers > or =50 W/cm(2), and (iii) singlet excitons are quenched by triplet excitons with an efficiency on the order of (1)/(2). The high efficiency of this latter process ensures that single molecule fluorescence spectroscopy can be effectively used to indirectly monitor triplet exciton population dynamics in conjugated polymers. Finally, correlation spectroscopy of MEH-PPV molecules in a multilayer device environment reveals that triplet excitons are efficiently quenched by hole polarons.     

Intermolecular interactions in pi-stacked conjugated molecules. Synthesis,structure, and spectral characterization of alkyl bithiazole oligomers

Syntheses are reported of new 4,4'-dialkyl-2,2'-bithiazole oligomers that have alkenoxy side chains that are capable of easy conversion to oligomers with functionalized side chains, e.g., terminally substituted hydroxy chains. The crystal structures of two representative oligomers (4,4',4' ',4' "-tetra-(2-propenoxymethyl)-2,2',5',5' ',2' ',2' "-quaterthiazole (3P2) and 4,4',4' ',4' "-tetra-(3-hydroxypropyloxymethyl)-2,2',5',5' ',2' ',2' "-quaterthiazole (3H2)) were determined; 3P2 crystallizes in a pi-stacked motif with two molecules per unit cell, whereas 3H2 forms pi-stacks that are linked with hydrogen bonds to form infinite two-dimensional sheets with one molecule per unit cell. A comparison of the UV-vis spectra of the compounds in solution and in the solid state provides unequivocal evidence for the presence of a Davydov splitting, W(D) approximately 0.2 eV, in solid 3P2. The spectra are interpreted in the framework of molecular exciton theory to extract a value of the intermolecular transfer integral, J approximately 0.2 eV, for a total exciton bandwidth of ca. 0.8 eV. Monte Carlo calculations were used to determine the density of states of the exciton band and the absorption and emission line shapes of the 0 <-- 0 transition. It is suggested that the "three-humped" absorption profile typical of partially crystalline, regioregular polymers is the "optical signature" of pi-stacking.     

Temperature-dependent relaxation of excitons in tubular molecular aggregates: Fluorescence decay and stokes shift

We report temperature-dependent steady-state and time-resolved fluorescence studies to probe the exciton dynamics in double-wall tubular J-aggregates formed by self-assembly of the dye 3,3'-bis(3-sulfopropyl)-5,5',6,6'-tetrachloro-1,1'-dioctylbenzimidacarbocyanine. We focus on the lowest energy fluorescence band, originating from the inner cylindrical wall. At low temperatures, the experiments reveal a nonexponential decay of the fluorescence, with a typical time scale that depends on the emission wavelength. At these temperatures we also find a dynamic Stokes shift of the fluorescence spectrum and its nonmonotonic dependence on temperature under steady-state conditions. All these data indicate that below about 20 K the excitons in the lowest fluorescence band do not reach thermal equilibrium before emission occurs, while above about 60 K thermalization on this time scale is complete. By comparing the two lowest fluorescence bands, we also find indications for fast energy transfer from the outer to the inner wall. We show that the Frenkel exciton model with diagonal disorder, which previously has been proposed to explain the absorption and linear dichroism spectra of these aggregates, yields a quantitative explanation to the observed dynamics. To this end, we extend the model to account for weak phonon-induced scattering of the localized exciton states; the spectral dynamics are then described by solving a Pauli master equation for the exciton populations.     

Ultrafast dynamical localization of photoexcited states in conformationally disordered poly(p-phenylenevinylene)

We consider two types of ultrafast dynamical localization of photoexcited states in conformationally disordered poly(p-phenylenevinylene). First, we discuss nonadiabatic interconversion from higher energy extended exciton states to lower energy more localized local exciton ground states. Second, we calculate the dynamics of local exciton ground states on their Born-Oppenheimer potential energy surfaces. We show that within the first C-C bond oscillation following photoexcitation (～35 fs) the exciton becomes self-trapped and localized over approximately eight monomers. This process is associated with a Calderia-Leggett type loss of phase coherence owing to the coupling of the polymer to a dissipative environment. Subsequent torsional relaxation (on a time scale of approximately picoseconds) has little effect on the localization. We conclude from this that the initial torsional disorder determines the spatial distribution and localization length of vertical excitations but that electron-phonon coupling is largely responsible for the localization length of self-trapped excitons. We next consider the effect of dynamical localization on fluorescence depolarization. We show that exciting higher energy states causes a larger fluorescence depolarization, because these states have a larger initial delocalization. Using the observation that fluorescence depolarization is a function of excitation wavelength and polymer conformation, we show how the models of exciton localization discussed here can be experimentally investigated.     

Dynamics and transient absorption spectral signatures of the single-wall carbon nanotube electronically excited triplet state

We utilize femtosecond-to-microsecond time domain pump-probe transient absorption spectroscopy to interrogate for the first time the electronically excited triplet state of individualized single-wall carbon nanotubes (SWNTs). These studies exploit (6,5) chirality-enriched SWNT samples and poly[2,6-{1,5-bis(3-propoxysulfonic acid sodium salt)}naphthylene]ethynylene (PNES), which helically wraps the nanotube surface with periodic and constant morphology (pitch length = 10 ± 2 nm), providing a self-assembled superstructure that maintains structural homogeneity in multiple solvents. Spectroscopic interrogation of such PNES-SWNT samples in aqueous and DMSO solvents using E(22) excitation and a white-light continuum probe enables E(11) and E(22) spectral evolution to be monitored concomitantly. Such experiments not only reveal classic SWNT singlet exciton relaxation dynamics and transient absorption signatures but also demonstrate spectral evolution consistent with formation of a triplet exciton state. Transient dynamical studies evince that (6,5) SWNTs exhibit rapid S(1)→T(1) intersystem crossing (ISC) (τ(ISC) ~20 ps), a sharp T(1)→T(n) transient absorption signal (λ(max)(T(1)→T(n)) = 1150 nm; full width at half-maximum ≈ 350 cm(-1)), and a substantial T(1) excited-state lifetime (τ(es) ≈ 15 μs). Consistent with expectations for a triplet exciton state, T(1)-state spectral signatures and T(1)-state formation and decay dynamics for PNES-SWNTs in aqueous and DMSO solvents, as well as those determined for benchmark sodium cholate suspensions of (6,5) SWNTs, are similar; likewise, studies that probe the (3)[(6,5) SWNT]* state in air-saturated solutions demonstrate (3)O(2) quenching dynamics reminiscent of those determined for conjugated aromatic hydrocarbon excited triplet states.     

Theoretical study of vibrational and optical spectra of methylene-bridged oligofluorenes

We report a systematic characterization of methylene-bridged fluorene oligomers constructed of two, four, six, and eight aromatic rings using time-dependent density functional theory (TDDFT), the ab initio approximate coupled-cluster singles and doubles (CC2) method, and semiempirical spectroscopic Zerner's intermediate neglect of differential overlap method (ZINDO/S). Geometry optimizations have been performed for the ground state and for the first electronically excited state. Vertical excitations and the fluorescence transition from the lowest excited state have been calculated. Computed ground-state geometries and infrared spectra for fluorene are in good agreement with experimental results. The RI-CC2 and ZINDO/S absorption and fluorescence spectra agree very well with the available experimental data for studied fluorene oligomers and for para oligophenylenes films. On the other hand, TDDFT calculations underestimate excitation and fluorescence energies systematically for larger systems (N > 4) in comparison with the above-mentioned results. The effective conjugation length was estimated to 13-14 repeat units. The computed radiative lifetimes for the fluorene molecule show good agreement with experiment within realistic expectations. The decrease of the radiatiave fluorescence lifetime with the increase in the conjugation length has been discussed also.     

Chirality induction and protonation-induced molecular motions in helical molecular strands

The long oligopyridinedicarboxamide strand 9, containing 15 heterocyclic rings has been synthesized and its helical structure determined by X-ray crystallography. It was shown that the shorter analogue 6 displays induced circular dichroism and amplification of induced chirality upon dissolution in an optically active solvent, diethyl-L-tartrate. A novel class of helical foldamers was prepared, strands 14-16, based on two oligopyridine carboxamide segments linked through a L-tartaric acid derived spacer. These tartro strands display internal chirality induction as well as chirality amplification. NMR spectroscopy (on 8 and 9) and circular dichroism (on 16) studies show that the oligopyridine carboxamide strands undergo reversible unfolding/folding upon protonation. The protonation-induced unfolding has been confirmed by X-ray crystallographic determination of the molecular structure of the extended protonated heptameric form 8(+). The molecular-scale mechano-chemical motions of the protonation-induced structural switching consist of a change of the length of the molecule, from 6 angstroms (6, coiled form) to 29 angstroms (8(+), uncoiled form) for the heptamer and from 12.5 angstroms (9, coiled form, X-ray structure) to 57 angstroms (9(+), uncoiled form, from modeling) for the pentadecamer. Similar unfolding/folding motional processes take place in the L-tartro strands 15 and 16 upon protonation/deprotonation, with loss of helicity-induced circular dichroism on unfolding as shown for the protonated form 16(+).     

α-Bridged BODIPY oligomers with switchable near-IR photoproperties by external-stimuli-induced foldamer formation and disruption

We designed and synthesized a series of new α-bridged linear BODIPY oligomers, which exhibited strong absorption and high fluorescence efficiency in the near infrared region. The oligomers can be reversibly converted to the first NIR emissive BODIPY foldamers upon selective complexation with Cs(+).     

Study of ultrafast dynamics of 2-picoline by time-resolved photoelectron imaging

The dynamics of electronically excited states in 2-picoline is studied using femtosecond time-resolved photoelectron imaging spectroscopy. The internal conversion from the S(2) state to the vibrationally excited S(1) state is observed in real time. The secondarily populated high vibronic S(1) state deactivates further to the S(0) state. Photoelectron energy and angular distributions reveal the feature of ionization from the singlet 3p Rydberg states. In addition, variation of time-dependent anisotropy parameters indicates the rotational coherence of the molecule.     

Optische Einzelmolekülspektroskopie. Einblicke in den Nanokosmos

Single‐molecule fluorescence spectroscopy evolved to a variety of tools to investigate molecular dynamics in thermodynamic equilibrium and to reveal subpopulations in heterogeneous molecular distributions which usually remain hidden in bulk experiments. Applications of single‐molecule experiments range from life sciences and material sciences to photo‐physics and photo‐chemistry. Some of these research fields, like chemical catalysis, have just recently been entered. This article summarizes major principles of single‐molecule fluorescence spectroscopy and gives an overview on some important applications up to the development of novel microscopic techniques with nanometer resolution.     

Synthesis and fluorescence characterization of MEHPPV oligomers

Trimer, tetramer, and pentamer oligomers based on the polymer backbone structure of poly[2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene] (MEHPPV) have been synthesized by Horner-Wadsworth-Emmons reactions. The fluorescence spectra, emission quantum yields, and lifetimes of the oligomers have been characterized in dilute chloroform solutions. The oligomers exhibit a sequential increase in absorption and emission wavelength maxima and a decrease in fluorescence lifetime as the π conjugation length is increased. The shortening in excited state lifetime is shown to be due to an increase in the rates of both radiative and nonradiative processes. The absence of a mirror-image relationship for the absorption and fluorescence spectra of the oligomers is attributed to the photoexcitation of a range of torsional configurations followed by relaxation to a more planar arrangement that then emits.     

Mechanically untying a protein slipknot: multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations

Protein structure is highly diverse when considering a wide range of protein types, helping to give rise to the multitude of functions that proteins perform. In particular, certain proteins are known to adopt a knotted or slipknotted fold. How such proteins undergo mechanical unfolding was investigated utilizing a combination of single molecule atomic force microscopy (AFM), protein engineering, and steered molecular dynamics (SMD) simulations to show the mechanical unfolding mechanism of the slipknotted protein AFV3-109. Our results reveal that the mechanical unfolding of AFV3-109 can proceed via multiple parallel unfolding pathways that all cause the protein slipknot to untie and the polypeptide chain to completely extend. These distinct unfolding pathways proceed via either a two- or three-state unfolding process involving the formation of a well-defined, stable intermediate state. SMD simulations predict the same contour length increments for different unfolding pathways as single molecule AFM results, thus providing a plausible molecular mechanism for the mechanical unfolding of AFV3-109. These SMD simulations also reveal that two-state unfolding is initiated from both the N- and C-termini, while three-state unfolding is initiated only from the C-terminus. In both pathways, the protein slipknot was untied during unfolding, and no tightened slipknot conformation was observed. Detailed analysis revealed that interactions between key structural elements lock the knotting loop in place, preventing it from shrinking and the formation of a tightened slipknot conformation. Our results demonstrate the bifurcation of the mechanical unfolding pathway of AFV3-109 and point to the generality of a kinetic partitioning mechanism for protein folding/unfolding.     

Excited‐State Dynamic Planarization of Cyclic Oligothiophenes in the Vicinity of a Ring‐to‐Linear Excitonic Behavioral Turning Point

Excited‐state dynamic planarization processes play a crucial role in determining exciton size in cyclic systems, as reported for π‐conjugated linear oligomers. Herein, we report time‐resolved fluorescence spectra and molecular dynamics simulations of π‐conjugated cyclic oligothiophenes in which the number of subunits was chosen to show the size‐dependent dynamic planarization in the vicinity of a ring‐to‐linear behavioral turning point. Analyses on the evolution of the total fluorescence intensity and the ratio between 0–1 to 0–0 vibronic bands suggest that excitons formed in a cyclic oligothiophene composed of six subunits fully delocalize over the cyclic carbon backbone, whereas those formed in larger systems fail to achieve complete delocalization. With the aid of molecular dynamics simulations, it is shown that distorted structures unfavorable for efficient exciton delocalization are more easily populated as the size of the cyclic system increases.