Strongly Polarized π-Extended 1,4-Dihydropyrrolo[3,2-b]pyrroles Fused with Tetrazolo[1,5-a]quinolines.

A straightforward route to 1,4-dihydropyrrolo[3,2-b]pyrroles comprised of two electron-withdrawing quinoline or tetrazolo[1,5-a]quinoline scaffolds has been developed. The versatile multicomponent reaction affording 1,4-dihydropyrrolo[3,2-b]pyrroles combined with intramolecular direct arylation enables assembly of these products in just three steps from anilines with overall yields exceeding 30%. The planarized, ladder-type heteroacenes possess up to 14 conjugated rings. These nominally quadrupolar materials exhibit efficient fluorescence with wavelengths spanning most of the visible spectrum from green-yellow for the dyes possessing biaryl bridges and orange-red for the fully fused systems. In many cases, the fluorescence quantum yields are large, the solvatofluorochromic effects are strong, and the fluorescence is maintained even in crystalline state. Analysis of the electronic structure of these molecular architectures using quantum chemical methods suggests that the character and position of the flanking heterocycle determine the shape of HOMO and LUMO and their extension to N-aryl substituents, influencing the values of molar absorption coefficient. An experimental study of the two-photon absorption (2PA) properties has revealed that it occurs in the 700-800 nm range with apparent deviation from the Laporte parity selection rule, which may be attributed to Hertzberg-Teller contribution to vibronically allowed 2PA transition.

Slow light and photon echoes in the 7F0→5D0 transition of Sm2+ in single-crystal BaFCl.

Slow light effects induced by transient spectral hole-burning in the 7F0→5D0 transition of Sm2+ in BaFCl at 688 nm are reported and a probe pulse delay of 1.25 µs was observed through a 5 mm thick crystal. This delay corresponds to a reduction of the group velocity vG of the transmitted light to ∼4000 m/s. An analysis of the dependence of the slow light effect on the probe pulse timing indicates some broadening of the spectral hole caused by relatively fast excitation energy transfer. We also demonstrate two-pulse (2PE) and (three-pulse) stimulated photon echoes (SPE) for the first time for Sm2+ in the solid state and a homogenous linewidth of 16 kHz (∼2.5·10-8 nm) was obtained at 1.8 K. The echoes in the optically dense medium were very efficient and revealed spectral diffusion on the 100-µs time scale possibly due to flipping of the fluorine and chlorine nuclear spins in the environment of the Sm2+ ions. Furthermore, the SPE also indicates relatively fast energy transfer, commensurate with the hole decay.

Surface Passivation Method for the Super-repellence of Aqueous Macromolecular Condensates.

Solutions of macromolecules can undergo liquid-liquid phase separation to form droplets with ultralow surface tension. Droplets with such low surface tension wet and spread over common surfaces such as test tubes and microscope slides, complicating in vitro experiments. The development of a universal super-repellent surface for macromolecular droplets has remained elusive because their ultralow surface tension requires low surface energies. Furthermore, the nonwetting of droplets containing proteins poses additional challenges because the surface must remain inert to a wide range of chemistries presented by the various amino acid side chains at the droplet surface. Here, we present a method to coat microscope slides with a thin transparent hydrogel that exhibits complete dewetting (contact angles θ ≈ 180°) and minimal pinning of phase-separated droplets in aqueous solution. The hydrogel is based on a swollen matrix of chemically cross-linked polyethylene glycol diacrylate of molecular weight 12 kDa (PEGDA), and can be prepared with basic chemistry laboratory equipment. The PEGDA hydrogel is a powerful tool for in vitro studies of weak interactions, dynamics, and the internal organization of phase-separated droplets in aqueous solutions.

Novel Lipophilic Fluorophores with Highly Acidity-Dependent Two-Photon Response.

Lipophilic fluorophores are widely implemented in nonlinear microscopy; however, few existing membrane-specific probes combine the high brightness of two-photon excited fluorescence (2PEF) with pH sensitivity. Herein we describe four novel two-photon excited fluorophores, based on a coumarin 151 core structure, where lipophilicity is induced by a covalently attached phosphazene moiety. Changing the environmental acidity using trifluoromethanesulfonic (triflic) acid leads to profound changes in the linear fluorescence and 2PEF characteristics, due to chromophores' switching between neutral- and protonated forms. We characterize this dependence by measuring the two-photon absorption (2PA) spectra over the region λ2PA =550-1000 nm, observing 2PA cross sections of σ2PA =10-20 GM, with an associated 2PEF brightness of 10-13 GM, in neutral solutions of both acetonitrile and n-octanol. Although quantum chemical modelling and NMR measurements show that, at high chromophore concentrations, protonation may be accompanied by a dimerization process, these dimers likely do not form at the lower concentrations used in optical spectroscopy.

Photophysical and Electrochemical Properties of Push-Pull Oligo(ferrocenyl-phenyleneethynylene)s: Supramolecular Orders in Molecular Films.

We report on the optoelectronic properties of a series of unsymmetrical π-conjugated phenyleneethynylene macromolecules bearing ferrocene (Fc) as the electron-donor group (D), (benzyl) benzoate (Bz) or benzoic acid (Ac) as the electron attractor group (A) and connected through 2,5-di(alcoxy) phenyleneethynylene(s) (nPE) with n = 1, 2, 3 as π-conjugated bridges. In the series, by increasing the distance between the electron-attracting and electron-donor groups, the push-pull effect decreases. The intramolecular charge transfer (D → π → A) was evaluated by static and dynamic spectroscopy, electrochemistry, and density functional theory (DFT) theoretical calculations. The longest oligomer Fc3PEBz formed the best optical quality films. A study at the atomic level by scanning tunneling microscopy (STM) revealed that the molecules self-assemble on highly ordered pyrolytic graphite (HOPG) in domains with a short-range order. Films are mesoporous and the molecules arrange in a lamellar-like pattern, with an edge-on conformation with respect to HOPG, where the conjugated backbones lie parallel to the surface. Two different assemblies were identified in the monoatomic film, which depends on the ferrocene-ferrocene or benzyl-benzyl interactions.

On-off-on Control of Molecular Inversion Symmetry via Multi-stage Protonation: Elucidating Vibronic Laporte Rule.

The Laporte rule dictates that one- and two-photon absorption spectra of inversion-symmetric molecules should display alternatively forbidden electronic transitions; however, for organic fluorophores, drawing clear distinction between the symmetric- and non-inversion symmetric two-photon spectra is often obscured due to prevalent vibronic interactions. We take advantage of consecutive single- and double-protonation to break and then reconstitute inversion symmetry in a nominally symmetric diketopyrrolopyrrole, causing large changes in two-photon absorption. By performing detailed one- and two-photon titration experiments, with supporting quantum-chemical model calculations, we explain how certain low-frequency vibrational modes may lead to apparent deviations from the strict Laporte rule. As a result, the system may be indeed considered as an on-off-on inversion symmetry switch, opening new avenues for two-photon sensing applications.

Stereochemical Effects on Platinum Acetylide Two-Photon Chromophores.

A series of cis-platinum(II) acetylide complexes containing two-photon-absorbing chromophores have been synthesized and characterized to explore the effects of stereochemistry on the nonlinear absorption properties. The molecules feature 4-(phenylethynyl)phenylethynylene (PE2), diphenylaminofluorene (DPAF), and benzothiazolylfluorene (BTF) ligands. The photophysical properties were investigated under one- and two-photon conditions and compared to the known trans analogues via UV-visible absorption, photoluminescence, femtosecond and nanosecond transient absorption (TA), nanosecond z-scan, and femtosecond two-photon absorption (2PA). The bent cis complexes exhibit blue shifts in the absorption, emission, femtosecond, and nanosecond TA spectra along with lower molar extinction coefficients and lower phosphorescence yields relative to the trans complexes suggesting less efficient Pt-induced spin-orbit coupling and intersystem crossing in the cis configuration. The cis chromophores are noncentrosymmetric and therefore show dipolar behavior with a pronounced 2PA in the 0-0 transition of the S0 → S1 band, while the trans complexes show quadrupolar behavior with a forbidden 0-0 transition. In the S0 → Sn region, both cis and trans complexes show intense two-photon-absorption bands (up to 3700 GM by the peak cross section for cis-BTF) which contain a significant contribution from the excited state absorption (S1 → Sn). All six complexes exhibit comparable nonlinear absorption response with a significant contribution from triplet-triplet absorption that slightly favors trans complexes but is more strongly dependent upon the structure of the π-conjugated chromophore.

Stability, folding dynamics, and long-range conformational transition of the synaptic t-SNARE complex.

Synaptic soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) couple their stepwise folding to fusion of synaptic vesicles with plasma membranes. In this process, three SNAREs assemble into a stable four-helix bundle. Arguably, the first and rate-limiting step of SNARE assembly is the formation of an activated binary target (t)-SNARE complex on the target plasma membrane, which then zippers with the vesicle (v)-SNARE on the vesicle to drive membrane fusion. However, the t-SNARE complex readily misfolds, and its structure, stability, and dynamics are elusive. Using single-molecule force spectroscopy, we modeled the synaptic t-SNARE complex as a parallel three-helix bundle with a small frayed C terminus. The helical bundle sequentially folded in an N-terminal domain (NTD) and a C-terminal domain (CTD) separated by a central ionic layer, with total unfolding energy of ∼17 kBT, where kB is the Boltzmann constant and T is 300 K. Peptide binding to the CTD activated the t-SNARE complex to initiate NTD zippering with the v-SNARE, a mechanism likely shared by the mammalian uncoordinated-18-1 protein (Munc18-1). The NTD zippering then dramatically stabilized the CTD, facilitating further SNARE zippering. The subtle bidirectional t-SNARE conformational switch was mediated by the ionic layer. Thus, the t-SNARE complex acted as a switch to enable fast and controlled SNARE zippering required for synaptic vesicle fusion and neurotransmission.

Kinetically coupled folding of a single HIV-1 glycoprotein 41 complex in viral membrane fusion and inhibition.

HIV-1 glycoprotein 41 (gp41) mediates viral entry into host cells by coupling its folding energy to membrane fusion. Gp41 folding is blocked by fusion inhibitors, including the commercial drug T20, to treat HIV/AIDS. However, gp41 folding intermediates, energy, and kinetics are poorly understood. Here, we identified the folding intermediates of a single gp41 trimer-of-hairpins and measured their associated energy and kinetics using high-resolution optical tweezers. We found that folding of gp41 hairpins was energetically independent but kinetically coupled: Each hairpin contributed a folding energy of ∼-23 kBT, but folding of one hairpin successively accelerated the folding rate of the next one by ∼20-fold. Membrane-mimicking micelles slowed down gp41 folding and reduced the stability of the six-helix bundle. However, the stability was restored by cooperative folding of the membrane-proximal external region. Surprisingly, T20 strongly inhibited gp41 folding by actively displacing the C-terminal hairpin strand in a force-dependent manner. The inhibition was abolished by a T20-resistant gp41 mutation. The energetics and kinetics of gp41 folding established by us provides a basis to understand viral membrane fusion, infection, and therapeutic intervention.

Ultra-slow light propagation by self-induced transparency in ruby in the superhyperfine limit.

Self-induced transparency is reported for circularly polarized light in the R1(-3/2) line of a 30 ppm ruby (α-Al2O3:Cr3+) at 1.7 K in a magnetic field of B‖c=4.5 T. In such a field and temperature, a 30 ppm ruby is in the so-called superhyperfine limit resulting in a long phase memory time, TM=50 µs, and a thousand-fold slower pulse propagation velocity of ∼300 m/s was observed, compared to the ∼300 km/s measured in the first observation of self-induced transparency (SIT) ∼50 years ago, that employed a ruby with a 500 ppm chromium concentration in zero field and at 4.2 K. To date, this is the slowest pulse propagation ever observed in a SIT experiment.

TD-DFT calculations of one- and two-photon absorption in Coumarin C153 and Prodan: attuning theory to experiment.

We use TD-DFT to calculate the one-photon absorption (1PA) and two-photon absorption (2PA) properties of C153 and Prodan in toluene and DMSO, and benchmark different methods relative to accurate experimental data available from the literature on these particular systems. As the first step, we modify the range-separated TD-DFT to provide the best prediction for the peak 1PA wavelength, and then apply the optimized functionals to achieve quantitative predictions of the corresponding two-photon absorption cross section, σ2PA, with an accuracy ∼10-20% in C153 and ∼20-30% in Prodan. To elucidate the origin of residual discrepancies between the theory and experimental observations, we invoked the two essential states model for σ2PA, which allows us to verify not only the transition wavelength and the σ2PA value, but also to quantitatively benchmark the calculation of key molecular parameters such as the transition dipole moment and the change of the permanent dipole moment. Such comprehensive cross-checking indicates that a larger discrepancy in Prodan is most likely caused by a noted failure of DFT to predict the relative intensity and relative ordering of closely lying excited states with different degrees of intramolecular charge transfer, which we further support by analyzing the predictions obtained by high-level coupled-cluster calculations in the gas phase. Our results highlight the utility of benchmarking the calculations not only relative to other theoretical methods, but also in comparison to the experimental measurements, wherever such data are available.

Two-Photon Spectroscopy of a Series of Platinum Acetylides: Conformation-Induced Ground-State Symmetry Breaking.

With the goal of elucidating electronic and conformational effects on structure-spectroscopic property relationships in platinum acetylides, we synthesized a series of nominally centrosymmetric chromophores trans-Pt(PBu3)2(C≡C-Phenyl-X)2, where X = diphenylamino (DPA), NH2, OCH3, t-Bu, CH3, H, F, benzothiazole (BTH), CF3, CN, and NO2. We collected one- and two-photon absorption spectra and also performed density functional theory (DFT) and time-dependent (TD) DFT calculations on the ground- and excited-state properties of these compounds. The DFT calculations revealed facile rotation between the two ligands, suggesting that the compounds exhibit nonplanar ground-state conformations in solution. TDDFT calculation of the S1 state energy and transition dipole moment for a nonplanar conformation gave good agreement with experiment. Two-photon absorption spectra obtained from these compounds allowed estimation of the change of permanent electric dipole moment upon vertical excitation from ground state to S1 state. The values are small Δµ < 1.0 D for neutral substituents such as CH3, H, and F but increase sharply to Δµ ≈ 11 D for electron-accepting NO2. When in a nonplanar conformation, the corresponding calculated Δµ values showed good agreement with the experimental data indicating that the two-photon spectra result from nonplanar ground-state conformations. Previously studied related chromophores having extended conjugation ( Rebane, A.; Drobizhev, M.; Makarov, N. S.; Wicks, G.; Wnuk, P.; Stepanenko, Y.; Haley, J. E.; Krein, D. M.; Fore, J. L.; Burke, A. R.; Slagle, J. E.; McLean, D. G.; Cooper, T. M. J. Phys. Chem. A 2014 , 118 , 3749 - 3759 ) show similar dependence of Δµ on the substituents, which allows us to conclude that the excited-state properties of these floppy chromophores are a function of the electronic properties of the substituents, ligand size, and nonplanar molecular conformation.

Hidden Markov Modeling with Detailed Balance and Its Application to Single Protein Folding.

Hidden Markov modeling (HMM) has revolutionized kinetic studies of macromolecules. However, results from HMM often violate detailed balance when applied to the transitions under thermodynamic equilibrium, and the consequence of such violation has not been well understood. Here, to our knowledge, we developed a new HMM method that satisfies detailed balance (HMM-DB) and optimizes model parameters by gradient search. We used free energy of stable and transition states as independent fitting parameters and considered both normal and skew normal distributions of the measurement noise. We validated our method by analyzing simulated extension trajectories that mimicked experimental data of single protein folding from optical tweezers. We then applied HMM-DB to elucidate kinetics of regulated SNARE zippering containing degenerate states. For both simulated and measured trajectories, we found that HMM-DB significantly reduced overfitting of short trajectories compared to the standard HMM based on an expectation-maximization algorithm, leading to more accurate and reliable model fitting by HMM-DB. We revealed how HMM-DB could be conveniently used to derive a simplified energy landscape of protein folding. Finally, we extended HMM-DB to correct the baseline drift in single-molecule trajectories. Together, we demonstrated an efficient, versatile, and reliable method of HMM for kinetics studies of macromolecules under thermodynamic equilibrium.

Structure-Based Derivation of Protein Folding Intermediates and Energies from Optical Tweezers.

Optical tweezers (OTs) measure the force-dependent time-resolved extension of a single macromolecule tethered between two trapped beads. From this measurement, it is possible to determine the folding intermediates, energies, and kinetics of the macromolecule. Previous data analysis generally has used the extension as a reaction coordinate to characterize the observed folding transitions. Despite its convenience, the extension poorly describes folding in the absence of force. Here, we chose the contour length of the unfolded polypeptide as a reaction coordinate and modeled the extensions of protein structures along their predicted folding pathways based on high-resolution structures of the proteins in their native states. We included the extension in our model to calculate the total extensions, energies, and transition rates of the proteins as a function of force. We fit these calculations to the corresponding experimental measurements and obtained the best-fit conformations and energies of proteins in different folding states. We applied our method to analyze single-molecule trajectories of two representative protein complexes responsible for membrane fusion, the HIV-1 glycoprotein 41 and the synaptic SNARE proteins, which involved transitions between two and five states, respectively. Nonlinear fitting of the model to the experimental data revealed the structures of folding intermediates and transition states and their associated energies. Our results demonstrate that the contour length is a useful reaction coordinate to characterize protein folding and that intrinsic extensions of protein structures should be taken into account to properly derive the conformations and energies of protein folding intermediates from single-molecule manipulation experiments.

High-accuracy reference standards for two-photon absorption in the 680-1050 nm wavelength range.

Degenerate two-photon absorption (2PA) of a series of organic fluorophores is measured using femtosecond fluorescence excitation method in the wavelength range, λ2PA = 680-1050 nm, and ~100 MHz pulse repetition rate. The function of relative 2PA spectral shape is obtained with estimated accuracy 5%, and the absolute 2PA cross section is measured at selected wavelengths with the accuracy 8%. Significant improvement of the accuracy is achieved by means of rigorous evaluation of the quadratic dependence of the fluorescence signal on the incident photon flux in the whole wavelength range, by comparing results obtained from two independent experiments, as well as due to meticulous evaluation of critical experimental parameters, including the excitation spatial- and temporal pulse shape, laser power and sample geometry. Application of the reference standards in nonlinear transmittance measurements is discussed.

Green fluorescent protein with anionic tryptophan-based chromophore and long fluorescence lifetime.

Spectral diversity of fluorescent proteins, crucial for multiparameter imaging, is based mainly on chemical diversity of their chromophores. Recently we have reported, to our knowledge, a new green fluorescent protein WasCFP-the first fluorescent protein with a tryptophan-based chromophore in the anionic state. However, only a small portion of WasCFP molecules exists in the anionic state at physiological conditions. In this study we report on an improved variant of WasCFP, named NowGFP, with the anionic form dominating at 37°C and neutral pH. It is 30% brighter than enhanced green fluorescent protein (EGFP) and exhibits a fluorescence lifetime of 5.1 ns. We demonstrated that signals of NowGFP and EGFP can be clearly distinguished by fluorescence lifetime in various models, including mammalian cells, mouse tumor xenograft, and Drosophila larvae. NowGFP thus provides an additional channel for multiparameter fluorescence lifetime imaging microscopy of green fluorescent proteins.

Pyrrolo[3,2-b]pyrroles-From Unprecedented Solvatofluorochromism to Two-Photon Absorption.

A combined experimental and theoretical study of the two-photon absorption (2PA) properties of a series of quadrupolar molecules possessing a highly electron-rich heterocyclic core, pyrrolo[3,2-b]pyrrole, is presented. In agreement with quantum-chemical calculations, large 2PA cross-section values, σ2PA ≈10(2) -10(3)  GM (1 GM=10(50)  cm(4) s photon(-1) ), are observed at wavelengths of 650-700 nm, which correspond to the two-photon allowed but one-photon forbidden transitions. The calculations also predict that increased planarity of this molecule through removal of two N-substituents leads to further increase in the σ2PA values. Surprisingly, the most quadrupolar pyrrolo[3,2-b]pyrrole derivative, containing two 4-nitrophenyl substituents at positions 2 and 5, demonstrates a very strong solvatofluorochromic effect, with a fluorescence quantum yield as high as 0.96 in cyclohexane, whereas the fluorescence vanishes in DMSO.

Two-photon voltmeter for measuring a molecular electric field.

We present a new approach for determining the strength of the dipolar solute-induced reaction field, along with the ground- and excited-state electrostatic dipole moments and polarizability of a solvated chromophore, using exclusively one-photon and two-photon absorption measurements. We verify the approach on two benchmark chromophores N,N-dimethyl-6-propionyl-2-naphthylamine (prodan) and coumarin 153 (C153) in a series of toluene/dimethyl sulfoxide (DMSO) mixtures and find that the experimental values show good quantitative agreement with literature and our quantum-chemical calculations. Our results indicate that the reaction field varies in a surprisingly broad range, 0-10(7)  V cm(-1) , and that at close proximity, on the order of the chromophore radius, the effective dielectric constant of the solute-solvent system displays a unique functional dependence on the bulk dielectric constant, offering new insight into the close-range molecular interaction.

Vascular targeting to the SST2 receptor improves the therapeutic response to near-IR two-photon activated PDT for deep-tissue cancer treatment.

BACKGROUND: Broader clinical acceptance of photodynamic therapy is currently hindered by (a) poor depth efficacy, and (b) predisposition towards establishment of an angiogenic environment during the treatment. Improved depth efficacy is being sought by exploiting the NIR tissue transparency window and by photo-activation using two-photon absorption (2PA). Here, we use two-photon activation of PDT sensitizers, untargeted and targeted to SST2 receptors or EGF receptors, to achieve deep tissue treatment. METHODS: Human tumor lines, positive or negative for SST2r expression were used, as well as murine 3LL cells and bovine aortic endothelial cells. Expression of SST2 receptors on cancer cells and tumor vasculature was evaluated in vitro and frozen xenograft sections. PDT effects on tumor blood flow were followed using in vivo scanning after intravenous injection of FITC conjugated dextran 150K. Dependence of the PDT efficacy on the laser pulse duration was evaluated. Effectiveness of targeting to vascular SST2 receptors was compared to that of EGF receptors, or no targeting. RESULTS: Tumor vasculature stained for SST2 receptors even in tumors from SST2 receptor negative cell lines, and SST2r targeted PDT led to tumor vascular shutdown. Stretching the pulse from ~120fs to ~3ps led to loss of the PDT efficacy especially at greater depth. PDT targeted to SST2 receptors was much more effective than untargeted PDT or PDT targeted to EGF receptors. GENERAL SIGNIFICANCE: The use of octreotate to target SST2 receptors expressed on tumor vessels is an excellent approach to PDT with few recurrences and some long term cures.

Two-photon absorption properties of fluorescent proteins.

Two-photon excitation of fluorescent proteins is an attractive approach for imaging living systems. Today researchers are eager to know which proteins are the brightest and what the best excitation wavelengths are. Here we review the two-photon absorption properties of a wide variety of fluorescent proteins, including new far-red variants, to produce a comprehensive guide to choosing the right fluorescent protein and excitation wavelength for two-photon applications.