2D-IR Spectroscopy of Nitrosyl Stretch of Sodium Nitroprusside Reveals the Elusive Two Anomalous Regions in the DMSO-Water Mixture.

DMSO-water mixtures provide an intriguing hydrogen-bonding environment which has been a subject of various theoretical and experimental investigations. The structural dynamics of aqueous DMSO solutions has been investigated, using nitrosyl stretch of sodium nitroprusside (SNP, Na2[Fe(CN)5NO]) as a local vibrational probe, with the help of infrared (IR) absorption spectroscopy, vibrational pump-probe spectroscopy, and two-dimensional IR spectroscopy (2D-IR). Fourier transform infrared spectra of the nitrosyl stretch of SNP reveals that both the peak position and spectral broadening are very sensitive to the composition of the DMSO-water mixture and the subsequent structural changes occurring due to the addition of DMSO to water. The vibrational lifetime of the nitrosyl stretch displays two different linear variation regimes as a function of mole fraction of DMSO which has been assigned presumably to two different predominant structures at these compositions. However, the rotational depolarization measurements show that the reorientational times follow a bell-shaped profile, imitating the changes in the composition-dependent physical properties (viscosity) of DMSO-water solvent mixtures. To get a holistic picture of the system, 2D-IR spectroscopy of the NO stretch of SNP has been employed to study time scales of hydrogen-bond reorganization dynamics existing at different compositions. The analysis of frequency-frequency correlation function (FFCF) decay times reveal that the dynamics gets slower in intermediate DMSO concentrations than that of pure DMSO or pure water. A careful analysis reveals two anomalous regions of hydrogen-bond dynamics: XDMSO ∼0.2 and 0.4, which indicates that different hydrogen-bonded structures exist in these regions that can be effectively probed by SNP which has remained mostly elusive to previous vibrational probe-based investigations.

Sensing lysozyme fibrils by salicylaldimine substituted BODIPY dyes - A correlation with molecular structure.

Quick and efficient detection of protein fibrils has enormous impact on the diagnosis and treatment of amyloid related neurological diseases. Among several methods, fluorescence based techniques have garnered most importance in the detection of amyloid fibrils due to its high sensitivity and extreme simplicity. Among other classes of molecular probes, BODIPY derivatives have been employed extensively for the detection of amyloid fibrils. However, there are very few studies on the relationship between the molecular structure of BODIPY dyes and their amyloid sensing activity. Here in a BODIPY based salicylaldimine Schiff base and its corresponding boron complex have been evaluated for their ability to sense amyloid fibrils from hen-egg white lysozyme using steady state and time-resolved spectroscopic techniques. Both dyes show fluorescence enhancement as well as increase in their excited state lifetime upon their binding with lysozyme fibrils. However, the BODIPY derivative which shows more emission enhancement in fibrillar solution has much lower affinity towards amyloid fibrils as compared to other derivative. This contrasting behaviour in the emission enhancement and binding affinity has been explained on the basis of differences in their photophysical properties in water and amyloid fibril originating from the difference in their molecular structure. Such correlation between the amyloid sensitivity and the molecular structure of the probe can open up a new strategy for designing new efficient amyloid probes.

Surfactant mediated suppression of aggregation and excited state ring puckering process in Pyrromethene 597-Application in water based dye laser.

Water is being considered as an economical, safe and environmental friendly alternative solvent for dye lasers. However, the use of water in dye laser is restricted due to the formation of non-emissive aggregates of dye molecules. In the present study we have explored the possibility of the use of commercially available surfactant molecules for the water based laser of Pyrromethene 597 (PM597) dye, which has emerged as an alternative for more commonly used Rhodamine dyes in dye laser systems. Our studies show that in water, PM597 forms non-emissive aggregates which can be dissociated into monomeric dye molecules by adding common surfactants. Further, the high microviscosity in the micellar media retarded energy wasting ring puckering process in the excited state of the dye leading to the increase in its emission yield and excited state lifetime to a significant extent. It has been demonstrated that the emission yield and excited state lifetime in surfactant solution is relatively higher than in ethanol, the most commonly used organic solvent for dye lasers. Lasing action has been demonstrated in the aqueous solution of dye and lasing efficiency is found to be comparable to ethanol.

Natural DNA assisted white light generation and stimuli responsive colour tuning.

The unique structure of a natural nucleic acid, calf thymus DNA, which can provide an appropriate scaffold for an efficient cascaded energy transfer among organic chromophores, has been used for the generation of bright and pure white light on UV light excitation. Two most commonly used DNA stains, 4',6-diamidino-2-phenylindole (DAPI) and ethidium bromide (EB) have been used as a part of the donor-acceptor pairs. We have judiciously selected 10-anthracene-10-yl-3-methylbenzothiazol-3-ium chloride (AnMBTZ), an ultrafast molecular rotor, to act as a bridge between DNA bound DAPI and EB for the cascaded flow of energy. The unique molecular rotor properties of AnMBTZ and its exceptional binding ability with natural DNA help to form a distinct tri-chromophoric system in DNA template which can produce bright and pure white light on UV excitation. Detailed flow of energy from photoexcited DAPI to EB via AnMBTZ has been explored using steady state and time-resolved emission spectroscopy. Further, unique binding nature of AnMBTZ with DNA molecules has been used to modulate the colour of the emission from the present tri-chromophoric system by external stimuli, like salt and temperature. Such unique stimuli responsive multi-chromophoric system in a bio-template has great potential for different lightening applications.

Monitoring the formation of insulin oligomers using a NIR emitting glucose-conjugated BODIPY dye.

Protein oligomers, which are formed due to the aggregation of protein molecules under physiological stress, are neurotoxic and responsible for several neurological diseases. Early detection of protein oligomers is essential for the timely intervention in the associated diseases. Although several probes have been developed for the detection of insoluble matured protein fibrils, fluorescent probes with emission in the near infrared (NIR) region for probing protein oligomers are very rare. In the present study we have designed and synthesized a glucose-conjugated BODIPY dye with emission in the NIR spectral range. Our detailed studies show that the new probe is not only capable of detecting matured fibrils but can also probe the formation of oligomers from the native protein. The new probe shows a large increase in its emission intensity upon association with oligomers and matured fibrils. Hence, the present probe has a great potential for the in vivo imaging of protein oligomers and matured fibrils. Detailed spectroscopic properties of the new probes in molecular solvents have been performed to understand its oligomers- and fibril- sensing mechanism.

Is DAPI assay of cellular nucleic acid reliable in the presence of protein aggregates?

DAPI is used extensively to identify and quantify DNA in cellular systems assuming its exclusive staining of nucleic acids. However, the present results show that DAPI has much higher affinity towards protein aggregates than DNA. Thus, the use of DAPI for the nucleic acid assay of cellular systems with protein aggregates may not be very reliable.

SYPRO Orange - a new gold standard amyloid probe.

SYPRO Orange, a zwitterionic merocyanine dye, can strongly interact with amyloid fibrils and shows enormous (∼1200 times) increase in its emission intensity. The sensitivity of the new probe is several times higher than that of the gold standard amyloid probe thioflavin T. Unlike thioflavin-T, the new probe has spectral properties suitable for in vivo imaging with detection sensitivity in the picomolar range.

Ultrafast Dynamics of a Molecular Rotor-Based Bioprobe-PicoGreen: Understanding toward Fibril Sensing Mechanism.

A recent report shows that the cyanine-based molecular rotor, PicoGreen, has very strong affinity toward amyloid fibrils and shows large increase in its emission yield upon binding with insulin amyloid fibrils. To gain deeper knowledge about the excited-state molecular processes that are responsible for its amyloid sensing behavior, detailed ultrafast dynamics of PicoGreen in molecular solvents with varying polarity and viscosity have been investigated. Our detailed studies on femtosecond time-resolved emission of PicoGreen show that both polarity and viscosity of the medium a play vital role in the deactivation of its photoexcited state. Detailed analysis of the time-resolved data suggests the formation of the intramolecular charge transfer (ICT) state, which is independent of solvent viscosity, takes place in ultrafast time scales (<2 ps), followed by the formation of a twisted ICT (TICT) state at a longer time scale in polar solvents. The formation of TICT from the ICT state due to the large amplitude torsional motion in its excited state has been supported by viscosity-dependent excited-state dynamics. Finally, the dynamical studies in fibrillar medium demonstrate the retardation in the excited-state torsional motion, which is primarily responsible for its observed large fluorescence enhancement in insulin amyloid fibrils.

Anthryl Benzothiazolium Molecular Rotor-Based Turn-On DNA Probe: Detailed Mechanistic Studies.

An efficient turn-on fluorescence probe for biomolecules not only helps in its sensitive detection but is also useful to understand the different interactions that are operating between biomolecules and probes. Polycyclic aromatic molecules are known to be strong interacting ligand for DNA and extensively studied as a model cancer drug. However, these molecules show large decrease in their emission intensity, i.e., a turn-off probe for DNA. In the present work, we have synthesized a benzothiazole-based anthracene derivative and studied its interaction with a natural DNA with the aim of having a turn-on DNA probe with a polycyclic aromatic moiety. Our detailed spectroscopic studies show that the new probe strongly interacts with DNA molecules and results in a significant increase in its emission yield. Time-resolved studies show a large increase in probe's excited-state lifetime in DNA solution. Detailed experiments have been performed to understand its mode of interaction with DNA molecules. The mode of interaction has also been supported by the blind molecular docking studies. Further, the viscosity-dependent photophysical properties and detailed quantum chemical calculations confirm that the new probe belongs to molecular rotor class of molecules. Association with DNA molecules results in a significant retardation in the nonradiative deactivation process due to the torsional motion in the excited state of the probe and leads to a significant increase in its emission yield. Thus, due its molecular rotor nature, despite with a turn-off fluorophore unit, anthracene, the new probe, acts as a sensitive turn-on fluorescence probe for DNA molecules.

Disentangling Time Scales of Vibrational Cooling, Solvation, and Hydrogen Bond Reorganization Dynamics Using Ultrafast Transient Infrared Spectroscopy of Formylperylene.

Unraveling dynamics of solvation and hydrogen bond (H-bond) reorganization between a solute and solvent is crucial to understand the importance of specific and nonspecific interactions in a solution-phase chemical reaction. Ultrafast time-resolved infrared (TRIR) spectroscopy provides direct opportunity to monitor site-specific intermolecular dynamics on a real-time scale by probing vibrational marker bands in the excited state of a solute. Herein, we report the real-time dynamics of vibrational cooling, solvation, and hydrogen bond reorganization of formylperylene (FPe) through TRIR spectroscopy of carbonyl (C═O) stretching mode in nonpolar, polar aprotic, and polar protic solvents. High sensitivity of the C═O stretch frequency (υ̅C═O) to photoinduced intramolecular charge transfer processes induced by specific and nonspecific solvent interactions led us to monitor the dynamics of dipolar solvation, site-specific H-bond formation, and reorganization processes by the TRIR method. In nonpolar cyclohexane, the υ̅C═O stretch band appears at 1610 cm-1 and exhibits negligible spectral shift over several tens of picoseconds. In acetonitrile, the υ̅C═O peak shifts to 1594 cm-1 and exhibits a further temporal red shift of about 5 cm-1 with a characteristic solvation time scale of acetonitrile (τ ∼ 0.5 ps). In methanol, υ̅C═O exhibits two bands corresponding to free and H-bonded FPe in early time scale. The free FPe population converts to the hydrogen-bonded population with a lifetime of about 10 ps. Vibrational cooling (τvc ∼ 12-20 ps) in the excited electronic state of FPe could independently be monitored from the temporal dynamics of the ring vibration mode, which is less sensitive to solvation and hydrogen bonding. The present study provides insight into the specific and nonspecific solvation-controlled charge transfer dynamics in aprotic and protic solvents using FPe as a probe.

Polymer-assisted drug sequestration from plasma protein by a surfactant with curtailed denaturing capacity.

The capability of a surfactant to sequester a drug bound to plasma protein was investigated using steady-state and time-resolved spectroscopic techniques. Surfactants are known to denature protein, and hence are not suitable for the sequestration of a drug from protein. Herein, we show that the denaturing capacity of a surfactant is curtailed completely and its drug sequestration power is enhanced in the presence of biocompatible Pluronic micelles due to the formation of unique supramolecular assemblies. Further, our detailed studies indicate that the concentration of surfactant required for the sequestration of a drug is less than its critical micellar concentration (CMC). The extent of sequestration of drug by polymer-surfactant supramolecular assemblies can be tuned finely by controlling the concentration of surfactant. Detailed analysis showed that up to ∼85% sequestration of a drug from plasma protein could be achieved using a sub-CMC concentration of surfactant. Our results clearly show that controlled sequestration of a drug from plasma protein can be achieved with a reduction in the protein denaturing properties of surfactants.

Synergistic enhancement in the drug sequestration power and reduction in the cytotoxicity of surfactants.

Surfactants have often been employed for the sequestration of drugs from DNA. However, for an effective sequestration, the concentration of the surfactant needs to be higher than its critical micellar concentration (CMC). Use of such high concentrations of the surfactant may limit its practical usage as a sequestering agent due to its cytotoxicity. In the present study we have shown that sodium dodecyl sulfate (SDS) itself at a concentration less than its CMC failed to sequester a drug from DNA. However, the sequestration power of SDS at sub-CMC concentration could be enhanced to a significant extent when incorporated into Pluronic polymer micelles in the form of supramolecular assemblies. Such a sequestration process was monitored through detailed photophysical properties of a model drug using steady-state and time-resolved fluorescence techniques. It has also been demonstrated that unlike a conventional surfactant, the sequestration of drugs by SDS-polymer supramolecular assemblies can be controlled by their compositions. Two Pluronic polymers with different compositions have been used to understand the effect of polymer composition on the sequestration process. It has been shown that with the increase in the length of the hydrophilic blocks of the polymer, the extent of sequestration decreases due to the decrease in the sequestering force exerted on the intercalated drug. Most importantly, our in vitro cell viability studies show that the toxicity of the SDS surfactant is reduced to a remarkable extent due to its incorporation into the polymer micelles.

Ultrafast Dynamics of Hydrogen Bond Breaking and Making in the Excited State of Fluoren-9-one: Time-Resolved Visible Pump-IR Probe Spectroscopic Study.

The fluoren-9-one (FL) molecule, with a single hydrogen bond-accepting site (C═O group), has been used as a probe for investigation of the dynamics of a hydrogen bond in its lowest excited singlet (S1) state using the subpicosecond time-resolved visible pump-IR probe spectroscopic technique. In 1,1,1,3,3,3-hexafluoroisopropanol (HFIP), a strong hydrogen bond-donating solvent, the formation of an FL-alcohol hydrogen-bonded complex in the ground electronic (S0) state is nearly complete, with a negligible concentration of the FL molecule remaining free in solution. In addition to the presence of a band due to the hydrogen-bonded complex in the transient IR spectrum recorded immediately after photoexcitation of FL in HFIP solution, appearance of the absorption band due to a free C═O stretch provides confirmatory evidence of ultrafast photodissociation of hydrogen bonds in some of the complexes formed in the S0 state. The peak-shift dynamics of the C═O stretch bands reveal two major relaxation pathways, namely, vibrational relaxation in the S1 state of the free FL molecules and the solvent reorganization process in the hydrogen-bonded complex. The latter process follows bimodal exponential dynamics involving hydrogen bond-making and hydrogen bond-reorganization processes. The similar lifetimes of the S1 states of the FL molecules, both free and hydrogen-bonded, suggest establishment of a dynamic equilibrium between these two species in the excited state. However, investigations in two other weaker hydrogen bond-donating solvents, namely, trifluoroethanol (TFE) and perdeuterated methanol (CD3OD), reveal different features of peak-shift dynamics because of the prominence of the vibrational relaxation process over the hydrogen bond-reorganization process during the early time.

Benzothiazole-Based Neutral Ratiometric Fluorescence Sensor for Amyloid Fibrils.

Early detection of amyloid fibrils is very important for the timely diagnosis of several neurological diseases. Thioflavin-T (ThT) is a gold standard fluorescent probe for amyloid fibrils and has been used for the last few decades. However, due to its positive charge, ThT is incapable of crossing the blood-brain barrier and cannot be used for in vivo imaging of fibrils. In the present work, we synthesized a neutral ThT derivative, 2-[2'-Me,4'-(dimethylamino)phenyl]benzothiazole (2Me-DABT), which showed a strong affinity towards the amyloid fibrils. On association with the amyloid fibrils, 2Me-DABT not only showed a large increase in its emission intensity, but also, unlike ThT, a large blueshift in its emission spectrum was observed. Thus, unlike ThT, 2Me-DABT is a potential candidate for the ratiometric sensor of the amyloid fibrils. Detailed photophysical properties of 2Me-DABT in amyloid fibrils and different solvent media were studied to understand its sensory activity. Fluorescence resonance energy transfer (FRET) studies suggested that the sites of localization for ThT and 2Me-DABT in amyloid fibrils are not same and their average distance of separation in amyloid fibrils was determined. The experimental data was nicely supported by molecular docking studies, which confirmed the binding of 2Me-DABT in the inner core of the amyloid fibrils.

PicoGreen: a better amyloid probe than Thioflavin-T.

PicoGreen, a cyanine based ultrafast molecular rotor, shows high affinity towards amyloid fibrils and scores a much better sensitivity than Thioflavin-T, a gold standard probe for amyloid fibrils. Detailed spectroscopic and molecular docking studies have been performed to understand the mode of interaction between PicoGreen and amyloid fibrils.

Interaction of a Julolidine-Based Neutral Ultrafast Molecular Rotor with Natural DNA: Spectroscopic and Molecular Docking Studies.

Ultrafast molecular rotors (UMRs) are reported to be one of the best fluorescent sensors to study different microenvironments, including biomolecules. In the present work, we have explored the possibility of application of a julolidine-based neutral UMR, 9-(2,2-dicyano vinyl) julolidine (DCVJ), as a DNA sensor and studied its mode of binding with DNA in detail using spectroscopic and molecular docking techniques. Our spectroscopic studies indicate that association of DCVJ with DNA leads to a very large enhancement in its emission intensity. Detailed investigation reveals that, despite being a neutral molecule, binding of DCVJ with DNA is largely modulated in the presence of salt. Such an unusual salt effect has been explained by invoking the ion-dipole interaction between DCVJ and the phosphate backbone of DNA. The ion-dipole interaction has also been established by studying the interaction of DCVJ with nucleosides. Detailed time-resolved studies show that the twisting motion around the vinyl bond in DCVJ gets retarded to a great extent because of its association with DNA molecules. Through competitive binding studies, it has also been established that DCVJ also binds to DNA through intercalation. Finally, quantum chemical calculations and molecular docking studies have been performed to confirm the mode of binding of DCVJ with DNA.

Controlled Sequestration of DNA Intercalated Drug by Polymer-Surfactant Supramolecular Assemblies.

Triblock copolymer and surfactant based supramolecular assemblies have been used for the controlled sequestration of the DNA intercalator. The triblock copolymer micelles do not affect the molecules that are intercalated in the DNA. However, on addition of charged surfactant to the triblock copolymer micellar solution, sequestration of the intercalated molecules from DNA to the polymer-surfactant supramolecular assemblies takes place. Such sequestration of the intercalated molecules in the polymer-surfactant supramolecular assemblies has been explained on the basis of the charged surface formed in the polymer micelles due to the addition of surfactants. Sequestration of the intercalated molecules from the DNA to the polymer-surfactant supramolecular assemblies has been monitored through the ground state absorption, steady state, and time-resolved emission measurements. It is shown that the extent of sequestration of the intercalated molecules can be finely tuned by tuning the concentration of the surfactant in the triblock copolymer solution. Quantitative sequestration of the intercalated molecules by the supramolecular assemblies has been achieved. Such controlled sequestration of the DNA intercalated molecules by polymer-surfactant supramolecular assemblies can be used to study the binding of drug with DNA and may be useful in applications like detoxification in the case of drug overdose.

Ultrafast Torsional Relaxation of Thioflavin-T in Tris(pentafluoroethyl)trifluorophosphate (FAP) Anion-Based Ionic Liquids.

Ultrafast spectroscopy on solutes, whose dynamics is very sensitive to the friction in its local environment, has strong potential to report on the microenvironment existing in complex fluids such as ionic liquids. In this work, the torsional relaxation dynamics of Thioflavin-T (ThT), an ultrafast molecular rotor, is investigated in two fluoroalkylphosphate ([FAP])-based ionic liquids, namely, 1-ethyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate ([EMIM][FAP]) and 1-(2-hydroxyethyl)-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate ([OHEMIM][FAP]), using ultrafast fluorescence up-conversion spectroscopy. The emission quantum yield and the excited-state fluorescence lifetime measurement suggest that the torsional relaxation of Thioflavin-T, in this class of ionic liquids, is guided by the viscosity of the medium. The temporal profile of the dynamic Stokes' shift of ThT, measured from time-resolved emission spectrum (TRES), displays a multiexponential behavior in both ionic liquids. The long time dynamics of the Stokes' shift is reasonably slower for the hydroxyethyl derivative as compared to the ethyl derivative, which is in accordance with their measured shear viscosity. However, the short time dynamics of Stokes' shift is very similar in both the ionic liquids, and seems to be independent of the measured shear viscosity of the ionic liquid. We rationalize these observations in terms of different locations of ThT in these ionic liquids. These results suggest that despite having a higher bulk viscosity in the ionic liquid, they can provide unique microenvironment in their complex structure, where the reaction can be faster than expected from their measured shear viscosity.

Ultrafast fluorescence spectroscopy reveals a dominant weakly-emissive population of fibril bound thioflavin-T.

In this communication, using sub-picosecond resolved fluorescence upconversion spectroscopy, we discover that despite a large fluorescence enhancement observed for thioflavin-T in insulin fibrils, the majority of fibril bound thioflavin-T undergoes efficient ultrafast conformational relaxation, and thus does not contribute to the characteristic fluorescence enhancement.

An ultrafast molecular rotor based ternary complex in a nanocavity: a potential "turn on" fluorescence sensor for the hydrocarbon chain.

Formation of a ternary complex by an ultrafast molecular rotor (UMR) with a macrocyclic cavitand has been investigated for the sensitive detection of the alkyl chain of a surfactant. A benzothiazole based UMR, Thioflavin-T (ThT), has been used as a fluorescent probe. It is shown that ThT forms a very weak inclusion complex with γ-cyclodextrin (γ-CD) with an association constant of 8.8 M(-1). However, the addition of a small amount of surfactant results in a significant increase in the emission intensity of ThT in γ-CD solution. From detailed steady-state and time-resolved fluorescence measurements and NMR studies, it has been inferred that the addition of the surfactant results in the formation of a ternary complex through the inclusion of its alkyl chain inside the γ-CD nanocavity. In such a ternary complex, the non-radiative torsional motion in ThT is largely prevented due to a large increase in the frictional force inside the nanocavity and results in a significant fluorescence enhancement. The formation of the binary and the ternary complexes in the present system has been further supported by the molecular docking and subsequent molecular dynamics simulation studies. The present result indicates that the inclusion complex with an UMR as a guest could be a potential candidate for the efficient detection of insoluble organic molecules, especially hydrocarbons.