Effect of Mixture Composition on the Photophysics of Indoline Dyes in Imidazolium Ionic Liquid-Molecular Solvent Mixtures: A Femtosecond Transient Absorption Study.

We conducted a study on the photophysics of three indoline dyes, D102, D149, and D205, in binary mixtures of ionic liquids (IL) and polar aprotic molecular solvents (MS). Specifically, we examined the behavior of these dyes in IL-MS mixtures containing four different imidazolium-based ILs and three different polar aprotic MSs. Our investigation involved several techniques, including stationary absorption and emission measurements, as well as femtosecond transient absorption (TA) spectroscopy.

Solvation structure and dynamics of coumarin 153 in an imidazolium-based ionic liquid with chloroform, benzene, and propylene carbonate.

In order to determine the self-diffusion coefficients of all the species in the solutions at 298.2 K, H and F NMR diffusion ordered spectroscopy (DOSY) has been conducted on coumarin 153 (C153) in binary mixed solvents of an imidazolium-based ionic liquid (IL), 1-dodecyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide (CmimTFSA), with three molecular liquids (MLs) of chloroform (CL), benzene (BZ), and propylene carbonate (PC) as a function of ML mole fraction . Below ≈ 0.

Insight to the Local Structure of Mixtures of Imidazolium-Based Ionic Liquids and Molecular Solvents from Molecular Dynamics Simulations and Voronoi Analysis.

While the physicochemical properties as well as the NMR and vibration spectroscopic data of the mixtures of ionic liquids (ILs) with molecular solvents undergo a drastic change around the IL mole fraction of 0.2, the local structure of the mixtures pertaining to this behavior remains unclear. In this work, the local structure of 12 mixtures of 1-butyl-3-methylimidazolium cation (Cmim) combined with perfluorinated anions, such as tetrafluoroborate (BF), hexafluorophosphate (PF), trifluoromethylsulfonate (TFO), and bis(trifluoromethanesulfonyl)imide, (TFSI), and aprotic dipolar solvents, such as acetonitrile (AN), propylene carbonate (PC), and gamma butyrolactone (γ-BL) is studied by molecular dynamics simulations in the entire composition range, with an emphasis on the IL mole fractions around 0.

Voronoi Polyhedra as a Tool for the Characterization of Inhomogeneous Distribution in 1-Butyl-3-methylimidazolium Cation-Based Ionic Liquids.

The inhomogeneity distribution in four imidazolium-based ionic liquids (ILs) containing the 1-butyl-3-methylimidazolium (Cmim) cation, coupled with tetrafluoroborate (BF), hexafluorophosphate (PF), bis(trifluoromethanesulfonyl)amide (TFSA), and trifluoromethanesulfonate (TfO) anions, was characterized using Voronoi polyhedra. For this purpose, molecular dynamic simulations have been performed on the isothermal-isobaric () ensemble. We checked the ability of the potential models to reproduce the experimental density, heat of vaporization, and transport properties (diffusion and viscosity) of these ionic liquids.

Dynamics in the BMIM PF/acetonitrile mixtures observed by femtosecond optical Kerr effect and molecular dynamics simulations.

We have performed the measurements of the optical Kerr effect signal time evolution up to 4 ns for a mixture of 1-alkyl-3-methyl-imidazolium hexafluorophosphate (BMIM PF) ionic liquid and acetonitrile in the whole mole fractions range. The long delay line in our experimental setup allowed us to capture the complete reorientational dynamics of the ionic liquid. We have analysed the optical Kerr effect signal in the time and frequency domains with help of molecular dynamics simulations.

A Picosecond Time-Resolved Spectroscopic Investigation of the Effect of pH on Morin Fluorescence.

In this work, we investigated for the first time morin in MeOH at different pH values by picosecond time-resolved fluorescence. We identified the two species responsible for the fluorescence at low and high pH. The solvated morin-solvent hydrogen-bonded complex has been experimentally observed for the first time.

Distance Angle Descriptors of the Interionic and Ion-Solvent Interactions in Imidazolium-Based Ionic Liquid Mixtures with Aprotic Solvents: A Molecular Dynamics Simulation Study.

The aim of this paper is to quantify the changes of the interionic and ion-solvent interactions in mixtures of imidazolium-based ionic liquids, having tetrafluoroborate (BmimBF), hexafluorophosphate (BmimPF), trifluoromethylsulfonate (BmimTFO), or bis(trifluoromethanesulfonyl)imide (BmimTFSI), anions, and polar aprotic molecular solvents, such as acetonitrile (AN), γ-butyrolactone (GBL), and propylene carbonate (PC). For this purpose, we calculate, using the nearest-neighbor approach, the average distance between the imidazolium ring H atom in positions 2, 4, and 5 (H) and the nearest high-electronegativity atom of the solvent or anion (X) as distance descriptors, and the mean angle formed by the C-H bond and the H···X axis around the H atom as angular descriptors of the cation-anion and cation-solvent interactions around the ring C-H groups. The behavior of these descriptors as a function of the ionic liquid mole fraction is analyzed in detail.

The local structure in the BmimPF/acetonitrile mixture: the charge distribution effect.

The changes of the local structure in the binary mixture of 1-butyl-3-methylimidazolium hexafluorophosphate (BmimPF6) ionic liquid and acetonitrile are investigated over the entire composition range. Two charge distribution models of the ions are considered: in the first one, the atomic fractional charges of the cations and anions are kept equal with those in the neat ionic liquid, and hence they are independent from the mole fraction of the ionic liquid, while in the second one the charge distribution is scaled up by a mole fraction dependent factor. The sum of these charges converge to +1e and -1e on the cation and anion, respectively, at infinite dilution.

Physicochemical and Electronic Properties of Cationic [6]Helicenes: from Chemical and Electrochemical Stabilities to Far-Red (Polarized) Luminescence.

The physicochemical properties of cationic dioxa (1), azaoxa (2), and diaza (3) [6]helicenes demonstrate a much higher chemical stability of the diaza adduct 3 (pK =20.4, Ered1/2 =-0.72 V) compared to its azaoxa 2 (pK =15.

Direct coupling of carbenium ions with indoles and anilines for the synthesis of cationic π-conjugated dyes.

A C-C bond forming reaction occurs spontaneously between tris-(2,6-dimethoxyphenyl)carbenium ions and indoles/anilines. The carbocation acts both as an electrophile and an oxidant. Effective cationic π-conjugated dyes are formed resulting in a strong hyper- and bathochromism.

Synthesis and photophysical characterisation of new fluorescent triazole adenine analogues.

Fluorescent nucleic acid base analogues are powerful probes of DNA structure. Here we describe the synthesis and photo-physical characterisation of a series of 2-(4-amino-5-(1H-1,2,3-triazol-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl) and 2-(4-amino-3-(1H-1,2,3-triazol-4-yl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl) analogues via Sonogashira cross-coupling and [3 + 2]-cycloaddition reactions as the key steps in the synthesis. Compounds with a nitrogen atom in position 8 showed an approximately ten-fold increase in quantum yield and decreased Stokes shift compared to analogues with a carbon atom in position 8.

Steroid receptor RNA activator (SRA) modification by the human pseudouridine synthase 1 (hPus1p): RNA binding, activity, and atomic model.

The most abundant of the modified nucleosides, and once considered as the "fifth" nucleotide in RNA, is pseudouridine, which results from the action of pseudouridine synthases. Recently, the mammalian pseudouridine synthase 1 (hPus1p) has been reported to modulate class I and class II nuclear receptor responses through its ability to modify the Steroid receptor RNA Activator (SRA). These findings highlight a new level of regulation in nuclear receptor (NR)-mediated transcriptional responses.

FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids.

Förster resonance energy transfer (FRET) is a technique commonly used to unravel the structure and conformational changes of biomolecules being vital for all living organisms. Typically, FRET is performed using dyes attached externally to nucleic acids through a linker that complicates quantitative interpretation of experiments because of dye diffusion and reorientation. Here, we report a versatile, general methodology for the simulation and analysis of FRET in nucleic acids, and demonstrate its particular power for modelling FRET between probes possessing limited diffusional and rotational freedom, such as our recently developed nucleobase analogue FRET pairs (base-base FRET).

A fluorescence-based assay for monitoring clinical drug resistance.

Background And Aims: Multidrug resistance (MDR) limits effectiveness in treating malignancy by modifying internalisation and/or externalisation of drugs through cancer cell membranes. In this study we describe an assay to monitor patients' responses to chemotherapy.

Methods: The assay is based on the fluorescent properties of doxorubicin alone as well as in combination with methotrexate, vinblastine, doxorubicin and cisplatin (MVAC).

Quadracyclic adenine: a non-perturbing fluorescent adenine analogue.

Fluorescent-base analogues (FBAs) comprise a group of increasingly important molecules for the investigation of nucleic acid structure and dynamics as well as of interactions between nucleic acids and other molecules. Here, we report on the synthesis, detailed spectroscopic characterisation and base-pairing properties of a new environment-sensitive fluorescent adenine analogue, quadracyclic adenine (qA). After developing an efficient route of synthesis for the phosphoramidite of qA it was incorporated into DNA in high yield by using standard solid-phase synthesis procedures.

Fluorescence of natural DNA: from the femtosecond to the nanosecond time scales.

The fluorescence of calf thymus DNA is studied by steady-state and time-resolved spectroscopy combining fluorescence upconversion and time-correlated single photon counting. The fluorescence spectrum is very similar to that of a stoichiometric mixture of monomeric chromophores, arising from bright pi pi* states, and contrasts with the existing picture of exciplex emission in natural DNA. Yet, the DNA fluorescence decays span over five decades of time, with 98% of the photons being emitted at times longer than 10 ps.

Excited-state dynamics of dGMP measured by steady-state and femtosecond fluorescence spectroscopy.

The room-temperature fluorescence of 2'-deoxyguanosine 5'-monophosphate (dGMP) in aqueous solution is studied by steady-state and time-resolved fluorescence spectroscopy. The steady-state fluorescence spectrum of dGMP shows one band centered at 334 nm but has an extraordinary long red tail, extending beyond 700 nm. Both the fluorescence quantum yield and the relative weight of the 334 nm peak increase with the excitation wavelength.

Ultrafast excited-state deactivation and energy transfer in guanine-cytosine DNA double helices.

The DNA double helix poly(dGdC).poly(dGdC) is studied by fluorescence upconversion spectroscopy with femtosecond resolution. It is shown that the excited-state relaxation of the duplex is faster than that of the monomeric components dGMP and dCMP.