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 D of all the species in the solutions at 298.2 K, 1H and 19F 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 (C12mimTFSA), with three molecular liquids (MLs) of chloroform (CL), benzene (BZ), and propylene carbonate (PC) as a function of ML mole fraction xML. Below xML ≈ 0.8, the D values of each species do not significantly depend on the MLs. However, above this mole fraction, the diffusion of C153 becomes smoother in the order of BZ ≈ CL > PC systems. The interactions among C153, C12mim+, TFSA-, and ML molecules have been investigated using infrared (IR) and 1H and 13C NMR spectroscopic techniques. The relations of the diffusion of the species with the interactions among them have been discussed on the molecular scale. In the IL solution, the C153 carbonyl oxygen atom is hydrogen-bonded with the imidazolium ring C2-H atom of C12mim+. C12mim+ also forms an ion pair with TFSA-. Thus, C153, C12mim+, and TFSA- cooperatively move in the CL and BZ solutions at a lower ML content, xML < ∼0.8. On the other hand, at a higher ML content, xML > ∼0.8, the C153 molecule diffuses with CL and BZ molecules because of the hydrogen bonding between the C153 carbonyl O atom and the CL H atom and the π-π interaction between the C153 and BZ ring planes, respectively. For the PC system, the change in the relative self-diffusion coefficients of each species with increasing xML differs from those for the CL and BZ systems because of both hydrogen bonding donor H and acceptor O atoms of PC for C153, the IL cation and anion, and PC themselves.

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. We give also the typical fluorescence spectra as well as the fluorescence lifetimes of the probable emitting species. In this work we put forward new insights concerning the contribution of free morin to the fluorescence. We hope that these new data improve the accuracy of the interpretation of the cation:morin complexes titration using fluorescence signal.

Dynamics in the BMIM PF6/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 PF6) 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. In our approximation of the slow picosecond dynamics with a multi-exponential decay, we distinguish three relaxation times. The highest two are assigned to the reorientation of the cation and acetonitrile molecules that are in the vicinity of the imidazolium ring. The third one is recognized as originating from cation rotations and reorientation of acetonitrile molecules in the bulk or in the vicinity of the aliphatic chains of the cation. With help of the simulation we interpret the intermolecular band in the reduced spectral density, obtained from Kerr signal, as follows: its low-frequency side results from oscillations of one of the components in the cage formed by its neighbors, while the high-frequency side is attributed to the librations of the cation and acetonitrile molecule as well as the intermolecular oscillations of system components involved in specific interactions. We use this assignment and concentration dependence of the spectra obtained from velocity and angular velocity correlations to explain the mole fraction dependence of Kerr reduced spectral density.

The local structure in the BmimPF6/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. All the other interactions and geometry parameters of the ions (i.e., Lennard-Jones, bond stretching, angle bending and dihedral parameters) are identical in the two cases. The effect of the fractional charge distribution on the hydrogen bonding between the counterions themselves and between the ions and solvent molecules, as well as on the stacking interactions between the cations, is analyzed. To this end, two distances, characteristic of the hydrogen bond formed by the donor moiety and its nearest neighbor acceptor, as well as a coordinate system that defines unambiguously the orientation between a reference cation and its nearest neighbor, are introduced. It is shown that, with the variable charge model, the neighboring cation-anion pairs maintain their relative arrangement similar to the neat ionic liquid down to an ionic liquid mole fraction of xIL = 0.10, whereas in the case of the constant charge model such changes occur already at xIL = 0.20. Furthermore, the analysis of the first and the second nearest neighbor distance distributions of an anion around a reference cation indicates that, at this mole fraction range, there are two different preferred arrangements of the anions around the cations. In the first one, similarly to the local structure around a reference cation in the neat ionic liquid, the anion forms a distorted hydrogen bond with the cation, while in the second one the anion is located farther from the cation, forming no hydrogen bond with it. The relative population of these two types of preferred nearest neighbor cation-anion arrangements is found to be sensitive to further decrease of the ionic liquid mole fraction. These findings correlate with experimental results concerning the behavior of many physical chemical properties (e.g., excess volume, excess viscosity, chemical shift, infrared and Raman vibrational mode shifts, diffusion, etc.) that were found to undergo a drastic change in this mole fraction range. Our results show that in this composition range a transition occurs from the situation where the macroscopic physical chemical properties of the system are determined primarily by the cation-anion hydrogen bonding interactions to that where they are determined by the solvation of the cation and the anion by the molecular solvent.

Local structure of dilute aqueous DMSO solutions, as seen from molecular dynamics simulations.

The information about the structure of dimethyl sulfoxide (DMSO)-water mixtures at relatively low DMSO mole fractions is an important step in order to understand their cryoprotective properties as well as the solvation process of proteins and amino acids. Classical MD simulations, using the potential model combination that best reproduces the free energy of mixing of these compounds, are used to analyze the local structure of DMSO-water mixtures at DMSO mole fractions below 0.2. Significant changes in the local structure of DMSO are observed around the DMSO mole fraction of 0.1. The array of evidence, based on the cluster and the metric and topological parameters of the Voronoi polyhedra distributions, indicates that these changes are associated with the simultaneous increase of the number of DMSO-water and decrease of water-water hydrogen bonds with increasing DMSO concentration. The inversion between the dominance of these two types of H-bonds occurs around XDMSO = 0.1, above which the DMSO-DMSO interactions also start playing an important role. In other words, below the DMSO mole fraction of 0.1, DMSO molecules are mainly solvated by water molecules, while above it, their solvation shell consists of a mixture of water and DMSO. The trigonal, tetrahedral, and trigonal bipyramidal distributions of water shift to lower corresponding order parameter values indicating the loosening of these orientations. Adding DMSO does not affect the hydrogen bonding between a reference water molecule and its first neighbor hydrogen bonded water molecules, while it increases the bent hydrogen bond geometry involving the second ones. The close-packed local structure of the third, fourth, and fifth water neighbors also is reinforced. In accordance with previous theoretical and experimental data, the hydrogen bonding between water and the first, the second, and the third DMSO neighbors is stronger than that with its corresponding water neighbors. At a given DMSO mole fraction, the behavior of the intensity of the high orientational order parameter values indicates that water molecules are more ordered in the vicinity of the hydrophilic group while their structure is close-packed near the hydrophobic group of DMSO.

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 (pKR+ =20.4, Ered1/2 =-0.72 V) compared to its azaoxa 2 (pKR+ =15.2, Ered1/2 =-0.45 V) and dioxa 1 (pKR+ =8.8, Ered1/2 =-0.12 V) analogues. The fluorescence of these cationic chromophores is established, and ranges from the orange to the far-red regions. From 1 to 3, a bathochromic shift of the lowest energy transitions (up to 614 nm in acetonitrile) and an enhancement of the fluorescence quantum yields and lifetimes (up to 31 % and 9.8 ns, respectively, at 658 nm) are observed. The triplet quantum yields and circularly polarized luminescence are also reported. Finally, fine tuning of the optical properties of the diaza [6]helicene core is achieved through selective and orthogonal post-functionalization reactions (12 examples, compounds 4-15). The electronic absorption is modulated from the orange to the far-red spectral range (560-731 nm), and fluorescence is observed from 591 to 755 nm with enhanced quantum efficiency up to 70 % (619 nm). The influence of the peripheral auxochrome substituents is rationalized by first-principles calculations.

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). These probes are positioned inside the DNA/RNA structures as a replacement for one of the natural bases, thus, providing unique control of their position and orientation and the advantage of reporting from inside sites of interest. In demonstration studies, not requiring molecular dynamics modelling, we obtain previously inaccessible insight into the orientation and nanosecond dynamics of the bases inside double-stranded DNA, and we reconstruct high resolution 3D structures of kinked DNA. The reported methodology is accompanied by a freely available software package, FRETmatrix, for the design and analysis of FRET in nucleic acid containing systems.

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. Furthermore, the analogues containing nitrogen in the 8-position showed a more red-shifted and structured absorption as opposed to those which have a carbon incorporated in the same position. Compared to the previously characterised C8-triazole modified adenine, the emissive potential was significantly lower (tenfold or more) for this new family of triazoles-adenine compounds. However, three of the compounds have photophysical properties which will make them interesting to monitor inside DNA.

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. Through our analysis, we discovered a peculiar behavior of several photophysical properties at low IL mole fractions (0 < XIL < 0.2). Indeed, in this range of mixture composition, the absorption maximum wavelength decreases noticeably, while the emission maximum wavelength and the Stokes shift, expressed in wavenumbers, reach a maximum. while a minimum occurs in the relative quantum yield and the excited state lifetime. These results indicate that the solvation of dye undergoes a large change in this range of mixture composition. We found that, at high ionic liquid content, the excited relaxation times are correlated with the high viscosity, while at low content, it is the polarity of the solvent that influences the behavior of the excited relaxation times. At a mixture composition of around 0.10, the behavior of the photophysical properties of the studied IL-MS mixtures indicates a crossover between situations where the solvation is dominated by that of ions and that dominated by the solvent.

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 (C4mim+) combined with perfluorinated anions, such as tetrafluoroborate (BF4-), hexafluorophosphate (PF6-), 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 0.2. Distributions of metric properties corresponding to the Voronoi polyhedra of the particles (volume assigned to the particles, local density, radius of spherical voids) are determined, using representative sites of the cations, anions, and the solvent molecules, to characterize the changes in the local structure of these mixtures. By analyzing the mole fraction dependence of the average value, fluctuation, and skewness parameter of these distributions, the present study reveals that, around the IL mole fraction of 0.2, the local structure of the mixture undergoes a transition between that determined by the interionic interactions and that determined by the interactions between the ions and solvent molecules. It should be noted that the strength of the interactions between the ions and the solvent molecules, modulated by the change in the composition of the mixture, plays an important role in the occurrence of this transition. The signature of the change in the local structure is traced back to the nonlinear change of the mean values, fluctuations, and skewness values of the metric Voronoi polyhedra distributions.

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. In DNA qA serves as an adenine analogue that preserves the B-form and, in contrast to most currently available FBAs, maintains or even increases the stability of the duplex. We demonstrate that, unlike fluorescent adenine analogues, such as the most commonly used one, 2-aminopurine, and the recently developed triazole adenine, qA shows highly specific base-pairing with thymine. Moreover, qA has an absorption band outside the absorption of the natural nucleobases (>300 nm) and can thus be selectively excited. Upon excitation the qA monomer displays a fluorescence quantum yield of 6.8 % with an emission maximum at 456 nm. More importantly, upon incorporation into DNA the fluorescence of qA is significantly less quenched than most FBAs. This results in quantum yields that in some sequences reach values that are up to fourfold higher than maximum values reported for 2-aminopurine. To facilitate future utilisation of qA in biochemical and biophysical studies we investigated its fluorescence properties in greater detail and resolved its absorption band outside the DNA absorption region into distinct transition dipole moments. In conclusion, the unique combination of properties of qA make it a promising alternative to current fluorescent adenine analogues for future detailed studies of nucleic acid-containing systems.

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. These findings, in association with recent studies on model duplexes, are explained by the involvement of dark states, possibly related to charge separation, serving as a reservoir for the repopulation of the bright pi pi* states.

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. The initial fluorescence anisotropy after excitation at 267 nm is lower than 0.2 for all emission wavelengths, indicating an ultrafast S(2) --> S(1) internal conversion. The fluorescence decays depend strongly on the emission wavelength, getting longer with the wavelength. A rise time of 100-150 fs was observed for wavelengths longer than 450 nm, in accordance with a gradual red shift of the time-resolved spectra. The results are discussed in terms of a relaxation occurring mainly on the lowest excited (1)pi pi*-state surface toward a conical intersection with the ground state, in line with recent theoretical predictions. Our results show that the excited-state population undergoes a substantial "spreading out" before reaching the CI, explaining the complex dynamics observed.

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 (C4mim) cation, coupled with tetrafluoroborate (BF4), hexafluorophosphate (PF6), 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 (NpT) 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. The inhomogeneity distribution of ions around the ring, methyl, and butyl chain terminal hydrogen atoms of the C4mim cation was investigated by means of Voronoi polyhedra analysis. For this purpose, the position of the C4mim cation was described successively by the ring, methyl, and butyl chain terminal hydrogen atoms, while that of the anions was described by their F or O atom. We calculated the Voronoi polyhedra distributions of the volume, the density, and the asphericity parameters as well as that of the radius of the spherical intermolecular voids. We carried out the analysis in two steps. In the first step, both ions were taken into account. The calculated distributions gave information on the neighboring ions around a reference one. In the second step, to distinguish between like and oppositely charged ions and then to get information on the inhomogeneity distribution of the like ions, we repeated the same calculations on the same sample configurations and removed one of the ions and considered only the other one. Detailed analysis of these distributions has revealed that the ring hydrogen atoms are mainly solvated by the anions, while the methyl and butyl terminal H atoms are surrounded by like atoms. The extent of this inhomogeneity was assessed by calculating the cluster size distribution that shows that the dimers are the most abundant ones.

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 (BmimBF4), hexafluorophosphate (BmimPF6), 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 (H2,4,5) and the nearest high-electronegativity atom of the solvent or anion (X) as distance descriptors, and the mean angle formed by the C2,4,5-H2,4,5 bond and the H2,4,5···X axis around the H2,4,5 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 obtained results show that the extent of the change of these descriptors with respect to their values in the neat ionic liquid depends both on the nature of the anion and on the mixture composition. Thus, in the case of the mixtures of the molecular solvents with BmimBF4 and BmimTFO, a small change of the distance and a drastic increase of the angular descriptor corresponding to the cation-anion interactions are observed with decreasing mole fraction of the ionic liquid, indicating that the anion moves from the above/below position (with respect to the imidazolium ring plane) to a position that is nearly linearly aligned with the C2-H2 bond and hinders the possible interaction between the C2-H2 group and the solvent molecules. On the other hand, in the case of mixtures of BmimTFSI and BmimPF6 with the molecular solvents, both the observed increase of the distance descriptor and the slight change of the angular descriptor with decreasing ionic liquid mole fraction are compatible with the direct interactions of the solvent with the C2-H2 group. The behavior of these descriptors is correlated with the experimentally observed 1H chemical shift of the C2-H2 group and the red shift of the C2-H2 vibrational mode, particularly at low ionic liquid mole fractions. The present results are thus of great help in interpreting these experimental observations.

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. This contrasts with the behavior of duplexes composed exclusively of adenine-thymine base pairs, for which an overall lengthening of the fluorescence lifetimes with respect to that of an equimolar mixture of dAMP and TMP was reported previously. Despite the difference in the excited-state deactivation rate between the two types of duplexes, the signature of ultrafast energy transfer is present in both of them. It is attested by the decrease of fluorescence anisotropy decay of the duplexes on the subpicosecond time scale, where molecular motions are inhibited, and is corroborated by the fact that their steady-state fluorescence spectra do not change with the excitation wavelength. Energy transfer involves excited states delocalized over at least two bases, whose existence is revealed by the UV absorption spectrum of the duplex, clearly different from that of an equimolar spectrum of dGMP and dCMP.

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.

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. We have characterised the RNA association and activity of the human Pus1p enzyme with its unusual SRA substrate. We validate that the minimal RNA fragment within SRA, named H7, is necessary for both the association and modification by hPus1p. Furthermore, we have determined the crystal structure of the catalytic domain of hPus1p at 2.0 Å resolution, alone and in a complex with several molecules present during crystallisation. This model shows an extended C-terminal helix specifically found in the eukaryotic protein, which may prevent the enzyme from forming a homodimer, both in the crystal lattice and in solution. Our biochemical and structural data help to understand the hPus1p active site architecture, and detail its particular requirements with regard to one of its nuclear substrates, the non-coding RNA SRA.