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The recognition of intrinsically disordered proteins (IDPs) is highly dependent on dynamics owing to the lack of structure. Here we studied the interplay between dynamics and molecular recognition in IDPs with a combination of time-resolving tools on timescales ranging from femtoseconds to nanoseconds. We interrogated conformational dynamics and surface water dynamics and its attenuation upon partner binding using two IDPs, IBB and Nup153FG, both of central relevance to the nucleocytoplasmic transport machinery. These proteins bind the same nuclear transport receptor (Importinß) with drastically different binding mechanisms, coupled folding-binding and fuzzy complex formation, respectively. Solvent fluctuations in the dynamic interface of the Nup153FG-Importinß fuzzy complex were largely unperturbed and slightly accelerated relative to the unbound state. In the IBB-Importinß complex, on the other hand, substantial relative slowdown of water dynamics was seen in a more rigid interface. These results show a correlation between interfacial water dynamics and the plasticity of IDP complexes, implicating functional relevance for such differential modulation in cellular processes, including nuclear transport.

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Spontaneous polarization of a nonpolar molecule upon photoexcitation (the sudden polarization effect) earlier discussed for 90°-twisted alkenes is observed and calculated for planar ring-fluorinated stilbenes, trans-2,3,5,6,2',3',5',6'-octofluorostilbene (tF2356) and trans-2,3,4,5,6,2',3',4',5',6'-decafluorostilbene (tF23456). Due to the fluorination, Franck-Condon states S1FC and S2FC are dominated by the quasi-degenerate HOMO-1 → LUMO and HOMO-2 → LUMO excitations, while their interaction gives rise to a symmetry-broken zwitterionic S1 state. After optical excitation of tF2356, one observes an ultrafast (∼0.06 ps) evolution that reflects relaxation from initial nonpolar S3FC to long-lived (1.3 ns in n-hexane and 3.4 ns in acetonitrile) polar S1. The polarity of S1 is evidenced by a solvatochromic shift of its fluorescence band. The experimental results provide a sensitive test for quantum-chemical calculations. In particular, our calculations agree with the experiment, and raise concerns about the applicability of the common TDDFT approach to relatively simple stilbenic systems.

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We monitor the time-dependent Stokes shift (TDSS) of fluorescence from the zwitterionic probe N-methyl-6-oxyquinolinium betaine in water. A spectral relaxation time τsolv = 0.57 ps (at 20.5 °C) is attributed to a solvation process involving water in the hydration layer. In this article we show that a tertiary butyl group, when attached to the chromophore, slows the dynamics to τsolv = 0.76 ps and increases the corresponding activation energy by 5 kJ/mol. In a companion paper (10.1021/acs.jpcb.7b05039), simulations suggest that the observed slow-down indicates coupling of solute vibrations to hydration water. Thus, a new angle on a thoroughly researched topic, solvation dynamics, has been opened.

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A 13mer DNA duplex containing the artificial 4-aminophthalimide:2,4-diaminopyrimidine (4AP:DAP) base pair in the central position was characterized by optical and NMR spectroscopy. The fluorescence of 4AP in the duplex has a large Stokes shift of Δλ=124 nm and a quantum yield of ΦF =24 %. The NMR structure shows that two interstrand hydrogen bonds are formed and confirms the artificial base pairing. In contrast, the 4-N,N-dimethylaminophthalimide moiety prefers the syn conformation in DNA. The fluorescence intensity of this chromophore in DNA is very low and the NMR structure shows no significant interaction with DAP. Primer-extension experiments with DNA polymerases showed that not only is the 4AP C nucleotide incorporated at the desired position opposite DAP in the template, but also that the polymerase is able to progress past this position to give the full-length product. The observed selectivity supports the NMR results.

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In the photoisomerization path of stilbene, a perpendicular state P on the S1 potential energy surface is expected just before internal conversion through a conical intersection S1/S0. For decades the observation of P was thwarted by a short lifetime τP in combination with slow population flow over a barrier. But these limitations can be overcome by ethylenic substitution. Following optical excitation of trans-1,1'-dicyanostilbene, P is populated significantly (τP = 27 ps in n-hexane) and monitored by an exited-state absorption band at 370 nm. Here we report stimulated Raman lines of P. The strongest, at 1558 cm-1, is attributed to stretching vibrations of the phenyl rings. Transient electronic states, resonance conditions, and corresponding Raman signals are discussed.

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Sum frequency mixing of fluorescence and ∼1300 nm gate pulses, in a thin ß-barium borate crystal and non-collinear type II geometry, is quantified as part of a femtosecond fluorimeter [X.-X. Zhang et al., Rev. Sci. Instrum. 82, 063108 (2011)]. For a series of fixed phasematching angles, the upconversion efficiency is measured depending on fluorescence wavelength. Two useful orientations of the crystal are related by rotation around the surface normal. Orientation A has higher efficiency (factor ∼3) compared to B at the cost of some loss of spectral coverage for a given crystal angle. It should be used when subtle changes of an otherwise stationary emission band are to be monitored. With orientation B, the fluorescence range λF > 420-750 nm is covered with a single setting of the crystal and less gate scatter around time zero. The accuracy of determining an instantaneous emission band shape is demonstrated by comparing results from two laboratories.

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ß-Carotene in n-hexane was examined by femtosecond transient absorption and stimulated Raman spectroscopy. Electronic change is separated from vibrational relaxation with the help of band integrals. Overlaid on the decay of S1 excited-state absorption, a picosecond process is found that is absent when the C9 -methyl group is replaced by ethyl or isopropyl. It is attributed to reorganization on the S1 potential energy surface, involving dihedral angles between C6 and C9 . In Raman studies, electronic states S2 or S1 were selected through resonance conditions. We observe a broad vibrational band at 1770 cm(-1) in S2 already. With 200 fs it decays and transforms into the well-known S1 Raman line for an asymmetric C=C stretching mode. Low-frequency activity (<800 cm(-1) ) in S2 and S1 is also seen. A dependence of solvent lines on solute dynamics implies intermolecular coupling between ß-carotene and nearby n-hexane molecules.

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Raman scattering with stimulating femtosecond probe pulses (FSR) was used to observe vibrational activity of all-trans ß-carotene in n-hexane. The short-lived excited electronic state S2 was accessed in two ways: (i) by transient FSR after an actinic pulse to populate the S2 state, exploiting resonance from an Sx ← S2 transition, and (ii) by FSR without actinic excitation, using S2 ↔ S0 resonance exclusively and narrow-band Raman/broad-band femtosecond probe pulses only. The two approaches have nonlinear optical susceptibilities χ((5)) and χ((3)), respectively. Both methods show low-frequency bands of the S2 state at 200, 400, and ∼600 cm(-1), which are reported for the first time. With (ii) the intensities of low-frequency vibrational resonances in S2 are larger compared to those in S0, implying strong anharmonicities/mode mixing in the excited state. In principle, for short-lived electronic states, the χ((3)) method should allow the best characterization of low-frequency modes.

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Solvation and rotational dynamics of 4-aminophthalimide (4AP) in four ionic liquids (ILs) are measured using a combination of fluorescence upconversion spectroscopy and time-correlated single photon counting. These data are compared with previously reported data for coumarin 153 (C153) to investigate the probe dependence of solvation dynamics. No fast component (<15 ps) in the fluorescence anisotropy is observed with 4AP. The differences between the solvation response functions of 4AP and C153 are significant in all four ILs, but these differences can be reduced by applying a correction for solute rotation using measured emission anisotropies. Response functions of other probes available in the literature are used to further examine the validity of this correction. The corrected data are also compared to predictions of dielectric continuum models of solvation. By replacing the measured static conductivity of the ILs with an estimated value, such predictions show good agreement with the observed spectral response functions, especially when the anion size is small.

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Solvation energies, rotation times, and 100 fs to 20 ns solvation response functions of the solute coumarin 153 (C153) in mixtures of 1-butyl-3-methylimidazolium tetrafluoroborate ([Im41][BF4]) + acetonitrile (CH3CN) at room temperature (20.5 °C) are reported. Available density, shear viscosity, and electrical conductivity data at 25 °C are also collected and parametrized, and new data on refractive indices and component diffusion coefficients presented. Solvation free energies and reorganization energies associated with the S0 ↔ S1 transition of C153 are slightly (≤15%) larger in neat [Im41][BF4] than in CH3CN. No clear evidence for preferential solvation of C153 in these mixtures is found. Composition-dependent diffusion coefficients (D) of Im41(+) and CH3CN as well as C153 rotation times (τ) are approximately related to solution viscosity (η) as D, τ ∝ η(p) with values of p = -0.88, -0.77, and +0.90, respectively. Spectral/solvation response functions (Sν(t)) are bimodal at all compositions, consisting of a subpicosecond fast component followed by a broadly distributed slower component extending over ps-ns times. Integral solvation times (⟨τ(solv)⟩ = ∫(0)(∞)Sν(t) dt) follow a power law on viscosity for mixturecompositions 0.2 ≤ x(IL) ≤ 1 with p = 0.79. With recent broad-band dielectric measurements [J. Phys. Chem. B 2012, 116, 7509] asinput, a simple dielectric continuum model provides predictions for solvation response functions that correctly capture thedistinctive bimodal character of the observed response. At x(IL) ∼ 1 predicted values of ⟨τ(solv)⟩ are smaller than those observed by a factor of 2-3, but the two become approximately equal at x(IL) = 0.2. Predictions of a recent semimolecular theory [J. Phys. Chem. B 2011, 115, 4011] are less accurate, being uniformly slower than the observed solvation dynamics.

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The terahertz (THz) absorption bands of biomolecular hydration layers are generally swamped by absorption from bulk water. Using the disaccharide trehalose, we show that this limitation can be overcome by attaching a molecular probe. By time-resolving the fluorescence shift of the probe, a local THz spectrum is obtained. From the dependence on temperature and H2O/D2O exchange, it is concluded that the trehalose hydration layer is being observed. The region of dynamic water perturbation by the disaccharide encompasses the probe and is therefore larger than the first two solvation layers.

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The solvation dynamics of molecular probes is studied by broad-band fluorescence upconversion. The time-dependent position of the S1 → S0 emission band or of a vibronic line shape is measured with ~80 fs, 10 cm(-1) resolution. Polar solutes in acetonitrile and acetone, when excited into S1 with excess vibrational energy, show a dynamic Stokes shift which extends to the red beyond the quasistationary state. Equilibrium is then reached by a slower blue shift on a 10 ps time scale. In methanol, excess vibrational energy as large as ~14,000 cm(-1) shows no such effect. Nonpolar solutes exhibit an excess red shift of the emission band in both polar and nonpolar solvents even upon excitation near the vibronic origin. The observed dynamics are discussed in terms of transient heating of the excited chromophore, conformational change, and changes of the molecular cavity size. For solvation studies the optical excitation should be chosen close to the band origin.

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Excited-state protonation of riboflavin in the oxidized form is studied in water. In the -1 < pH < 2 range, neutral and N(1)-protonated riboflavin coexist in the electronic ground state. Transient absorption shows that the protonated form converts to the ground state in <40 fs after optical excitation. Broadband fluorescence upconversion is therefore used to monitor solvation and protonation of the neutral species in the excited singlet state exclusively. A weak fluorescence band around 660 nm is assigned to the product of protonation at N(5). Its radiative rate and quantum yield relative to neutral riboflavin are estimated. Protonation rates agree with proton diffusion times for H(+) concentrations below 5 M but increase at higher acidities, where the average proton distance is below the diameter of the riboflavin molecule.

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The 4-aminophthalimide C-nucleoside 1 was designed as an isosteric DNA base surrogate, and a synthetic route to nucleoside 1 together with the 2,4-diaminopyrimidine-C-nucleoside 2 as a potential counterbase was worked out. The key steps in both synthetic routes represent a stereoselective Heck-type palladium-catalyzed cross-coupling with 2'-deoxyribofuranoside glycal followed by stereoselective reduction with NaBH(OAc)3. The nucleoside 1 shows a solvatofluorochromic behavior and significantly red-shifted fluorescence in solvents of high polarity and with hydrogen bonding capabilities. Both nucleosides 1 and 2 can be further processed to the corresponding phosphoramidite as DNA building blocks that allow incorporation of these chromophores as artificial DNA bases by automated DNA synthesis. The combination of the poor stacking properties of 1 and the hydrogen bonding interface at the phthalimide functionality that does not fit to any of natural DNA bases in the counterstrand yields destabilization of the duplex by 4-11 °C. The fluorescence of 1 in a representative double stranded DNA is characterized by a large Stokes' shift and a quantum yield of approximately 12%. These are remarkable optical properties considering the very small size of the chromophore and indicate a high potential of these nucleoside analogues for fluorescent DNA analytics and imaging.

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It was shown recently that a simple dielectric continuum model predicts the integral solvation time of a dipolar solute ⟨τsolv⟩ to be inversely proportional to the electrical conductivity σ0 of an ionic solvent or solution. In this Letter, we provide a more general derivation of this connection and show that available data on coumarin 153 (C153) in ionic liquids generally support this prediction. The relationship between solvation time and conductivity can be expressed by ln(⟨τsolv⟩/ps) = 4.37 - 0.92 ln (σ0/S m(-1)) in 34 common ionic liquids.

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The dynamic Stokes shift of coumarin 153, measured with a combination of broad-band fluorescence upconversion (80 fs resolution) and time-correlated single photon counting (to 20 ns), is used to determine the complete solvation response of 21 imidazolium, pyrrolidinium, and assorted other ionic liquids. The response functions so obtained show a clearly bimodal character consisting of a subpicosecond component, which accounts for 10-40% of the response, and a much slower component relaxing over a broad range of times. The times associated with the fast component correlate with ion mass, confirming its origins in inertial solvent motions. Consistent with many previous studies, the slower component is correlated to solvent viscosity, indicating that its origins lie in diffusive, structural reorganization of the solvent. Comparisons of observed response functions to the predictions of a simple dielectric continuum model show that, as in dipolar solvents, solvation and dielectric relaxation involve closely related molecular dynamics. However, in contrast to dipolar solvents, dielectric continuum predictions systematically underestimate solvation times by factors of at least 2-4.

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The photoisomerisation of 1,1'-diethyl-2,2'-pyridocyanine, regarded by Brooker as the simplest cyanine, is examined in methanol by time-resolved experiments and PCM/TD-CAM-B3LYP calculations. Femtosecond transient absorption, fluorescence upconversion, and stimulated Raman scattering, all with broadband coverage, provide a panoramic view of the photoreaction. On the computational side, evolving distributions on an S(1) minimum-energy path are obtained by solving the Smoluchowski equation for drift and diffusion of torsional motion. Absorption and fluorescence bandshapes are calculated and compared to the observations; near-quantitative agreement implies that the entire S(1) path has been observed. Most importantly the global S(1) minimum, i.e. the perpendicular "phantom state" P*, can be identified and characterized in this way. Internal conversion of P* (3.7 ps), assisted by solvent equilibration, leads to the hot ground state. Within 5 ps, vibrational bands of cis and trans isomers are recognized with the help of calculated Raman spectra. The differences between observed and simulated spectra are discussed.

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The complete solvation response of coumarin 153 (C153) has been determined over the range 10(-13)-10(-8) s in a variety of ionic liquids by combining femtosecond broad-band fluorescence upconversion and picosecond time-correlated single photon counting measurements. These data are used together with recently reported dielectric data in eight ionic liquids to test the accuracy of a simple continuum model for predicting solvation dynamics. In most cases the features of the solvation response functions predicted by the dielectric continuum model are similar to the measured dynamics of C153. The predicted dynamics are, however, systematically faster than those observed, on average by a factor of 3-5. Computer simulations of a model solute/ionic liquid system also exhibit the same relationship between dielectric predictions and observed dynamics. The simulations point to spatial dispersion of the polarization response as an important contributor to the over-prediction of solvation rates in ionic liquids.

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