The dynamics of dimethyl sulfoxide (DMSO)/water solutions with a wide range of water concentrations are studied using polarization selective infrared pump–probe experiments, two-dimensional infrared (2D IR) vibrational echo spectroscopy, optical heterodyne detected optical Kerr effect (OHD-OKE) experiments, and IR absorption spectroscopy. Vibrational population relaxation of the OD stretch of dilute HOD in H2O displays two vibrational lifetimes even at very low water concentrations that are associated with water–water and water–DMSO hydrogen bonds. The IR absorption spectra also show characteristics of both water–DMSO and water–water hydrogen bonding. Although two populations are observed, water anisotropy decays (orientational relaxation) exhibit single ensemble behavior, indicative of concerted reorientation involving water and DMSO molecules. OHD-OKE experiments, which measure the orientational relaxation of DMSO, reveal that the DMSO orientational relaxation times are the same as orientational relaxation times found for water over a wide range of water concentrations within experimental error. The fact that the reorientation times of water and DMSO are basically the same shows that the reorientation of water is coupled to the reorientation of DMSO itself. These observations are discussed in terms of a jump reorientation model. Frequency–frequency correlation functions determined from the 2D IR experiments on the OD stretch show both fast and slow spectral diffusion. In analogy to bulk water, the fast component is assigned to very local hydrogen bond fluctuations. The slow component, which is similar to the slow water reorientation time at each water concentration, is associated with global hydrogen bond structural randomization.

The long time scale orientational relaxation of nematogens in the isotropic phase is associated with the randomization of pseudonematic domains, which have a correlation length that grows as the isotropic-to-nematic phase transition temperature is approached from above. Here we begin to address the fast dynamics of the nematogen molecules within the domains using two-dimensional infrared (2D IR) vibrational echo experiments. The problems of performing ultrafast IR experiments in pure liquids are discussed, and solutions are presented. In addition, the issue of short vibrational lifetimes, which limit the ability of 2D IR experiments to examine dynamics over a wide range of times, is addressed. The experiments were performed on the nematogen 4-cyano-4'-pentylbiphenyl (5CB), with the CN stretch initially used as the vibrational probe. Although the CN stretch has a small transition dipole, because the sample is a pure liquid it is necessary to use an exceedingly thin sample to perform the experiments. The small sample volume leads to massive heating effects that distort the results. In addition, the high concentration in the pure liquid can result in vibrational excitation transfer that interferes with the measurements of structural dynamics, and the CN vibrational lifetime is very short (3.6 ps). These problems were overcome by performing the experiments on the natural-abundance (13)CN stretch (5(13)CB), which greatly reduced the absorbance, eliminating the heating problems; also, this stretch has a longer lifetime (7.9 ps). Experiments were also performed on benzonitrile, which showed that the heating problems associated with pure liquids are not unique to 5CB. Again, the problems were eliminated by conducting measurements on the (13)CN stretch, which has an even longer lifetime (20.2 ps) compared with the (12)CN stretch (5.6 ps). Finally, to extend the range of the dynamical measurements, 4-pentyl-4'-thiocyanobiphenyl (5SCB) was synthesized and studied as a dilute solute in 5CB. The CN stretch of 5SCB has a vibrational lifetime of 103 ps, which permits dynamical measurements to 200 ps, revealing the full range of fast structural dynamics in the isotropic phase of 5CB. It is shown that the 5SCB probe reports essentially the same dynamics as 5(13)CB on the short time scale that is observable with the 5(13)CB vibrational probe.

The isotropic phase of nematogenic liquid crystals has nanometer length scale domains with pseudonematic ordering. As the isotropic to nematic phase transition temperature (TNI) is approached from above, the orientational correlation length, ξ, of the pseudonematic domains grows as (T - T(*))(-1/2), where T(*) is 0.5-1 K below TNI. The orientational relaxation, which is a collective property of the pseudonematic domains, was measured with optical heterodyne detected-optical Kerr effect (OHD-OKE). The orientational relaxation obeys Landau-de Gennes theory, as has been shown previously. To examine the environmental evolution experienced by molecules in the pseudonematic domains, two-dimensional infrared (2D IR) vibrational echo experiments on the CN stretching mode of the non-perturbative vibrational probes 4-pentyl-4(')-selenocyanobiphenyl (5SeCB) and 4-pentyl-4(')-thiocyanobiphenyl (5SCB) in the nematogen 4-cyano-4(')-pentylbiphenyl (5CB) were performed. The 2D IR experiments measure spectral diffusion, which is caused by structural fluctuations that couple to the CN vibrational frequency. Temperature dependent studies were performed just above TNI, where the correlation length of pseudonematic domains is large and changing rapidly with temperature. These studies were compared to 2D IR experiments on 4-pentylbiphenyl (5B), a non-mesogenic liquid that is very similar in structure to 5CB. The time constants of spectral diffusion in 5CB and 5B are practically identical at temperatures ≥5 K above TNI. As the temperature is lowered, spectral diffusion in 5B slows gradually. However, the time constants for spectral diffusion in 5CB slow dramatically and diverge as T(*) is approached. This divergence has temperature dependence proportional to (T - T(*))(-1/2), precisely the same as seen for the correlation length of pseudonematic domains, but different from the observed orientational relaxation times, which are given by the Landau-de Gennes theory. The data and previous results show that spectral diffusion in 5CB has no contributions from orientational relaxation, and the structural dynamics responsible for the spectral diffusion are likely a result of density fluctuations. The results suggest that the correlation length of the density fluctuations is diverging with the same temperature dependence as the pseudonematic domain correlation length, ξ. The isotropic-nematic phase transition in liquid crystals is described in the context of the slowing of orientational relaxation associated with divergent growth of the orientational correlation length. The results presented here show that there is another divergent dynamical process, likely associated with density fluctuations.

Binding of a cis,syn-cyclobutane pyrimidine dimer (CPD) to Escherichia coli DNA photolyase was examined as a function of temperature, enzyme oxidation state, salt, and substrate conformation using isothermal titration calorimetry. While the overall ΔG° of binding was relatively insensitive to most of the conditions examined, the enthalpic and entropic terms that make up the free energy of binding are sensitive to the conditions of the experiment. Substrate binding to DNA photolyase is generally driven by a negative change in enthalpy. Electrostatic interactions and protonation are affected by the oxidation state of the required FAD cofactor and substrate conformation. The fully reduced enzyme appears to bind approximately two additional water molecules as part of substrate binding. More significantly, the experimental change in heat capacity strongly suggests that the CPD lesion must be flipped out of the intrahelical base stacking prior to binding to the protein; the DNA repair enzyme appears to recognize a solvent-exposed CPD as part of its damage recognition mechanism.

Nematogen liquids in the isotropic phase are macroscopically homogeneous but on multinanometer length scales have pseudonematic domains with correlation lengths that grow as the isotropic to nematic phase transition temperature (TNI) is approached from above. Orientational relaxation of nematogens in the isotropic phase manifests as two fast power laws and a slow exponential decay when measured by optical heterodyne detected optical Kerr effect (OHD-OKE) experiments. The long time exponential relaxation is associated with complete randomization of pseudonematic domains. We examine the effect of local orientational correlation on spectral diffusion (structural evolution) experienced by a vibrational probe molecule within the pseudonematic domains of 4-cyano-4'-pentylbiphenyl (5CB) using two-dimensional infrared (2D IR) vibrational echo spectroscopy. The addition of low concentration 4-pentyl-4'-thiocyanobiphenyl (5SCB) as a long-lived vibrational probe to 5CB is shown to lower TNI of the sample slightly, but the fast power law dynamics and exponential decays observed by OHD-OKE spectroscopy are unchanged. We compare the complete orientational relaxation and spectral diffusion for samples of 5SCB in 5CB to 5SCB in 4-pentylbiphenyl (5B) at four temperatures above TNI. 5B has a molecular structure similar to 5CB but is not a nematogen. At all but the lowest temperature, the spectral diffusion in 5CB and 5B is described well as a triexponential decay with very similar time constants. The results demonstrate that the presence of local orientational order at temperatures well above TNI does not affect the spectral diffusion (structural evolution) within pseudonematic domains when the correlation lengths are short. However, when the temperature of the sample is held very close to TNI, the spectral diffusion in 5CB slows dramatically while that in 5B does not. It is only as the correlation length becomes very long that its presence impacts the spectral diffusion (structural fluctuations) sensed by the vibrational probes located in pseudonematic domains. The orientational relaxation is modeled with schematic mode coupling theory (MCT). Fitting with MCT provides density and orientational correlation functions. The density correlation decays are similar for 5B and 5CB, but the orientational correlation decays are much slower for 5CB. Additionally, the time dependence of the spectral diffusion in 5CB is strikingly similar to that of the density correlation function decay, while the orientational correlation function decay is far too slow to contribute to the spectral diffusion. Therefore, density fluctuations are likely the source of spectral diffusion at temperatures at least 5 K above TNI.

Escherichia coli DNA photolyase and cryptochrome 1 isolated from Vibrio cholerae, a member of the CRY-DASH family, are directly compared using a variety of experimental methods including UV-vis and Raman spectroscopy, reduction potential measurements, and isothermal titration calorimetry. The semiquinone form of the cryptochrome has an absorption spectrum that is red-shifted from that of the photolyase, but the Raman spectrum indicates that the FAD binding pocket is similar to that of photolyase. The FADH(-)/FADH* reduction potential of the cryptochrome is significantly higher than that of the photolyase at 164 mV vs NHE, but it also increases upon substrate binding (to 195 mV vs NHE), an increase similar to what is observed in photolyase. The FADH(-)/FADH* reduction potential for both proteins was found to be insensitive to ATP binding. Isothermal titration calorimetry found that photolyase binds tighter to substrate (K(A) approximately 10(5) M(-1) for photolyase and approximately 10(4) M(-1) for cryptochrome 1), and the binding constants for both proteins were slightly sensitive to oxidation state. Based upon this work, it appears that this cryptochrome has significant spectroscopic and electrochemical similarities to CPD photolyase. The thermodynamic cycle of the enzymatic repair in the context of this work is discussed.

The dynamics of supercooled liquids of the molecular glass formers benzophenone and ortho-terphenyl were investigated with 2D IR spectroscopy using long-lived vibrational probes. The long lifetimes of the probes enabled structural dynamics of the liquids to be studied from a few hundred femtoseconds to a nanosecond. 2D IR experiments measured spectraldiffusion of a vibrational probe, which reports on structural fluctuations of the liquid. Analysis of the 2D IR data provides the frequency-frequency correlation function (FFCF). Two vibrational probes were examined with equivalent results, demonstrating the observed liquid dynamics are not significantly influenced by the probe molecules. At higher temperatures, the FFCF is a biexponential decay. However, at mild supercooling, the biexponential decay is no longer sufficient, indicating a dynamic crossover. The crossover occurs at a temperature well above the mode-coupling theory critical temperature for the given liquid, indicating dynamic heterogeneity above the critical temperature. Examination of the low temperature data with lifetime density analysis shows that the change is best described as an additional, distinct relaxation that shows behavior consistent with a slow β-process.

Two-dimensional infrared (2D IR) data are presented for a vibrational probe in three nematogens: 4-cyano-4'-pentylbiphenyl, 4-cyano-4'-octylbiphenyl, and 4-(trans-4-amylcyclohexyl)-benzonitrile. The spectral diffusion time constants in all three liquids in the isotropic phase are proportional to [T*/(T - T*)](1/2), where T* is 0.5-1 K below the isotropic-nematic phase transition temperature (TNI). Rescaling to a reduced temperature shows that the decays of the frequency-frequency correlation function (FFCF) for all three nematogens fall on the same curve, suggesting a universal dynamic behavior of nematogens above TNI. Spectral diffusion is complete before significant orientational relaxation in the liquid, as measured by optically heterodyne detected-optical Kerr effect (OHD-OKE) spectroscopy, and before any significant orientational randomization of the probe measured by polarization selective IR pump-probe experiments. To interpret the OHD-OKE and FFCF data, we constructed a mode coupling theory (MCT) schematic model for the relationships among three correlation functions: ϕ1, a correlator for large wave vector density fluctuations; ϕ2, the orientational correlation function whose time derivative is the observable in the OHD-OKE experiment; and ϕ3, the FFCF for the 2D IR experiment. The equations for ϕ1 and ϕ2 match those in the previous MCT schematic model for nematogens, and ϕ3 is coupled to the first two correlators in a straightforward manner. Resulting models fit the data very well. Across liquid crystals, the temperature dependences of the coupling constants show consistent, nonmonotonic behavior. A remarkable change in coupling occurs at ∼5 K above TNI, precisely where the rate of spectral diffusion in 5CB was observed to deviate from that of a similar nonmesogenic liquid.