Dynamics of molecular reorientational motion and vibrational relaxation in liquids. Chloroform

Ultrafast electronic deactivation dynamics of the inosine dimer--a model case for H-bonded purine bases

The structural properties and ultrafast electronic deactivation dynamics of the inosine dimer in CHCl3 have been investigated by two-dimensional (1)H NMR and static FTIR spectroscopy and by femtosecond time-resolved transient absorption spectroscopy, respectively. The (1)H NMR and IR spectra show the formation of a well-defined, symmetric dimer with an association equilibrium constant of KI·I = 690 ± 100 M(-1). The excited-state dynamics after photoexcitation at λpump = 260 nm monitored by ultrafast absorption spectroscopy show great similarity with those of the monomer inosine in an aqueous solution and are governed by a decay time of τ = 90 ± 10 fs, which is one of the shortest electronic lifetimes of all nucleobases and nucleobase dimers studied so far. On the basis of these observations, the inosine dimer is expected to follow a similar relaxation pathway as the monomer, involving an out-of-plane deformation of the six-membered ring. The importance of the C(2) position for the electronic deactivation of hypoxanthine and guanine is discussed. The obtained well-determined structure and straightforward dynamics qualify the inosine dimer as an excellent reference case for more complicated systems such as the G·G dimer and the G·C and A·T Watson-Crick pairs.

Molecular reorientation in hydrogen-bonding liquids: Through algebraic ∼t−3∕2 relaxation toward exponential decay

We present a model for the description of orientational relaxation in hydrogen-bonding liquids. The model contains two relaxation parameters which regulate the intensity and efficiency of dissipation, as well as the memory function which is responsible for the short-time relaxation effects. It is shown that the librational portion of the orientational relaxation is described by an algebraic approximately t(-32) contribution, on top of which more rapid and nonmonotonous decays caused by the memory effects are superimposed. The long-time behavior of the orientational relaxation is exponential, although nondiffusional. It is governed by the rotational energy relaxation. We apply the model to interpret recent molecular dynamic simulations and polarization pump-probe experiments on HOD in liquid D(2)O [C. J. Fecko et al., J. Chem. Phys. 122, 054506 (2005)].

Time-Domain Theoretical Analysis of the Noncoincidence Effect, Diagonal Frequency Shift, and the Extent of Delocalization of the CO Stretching Mode of Acetone/Dimethyl Sulfoxide Binary Liquid Mixtures

A time-domain method for simulating vibrational band profiles that simultaneously takes into account both the diagonal and off-diagonal effects is developed and applied to the C=O stretching bands of neat liquid acetone and the acetone/dimethyl sulfoxide (DMSO) binary liquid mixtures. By using this method, it is possible to examine the influence of liquid dynamics on the noncoincidence effect (NCE), which arises from the off-diagonal vibrational interactions, as well as the frequency shifts and band broadening, which are related to both the diagonal and off-diagonal effects. It is shown that the simulations for the C=O stretching bands of acetone in acetone/DMSO binary liquid mixtures on the basis of this method can reproduce the experimentally observed concave curvature of the concentration dependence of the NCE and the unusually large frequency shift of the anisotropic Raman band. The widths of the infrared, isotropic Raman, and anisotropic Raman bands calculated for neat liquid acetone are also in good agreement with those observed. Based on these calculations, the extent of delocalization of the C=O stretching vibrational motions is examined by referring to two quantitative measures of this property, one calculated in the frequency domain and the other in the time domain. It is shown that the extent of delocalization gets larger as the mole fraction of acetone increases, the C=O stretching vibrations being delocalized over a few tens of molecules in neat liquid acetone. It is also shown that the extent of delocalization is related to the quantity called NCE detectability, which is the ratio between the magnitude of NCE and the bandwidth. It is therefore suggested that the extent of delocalization of vibrational motions may be estimated from observable features of Raman band profiles.

Cytochrome c oxidase: evidence for interaction of water molecules with cytochrome a

The resonance Raman spectra of cytochrome c oxidase in protonated buffer compared to that in deuterated buffer indicate that water molecules are near the heme of cytochrome a. Differences in widths of the heme line at 1610 cm-1, after short exposure to D2O, and, additionally, of the heme line at 1625 cm-1, after long exposure, can be accounted for by changes in resonance vibrational energy transfer between modes of cytochrome a2+ and the bending mode of water molecules in the heme pocket. On the basis of the assignment of these modes, we place one water molecule near the vinyl group and one water molecule near the formyl group of the cytochrome a heme. These water molecules may play several possible functional roles.