Vibrational Relaxation of OH and CH Fundamentals of Polar and Nonpolar Molecules in the Condensed Phase

Shortwave infrared polymethine dyes for bioimaging: ultrafast relaxation dynamics and excited-state decay pathways

Excited-state relaxation in two prototypical shortwave infrared (SWIR) polymethine dyes developed for bioimaging, heptamethine chromenylium Chrom7 and flavylium Flav7, is studied by means of femtosecond transient absorption with broadband ultraviolet-to-SWIR probing complemented by steady-state and time-resolved fluorescence and phosphorescence measurements. The relaxation processes of the dyes in dichloromethane are resolved with sub-100 fs temporal resolution using SWIR, near-IR, and visible photoexcitation. Different population members of the ground-state inhomogeneous ensemble are found to equilibrate via skeletal deformation changes with time constants of 90 fs and either 230 fs (Chrom7) and 350 fs (Flav7) followed by slower evolution matching the 1-ps timescale of diffusive solvation dynamics. Molecules excited into high-lying singlet electronic states (Sn) by visible excitation repopulate with time constants of 400 fs (Chrom7) and 450 fs (Flav7) the corresponding first excited singlet S1 states, which decay within several hundreds of picoseconds in dichloromethane and chloroform solvents. Vibrational relaxation in S1 for both Chrom7 and Flav7 in dichloromethane occurs with time constants of 350 and 800 fs for excess of vibrational energy of ∼1000 and 10 000 cm-1 deposited by near-IR and visible excitation, respectively. Two competing non-radiative processes are present in S1: temperature-independent internal conversion, and thermally-activated twisting about a carbon-carbon bond of the conjugated chain, which is substantial at room temperature but essentially nonreactive, producing traces of isomer product. Intersystem crossing in S1, and thus the triplet quantum yield, is minor. The importance of absorption bands from the excited S1 state in applications requiring high-intensity excitation conditions is discussed.

Vibrational Lifetime of the SCN Protein Label in H2O and D2O Reports Site-Specific Solvation and Structure Changes During PYP's Photocycle

The application of vibrational labels such as thiocyanate  (-S-C≡N) for studying protein structure and dynamics is thriving. Absorption spectroscopy is usually employed to obtain wavenumber and line shape of the label. An observable of great significance might be the vibrational lifetime, which can be obtained by pump probe or 2D-IR spectroscopy. Due to the insulating effect of the heavy sulfur atom in the case of the SCN label, the lifetime of the C≡N oscillator is expected to be particularly sensitive to its surrounding as it is not dominated by through-bond relaxation. We therefore investigate the vibrational lifetime of the SCN label at various positions in the blue light sensor protein Photoactive Yellow Protein (PYP) in the ground state and signaling state of the photoreceptor. We find that the vibrational lifetime of the C≡N stretching mode is strongly affected both by its protein environment and by the degree of exposure to the solvent. Even for label positions where the line shape and wavenumber observed by FTIR are barely changing upon activation of the photoreceptor, we find that the lifetime can change considerably. To obtain an unambiguous measure for the solvent exposure of the labeled site, we show that it is imperative to compare the lifetimes in H₂O and D₂O. Importantly, the lifetimes shorten in H₂O as compared to D₂O for water exposed labels, while they stay largely the same for buried labels. We quantify this effect by defining a solvent exclusion coefficient (SEC). The response of the label's vibrational lifetime to its solvent exposure renders it a suitable universal probe for protein investigations. This applies even to systems that are otherwise hard to address, such as transient or short-lived states, which could be created during a protein's working cycle (as here in PYP) or during protein folding. It is also applicable to flexible systems (intrinsically disordered proteins), protein-protein and protein-membrane interactions.

Density functional theory study of the OH, Cl and H2O coadsorption on the step-defect Al2O3 film surface

Density functional theory has been performed on the step-defect Al2O3 film surfaces with the OH, Cl and H2O molecules coadsorption. Three kinds of step-defect (Al, O2, Al3) surfaces are optimized and the adsorption energy, the binding energies of film and adsorbates are calculated. The energy properties are similar in H2O or Cl coadsorption configurations, but have obvious differences for the OH group coadsorption configuration due to large numbers of adsorbate species and numbers. After structural relaxation, most of the step-defect surfaces could be easily hydroxylated. The Al3 step-defect surfaces are easier to be corroded by H2O and coadsorption molecules due to lots of unsaturated dangling bonds, some H2O molecules are located into the step-defect, surface Al atoms collapse inside the steps and several inner O atoms move outside the film. When the Cl exists in the aqueous solution, it would restrict H2O molecules from dissociating into OH groups. Moreover, the dissociation and recombination of H2O molecules could be promoted by OH groups.

Labelling and determination of the energy in reactive intermediates in solution enabled by energy-dependent reaction selectivity

Any long-lived chemical structure in solution is subject to statistical energy equilibration, so the history of any specific structure does not affect its subsequent reactions. This is not true for very short-lived intermediates, since energy equilibration takes time. Here, this idea is applied to achieve the energy labeling of a reactive intermediate. The selectivity of the ring-opening α-cleavage reaction of 1-methylcyclobutoxy radical is found here to vary broadly depending on how the radical was formed. Reactions that provide little excess energy to the intermediate lead to high selectivity in the subsequent cleavage (measured as a kinetic isotope effect) while reactions that provide more excess energy to the intermediate exhibit lower selectivity. Allowing for the expected excess energy allows the prediction of the observed product ratios, and in turn the product ratios can be used to obtain a read-out of the energy present in a intermediate.

Vibrational dynamics and solvatochromism of the label SCN in various solvents and hemoglobin by time dependent IR and 2D-IR spectroscopy

The vibrational label SCN is used to report on local structural dynamics in a protein revealing spectral diffusion on a picosecond scale. The SCN spectra are compared to the response of methylthiocyanate in solvents with different polarity and hydrogen-bonding capabilities.

Vibrational relaxation of chloroiodomethane in cold argon

Electronically exciting the C-I stretch in the molecule chloroiodomethane CH2ClI embedded in a matrix of argon at 12 K can lead to an isomer, iso-chloroiodomethane CH2Cl-I, that features a chlorine iodine bond. By temporally probing the isomer at two different frequencies of 435 nm and 485 nm, multiple timescales for isomerization and vibrational energy relaxation were inferred [T. J. Preston, et al., J. Chem. Phys. 135, 114503 (2011)]. This relaxation is studied theoretically using molecular dynamics by considering 2 and 3 dimensional models. Multiple decay rate constants of the same order of magnitude as the experiment are observed. These decay rate constants are interpreted within the context of the Landau-Teller theory. Sensitivity of the decay rate constants on the bath and system parameters shed more light into the mechanism of vibrational energy relaxation.

Tracking energy transfer from excited to accepting modes: application to water bend vibrational relaxation

We extend, via a reformulation in terms of Poisson brackets, the method developed previously (Rey et al., J. Phys. Chem. A, 2009, 113, 8949) allowing analysis of the pathways of an excited molecule's ultrafast vibrational relaxation in terms of intramolecular and intermolecular contributions. In particular we show how to ascertain, through the computation of power and work, which portion of an initial excess molecular energy (e.g. vibrational) is transferred to various degrees of freedom (e.g. rotational, translational) of the excited molecule itself and its neighbors. The particular case of bend excess energy relaxation in pure water is treated in detail, completing the picture reported in the work cited above. It is shown explicitly, within a classical description, that almost all of the initial water bend excitation energy is transferred-either indirectly, via Fermi resonance centrifugal coupling to the bend-excited water's rotation, or directly via intermolecular coupling- to local water librations, only involving molecules in the first two hydration shells of the vibrationally excited water molecule. Finally, it is pointed out that the Poisson bracket formulation can also be applied to elucidate the microscopic character of solvation and rotational dynamics, and should prove useful in developing a quantum treatment for energy flow in condensed phases.