Femtosecond wave packet spectroscopy: Coherences, the potential, and structural determination

Recently, we presented a formalism for extracting highly resolved spectral information and the potential of bound isolated systems from coherent ultrafast laser experiments, using I2 as a model system [Gruebele et al., Chem. Phys. Lett. 166, 459 (1990)]. The key to this approach is the formation of coherent wave packets on the potential energy curve (or surface) of interest, and the measurement of their scalar and vector properties. Here we give a full account of the method by analyzing the coherences of the wave packet in the temporal transients of molecules excited by ultrashort laser pulses, either at room temperature, or in a molecular beam. From this, some general considerations for properly treating temporal data can be derived. We also present a direct inversion to the potential and quantum and classical calculations for comparison with the experiments

Femtosecond probing of bimolecular reactions: The collision complex

Progress has been made in probing the femtosecond dynamics of transition states of chemical reactions.(1) The "half-collision" case of unimolecular reactions has been experimentally investigated for a number of systems and much theoretical work has already been developed.(2) For bimolecular reactions, the case of full collision, the zero of time is a problem which makes the femtosecond temporal resolution of the dynamics a difficult task

Femtosecond real-time probing of reactions. VIII. The bimolecular reaction Br+I2

In this paper, we discuss the experimental technique for real-time measurement of the lifetimes of the collision complex of bimolecular reactions. An application to the atom–molecule Br+I_2 reaction at two collision energies is made. Building on our earlier Communication [J. Chem. Phys. 95, 7763 (1991)], we report on the observed transients and lifetimes for the collision complex, the nature of the transition state, and the dynamics near threshold. Classical trajectory calculations provide a framework for deriving the global nature of the reactive potential energy surface, and for discussing the real-time, scattering, and asymptotic (product-state distribution) aspects of the dynamics. These experimental and theoretical results are compared with the extensive array of kinetic, crossed beam, and theoretical studies found in the literature for halogen radical–halogen molecule exchange reactions

Femtosecond real-time probing of reactions. V. The reaction of IHgI

The dissociation reaction of HgI2 is examined experimentally using femtosecond transition-state spectroscopy (FTS). The reaction involves symmetric and antisymmetric coordinates and the transition-state is well-defined: IHgI*-->[IHgI][double-dagger]@B|Q[sub S[script ']]Q[sub a[script ']]q-->HgI+I. FTS is developed for this class of ABA-type reactions and recurrences are observed for the vibrating fragments (symmetric coordinate) along the reaction coordinate (antisymmetric coordinate). The translational motion is also observed as a "delay time" of the free fragments. Analysis of our FTS results indicates that the reaction wave packet proceeds through two pathways, yielding either I(2P3/2) or I*(2P1/2) as one of the final products. Dissociation into these two pathways leads to HgI fragments with different vibrational energy, resulting in distinct trajectories. Hence, oscillatory behaviors of different periods in the FTS transients are observed depending on the channel probed (~300 fs to ~1 ps). These results are analyzed using the standard FTS description, and by classical trajectory calculations performed on model potentials which include the two degrees of freedom of the reaction. Quantum calculations of the expected fluorescence of the fragment are also performed and are in excellent agreement with experiments

Vibrational energy relaxation in proteins

An overview of theories related to vibrational energy relaxation (VER) in proteins is presented. VER of a selected mode in cytochrome c is studied using two theoretical approaches. One is the equilibrium simulation approach with quantum correction factors, and the other is the reduced model approach which describes the protein as an ensemble of normal modes interacting through nonlinear coupling elements. Both methods result in estimates of the VER time (sub ps) for a CD stretching mode in the protein at room temperature. The theoretical predictions are in accord with the experimental data of Romesberg's group. A perspective on future directions for the detailed study of time scales and mechanisms for VER in proteins is presented.Comment: 12 pages, 4 figures, accepted for publication in PNA

Extended Gaussian wave packet dynamics

We examine an extension to the theory of Gaussian wave packet dynamics in a one-dimensional potential by means of a sequence of time dependent displacement and squeezing transformations. Exact expressions for the quantum dynamics are found, and relationships are explored between the squeezed system, Gaussian wave packet dynamics, the time dependent harmonic oscillator, and wave packet dynamics in a Gauss-Hermite basis. Expressions are given for the matrix elements of the potential in some simple cases. Several examples are given, including the propagation of a non-Gaussian initial state in a Morse potential

Protein folding mediated by solvation: water expelling and formation of the hydrophobic core occurs after the structure collapse

The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is achieved before water is expelled from the hydrophobic core. This view integrates water expulsion effects into the funnel energy landscape theory of protein folding. Comparisons to experimental results are shown for the SH3 protein. After the folding transition, a near-native intermediate with partially solvated hydrophobic core is found. This transition is followed by a final step that cooperatively squeezes out water molecules from the partially hydrated protein core.Comment: Proceedings of the National Academy of Science, 2002, Vol.99. 685-69

Determination of the Born–Oppenheimer potential function of CCl+ by velocity modulation diode laser spectroscopy

Over 70 transitions among the lowest six vibrational states of C35Cl+ and C37Cl+ have been measured between 1070–1210 cm^−1. The spectrum has been fitted to a sixth order Dunham expansion to yield an accurate mapping of the Born–Oppenheimer potential function of CCl+. The spectroscopic constants obtained are ωe = 1177.7196(8) cm^−1, ωexe = 6.6475(3) cm^−1, and Be = 0.797 940(3) cm^−1. The rotational constants for both CCl+ isotopes reported here show the results of the previous electronic emission studies to be incorrect. A fit of the data to a Morse function yields a dissociation energy D of 52 828(50) cm^−1. The rotational temperature has been determined as 540 K±30%. The increase in the effective vibrational temperature with vibrational excitation indicates that CCl+ is formed with high internal energy