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

Intramolecular vibrational energy redistribution as state space diffusion: Classical-quantum correspondence

We study the intramolecular vibrational energy redistribution (IVR) dynamics of an effective spectroscopic Hamiltonian describing the four coupled high frequency modes of CDBrClF. The IVR dynamics ensuing from nearly isoenergetic zeroth-order states, an edge (overtone) and an interior (combination) state, is studied from a state space diffusion perspective. A wavelet based time-frequency analysis reveals an inhomogeneous phase space due to the trapping of classical trajectories. Consequently the interior state has a smaller effective IVR dimension as compared to the edge state.Comment: 5 pages, 3 figure

On Readout of Vibrational Qubits Using Quantum Beats

Readout of the final states of qubits is a crucial step towards implementing quantum computation in experiment. Although not scalable to large numbers of qubits per molecule, computational studies show that molecular vibrations could provide a significant (factor 2–5 in the literature) increase in the number of qubits compared to two-level systems. In this theoretical work, we explore the process of readout from vibrational qubits in thiophosgene molecule, SCCl2, using quantum beat oscillations. The quantum beats are measured by first exciting the superposition of the qubit-encoding vibrational states to the electronically excited readout state with variable time-delay pulses. The resulting oscillation of population of the readout state is then detected as a function of time delay. In principle, fitting the quantum beat signal by an analytical expression should allow extracting the values of probability amplitudes and the relative phases of the vibrational qubit states. However, we found that if this procedure is implemented using the standard analytic expression for quantum beats, a non-negligible phase error is obtained. We discuss the origin and properties of this phase error, and propose a new analytical expression to correct the phase error. The corrected expression fits the quantum beat signal very accurately, which may permit reading out the final state of vibrational qubits in experiments by combining the analytic fitting expression with numerical modelling of the readout process. The new expression is also useful as a simple model for fitting any quantum beat experiments where more accurate phase information is desired

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

Direct Imaging of Two-State Dynamics on the Amorphous Silicon Surface

Amorphous silicon is an important material, amidst a debate whether or not it is a glass. We produce amorphous Si surfaces by ion bombardment and vapor growth, and image discrete Si clusters which hop by two-state dynamics at 295 K. Independent of surface preparation, these clusters have an average diameter of ~5 atoms. Given prior results for metallic glasses, we suggest that this cluster size is a universal feature. The hopping activation free energy of 0.93 ± 0.15 eV is rather small, in agreement with a previously untested surface glass model. Hydrogenation quenches the two-state dynamics, apparently by increasing surface crystallinity

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

Three-body Interactions Improve the Prediction of Rate and Mechanism in Protein Folding Models

Here we study the effects of many-body interactions on rate and mechanism in protein folding, using the results of molecular dynamics simulations on numerous coarse-grained C-alpha-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Go-like Hamiltonian with native pair-wise interactions only, we have found 1) a significantly increased correlation with experimental phi-values and folding rates, 2) a stronger correlation of folding rate with contact order, matching the experimental range in rates when the fraction of three-body energy in the native state is ~ 20%, and 3) a considerably larger amount of 3-body energy present in Chymotripsin inhibitor than other proteins studied.Comment: 9 pages, 2 tables and 5 figure