Biomedical subjects

J Spencer Baskin

Publications and source records attributed to J Spencer Baskin.

7 recordsLinked to original sources

PubMed2006

Ultrafast vectorial and scalar dynamics of ionic clusters: azobenzene solvated by oxygen.

The ultrafast dynamics of clusters of trans-azobenzene anion (A-) solvated by oxygen molecules was investigated using femtosecond time-resolved photoelectron spectroscopy. The time scale for stripping off all oxygen molecules from A- was determined by monitoring in real time the transient of the A- rise, following an 800 nm excitation of A- (O2)n, where n = 1-4. A careful analysis of the time-dependent photoelectron spectra strongly suggests that for n > 1 a quasi-O4 core is formed and that the dissociation occurs by a bond cleavage between A- and conglomerated (O2)n rather than a stepwise evaporation of O2. With time and energy resolutions, we were able to capture the photoelectron signatures of transient species which instantaneously rise (<100 fs) then decay. The transient species are assigned as charge-transfer complexes: A.O2- for A- O2 and A.O4-(O2)n-2 for A-(O2)n, where n = 2-4. Subsequent to an ultrafast electron recombination, A- rises with two distinct time scales: a subpicosecond component reflecting a direct bond rupture of the A- -(O2)n nuclear coordinate and a slower component (1.6-36 ps, increasing with n) attributed to an indirect channel exhibiting a quasistatistical behavior. The photodetachment transients exhibit a change in the transition dipole direction as a function of time delay. Rotational dephasing occurs on a time scale of 2-3 ps, with a change in the sign of the transient anisotropy between A- O2 and the larger clusters. This behavior is a key indicator of an evolving cluster structure and is successfully modeled by calculations based on the structures and inertial motion of the parent clusters.

Journal Article↗

PubMed2006

Oriented ensembles in ultrafast electron diffraction.

Electron scattering expressions are presented which are applicable to very general conditions of implementation of anisotropic ultrafast electron diffraction (UED) experiments on the femto- and picosecond time scale. "Magic angle" methods for extracting from the experimental diffraction patterns both the isotropic scalar contribution (population dynamics) and the angular (orientation-dependent) contribution are described. To achieve this result, the molecular scattering intensity is given as an expansion in terms of the moments of the transition-dipole distribution created by the linearly polarized excitation laser pulse. The isotropic component (n=0 moment) depends only on population and scalar internuclear separations, and the higher moments reflect bond angles and evolve in time due to rotational motion of the molecules. This clear analytical separation facilitates assessment of the role of experimental variables in determining the influence of anisotropic orientational distributions of the molecular ensembles on the measured diffraction patterns. Practical procedures to separate the isotropic and anisotropic components of experimental data are evaluated and demonstrated with application to reactions. The influence of vectorial properties (bond angles and rotational dynamics) on the anisotropic component adds a new dimension to UED, arising through the imposition of spatial order on otherwise randomly oriented ensembles.

Journal Article↗

PubMed2006

Dynamics of clusters: from elementary to biological structures.

Between isolated atoms or molecules and bulk materials there lies a class of unique structures, known as clusters, that consist of a few to hundreds of atoms or molecules. Within this range of "nanophase," many physical and chemical properties of the materials evolve as a function of cluster size, and materials may exhibit novel properties due to quantum confinement effects. Understanding these phenomena is in its own rights fundamental, but clusters have the additional advantage of being controllable model systems for unraveling the complexity of condensed-phase and biological structures, not to mention their vanguard role in defining nanoscience and nanotechnology. Over the last two decades, much progress has been made, and this short overview highlights our own involvement in developing cluster dynamics, from the first experiments on elementary systems to model systems in the condensed phase, and on to biological structures.

Biology↗

PubMed2005

Ultrafast electron diffraction: oriented molecular structures in space and time.

The technique of ultrafast electron diffraction allows direct measurement of changes which occur in the molecular structures of isolated molecules upon excitation by femtosecond laser pulses. The vectorial nature of the molecule-radiation interaction also ensures that the orientation of the transient populations created by the laser excitation is not isotropic. Here, we examine the influence on electron diffraction measurements--on the femtosecond and picosecond timescales--of this induced initial anisotropy and subsequent inertial (collision-free) molecular reorientation, accounting for the geometry and dynamics of a laser-induced reaction (dissociation). The orientations of both the residual ground-state population and the excited- or product-state populations evolve in time, with different characteristic rotational dephasing and recurrence times due to differing moments of inertia. This purely orientational evolution imposes a corresponding evolution on the electron scattering pattern, which we show may be similar to evolution due to intrinsic structural changes in the molecule, and thus potentially subject to misinterpretation. The contribution of each internuclear separation is shown to depend on its orientation in the molecular frame relative to the transition dipole for the photoexcitation; thus not only bond lengths, but also bond angles leave a characteristic imprint on the diffraction. Of particular note is the fact that the influence of anisotropy persists at all times, producing distinct differences between the asymptotic "static" diffraction image and the predictions of isotropic diffraction theory.

Journal Article↗

PubMed2004

Human myoglobin recognition of oxygen: dynamics of the energy landscape.

Femtosecond to nanosecond dynamics of O(2) rebinding to human WT myoglobin and its mutants, V68F and I107F, have been studied by using transient absorption. The results are compared with NO rebinding. Even though the immediate environment around the heme binding site is changed by the mutations, the picosecond geminate rebinding of oxygen is at most minimally affected. On the other hand, the V68F (E11) mutation causes drastic differences in rebinding on the nanosecond time scale, whereas the effect of the I107F (G8) mutation remains relatively small within our 10-ns time window. Unlike traditional homogeneous kinetics and molecular dynamics collisional simulations, we propose a "bifurcation model" for populations of directed and undirected dynamics on the ultrafast time scale, reflecting the distribution of initial protein conformations. The major mutation effect occurs on the time scale on which global protein conformational change is possible, consistent with transitions between the conformations of directed and undirected population playing a role in the O(2) binding. We discuss the relevance of these findings to the bimolecular function of the protein.

Biochemical Phenomena↗

PubMed2004

Electrons in finite-sized water cavities: hydration dynamics observed in real time.

We directly observed the hydration dynamics of an excess electron in the finite-sized water clusters of (H2O)n- with n = 15, 20, 25, 30, and 35. We initiated the solvent motion by exciting the hydrated electron in the cluster. By resolving the binding energy of the excess electron in real time with femtosecond resolution, we captured the ultrafast dynamics of the electron in the presolvated ("wet") and hydrated states and obtained, as a function of cluster size, the subsequent relaxation times. The solvation time (300 femtoseconds) after the internal conversion [140 femtoseconds for (H2O)35-] was similar to that of bulk water, indicating the dominant role of the local water structure in the dynamics of hydration. In contrast, the relaxation in other nuclear coordinates was on a much longer time scale (2 to 10 picoseconds) and depended critically on cluster size.

Journal Article↗

PubMed2002

Molecular recognition of oxygen by protein mimics: dynamics on the femtosecond to microsecond time scale.

Molecular recognition by biological macromolecules involves many elementary steps, usually convoluted by diffusion processes. Here we report studies of the dynamics, from the femtosecond to the microsecond time scale, of the different elementary processes involved in the bimolecular recognition of a protein mimic, cobalt picket-fence porphyrin, with varying oxygen concentration at controlled temperatures. Electron transfer, bond breakage, and thermal "on" (recombination) and "off" (dissociation) reactions are the different processes involved. The reaction on-rate is 30 to 60 times smaller than that calculated from standard Smoluchowski theory. Introducing a two-step recognition model, with reversibility being part of both steps, removes the discrepancy and provides consistency for the reported thermodynamics, kinetics, and dynamics. The transient intermediates are configurations defined by the contact between oxygen (diatomic) and the picket-fence porphyrin (macromolecule). This intermediate is critical in the description of the potential energy landscape but, as shown here, both enthalpic and entropic contributions to the free energy are important. In the recognition process, the net entropy decrease is -33 cal mol(-1) K(-1); Delta H is -13.4 kcal mol(-1).

Kinetics↗