			Home About us Contact

Atomic Motion (atomic + motion)

Distribution by Scientific Domains

Chemistry	80%

Selected Abstracts

Epicurean and Galilean Motion in Gassendi's Physics

PHILOSOPHY COMPASS (ELECTRONIC), Issue 2 2008
Antonia LoLordo
Pierre Gassendi held a Galilean theory of the motion of composite bodies. He also accepted an Epicurean theory of the motion of atoms according to which atoms can never gain or lose speed. The conjunction of these two theories is awkward and, from the point of view of physics, unfruitful. I offer metaphysical reasons why Gassendi might have thought he needed to adopt the Epicurean view of atomic motion. [source]

X-ray diffraction by a crystal in a permanent external electric field: general considerations

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2005
Semen V. Gorfman
The variations of X-ray diffraction intensities from a crystal in the presence of a permanent external electric field is modeled analytically using a first-order stationary perturbation theory. The change in a crystal, induced by an external electric field, is separated into two contributions. The first one is related to a pure polarization of an electron subsystem, while the second contribution can be reduced to the displacements of the rigid pseudoatoms from their equilibrium positions. It is shown that a change of the X-ray diffraction intensities mainly originates from the second contribution, while the influence of the pure polarization of a crystal electron subsystem is negligibly small. The quantities restored from an X-ray diffraction experiment in the presence of an external electric field were analyzed in detail in terms of a rigid pseudoatomic model of electron density and harmonic approximation for the atomic thermal motion. Explicit relationships are derived that link the properties of phonon spectra with E -field-induced variations of a structure factor, pseudoatomic displacements and piezoelectric strains. The displacements can be numerically estimated using a model of independent atomic motion if the Debye,Waller factors and pseudoatomic charges are known either from a previous single-crystal X-ray diffraction study or from density functional theory calculations. The above estimations can be used to develop an optimum strategy for a data collection that avoids the measurements of reflections insensitive to the electric-field-induced variations. [source]

Atomic resolution structure of pseudoazurin from the methylotrophic denitrifying bacterium Hyphomicrobium denitrificans: structural insights into its spectroscopic properties

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2009
Daisuke Hira
The crystal structure of native pseudoazurin (HdPAz) from the methylotrophic denitrifying bacterium Hyphomicrobium denitrificans has been determined at a resolution of 1.18,Å. After refinement with SHELX employing anisotropic displacement parameters and riding H atoms, Rwork and Rfree were 0.135 and 0.169, respectively. Visualization of the anisotropic displacement parameters as thermal ellipsoids provided insight into the atomic motion within the perturbed type 1 Cu site. The asymmetric unit includes three HdPAz molecules which are tightly packed by head-to-head cupredoxin dimer formation. The shape of the Cu-atom ellipsoid implies significant vibrational motion diagonal to the equatorial xy plane defined by the three ligands (two His and one Cys). The geometric parameters of the type 1 Cu site in the HdPAz structure differ unambiguously from those of other pseudoazurins. It is demonstrated that their structural aspects are consistent with the unique visible absorption spectrum. [source]

`Making the molecular movie': first frames

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2010
R. J. Dwayne Miller
Recent advances in high-intensity electron and X-ray pulsed sources now make it possible to directly observe atomic motions as they occur in barrier-crossing processes. These rare events require the structural dynamics to be triggered by femtosecond excitation pulses that prepare the system above the barrier or access new potential energy surfaces that drive the structural changes. In general, the sampling process modifies the system such that the structural probes should ideally have sufficient intensity to fully resolve structures near the single-shot limit for a given time point. New developments in both source intensity and temporal characterization of the pulsed sampling mode have made it possible to make so-called `molecular movies', i.e. measure relative atomic motions faster than collisions can blur information on correlations. Strongly driven phase transitions from thermally propagated melting to optically modified potential energy surfaces leading to ballistic phase transitions and bond stiffening are given as examples of the new insights that can be gained from an atomic level perspective of structural dynamics. The most important impact will likely be made in the fields of chemistry and biology where the central unifying concept of the transition state will come under direct observation and enable a reduction of high-dimensional complex reaction surfaces to the key reactive modes, as long mastered by Mother Nature. [source]

Photolysis of Br2 in CCl4 studied by time-resolved X-ray scattering

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2010
Qingyu Kong
A time-resolved X-ray solution scattering study of bromine molecules in CCl4 is presented as an example of how to track atomic motions in a simple chemical reaction. The structures of the photoproducts are tracked during the recombination process, geminate and non-geminate, from 100,ps to 10,µs after dissociation. The relaxation of hot Br2* molecules heats the solvent. At early times, from 0.1 to 10,ns, an adiabatic temperature rise is observed, which leads to a pressure gradient that forces the sample to expand. The expansion starts after about 10,ns with the laser beam sizes used here. When thermal artefacts are removed by suitable scaling of the transient solvent response, the excited-state solute structures can be obtained with high fidelity. The analysis shows that 30% of Br2* molecules recombine directly along the X potential, 60% are trapped in the A/A, state with a lifetime of 5.5,ns, and 10% recombine non-geminately via diffusive motion in about 25,ns. The Br,Br distance distribution in the A/A, state peaks at 3.0,Å. [source]