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Ammonia Molecule (ammonia + molecule)

Distribution by Scientific Domains

Chemistry	100%

Selected Abstracts

Positive width function and energy indeterminacies in ammonia molecule

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 8 2007
Theodosios G. Douvropoulos
A recently published methodology based on the semiclassical path integral theory was applied in a double well structure and gave the analytic form of the system's Green's function. This type of potential can describe the ammonia molecule as far as the motion of the nitrogen atom perpendicular to the hydrogen plane is discussed. Because of the fact that a double well describes a bound system and correspondingly stationary states (constructed by the symmetric and antisymmetric superposition of the eigenstates of the two unperturbed wells), it was expected that the energy spectrum would be real, in a form of doublets due to the splitting effect that takes place. However, the result was a pair of complex poles, which had a clearly positive imaginary part for each member. The present work explains the role of the imaginary parts of the complex poles as the decay rate of quantities defined as the energy indeterminacies, which are directly related to the fact that energy is not well determined in a classically forbidden region of motion. These quantities come as a function of (d,)/dE, which is the derivative of the classical action inside the potential barrier, with respect to energy. The major contribution comes from the turning points, and then the imaginary parts are responsible, not only for the conservation of energy, but for the correct sign of time as well. In this way, a different approach for the tunneling process is adopted, in which the entry or exit of the particle from the potential barrier takes place inside a neighborhood of the turning point, as though the latter was broadened and fluctuating. The magnitude of the previously mentioned decay rate is equal to ,/,, where , is the frequency of the classical oscillations inside one well. In contrast, the inversion frequency is generated by the part of the complex pole that is unrelated to (d,)/dE and is much smaller in magnitude than the classical frequency, since it is given as ,/, exp(,,). In this way, the period of the energy fluctuations is much smaller than the internal period of the system produced by the oscillating communication of the two classically allowed regions of motion. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source]

Cleavage of the iron-methionine bond in c-type cytochromes: Crystal structure of oxidized and reduced cytochrome c2 from Rhodopseudomonas palustris and its ammonia complex

PROTEIN SCIENCE, Issue 1 2002
Silvano Geremia
Abstract The three-dimensional structures of the native cytochrome c2 from Rhodopseudomonas palustris and of its ammonia complex have been obtained at pH 4.4 and pH 8.5, respectively. The structure of the native form has been refined in the oxidized state at 1.70 Å and in the reduced state at 1.95 Å resolution. These are the first high-resolution crystal structures in both oxidation states of a cytochrome c2 with relatively high redox potential (+350 mV). The differences between the two oxidation states of the native form, including the position of internal water molecules, are small. The unusual six-residue insertion Gly82-Ala87, which precedes the heme binding Met93, forms an isolated 310 -helix secondary structural element not previously observed in other c-type cytochromes. Furthermore, this cytochrome shows an external methionine residue involved in a strained folding near the exposed edge of the heme. The structural comparison of the present cytochrome c2 with other c-type cytochromes has revealed that the presence of such a residue, with torsion angles , and , of approximately ,140 and ,130°, respectively, is a typical feature of this family of proteins. The refined crystal structure of the ammonia complex, obtained at 1.15 Å resolution, shows that the sulphur atom of the Met93 axial ligand does not coordinate the heme iron atom, but is replaced by an exogenous ammonia molecule. This is the only example so far reported of an X-ray structure with the heme iron coordinated by an ammonia molecule. The detachment of Met93 is accompanied by a very localized change in backbone conformation, involving mainly the residues Lys92, Met93, and Thr94. Previous studies under typical denaturing conditions, including high-pH values and the presence of exogenous ligands, have shown that the detachment of the Met axial ligand is a basic step in the folding/unfolding process of c-type cytochromes. The ammonia adduct represents a structural model for this important step of the unfolding pathway. Factors proposed to be important for the methionine dissociation are the strength of the H-bond between the Met93 and Tyr66 residues that stabilizes the native form, and the presence in this bacterial cytochrome c2 of the rare six-residue insertion in the helix 310 conformation that increases Met loop flexibility. [source]