Molecular isomerism

Leitner D M 1999 influence of quantum energy flow and localization on molecular isomerization in gas and condensed phases Int. J. Quant. Chem. 75 523-31... 

For the first time, the primary nitrone (formaldonitrone) generation and the comparative quantum chemical analysis of its relative stability by comparison with isomers (formaldoxime, nitrosomethane and oxaziridine) has been described (357). Both, experimental and theoretical data clearly show that the formal-donitrones, formed in the course of collision by electronic transfer, can hardly be molecularly isomerized into other [C,H3,N,0] molecules. Methods of quantum chemistry and molecular dynamics have made it possible to study the reactions of nitrone rearrangement into amides through the formation of oxaziridines (358). 

Referring to the plot of G vs. T for the isotropic and nematic fluids, a uni-molecular isomerization process would show the same characteristics if one of the isomers had a higher entropy of formation than the other. In the molecular case, however, the equilibrium constant at a given temperature would derive from the free energies on a per molecule basis, while for the phases this free energy is per collective volume of molecules. The similarities to a molecular isomerization, however, are more important than the differences for the purposes of this discussion. The transition from isotropic fluid to nematic LC can be considered a temperature-driven, or thermotropic, isomerization. 

The main diagnostic tools employed in studying molecular isomerizations are electronic absorption and infrared spectroscopy. Changes of the molecular conformation can be indicated by variations in energy, intensity, or number of electronic peaks, as well as by shifts, splitting, and appearance-disappearance of vibrational bands. 

As an example of why linear interpolation is not always a useful way to initialize an NEB calculation, consider the molecule HCN in the gas phase. This molecule can rearrange to form CNH. Optimize the structures of HCN and CNH, then use these states to examine the bond lengths in the structures that are defined by linear interpolation between these two structures. Why are the intermediate structures defined by this procedure not chemically reasonable Construct a series of initial images that are chemically reasonable and use them in an NEB calculation to estimate the activation energy for this molecular isomerization reaction. 

Cycloalkanes. Methylene reacts with the C—H bonds of cycloalkanes to form excited methyl cycloalkanes, which may undergo uni-molecular isomerization or dissociation (dissociation would constitute an abstraction reaction) or may be collisionally deactivated. 

Figure 4. Poincare surface of section of molecular isomerization of cyclobutanone (C4H6O) for the total reaction energy E = O.Ola.u, showing a 3 1 resonance.

MacFadyen and Andricioaei used as scheme whereby the initial distribution is modified by increasing the variance of the momentum distribution. They show that the results obtained significantly improve the accuracy of the results for a simple model of molecular isomerization. 

As previously stated, molecular isomerization does not provide an explanation for the quantum deficit following excitation of benzene the first band does not bear close scrutiny. However, an investigation of the photochemistry of excited benzene is of interest, in view of the variety and complexity of the isomeric products. An extensive review of conditions under which the formation of Isomers of benzene and its derivatives can be found has been compiled by Scott and Jones (250). Interconversion of the isomers which would be relevant to photophysical effects are governed by orbital symmetry considerations, and examples of this type of treatment are now appearing (251,252). 

This result may be explained by the possible molecular isomerization of the molecular ions of these two isomers (Fig. 17), which may occur as a result of the particularly long lifetime (10 - second [Pg.173]

In the case of bicyclic ketones, such as ethyl hydrindanones (a and b) [125], such a partial molecular isomerization does not prevent their identification (Fig. 18), since their MIKE spectra are quite different (Fig. 19). 

Figure 18. Molecular isomerization prior to the C2H3 loss, and partial isomerization of fragment [M-CjHJ ions [125].

Although thermally induced 0-> N methyl group migrations are well documented for the methoxy analogs of xanthine and uric acid, the inter-molecular isomerization of 6-methoxy-7,9-dimethylpurinium chloride (53) to 1,7,9-trimethylhypoxanthinium chloride, in methanol, appears to be the first reported example of a Hilbert-Johnson type reaction involving mono-oxopurines [Eq. (7)]. ° ... 

Furthermore, the pyrolysis of cyc/o-alkanes is a chain radical process where several molecular reactions also play a significant role. Specifically, the molecular isomerizations between cyc/o-alkanes and alkenes are typical examples of four- and six-centre concerted reactions. 

Leitner D M and Wolynes P G 1997 Quantum energy flow during molecular isomerization Chem. Phys. Lett. 280 411-18... 

Isomerases catalyze molecular isomerizations and include the epimerases, racemases, and intramolecular transferases. An example is shown in Figure 4.8, with the xylose isomerase (EC 5.3.1.5 systematic name, D-xylose ketol-isomerase commonly called glucose isomerase) transformation of a-D-glucopyranose to a-o-fructofuranose. 

Figure 3 Fraaional population decay curves for a model of three-state molecular isomerization with all trajectories initially distributed uniformly on the constant-energy shell within a single isomer...

A. Bosco, M.G.M. Jongejan, R. Eelkema, N. Katsonis, E. Lacaze, A. Ferrarini, B.L. Eeringa, Photoinduced reoiganization of motOT-doped chiral liquid crystals bridging molecular isomerization and texture rotation. J. Am. Chem. Soc. 130, 14615-14624 (2008)... 

Each state is split into numerous components by the effects of nuclear hyperfine structure, vibrational excitation, and molecular isomerism. 

Since 1952, most of the tritium measured in the atmosphere originates from thermonuclear explosions. Like hydrogen, deuterium and tritium also exhibit molecular isomerism. Because of the important differences between the relative atomic masses of the three isotopes, their physical properties (e.g., density, enthalpy of vaporization) differ greatly. This allows an easier isotopic separation than for any other element. Several separation processes are used for the enrichment and separation of hydrogen isotopes. Most of these processes use isotopic exchange reactions (e.g., H D-H O or NH3-HD) and to a lesser extent fractional distillation and water electrolysis (e.g., Norway, Canada). 

Moulton and Zaworotko" suggested that supramolecular isomers could be considered in four categories on the basis of analogies drawn from molecular isomerism. 

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