Holistic molecule

Well-defined products from the chaotic turmoil, which is a chemical reaction, result from a balance between external thermodynamic factors and the internal molecular parameters of chemical potential, electron density and angular momentum. Each of the molecular products, finally separated from the reaction mixture, is a new equilibrium system that balances these internal factors. The composition depends on the chemical potential, the connectivity is determined by electron-density distribution and the shape depends on the alignment of vectors that quenches the orbital angular momentum. The chemical, or quantum, potential at an equilibrium level over the entire molecule, is a measure of the electronegativity of the molecule. This is the parameter that contributes to the activation barrier, should this molecule engage in further chemical activity. Molecular cohesion is a holistic function of the molecular quantum potential that involves all sub-molecular constituents on an equal basis. The practically useful concept of a chemical bond is undefined in such a holistic molecule. 

The key to the understanding of molecular geometry is in the definition of an holistic molecule described by one of the factors in a product function, equation 5.7. This factor represents the molecular wave function for the molecule of interest and defines non-local entanglement within a limited region of space that varies as a function of the environment. The relative confinement of the molecule means that the boundary conditions on the molecular wave function are variable, in the same sense as for the compressed atom. Different solutions are therefore found in different settings and particularly in different states of aggregation. Any structure revealed by the wave functions must likewise be a function of the surroundings. 

To understand why and how chemical reactions happen it is necessary to consider also intermolecular interactions. It is only in the hypothetical case of an ideal gas that intermolecular interactions are totally absent. In all other systems they represent an important factor that affects molecular conformation, reactivity and stability. Whenever molecules co-exist in equilibrium it means that intermolecular forces are not sufficient to pull the molecules apart or together into larger aggregates. Equilibrium implies a balance of thermodynamic factors, and when these factors change, intermolecular interactions may overcome the integrity of a partially holistic molecule, and lead on to chemical reaction. Onset of the reaction is said to be controlled by an activation energy barrier. This barrier must clearly be closely allied to the quanmm potential of the molecule. 

To understand this, and other intramolecular rearrangements, it is necessary to give up the naive notion of Lewis-type electron-pair bonds. The alternative is to view all interaction within a partially holistic molecule as mediated by its quantum potential and quantum torque. Both of these quantities are specified by the total molecular wave function. The necessary theory for this approach has not been worked out. 

The mysterious behaviour of bio-macromolecules is one of the outstanding problems of molecular biology. The folding of proteins and the replication of DNA transcend all classical mechanisms. At this stage, non-local interaction within such holistic molecules appears as the only reasonable explanation of these phenomena. It is important to note that, whereas proteins are made up of many partially holistic amino-acid units, DNA consists of essentially two complementary strands. Nonlocal interaction in DNA is therefore seen as more prominent, than for proteins. Non-local effects in proteins are sufficient to ensure concerted response to the polarity and pH of suspension media, and hence to direct tertiary folding. The induced fit of substrates to catalytic enzymes could be promoted in the same way. Future analysis of enzyme catalysis, allosteric effects and protein folding should therefore be, more ambitiously, based on an understanding of molecular shape as a quantum potential response. The function of DNA depends even more critically on non-local effects. 

Fig. 18 (a) Fine cutting of SWNT with oxygen plasma introduced through an opening in a window of PMMA defined with e-beam lithography, (b) Schematic demonstration of holistic construction of a single molecule circuit. (Reprinted with permission from [153])... 

While the ability to relate the chemistry of C60 to that of other organic molecules has been beneficial for many studies, the novel reactivity of the spherical form is of particular interest. The quantitative thermal decomposition of C60Br24 to C60 and Br2 is one example with little precedent in traditional reactions. Another is the observation by Paul Krusic that up to thirty-four methyl radicals can be added to the fullerene. This holistic behaviour is promising for other novel chemistry. 

Intramolecular cohesion evidently is a holistic quantum-mechanical property, which cannot be reduced to pairwise interactions. Molecules are formed during the interaction of atoms and/or radicals in their valence states, to be understood in terms of valence-state wave functions of appropriate symmetry. 

A schematic diagram to illustrate the course of reaction is shown in hgure 7.1. The energy level of the valence state corresponds to the promotion of two atoms involved in the reaction. The energy of the system drops as the valence electrons spread out across the larger accessible space surrounding the atomic cores. Holistic interaction between the two valence electrons and the cores stabilizes the molecule by an amount De. According to the classical model this corresponds to an internuclear distance re. 

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