Multidimensional scaling products spaces

The Oriented Substituent Pharmacophore PRopErtY Space (OSPPREYS) approach, introduced by Martin and Hoeffel [6], is in software terms an extension of CCG s MOE package, written using SVL. The 3D oriented substituent pharmacophores are aimed towards better representation of diversity and similarity in combinatorial libraries in the 3D pharmacophore space. Combinatorial library design often operates only on substituents rather than on the final products as the complications related to the conformational coverage in the 3D space and the scaffold dependency limit the product-based approaches to smaller libraries. The 3D oriented substituent pharmacophores add two more points and the corresponding distances to each substituent pharmacophore which represent the relationship of the substituents in the product with only little additional information. The fingerprints permit the creation of property space by multidimensional scaling (MDS) and, since scaffold independent, can be stored separately and applied to different libraries [6],... 

A question that arises in consideration of the annihilation pathways is why the reactions between radical ions lead preferentially to the formation of excited state species rather than directly forming products in the ground state. The phenomenon can be explained in the context of electron transfer theory [34-38], Since electron transfer occurs on the Franck-Condon time scale, the reactants have to achieve a structural configuration that is along the path to product formation. The transition state of the electron transfer corresponds to the area of intersection of the reactant and product potential energy surfaces in a multidimensional configuration space. Electron transfer rates are then proportional to the nuclear frequency and probability that a pair of reactants reaches the energy in which they have a common conformation with the products and electron transfer can occur. The electron transfer rate constant can then be expressed as... 

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