Chemical space coordinate-based

We established [54] that, in conjunction with 2D-based descriptors, ChemGPS can provide global chemical space coordinates by performing extensive comparisons with GRID-based principal properties for heteroaromatic compounds [59], principal properties ( z-scores ) of a-amino acids [60], as well as by comparison to several local PCA models. The initial ChemGPS map turned out to be 9-dimensional [54]. 

Fig. 1. Clustering versus partitioning. In cluster analysis, compounds (gray dots) are grouped together based on the calculation of pairwise intermolecular distances in chemical space. By contrast, partitioning methods subdivide chemical space into sections into which compounds fall based on their calculated descriptor coordinates.

Transfer of solute with and relative to the moving water and competitive adsorption of solutes are central to amelioration of saline and alkali soils, agricultural chemical location in soils and management of wastes in soils. This paper illustrates how space-like coordinates based on the distribution of the solid and the water help analyse these problems. We focus on the macroscopic or Darcy scale of discourse [6], which permits unambiguous measurement of the key elements of the flow equations, and we restrict ourselves to 1-dimensional flow, because that seems to limit analysable experiments. 

The measurement of molecular diversity requires the definition of a chemical space. This A-dimensional chemical space is represented by a group of selected molecular descriptors. Each compound in a collection can be assigned coordinates based on the measurement of its descriptor values. Increasing distance, within the dimensions of the assigned coordinate space, should correlate with increasing diversity (or decreasing similarity) between compounds. 

Rg. 6-10 Mapping chemical space [76]. Principle component models of chemical space are shown for 480 small molecules analyzed using 24 computed molecular descriptors and 60 measured phenotypic descriptors derived from a cell-based assay of cell proliferation. By considering the elements of S as coordinates, small molecules can be modeled as vectors,... 

On the other hand, bulk concentrations are required for estimation of the respective surface concentrations that are the terms of kinetic equations. To obtain the data for the solution layer adjacent to the electrode surface, mass transport of chemically interacting species should be considered. Quantitative formulation of this problem is based on differential equations representing Pick s second law and supplemented with the respective kinetic terms. It turns out that some linear combinations of these equations make it possible to eliminate kinetic terms. So produced common diffusion equations involve total concentrations of metal, ligand and proton donors (cj j, c, and Cj4, respectively) as functions of time and space coordinates. It follows from the relationships obtained that the total metal concentration varies in the same manner as the concentration of free metal ions in the absence of ligand. Simultaneously, the total ligand concentration remains constant within the whole region of the diffusion layer. This proposition also remains valid for proton donors and acceptors. 

Fig. 12 (A) The d(CGCGAATTCGCG)2 duplex with a narrow groove and a sodium ion coordinated at the ApT step. (I) The DNA is shown in stick representation and the ion in space-filling size. Left view is directly into the central minor groove. Right view left view rotated 90° counterclockwise and tilted 30° to show the ion in the minor groove. (II) The base pair views are of the central ApT step. Top view is down the helix axis, bottom view is directly into the minor groove. (B) The DNA duplex with a phosphate-oxygen pair-sodium ion interaction and a water molecule coordinated at the ApT step. (II) Views as in Fig. 12A for the phosphate-ion-water-base complex at the AT site. Reproduced with permission from Ref. (42). Copyright 2000, American Chemical Society.

---