Bader structure

Tsirelson, V.G., Zou, P.F. and Bader, R.F.W. (1995) Topological definition of crystal structure determination of the bonded interactions in solid molecular chlorine, Ada Cryst., A51, 143-153. 

Carroll, M.T., Chang, C. and Bader, R.F.W. (1988) Prediction ofthe structures of hydrogen-bonded complexes using the Laplacian of the charge density, Mol. Phys., 63, 387 105. 

Bader et al. have developed a theory of molecular structure [8], based on the topological properties of the electron density p(r). In this theory, a molecule may be partitioned into atoms or fragments by using zero-flux surfaces that satisfy the condition... 

The first step in our procedure is to compute an optimized structure for each molecule and then to use this geometry to compute the electronic density and the electrostatic potential. A large portion of our work in this area has been carried out at the SCF/STO-5G //SCF/STO-3G level, although some other basis sets have also been used. We then compute V(r) on 0.28 bohr grids over molecular surfaces defined as the 0.001 au contour of the electronic density (Bader et al. 1987). The numbers of points on these grids are converted to surface areas (A2), and the and Fs min are determined. Our statistically based interaction in-... 

By a careful fractionation of normal horse serum, involving as an essential part of the process a separation of closely related substances by the Schtitz168 foam technique, Bader, Schiitz and Stacey16 obtained a crystalline mucoprotein with high choline esterase activity. This appears to be the first mucoprotein obtained without the use of heat or alcohol, and while it is not yet claimed that the crystalline material is indeed the enzyme itself, arguments are advanced to show that the enzymic activity is closely bound up with mucoprotein structure. 

C. F. Matta, R. F.W. Bader, Proteins Structure Function Genetics, 2002, submitted. 

One further theoretical method that merits consideration at this point is the topological theory of molecular structure exemplified by Bader (1985, 1990). In this method a topological description of the total electron density in the molecule is used. A major advantage of this method is that it allows the total interaction between various centres to be probed. Cremer et al. (1983) used the Bader method to examine the homotropylium cation [12] and concluded that it was indeed homoaromatic. 

The microscopic world of atoms is difficult to imagine, let alone visualize in detail. Chemists and chemical engineers employ different molecular modelling tools to study the structure, properties, and reactivity of atoms, and the way they bond to one another. Richard Bader, a chemistry professor at McMaster University, has invented an interpretative theory that is gaining acceptance as an accurate method to describe molecular behaviour and predict molecular properties. According to Dr. Bader, shown below, small molecules are best represented using topological maps, where contour lines (which are commonly used to represent elevation on maps) represent the electron density of molecules. 

Figure 8,1 Structural models for H2O molecule. (A) Electrostatic point-charge model (from Eisemberg and Kauzmann, 1969 redrawn). (B) Electron density map (from Bader and Jones, 1963). (C) Formation of MOs and starting from AOs 2p and Is of oxygen and 1 of hydrogen.

The theory of molecular structure based on the topology of molecular charge distribution, developed by Bader and co-workers (83MI2 85ACR9), enables certain features to be revealed that are characteristic of the systems with aromatic cyclic electron delocalization. To describe the structure of a molecule, it is necessary to determine the number and kind of critical points in its electronic charge distribution, i.e., the points where for the gradient vector of the charge density the condition Vp = 0 is fulfilled. 

The topological analysis of the total density, developed by Bader and coworkers, leads to a scheme of natural partitioning into atomic basins which each obey the virial theorem. The sum of the energies of the individual atoms defined in this way equals the total energy of the system. While the Bader partitioning was initially developed for the analysis of theoretical densities, it is equally applicable to model densities based on the experimental data. The density obtained from the Fourier transform of the structure factors is generally not suitable for this purpose, because of experimental noise, truncation effects, and thermal smearing. 

When space is partitioned with discrete boundaries, as in Eq. (6.7) and in the Bader virial partitioning method, the moments can be derived directly from the structure factors by a modified Fourier summation, as described for the net charge in chapter 6. 

The qualitative study of electronic structure through the electron (number) density p(r) relies heavily on linecut diagrams, contour plots, perspective plots, and other representations of the density and density differences. There is a review article by Smith and coworkers [302] devoted entirely to classifying and explaining the different techniques available for the pictorial representation of electron densities. Beautiful examples of this type of analysis can be seen in the work of Bader, Coppens, and others [303,304]. 

An alternative physical observable that has been used to define partial atomic charges is the electron density. In X-ray crystallography, the electron density is direedy measured, and by comparison to, say, spherically symmetric neutral atoms, atomic partial charges may be defined experimentally, following some decisions about what to do with respect to partitioning space between the atoms (Coppens 1992). Bader and co-workers have adopted a particular partitioning scheme for use with electronic structure calculations that defines the atoms-in-molecules (AIM) method (Bader 1990). In particular, an atomic volume is... 

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