Functional groups quantum chemical description

Apparently, the concept of similarity plays an important role in the chemistry of functional groups. Motivated by the recent revival of interest in molecular similarity [7-39], we shall present a systematic approach towards a quantum chemical description of functional groups. There are two main components of the approach described in this report. The first component is shape-similarity, based on the topological shape groups and topological similarity measures of molecular electron densities[2,19-34], whereas the second component is the Density Domain approach to chemical bonding [4]. The topological Density Domain is a natural basis for a quantum... 

Within the quantum chemical description of molecular electron density clouds, a natural criterion, the Density Domain criterion, provides a quantum chemical definition for functional groups [14-18]. Furthermore, techniques that generate fuzzy electron density contributions for local molecular moieties that are analogous to the fuzzy electron density clouds of complete molecules, determined by the analytic Additive Fuzzy Density Fragmentation (AFDF) method [19-21], or the earlier numerical-grid MEDLA method [22,23], are also... 

For the description of a solution of alanine in water two models were compared and combined with one another (79), namely the continuum model approach and the cluster ansatz approach (148,149). In the cluster approach snapshots along a trajectory are harvested and subsequent quantum chemical analysis is carried out. In order to learn more about the structure and the effects of the solvent shell, the molecular dipole moments were computed. To harvest a trajectory and for comparison AIMD (here CPMD) simulations were carried out (79). The calculations contained one alanine molecule dissolved in 60 water molecules. The average dipole moments for alanine and water were derived by means of maximally localized Wannier functions (MLWF) (67-72). For the water molecules different solvent shells were selected according to the three radial pair distributions between water and the functional groups. An overview about the findings is given in Tables II and III. 

This has opened the way to a systematic, quantum chemical definition and description of functional groups, to macromolecular shape analysis, to macromolec-ular force computations, and to shape-code-based macromolecular similarity analysis [20-25],... 

In a quantum mechanical description, the simple spring-like picture of chemical bonds, of course, breaks down and the molecule has to be described as a many-body system of interacting particles including electrons and nuclei. Nevertheless, the normal mode vibrations have their counterpart in the fundamental excitations of the nuclear vibrational degrees of freedom (DOF) of the molecule. The fundamentals can be excited by infrared radiation (IR) and characteristic absorption bands in the IR spectra immediately point to the existence of certain chemical bonds or to functional groups and hence IR (and Raman) spectroscopy are powerful tools to investigate and study the chemical structure of molecules. 

An advantage of the method of increments in comparison with other local correlation methods is that the translational symmetry of the system can be used to reduce the effort of the calculation. Translational symmetry is, however, not a prerequisite of the method. Therefore it is possible to extend the method to systems with reduced symmetry like surfaces and molecules on the surface. " Impurities and functional groups in large biological molecules can be described as well. If the description for metals and the one for impurities are combined, the whole field of Kondo physics opens up. But one has to be aware of the fact that for the small energy scales involved in the Kondo effect require highly accurate quantum-chemical methods, and very extended basis sets are necessary to achieve reliable results. 

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