Quantum mechanics electron cloud representation

Classical shape representations of molecules are based on assumed analogies between quantum mechanical molecules and macroscopic, classical objects. Since most of the mass of molecules is concentrated in the nuclei, it has appeared natural to place emphasis on nuclear arrangements, and the chemically more relevant shapes of electron densities have become the focus of molecular shapes analysis only recently. It is important to distinguish stereochemistry and molecular shape analysis. The term stereochemistry is commonly used for the 3D pattern of formal bonds, whereas molecular shape often refers to the shape of the fuzzy electron density cloud, or to simpler representations of large-scale molecular features, such as an a-helix or a -sheet of a protein. Several alternative shape representations are also used, such as fused sphere van der Waals (VDW) surfaces, Connolly surfaces, solvent accessibility surfaces, or molecular electrostatic potential (MEP) surfaces. 

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