Download Molecular Modeling: Basic Principles and Applications by Hans-Dieter Höltje PDF

By Hans-Dieter Höltje

Written via skilled specialists in molecular modeling, this books describes the fundamentals to the level that's important if one desires to be capable to reliably pass judgement on the consequences from molecular modeling calculations.
Its major target is the outline of many of the pitfalls to be kept away from. with out pointless overhead it leads the reader from uncomplicated calculations on small molecules to the modeling of proteins and different appropriate biomolecules.
A textbook for rookies in addition to a useful reference for all these facing molecular modeling of their day-by-day paintings!

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The third method for displaying the molecular electrostatic potential is associated with the calculation and visualization of the molecular surfaces. We will therefore dwell only shortly on the various definitions of the molecular surface. In the formal treatment of molecular surfaces the atomic positions are treated as points, whereas the electron clouds are approximated by spheres centered on the atomic centers. If the electron spheres are represented by the van der Waals radii, then the surface generated by summing all spheres is called the van der Wads surface.

Comput. Chem. 10,209-220 (1 989). (311 Stewart, J. J. J. Comput. Chem. 3 Conformational Analysis Molecules are not rigid. The motional energy at room temperature is large enough to let all atoms in a molecule move permanently. That means that the absolute positions of atoms in a molecule, and of a molecule as a whole, are by no means fixed and that the relative location of substituents on a single bond may vary in the course of time. Therefore, each compound containing one or several single bonds is existing at each moment in many different so-called rotamers or conformers.

Very often the validation procedure simply is omitted. Of course this renders the corresponding study useless. Topological methods often are implemented into commercial software packages as standard tools for charge calculation. Quantum Chemical Methods All other methods for the calculation of atomic partial charges are based on the quantum mechanical computation of wavefunctions. Wavefunctions either can be obtained using semiempirical or ab initio methods depending on the requested accuracy of the wavefunction and also on the available computational resources.

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