This book introduces the reader to the theory and methodology of quantum-mechanical modeling of chemical and biological systems. Given the immense complexity of such systems, there is a constant search for new methods. The goal of this text is to derive approximate (semi-empirical) methods to address this class of problems and to provide insight for their continued development. The authors cover such important topics as molecular dynamics, high performance computing, free energy calculations, statistical mechanics, long-range electrostatics, and many-electron systems. They also discuss applications for water salvation, chemical reactions, conformational sampling, and structure relaxation.