Levels of Theory Used

Molecular Mechanics

• assumes atoms to be like spheres at the end of a spring
• atoms obey classical mechanics (laws of motion)
  • Hooke's Law: F=-kx (for springs)
  • Newton's Second Law: F=ma (for all objects)
• used almost exclusively for molecules of 100 atoms or more
  • proteins
  • pharmaceuticals
  • large biologicals

Semi-Empirical Methods

• used for calculation of molecules from 50-100 atoms
• borrows from both experimental and ab initio methods: simplifies difficult mathematical equations in ab initio with some real (empirical) data, i.e. from the lab
• has advantage in being well-suited for studying the behavior of molecules in solution (i.e., dissolved in water)

ab initio methods

• Latin for "from scratch" or "from the beginning"
• used for calculation of 1 to 50 atoms - "small molecules"
• all results come from significant computational analysis fo Schroedinger's equation
• generally considered to be the most accurate but also the most computationally expensive

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