分子建模-1.pdfVIP

Advanced Molecular Modeling and Design (一一) 一一 Jie-Lou Liao, USTC 2013- Spring-Summer Semester Lecture 1 Molecular Modeling 1.1 Introduction 1.1.1 Computational Methods • Quantum Mechanics/Quantum Chemistry -Valence-Bond Walter Heitler and Fritz London --H2 (1927) John Slater and Linus Pauling (1930) -Molecular-Orbital Hund-Mulliken (1929), Huckel (1931) -Density Functional Thomas, Fermi (1927), Kohn -abinitio Quantum Chemistry Parr (1950), John A. Pople • Molecular Dynamics (MD) • Monte Carlo Method (MC) • Others • 1.1.3 Quantum Mechanics/Chemistry 1.2 Molecular Mechanics (MM) 1.2 Molecular Mechanics Force Fields 1.2.1 MM force field 1.2.2 Bonded Terms 1.2.3 Non-Bonded Terms • Electrostatic interaction energy • Methods • Examples • Calculations of partial charges • Polarization • Solvent dielectric models 1.3 Force Field Models for the simulation of Liquid Water 1.3.1 History • 1932-- Spectroscopic proofs of the V-shaped water molecule • 1933-- Bernal and Fowler (BF) propose the 1st realistic interaction potential for water • 1953-- Metropolis present the 1st Monte Carlo sampling scheme • 1957—Adler and Wainwright performed the 1st MD simulation • 1969– Pink and Watts 1st computer simulations of water • 1976– Lie et al 1st pair potential from ab initio calculations • 1981– Berendsen et al construct the 1st SPC model • 1983– Jorgensen proposed TIP3P model • 1.3.2 Representation of Water Molecule • 1.3.3 Liquid Water (1) Rigid water model 3-site model SPC TIP3P r (OH), Å 1.0 0.9572 H