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Unformatted text preview: 1 Basic Electrostatics BIOL 7110 / CHEM 8901 / BIOL 4105 / 4804 January 20, 2011 Outline of Talk Significance of electrostatics in macromolecular simulations Classical treatment of electrostatics: Point charges and Coulomb’s law Polarization of nonconducting media by electric fields The dielectric constant Outline of Talk Significance of electrostatics in macromolecular simulations Contributions to conformational energy: • Bond stretching Bond lengths and bond energies don’t change much with conformation • Angle bending Angles and angle energies don’t change much with conformation • Torsional rotations Torsions change a lot with conformation, but energy changes are small • van der Waals Affect local structure but usually not the overall conformation • Electrostatics Electrostatic forces act over both long and short distances At short distances, electrostatic forces are very strong Salt bridges Hydrogen bonds are largely electrostatic Solvation forces (including hydrophobicity) are largely electrostatic Conformational energy differences are therefore dominated by electrostatics Significance The most important factor for determining the conformation of macromolecules is electrostatics. The least accurate term in the potential energy function is the electrostatic term. Outline of Talk Significance of electrostatics in macromolecular simulations Classical treatment of electrostatics: Point charges and Coulomb’s law 2 Atomic Charges in Molecular Mechanics Groups of atoms may be neutral or carry a net charge Individual atoms generally carry nonzero partial charges Real atoms: The nucleus has positive charge (point charge) Electron clouds are negative (distributed charges) The distribution may be symmetric or asymmetric Net atomic charge may be positive, negative, or zero Atoms in molecular mechanics models: All charge is located at the center of the atom (the nucleus) All atomic charges are treated as point charges (No electrons; no distributed charges) Net atomic charge may be positive, negative, or zero 27 !NATOM . . . 10 X 2 ALA N NH1 -0.470000 14.0070 11 X 2 ALA HN H 0.310000 1.0080 12 X 2 ALA CA CT1 0.070000 12.0110 13 X 2 ALA HA HB 0.090000 1.0080 14 X 2 ALA CB CT3 -0.270000 12.0110 15 X 2 ALA HB1 HA 0.090000 1.0080 16 X 2 ALA HB2 HA 0.090000 1.0080 17 X 2 ALA HB3 HA 0.090000 1.0080 18 X 2 ALA C C 0.510000 12.0110 19 X 2 ALA O O -0.510000 15.9990 ....
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This note was uploaded on 09/22/2011 for the course BIOL 7110 taught by Professor Steveharvey during the Spring '11 term at Georgia Tech.
- Spring '11