Intra- and Inter-molecular Forces

Table of Contents

{1} Intra- and Inter-molecular Forces

{2} Describing molecular forces...

{3} A further look at vdW radii

{4} A further look at vdW radii...

{5} A further look at vdW radii...

{6} Non-bonding Interactions

{7} The basis of non-bonded interactions

{8} With a neutral species...

{9} Within proteins there are some fairly large and more permenant charge separations.

{10} Interactions of dipoles...

{11} The aromatic residues of proteins have quadrupole moments

{12} What prevents an attraction between charged groups from fusing the atoms?

{13} Combined short range interactions, the Lennard-Jones potential

{14} A and B must be functions of...

{15} There is little theoretical support for 12 power repulsion term.

{16} Example: potential well shapes...

{17} The van der Waals potential...

{18} The Hydrogen Bond

{19} The approach of H-bond acceptor polarizes donar-H bond

{20} H-bonds also have a distinct, but small angle dependence

{21} Bonding Interactions

{22} Covalent Bonds

{23} Example, ab initio energies for the carbonyl stretch of formaldehyde.

{24} A good fit to this shape is the Morse potential...

{25} Example, Morse potential fit to the formaldehyde carbonyl stretch

{26} Angle Preferences

{27} Example, the H-C-H bending of formaldehyde

{28} Example cont., harmonic fit to the H-C-H bending of formaldehyde*

{29} Rotation Angle Preferences

{30} The less symmetrical N-methyl-amide...

{31} Removing the 1-4 non-bonded interactions...

{32} Interdependence

{33} Interdependence...

References:

Atkins, P. W. (1990) Physical Chemistry, W. H. Freeman and Company, NY. Chapter 22.

Burley, S. K., and G. A. Petsko (1988), "Weakly Polar Interactions in Proteins," in Advances in Protein Chemistry vol. 39, pp. 125-189.

Creighton, T. E. (1993) Proteins Structures and Molecular Properties, W. H. Freeman and Company, NY. Chapter 4, Section 4.1.4

J-H. Lii & N. L. Allinger (1998), "Directional Hydrogen Bonding in the MM3 Force Field. II," J. Comp. Chem. 19, 1001-1016.

Pauling, L (1960) The Nature of the Chemical Bond, Cornell University Press, Ithaca, NY. Chapter 12

Stewart, D. E., A. Sarkar, J. E. Wampler, "The Occurrence and Role of cis Peptide Bonds in Protein Structures," J. Mol. Biol. 214, 253-260 (1990).