Table of Contents
Size Matters
Does size matter?
Does size matter?...
For example, data like...
What defines the extent of an atom?
Various Radii for atoms found in proteins
Carbon radii illustrated:
Carbon:
Surface definitions and calculations
Accessible surface determines how many solvent molecules can “touch”
The molecular surface is identified by concave regions.
Connolly’s MS program:
Connolly program...
Advantages of dot surface:
Electrostatic potential...
Coulombic electrostatic potential on a Molecular Surface
and the spatial derivatives indicate the contours of the electrostatic field...
Potential gradients around the Glu-Arg dipeptide
van der Waals radii are not standardized!
Applying some literature vdW’s to acetylene
Why does this matter?
Best combination of energy components
Solvation energy of charged molecules is very different from those of uncharged species
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Author: John E. Wampler
References:
Links:
http://wulff.mit.edu/pt/pert1.html - broken link to half distance between centers in
solid metal
http://www.lumsc.indiana.edu/helps/radii.html - broken link to Nat Alcock's Atomic Radii Tables.
See Alcock (1990) below
AMBER- for references, force field details etc for the AMBER Force Field and the AMBER molecular simulation
programs see here.
Sources of van der Waals Radii:
Allcock, N. W. (1990) Bonding and Structure (Ellis Horwood)
Bondi, A. (1964) "van der Waals Volumes and Radii," J. Phys. Chem.
68, 441 (1964)
Bondi, A. (1968) Physical Properties of Molecular Crystals, Liquids,
and Glasses, John Wiley & Sons, Inc., NY (1968), chapter 14
Nyburg, S. C., and Faerman, C. H. (1985) "A Revision of van der Waals
Atomic Radii for Molecular Crystals," Acta Crystallogr. B41, 274-279
(1985).
Pauling, L (1960) The Nature of the Chemical Bond, Cornell
University Press, Ithaca, NY
Surface Types and Calculations:
Connolly, M. L. (1983a) “Solvent-accessible surfaces of proteins and
nucleic acids,” Science 221, 709-713.
Connolly, M. L. (1983b) “Analytical Molecular Surface Calculation,”
J. Applied Cryst. 16, 548-558.
Connolly, M. L. (1993) "The Molecular Surface Package," J. Mol.
Graphics 11, 139-141.
Duncan, B. S., and Olson, A. J. (1993) "Approximation and
Characterization of Molecular Surfaces," Biopolymers 33, 219-229.
Grant, J. A., and B. T. Pickup (1995) "A Gaussian Descripton of
Molecular Shape," J. Phys. Chem. 99, 3503-3510.
Richards, F. M. (1977) “Areas, volumes, packing and protein
structure,” Ann. Rev. in Biophys. & Bioengin. 6, 151-176.
Richards, F. M. (1985) "Calculation of Molecular Volumes and Areas for
Structures of Known Geometry," Methods in Enzymology 115, 440-464.
Solvation energies from surface and volume calculations:
Furuki, T. A. Umeda, M. Sakurai, Y. Inoue and R. Chujo (1994)
"General Parameterization of a Reaction Field Theory Combined with
the Boundary Element Method," J. Comp. Chem. 15, 90-104.
Giesen, D. J., C. J. Cramer & D. G. Truhlar (1994) "Entropic
contributions to free energies of solvation," J. Phys. Chem. 98,
4141-4147.
Gilson, M. & B. Honig (1987), Nature 330, 84-86
Rashin, A.A., & M. A. Bukatin (1994) "A view of thermodynamics of
hydration emerging from continuum studies," Biophys. Chem. 51,
167-192
Rashin, A. A., & K. Namboodiri (1987) "A simple method for the
calculation of hydration enthalpies of polar molecules with
arbitrary shapes," J. Phys. Chem. 91, 6003-6012.
Rashin, A. A., L. Young and I. A. Topol (1994) "Quantitative Evaluation
of Hydration Thermodynamics with a Continuum Model," Biophys. Chem.
51, 359-374
Richards, W. G., P. M. King, & C. A. Reynolds (1989) "Solvation
effects," Protein Engineering 2, 319-327
Tannor, D. J., B. Marten, R. Murphy, R. A. Friesner, D. Sitkof, A. Nicholls,
M. Ringnalda, W. A. Goddard III and B. Honig (1994) J. Am. Chem. Soc. 116, 11875-11882.
Warshell, A., & S. T. Russell (1984), Quart. Rev. Biophys. 17, 283-422.
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