Method and apparatus for designing molecular structures using an analytical solution for effective born radii

US5420805A · kind A · utility

Assignee

• The Trustees of Columbia University in the City of New York · US

Inventors

• William Still · Atlanta, US
• Frank Hollinger · Barwala, IN

Key dates

• Filing date: May 5, 1992
• Grant date: May 30, 1995
• Expiry date: May 5, 2012

Classification

• Technology area (CPC G): Physics
• CPC primary: G16C20/50
• WIPO field: Biotechnology
• WIPO sector: Chemistry

Abstract

The effective Born radii of atoms in a molecule are determined using a new molecular modeling technique. In this approach, the electrical polarization component of solvation energy of an atom i is approximated as the electrical polarization energy given by the classical Born equation (Eq. 2), assuming that the Born radius .alpha. is equal to the van der Waals radius of the atom, minus the effects of all surrounding atoms, j, which displace solvent from around atom i. This displacement effect increases with the volume of the atom j and decreases as the fourth power of the separation between atom i and atom j. E.sub.pol for atom i can therefore be calculated using the following equation: EQU E.sub.pol,i =-166(1-1/.epsilon.)q.sub.i [1/(P.sub.0 +R.sub.i)-.SIGMA.PV.sub.j /r.sub.ij.sup.4 ] wherein R.sub.i is the van der Waals radius of atom i, V.sub.j is the volume of an atom j, and P.sub.0 and P are empirically determined, solvent-dependant constants or functions of r.sub.ij, This value of E.sub.pol,i is then substituted into a rearranged form of the Born equation EQU .alpha..sub.i =-166(1-1/.epsilon.)q.sub.i.sup.2 /E.sub.pol,i to give the effective Born radius for atom i, .alpha..sub.i…