The Introduction of Atom Types and Calculations of New Parameters for Charge Equilibrium Method

Akifumi ODAa,b* and Shuichi HIRONOb

aDiscovery Laboratories, Toyama Chemical Co., Ltd.,
2-4-1 Shimookui, Toyama 930-8508, Japan
bSchool of Pharmaceutical Sciences, Kitasato University
5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan

(Received: January 17, 2003; Accepted for publication: February 17, 2003; Published on Web: March 20, 2003)

The calculations of atomic charges play important roles in the non-bonded interaction terms of energy functions of molecular mechanics (MM) and molecular dynamics (MD) methods. In this study, we introduce atom types for the charge equilibrium method (QEq method), which can be easily calculated and can derive different charges for different conformations. Since this method requires one-center Coulombic terms and electronegativities as parameters, we determine these parameters by using 153 compounds. We also determined the parameters for carboxylic acid ion carbon, pyrrole nitrogen, ammonium ion nitrogen, nitro nitrogen, furan oxygen, trivalent and quintivalent phosphorus, bivalent and sexivalent sulfur, thiophene sulfur, chlorine and bromine, see Table 3. Using these atom types and parameters, appropriate atomic charges can be obtained for various molecules by the QEq method and, thus, more accurate molecular energy becomes available in MM and MD.

Keywords: Atomic charge, Charge equilibrium method, Atom type, Molecular mechanics


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