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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 24, Number 3
BKCSDE 24(3)
March 20, 2003 

An Efficient Method to Compute Partial Atomic Charges of Large Molecules Using Reassociation of Fragments
Jung-Goo Lee, Ho Young Jeong, Hosull Lee
Population analysis, Fragment reassociation
Coulson (ZINDO), Mulliken (MP2/6-31G*) and Natural (MP2/6-31G*) population analyses of several large molecules were performed by the Fragment Reassociation (FR) method. The agreement between the conventional ZINDO (or conventional MP2) and FR-ZINDO (or FR-MP2) charges of these molecules was excellent. The standard deviations of the FR-ZINDO net atomic charges from the conventional ZINDO net atomic charges were 0.0008 for C10H22 (32 atoms), 0.0012 for NH2-C16O2H28-COOH (53 atoms), 0.0014 for NH3 +-C16O2H28-COOH (54 atoms), 0.0017 for NH2-C16O2H28-COO- (52 atoms), 0.0019 for NH3 +-C16O2H28- COO- (53 atoms), 0.0024 for a conjugated model (O=CH-(CH=CH)15-C=O-(CH=CH)12-CH=CH2), 118 atoms), 0.0038 for aglycoristocetin (C60N7O19H52 +, 138 atoms), 0.0023 for a polypropylene model complexed with a zirconocene catalyst (C68H121Zr+, 190 atoms) and 0.0013 for magainin (C112N29O28SH177, 347 atoms), respectively. The standard deviations of the FR-MP2 Mulliken (or Natural) partial atomic charges from the conventional ones were 0.0016 (or 0.0016) for C10H22, 0.0019 (or 0.0018) for NH2-C16O2H28-COOH and 0.0033 (or 0.0023) for NH3 +-C16O2H28-COO-, respectively. These errors were attributed to the shape of molecules, the choice of fragments and the degree of ionic characters of molecules as well as the choice of methods. The CPU time of aglycoristocetin, conjugated model, polypropylene model complexed with zirconocene and magainin computed by the FR-ZINDO method was respectively 2, 4, 6 and 21 times faster than that by the normal ZINDO method. The CPU time of NH2-C16O2H28-COOH and NH3 +-C16O2H28-COO- computed by the FR-MP2 method was, respectively, 6 and 20 times faster than that by the normal MP2 method. The largest molecule calculated by the FR-ZINDO method was B-DNA (766 atoms). These results will enable us to compute atomic charges of huge molecules near future.
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