title: Computation of large systems with an economic basis set: structures and reactivity indices of nucleic acid base pairs from density functional theory.
abstract: We show here that an economic basis set can describe nucleic acid base pairs involving the hydrogen bond interactions in density functional calculations. The economic basis set in which the polarization function is added only to oxygen and nitrogen atoms of strong electronegativity can predict reliable geometric structures and dipole moment of nucleic acid base pairs, comparable to those obtained from the basis set of 6-31G* in B3LYP calculations. Combining single point calculations with the standard basis set on the geometric structures optimized by the economic basis set, the present approach has predicted accurate natural bond orbital charge, binding energy, electronegativity, hardness, softness, and electrophilicity index. The principle for basis selection presented in this study can be regarded as a general guideline in the computation of large biological systems with considerably high accuracy and low computational expense.
authors.affiliation: Center of Super-Diamond and Advanced Films (COSDAF) & Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, People's Republic of China.
authors.forename: W J
authors.initials: WJ
authors.lastname: Fan
authors.forename: R Q
authors.initials: RQ
authors.lastname: Zhang
authors.forename: Shubin
authors.initials: S
authors.lastname: Liu
mesh_terms: D000225:Adenine / Q000737:chemistry; D000465:Algorithms; D001482:Base Composition; D020029:Base Pairing; D003198:Computer Simulation; D003596:Cytosine / Q000737:chemistry; D006860:Hydrogen Bonding; D009584:Nitrogen / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D009705:Nucleosides / Q000737:chemistry*; D010100:Oxygen / Q000737:chemistry; D011789:Quantum Theory; D012984:Software / Q000191:economics; D013941:Thymine / Q000737:chemistry
chemical_list: D009696:Nucleic Acids; D009705:Nucleosides; D003596:Cytosine; D000225:Adenine; D009584:Nitrogen; D013941:Thymine; D010100:Oxygen