Journal of the Korean Physical Society, Vol. 60, No. 9, May 2012, pp. 1452∼1456 First-principles Studies of the Energetics and the Electronic Structures of Methylguanine Geunjung Lee and Young-Gui Yoon ∗ Department of Physics, Chung-Ang University, Seoul 156-756, Korea (Received 1 February 2012) We calculate the total energies, the equilibrium geometries, and the HOMO-LUMO energy gaps of keto 9-H guanine (N9H), keto 7-H guanine (N7H), and various guanine, methylguanine, and dimethylguanine molecules related to N9H and N7H. Bond orders are found to be crucial in de- termining the HOMO-LUMO energy gaps. The impact of structural changes such as methylation and the rearrangement of the hydrogen atoms of guanine molecules on the geometries and the elec- tronic properties can be understood in terms of the bond orders, the steric effects, and the specific molecular topologies. PACS numbers: 87.14.Gg, 87.15.Aa, 87.15.-v Keywords: Energetics, Guanine, Methylguanine, Dimethylguanine, HOMO-LUMO DOI: 10.3938/jkps.60.1452 I. INTRODUCTION DNA nanotechnology is a rapidly growing field [1]. En- gineered DNA strands have been used as building blocks for DNA-based nanostructures [2], and a methylation- stimulated DNA machine has been implemented [3]. DNA methylation is also involved in many important biochemical processes [4,5], epigenetic regulation of gene expression [6], the genome’s immune system [7], and mu- tagenesis [8]. Recently, modified forms of DNA bases and their electronic properties have been receiving great at- tention [9–11]. DNA guanine molecules can be functionalized with a methyl group (-CH 3 ) at experimentally known sites (N1, N 2 , N3, O 6 , N7, C8, and N9) [12–16], and theoretical in- vestigations on those molecules are growing rapidly [17– 20]. Electronic structure calculations of those bases may help us to understand the mechanisms involving func- tionalized DNA bases and to engineer biomaterials with desired electronic properties. Therefore, we have per- formed first-principles electronic structure calculations on the guanine and the methylguanine molecules. II. CALCULATION We have calculated the energetics, the equilibrium gas phase geometries, and the electronic properties of guanine and methylguanine molecules. The structures ∗ E-mail: yyoon@cau.ac.kr; Fax: +82-2-825-4988 are studied in a fcc supercell with primitive vectors of 25 ˚ A to minimize spurious image image interactions. The calculations are performed using the ab-initio total- energy and molecular-dynamics program VASP (Vienna ab-initio simulation program) developed at the Institute f¨ ur Materialphysic of the Universitat Wien, using the projector-augmented-wave (PAW) approach [21]. We adopt the generalized gradient approximation (GGA) implemented by Perdew, Burke, and Ernzerhof (PBE) [22] for the exchange-correlation energy functional. We employ a plane-wave basis set with a cutoff energy of 500 eV. The structures are relaxed until the maximum of the remaining forces on the atoms is less than 0.01 eV/ ˚ A. III. RESULTS AND DISCUSSION We investigate keto 9-H guanine (N9H), keto 7-H gua- nine (N7H), and various guanine, methylguanine, and dimethylguanine molecules related to N9H and N7H. The ball and stick model structures of the calculated equilib- rium geometries are shown in Figs. 1, 2, and 3. The stan- dard numbering for the C, N, and O atoms in Fig. 1 is also applicable to the C, N, and O atoms in Figs. 2 and 3. The equilibrium gas phase geometries are analyzed in terms of the dihedral angles. The calculated rela- tive energies, angles for all the optimized structures, and HOMO-LUMO energy gaps are presented in Tables 1, 2, and 3. In Fig. 1, the calculated guanine structures are related to the N9H and the N7H guanine structures in the fol- lowing manner: The N1H hydrogen atom is removed, -1452-