Quantum Chemical Calculations on the Conformational Structure of the Alanine Oligomer Model

알라닌 올리고머의 배좌구조에 관한 양자화학적 계산

  • Sim, Jae-Ho (Department of Advanced Materal and Chemical Engineering, Halla University)
  • 심재호 (한라대학교 공과대학 신소재화학공학과)
  • Received : 2014.10.10
  • Accepted : 2015.02.12
  • Published : 2015.02.28


Conformational change during chain propagation of alanine oligomer was investigated by quantum chemical calculation(QCC) using 2~5mers(${\times}=2{\sim}5$) models. For estimation of the end group effects, two types of end group. "amide type" ($CH_3CONH-and-CONHCH_3$) and "methyl type" ($CH_3CONH-and-CONHCH_3$), were prepared as both ends(N-and-C). Conformers optimized for 5-mer converged to three types of ${\Phi}/{\Psi}$ : ${\alpha}$-helix(g+/g+, or g-/g-), PPII-like(extended helix-like, g+/g-, or g-/g+), and ${\beta}$-extended (t+/t-, or t-/t+), in the order of lower energy, and the energies of left- and right- handed conformers were the same (5-mer. amide type ${\Delta}E=-1.05$, right type ${\Delta}E=-1.62$). Energies of the monomer unit(${\Delta}E$) of ${\alpha}$-helix decreased with increases of monomer.


  1. J. Graf, P. H. Nguyen, G. Stock, and H. Schwalbe, "Structure and Dynamics of the Homologous Series of Alanine Peptides", J. Am. Chem. Soc., Vol. 129, 1179-1189 (2007). DOI:
  2. N. G. Mirkin and S. Krimm, "Conformation Dependence of the C$C^{\alpha}D^{\alpha}$ Stretch Mode in Peptides. I. Isolated Alanine Peptide Structures", J. Phys. Chem., A, Vol. A111, 5300-5303 (2007). DOI:
  3. A. Kentsis, M. Mezei, T. Gindin, and R. Osman, "Unfolded State of Polyalanine is a Segmented Polyproline II Helix", PROTEINS: Structure, Function, and Bioinformatics, Vol. 55, 493-501 (2004). DOI:
  4. M. Kobayashi and H. Sato, "Examinaion of Conformations of Isotactic Methyl Methacrylate Oligomers by Quantum Chemical Calculation", Kobunshi Ronbun shu, Vol. 64, No. 2. 119-127 (2007). DOI:
  5. M. Kobayashi and H. Sato, "Conformational Analysis of Ethylene oxide and Ethylene Imine Oligomers by Quantum Chemical Calculation", Polymer Journal, Vol. 40, No. 4, 343-349 (2008). DOI:
  6. M. Kobayashi, M. Takahashi, and H. Sato, "Conformational Analysis for Hydrated Ethylene Imine Oligomer Model by Quantum Chemical Calculations", Polymer Journal, Vol. 41, No. 10, 880-887 (2009). DOI:
  7. M. Kobayashi and H. Sato, "Structure Analysis for Hydrate Model of Ethyleneimine Oligomer by Quantum Chemical Calculation", Pharmacology & Pharmacy; Vol. 1, 60-68 (2010). DOI:
  8. N. G. Mirkin, S. Krimm, "Conformation Dependence of the $C^{\alpha}D^{\alpha}$ Stretch Mode in Peptides. II. Explicitly Hydrated Alanine Peptide Structures", Biopolymer, Vol. 91, 791-800 (2009) DOI:
  9. "Gaussian 03 User's Reference", Gaussian Inc., Carnegie, PA, 2003
  10. J. Makowska, A. Liwo, W. Zmudzinska, A. Lewandowska, L. Chmurzynski, and H. A Scheraga, "Like-Charged Residues at the Ends of Oligoalanine Sequences Might Induce a Chain Reversal", Biopolymers, Vol. 97, No. 4, 240-249 (2011). DOI: