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Biochemistry Research International
Volume 2013 (2013), Article ID 939865, 12 pages
Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides
Department of Chemistry, North Eastern Hill University, Shillong 793022, India
Received 9 July 2013; Accepted 15 August 2013
Academic Editor: Emil Pai
Copyright © 2013 Gunajyoti Das and Shilpi Mandal. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- M. Rother and J. A. Krzycki, “Selenocysteine, pyrrolysine, and the unique energy metabolism of methanogenic archaea,” Archaea, vol. 2010, Article ID 453642, 14 pages, 2010.
- I. Chambers, J. Frampton, P. Goldfarb, N. Affara, W. McBain, and P. R. Harrison, “The structure of the mouse glutathione peroxidase gene: the selenocysteine in the active site is encoded by the ‘termination’ codon, TGA,” The EMBO Journal, vol. 5, no. 6, pp. 1221–1227, 1986.
- F. Zinoni, A. Birkmann, T. C. Stadtman, and A. Bock, “Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked) from Escherichia coli,” Proceedings of the National Academy of Sciences of the United States of America, vol. 83, no. 13, pp. 4650–4654, 1986.
- A. Bock, K. Forchhammer, J. Heider et al., “Selenocysteine: the 21st amino acid,” Molecular Microbiology, vol. 5, no. 3, pp. 515–520, 1991.
- N. P. Lukashenko, “Expanding genetic code: amino acids 21 and 22, selenocysteine and pyrrolysine,” Russian Journal of Genetics, vol. 46, no. 8, pp. 899–916, 2010.
- T. C. Stadtman, “Selenocysteine,” Annual Review of Biochemistry, vol. 65, pp. 83–100, 1996.
- D. L. Hatfield and V. N. Gladyshev, “How selenium has altered our understanding of the genetic code,” Molecular and Cellular Biology, vol. 22, no. 11, pp. 3565–3576, 2002.
- R. H. Garrett and C. M. Grisham, Biochemistry, Chapter 6, Saunders College Publishing, New York, NY, USA, 1999.
- M. R. Wormald, A. J. Petrescu, Y.-L. Pao, A. Glithero, T. Elliott, and R. A. Dwek, “Conformational studies of oligosaccharides and glycopeptides: complementarity of NMR, X-ray crystallography, and molecular modelling,” Chemical Reviews, vol. 102, no. 2, pp. 371–386, 2002.
- N. Foloppe, B. Hartmann, L. Nilsson, and A. D. MacKerell Jr., “Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study,” Biophysical Journal, vol. 82, no. 3, pp. 1554–1569, 2002.
- J. Sponer, M. Zgarbova, P. Jurecka, K. E. Riley, J. E. Sponer, and P. Hobza, “Reference quantum chemical calculations on RNA base pairs directly involving the 2′-OH group of ribose,” Journal of Chemical Theory and Computation, vol. 5, pp. 1166–1179, 1999.
- S. Ghosh, S. Mondal, A. Misra, and S. Dalai, “Investigation on the structure of dipeptides: a DFT study,” Journal of Molecular Structure, vol. 805, no. 1–3, pp. 133–141, 2007.
- C. D. Keefe and J. K. Pearson, “Ab initio investigations of dipeptide structures,” Journal of Molecular Structure, vol. 679, no. 1-2, pp. 65–72, 2004.
- I. Saada and J. K. Pearson, “A theoretical study of the structure and electron density of the peptide bond,” Computational and Theoretical Chemistry, vol. 969, no. 1–3, pp. 76–82, 2011.
- R. Vargas, J. Garza, B. P. Hay, and D. A. Dixon, “Conformational study of the alanine dipeptide at the MP2 and DFT levels,” Journal of Physical Chemistry A, vol. 106, no. 13, pp. 3213–3218, 2002.
- D. J. Tobiast and C. L. Brooks III, “Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution: a comparison of theoretical results,” Journal of Physical Chemistry A, vol. 96, pp. 3864–3874, 1992.
- Z.-X. Wang and Y. Duan, “Solvation effects on alanine dipeptide: a MP2/cc-pVTZ//MP2/6-31G** study of (Φ, Ψ) energy maps and conformers in the gas phase, ether, and water,” Journal of Computational Chemistry, vol. 25, no. 14, pp. 1699–1716, 2004.
- F. F. García-Prieto, I. F. Galvan, M. A. Aguilar, and M. E. Martín, “Study on the conformational equilibrium of the alanine dipeptide in water solution by using the averaged solvent electrostatic potential from molecular dynamics methodology,” Journal of Chemical Physics, vol. 135, pp. 194502–194509, 2011.
- I. R. Gould, W. D. Cornell, and I. H. Hillier, “A quantum mechanical investigation of the conformational energetics of the alanine and glycine dipeptides in the gas phase and in aqueous solution,” Journal of the American Chemical Society, vol. 116, no. 20, pp. 9250–9256, 1994.
- T. Head-Gordon, M. Head-Gordon, M. J. Frisch, C. L. Brooks III, and J. A. Pople, “Theoretical study of blocked glycine and alanine peptide analogues,” Journal of the American Chemical Society, vol. 113, no. 16, pp. 5989–5997, 1991.
- C. Adamo, V. Dillet, and V. Barone, “Solvent effects on the conformational behavior of model peptides. A comparison between different continuum models,” Chemical Physics Letters, vol. 263, no. 1-2, pp. 113–118, 1996.
- G. Das, “Investigations of dipeptide structures containing pyrrolysine as N-terminal residues: a DFT study in gas and aqueous phase,” Journal of Molecular Modeling, vol. 19, no. 4, pp. 1901–1911, 2013.
- S. Mandal and G. Das, “Structure of dipeptides having N-terminal selenocysteine residues: a DFT study in gas and aqueous phase,” Journal of Molecular Modeling, vol. 19, pp. 2613–2613, 2013.
- G. N. Ramachandran, “Need for nonplanar peptide units in polypeptide chains,” Biopolymers, vol. 6, pp. 1494–1496, 1963.
- G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, “Stereochemistry of polypeptide chain configurations,” Journal of Molecular Biology, vol. 7, pp. 95–99, 1963.
- G. A. Chasse, A. M. Rodriguez, M. L. Mak et al., “Peptide and protein folding,” Journal of Molecular Structure, vol. 537, no. 1, pp. 319–361, 2001.
- A. D. Becke, “Density-functional thermochemistry. III. The role of exact exchange,” Journal of Chemical Physics, vol. 98, pp. 5648–5662, 1993.
- C. Lee, W. Yang, and R. G. Parr, “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density,” Physical Review B, vol. 37, no. 2, pp. 785–789, 1988.
- M. J. Frisch, et al., Gaussian 03, Revision C. 01, Wallingford, Conn, USA, 2004.
- Z. A. Tehrani, E. Tavasoli, and A. Fattahi, “Conformational behavior and potential energy profile of gaseous histidine,” Journal of Molecular Structure, vol. 960, no. 1–3, pp. 73–85, 2010.
- S. Miertus, E. Scrocco, and J. Tomasi, “Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects,” Chemical Physics, vol. 55, no. 1, pp. 117–129, 1981.
- I. R. Gould and I. H. Hillier, “Solvation of alanine dipeptide: a quantum mechanical treatment,” Journal of the Chemical Society, Chemical Communications, pp. 951–952, 1993.
- M. P. Andersson and P. Uvdal, “New scale factors for harmonic vibrational frequencies using the B3LYP density functional method with the triple-ζ basis Set 6-311+G(d,p),” Journal of Physical Chemistry A, vol. 109, no. 12, pp. 2937–2941, 2005.
- J. B. Foresman and A. Frisch, Exploring Chemistry with Electronic Structure Methods, Gaussian, Pittsburgh, Pa, USA, 2nd edition, 1996.
- F. Freeman and K. T. Le, “A computational study of conformations and conformers of 1,3-dithiane (1,3-dithiacyclohexane),” Journal of Physical Chemistry A, vol. 107, no. 16, pp. 2908–2918, 2003.
- S. G. Stepanian, I. D. Reva, E. D. Radchenko et al., “Matrix-isolation infrared and theoretical studies of the glycine conformers,” Journal of Physical Chemistry A, vol. 102, no. 6, pp. 1041–1054, 1998.
- S. G. Stepanian, I. D. Reva, E. D. Radchenko, and L. Adamowicz, “Conformational behavior of α-alanine. Matrix-isolation infrared and theoretical DFT and ab initio study,” Journal of Physical Chemistry A, vol. 102, no. 24, pp. 4623–4629, 1998.
- Z. Huang and Z. Lin, “Detailed Ab initio studies of the conformers and conformational distributions of gaseous tryptophan,” Journal of Physical Chemistry A, vol. 109, no. 11, pp. 2656–2659, 2005.
- M. T. Baei and S. Zahra Sayyed-Alangi, “Effects of zinc binding on the structure and stability of glycylglycine dipeptide: a computational study,” E-Journal of Chemistry, vol. 9, no. 3, pp. 1244–1250, 2012.
- K. Fukui, T. Yonezawa, and H. Shingu, “A molecular orbital theory of reactivity in aromatic hydrocarbons,” The Journal of Chemical Physics, vol. 20, no. 4, pp. 722–725, 1952.
- L. Padmaja, C. Ravikumar, D. Sajan et al., “Density functional study on the structural conformations and intramolecular charge transfer from the vibrational spectra of the anticancer drug combretastatin-A2,” Journal of Raman Spectroscopy, vol. 40, no. 4, pp. 419–428, 2009.
- C. Ravikumar, J. I. Hubert, and V. S. Jayakumar, “Charge transfer interactions and nonlinear optical properties of push-pull chromophore benzaldehyde phenylhydrazone: a vibrational approach,” Chemical Physics Letters, vol. 460, pp. 552–558, 2008.
- Z. Slanina, M.-A. Hsu, and T. J. Chow, “Computations on a series of substituted quinolines,” Journal of the Chinese Chemical Society, vol. 50, no. 3, pp. 593–596, 2003.