Abstract
The molecular structures of a series of selenocysteine-containing dipeptides in their zwitterionic forms were studied using the B3LYP/6-311++G(d,p) level in the aqueous phase. The B3LYP and BH and HLYP functionals in combination with 6-311++G(d,p) and LANL2DZ basis sets were used to investigate the effects of metal coordination on the structural and molecular properties of the dipeptides by complexing them with bivalent copper ions. The results from this DFT study provide valuable insights into the interaction enthalpies (metal ion-binding affinities) and free energies, the influence of the C-terminal moiety on the backbone structural features, the existence of various types of intramolecular H-bond interactions, harmonic vibrational frequencies, along with various other electronic properties pertaining to the zwitterions of the dipeptide molecules as well as their metallic complexes. Metal coordination via the carboxylate groups tends to enhance the planarity of the amide planes. The participations of the N- and C-terminal side-chain moieties in metal-binding markedly enhance the thermodynamic stability of the metalated dipeptides. The theoretical λmaxvalues, calculated using the TD/DFT level for all the systems, well represent the occurrence of d-d transitions in the Cu-dipeptide complexes.
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Andersson, M. P., & Uvdal, P. (2005). New scale factors for harmonic vibrational frequencies using the B3LYP density functional method with the triple-ζ basis set 6-311+G(d,p). The Journal of Physical Chemistry A, 109, 2937–2941. DOI: 10.1021/jp045733a.
Arunan, E., Desiraju, G. R., Klein, R. A., Sadlej, J., Scheiner, S., Alkorta, I., Clary, D. C., Crabtree, R. H., Dannenberg, J. J., Hobza, P., Kjaergaard, H. G., Legon, A. C., Mennucci, B., & Nesbitt, D. J. (2011). Definition of the hydrogen bond (IU-PAC Recommendations 2011). Pure and Applied Chemistry, 83, 1637–1641. DOI: 10.1351/pAC-REC-10-01-02.
Bauernschmitt, R., & Ahlrichs, R. (1996). Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory. Chemical Physics Letters, 256, 454–464. DOI: 10.1016/0009-2614(96)00440-x.
Becke, A. D. (1993). Density-functional thermochemistry. III. The role of exact exchange. The Journal of Chemical Physics, 98, 5648–5652. DOI: 10.1063/1.464913.
Böck, A., Forchhammer, K., Heider, J., Leinfelder, W., Sawers, G., Veprek, B., & Zinoni, F. (1991a). Selenocysteine: the 21st amino acid. Molecular Microbiology, 5, 515–520. DOI: 10.1111/j.1365-2958.1991.tb00722.x.
Böock, A., Forchhammer, K., Heider, J., & Baron, C. (1991b). Selenoprotein synthesis: an expansion of the genetic code. Trends in Biochemical Sciences, 16, 463–467. DOI: 10.1016/0968-0004(91)90180-4.
Cheam, T. C., & Krimm, S. (1989). Ab initio force fields of alanine dipeptide in C5 and C7 conformations. Journal of Molecular Structure (Theochem), 188, 15–43. DOI: 10.1016/0166-1280(89)85023-7.
Constantino, E., Rimola, A., Rodríguez-Santiago, L., & Sodupe, M. (2005). Coordination properties of glycylglycine to Cu+, Ni+ and Co+. Influence of metal cation electronic configuration. New Journal of Chemistry, 29, 1585–1593. DOI: 10.1039/b512618e.
Das, G. (2014). Rotational aspects of non-ionized creatine in the gas phase. Monatshefte für Chemie — Chemical Monthly, 145, 1431–1441. DOI: 10.1007/s00706-014-1210-0.
Das, G., & Mandal, S. (2014). Ab initio- and density-functional studies of conformational behavior of N-formylmethionine in gaseous phase. Chemical Papers, 68, 1608–1620. DOI: 10.2478/s11696-014-0614-y.
DeGrado, W. F., Summa, C. M., Pavone, V., Nastri, F., & Lombardi, A. (1999). De novo design and structural characterization of proteins and metalloproteins. Annual Review of Biochemistry, 68, 779–819. DOI: 10.1146/annurev.biochem.68.1.779.
Dudev, T., & Lim, C. (2009). Metal-binding affinity and selectivity of nonstandard natural amino acid residues from DFT/CDM calculations. The Journal of Physical Chemistry B, 113, 11754–11764. DOI: 10.1021/jp904249s.
Fraústo da Silva, J. J. R., & Williams, R. J. P. (1991). The biological chemistry of the elements: The inorganic chemistry of life. Oxford, UK: Clarednon Press.
Foresman, J. B., & Frisch, A. (1996). Exploring chemistry with electronic structure methods (2nd ed.). Pittsburgh, PA, USA: Gaussian.
Freeman, F., & Le, K. T. (2003). A computational study of conformations and conformers of 1,3-dithiane (1,3-dithiacyclohexane). The Journal of Physical Chemistry A, 107, 2908–2918. DOI: 10.1021/jp0138633.
Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., Zheng, G., Sonnenberg, J. L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J. A., Jr., Peralta, J. E., Ogliaro, F., Bearpark, M., Heyd, J. J., Brothers, E., Kudin, K. N., Staroverov, V. N., Keith, T., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J. C., Iyengar, S. S., Tomasi, J., Cossi, M., Rega, N., Millam, N. J., Klene, M., Knox, J. E., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Martin, R. L., Morokuma, K., Zakrzewski, V. G., Voth, G. A., Salvador, P., Dannenberg, J. J., Dapprich, S., Daniels, A. D., Farkas, Ö., Foresman, J. B., Ortiz, J. V., Cioslowski, J., & Fox, D. J. (2009). Gaussian 09, Revision B.01 [computer software]. Wallingford, CT, USA: Gaussian.
Fukui, K., Yonezawa, T., & Shingu, H. (1952). A molecular orbital theory of reactivity in aromatic hydrocarbons. The Journal of Chemical Physics, 20, 722–725. DOI: 10.1063/1.1700523.
Gould, I. R., & Hillier, I. H. (1993). Solvation of alanine dipeptide: a quantum mechanical treatment. Journal of the Chemical Society, Chemical Communications, 1993, 951–952. DOI: 10.1039/c39930000951.
Gould, I. R., Cornell, W. D., & Hillier, I. H. (1994). 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, 116, 9250–9256. DOI: 10.1021/ja00099a048.
Hatfield, D. L., & Gladyshev, V. N. (2002). How selenium has altered our understanding of the genetic code. Molecular and Cellular Biology, 22, 3565–3576. DOI: 10.1128/mcb.22.11.3565-3576.2002.
Hay, P. J. (1977). Gaussian basis sets for molecular calculations. The representation of 3d orbitals in transition-metal atoms. The Journal of Chemical Physics, 66, 4377–4384. DOI: 10.1063/1.433731.
Hay, P. J., & Wadt, W. R. (1985a). Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg. The Journal of Chemical Physics, 82, 270–283. DOI: 10.1063/1.448799.
Hay, P. J., & Wadt, W. R. (1985b). Ab initio effective core potentials for molecular calculations. Potentials for main group elements K to Au including the outermost core orbitals. The Journal of Chemical Physics, 82, 299–310. DOI: 10.1063/1.448975.
Hehre, W. J., Radom, L., Schleyer, P. v. R., & Pople, J. A. (1986). Ab initio molecular orbital theory. New York, NY, USA: Wiley.
Jeanvoine, Y., & Spezia, R. (2009). Mn2+-, Fe2+-, Co2+-, Ni2+-, Cu2+-, and Zn2+-binding chalcogen-chalcogen bridges: A compared MP2 and B3LYP study. The Journal of Physical Chemistry A, 113, 7878–7887. DOI: 10.1021/jp811460f.
Kaur, D., Sharma, P., Bharatam, P. V., & Kaur, M. (2008). Understanding selenocysteine through conformational analysis, proton affinities, acidities and bond dissociation energies. International Journal of Quantum Chemistry, 108, 983–991. DOI: 10.1002/qua.21556.
Keefe, C. D., & Pearson, J. K. (2004). Ab initio investigations of dipeptide structures. Journal of Molecular Structure (Theochem), 679, 65–72. DOI: 10.1016/j.theochem.2004.04.005.
Kroneck, P. M. H., Vortisch, V., & Hemmerich, P. (1980). Model studies on the coordination of copper in biological systems. The deprotonated peptide nitrogen as a potential binding site for copper(II). European Journal of Biochemistry, 109, 603–612. DOI: 10.1111/j.1432-1033.1980.tb04833.x.
Lee, C., Yang, W., & Parr, R. G. (1988). Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical Review B, 37, 785–789. DOI: 10.1103/PhysRevB.37.785.
Lippard, S. J., & Berg, J. M. (1994). Principles of bioinorganic chemistry. Mill Valley, CA, USA: University Science Books.
Lu, Y., Berry, S. M., & Pfister, T. D. (2001). Engineering novel metalloproteins: Design of metal-binding sites into native protein scaffolds. Chemical Reviews, 101, 3047–3080. DOI: 10.1021/cr0000574.
Lukashenko, N. P. (2010). Expanding genetic code: Amino acids 21 and 22, selenocysteine and pyrrolysine. Russian Journal of Genetics, 46, 899–916. DOI: 10.1134/s1022795410080016.
Mandal, S., & Das, G. (2013). Structure of dipeptides having N-terminal selenocysteine residues: a DFT study in gas and aqueous phase. Journal of Molecular Modeling, 19, 2613–2623. DOI: 10.1007/s00894-013-1808-x.
Mandal, S., Das, G., & Askari, H. (2014). Experimental and quantum chemical modeling studies of the interactions of L-phenylalanine with divalent transition metal cations. Journal of Chemical Information and Modeling, 54, 2524–2535. DOI: 10.1021/ci500500k.
Marques, M. A. L., & Gross, E. K. U. (2004). Time-dependent density functional theory. Annual Review of Physical Chemistry, 55, 427–455. DOI: 10.1146/annurev.physchem.55.091602.094449.
Miertuš, S., Scrocco, E., & Tomasi, J. (1981). Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects. Chemical Physics, 55, 117–129. DOI: 10.1016/0301-0104(81)85090-2.
Ramachandhan, G. N. (1963). Need for nonplanar peptide units in polypeptide chains. Biopolymers, 6, 1494–1496. DOI: 10.1002/bip.1968.360061013.
Ramachandran, G. N., Ramakrishnan, C., & Sasisekharan, V. (1963). Stereochemistry of polypeptide chain configurations. Journal of Molecular Biology, 7, 95–99. DOI: 10.1016/s0022-2836(63)80023-6.
Remko, M., & Rode, B. M. (2000). Bivalent cation binding effect on formation of the peptide bond. Chemical Physics Letters, 316, 489–494. DOI: 10.1016/s0009-2614(99)01322-6.
Remko, M., Fitz, D., & Rode, B. M. (2008). Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water coordination on the structure and properties of L-arginine and zwitterionic L-arginine. The Journal of Physical Chemistry A, 112, 7652–7661. DOI: 10.1021/jp801418h.
Remko, M., Fitz, D., Broer, R., & Rode, B. M. (2011). Effect of metal ions (Ni2+, Cu2+ and Zn2+) and water coordination on the structure of L-phenylalanine, L-tyrosine, L-tryptophan and their zwitterionic forms. Journal of Molecular Modeling, 17, 3117–3128. DOI: 10.1007/s00894-011-1000-0.
Rode, B. M. (1999). Peptides and the origin of life. Peptides, 20, 773–786. DOI: 10.1016/s0196-9781(99)00062-5.
Rother, M., & Krzycki, J. A. (2010). Selenocysteine, pyrrolysine, and the unique energy metabolism of methanogenic archaea. Archaea, 2010, 453642. DOI: 10.1155/2010/453642.
Saada, I., & Pearson, J. K. (2011). A theoretical study of the structure and electron density of the peptide bond. Computational and Theoretical Chemistry, 969, 76–82. DOI: 10.1016/j.comptc.2011.05.023.
Spezia, R., Tournois, G., Cartailler, T., Tortajada, J., & Jeanvoine, Y. (2006). Co2+ binding cysteine and selenocysteine: A DFT study. The Journal of Physical Chemistry A, 110, 9727–9735. DOI: 10.1021/jp0614998.
Stadtman, T. C. (1996). Selenocysteine. Annual Review of Biochemistry, 65, 83–100. DOI: 10.1146/annurev.bi.65.070196.000503.
Stepanian, S. G., Reva, I. D., Radchenko, E. D., Rosado, M. T. S., Duarte, M. L. T. S., Fausto, R., & Adamowicz, L. (1998). Matrix-isolation infrared and theoretical studies of the glycine conformers. The Journal of Physical Chemistry A, 102, 1041–1054. DOI: 10.1021/jp973397a.
Stratmann, R. E., Scuseria, G. E., & Frisch, M. J. (1998). An efficient implementation of time-dependent density-functional theory for the calculation of excitation energies of large molecules. The Journal of Chemical Physics, 109, 8218–8224. DOI: 10.1063/1.477483.
Tobias, D. J., & Brooks, C. L., III (1992). Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution: A comparison of theoretical results. The Journal of Physical Chemistry, 96, 3864–3870. DOI: 10.1021/j100188a054.
Wachters, A. J. H. (1970). Gaussian basis set for molecular wavefunctions containing third-row atoms. The Journal of Chemical Physics, 52, 1033–1036. DOI: 10.1063/1.1673095.
Wadt, W. R., & Hay, P. J. (1985). Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi. The Journal of Chemical Physics, 82, 284–298. DOI: 10.1063/1.448800.
Wang, Z. X., & Duan, Y. (2004). 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, 25, 1699–1716. DOI: 10.1002/jcc.20092.
Yokota, K., Hagimori, M., Mizuyama, N., Nishimura, Y., Fujito, H., Shigemitsu, Y., & Tominaga, Y. (2012). Synthesis, solid-state fluorescence properties, and computational analysis of novel 2-aminobenzo[4,5]thieno[3,2-d]pyrimidine 5,5-dioxides. Beilstein Journal of Organic Chemistry, 8, 266–274. DOI: 10.3762/bjoc.8.28.
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Das, G., Mandal, S. Zwitterionic structures of selenocysteine-containing dipeptides and their interactions with Cu(II) ions. Chem. Pap. 69, 616–626 (2015). https://doi.org/10.1515/chempap-2015-0064
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DOI: https://doi.org/10.1515/chempap-2015-0064