REFERENCES
- AhnDS, ParkSW, JeonIS, LeeMK, KimNH, KimYH, HanYH, LeeS. Effects of microsolvation on the structures and reactions of neutral and zwitterionic alanine: computational study. J Phys Chem B. 2003;107:14109–14118.
- HalleB. Protein hydration dynamics in solution: a critical survey. Philos Trans Soc Lond B. 2004;359:1207–1224.
- CreightonT. Proteins. 2nd ed. New York: Freeman and company; 1993.
- BakerEN. Solvent interactions with proteins as revealed by X-ray crystallographic studies. In protein-solvent interactions. New York: Marcel Dekker; 1995.
- DanielRM, DunnRV, FinneyJL, SmithJC. The role of dynamics in enzyme activity. Annu Rev Biophys Biomol Struct. 2003;32:69–92.
- LanghorstU, BackmannJ, LorisR, StevaertJ. Analysis of water mediated protein-protein interactions within RNase T1. Biochemistry. 2000;39:6586–6593.
- DenisovVP, JonssonBH, HalleB. Hydration of denaturated and molten globule proteins. Nat Struct Biol. 1999;6:253–260.
- TorozD, MourikTV. Structure of the gas-phase glycine tripeptide. Phys Chem Chem Phys. 2010;12:3463–3473.
- SrikrishnanT, WiniewiczN, ParthasarathyR. New patterns of hydrogen bonded interactions between polypeptide chains. Int J Pept Protein Res. 1982;19:103–113.
- WrightLR, BorkmanRF. Ab initio self-consistent field studies of the peptides Gly-Gly, Gly-Ala, Ala-Gly, and Gly-Gly-Gly. J Phys Chem. 1982;86:3956–3962.
- ShipmanLL, ChristoffersenRE. Ab initio calculations on large molecules using molecular fragments. Evidence of hydrogen bonding in polypeptides of glycine. Proc Nat Acad Sci USA. 1972;69:3301–3304.
- RodgriquezCF, CunjeA, ShoeibT, ChuIK, HopkinsonAC, SiuKWM. Solvent-assisted rearrangements between tautomers of protonated peptides. J Phys Chem A. 2000;104:5023–5028.
- TorriH, TasumiM. Ab initio molecular orbital study of the amide I vibrational interactions between the peptide groups in di- and tripeptides and considerations on the conformation of the extended helix. J Raman Spectrosc. 1998;29:81–86.
- StennerRS. Dihedral angles of tripeptides in solution directly determined by polarized Raman and FTIR spectroscopy. Biophys J. 2002;83:523–532.
- ChatterjeeA, ZhaoL, ZhangL, PradhanD, ZhouX, LeungKT. Core-level electronic structure of solid-phase glycine, glycyl-glycine, diglycyl-glycine, and polyglycine: X-ray photoemission analysis and Hartree-Fock calculations of their zwitterions. J Chem Phys. 2008;129 105104-1–105104-6.
- GordonML, CooperG, MorinC, ArakiT, TureiCC, KaznatcheevK, HitchcockAP. Inner-shell excitation spectroscopy of the peptide bond: comparison of the C 1s, N 1s, and O 1s spectra of glycine, glycyl-glycine, and glycyl-glycyl-glycine. J Phys Chem A. 2003;107:6144–6159.
- SanthanamoorthiN, KolandaivelP, SenthilkumarK. Effect of conformational degrees of freedom on the charge transfer in model tripeptide. J Mol Graph Model. 2009;27:784–791.
- YakubovitchAV, Solov'yovIA, Solov'yovAV, GreinerW. Conformational changes in glycine tri-and hexapeptide. Eur Phys J. 2005;39:23–34.
- ParkC, CarlsonMJ, GoddardWAIII. Solvent effects on the secondary structures of proteins. J Phys Chem A. 2000;104:2498–2503.
- GorbunovRD, StockG. Ab initio based building block model of amide I vibrations in peptides. Chem Phys Lett. 2007;437:272–276.
- BrandenC, ToozeJ. Introduction to protein structure. London: Imperial Cancer Research Fund Laboratories; 1999.
- YogeswariB, KanakarajuR, AbiramA, KolandaivelP. Molecular dynamics and quantum chemical studies on incremental solvation of glycine. Comput Theor Chem. 2011;967:81–92.
- YogeswariB, KanakarajuR, BoopathiS, KolandaivelP. Microsolvation and hydrogen bond interactions in glycine dipeptide: molecular dynamics and density functional theory studies. J Mol Graph Model. 2012;35:11–20.
- YogeswariB, KanakarajuR, BoopathiS, KolandaivelP. Molecular dynamics and quantum chemical studies of solvent effects on cyclo glycylglycine and glycylalanine dipeptides. J Mol Simul. 2013;8: 670–687.
- GuimaraesCRW, BarreiroG, AugustoC, OliveiraFD, AlencastroRBD. On the application of simple explicit water models to the simulations of Biomolecules. Braz J Phys. 2004;34:126–136.
- CaseDA, DardenTA, CheathamTEIII, SimmerlingCL, WangJ, DukeRE, LuoR, MerzKM, WangB, PearlmanDA, CrowleyM, BrozellS, TsuiV, GohlkeH, MonganJ, HornakV, CuiG, BerozaP, SchafmeisterC, CaldwellJW, RossWS, KollmanPA. Amber 8. San Francisco, CA: University of California; 2004.
- JorgensenWL, ChandrasekharJ, MaduraJD, KleinML, ImpeyRW. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79:926–935.
- DardenT, YorkD, PedersonL. Particle Mesh Ewald: An N*logN method for Ewald sums in large systems. J Chem Phys. 1993;98:227–234.
- RyckaertJP, CiccottiG, BadersenHJC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys. 1977;23:327–341.
- LeeC, YangW, ParrRG. Development of the Colle-Salvetti correlation energy formulae into a functional of the electron density. Phys Rev B. 1988;37:785–789.
- PerdewJP, WangY. Accurate and simple analytic representation of the electron-gas correlation energy. Phys Rev B. 1992;45:13244–13249.
- MollarC, PlessetMS. Note on an approximation treatment for many-electron systems. Phys Rev. 1934;46:618–622.
- BoysSF, BernardiF. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol Phys. 1970;19:553–566.
- BaderRFW. Atoms in molecules: a quantum theory. Oxford: Oxford University Press; 1990.
- FrischMJ, TrucksGW, SchlegelHB, ScuseriaGE, RobbMA, CheesemanJR, ZakrzewskiVG, MontgomeryJAJr., StratmannRE, BurantJC, DapprichS, MillamJM, DanielsAD, KudinKN, StrainMC, FarkasO, TomasiJ, BaroneV, CossiM, CammiR, MennucciB, PomelliC, AdamoC, CliffordS, OchterskiJ, PeterssonGA, AyalaPY, CuiQ, MorokumaK, RegaN, SalvadorP, DannenbergJJ, MalickDK, RabuckAD, RaghavachariK, ForesmanJB, CioslowskiJ, OrtizJV, BaboulAG, StefanovBB, LiuG, LiashenkoA, PiskorzP, KomaromiI, GompertsR, MartinRL, FoxDJ, KeithT, Al-LahamMA, PengCY, NanayakkaraA, ChallacombePMW, GillB, JohnsonW, ChenMW, WongJL, AndresC, GonzalezM, Head-GordonES, Replogle, PopleJA. Gaussian 03, Revision B.05. Pittsburgh PA: Gaussian, Inc; 2003.
- GrabowskiSJ. Hydrogen bonding: new insights. Dordrecht: Springer; 2006.
- BaldwinRL. Energetics of protein folding. J Mol Biol. 2007;371:283–301.
- CoxPJ, KumarasamyY, NaharL, SarkerSD, ShoebM. Luteolin. Acta Cryst E. 2003;59:975–977.
- SamantaAK, PandeyP, BandyopadhyayB, ChakrabortyT. Co-operative strengthening of an intramolecular O = H..O hydrogen bond by a weak C–H..O counterpart: matrix-isolation infrared spectroscopy and quantum chemical studies on 3-methyl-1,2-cyclohexanedione. J Phys Chem A. 2010;114:1650–1656.