Abstract
We present the results of a computational study of the NMR properties of glycine in water solution at the level of density functional theory employing the B3LYP functional and the 6-31G(d,p) and pcSseg-2 basis sets, describing the solvent either via the PCM continuous solvation model or PCM with additional explicit water molecules hydrogen-bonded to the solute. We observe that the solvent causes considerable changes in the predicted magnetic shieldings and that the results depend significantly on the number of solvent molecules included in the quantum mechanical treatment.
Similar content being viewed by others
References
Jensen JH, Gordon MS (1995) On the number of water molecules necessary to stabilize the glycine zwitterion. J Am Chem Soc 117:8159–8170
Fernandez-Ramos A, Smedarchina Z, Siebrand W, Zgierski MZ (2000) A direct-dynamics study of the zwitterion-to-neutral interconversion of glycine in aqueous solution. J Chem Phys 113:9714–9721
Karmacharya R, Antoniou D, Schwartz SD (2001) Nonequilibrium solvation and the quantum kramers problem: proton transfer inaqueous glycine. J Phys Chem A 105:2563–2567
Aikens CM, Gordon MS (2006) Incremental solvation of nonionized and zwitterionic glycine. J Am Chem Soc 128:12835–12850
Leung K, Rempe SB (2005) Ab initio molecular dynamics study of glycine intramolecular proton transfer in water. J Chem Phys 122(1–13):184506
Campo MG (2006) Molecular dynamics simulation of glycine zwitterion in aqueous solution. J Chem Phys 125(1–9):114511
Sauer SPA, Oddershede J, Sabin John R (2006) Directional dependence of the mean excitation energy and spectral moments of the dipole oscillator strength distribution of glycine and its zwitterion. J Phys Chem A 110:8811–8817
Balabin RM (2010) The first step in glycine solvation: the glycine–water complex. J Phys Chem B 114:15075–15078
Aidas K, Kongsted J, Sabin JR, Oddershede J, Mikkelsen KV, Sauer SPA (2010) The effect of solvation on the mean excitation energy of glycine. J Phys Chem Lett 1:242–245
Bruun-Ghalbia S, Sauer SPA, Oddershede J, Sabin JR (2010) Comparison of the directional characteristics of swift ion excitation for two small biomolecules: glycine and alanine. Eur Phys J D 60:71–76
Takenaka N, Kitamura Y, Koyano Y, Asada T, Nagaoka M (2011) Reaction path optimization and vibrational frequency analysis via ab initio qm/mm free energy gradient (feg) method: application to isomerization process of glycine in aqueous solution. Theor Chem Acc 130:215–226
Sauer SPA, Oddershede J, Sabin JR (2011) Mean excitation energies for biomolecules: glycine to DNA. Adv Quantum Chem 62:215–242
Sabin JR, Oddershede J, Sauer SPA (2013) Glycine: theory of the interaction with fast ion radiation. In: Vojak W (ed) Glycine: biosynthesis, physiological functions and commercial uses, chapter 4. Nova Science Publisher, Hauppauge, pp 79–96
Kim JY, Ahn DS, Park SW, Lee S (2014) Gas phase hydration of amino acids and dipeptides: effects on the relative stability of zwitterion vs. canonical conformers. RSC Adv 4:16352–16361
Wu R, McMahon TB (2008) Stabilization of zwitterionic structures of amino acids (Gly, Ala, Val, Leu, Ile, Ser and Pro) by ammonium ions in the gas phase. J Am Chem Soc 130:3065–3078
Hwang T, Eom G, Choi M, Jang S, Kim J, Le S (2011) Microsolvation of lysine by water: computational study of stabilized zwitterion. J Phys Chem B 115:10147–10153
Wada G, Tamura E, Okina M, Nacamura M (1982) On the ratio of zwitterion form to uncharged form of glycine at equilibrium in various aqueous media. Bull Chem Soc Jpn 55:3064–3067
Slifkin MA, All SM (1984) Thermodynamic parameters of the activation of glycine zwitterion protonation reactions. J Mol Liq 28:215–221
Peteanu LA, Levy DH (1988) Spectroscopy of complexes of tryptamine and 3-indolepropionic acid with various solvents. J Phys Chem 92:6554–6561
Xu S, Nilles JM, Bowen KH (2003) Zwitterion formation in hydrated amino acid, dipole bound anions: How many water molecules are required? J Chem Phys 119(1–7):10696
Diken EG, Hammer NI, Johnson MA (2004) Preparation and photoelectron spectrum of the glycine molecular anion: assignment to a dipole-bound electron species with a high-dipole moment, non-zwitterionic form of the neutral core. J Chem Phys 120:9899–9902
Nonose S, Iwaoka S, Mori K, Shibata Y, Fuke K (2005) Structures and reactions of hydrated biomolecular cluster ions. Eur Phys J D 34:315–319
Alonso JL, Cocinero EJ, Lesarri A, Sanz ME, López JC (2006) The glycine–water complex. Angew Chem 118:3551–3554
Császár AG (1992) Conformers of gaseous glycine. J Am Chem Soc 114:9568–9575
Godfrey PD, Brown RD, Rodgers FM (1996) The missing conformers of glycine and alanine: relaxation in seeded supersonic jets’. J Mol Struct 376:65–81
Miertus S, Scroco E, Tomasi J (1981) Electrostatic interaction of a solute with a continuum. A direct utilizaion of ab initio molecular potentials for the prevision of solvent effects. Chem Phys 55:117–129
Miertus S, Tomasi J (1982) Approximate evaluations of the electrostatic free energy and internal energy changes in solution processes. Chem Phys 65:239–245
Cossi M, Barone V, Cammi R, Tomasi J (1996) Ab initio study of solvated molecules: a new implementation of the polarizable continuum model. Chem Phys Lett 255:327–335
Cossi M, Barone V, Robb MA (1999) A direct procedure for the evaluation of solvent effects in mc-scf calculations. J Chem Phys 111:5295–5302
Cossi M, Barone V (2000) Solvent effect on vertical electronic transitions by the polarizable continuum model. J Chem Phys 112:2427–2435
Cossi M, Rega N, Scalmani G, Barone V (2001) Polarizable dielectric model of solvation with inclusion of charge penetration effects. J Chem Phys 114:5691–5701
Cossi M, Barone V (2001) Time-dependent density functional theory for molecules in liquid solutions. J Chem Phys 115:4708–4717
Cossi M, Scalmani G, Rega N, Barone VJ (2002) New developments in the polarizable continuum model for quantum mechanical and classical calculations on molecules in solution. J Chem Phys 117:43–54
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09 revision D.01. Gaussian Inc., Wallingford, CT
Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98:5648–5652
Lee C, Yang W, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37:785–789
Mennucci B, Tomasi J (1997) Continuum solvation models: a new approach to the problem of solute’s charge distribution and cavity boundaries. J Chem Phys 106:5151–5158
Hehre WJ, Ditchfield R, Pople JA (1972) Self-consistent molecular orbital methods. XII. Further extensions of Gaussian-type basis sets for use in molecular orbital studies of organic molecules. J Chem Phys 56:2257–2261
Hariharan PC, Pople JA (1973) Influence of polarization functions on molecular-orbital hydrogenation energies. Theor Chem Acc 28:213–222
Jensen F (2015) Segmented contracted basis sets optimized for nuclear magnetic shielding. J Chem Theory Comput 11:132–138
Ramsey NF (1950) Magnetic shielding of nuclei in molecule. Phys Rev 78:699–703
Helgaker T, Jaszuński M, Ruud K (1999) Ab initio methods for the calculation of nmr shielding and indirect spin–spin coupling constants. Chem Rev 99:293–352
Vaara J (2007) Theory and computation of nuclear magnetic resonance parameters. Phys Chem Chem Phys 9:5399–5418
Sauer SPA (2011) Molecular electromagnetism: a computational chemistry approach. Oxford University Press, Oxford
Helgaker T, Coriani S, Jørgensen P, Kristensen K, Olsen J, Ruud K (2012) Recent advances in wave function-based methods of molecular-property calculations. Chem Rev 112:543–631
Wolinski K, Hinton JF, Pulay P (1990) Efficient implementation of the gauge-independent atomic orbital method for nmr chemical shift calculations. J Am Chem Soc 112:8251–8260
Ligabue A, Sauer SPA, Lazzeretti P (2003) Correlated and gauge invariant calculations of nuclear magnetic shielding constants using the continuous transformation of the origin of the current density approach. J Chem Phys 118:6830–6845
Ligabue A, Sauer SPA, Lazzeretti P (2007) Gauge invariant calculations of nuclear magnetic shielding constants using the continuous transformation of the origin of the current density approach. II. Density functional and coupled cluster theory. J Chem Phys 126:154111
Acknowledgements
MCC acknowledge financial support to the present research from CONICET (PIP0369) and Universidad de Buenos Aires (UBACYT,W197), PFP acknowledge financial support from CONICET and UNNE (PI:F002-15 Res.1017/15); and SPAS thanks the Danish Center for Scientific Computing (DCSC) and the TWAS Visiting Expert Programme (F.R. 3240301376) for financial support.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Caputo, M.C., Provasi, P.F. & Sauer, S.P.A. The role of explicit solvent molecules in the calculation of NMR chemical shifts of glycine in water. Theor Chem Acc 137, 88 (2018). https://doi.org/10.1007/s00214-018-2261-9
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00214-018-2261-9