Conformational analysis of alkali metal complexes of anionic species of aspartic acid, their interconversion and deprotonation: A DFT investigation

Journal of Molecular Graphics and Modelling

Volumn 26, Issue 6, 2008, Pages 982-990

  Sang Aroon, Wichien ^a   Ruangpornvisuti, Vithaya ^a  

^a Faculty of Science   (Thailand)

Author keywords

Alkali cation; Aspartate anion; Complexation; Lithium; Metal ion affinity; Potassium; Sodium

Indexed keywords

ACIDS; COMPLEXATION; DENSITY FUNCTIONAL THEORY; DEPROTONATION; EQUILIBRIUM CONSTANTS; METAL IONS;

ALKALI CATIONS; ANIONIC SPECIES; ASPARTATE ANIONS; ASPARTATE COMPLEXES;

ALKALI METALS;

ALKALI METAL; ANION; ASPARTIC ACID; CATION; LITHIUM ION; METAL ION; POTASSIUM ION; SODIUM ION;

ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; CONFORMATION; DENSITY FUNCTIONAL THEORY; ENERGY; EQUILIBRIUM CONSTANT; GEOMETRY; PRIORITY JOURNAL; PROTON TRANSPORT; THERMODYNAMICS;

ANIONS; ASPARTIC ACID; COMPUTATIONAL BIOLOGY; GASES; LIGANDS; LITHIUM; METALS, ALKALI; MOLECULAR CONFORMATION; POTASSIUM; PROTONS; SODIUM; THERMODYNAMICS;

EID: 37349104590     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2007.08.004     Document Type: Article

References (49)

1. Jensen J.H., and Gordon M.S. On the number of water molecules necessary to stabilize the glycine zwitterion. J. Am. Chem. Soc. 117 (1995) 8159-8170
2. Gluster J.P. Structural aspects of metal liganding to functional groups in proteins. Adv. Protein Chem. 42 (1991) 1-76
3. Lippard S.A., and Berg J.M. Principles of Bioinorganic Chemistry (1994), University Science Books, Mill Valley, CA
4. Hughes M.N. The Inorganic Chemistry of Biological Process. 2nd ed. (1981), John Wiley and Sons, Chichester
5. Dougherty D.A. Cation interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp. Science 271 (1996) 163-168
6. In: Freiser B.S. (Ed). Organometallic Ion Chemistry (1996), Kluwer, Dordrecht
7. Kaim W., and Schwederski B. Bioinorganic Chemistry: Inorganic Elements in Chemistry of Life (1994), Wiely, Chichester
8. +, M = H, Li, Na, K, Rb, and Cs) in the gas phase: further evidence for zwitterionic arginine. J. Phys. Chem. A 103 (1999) 9266-9274
9. 2+ (M = Be, Mg, Ca, Sr, Ba), in the gas phase: intrinsic effect of cation size on zwitterion stability. J. Phys. Chem. A 104 (2000) 9793-9796
10. +) affinities of glycine and alanine. J. Inorg. Biochem. 79 (2000) 179-185
11. +). A density functional study. Inorg. Chem. 40 (2001) 6439-6443
12. + with the proline amino acid. Complexation modes, potential energy profiles, and metal ion affinities. J. Phys. Chem. B 107 (2003) 2588-2594
13. 2+): Existence of zwitterionic structures?. Chem.-Eur. J. 6 (2000) 4393-4399
14. 2+) and water coordination on the structure of glycine and zwitterionic glycine. J. Phys. Chem. A 110 (2006) 1960-1967
15. Yu B.M., Paroutis P., Davidson A.R., and Howell P.L. Disruption of a salt bridge dramatically accelerates subunit exchange in duck delta2 crystallin. J. Biol. Chem. 279 (2004) 40972-40979
16. de Vos A.M., Ulsch M., and Kossiakoff A.A. Human growth hormone and extracellular domain of its receptor: crystal structure of the complex. Science 255 (1992) 306-312
17. Lee S.W., Kim H.S., and Beauchamp J.L. Salt bridge chemistry applied to gas-phase peptide sequencing: selective fragmentation of sodiated gas-phase peptide ions adjacent to aspartic acid residues. J. Am. Chem. Soc. 120 (1998) 3188-3195
18. Teesch L.M., Orlando R.C., and Adams J. Location of the alkali metal ion in gas-phase peptide complexes. J. Am. Chem. Soc. 113 (1991) 3668
19. +,M = H, Li, Na, K, Rb, and Cs) in the gas phase: further evidence for zwitterionic arginine. Org. Mass Spectrom. 28 (1993) 1047-1050
20. + to aromatic amino acids: a density functional computational study of cation-π interactions. J. Phys. Chem. A 104 (2000) 8067-8074
21. + with the aromatic amino acids, phenylalanine, tyrosine, and tryptophan. J. Am. Chem. Soc. 126 (2004) 14600-14610
22. Wyttenbach T., Witt M., and Bowers M.T. On the question of salt bridges of cationized amino acids in the gas phase: glycine and arginine. Int. J. Mass Spectrom. 183 (1999) 243-252
23. Wyttenbach T., Witt M., and Bowers M.T. On the stability of amino acid zwitterions in the gas phase: the influence of derivatization, proton affinity, and alkali ion addition. J. Am. Chem. Soc. 122 (2000) 3458-3464
24. Jockusch R.A., Lemoff A.S., and Williams E.R. Effect of metal ion and water coordination on the structure of a gas-phase amino acid. J. Am. Chem. Soc. 123 (2001) 12255-12265
25. Jockusch R.A., Lemoff A.S., and Williams E.R. Hydration of valine-cation complexes in the gas phase: on the number of water molecules necessary to form a zwitterion. J. Phys. Chem. A 105 (2001) 10929-10942
26. Lemoff A.S., and Williams E.R. Binding energies of water to lithiated valine: formation of solution-phase structure in vacuo. J. Am. Soc. Mass Spectrom. 15 (2004) 1014-1024
27. Lemoff A.S., Bush M.F., and Williams E.R. Binding energies of water to sodiated valine and structural isomers in the gas phase: the effect of proton affinity on zwitterion stability. J. Am. Chem. Soc. 125 (2003) 13576-13584
28. Lemoff A.S., Bush M.F., and Williams E.R. Structures of cationized proline analogues: evidence for the zwitterionic form. J. Phys. Chem. A 109 (2005) 1903-1910
29. Lemoff A.S., Bush M.F., Wu C.C., and Williams E.R. Structures and hydration enthalpies of cationized glutamine and structural analogues in the gas phase. J. Am. Chem. Soc. 127 (2005) 10276-10286
30. + affinities of α-amino acids: side-chain substituent effects. Int. J. Mass Spectrom. 227 (2003) 509-524
31. Cox H.A., Julian R.R., Lee S.W., and Beauchamp J.L. Gas-phase H/D exchange of sodiated glycine oligomers with ND3: exchange kinetics do not reflect parent ion structures. J. Am. Chem. Soc. 126 (2004) 6485-6490
32. Rožman M., Bertoša B., Klasinc L., and Srzić D. Gas phase H/D exchange of sodiated amino acids: why do we see zwitterions?. J. Am. Soc. Mass Spectrom. 17 (2006) 29-36
33. Ye S.J., Moision R.M., and Armentrout P.B. Sequential bond energies of water to sodium glycine cation. Int. J. Mass Spectrum. 240 (2005) 233-248
34. Rodgers M.T., and Armentrout P.B. A thermodynamic "vocabulary" for metal ion interactions in biological systems. Acc. Chem. Res. 37 (2004) 989-998
35. Moision R.M., and Armentrout P.B. Experimental and theoretical dissection of sodium cation/glycine interactions. J. Phys. Chem. A 106 (2002) 10350-10362
36. Moision R.M., and Armentrout P.B. An experimental and theoretical dissection of potassium cation/glycine interactions. Phys. Chem. Chem. Phys. 6 (2004) 2588-2599
37. Polfer N.C., Paizs B., Snoek L.C., Compagnon I., Suhai S., Meijer G., von Helden G., and Oomens J. Infrared fingerprint spectroscopy and theoretical studies of potassium ion tagged amino acids and peptides in the gas phase. J. Am. Chem. Soc. 127 (2005) 8571-8579
38. Sang-aroon W., and Ruangpornvisuti V. Conformational study of cationic, zwitterionic, anionic species of aspartic acid, water-added forms and their protonation. A DFT method. J. Mol. Struct. (THEOCHEM) 758 (2006) 181-187
39. Feng W.Y., Gronert S., and Lebrilla C. The lithium cation binding energies of gaseous amino acids. J. Phys. Chem. A 107 (2003) 405-410
40. + affinities of gas phase amino acids by ligand exchange equilibrium. Int. J. Mass Spectrom. 228 (2003) 825-839
41. Sang-Aroon W., and Ruangpornvisuti V. Conformational analysis of alkali metal complexes of aspartate dianion and their interactions in gas phase. J. Mol. Graph. Model. 26 (2007) 342-351
42. Becke A.D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98 (1993) 5648-5652
43. Lee C., Yang W., and Parr R.G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 37 (1988) 785-789
44. Barone V., and Cossi M. J. Phys. Chem A 102 (1998) 1995-2001
45. 2. J. Chem. Phys. 84 (1986) 2279-2289
46. Schwenke D.W., and Truhlar D.G. Systematic study of basis set superposition errors in the calculated interaction energy of two HF molecules. J. Chem. Phys. 82 (1985) 2418-2426
47. Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Montgomery Jr. J.A., Vreven T., Kudin K.N., Burant J.C., Millam J.M., Iyengar S.S., Tomasi J., Barone V., Mennucci B., Cossi M., Scalmani G., Rega N., Petersson G.A., Nakatsuji H., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Klene M., Li X., Knox J.E., Hratchian H.P., Cross J.B., Adamo C., Jaramillo J., Gomperts R., Stratmann R.E., Yazyev O., Austin A.J., Cammi R., Pomelli C., Ochterski J.W., Ayala P.Y., Morokuma K., Voth G.A., Salvador P., Dannenberg J.J., Zakrzewski V.G., Dapprich S., Daniels A.D., Strain M.C., Farkas O., Malick D.K., Rabuck A.D., Raghavachari K., Foresman J.B., Ortiz J.V., Cui Q., Baboul A.G., Clifford S., Cioslowski J., Stefanov B.B., Liu G., Liashenko A., Piskorz P., Komaromi I., Martin R.L., Fox D.J., Keith T., Al-Laham M.A., Peng C.Y., Nanayakkara A., Challacombe M., Gill P.M.W., Johnson B., Chen W., Wong M.W., Gonzalez C., and Pople J.A. Gaussian 03, Revision D. 02 (2006), Gaussian, Inc., Pittsburgh, PA
48. Schaftenaar G. Molden 3.7, CAOS/CAMM Center (1991), Nijmegen Toernooiveld, Nijmegen, Netherlands
49. Flükiger P., Lüthi H.P., Portmann S., and Weber J. Molekel 4.3 (2000), Swiss Center for Scientific Computing, Manno, Switzerland