A DFT Study on Magnesium Ion Affinity of Glycine
A DFT Study on Magnesium Ion Affinity of Glycine
Journal of the Korean Chemical Society. 2008. Apr, 52(2): 207-211
Copyright © 2008, The Korean Chemical Society
  • Received : February 21, 2008
  • Published : April 20, 2008
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혁재, 권
갑용, 이

Prior to the calculations for the Mg 2+ -glycine complexes, the geometry optimization for various glycine conformers was performed starting from the 13 possible structures that had been reported by Csaszar. 24 Our DFT calculations at the 6-311++G(d,p) level revealed a total of 7 stable conformers among them. A zwitterionic form, along with these 7 optimized glycines was also considered as an additional trial structure in this study. The optimized 7 glycine isomers and the zwitterionic form are shown in . 1 .
It should be noted that the zwitterionic form is not optimized in the gaseous state. That is, the zwitterionic form, structure G3, degenerates into structure G2 when G3 is optimized in the gaseous state. This implies that glycine exists as a zwitterion in the crystalline state and in solution due to strong electrostatic and polarization interactions with its environment. 24 Many studies have shown that glycine also exists in a neutral form in the gas phase. 25 - 27 The studies have also demonstrated that the zwitterionic form of glycine can be stabilized by the presence of metal ions, thereby forming a bridging complex. 28
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B3LPY optimized neutral glycines including ground state glycine, G1, and zwitterionic conformer, G3.
The ground state glycine(G1) is compared to a previously studied conformer and the structural parameters are found to be in good agreement with the results of the theoretical 24 and experimental 29 method. On the basis of this result, we have chosen to use the B3LYP functional couples with the 6-311++G(d,p) basis sets to determine the geometrical structures of the Mg 2+ -glycine complexes and the Mg 2+ affinity of glycine.
The lowest energy form of neutral glycine in the gas phase, as determined experimentally 29 and theoretically, 30 - 31 is the G1 conformer with a planar heavy-atom structure and two equal N-H...O Hbonds. Further, the relative energies for the 7 optimized glycines at the B3LYP level in this study are close to those of the MP2 results. 24
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Optimized structures at B3LYP/6-311++G(d,p) level of theory of Mg2+-glycine complexes.
The geometry was optimized to one structure, GM2, for the G1- and G4-Mg 2+ complexes even though they were started from the two glycine conformers, G1 and G4. The optimized geometries of the Mg 2+ -glycine complexes associated with the coordination sites of the glycine conformers are shown in . 2 .
As shown in . 2 , the mode of Mg 2+ coordination with glycine can be classified into four different groups. The first structure is GM1, in which Mg 2+ is coordinated to two oxygens, i.e. , complexation to the zwitterionic form of glycine. The second group consists of structures GM2, GM3, and GM4 each having a five-membered ring along with Mg 2+ coordinated to both amino nitrogen and oxygen. The ring in GM4 complex is slightly enveloped-shaped, similar to cyclopentane. All the other structures with the five-membered ring have C s symmetric geometry. The third structure is GM5 that represents a structure corresponding to the coordination with two carboxylic oxygens. The fourth group consists of structures GM6 and GM7, in which Mg 2+ is coordinated only to the carbonyl oxygen and amino nitrogen, respectively.
It should be noted that the amino hydrogens in the glycines rotate to reduce the repulsion for the Mg 2+ with complexation in bidentate complexes. The relative and binding energies of the optimized Mg 2+ -glycine complexes, including the MP2 results, are presented in 1 .
Relative and binding energies for optimized Mg2+-glycine complexesa
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aMP2 results are on B3LYP/6-311++G(d,p) optimized geometries. bB3LYP binding energies are included BSSE correction. cBetween glycine G4 and Mg2+. dBetween glycine G1 and Mg2+.
As given in 1 , the MP2 energies are similar to the B3LYP energies. The most stable Mg 2+ -glycine complex is GM1, in which Mg 2+ is bound to both the oxygens at the ends of the zwitterionic glycine in both the methods. The next stable isomer is GM2, in which Mg 2+ is coordinated to the amino nitrogen and carbonyl oxygen. This complex has been found to be less stable than the zwitterionic complex by 6.4 kcal/mol at the B3LYP level. The third stable isomer for the Mg 2+ -glycine complex is GM3 that is computed to be 12.1 kcal/mol less stable than GM1. The important structural difference between GM2 and GM3 is in the orientation of the hydroxyl hydrogen, which is anti to that of the carbonyl oxygen in GM3 and results in 5.7(6.0 in MP2) kcal/mol higher than GM2. The next stable complex is GM4, in which Mg 2+ is bound to the amino nitrogen and hydroxyl oxygen. GM4 is different from above the most stable three C s-symmetric isomers, it is a drastically distorted structure, in which Mg 2+ is coordinated to the amino nitrogen with 24.4˚ above the NCC plane. The last three complexes are GM5, GM6, and GM7 which is 44.8, 48.9, and 60.8 kcal/mol above GM1, respectively. In GM5, similar to GM1, Mg 2+ is bound to the two carboxylic oxygens. In GM6 and GM7, Mg 2+ is bound only to the carboxylic oxygen (at distance 1.873Å) and amino nitrogen (at distance 2.090Å), respectively.
On the other hand, the binding energies between glycine and Mg 2+ at the B3LYP/6-31++G (d,p) level are also presented in 1 . As has been introduced above, the binding energy is obtained from the difference between the energy of the Mg 2+ -coordinated glycine complex, and the sum of the energy of corresponding free glycine and the magnesium cation. As given 1 , the zwitterionic form, GM1, has the greatest binding energy with 164.3 kcal/mol due to its more electrostatic and polarity and smaller metal-ligand repulsion than the other complexes. 7 , 11 , 15 The binding energies of GM2 and GM3 are almost the same (157.9 and 156.6kcal/mol in GM2 and 157.5 kcal/mol in GM3) due to the similarity of the glycine structure and Mg 2+ coordinated site.
In conclusion, structure GM1, in which Mg 2+ ion coordinates with two oxygens in the carboxylic moiety of the zwitter ionic glycine, exhibited the largest binding energy.
Voet D. , Voet J. G. 1995 Biochemistry 2nd ed. J. Wiley & Sons New York
Lippard S. A. , Berg J. M. 1994 Principles of Bioinorganic Chemistry University Science Books Mill Valley, CA
Cerda B. A. , Wesdemiotis C. 1996 J. Am. Chem. Soc. 118 11884 -    DOI : 10.1021/ja9613421
Jockusch R. A. , Lemoff A. , Williams E. R. 2001 J. Am. Chem. Soc. 123 12255 -    DOI : 10.1021/ja0106873
Kim H. T. 2005 Bull. Korean Chem. Soc. 26 679 -    DOI : 10.5012/bkcs.2005.26.4.679
Rogalewicz F. , Ohanesian G. , Gresh H. 2000 J. Comput. Chem. 21 963 -    DOI : 10.1002/1096-987X(200008)21:11<963::AID-JCC6>3.0.CO;2-3
Marino T. , Russo M. , Toscano M. 2000 J. Inorg. Biochem. 79 179 -    DOI : 10.1016/S0162-0134(99)00242-1
Remko M. , Rode B. M. 2000 Chem Phys. Lett. 316 489 -    DOI : 10.1016/S0009-2614(99)01322-6
Ai H. , Bu Y. , Chen Z. 2003 J. Chem Phys. 118 1761 -    DOI : 10.1063/1.1531107
Ai H. , Bu Y. , Chen Z. 2003 J. Chem Phys. 118 10973 -    DOI : 10.1063/1.1575192
Remko M. , Rode B. M. 2004 Struct. Chem. 15 223 -    DOI : 10.1023/B:STUC.0000021531.69736.00
Liu H. , Sun J. , Yang S. 2003 J. Phys. Chem. A 107 5681 -    DOI : 10.1021/jp034757z
Li P. , Bu Y. , Ai H. 2003 J. Phys. Chem. A 107 6419 -    DOI : 10.1021/jp034886f
Hwang S. G. , Jang Y. H. , Chung D. S. 2005 Bull. Korean Chem. Soc. 26 585 -    DOI : 10.5012/bkcs.2005.26.4.585
Topol LA. , Burt S. K. , Toscano M. , Russo N. 1998 J. Mol. Struc.(THEOCHEM) 430 41 -    DOI : 10.1016/S0166-1280(98)90213-5
Marino T. , Russo M. , Sicilia E. , Toscano M. , Mineva T. 2000 Adv. Quantum Chem. 36 93 -
Hoyau S. , Ohanesian G. 1997 J. Am. Chem. Soc. 119 2016 -    DOI : 10.1021/ja963432b
Bertran J. , Rodriguez-Santiago L. , Sodupe M. 1999 J. Phys. Chem. B 103 2310 -    DOI : 10.1021/jp984534m
Remko M. , Rode B. M. 2006 J. Phys. Chem. A 110 1960 -    DOI : 10.1021/jp054119b
Becke A. D. 1993 J. Chem. Phys. 98 5648 -    DOI : 10.1063/1.464913
Lee C. , Yang W. , Parr R. G. 1988 Phys. Rev. B 37 785 -    DOI : 10.1103/PhysRevB.37.785
Frisch M. J. , Trucks G. W. , Schlegel H. B. , Scuseria G. E. , Robb M. A. , Cheeseman J. R. , Montgomery J. A. , Vreven. Jr. 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. , Peterson 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. , Dennenberg 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. , Pople J. A. 2003 Gaussian 03, Revision A.1 Gaussian, Inc. Pittsburgh PA
Jensen F. 1992 J. Am. Chem. Soc. 114 9533 -    DOI : 10.1021/ja00050a036
Csaszar. G. 1992 J. Am. Chem. Soc. 114 9568 -    DOI : 10.1021/ja00050a041
Godfrey P. D. , Brown R. D. 1995 J. Am. Chem. Soc. 117 2019 -    DOI : 10.1021/ja00112a015
Chapo C. J , Paul J. B. , Provencal R. A. , Roth K. , Saykally I. J. 1998 J. Am. Chem. Soc. 120 12956 -    DOI : 10.1021/ja982991a
Stepanian S. J. , Reva I. D. , Radchenko E. D. , Rosado M. T. S. , Duarte M. L. T. S , Fausto R. , Adamowicz L. 1995 J. Phys. Chem. A 102 1041 -    DOI : 10.1021/jp973397a
Jockusch R. A. , Price W. D. , Williams E. R. 1999 J. Phys. Chem. A 103 9266 -    DOI : 10.1021/jp9931307
Iijima K. , Tanaka K. , Onuma S. 1991 J. Mol. Spectrosc. 246 257 -