How Metal Coordination in the Ca-, Ce- and Eu-Containing …
501
42. Grimme S, Ehrlich S, Goerigk L (2011) Effect of the damping function in dispersion corrected
density functional theory. J Comput Chem 32:1456–1465. https://doi.org/10.1002/jcc.21759
43. Cossi M, Rega N, Scalamani V, Barone V (2003) Energies, structures, and electronic properties
of molecules in solution with the C-PCM solvation model. J Comput Chem 24:669–681. https://
doi.org/10.1002/chem.201700381
44. Barone V, Cossi M (1998) Quantum calculation of molecular energies and energy gradients
in solution by a conductor solvent model. J Phys Chem A 102:1995–2001. https://doi.org/10.
1021/jp9716997
45. Chen W, Fang WH, Himo F (2009) Reaction mechanism of the binuclear zinc enzyme
glyoxalase II—a theoretical study. J Inorg Biochem 103:274–281. https://doi.org/10.1016/j.
jinorgbio.2008.10.016
46. Ziao RZ, Himo F Yu JG, Liu RZ (2010) Dipeptide hydrolysis by the dinuclear zinc enzyme
human renal dipeptidase: mechanistic insights from DFT calculations. J Inorg Biochem
104:37–46. https://doi.org/10.1016/j.jinorgbio.2009.09.025
47. Sousa SF, Fernandes PA, Ramos MJ (2009) The search for the mechanism of the reaction
catalyzed by farnesyltransferase. Chem Eur J 15:4243–4247. https://doi.org/10.1002/chem.
200802745
48. Alberto ME, Marino T, Ramos MJ, Russo N (2010) Atomistic details of the catalytic mechanism
of Fe(III)–Zn(II) purple acid phosphatase. J Chem Theory Comput 6:2424–2433. https://doi.
org/10.1021/ct100187c
49. Siegbahn PEM, Eriksson LA, Himo F, Pavlov M (1998) Hydrogen atom transfer in
ribonucleotide reductase (RNR). J Phys Chem B 102:10622–10629. https://doi.org/10.1021/
jp9827835
50. Warshel A (1991) Computer modeling of chemical reactions in enzymes and solutions. Wiley,
New York
51. Piazzetta P, Marino T, Russo N (2014) Insight into the promiscuous activity of human carbonic
anhydrase against the cyanic acid substrate from a combined QM and QM/MM investigation.
Phys Chem Chem Phys 16:16671–16676. https://doi.org/10.1039/C4CP02363C
52. Ribeiro AJM, Alberto ME, Ramos MJ, Fernandes PA, Russo N (2013) The catalytic mechanism
of protein phosphatase 5 established by DFT calculations. Chem Eur J 114:3601–3658. https://
doi.org/10.1002/chem.201301565
53. Prejanò M, Marino T, Russo N (2017) How can methanol dehydrogenase from Methylacidiphilum fumariolicum work with the alien CeIII ion in the active center? A theoretical
study. Eur Chem J 23:8652–8657. https://doi.org/10.1002/chem.201700381
54. Prejanò M, Marino T, Rizzuto C, Madrid JCM, Russo N, Toscano M (2017) Reaction mechanism of low-spin iron(III)- and cobalt(III)-containing nitrile hydratases: a quantum mechanics
investigation. Inorg Chem 56:13390–13400. https://doi.org/10.1021/acs.inorgchem.7b02121
55. Bogart JA, Lewis AJ, Schelter EJ (2015) DFT study of the active site of the XoxF-type natural,
cerium-dependent methanol dehydrogenase enzyme. Chem Eur J 21:1743–1748. https://doi.
org/10.1002/chem.201405159
56. E. D. Glendening, A. E. Reed, J. E. Carpenter, F. Weinhold, NBO, version 3.1
57. Anthony C (1996) Quinoprotein-catalysed reactions. Biochem J 320:697–711. https://doi.org/
10.1042/bj3200697
58. Simon S, Duran M, Dannenberg JJ (1996) How does basis set superposition error change the
potential surfaces for hydrogen-bonded dimers? J Phys Chem 105:11024–11031. https://doi.
org/10.1063/1.472902
59. Boys SF, Bernardi F (1970) The calculation of small molecular interactions by the differences
of separate total energies. Some procedures with reduced errors. Mol Phys 19:553–566. https://
doi.org/10.1080/00268977000101561
501
42. Grimme S, Ehrlich S, Goerigk L (2011) Effect of the damping function in dispersion corrected
density functional theory. J Comput Chem 32:1456–1465. https://doi.org/10.1002/jcc.21759
43. Cossi M, Rega N, Scalamani V, Barone V (2003) Energies, structures, and electronic properties
of molecules in solution with the C-PCM solvation model. J Comput Chem 24:669–681. https://
doi.org/10.1002/chem.201700381
44. Barone V, Cossi M (1998) Quantum calculation of molecular energies and energy gradients
in solution by a conductor solvent model. J Phys Chem A 102:1995–2001. https://doi.org/10.
1021/jp9716997
45. Chen W, Fang WH, Himo F (2009) Reaction mechanism of the binuclear zinc enzyme
glyoxalase II—a theoretical study. J Inorg Biochem 103:274–281. https://doi.org/10.1016/j.
jinorgbio.2008.10.016
46. Ziao RZ, Himo F Yu JG, Liu RZ (2010) Dipeptide hydrolysis by the dinuclear zinc enzyme
human renal dipeptidase: mechanistic insights from DFT calculations. J Inorg Biochem
104:37–46. https://doi.org/10.1016/j.jinorgbio.2009.09.025
47. Sousa SF, Fernandes PA, Ramos MJ (2009) The search for the mechanism of the reaction
catalyzed by farnesyltransferase. Chem Eur J 15:4243–4247. https://doi.org/10.1002/chem.
200802745
48. Alberto ME, Marino T, Ramos MJ, Russo N (2010) Atomistic details of the catalytic mechanism
of Fe(III)–Zn(II) purple acid phosphatase. J Chem Theory Comput 6:2424–2433. https://doi.
org/10.1021/ct100187c
49. Siegbahn PEM, Eriksson LA, Himo F, Pavlov M (1998) Hydrogen atom transfer in
ribonucleotide reductase (RNR). J Phys Chem B 102:10622–10629. https://doi.org/10.1021/
jp9827835
50. Warshel A (1991) Computer modeling of chemical reactions in enzymes and solutions. Wiley,
New York
51. Piazzetta P, Marino T, Russo N (2014) Insight into the promiscuous activity of human carbonic
anhydrase against the cyanic acid substrate from a combined QM and QM/MM investigation.
Phys Chem Chem Phys 16:16671–16676. https://doi.org/10.1039/C4CP02363C
52. Ribeiro AJM, Alberto ME, Ramos MJ, Fernandes PA, Russo N (2013) The catalytic mechanism
of protein phosphatase 5 established by DFT calculations. Chem Eur J 114:3601–3658. https://
doi.org/10.1002/chem.201301565
53. Prejanò M, Marino T, Russo N (2017) How can methanol dehydrogenase from Methylacidiphilum fumariolicum work with the alien CeIII ion in the active center? A theoretical
study. Eur Chem J 23:8652–8657. https://doi.org/10.1002/chem.201700381
54. Prejanò M, Marino T, Rizzuto C, Madrid JCM, Russo N, Toscano M (2017) Reaction mechanism of low-spin iron(III)- and cobalt(III)-containing nitrile hydratases: a quantum mechanics
investigation. Inorg Chem 56:13390–13400. https://doi.org/10.1021/acs.inorgchem.7b02121
55. Bogart JA, Lewis AJ, Schelter EJ (2015) DFT study of the active site of the XoxF-type natural,
cerium-dependent methanol dehydrogenase enzyme. Chem Eur J 21:1743–1748. https://doi.
org/10.1002/chem.201405159
56. E. D. Glendening, A. E. Reed, J. E. Carpenter, F. Weinhold, NBO, version 3.1
57. Anthony C (1996) Quinoprotein-catalysed reactions. Biochem J 320:697–711. https://doi.org/
10.1042/bj3200697
58. Simon S, Duran M, Dannenberg JJ (1996) How does basis set superposition error change the
potential surfaces for hydrogen-bonded dimers? J Phys Chem 105:11024–11031. https://doi.
org/10.1063/1.472902
59. Boys SF, Bernardi F (1970) The calculation of small molecular interactions by the differences
of separate total energies. Some procedures with reduced errors. Mol Phys 19:553–566. https://
doi.org/10.1080/00268977000101561