Assessment of density functionals for predicting the infrared spectrum of sodiated octa-glycine

International Journal of Mass Spectrometry

Volumn 297, Issue 1-3, 2010, Pages 152-161

  Semrouni, David ^a   Clavaguéra, Carine ^a   Dognon, Jean Pierre ^b   Ohanessian, Gilles ^a  

^a LABORATOIRE HÉTÉROÉLÉMENTS ET COORDINATION   (France)

^b DIF   (France)

Author keywords

Density functional theory; Infrared spectra; Peptides

Indexed keywords

EID: 78049258716     PISSN: 13873806     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijms.2010.08.006     Document Type: Article

References (51)

1. MacAleese L., Maître P. Infrared spectroscopy of organometallic ions in the gas phase: from model to real world complexes. Mass Spectrom. Rev. 2007, 26(4):583-605.
2. Asmis K.R., Sauer J. Mass-selective vibrational spectroscopy of vanadium oxide cluster ions. Mass Spectrom. Rev. 2007, 26(4):542-562.
3. Polfer N.C., Oomens J. Vibrational spectroscopy of bare and solvated ionic complexes of biological relevance. Mass Spectrom. Rev. 2009, 28(3):468-494.
4. Fridgen T.D. Infrared consequence spectroscopy of gaseous protonated and metal ion cationized complexes. Mass Spectrom. Rev. 2009, 28(4):586-607.
5. Semrouni D., Balaj O.P., Calvo F., Correia C.F., Clavaguéra C., Ohanessian G. Structure of sodiated octa-glycine: IRMPD spectroscopy and molecular modeling. J. Am. Soc. Mass Spectrom. 2010, 21:728-738.
6. Kish M.M., Wesdemiotis C., Ohanessian G. The sodium ion affinity of glycylglycine. J. Phys. Chem. B 2004, 108(9):3086-3091.
7. Wang P., Wesdemiotis C., Kapota C., Ohanessian G. The sodium ion affinities of simple di-, tri-, and tetrapeptides. J. Am. Soc. Mass Spectrom. 2007, 18(3):541-552.
8. +) in the gas phase. Int. J. Mass Spectrom. 2008, 269(3):196-209.
9. Roscioli J.R., McCunn L.R., Johnson M.A. Quantum structure of the intermolecular proton bond. Science 2007, 316(5822):249-254.
10. Riley K.E., Pitoňák M., Jurečka P., Hobza P. Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories. Chem. Rev. ASAP 2010.
11. Cerny J., Hobza P. Non-covalent interactions in biomacromolecules. Phys. Chem. Chem. Phys. 2007, 9:5291-5303.
12. Riley K.E., Hobza P. Assessment of the MP2 method, along with several basis sets, for the computation of interaction energies of biologically relevant hydrogen bonded and dispersion bound complexes. J. Phys. Chem. A 2007, 111(33):8257-8263.
13. Bouteiller Y., Poully J.C., Desfrançois C., Grégoire G. Evaluation of MP2, DFT, and DFT-D methods for the prediction of infrared spectra of peptides. J. Phys. Chem. A 2009, 113(22):6301-6307.
14. Gloaguen E., Valdes H., Pagliarulo F., Pollet R., Tardivel B., Hobza P., Piuzzi F., Mons M. Experimental and theoretical investigation of the aromatic-aromatic interaction in isolated capped dipeptides. J. Phys. Chem. A 2000, 114(9):2973-2982.
15. Schwabe T., Grimme S. Theoretical thermodynamics for large molecules: walking the thin line between accuracy and computational cost. Acc. Chem. Res. 2008, 41(4):569-579.
16. Zhao Y., Truhlar D.G. Density functionals with broad applicability in chemistry. Acc. Chem. Res. 2008, 41(2):157-167.
17. Zhao Y., Truhlar D.G. A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions. J. Chem. Phys. 2006, 125(19):194101-194118.
18. Zhao Y., Truhlar D. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four m06-class functionals and 12 other functionals. Theor. Chem. Acc. 2008, 120(1):215-241.
19. Zhao Y., Truhlar D.G. Exploring the limit of accuracy of the global hybrid meta density functional for main-group thermochemistry, kinetics, and noncovalent interactions. J. Chem. Theory Comput. 2008, 4(11):1849-1868.
20. Zhao Y., Truhlar D.G. Density functional for spectroscopy: no long-range self-interaction error, good performance for Rydberg and charge-transfer states, and better performance on average than B3LYP for ground states. J. Phys. Chem. A 2006, 110(49):13126-13130.
21. Grimme S. Semiempirical hybrid density functional with perturbative second-order correlation. J. Chem. Phys. 2006, 124(3):034108.
22. Schwabe T., Grimme S. Double-hybrid density functionals with long-range dispersion corrections: higher accuracy and extended applicability. Phys. Chem. Chem. Phys. 2007, 9:3397-3406.
23. Korth M., Grimme S. " Mindless" DFT Benchmarking. J. Chem. Theory Comput. 2009, 5(4):993-1003.
24. Ahlrichs R., Bar M., Haser M., Horn H., Kolmel C. Electronic-structure calculations on workstation computers-the program system TURBOMOLE. Chem. Phys. Lett. 1989, 162(3):165-169.
25. Hattig C., Weigend F. CC2 excitation energy calculations on large molecules using the resolution of the identity approximation. J. Chem. Phys. 2000, 113(13):5154-5161.
26. Eichkorn K., Treutler O., Öhm H., Häser M., Ahlrichs R. Auxiliary basis sets to approximate Coulomb potentials. Chem. Phys. Lett. 1995, 242(6):652-660.
27. Eichkorn K., Weigend F., Treutler O., Ahlrichs R. Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentials. Theor. Chem. Acc. 1997, 97:119-124.
28. Perdew J.P., Burke K., Ernzerhof M. Generalized gradient approximation made simple. Phys. Rev. Lett. 1996, 77:3865-3868.
29. Tao J., Perdew J.P., Staroverov V.N., Scuseria G.E. Climbing the density functional ladder: nonempirical meta-generalized gradient approximation designed for molecules and solids. Phys. Rev. Lett. 2003, 91(14):146401.
30. Staroverov V.N., Scuseria G.E., Tao J., Perdew J.P. Comparative assessment of a new nonempirical density functional: molecules and hydrogen-bonded complexes. J. Chem. Phys. 2003, 119(23):12129-12137.
31. Perdew J.P., Ernzerhof M., Burke K. Rationale for mixing exact exchange with density functional approximations. J. Chem. Phys. 1996, 105:9982-9985.
32. Becke A.D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 1993, 98(7):5648-5652.
33. Semrouni D., Ohanessian G., Clavaguéra C. Structural, energetic and dynamical properties of sodiated oligoglycines: relevance of a polarizable force field. Phys. Chem. Chem. Phys. 2010, 12:3450-3462.
34. Vaden T.D., de Boer T.S.J.A., Simons J.P., Snoek L.C., Suhai S., Paizs B. Vibrational spectroscopy and conformational structure of protonated polyalanine peptides isolated in the gas phase. J. Phys. Chem. A 2008, 112(20):4608-4616.
35. Grimme S. Semiempirical GGA-type density functional constructed with a long-range dispersion contribution. J. Comput. Chem. 2006, 27(15):1787-1799.
36. Becke A.D. Density-functional thermochemistry. V. Systematic optimization of exchange-correlation functionals. J. Chem. Phys. 1997, 107(20):8554-8560.
37. Grimme S. Accurate description of van der waals complexes by density functional theory including empirical corrections. J. Comput. Chem. 2004, 25(12):1463-1473.
38. Schmidt M.W., Baldridge K.K., Boatz J.A., Elbert S.T., Gordon M.S., Jensen J.H., Koseki S., Matsunaga N., Nguyen K.A., Su S., Windus T.L., Dupuis M., Montgomery J.A. General atomic and molecular electronic structure system. J. Comput. Chem. 1993, 14:1347-1363.
39. Gordon M.S., Schmidt M.W. Advances in electronic structure theory: GAMESS a decade later 2005, Elsevier, Amsterdam, pp. 1167-1189.
40. ADF2009.01, SCM, Theoretical Chemistry, Vrije Universiteit, Amsterdam, The Netherlands, 2009, http://www.scm.com.
41. te Velde G., Bickelhaupt F.M., Baerends E.J., Guerra C.F., van Gisbergen S.J.A., Snijders J.G., Ziegler T. Chemistry with ADF. J. Comput. Chem. 2001, 931-967.
42. N2 barriers. J. Chem. Phys. 2009, 131(9):094103.
43. Morokuma K. Molecular orbital studies of hydrogen bonds. III. J. Chem. Phys. 1971, 55(3):1236-1244.
44. Kitaura K., Morokuma K. A new energy decomposition scheme for molecular interactions within the Hartree-Fock approximation. Int. J. Quantum Chem. 1976, 10(2):325-340.
45. Ziegler T., Rauk A. On the calculation of bonding energies by the Hartree Fock Slater Method. Theor. Chem. Acta 1977, 46:1-10.
46. M. Kohout, Program DGrid, Version 4.5, Max-Planck Institut für Chemische Physik fester Stoffe, Dresden, 2009.
47. Guerra C.F., Handgraaf J.W., Baerends E.J., Bickelhaupt F.M. Voronoi deformation density (VDD) charges: assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis. J. Comput. Chem. 2004, 25(2):189-210.
48. Noury S., Silvi B., Gillespie R.J. Chemical bonding in hypervalent molecules: is the octet rule relevant?. Inorg. Chem. 2002, 41(8):2164-2172.
49. Alikhani M.E., Fuster F., Silvi B. What can tell the topological analysis of elf on hydrogen bonding?. Struct. Chem. 2005, 16(3):203-210.
50. 3+ complex. Features of the electron density distribution. J. Struct. Chem. 2010, 51(1):166-169.
51. Prell J.S., Flick T.G., Oomens J., Berden G., Williams E.R. Coordination of trivalent metal cations to peptides: results from IRMPD spectroscopy and theory. J. Phys. Chem. A 2009, 114(2):854-860.