Abstract
The performances of quantum chemistry methods (i.e., DFT and ab initio) in calculating the structural and vibrational properties of phosphates and phosphorylated compounds have been evaluated. Diethyl-phosphate, phosphonic acid, dihydrogen phosphate anion, phosphoric acid dimer and protonated glycylphosphotyrosine dipeptide were selected for our study. Geometry and harmonic frequency deviations were investigated, pointing out the contribution of dispersion interactions on diethyl-phosphate, [Gly-pTyr+H]+ and the phosphoric acid dimer. The B3LYP-D functional, followed by CC2 and MP2 methods, revealed significant accuracy for frequency calculations of the majority of the phosphorylated compounds in comparison with available experimental data. These investigations provide a guide to the accurate computation of phosphorylated biological compounds.
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Blom N, Kreegipuu A, Brunak S (1998) Nucleic Acids Res 26:382
Diella F, Cameron S, Gemünd C, Linding R, Via A, Kuster B, Sicheritz-Pontén T, Blom N, Gibson T (2004) J BMC Bioinforma 5:79
Johnson LN, Lewis RJ (2001) Chem Rev 101:2209
Kreegipuu A, Blom N, Brunak S (1999) Nucleic Acids Res 27:237
Engel D, Nudelman A, Levovich I, Gruss-Fischer T, Entin-Meer M, Phillips DR, Cutts SM, Rephaeli A (2006) J Cancer Res Clin Oncol 132:673
Park J, Singh B, Maj MC, Gupta RS (2004) Protein J 23:167
Cuisset A, Mouret G, Pirali O, Roy P, Cazier F, Nouali H, Demaison J (2008) J Phys Chem B 112:12516
Smirnova IN, Cuisset A, Hindle F, Mouret G, Bocquet R, Pirali O, Roy P (2010) J Phys Chem B 114:16936
Salpin JY, Guillaumont S, Ortiz D, Tortajada J, Maître P (2011) Inorg Chem 50:7769
Chiavarino B, Crestoni ME, Fornarini S, Lanucara F, Lemaire J, Maitre P, Scuderi D (2008) Int J Mass Spectrom 270:111
Fales BS, Fujamade NO, Oomens J, Rodgers MT (2011) J Am Soc Mass Spectrom 22:1862
Nei YW, Hallowita N, Steill JD, Oomens J, Rodgers MT (2013) J Phys Chem A 117:1319
Rummel JL, Steill JD, Oomens J, Contreras CS, Pearson WL, Szczepanski J, Powell DH, Eyler JR (2011) Anal Chem 83:4045
Fales BS, Fujamade NO, Nei YW, Oomens J, Rodgers MT (2011) J Am Soc Mass Spectrom 22:81
Nei YW, Crampton KT, Berden G, Oomens J, Rodgers MT (2013) J Phys Chem A 117:10634
Lanucara F, Crestoni ME, Chiavarino B, Fornarini S, Hernandez O, Scuderi D, Maitre P (2013) RSC Adv 3:12711
Dahlke EE, Orthmeyer MA, Truhlar DG (2008) J Phys Chem B 112:2372
Riley KE, Hobza P (2007) J Phys Chem A 111:8257
Van Mourik T (2008) J Chem Theory Comput 4:1610
Perdew JP, Kurth S, Zupan A, Blaha P (1991) Phys Rev Lett 82:2544
Adamo C, Ernzerhof M, Scuseria GE (2000) J Chem Phys 112:2643
Peverati R, Truhlar DG (2011) J Phys Chem Lett 2:2810
Savin A (1996) In: Seminario JM (ed) Recent developments and applications of modern density functional theory. Elsevier, Amsterdam, pp 327–357
Song JW, Watson MA, Hirao K (2009) J Chem Phys 131:144108
Iikura H, Tsuneda T, Yanai T, Hirao K (2001) J Chem Phys 115:3540
Jacquemin D, Perpète EA, Scalmani G, Frisch MJ, Kobayashi R, Adamo C (2007) J Chem Phys 126:144105
Becke AD, Johnson ER (2005) J Chem Phys 122:154104
Tkatchenko A, Scheffler M (2009) Phys Rev Lett 102:073005
Gritsenko O, Baerends EJ (2006) J Chem Phys 124:1
Dion M, Rydberg H, Schröder E, Langreth DC, Lundqvist BI (2004) Phys Rev Lett 92:246401
Waller MP, Robertazzi A, Platts JA, Hibbs DE, Williams PA (2006) J Comput Chem 27:491
Černý J, Hobza P (2005) Phys Chem Chem Phys 7:1624
Cohen AJ, Mori-Sánchez P, Yang W (2008) Science 321:792
Hohenstein EG, Chill ST, Sherrill CD (2008) J Chem Theory Comput 4:1996
Jacquemin D, Perpète EA, Ciofini I, Adamo C, Valero R, Zhao Y, Truhlar DG (2010) J Chem Theory Comput 6:2071
Bouteiller Y, Poully JC, Desfrancois C, Gregoire G (2009) J Phys Chem A 113:6301
Foster ME, Sohlberg K (2010) Phys Chem Chem Phys 12:307
Morgado CA, McNamara JP, Hillier IH, Burton NA, Vincent MA (2007) J Chem Theory Comput 3:1656
Grimme S (2004) J Comput Chem 25:1463
Grimme S (2006) J Comput Chem 27:1787
Grimme S, Antony J, Ehrlich S, Krieg HA (2010) J Chem Phys 132:154104
Hujo W, Grimme S (2011) Phys Chem Chem Phys 13:13942
Ehrlich S, Moellmann J, Grimme S (2013) Acc Chem Res 46:916
Potrzebowski MJ, Assfeld X, Ganicz K, Olejniczak S, Cartier A, Gardiennet C, Tekely P (2003) J Am Chem Soc 125:4223
Mládek A, Šponer JE, Jurečka P, Banáš P, Otyepka M, Svozil D, Šponer J (2010) J Chem Theory Comput 6:3817
Ahlrichs R, Bär M, Häser M, Horn H, Kölmel C (1989) Chem Phys Lett 162:165
Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, John A, Montgomery JJ (1993) J Comput Chem 14:1347
Gordon MS, Schmidt MW (2005) In: Dykstra CE, Frenking G, Kim KS, Scuseria GE (eds) Theory and applications of computational chemistry: the first forty years; Elsevier, Amsterdam, pp 1167
Scott AP, Radom L (1996) J Phys Chem 100:16502
Wong MW (1996) Chem Phys Lett 256:391
Carauta ANM, De Souza V, Hollauer E, Téllez SCA (2004) Spectrochim Acta Part A 60:41
Katsyuba S, Vandyukova E (2003) Chem Phys Lett 377:658
Correia CF, Balaj PO, Scuderi D, Maitre P, Ohanessian G (2008) J Am Chem Soc 130:3359
Correia CF, Clavaguera C, Erlekam U, Scuderi D, Ohanessian G (2008) Chem Phys Chem 9:2564
Scuderi D, Correia CF, Balaj OP, Ohanessian G, Lemaire J, Maitre P (2009) Chem Phys Chem 10:1630
Withnall R, Andrews L (1987) J Phys Chem 91:784
Jiang L, Sun ST, Heine N, Liu JW, Yacovitch TI, Wende T, Liu ZF, Neumark DM, Asmis KR (2014) Phys Chem Chem Phys 16:1314
Acknowledgments
A.S. thanks the vice-presidency for external relations in Ecole Polytechnique for support from the international internship program, and for a 1-year post-doctoral fellowship.
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Sharma, A., Ohanessian, G. & Clavaguéra, C. Accuracy of density functionals in the description of dispersion interactions and IR spectra of phosphates and phosphorylated compounds. J Mol Model 20, 2426 (2014). https://doi.org/10.1007/s00894-014-2426-y
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DOI: https://doi.org/10.1007/s00894-014-2426-y