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Fast and accurate hybrid QM//MM approach for computing anharmonic corrections to vibrational frequencies

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Abstract

We have developed and tested a new time-effective and accurate hybrid QM//MM generalized second-order vibrational perturbation theory (GVPT2) approach. In this approach, two different levels of theory were used, a high level one (DFT) for computing the harmonic spectrum and a lower fast one (Molecular Mechanic) for the anharmonic corrections. To validate our approach, we used B2PLYP/def2-TZVPP as the high-level method, and the MMFF94 method for the anharmonic corrections as the low-level method. The calculations were carried out on 28 molecules (containing from 2 to 47 atoms) covering a broad range of vibrational modes present in organic molecules. We find that this fast hybrid method reproduces the experimental frequencies with a very good accuracy for organic and bio-molecules. The root-mean-square deviation (RMSD) is about 27 cm -1 while the full B3LYP/SNSD simulation reproduces the experimental values with a RMSD of about 41 cm -1. Concerning the computational time, the hybrid B2PLYP//MMFF94 approach considerably outperforms the full B3LYP/SNSD: for the larger molecule of our set (a dipeptide containing 47 atoms), the anharmonic corrections are 2300 times faster using hybrid MMFF94 rather than full B3LYP, which represents an additional computation time to the harmonic calculation of merely 9 %, instead of 32100 % with the full B3LYP approach. This time-effective and accurate alternative to the traditional GVPT2 approach will allow the spectroscopy community to explore anharmonic effects in larger biomolecules, which are generally unaffordable.

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References

  1. Adesokan AA, Gerber RB (2009) Anharmonic vibrational spectroscopy calculations for proton-bound amino acid dimers. J Phys Chem A 113:1905–1912

    Article  CAS  Google Scholar 

  2. Barnes L, Schindler B, Allouche AR, Simon D, Chambert S, Oomens J, Compagnon I (2015) Anharmonic simulations of the vibrational spectrum of sulfated compounds: application to the glycosaminoglycan fragment glucosamine 6-sulfate. Phys Chem Chem Phys 17:25,705–25,713

    Article  CAS  Google Scholar 

  3. Barone V (2005) Anharmonic vibrational properties by a fully automated second-order perturbative approach. J Chem Phys 122(014):108

    Google Scholar 

  4. Barone V, Biczysko M, Bloino J (2014a) Fully anharmonic IR and Raman spectra of medium-size molecular systems: accuracy and interpretation. Phys Chem Chem Phys 16:1759–1787

  5. Barone V, Biczysko M, Bloino J, Puzzarini C (2014b) Accurate molecular structures and infrared spectra of trans-2,3-dideuterooxirane, methyloxirane, and trans-2,3-dimethyloxirane. J Chem Phys 141(034):107

  6. Barone V, Biczysko M, Bloino J, Cimino P, Penocchio E, Puzzarini C (2015) Cc/dft route toward accurate structures and spectroscopic features for observed and elusive conformers of flexible molecules: pyruvic acid as a case study. J Chem Theory Comput 11:4342–4363

    Article  CAS  Google Scholar 

  7. Becke A (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38:3098–3100

    Article  CAS  Google Scholar 

  8. Becke A (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98:5648–5652

    Article  CAS  Google Scholar 

  9. Bowman JM (1978) Self-consistent field energies and wavefunctions for coupled oscillators. J Chem Phys 68:608–610

    Article  CAS  Google Scholar 

  10. Brauer B, Chaban GM, Gerber RB (2004) Spectroscopically-tested, improved, semi-empirical potentials for biological molecules: calculations for glycine, alanine and proline. Phys Chem Chem Phys 6:2543–2556

    Article  CAS  Google Scholar 

  11. Carbonniere P, Barone V (2004) Performances of different density functionals in the computation of vibrational spectra beyond the harmonic approximation. Chem Phys Lett 399:226–229

    Article  CAS  Google Scholar 

  12. Carbonniere P, Lucca T, Pouchan C, Rega N, Barone V (2005) Vibrational computations beyond the harmonic approximation: performances of the b3lyp density functional for semirigid molecules. J Comput Chem 26:384–388

    Article  CAS  Google Scholar 

  13. Carbonnière P, Dargelos A, Pouchan C (2010) The vci-p code: an iterative variation–perturbation scheme for efficient computations of anharmonic vibrational levels and IR intensities of polyatomic molecules. Theor Chem Acc 125:543–554

    Article  Google Scholar 

  14. Constans P, Ayala PY, Scuseria GE (2000) Scaling reduction of the perturbative triples correction (T) to coupled cluster theory via Laplace transform formalism. J Chem Phys 113:10,451– 10,458

    Article  CAS  Google Scholar 

  15. Dian BC, Longarte A, Mercier S, Evans DA, Wales DJ, Zwier TS (2002) The infrared and ultraviolet spectra of single conformations of methyl-capped dipeptides: N-acetyl tryptophan amide and n-acetyl tryptophan methyl amide. J Chem Phys 117:10,688–10,702

    Article  CAS  Google Scholar 

  16. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery J A Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas d Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09 Revision D.01. Gaussian Inc, Wallingford CT, p 2009

    Google Scholar 

  17. Grimme S (2006) Semiempirical hybrid density functional with perturbative second-order correlation. J Chem Phys 124(034):108

    Google Scholar 

  18. Halgren TA (1996) Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J Comput Chem 17:490–519

    Article  CAS  Google Scholar 

  19. Huber K, Herzberg G (2005) Gaithersburg MD, 20899

  20. Jacox M (2005) Vibrational and Electronic Energy Levels of Polyatomic Transient Molecules in the NIST Chemistry WebBook, NIST Standard Reference Database Number 69. National Institute of Standards and Technology, Gaithersburg MD, 20899

  21. Jung JO, Gerber RB (1996) Vibrational wave functions and spectroscopy of (H 2 O) n , n=2,3,4,5: vibrational self-consistent field with correlation corrections. J Chem Phys 105:10,332–10,348

    Article  CAS  Google Scholar 

  22. Kalescky R, Zou W, Kraka E, Cremer D (2012) Local vibrational modes of the water dimer comparison of theory and experiment. Chem Phys Lett 554:243–247

    Article  CAS  Google Scholar 

  23. Klopper W, Noga J, Koch H, Helgaker T (1997) Multiple basis sets in calculations of triples corrections in coupled-cluster theory. Theor Chem Acc 97:164–176

    Article  CAS  Google Scholar 

  24. Lee C, Yang W, Parr R (1988) Development of the Colle–Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37:785–789

    Article  CAS  Google Scholar 

  25. Martin JML, Lee TJ, Taylor PR, Franois J (1995) The anharmonic force field of ethylene, C 2 H 4, by means of accurate ab initio calculations. J Chem Phys 103:2589–2602

    Article  CAS  Google Scholar 

  26. Masiello T, Maki A, Blake TA (2009) Analysis of the high-resolution infrared spectrum of cyclopropane. J Mol Spec 255:45–55

    Article  CAS  Google Scholar 

  27. Maslen PE, Handy NC, Amos RD, Jayatilaka D (1992) Higher analytic derivatives. IV. anharmonic effects in the benzene spectrum. J Chem Phys 97:4233–4254

    Article  CAS  Google Scholar 

  28. Neese F (2012) The ORCA program system. WIRES Comput Mol Sc 2:73–78

    Article  CAS  Google Scholar 

  29. Nielsen HH (1951) The vibration-rotation energies of molecules. Rev Mod Phys 23:90–136

    Article  CAS  Google Scholar 

  30. O’Boyle N, Banck M, James C, Morley C, Vandermeersch T, Hutchison G (2011) Open Babel: an open chemical toolbox. J Cheminform 3:33

    Article  Google Scholar 

  31. Oh HB, Lin C, Hwang HY, Zhai H, Breuker K, Zabrouskov V, Carpenter BK, McLafferty FW (2005) Infrared photodissociation spectroscopy of electrosprayed ions in a Fourier transform mass spectrometer. J Am Chem Soc 127:4076–4083

    Article  CAS  Google Scholar 

  32. Piccardo M, Bloino J, Barone V (2015) Generalized vibrational perturbation theory for rotovibrational energies of linear, symmetric and asymmetric tops: theory, approximations, and automated approaches to deal with medium-to-large molecular systems. Int J Quant Chem 115:948–982

    Article  CAS  Google Scholar 

  33. Plath KL, Takahashi K, Skodje RT, Vaida V (2009) Fundamental and overtone vibrational spectra of gas-phase pyruvic acid. J Phys Chem A 113:7294–7303

    Article  CAS  Google Scholar 

  34. Rauhut G, Knizia G, Werner HJ (2009) Accurate calculation of vibrational frequencies using explicitly correlated coupled-cluster theory. J Chem Phys 130(054):105

    Google Scholar 

  35. Roy TK, Gerber RB (2013) Vibrational self-consistent field calculations for spectroscopy of biological molecules: new algorithmic developments and applications. Phys Chem Chem Phys 15:9468–9492

    Article  CAS  Google Scholar 

  36. Roy TK, Sharma R, Gerber RB (2016) First-principles anharmonic quantum calculations for peptide spectroscopy: Vscf calculations and comparison with experiments. Phys Chem Chem Phys 18:1607–1614

    Article  CAS  Google Scholar 

  37. Schindler B, Joshi J, Allouche AR, Simon D, Chambert S, Brites V, Gaigeot MP, Compagnon I (2014) Distinguishing isobaric phosphated and sulfated carbohydrates by coupling of mass spectrometry with gas phase vibrational spectroscopy. Phys Chem Chem Phys 16:22,131–22,138

    Article  CAS  Google Scholar 

  38. Stewart JJP (2012) Mopac2012. Stewart Computational Chemistry

  39. Sunahori FX, Su Z, Kang C, Xu Y (2010) Infrared diode laser spectroscopic investigation of four C–H stretching vibrational modes of propylene oxide. Chem Phys Lett 494:14–20

    Article  CAS  Google Scholar 

  40. Unterberg C, Gerlach A, Schrader T, Gerhards M (2003) Structure of the protected dipeptide ac-val-phe-ome in the gas phase: towards a ß-sheet model system. J Chem Phys 118:8296–8300

    Article  CAS  Google Scholar 

  41. Weigend F, Ahlrichs R (2005) Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: design and assessment of accuracy. Phys Chem Chem Phys 7:3297–3305

    Article  CAS  Google Scholar 

  42. Yagi K, Taketsugu T, Hirao K, Gordon MS (2000) Direct vibrational self-consistent field method: applications to H 2 O and H 2 C O. J Chem Phys 113:1005–1017

    Article  CAS  Google Scholar 

  43. Yagi K, Hirao K, Taketsugu T, Schmidt MW, Gordon MS (2004) Ab initio vibrational state calculations with a quartic force field: applications to H 2 C O, C 2 H 4, C H 3 O H, C H 3 C C H, and C 6 H 6. J Chem Phys 121:1383–1389

    Article  CAS  Google Scholar 

  44. van Zundert GCP, Jaeqx S, Berden G, Bakker JM, Kleinermanns K, Oomens J, Rijs AM (2011) Ir spectroscopy of isolated neutral and protonated adenine and 9-methyladenine. ChemPhysChem 12:1921–1927

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was granted access to the HPC resour ces of the FLMSN, “Fédération Lyonnaise de Modélisation et Sciences Numériques”, partner of EQUIPEX EQUIP@MESO, and to the “Centre de calcul CC-IN2P3” at Villeurbanne, France. The authors are members of the Glycophysics Network (http://www.glyms.univ-lyon1.fr).

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Authors and Affiliations

  1. Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France

    Loïc Barnes, Baptiste Schindler, Isabelle Compagnon & Abdul-Rahman Allouche

  2. Institut Universitaire de France IUF, 103 Blvd St Michel, 75005, Paris, France

    Isabelle Compagnon

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  1. Loïc Barnes
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  2. Baptiste Schindler
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  4. Abdul-Rahman Allouche
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Correspondence to Abdul-Rahman Allouche.

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This paper belongs to Topical Collection Festschrift in Honor of Henry Chermette

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Barnes, L., Schindler, B., Compagnon, I. et al. Fast and accurate hybrid QM//MM approach for computing anharmonic corrections to vibrational frequencies. J Mol Model 22, 285 (2016). https://doi.org/10.1007/s00894-016-3135-5

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