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The relative energies of polypeptide conformers predicted by linear scaling second-order Møller-Plesset perturbation theory

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  • Special Issue Quantum Chemistry for Extended Systems—In honor of Prof. J.M. André for his 70th birthday
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Abstract

We describe an implementation of the cluster-in-molecule (CIM) resolution of the identity (RI) approximation second-order Møller-Plesset perturbation theory (CIM-RI-MP2), with the purpose of extending RI-MP2 calculations to very large systems. For typical conformers of several large polypeptides, we calculated their conformational energy differences with the CIM-RI-MP2 and the generalized energy-based fragmentation MP2 (GEBF-MP2) methods, and compared these results with the density functional theory (DFT) results obtained with several popular functionals. Our calculations show that the conformational energy differences obtained with CIM-RI-MP2 and GEBF-MP2 are very close to each other. In comparison with the GEBF-MP2 and CIM-RI-MP2 relative energies, we found that the DFT functionals (CAM-B3LYP-D3, LC-ωPBE-D3, M05-2X, M06-2X and ωB97XD) can give quite accurate conformational energy differences for structurally similar conformers, but provide less-accurate results for structurally very different conformers.

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References

  1. Grimme S, Diedrich C, Korth M. The importance of inter- and intramolecular van der Waals interactions in organic reactions: the dimerization of anthracene revisited. Angew Chem Int Ed, 2006, 45: 625–629

    Article  CAS  Google Scholar 

  2. Grimme S. Seemingly simple stereoelectronic effects in alkane isomers and the implications for Kohn-Sham density functional theory. Angew Chem Int Ed, 2006, 45: 4460–4464

    Article  CAS  Google Scholar 

  3. Grimme S, Antony J, Ehrlich S, Krieg H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 Elements H-Pu. J Chem Phys, 2010, 132: 154104

    Article  Google Scholar 

  4. Pulay P. Localizability of dynamic electron correlation. Chem Phys Lett, 1983, 100: 151–154

    Article  CAS  Google Scholar 

  5. Li SH, Li W, Fang T. An efficient fragment-based approach for predicting the ground-state energies and structures of large molecules. J Am Chem Soc, 2005, 127: 7215–7226

    Article  CAS  Google Scholar 

  6. Li W, Li SH, Jiang YS. Generalized energy-based fragmentation approach for computing the ground-state energies and properties of large molecules. J Phys Chem A, 2007, 111: 2193–2199

    Article  CAS  Google Scholar 

  7. Hua SG, Hua WJ, Li SH. An efficient implementation of the generalized energy-based fragmentation approach for general large molecules. J Phys Chem A, 2010, 114: 8126–8134

    Article  CAS  Google Scholar 

  8. Deev V, Collins MA. Approximate ab initio energies by systematic molecular fragmentation. J Chem Phys, 2005, 122: 154102

    Article  Google Scholar 

  9. Collins MA, Deev VA. Accuracy and efficiency of electronic energies from systematic molecular fragmentation. J Chem Phys, 2006, 125: 104104

    Article  Google Scholar 

  10. Mullin JM, Roskop LB, Pruitt SR, Collins MA, Gordon MS. Systematic fragmentation method and the effective fragment potential: an efficient method for capturing molecular energies. J Phys Chem A, 2009, 113: 10040–10049

    Article  CAS  Google Scholar 

  11. Kitaura K, Ikeo E, Asada T, Nakano T, Uebayasi M. Fragment molecular orbital method: an approximate computational method for large molecules. Chem Phys Lett, 1999, 313: 701–706

    Article  CAS  Google Scholar 

  12. Fedorov DG, Kitaura K. Second order moller-plesset perturbation theory based upon the fragment molecular orbital method. J Chem Phys, 2004, 121: 2483–2490

    Article  CAS  Google Scholar 

  13. Fedorov DG, Kitaura K. Coupled-cluster theory based upon the fragment molecular-orbital method. J Chem Phys, 2005, 123: 134103

    Article  Google Scholar 

  14. Saebø S, Pulay P. Local configuration interaction: an efficient approach for larger molecules. Chem Phys Lett, 1985, 113: 13–18

    Article  Google Scholar 

  15. Saebø S, Pulay P. Fourth-order Møller-Plessett perturbation theory in the local correlation treatment. I. Method. J Chem Phys, 1987, 86: 914–922

    Article  Google Scholar 

  16. Hampel C, Werner HJ. Local treatment of electron correlation in coupled cluster theory. J Chem Phys, 1996, 104: 6286–6297

    Article  CAS  Google Scholar 

  17. Schutz M, Hetzer G, Werner HJ. Low-order scaling local electron correlation methods. I. Linear scaling local MP2. J Chem Phys, 1999, 111: 5691–5705

    Article  CAS  Google Scholar 

  18. Schutz M, Werner HJ. Low-order scaling local electron correlation methods. IV. Linear scaling local coupled-cluster (LCCSD). J Chem Phys, 2001, 114: 661–681

    Article  CAS  Google Scholar 

  19. Li S, Ma J, Jiang Y. Linear scaling local correlation approach for solving the coupled cluster equations of large systems. J Comput Chem, 2002, 23: 237–244

    Article  CAS  Google Scholar 

  20. Li S, Shen J, Li W, Jiang Y. An efficient implementation of the “cluster-in-molecule” approach for local electron correlation calculations. J Chem Phys, 2006, 125: 074109

    Article  Google Scholar 

  21. Li W, Piecuch P, Gour JR, Li S. Local correlation calculations using standard and renormalized coupled-cluster approaches. J Chem Phys, 2009, 131: 114109

    Article  Google Scholar 

  22. Li W, Guo Y, Li S. A refined cluster-in-molecule local correlation approach for predicting the relative energies of large systems. Phys Chem Chem Phys, 2012, 14: 7854–7862

    Article  CAS  Google Scholar 

  23. Vahtras O, Almlöf J, Feyereisen MW. Integral approximations for Lcao-Scf calculations. Chem Phys Lett, 1993, 213: 514–518

    Article  CAS  Google Scholar 

  24. Weigend F, Haser M, Patzelt H, Ahlrichs R. RI-MP2: optimized auxiliary basis sets and demonstration of efficiency. Chem Phys Lett, 1998, 294: 143–152

    Article  CAS  Google Scholar 

  25. Katouda M, Nagase S. Efficient parallel algorithm of second-order Møller-Plesset perturbation theory with resolution-of-identity approximation (RI-MP2). Int J Quant Chem, 2009, 109: 2121–2130

    Article  CAS  Google Scholar 

  26. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su SJ, Windus, TL, Dupuis M, Montgomery JA. General atomic and molecular electronic-structure system. J Comput Chem, 1993, 14: 1347–1363

    Article  CAS  Google Scholar 

  27. Gordon MS, Schmidt MW. Advances in electronic structure theory: gamess a decade later. In: Dykstra CE, Frenking G, Kim KS, Scuseria GE, Eds. Theory and Applications of Computational Chemistry: the First Forty Years. Amsterdam: Elsevier B.V., 2005

    Google Scholar 

  28. 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 JA, 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 O, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ. Gaussian 09, A.01. Wallingford CT: Gaussian, Inc., 2009

    Google Scholar 

  29. Yanai T, Tew DP, Handy NC. A new hybrid exchange-correlation functional using the coulomb-attenuating method (CAM-B3LYP). Chem Phys Lett, 2004, 393: 51–57

    Article  CAS  Google Scholar 

  30. Tawada Y, Tsuneda T, Yanagisawa S, Yanai T, Hirao K. A long-range-corrected time-dependent density functional theory. J Chem Phys, 2004, 120: 8425–8433

    Article  CAS  Google Scholar 

  31. Zhao Y, Schultz NE, Truhlar DG. Design of density functionals by combining the method of constraint satisfaction with parametrization for thermochemistry, thermochemical kinetics, and noncovalent interactions. J Chem Theory Comput, 2006, 2: 364–382

    Article  Google Scholar 

  32. Zhao Y, Truhlar DG. 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: 215–241

    Article  CAS  Google Scholar 

  33. Chai JD, Head-Gordon M. Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. Phys Chem Chem Phys, 2008, 10: 6615–6620

    Article  CAS  Google Scholar 

  34. Chai JD, Head-Gordon M. Systematic optimization of long-range corrected hybrid density functionals. J Chem Phys, 2008, 128: 084106

    Article  Google Scholar 

  35. Krivov SV, Karplus M. Hidden complexity of free energy surfaces for peptide (protein) folding. Proc Natl Acad Sci USA, 2004, 101: 14766–14770

    Article  CAS  Google Scholar 

  36. Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins: Struct Func Bioinf, 2006, 65: 712–725

    Article  CAS  Google Scholar 

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Guo, Y., Li, W., Yuan, D. et al. The relative energies of polypeptide conformers predicted by linear scaling second-order Møller-Plesset perturbation theory. Sci. China Chem. 57, 1393–1398 (2014). https://doi.org/10.1007/s11426-014-5181-0

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  • DOI: https://doi.org/10.1007/s11426-014-5181-0

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