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Séminaire Chimie ED459

Introduction to quantum chemical calculations of peptides

Prof. Young Kee Kang (Department of Chemistry and BK21+ Research Team, Chungbuk National University, Korea | Prof. invité LabEx ChemiSyst)

publié le

Introduction to quantum chemical calculations of peptides

Le Jeudi 09 juin 2016 à 13h45
UM FdS, salle SC-16.01

For the last two decades, the wave function theories such as HF and MP2 methods and the density functional theories (DFTs) have been widely used in conformational study of peptides and models for protein active sites.[1,2] Because MP2 usually requires a higher computational cost than DFTs, it is especially not attractive for peptides, although the former has some merits for certain classes of systems. It has been known that the DFT has a better performance compared with correlated wave function theories. Recently, several DFTs have been proposed to correct long-range and/or dispersion interactions.[3] Many attempts have been made using the complete basis set (CBS) extrapolation and CCSD(T) corrections to reproduce accurately experimental thermochemical data, barrier heights of chemical reactions, and noncovalent interaction energies.[4,5] However, the computational cost restricted their applicability to conformational study of peptides.

Considerable quantum mechanical studies have been carried out using HF, MP2, DFT, and coupled-cluster methods with various basis sets to explore the conformational preferences of Ac-Ala-NHMe (the Ala dipeptide) and Ac-Pro-NHMe (the Pro dipeptide), which have been used as prototypes for amino acid residues of peptides. Here, we assessed the CCSD(T), MP2, dispersion-corrected DFT methods with various basis sets to describe the conformational preferences of the Ala and Pro dipeptides in the gas phase.[6,7] In particular, the double-hybrid density functionals B2PLYP[8] and DSD-PBEP86[9] using the D3 version of Grimme’s dispersion with Becke-Johnson damping were also assessed for the relative conformational energies obtained by the CCSD(T)/CBS limit approach.

References

1. Császár, A. G. ; Perczel, A. Prog. Biophys. Mol. Biol. 1999, 71, 243.
2. Jalkanen, K. J. ; Elstner, M. ; Suhai, S. J. Mol. Struct. TheoChem 2004, 675, 61.
3. Goerigk, L. ; Grimme, S. Phys. Chem. Chem. Phys. 2011, 13, 6670.
4. Riley, K. E. ; Pitoňák, M. ; Jurečka, P. ; Hobza, P. Chem. Rev. 2010, 110, 5023.
5. Vasiliu, M. ; Arduengo, A. J. ; Dixon, D. A. J. Phys. Chem. C 2012, 116, 22196.
6. Kang, Y. K. ; Byun, B. J. J. Comput. Chem. 2010, 31, 2915.
7. Kang, Y. K. ; Park, H. S. Chem. Phys. Lett. 2014, 600, 112.
8. Schwabe, T. ; Grimme, S. Phys. Chem. Chem. Phys. 2007, 9, 3397.
9. Kozuch, S. ; Martin, J. M. L. Phys. Chem. Chem. Phys. 2011, 13, 20104.

Contact local IBMM : Dr. Ludovic Maillard (DAPP)

Voir en ligne : communiqué LabEx / Pôle Balard

Agenda

séminaire

  • Jeudi 9 juin 2016 13:45-15:00 -

    Introduction to quantum chemical calculations of peptides

    Résumé : Séminaire Chimie ED459 – Young Kee Kang (conf. 1/2)

    Lieu : UM FdS, salle SC-16.01


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