Literature DB >> 23379303

The melatonin conformer space: benchmark and assessment of wave function and DFT methods for a paradigmatic biological and pharmacological molecule.

Uma R Fogueri1, Sebastian Kozuch, Amir Karton, Jan M L Martin.   

Abstract

Reference quality conformational energies have been obtained for the 52 unique conformers of melatonin by means of explicitly correlated ab initio methods as well as the ccCA composite method. These data have then been used to evaluate more approximate methods, including a variety of density functionals both on their own and paired with various empirical dispersion corrections. Owing to the presence of internal contacts of the C-H···O and C-H···N variety, basis set convergence is much slower than for alkane conformers, for example, and basis sets of aug-cc-pVQZ or def2-QZVP quality seem to be required to obtain firm estimates of the basis set limit. Not just HF, but also many DFT functionals, will transpose the two lowest conformers unless empirical dispersion corrections are added. Somewhat surprisingly, many DFT functionals reproduce the reference data to fairly high accuracy when combined with the D3BJ empirical dispersion correction or the "nonlocal" Vydrov-Van Voorhis dispersion model. The two best performers including dispersion corrections are the double hybrids DSD-PBEP86-D3BJ and B2GP-PLYP-D; if no such correction is permitted, then M06-2X puts in the best performance. Of lower-cost ab initio-like models, MP2.5 yields the best performance, followed by SCS-MP2.

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Year:  2013        PMID: 23379303     DOI: 10.1021/jp312644t

Source DB:  PubMed          Journal:  J Phys Chem A        ISSN: 1089-5639            Impact factor:   2.781


  9 in total

1.  Survival of the most transferable at the top of Jacob's ladder: Defining and testing the ωB97M(2) double hybrid density functional.

Authors:  Narbe Mardirossian; Martin Head-Gordon
Journal:  J Chem Phys       Date:  2018-06-28       Impact factor: 3.488

2.  Informing geometric deep learning with electronic interactions to accelerate quantum chemistry.

Authors:  Zhuoran Qiao; Anders S Christensen; Matthew Welborn; Frederick R Manby; Anima Anandkumar; Thomas F Miller
Journal:  Proc Natl Acad Sci U S A       Date:  2022-07-28       Impact factor: 12.779

Review 3.  Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources.

Authors:  Rebecca Sure; Jan Gerit Brandenburg; Stefan Grimme
Journal:  ChemistryOpen       Date:  2015-11-25       Impact factor: 2.911

4.  Structure of Diferrocenyl Thioketone: From Molecule to Crystal.

Authors:  Piotr Matczak; Grzegorz Mlostoń; Róża Hamera-Fałdyga; Helmar Görls; Wolfgang Weigand
Journal:  Molecules       Date:  2019-10-31       Impact factor: 4.411

5.  Automatic generation of complementary auxiliary basis sets for explicitly correlated methods.

Authors:  Emmanouil Semidalas; Jan M L Martin
Journal:  J Comput Chem       Date:  2022-07-19       Impact factor: 3.672

6.  Explicitly Correlated Double-Hybrid DFT: A Comprehensive Analysis of the Basis Set Convergence on the GMTKN55 Database.

Authors:  Nisha Mehta; Jan M L Martin
Journal:  J Chem Theory Comput       Date:  2022-09-13       Impact factor: 6.578

7.  Reduced-Scaling Double Hybrid Density Functional Theory with Rapid Basis Set Convergence through Localized Pair Natural Orbital F12.

Authors:  Nisha Mehta; Jan M L Martin
Journal:  J Phys Chem Lett       Date:  2022-09-30       Impact factor: 6.888

8.  PEPCONF, a diverse data set of peptide conformational energies.

Authors:  Viki Kumar Prasad; Alberto Otero-de-la-Roza; Gino A DiLabio
Journal:  Sci Data       Date:  2019-01-22       Impact factor: 6.444

9.  Minimally Empirical Double-Hybrid Functionals Trained against the GMTKN55 Database: revDSD-PBEP86-D4, revDOD-PBE-D4, and DOD-SCAN-D4.

Authors:  Golokesh Santra; Nitai Sylvetsky; Jan M L Martin
Journal:  J Phys Chem A       Date:  2019-06-12       Impact factor: 2.944

  9 in total

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