A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+

PeerJ

Volumn 2014, Issue 1, 2014, Pages

  Kromann, Jimmy C ^a   Christensen, Anders S ^a   Steinmann, Casper ^b   Korth, Martin ^c   Jensen, Jan H ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^c UNIVERSITY OF ULM   (Germany)

Author keywords

Biochemistry; Computational biochemistry; Computational chemistry; Molecular modeling; Proteins

Indexed keywords

ANALYTIC METHOD; ARTICLE; BINOCULAR CONVERGENCE; COMPUTER PROGRAM; GAMESS; GEOMETRY; HYDROGEN BOND; PM6; PM6 D3H; PROTEIN STRUCTURE; REACTION OPTIMIZATION;

EID: 84903826931     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.449     Document Type: Article

References (35)

1. Fedorov DG, Kitaura K. 2007. Extending the power of qantum chemistry to large systems with the fragment molecular orbital method. The Journal of Physical Chemistry 111:6904-6914 DOI 10.1021/jp0716740.
2. Francl MM, Pietro WJ, Hehre WJ, Binkley JS, Gordon MS, DeFrees DJ, Pople JA. 1982. Self-consistent molecular orbital methods. XXIII. A polarization-type basis set for second-row elements. The Journal of Chemical Physics 77(7):3654-3665 DOI 10.1063/1.444267.
3. Gordon MS, Binkley JS, Pople JA, Pietro WJ, Hehre WJ. 1982. Self-consistent molecular-orbital methods. 22. Small split-valence basis sets for second-row elements. Journal of the American Chemical Society 104(10):2797-2803 DOI 10.1021/ja00374a017.
4. Grimme S. 2012. Supramolecular binding thermodynamics by dispersion-corrected density functional theory. Chemistry-A European Journal 18(32):9955-9964 DOI 10.1002/chem.201200497.
5. Grimme S, Antony J, Ehrlich S, Krieg H. 2010. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. The Journal of Chemical Physics 132:154104 DOI 10.1063/1.3382344.
6. Hariharan PC, Pople JA. 1973. The influence of polarization functions on molecular orbital hydrogenation energies. Theoretica Chimica Acta 28:213-222 DOI 10.1007/BF00533485.
7. JensenGroup. 2014a. Github: optimized protein structures. Available at https://github.com/jensengroup/optimized-protein-structures.
8. JensenGroup. 2014b. Github: Third-generation hydrogen-bonding correction. Available at https://github.com/jensengroup/hydrogen-bond-correction-f3.
9. Jmol: an open-source Java viewer for chemical structures in 3D. Available at http://www.jmol.org.
10. Jurečka P, Cerný J, Hobza P, Salahub DR. 2007. Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations. Journal of Computational Chemistry 28(2):555-569 DOI 10.1002/jcc.20570.
11. Jurečka P, Šponer J, Černý J, Hobza P. 2006. Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, dna base pairs, and amino acid pairs. Physical Chemistry Chemical Physics 8:1985-1993 DOI 10.1039/b600027d.
12. Kabsch W. 1976. A solution for the best rotation to relate two sets of vectors. Acta Crystallographica A32:922-923 DOI 10.1107/S0567739476001873.
13. Klamt A, Schuurmann G. 1993. COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. Journal of the Chemical Society, Perkin Transactions 2:799-805 DOI 10.1039/p29930000799.
14. Kobko N, Dannenberg JJ. 2003. Cooperativity in amide hydrogen bonding chains. Relation between energy, position, and h-bond chain length in peptide and protein folding models. The Journal of Physical Chemistry A 107(48):10389-10395 DOI 10.1021/jp0365209.
15. Kobko N, Paraskevas L, Rio E, Dannenberg JJ. 2001. Cooperativity in amide hydrogen bonding chains: implications for protein-folding models. Journal of the American Chemical Society 123(18):4348-4349 DOI 10.1021/ja004271l.
16. Korth M. 2010. Third-generation hydrogen-bonding corrections for semiempirical QM methods and force fields. Journal of Chemical Theory and Computation 12:803-3816.
17. Korth M. 2011. Empirical hydrogen-bond potential functions-an old hat reconditioned. ChemPhysChem 12(17):3131-3142 DOI 10.1002/cphc.201100540.
18. Korth M, Pitońak M, Rezác J, Hobza P. 2010. A transferable H-bonding correction for semiempirical quantum-chemical methods. Journal of Chemical Theory and Computation 6:344-352 DOI 10.1021/ct900541n.
19. Korth M, Thiel W. 2011. Benchmarking semiempirical methods for thermochemistry, kinetics, and noncovalent interactions: OMx methods are almost as accurate and robust as DFT-GGA methods for organic molecules. Journal of Chemical Theory and Computation 7(9):2929-2936 DOI 10.1021/ct200434a.
20. Maia JDC, Carvalho GAU, Mangueira CP, Santana SR, Cabral LAF, Rocha GB. 2012. GPU linear algebra libraries and GPGPU programming for accelerating MOPAC semiempirical quantum chemistry calculations. Journal of Chemical Theory and Computation 8(9):3072-3081 DOI 10.1021/ct3004645.
21. Muddana HS, Gilson MK. 2012. Calculation of host-guest binding affinities using a quantummechanical energy model. Journal of Chemical Theory and Computation 8:2023-2033 DOI 10.1021/ct3002738.
22. Nagata T, Brorsen K, Fedorov DG, Kazuo K, Gordon MS. 2011. Fully analytic energy gradient in the fragment molecular orbital method. Journal of Chemical Physics 134:124115 DOI 10.1063/1.3568010.
23. Nagata T, Fedorov DG, Li H, Kitaura K. 2012. Analytic gradient for second order Møller-Plesset perturbation theory with the polarizable continuum model based on the fragment molecular orbital method. Journal of Chemical Physics 136:204112 DOI 10.1063/1.4714601.
24. Peverati R, Baldridge KK. 2008. Implementation and performance of DFT-D with respect to basis set and functional for study of dispersion interactions in nanoscale aromatic hydrocarbons. Journal of Chemical Theory and Computation 12:2030-2048 DOI 10.1021/ct800252z.
25. Rezáč J, Hobza P. 2012. Advanced corrections of hydrogen bonding and dispersion for semiempirical quantum mechanical methods. Journal of Chemical Theory and Computation 8:141-151 DOI 10.1021/ct200751e.
26. Řezáč J, Jurečka P, Riley KE, Černý J, Valdes H, Pluháčková K, Berka K, Řezáč T, Pitońák M, Vondrášek J, Hobza P. 2008. Quantum chemical benchmark energy and geometry database for molecular clusters and complex molecular systems (www.begdb.com): a users manual and examples. Collection of Czechoslovak Chemical Communications 73(10):1261-1270 DOI 10.1135/cccc20081261.
27. Řezáč J, Riley KE, Hobza P. 2011. S66: a well-balanced database of benchmark interaction energies relevant to biomolecular structures. Journal of Chemical Theory and Computation 7(8):2427-2438 DOI 10.1021/ct2002946.
28. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA. 1993. General atomic and molecular electronic structure system. Journal of Computational Chemistry 14:1347-1363 DOI 10.1002/jcc.540141112.
29. Schrodinger LLC. The PyMOL Molecular Graphics System, Version 1.5.0.4. Available at http://www.pymol.org.
30. Steinmann C, Blædel KL, Christensen AS, Jensen JH. 2013. Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program. PLoS ONE 8(7):e67725 DOI 10.1371/journal.pone.0067725.
31. Stewart JJP. 2007. Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements. Journal of Molecular Modelling 13:1172-1213 DOI 10.1007/s00894-007-0233-4.
32. Stewart JJP. 2012. MOPAC2012. Colorado Springs, CO: Stewart Computational Chemistry. Available at http://openmopac.net.
33. Su P, Li H. 2009. Continuous and smooth potential energy surface for conductorlike screening solvation model using fixed points with variable areas. Journal of Chemical Physics 130:074109 DOI 10.1063/1.3077917.
34. Tomansi J, Mennucci B, Cammi R. 2005. Quantum mechanical continuum solvation models. Chemical Reviews 105:2999-3093 DOI 10.1021/cr9904009.
35. Yilmazer ND, Korth M. 2013. Comparison of molecular mechanics, semi-empirical quantum mechanical, and density functional theory methods for scoring protein-ligand interactions. The Journal of Physical Chemistry 117(27):8075-8084 DOI 10.1021/jp402719k.