The accuracy of quantum chemical methods for large noncovalent complexes
Status PubMed-not-MEDLINE Jazyk angličtina Země Spojené státy americké Médium print
Typ dokumentu časopisecké články
Grantová podpora
P30 GM103450
NIGMS NIH HHS - United States
PubMed
24098094
PubMed Central
PMC3789125
DOI
10.1021/ct400036b
Knihovny.cz E-zdroje
- Publikační typ
- časopisecké články MeSH
We evaluate the performance of the most widely used wavefunction, density functional theory, and semiempirical methods for the description of noncovalent interactions in a set of larger, mostly dispersion-stabilized noncovalent complexes (the L7 data set). The methods tested include MP2, MP3, SCS-MP2, SCS(MI)-MP2, MP2.5, MP2.X, MP2C, DFT-D, DFT-D3 (B3-LYP-D3, B-LYP-D3, TPSS-D3, PW6B95-D3, M06-2X-D3) and M06-2X, and semiempirical methods augmented with dispersion and hydrogen bonding corrections: SCC-DFTB-D, PM6-D, PM6-DH2 and PM6-D3H4. The test complexes are the octadecane dimer, the guanine trimer, the circumcoronene…adenine dimer, the coronene dimer, the guanine-cytosine dimer, the circumcoronene…guanine-cytosine dimer, and an amyloid fragment trimer containing phenylalanine residues. The best performing method is MP2.5 with relative root mean square deviation (rRMSD) of 4 %. It can thus be recommended as an alternative to the CCSD(T)/CBS (alternatively QCISD(T)/CBS) benchmark for molecular systems which exceed current computational capacity. The second best non-DFT method is MP2C with rRMSD of 8 %. A method with the most favorable "accuracy/cost" ratio belongs to the DFT family: BLYP-D3, with an rRMSD of 8 %. Semiempirical methods deliver less accurate results (the rRMSD exceeds 25 %). Nevertheless, their absolute errors are close to some much more expensive methods such as M06-2X, MP2 or SCS(MI)-MP2, and thus their price/performance ratio is excellent.
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Riley KE, Hobza P. Acc Chem Res. 2013;46:927–936. PubMed
Hohenstein EG, Sherrill CD. Wiley Interdiscip Rev: Comput Mol Sci. 2012;2:304–326.
Vondrášek J, Kubař T, Jenney FE, Adams MWW, Kožíšek M, Černý J, Sklenář V, Hobza P. Chem-Eur J. 2007;13:9022–9027. PubMed
Šponer J, Leszczynski J, Hobza P. Biopolymers. 2001;61:3–36. PubMed
Šponer J, Leszczynski J, Hobza P. J Mol Struct (THEOCHEM) 2001;573:43–53.
Kristyán S, Pulay P. Chem Phys Lett. 1994;229:175–180.
Perez-Jorda JM, Becke AD. Chem Phys Lett. 1995;233:134–137.
Hobza P, Šponer J, Reschel T. J Comput Chem. 1995;16:1315–1325.
Janowski T, Pulay P. Chem Phys Lett. 2007;447:27–32.
Sinnocrot MO, Valeev EF, Sherrill CD. J Am Chem Soc. 2002;124:10887–10893. PubMed
Riley KE, Pitoňák M, Jurečka P, Hobza P. Chem Rev. 2010;110:5023–5063. PubMed
Grimme S. J Chem Phys. 2003;118:9095–9102.
Marchelli O, Werner HJ. J Phys Chem A. 2009;113:11580–11585. PubMed
Distasio AR, Jr, Head-Gordon M. Mol Phys. 2007;105:1073–1083.
Takatani T, Hohenstein EG, Sherrill CD. J Chem Phys. 2008;128:124111/1–7. PubMed
Zhao Y, Truhlar DG. Acc Chem Res. 2008;41:157–167. PubMed
Hesselmann A. J Chem Phys. 2008;128:144112. PubMed
Chermak E, Mussard B, Angyan JjG, Reinhardt P. Chem Phys Lett. 2012;550:162–169.
Grimme S, Antony J, Ehrlich S, Krieg H. J Chem Phys. 2010;132:154104/1–17. PubMed
Schütz M, Werner HJ. Chem Phys Lett. 2000;318:370–378.
Jeziorski B, Moszynski R, Szalewicz K. Chem Rev. 1994;94:1887–1930.
Misquitta AJ, Szalewicz K. Chem Phys Lett. 2002;357:301–306.
Hesselmann A, Jansen G. Chem Phys Lett. 2002;357:464–470.
von Lilienfeld OA, Tavernelli I, Rothlisberger U, Sebastiani D. Phys Rev Lett. 2004;93:153004/1–4. PubMed
DiLabio GA. Chem Phys Lett. 2008;455:348–353.
Dion M, Rydberg H, Schröder E, Langreth DC, Lundqvist BI. Phys Rev Lett. 2004;92:246401/1–4. PubMed
Dion M, Rydberg H, Schröder E, Langreth DC, Lundqvist BI. Phys Rev Lett. 2005;95:109902/1. PubMed
Becke AD, Johnson ER. J Chem Phys. 2007;127:154108/1–6. PubMed
Pitoňák M, Neogrády P, Černý J, Grimme S, Hobza P. Phys Chem Chem Phys. 2009;10:282–289. PubMed
Riley EK, Řezáč J, Hobza P. Phys Chem Chem Phys. 2011;13:21121–21125. PubMed
Grimme S. J Comput Chem. 2006;27:1787–1799. PubMed
Jurečka P, Černý J, Hobza P, Salahub DR. J Comput Chem. 2007;28:555–569. PubMed
Zhao Y, Truhlar DG. Theor Chem Acc. 2008;120:215–241.
Dewar JSM, Thiel W. J Am Chem Soc. 1977;99:4899–4907.
Martin B, Clark T. Int J Quantum Chem. 2006;106:1208–1216.
Stewart JJP. J Mol Model. 2007;13:1173–1213. PubMed PMC
Řezáč J, Fanfrlik J, Salahub D, Hobza P. J Chem Theory Comput. 2009;5:1749–1760. PubMed
Řezáč J, Hobza P. J Chem Theory Comput. 2012;8:141–151. PubMed
Jurečka P, Šponer J, Černý J, Hobza P. Phys Chem Chem Phys. 2006;8:1985–1993. PubMed
Gráfová L, Pitoňák M, Řezáč J, Hobza P. J Chem Theory Comput. 2010;6:2365–2376. PubMed
Molnar L, He X, Wang B, Merz K. J Chem Phys. 2009;131:065102/1–16. PubMed PMC
Řezáč J, Riley KE, Hobza P. J Chem Theory Comput. 2011;7:2427–2438. 3466–3470. PubMed PMC
Goerigk L, Grimme S. J Chem Theory Comput. 2010;6:107–126. PubMed
Goerigk L, Grimme S. J Chem Theory Comput. 2011;7:291–309. PubMed
Zhao Y, Truhlar DG. J Chem Theory Comput. 2005;1:415–432. PubMed
Zhao Y, Truhlar DG. J Phys Chem A. 2005;109:5656–5667. PubMed
Zhao Y, Truhlar DG. J Chem Theory Comput. 2007;3:289–300. PubMed
Berka K, Laskowski R, Hobza P, Vondrášek J. J Chem Theory Comput. 2010;6:2191–2203. PubMed
Risthaus T, Grimme S. J Chem Theory Comput. 2013;9:1580–1591. PubMed
Granatier J, Pitoňák M, Hobza P. J Chem Theory Comput. 2012;7:2282–2292. PubMed
Janowski T, Pulay P. J Amer Chem Soc. 2012;134:17520–17525. PubMed PMC
Pitoňák M, Neogrády P, Hobza P. Phys Chem Chem Phys. 2010;12:1369–1378. PubMed
Janowski T, Ford AR, Pulay P. Mol Phys. 2010;108:249–257.
Hays FA, Teegarden A, Jones ZJ, Harms M, Raup D, Watson J, Cavaliere E, Ho PS. Proc Natl Acad Sci USA. 2005;102:7157–7162. PubMed PMC
Case AD, Darden AT, Cheatham ET, III, Simmerling LC, Wang J, Duke ER, Luo R, Merz MK, Pearlman AD, Crowley M, Walker CR, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong FK, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews HD, Schafmeister C, Ross SW, Kollman AP. AMBER 9. University of California; San Francisco: 2006.
Řezáč J, Jurečka P, Riley KE, Černý J, Valdes H, Pluháčková K, Berka K, Řezáč T, Pitoňák M, Vondrášek J, Hobza P. Collect Czech Chem Commun. 2008;73:1261–1270.
Boys SF, Bernardi F. Mol Phys. 1970;19:553–566.
Baker J, Wolinski K, Janowski T, Saebo S, Pulay P. PQS version 4.0. Parallel Quantum Solutions; Fayetteville, Arkansas, USA: 2012. www.pqs-chem.com.
Janowski T, Pulay P. Chem Phys Lett. 2007;447:27–32.
Jurečka P, Hobza P. Chem Phys Lett. 2002;365:89–94.
van Lenthe JH, vanDuijneveldt-van de Rijdt JGCM, van Duijneveldt FB. Adv Chem Phys. 1987;69:521–544.
Hobza P, Šponer J Chem Rev. 1999;99:3247–3276. PubMed
Svozil D, Hobza P, Šponer J. J Phys Chem B. 2010;114:1191–1203. PubMed
Riley EK, Řezáč J, Hobza P. Phys Chem Chem Phys. 2011;13:21121–21125. PubMed
Halkier A, Helgaker T, Jorgensen P, Klopper W, Koch HJ, Wilson KA. Chem Phys Lett. 1998;286:243–252.
Halkier A, Helgaker T, Jorgensen P, Klopper W, Olsen J. Chem Phys Lett. 1999;302:437–446.
Kendall RA, Dunning TH, Jr, Harrison RJ. J Chem Phys. 1992;96:6796–806.
Woon DE, Dunning TH., Jr J Chem Phys. 1993;98:1358–1371.
Dunning TH., Jr J Chem Phys. 1989;90:1007–1023.
Schwenke DW. J Chem Phys. 2007;122:014107/1–7.
Pitoňák M, Hesselmann A. J Chem Theory Comput. 2010;6:168–178. PubMed
Pitoňák M, Neogrády P, Černý J, Grimme S, Hobza P. Chem Phys Chem. 2009;10:282–289. PubMed
Grimme S, Ehrlich S, Goerigk L. J Comput Chem. 2011;32:1456–1465. PubMed
Johnson ER, Becke AD. J Chem Phys. 2005;123:024101/1–7. PubMed
Becke AD, Johnson ER. J Chem Phys. 2005;123:154101/1–9. PubMed
Johnson ER, Becke AD. J Chem Phys. 2006;124:174104/1–9. PubMed
Goerigk L, Kruse H, Grimme S. Chem Phys Chem. 2011;12:3421–3433. PubMed
Korth M, Pitoňák M, Řezáč J, Hobza P. J Chem Theory Comput. 2010;6:168–178. PubMed
Elstner M, Porezag D, Jungnickel G, Elsner J, Haugk M, Frauenheim T, Suhai S, Seifert G. Phys Rev B. 1998;58:7260–7268.
Elstner M, Hobza P, Frauenheim T, Suhai S, Kaxiras E. J Chem Phys. 2001;114:5149–5155.
Ahlrichs R, Bär M, Häser M, Horn H, Kölmel C. Chem Phys Lett. 1989;162:165–169.
Werner H-J, Knowles PJ, Lindh R, Manby FR, Schütz M, Celani P, Korona T, Mitrushenkov A, Rauhut G, Adler TB, Amos RD, Bernhardsson A, Berning A, Cooper DL, Deegan MJO, Dobbyn AJ, Eckert F, Goll E, Hampel C, Hetzer G, Hrenar T, Knizia G, Köppl C, Liu Y, Lloyd AW, Mata RA, May AJ, McNicholas SJ, Meyer W, Mura ME, Nicklass A, Palmieri P, Pflüger K, Pitzer R, Reiher M, Schumann U, Stoll H, Stone AJ, Tarroni R, Thorsteinsson T, Wang M, Wolf A. MOLPRO, version 2009.1, a package of ab initio programs. see http://www.molpro.net.
Karlstrom G, Lindh R, Malmqvist PA, Roos BO, Ryde U, Veryazov V, Widmark PO, Cossi M, Schimmelpfennig B, Neogrady P, Seijo L. Comput Mater Sci. 2003;28:222–239.
Malmqvist PA, Rendell A, Roos BO. J Phys Chem. 1990;94:5477–5482.
Roos BO, Taylor PR. Chem Phys. 1980;48:157–173.
Beebe NHF, Linderberg J. Int J Quantum Chem. 1977;12:683–705.
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, 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 NJ, 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 Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ. Gaussian 09, Revision A.1. Gaussian, Inc; Wallingford CT: 2009.
Stewart JJP. MOPAC2009. Stewart Computational Chemistry. Colorado Springs, CO, USA: 2008. HTTP://OpenMOPAC.net.
Antony J, Grimme S. J Phys Chem, A. 2007;111:4862–4868. PubMed
Goerigk L, Grimme S. Phys Chem Chem Phys. 2011;13:6670–6688. PubMed
Antony J, Brüske B, Grimme S. Phys Chem Chem Phys. 2009;11:8440–8447. PubMed
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