title: Enhanced semiempirical QM methods for biomolecular interactions.
abstract: Recent successes and failures of the application of 'enhanced' semiempirical QM (SQM) methods are reviewed in the light of the benefits and backdraws of adding dispersion (D) and hydrogen-bond (H) correction terms. We find that the accuracy of SQM-DH methods for non-covalent interactions is very often reported to be comparable to dispersion-corrected density functional theory (DFT-D), while computation times are about three orders of magnitude lower. SQM-DH methods thus open up a possibility to simulate realistically large model systems for problems both in life and materials science with comparably high accuracy.
authors.affiliation: Institute of Theoretical Chemistry, Ulm University, D-89069 Ulm, Germany.
authors.forename: Nusret Duygu
authors.initials: ND
authors.lastname: Yilmazer
authors.affiliation: Institute of Theoretical Chemistry, Ulm University, D-89069 Ulm, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Korth
keywords: Biomolecular interactions; Computational chemistry; Dispersion interactions; Hydrogen-bond-interactions; Semi-empirical QM methods
references.citation: Langmuir. 2014 May 27;30(20):5957-64
references.pmid: 24802522
references.citation: J Phys Chem A. 2005 Apr 21;109(15):3425-32
references.pmid: 16833679
references.citation: J Pharm Sci. 2013 Jun;102(6):1970-1980
references.pmid: 23595896
references.citation: J Am Chem Soc. 2014 Apr 2;136(13):5006-22
references.pmid: 24611543
references.citation: J Chem Theory Comput. 2014 Jun 10;10(6):2615-29
references.pmid: 26580782
references.citation: J Phys Chem B. 2010 Dec 16;114(49):16574-83
references.pmid: 21087024
references.citation: J Mol Graph Model. 2010 Nov;29(3):321-5
references.pmid: 20801066
references.citation: PeerJ. 2014 Jun 19;2:e449
references.pmid: 25024918
references.citation: Carbohydr Polym. 2013 Oct 15;98(1):122-31
references.pmid: 23987325
references.citation: PLoS One. 2011 Apr 25;6(4):e18868
references.pmid: 21541343
references.citation: J Chem Phys. 2014 Jul 21;141(3):034106
references.pmid: 25053300
references.citation: Phys Chem Chem Phys. 2007 May 21;9(19):2362-70
references.pmid: 17492099
references.citation: J Chem Theory Comput. 2012 Oct 9;8(10):3769-3776
references.pmid: 23413365
references.citation: Acta Biochim Pol. 2011;58(2):255-60
references.pmid: 21633729
references.citation: J Chem Inf Model. 2009 Apr;49(4):913-24
references.pmid: 19309119
references.citation: Phys Chem Chem Phys. 2010 Jan 14;12(2):307-22
references.pmid: 20023806
references.citation: Drug Discov Today. 2007 Sep;12(17-18):725-31
references.pmid: 17826685
references.citation: J Org Chem. 2013 Sep 20;78(18):9444-9
references.pmid: 23998190
references.citation: J Mol Graph Model. 2011 Jun;29(7):928-34
references.pmid: 21470886
references.citation: J Chem Theory Comput. 2014 Oct 14;10(10):4708-17
references.pmid: 26588160
references.citation: Phys Chem Chem Phys. 2013 Dec 28;15(48):20937-42
references.pmid: 24202112
references.citation: J Comput Chem. 2005 Oct;26(13):1347-58
references.pmid: 16021597
references.citation: ACS Chem Biol. 2013 Nov 15;8(11):2484-92
references.pmid: 23988122
references.citation: J Chem Theory Comput. 2010 Jul 13;6(7):2153-66
references.pmid: 26615942
references.citation: J Chem Theory Comput. 2009 Sep 8;5(9):2206-11
references.pmid: 26616606
references.citation: ACS Appl Mater Interfaces. 2011 Nov;3(11):4451-8
references.pmid: 22017301
references.citation: J Comput Aided Mol Des. 2014 Apr;28(4):305-17
references.pmid: 24599514
references.citation: J Biol Chem. 2011 Oct 14;286(41):35770-35781
references.pmid: 21832058
references.citation: Int J Mol Sci. 2011;12(5):3102-16
references.pmid: 21686172
references.citation: Anal Chem. 2014 May 6;86(9):4249-55
references.pmid: 24712714
references.citation: Chemphyschem. 2013 Feb 25;14(3):532-42
references.pmid: 23401373
references.citation: Anal Sci. 2014;30(9):865-70
references.pmid: 25213814
references.citation: J Phys Chem B. 2013 Jan 17;117(2):484-9
references.pmid: 23249437
references.citation: Org Biomol Chem. 2012 Aug 21;10(31):6341-9
references.pmid: 22751934
references.citation: J Chem Inf Model. 2014 Aug 25;54(8):2255-60
references.pmid: 25089840
references.citation: J Phys Chem B. 2010 Oct 7;114(39):12666-78
references.pmid: 20839830
references.citation: J Comput Aided Mol Des. 2012 May;26(5):647-59
references.pmid: 22476578
references.citation: J Chem Theory Comput. 2012 Jan 10;8(1):141-51
references.pmid: 26592877
references.citation: J Phys Chem B. 2013 Dec 5;117(48):14973-82
references.pmid: 24195769
references.citation: J Comput Aided Mol Des. 2011 Mar;25(3):223-35
references.pmid: 21286784
references.citation: J Chem Inf Model. 2010 Apr 26;50(4):585-8
references.pmid: 20356088
references.citation: J Comput Chem. 2002 Dec;23(16):1601-22
references.pmid: 12395428
references.citation: J Chem Theory Comput. 2011 Sep 13;7(9):2929-36
references.pmid: 26605482
references.citation: J Phys Chem A. 2007 Oct 25;111(42):10861-73
references.pmid: 17914769
references.citation: Carbohydr Res. 2011 Dec 13;346(17):2746-51
references.pmid: 22024568
references.citation: J Comput Chem. 2004 Sep;25(12):1463-73
references.pmid: 15224390
references.citation: Acta Crystallogr D Biol Crystallogr. 2014 May;70(Pt 5):1233-47
references.pmid: 24816093
references.citation: Eur J Pharm Sci. 2012 Aug 15;46(5):336-45
references.pmid: 22406295
references.citation: J Comput Chem. 2012 Feb 15;33(5):490-501
references.pmid: 22170247
references.citation: J Chem Phys. 2010 Apr 21;132(15):154104
references.pmid: 20423165
references.citation: J Chem Theory Comput. 2013 Aug 13;9(8):3364-3374
references.pmid: 24098094
references.citation: J Chem Theory Comput. 2012 Nov 13;8(11):4285-92
references.pmid: 26605592
references.citation: J Phys Chem B. 2012 Feb 23;116(7):2031-9
references.pmid: 22324459
references.citation: Photochem Photobiol Sci. 2013 Aug;12(8):1496-508
references.pmid: 23824308
references.citation: Bioorg Med Chem Lett. 2014 May 15;24(10):2340-5
references.pmid: 24731280
references.citation: Chemistry. 2012 Aug 6;18(32):9955-64
references.pmid: 22782805
references.citation: J Phys Chem A. 2010 Dec 2;114(47):12479-89
references.pmid: 21049959
references.citation: J Comput Chem. 2013 Oct 30;34(28):2403-11
references.pmid: 23913712
references.citation: J Phys Chem B. 2012 Mar 22;116(11):3659-69
references.pmid: 22393912
references.citation: Small. 2009 Mar;5(5):587-90
references.pmid: 19242950
references.citation: J Am Chem Soc. 1974 Aug 21;96(17):5319-27
references.pmid: 4851860
references.citation: J Chem Theory Comput. 2014 Aug 12;10(8):3129-39
references.pmid: 26588284
references.citation: Biopolymers. 2013 Dec;99(12):989-1005
references.pmid: 23828641
references.citation: Proteins. 2014 Dec;82(12):3335-46
references.pmid: 25212393
references.citation: Acta Biochim Pol. 2012;59(4):653-60
references.pmid: 23074704
references.citation: Chemphyschem. 2011 Dec 9;12(17):3131-42
references.pmid: 22038888
references.citation: J Phys Chem B. 2014 May 1;118(17):4514-26
references.pmid: 24702603
references.citation: J Comput Chem. 2012 May 5;33(12):1179-89
references.pmid: 22396176
references.citation: J Phys Chem A. 2011 Oct 20;115(41):11423-7
references.pmid: 21888324
references.citation: J Phys Chem A. 2014 Oct 9;118(40):9561-7
references.pmid: 25208095
references.citation: J Phys Chem A. 2011 Jul 7;115(26):7773-7
references.pmid: 21595443
references.citation: J Comput Chem. 2013 Jul 15;34(19):1672-85
references.pmid: 23670872
references.citation: J Chem Theory Comput. 2012 Jun 12;8(6):2023-2033
references.pmid: 22737045
references.citation: J Chem Theory Comput. 2007 Sep;3(5):1656-64
references.pmid: 26627611
references.citation: J Chem Theory Comput. 2013 Jan 8;9(1):33-45
references.pmid: 23704835
references.citation: J Chem Theory Comput. 2011 Mar 8;7(3):790-797
references.pmid: 21666841
references.citation: Chemphyschem. 2014 Oct 20;15(15):3218-25
references.pmid: 24954803
references.citation: Phys Chem Chem Phys. 2013 Nov 21;15(43):18815-21
references.pmid: 24092233
references.citation: J Chem Theory Comput. 2014 Mar 11;10(3):897-907
references.pmid: 26580168
references.citation: Phys Chem Chem Phys. 2010 Jul 28;12(28):7959-67
references.pmid: 20517573
references.citation: Phys Chem Chem Phys. 2008 Jan 7;10(1):128-35
references.pmid: 18075691
references.citation: J Phys Chem A. 2010 Sep 9;114(35):9529-36
references.pmid: 20707378
references.citation: J Chem Phys. 2011 Oct 7;135(13):134120
references.pmid: 21992295
references.citation: Nat Commun. 2013;4:1379
references.pmid: 23340419
references.citation: J Phys Chem Lett. 2014 Dec 18;5(24):4275-84
references.pmid: 26273974
references.citation: J Chromatogr A. 2013 Jul 12;1298:103-8
references.pmid: 23746371
references.citation: Chempluschem. 2013 Sep;78(9):921-931
references.pmid: 31986741
references.citation: J Comput Aided Mol Des. 2014 Apr;28(4):463-74
references.pmid: 24510191
references.citation: J Chem Theory Comput. 2014;10:4694-4707
references.pmid: 26120288
references.citation: J Chem Theory Comput. 2010;6(4):1018-1027
references.pmid: 20467461
references.citation: J Chem Theory Comput. 2009 Jul 14;5(7):1749-60
references.pmid: 26610000
references.citation: J Mol Graph Model. 2013 Jul;44:220-31
references.pmid: 23911931
references.citation: J Phys Chem B. 2013 Jul 11;117(27):8075-84
references.pmid: 23758433
references.citation: J Comput Chem. 2012 Nov 5;33(29):2310-7
references.pmid: 22782845
references.citation: Chempluschem. 2013 Sep;78(9):1149-1156
references.pmid: 31986736
references.citation: Acc Chem Res. 2012 Apr 17;45(4):663-72
references.pmid: 22225511
references.citation: J Chem Theory Comput. 2013 Jun 11;9(6):2672-86
references.pmid: 26583861
references.citation: J Chem Theory Comput. 2011 Apr 12;7(4):857-867
references.pmid: 23378824
references.citation: J Chem Theory Comput. 2014 Apr 8;10(4):1563-1575
references.pmid: 24803867
references.citation: Chemistry. 2014 Jan 13;20(3):760-71
references.pmid: 24339217
references.citation: Phys Chem Chem Phys. 2008 Apr 28;10(16):2159-66
references.pmid: 18404221
references.citation: J Mol Model. 2013 Jan;19(1):1-32
references.pmid: 23187683
references.citation: Org Lett. 2014 Jan 17;16(2):472-5
references.pmid: 24350666
references.citation: J Phys Chem Lett. 2013 May 2;4(9):1365-70
references.pmid: 26282286
references.citation: J Chem Theory Comput. 2013 Apr 9;9(4):2137-49
references.pmid: 26583559
references.citation: J Chem Theory Comput. 2012 Sep 11;8(9):3072-81
references.pmid: 26605718
references.citation: J Chem Theory Comput. 2014 Mar 11;10(3):1314-1325
references.pmid: 24803861
references.citation: Phys Chem Chem Phys. 2010 Jul 14;12(26):7117-25
references.pmid: 20480085
references.citation: Phys Chem Chem Phys. 2008 May 21;10(19):2767-74
references.pmid: 18464992
references.citation: J Chem Theory Comput. 2013 Dec 10;9(12):5567-77
references.pmid: 26592290
references.citation: Eur J Med Chem. 2015 Jan 7;89:189-97
references.pmid: 25462239
references.citation: J Mol Graph Model. 2014 Jun;51:137-48
references.pmid: 24907933
references.citation: J Chem Inf Model. 2011 Oct 24;51(10):2549-59
references.pmid: 21942911
references.citation: J Chem Theory Comput. 2010 Jan 12;6(1):344-52
references.pmid: 26614342
references.citation: J Phys Chem A. 2009 Oct 29;113(43):11938-48
references.pmid: 19848431
references.citation: J Chem Inf Model. 2009 Apr;49(4):944-55
references.pmid: 19309094
references.citation: J Chem Theory Comput. 2014 Aug 12;10(8):2881-90
references.pmid: 26588263
references.citation: J Chem Phys. 2013 Jun 14;138(22):224504
references.pmid: 23781802
references.citation: J Am Chem Soc. 2014 Jul 2;136(26):9443-52
references.pmid: 24915305
references.citation: J Chem Theory Comput. 2013 Feb 12;9(2):995-1006
references.pmid: 26588742
references.citation: J Med Chem. 2005 Jul 14;48(14):4558-75
references.pmid: 15999994
references.citation: J Mol Model. 2013 Jan;19(1):193-203
references.pmid: 22846926
references.citation: Biomacromolecules. 2013 Apr 8;14(4):1035-43
references.pmid: 23425034
references.citation: J Med Chem. 2012 Aug 23;55(16):7182-92
references.pmid: 22788918
references.citation: J Chem Theory Comput. 2007;3(4):1609-1619
references.pmid: 18728758