Abstract
Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid methods have become very popular schemes to incorporate environmental effects in the calculation of molecular properties, when it is mandatory to have both a quantum description of electrons to compute these properties and an atomistic description of the environment. However, even Density Functional Theory/MM schemes may become timecosting when a large part of the system should be treated at the QM level or when plenty of single point energy calculations are intended to be done. We report a new implementation, within the deMonNano code, of a hybrid QM/MM scheme combining the density functional based tight binding with class 1 force fields. Two types of additive couplings can be chosen, namely the mechanical coupling, consisting of a Lennard-Jones potential and the electrostatic coupling, in which the MM part of the system is also polarizing the region described at the QM level. As first test-case application, the harmonic infrared spectra of simple molecules in the gas phase and in water clusters are computed and compared to those obtained at the DFT/MM level. Binding energies are also compared. Similar trends are obtained with the two levels of calculations and the main differences are discussed.
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Notes
The present version of the code corresponding to this work can be downloaded from deMonNano website (10.12.2021) and corresponds to git hash commit f3707842dd69b9629954a55a28693189d572f425.
References
Warshel A, Karplus M (1972) J Am Chem Soc 94(16):5612
Warshel A, Levitt M (1976) J Mol Biol 103(2):227
Groenhof G (2013) Introduction to QM/MM simulations. Humana Press, Totowa, pp 43–66
Maseras F, Morokuma K (1995) J Comput Chem 16(9):1170
Senn HM, Thiel W (2007) Curr Opin Chem Biol 11(2):182
Marcolongo JP, Zeida A, Semelak JA, Foglia NO, Morzan UN, Estrin DA, González Lebrero MC, Scherlis DA (2018) Front Chem 6:70
Biswas PK, Chakraborty S (2019) Nucleic Acids Res 47(6):2757
Klähn M, Schlitter J, Gerwert K (2005) Biophys J 88(6):3829
Zhekova HR, Ngo V, da Silva MC, Salahub D, Noskov S (2017) Coord Chem Rev 345:108
Porezag D, Frauenheim T, Köhler T, Seifert G, Kaschner R (1995) Phys Rev B 51:12947
Seifert G, Porezag D, Frauenheim T (1996) Int J Quantum Chem 58:185
Elstner M, Porezag D, Jungnickel G, Elsner J, Haugk M, Frauenheim T, Suhai S, Seifert G (1998) Phys Rev B 58:7260
Elstner M, Seifert G (2014) Philosophical transactions of the royal society a: mathematical. Phys Eng Sci 372(2011):20120483
Spiegelman F, Tarrat N, Cuny J, Dontot L, Posenitskiy E, Martí C, Simon A, Rapacioli M (2020) Adv Phys X 5(1):1710252
Slater JC, Koster GF (1954) Phys Rev 94:1498
Gruden M, Andjeklovic L, Jissy AK, Stepanovic S, Zlatar M, Cui Q, Elstner M (2017) J Comput Chem 38(25):2171
Zheng L, Zamith S, Rapacioli M (2021) Theoret Chem Acc 140(2):19
Niehaus TA, Suhai S, Della Sala F, Lugli P, Elstner M, Seifert G, Frauenheim T (2001) Phys Rev B 63:085108
Witek H, Morokuma K, Stradomska A (2005) J Theor Comput Chem 4:639
Dontot L, Spiegelman F, Zamith S, Rapacioli M (2020) Eur Phys J D 74(11):216
Chakraborty S, Mulas G, Rapacioli M, Joblin C (2021) J Mol Spectrosc 378:111466
Witek H, Morokuma K, Stradomska A (2004) J Chem Phys 121(11):5171
Cuny J, Tarrat N, Spiegelman F, Huguenot A, Rapacioli M (2018) J Phys Condens Matter 30(30):303001
Wahiduzzaman M, Oliveira AF, Philipsen P, Zhechkov L, van Lenthe E, Witek HA, Heine T (2013) J Chem Theor Comp 9(9):4006
Elstner M, Porezag D, Seifert G, Frauenheim T, Suhai S (1998) MRS Online Proc Libr 538:541
Salomon-Ferrer R, Case DA, Walker RC (2013) WIREs Comput Mol Sci 3(2):198
Seabra GDM, Walker RC, Elstner M, Case DA, Roitberg AE (2007) J Phys Chem A 111(26):5655
Kubar T, Welke K, Groenhof G (2015) J Comput Chem 36(26):1978
Cui Q, Elstner M, Kaxiras E, Frauenheim T, Karplus M (2001) J Phys Chem B 105(2):569
Lima GFd, Heine T, Duarte HA, Sabin JR, Brändas E (2010) Chapter 5: Molecular dynamics of polypeptides and their inclusion compounds with cyclodextrin in aqueous solution using DC-SCC-DFTB/UFF approach. Academic Press, Cambridge, pp 145–180
Iftner C, Simon A, Korchagina K, Rapacioli M, Spiegelman F (2014) J Chem Phys 140(3):034301
Hou G, Zhu X, Cui Q (2010) J Chem Theory Comput 6(8):2303
Nishimoto Y (2016) J Phys Chem A 120(5):771
Kubař T, Woiczikowski PB, Cuniberti G, Elstner M (2008) J Phys Chem B 112:7937
Lundberg M, Sasakura Y, Zheng G, Morokuma K (2010) J Chem Theo Comput 6(4):1413
Heine T, Rapacioli M, Patchkovskii S, Frenzel J, Koster A, Calaminici P, Duarte HA, Escalante S, Flores-Moreno R, Goursot A, Reveles J, Salahub D, Vela A, deMonNano (2009) http://demon-nano.ups-tlse.fr
Gillet N, Elstner M, Kubař T (2018) J Chem Phys 149(7):072328
Hourahine B, Aradi B, Blum V, Bonafé F, Buccheri A, Camacho C, Cevallos C, Deshaye MY, Dumitrică T, Dominguez A, Ehlert S, Elstner M, van der Heide T, Hermann J, Irle S, Kranz JJ, Köhler C, Kowalczyk T, Kubař T, Lee IS, Lutsker V, Maurer RJ, Min SK, Mitchell I, Negre C, Niehaus TA, Niklasson AMN, Page AJ, Pecchia A, Penazzi G, Persson MP, Řezáč J, Sánchez CG, Sternberg M, Stöhr M, Stuckenberg F, Tkatchenko A, Yu VWz, Frauenheim T (2020) J Chem Phys 152(12): 124101
de Seabra MG, Walker RC, Elstner M, Case DA, Roitberg AE (2007) J Phys Chem A 111(26):5655
Götz AW, Clark MA, Walker RC (2014) J Comput Chem 35(2):95
Oliveira A, Seifert G, Heine T, Duarte H (2009) J Braz Chem Soc 20:1193
Koskinen P, Makinen V (2009) Comput Mater Sci 47(1):237
Foulkes WMC, Haydock R (1989) Phys Rev B 39:12520
Elstner M, Porezag D, Jungnickel G, Elsner J, Haugk M, Frauenheim T, Suhai S, Seifert G (1998) Phys Rev B 58(11):7260
Yang Y, Yu H, Uork D, Cui Q, Elstner M (2007) J Phys Chem A 111:10861
Gaus M, Cui Q, Elstner M (2011) J Chem Theory Comput 7(4):931
Gaus M, Goez A, Elstner M (2013) J Chem Theo Comp 9(1):338
Monticelli L, Tieleman DP (2013) Force fields for classical molecular dynamics. Humana Press, Totowa, pp 197–213
González MA (2011) JDN 12:169
Vanommeslaeghe K, Guvench O, MacKerell J, Alexander D (2014) Curr Pharm Des 20(20):3281
Field MJ, Bash PA, Karplus M (1990) J Comput Chem 11(6):700
de la Lande A, Alvarez-Ibarra A, Hasnaoui K, Cailliez F, Wu X, Mineva T, Cuny J, Calaminici P, López-Sosa L, Geudtner G, Navizet I, Garcia-Iriepa C, Salahub DR, Köster AM (2019) Molecules 24(9):1666
Koster A, Geudtner G, Alvarez-Ibarra A, Calaminici P, Casida M, Carmona-Espindola J, Dominguez V, Flores-Moreno R, Gamboa G, Goursot A, Heine T, Ipatov A, de la Lande A, Janetzko F, del Campo J, Mejia-Rodriguez D, Reveles JU, Vasquez-Perez J, Vela A, Zuniga-Gutierrez B, Salahub D (2018) deMon2k Version 6
Perdew JP, Burke K, Ernzerhof M (1996) Phys Rev Lett 77(18):3865
Godbout N, Salahub DR, Andzelm J, Wimmer E (1992) Can J Chem 70(2):560
Köster AM, Reveles JU, del Campo JM (2004) J Chem Phys 121(8):3417
Nosé S (1984) J Chem Phys 81(1):511
Hoover WG (1985) Phys Rev A 31(3):1695
Oliveira AF, Philipsen P, Heine T (2015) J Chem Theor Comput 11(11):5209
Gutmann V, Resch G (1995) Lecture notes on solution chemistry. World Scientific Co. Pte.Ltd
Miller TM, Bederson B, Bates DR (1978) Atomic and molecular polarizabilities: a review of recent advances. Academic Press, Cambridge, pp 1–55
Olney TN, Cann NM, Cooper G, Brion CE (1997) Chem Phys 223(1):59
Wu X, Teuler JM, Cailliez F, Clavaguéra C, Salahub DR, de la Lande A (2017) J Chem Theory Comput 13(9):3985
Acknowledgements
The authors acknowledge the ANR agency (Project ANR-19-CE29-0011-02 RUBI) for financial support and the supercomputing facilities of CALMIP for generous allocation of computer resources (Project P0059 and P18009).
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Yusef Buey, M., Mineva, T. & Rapacioli, M. Coupling density functional based tight binding with class 1 force fields in a hybrid QM/MM scheme. Theor Chem Acc 141, 16 (2022). https://doi.org/10.1007/s00214-022-02878-6
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DOI: https://doi.org/10.1007/s00214-022-02878-6