An algorithm for very high pressure molecular dynamics simulations.
barostat
butadiene
chemistry under extremely high pressures
molecular dynamics
Journal
Journal of computational chemistry
ISSN: 1096-987X
Titre abrégé: J Comput Chem
Pays: United States
ID NLM: 9878362
Informations de publication
Date de publication:
29 Aug 2024
29 Aug 2024
Historique:
revised:
28
05
2024
received:
13
03
2024
accepted:
17
06
2024
medline:
31
8
2024
pubmed:
31
8
2024
entrez:
29
8
2024
Statut:
aheadofprint
Résumé
We describe a method to run simulations of ground or excited state dynamics under extremely high pressures. The method is based on the introduction of a fictitious ideal gas that exerts the required pressure on a molecular sample and is therefore called XP-GAS (eXtreme Pressure by Gas Atoms in a Sphere). The algorithm is most suitable for approximately spherical clusters of molecules described by quantum chemistry methods, Molecular Mechanics or mixed QM/MM approaches. We compare the results obtained by the algorithm here presented and by the XP-PCM approach, based on a continuum description of the environment. As a test case, we study the conformational dynamics of 1,3-butadiene either as an isolated molecule ("naked" butadiene) or embedded in a cluster of argon atoms, under pressures up to 15 GPa. Overall, our results show that the XP-GAS QM/MM simulation method is in good agreement with the XP-PCM QM/Continuum model (Cammi model) in describing the effect of the pressure on static properties as the equilibrium geometry of butadiene in the ground state. Furthermore, the comparison of XP-GAS simulations with naked butadiene and butadiene in argon shows the importance, for XP-GAS and related methods, of a realistic representation of the medium in modelling pressure effects.
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2024 The Author(s). Journal of Computational Chemistry published by Wiley Periodicals LLC.
Références
V. Schettino, R. Bini, Chem. Soc. Rev. 2007, 36, 869.
X.‐D. Wen, L. Hand, V. Labet, T. Yang, R. Hoffmann, N. W. Ashcroft, A. R. Oganov, A. O. Lyakhov, Proc. Nat. Acad. Sci. 2011, 108, 6833.
T. Scheler, M. Marqués, Z. Konôpková, C. L. Guillaume, R. T. Howie, E. Gregoryanz, Phys. Rev. Lett. 2013, 111, 215503.
H.‐K. Mao, B. Chen, J. Chen, K. Li, J.‐F. Lin, W. Yang, H. Zheng, Matter Rad. Extr. 2016, 1, 59.
J. Sun, X. Dong, Y. Wang, K. Li, H. Zheng, L. Wang, G. D. Cody, C. A. Tulk, J. J. Molaison, X. Lin, Y. Meng, C. Jin, H. K. Mao, Angew. Chem., Int. Ed. 2017, 56, 6553.
B. Chen, R. Hoffmann, N. W. Ashcroft, J. V. Badding, E. Xu, V. Crespi, J. Am. Chem. Soc. 2015, 137, 14373.
T. A. Singleton, K. S. Ramsay, M. M. Barsan, I. S. Butler, C. J. Barrett, J. Phys. Chem. B 2012, 116, 9860.
T. Kinoshita, S. Nakamura, M. Harada, T. Hasobe, G. Fukuhara, Chem. Sci. 2023, 14, 3293.
M. Mugnai, G. Cardini, V. Schettino, Phys. Rev. B 2004, 70, 020101.
Z. Cui, Y. Sun, J. Qu, J. Comput. Theor. Nanosci. 2008, 5, 1646.
R. Cammi, C. Cappelli, B. Mennucci, J. Tomasi, J. Chem. Phys. 2012, 137, 154112.
R. Cammi, J. Comput. Chem. 2015, 36, 2246.
R. Cammi, B. Chen, J. Chem. Phys. 2022, 157, 114101.
R. Fukuda, T. Yang, R. Cammi, J. Chem. Theory Comput. 2015, 11, 2063.
T. Yang, R. Fukuda, R. Cammi, M. Ehara, J. Phys. Chem. A 2017, 121, 4363.
B. Chen, R. Hoffmann, R. Cammi, Angew. Chem., Int. Ed. 2017, 56, 11126.
M. Rahm, R. Cammi, N. W. Ashcroft, R. Hoffmann, J. Am. Chem. Soc. 2019, 141, 10253.
T. Stauch, J. Chem. Phys. 2020, 153, 134503.
T. Pongratz, P. Kibies, L. Eberlein, N. Tielker, C. Hölzl, S. Imoto, M. B. Erlach, S. Kurrmann, P. H. Schummel, M. Hofmann, O. Reiser, R. Winter, W. Kremer, H. R. Kalbitzer, D. Marx, D. Horinek, S. M. Kast, Biophys. Chem. 2020, 257, 106258.
S. Imoto, D. Marx, Phys. Rev. Lett. 2020, 125, 086001.
C. Förster, H. Osthues, D. Schwab, N. L. Doltsinis, K. Heinze, ChemPhysChem 2023, 24, e202300165.
J. Tomasi, B. Mennucci, R. Cammi, Chem. Rev. 2005, 105, 2999.
A. V. Akimov, Foundamentals of Trajectory Based Methods for Nonadiabatic Dynamics, in Comprehensive Computational Chemistry, Vol. 4 (Eds: M. Yáñez, R. J. Boyd), Elsevier, Amsterdam 2023, p. 235.
M. Persico, G. Granucci, D. Accomasso, The Quantum Decoherence Problem in Nonadiabatic Trajectory Methods In Comprehensive Computational Chemistry, Vol. 4 (Eds: M. Yáñez, R. J. Boyd), Elsevier, Amsterdam 2023, p. 273.
G. Granucci, M. Persico, A. Toniolo, J. Chem. Phys. 2001, 114, 10608.
P. Mondal, G. Granucci, D. Rastädter, M. Persico, I. Burghardt, Chem. Sci. 2018, 9, 4671.
J. Fregoni, G. Granucci, M. Persico, S. Corni, Chem 2020, 6, 250.
S. Osella, G. Granucci, M. Persico, S. Knippenberg, J. Mat. Chem. B 2023, 11, 2518.
S. M. J. Rogge, L. Vanduyfhuys, A. Ghysels, M. Waroquier, T. Verstraelen, G. Maurin, V. Van Speybroeck, J. Chem. Theory Comput. 2015, 11, 5583.
T. Vasilevskaya, W. Thiel, J. Chem. Theory Comput. 2016, 12, 3561.
H. Nishizawa, H. Okumura, J. Comput. Chem. 2016, 37, 2701.
Y. Kawashima, K. Ishimura, M. Shiga, J. Chem. Phys. 2019, 150, 124103.
M. Bondanza, M. Nottoli, L. Cupellini, F. Lipparini, B. Mennucci, Phys. Chem. Chem. Phys. 2020, 22, 14433.
S. Bonfrate, N. Ferré, M. Huix‐Rotllant, J. Chem. Phys. 2023, 158, 021101.
S. Bonfrate, N. Ferré, M. Huix‐Rotllant, J. Chem. theory Comput. 2024, 20, 4338. https://doi.org/10.26434/chemrxiv-2024-5tzsf
S. Kodiyalam, R. K. Kalia, H. Kikuchi, A. Nakano, F. Shimojo, P. Vashishta, Phys. Rev. Lett. 2001, 86, 55.
S. Kodiyalam, R. K. Kalia, A. Nakano, P. Vashishta, Phys. Rev. Lett. 2004, 93, 203401.
R. Martoňák, L. Colombo, C. Molteni, M. Parrinello, J. Chem. Phys. 2002, 117, 11329.
B. J. Morgan, P. A. Madden, Nano Lett. 2004, 4, 1581.
M. Grünwald, C. Dellago, Mol. Phys. 2006, 104, 3709.
M. Grünwald, E. Rabani, C. Dellago, Phys. Rev. Lett. 2006, 96, 255701.
M. Grünwald, C. Dellago, P. Geissler, J. Chem. Phys. 2007, 127, 154718.
N. Plotnikov, T. Martínez, J. Phys. Chem. C 2016, 120, 17898.
D. Beeman, J. Comp. Phys. 1976, 20, 130.
W. F. van Gunsteren, H. J. C. Berendsen, Mol. Phys. 1982, 45, 637.
J. J. P. Stewart, Mopac, Fujitsu Limited, Tokyo, Japan 2002.
G. Granucci, M. Persico, D. Accomasso, E. Sangiogo Gil, S. Corni, J. Fregoni, T. Laino, M. Tesi, A. Toniolo, MOPAC‐PI package. https://gitlab.com/granucci/mopacpi
J. A. Rackers, Z. Wang, C. Lu, M. L. Laury, L. Lagardère, M. J. Schniders, J.‐P. Piquemal, P. Ren, J. W. Ponder, J. Chem. Theory Comput. 2018, 14, 5273.
D. Accomasso, M. Persico, G. Granucci, J. Mat. Chem. A 2021, 9, 21897.
C. Pieroni, F. Becuzzi, L. Creatini, G. Granucci, M. Persico, J. Chem. Theory Comput. 2023, 19, 2430.
E. Sangiogo Gil, M. Persico, G. Granucci, J. Chem. Phys. 2022, 157, 161101.
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. V. Marenich, J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams‐Young, F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, K. Throssell, J. A. Montgomery Jr., J. E. Peralta, F. Ogliaro, M. J. Bearpark, J. J. Heyd, E. N. Brothers, K. N. Kudin, V. N. Staroverov, T. A. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. P. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, J. B. Foresman, D. J. Fox, Gaussian 16, Revision C.01, Gaussian, Inc, Wallingford, CT 2016.
W. L. Jorgensen, D. S. Maxwell, J. Tirado‐Rives, J. Am. Chem. Soc. 1996, 118, 11225.
S. Batsanov, Inorg. Mat. 2001, 37, 871.
M. Citroni, M. Ceppatelli, R. Bini, V. Schettino, Chem. Phys. Lett. 2003, 367, 186.
D. Feller, N. C. Craig, J. Phys. Chem. A 2009, 113, 1601.
R. Engeln, D. Consalvo, J. Reuss, Chem. Phys. 1992, 160, 427.
A. S. Christensen, T. Kubař, Q. Cui, M. Elstner, Chem. Rev. 2016, 116, 5301.
T. Cusati, G. Granucci, E. Martínez‐Núñez, F. Martini, M. Persico, S. Vázquez, J. Phys. Chem. A 2012, 116, 98.
Y. N. Panchenko, J. V. Auwera, Y. Moussaoui, G. R. De Maré, Struct. Chem. 2003, 14, 337.
J. Buša, J. Džurina, E. Hayryan, S. Hayryan, C. Hu, J. Plavka, I. Pokorný, J. Skřivánek, M. Wu, Comp. Phys. Commun. 2005, 165, 59.
M. Ross, H. K. Mao, P. M. Bell, J. A. Xu, J. Chem. Phys. 1986, 85, 1028.
K. Patkowski, G. Murdachaew, C.‐M. Fou, K. Szalewicz, Mol. Phys. 2005, 103, 2031.