Application of the ChIMES Force Field to Nonreactive Molecular Systems

(22) Schwegler, E.; Galli, G.; Gygi, F.; Hood, R. Q. Phys. Rev. Lett. 2001, 87, 265501–1. (23) Goldman, N.; Reed, E. J.; Kuo, I.-F. W.; Fried, L. E.; Mundy, C. J.; Curioni, A. Ab initio simulation of the equation of state and kinetics of shocked water. J. Chem. Phys. 2009, 130, 124517. (24) Goldman, N.; Reed, E. J.; Fried, L. E. Quantum Corrections to Shock Hugoniot Temperatures. J. Chem. Phys. 2009, 131, 204103. (25) Gillian, M. J.; Michaelides, A. Perspective: How good is DFT for water? J. Chem. Phys. 216, 144, 130901. (26) Alfè, D.; Bartók, A.; Csanyi, G.; Gillan, M. Analyzing the errors of DFT approximations for compressed water systems. J. Chem. Phys. 2014, 141, 014104. (27) Becke, A. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys 1993, 98, 5648–5652. (28) Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 1988, 37, 785–789. (29) Perdew, J. P.; Ernzerhof, M.; Burke, K. Rationale for mixing exact exchange with density functional approximations. J. Chem. Phys. 1996, 105, 9982–9985. 33

ACS Paragon Plus Environment

Journal of Chemical Theory and Computation 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

(30) Adamo, C.; Cossi, M.; Scalmani, G.; Barone, V. Accurate static polarizabilities by density functional theory: assessment of the PBE0 model. Chem. Phys. Lett. 1999, 307, 265–271. (31) Mardirossian, N.; Ruiz Pestana, L.; Womack, J. C.; Skylaris, C.-K.; Head-Gordon, T.; Head-Gordon, M. Use of the rVV10 Nonlocal Correlation Functional in the B97MV Density Functional: Defining B97M-rV and Related Functionals. J. Phys. Chem. Letters 2017, 8, 35–40. (32) Mardirossian, N.; Head-Gordon, M. Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V. J. Chem. Phys. 2015, 142, 074111. (33) Zhao, Y.; Truhlar, D. G. A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions. J. Chem. Phys. 2006, 125, 194101. (34) Grimme, S. Accurate description of van der Waals complexes by density functional theory including empirical corrections. J. Comput. Chem. 2004, 25, 1463–1473. (35) Grimme, S. Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J. Comput. Chem. 2006, 27, 1787–1799. (36) Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys. 2010, 132, 154104. (37) Von Lilienfeld, O. A.; Tavernelli, I.; Rothlisberger, U.; Sebastiani, D. Optimization of effective atom centered potentials for London dispersion forces in density functional theory. Phys. Rev. Lett. 2004, 93, 153004.

34


Page 34 of 41

Page 35 of 41 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Journal of Chemical Theory and Computation

(38) Tkatchenko, A.; Scheffler, M. Accurate molecular van der Waals interactions from ground-state electron density and free-atom reference data. Phys. Rev. Lett. 2009, 102, 073005. (39) Dion, M.; Rydberg, H.; Schröder, E.; Langreth, D. C.; Lundqvist, B. I. Van der Waals density functional for general geometries. Phys. Rev. Lett. 2004, 92, 246401. (40) Izvekov, S.; Parrinello, M.; Burnham, C. J.; Voth, G. A. Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching. J. Chem. Phys. 2004, 120, 10896–10913. (41) Paesani, F.; Zhang, W.; Case, D. A.; Cheatham III, T. E.; Voth, G. A. An accurate and simple quantum model for liquid water. J. Chem. Phys. 2006, 125, 184507. (42) Pinilla, C.; Irani, A. H.; Seriani, N.; Scandolo, S. Ab initio parameterization of an allatom polarizable and dissociable force field for water. The Journal of Chemical Physics 2012, 136, 114511. (43) Fritsch, S.; Potestio, R.; Donadio, D.; Kremer, K. Nuclear Quantum Effects in Water: A Multiscale Study. J. Chem. Theory Comput. 2014, 10, 816–824. (44) Spura, T.; John, C.; Habershon, S.; Kühne, T. D. Nuclear quantum effects in liquid water from path-integral simulations using an ab initio force-matching approach. Molecular Physics 2015, 113, 808–822. (45) Van Duin, A. C.; Dasgupta, S.; Lorant, F.; Goddard, W. A. ReaxFF: a reactive force field for hydrocarbons. J. Phys. Chem. A 2001, 105, 9396–9409. (46) Brenner, D. W.; Shenderova, O. A.; Harrison, J. A.; Stuart, S. J.; Ni, B.; Sinnott, S. B. A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons. J. Phys. Condens. Matter 2002, 14, 783.

35



(47) Bartók, A. P.; Payne, M. C.; Kondor, R.; Csányi, G. Gaussian approximation potentials: The accuracy of quantum mechanics, without the electrons. Phys. Rev. Lett. 2010, 104, 136403. (48) Bartók, A. P.; Gillan, M. J.; Manby, F. R.; Csányi, G. Machine-learning approach for one-and two-body corrections to density functional theory: Applications to molecular and condensed water. Phys. Rev. B 2013, 88, 054104. (49) Alfè, D.; Bartók, A.; Csanyi, G.; Gillan, M. Analyzing the errors of DFT approximations for compressed water systems. J. Chem. Phys. 2014, 141, 014104. (50) Lindsey, R. K.; Fried, L. E.; Goldman, N. ChIMES: A Force Matched Potential with Explicit Three-Body Interactions for Molten Carbon. J. Chem. Theory Comput. 2017, 13, 6222–6229. (51) Heyes, D. M. The Liquid State: Applications of Molecular SImulations; John Wiley and Sons Ltd: West Sussex, UK, 1998; p 68. (52) Heyes, D. M. Pressure tensor of partial-charge and point-dipole lattices with bulk and surface geometries. Phys. Rev. B 1994, 49, 755–764. (53) Friedman, J.; Hastie, T.; Tibshirani, R. Numerical Recipes: The Art of Scientific Computing,3rd ed.; Cambridge University Press: Cambridge, U.K., 2007. (54) Kresse, G.; Hafner, J. Ab initio molecular dynamics for liquid metals. Phys. Rev. B: Condens. Matter Mater. Phys. 1993, 47, 558. (55) Kresse, G.; Hafner, J. Ab initio molecular-dynamics simulation of the liquid-metal– amorphous-semiconductor transition in germanium. Phys. Rev. B: Condens. Matter Mater. Phys. 1994, 49, 14251. (56) Kresse, G.; Furthmüller, J. Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set. Comput. Mater. Sci. 1996, 6, 15–50. 36


Page 36 of 41

Page 37 of 41 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(57) Kresse, G.; Furthmüller, J. Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Phys. Rev. B: Condens. Matter Mater. Phys. 1996, 54, 11169. (58) Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized gradient approximation made simple. Phys. Rev. Lett. 1996, 77, 3865. (59) Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized gradient approximation made simple [Erratum to Phys. Rev. Lett. 77, 3865 (1996)]. Phys. Rev. Lett. 1997, 78, 1396– 1396. (60) Blöchl, P. E. Projector augmented-wave method. Phys. Rev. B: Condens. Matter Mater. Phys. 1994, 50, 17953. (61) Kresse, G.; Joubert, D. From ultrasoft pseudopotentials to the projector augmentedwave method. Phys. Rev. B: Condens. Matter Mater. Phys. 1999, 59, 1758. (62) Nosé, S. A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys. 1984, 81, 511–519. (63) Hoover, W. G. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A: At., Mol., Opt. Phys. 1985, 31, 1695. (64) Parrinello, M.; Rahman, A. Crystal structure and pair potentials: A moleculardynamics study. Phys. Rev. Lett. 1980, 45, 1196. (65) Parrinello, M.; Rahman, A. Polymorphic transitions in single crystals: A new molecular dynamics method. J. Appl. Phys. 1981, 52, 7182–7190. (66) Plimpton, S. Fast parallel algorithms for short-range molecular dynamics. J. Phys. Chem. C 1995, 117, 1–19.

37



(67) Koziol, L.; Fried, L. E.; Goldman, N. Using force-matching to determine reactive force fields for bulk water under extreme thermodynamic conditions. J. Chem. Theory Comput. 2017, 13, 135. (68) Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926–935. (69) Berendsen, H.; Grigera, J.; Straatsma, T. The missing term in effective pair potentials. J. Phys. Chem. 1987, 91, 6269–6271. (70) Braams, B. J.; Bowman, J. M. Permutationally invariant potential energy surfaces in high dimensionality. Int. Rev. Phys. Chem. 2009, 28, 577–606. (71) Skinner, L. B.; Huang, C.; Schlesinger, D.; Pettersson, L. G.; Nilsson, A.; Benmore, C. J. Benchmark oxygen-oxygen pair-distribution function of ambient water from x-ray diffraction measurements with a wide Q-range. J. Chem. Phys. 2013, 138, 074506. (72) Walrafen, G. Water. A Comprehensive Treatise, ed. F. Franks. 1972. (73) Downing, H. D.; Williams, D. Optical constants of water in the infrared. J. Geophys. Res. 1975, 80, 1656–1661. (74) Chen, S.; Teixeira, J. Structure and dynamics of low-temperature water as studied by scattering techniques. Adv. Chem. Phys 1986, 64 . (75) Bertie, J. E.; Ahmed, M. K.; Eysel, H. H. Infrared intensities of liquids. 5. Optical and dielectric constants, integrated intensities, and dipole moment derivatives of water and water-d2 at 22. degree. C. J. Phys. Chem. 1989, 93, 2210–2218. (76) Shimanouchi, T. Tables of Molecular Vibrational Frequencies Consolidated Volume I; National Bureau of Standards: Washington, DC, 1972. 2005, 1–160.

38


Page 38 of 41

Page 39 of 41 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(77) Mills, R. Self-diffusion in normal and heavy water in the range 1-45. deg. J. Phys. Chem. 1973, 77, 685–688. (78) O’Reilly, D.; Peterson, E. Self-Diffusion Coefficients and Rotational Correlation Times in Polar Liquids. II. J. Chem. Phys. 1971, 55, 2155–2163. (79) Pranami, G.; Lamm, M. H. Estimating error in diffusion coefficients derived from Molecular Dynamics simulations. J. Chem. Theory Comput. 2015, 11, 4586–4592. (80) Stubbs, J. M.; Siepmann, J. I. Aggregation in dilute solutions of 1-hexanol in n-hexane: A Monte Carlo simulation study. J. Phys. Chem. B 2002, 106, 3968–3978. (81) Zhang, L.; Rafferty, J. L.; Siepmann, J. I.; Chen, B.; Schure, M. R. Chain conformation and solvent partitioning in reversed-phase liquid chromatography: Monte Carlo simulations for various water/methanol concentrations. J. Chromatogr. A 2006, 1126, 219–231. (82) Stubbs, J. M.; Siepmann, J. I. Elucidating the vibrational spectra of hydrogen-bonded aggregates in solution: Electronic structure calculations with implicit solvent and firstprinciples molecular dynamics simulations with explicit solvent for 1-hexanol in nhexane. J. Am. Chem. Soc. 2005, 127, 4722–4729. (83) Rapaport, D. Hydrogen bonds in water: Network organization and lifetimes. Mol. Phys. 1983, 50, 1151–1162. (84) Voloshin, V.; Naberukhin, Y. I. Hydrogen bond lifetime distributions in computersimulated water. J. Struct. Chem. 2009, 50, 78–89. (85) Molinero, V.; Moore, E. B. Water modeled as an intermediate element between carbon and silicon. J. Phys. Chem. B 2008, 113, 4008–4016. (86) Friedman, J.; Hastie, T.; Tibshirani, R. The elements of statistical learning; Springer series in statistics New York, 2001; Vol. 1. 39



(87) Goldman, N.; Fried, L. E.; Koziol, L. Using Force-matched potentials to improve the accuracy of density functional tight binding for reactive conditions. J. Chem. Theory Comput. 2015, 11, 4530.

40


Page 40 of 41

Page 41 of 41 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Graphical TOC Entry

Predictive, Scale-limited DFT-MD

ChIMES

41

Scalable, Quantum-Accurate MM-MD


Application of the ChIMES Force Field to Nonreactive Molecular Systems

Recommend Documents