Application of the Electrostatically Embedded Many-Body Expansion to Microsolvation of Ammonia in Water Clusters

Abstract

The electrostatically embedded many-body expansion (EE-MB), at both the second and third order, that is, the electrostatically embedded pairwise additive (EE-PA) approximation and the electrostatically embedded three-body (EE-3B) approximation, are tested for mixed ammonia-water clusters. We examine tetramers, pentamers, and hexamers for three different density functionals and two levels of wave function theory, We compare the many-body results to the results of full calculations performed without many-body expansions. Because of the differing charge distributions in the two kinds of monomers, this provides a different kind of test of the usefulness of the EE-MB method than was provided by previous tests on pure water clusters. We find only small errors due to the truncation of the many-body expansion for the mixed clusters. In particular, for tests on tetramers and pentamers, the mean absolute deviations for truncation at second order are 0.36-0.98 kcal/mol (average: 0.66 kcal/mol), and the mean absolute deviations for truncation at third order are 0.04-0.28 (average: 0.16 kcal/mol). These may be compared to a spread of energies as large as 4.24 kcal/mol in the relative energies of various structures of pentamers and to deviations of up to 8.57 kcal/mol of the full calculations of relative energies from the best estimates of the relative energies. When the methods are tested on hexamers, the mean unsigned deviation per monomer remains below 0.10 kcal/mol for EE-PA and below 0.03 kcal/mol for EE-3B. Thus the additional error due to the truncation of the expansion is small compared to the accuracy needed or the other approximations involved in practical calculations. This means that the EE-MB expansion in combination with density functional theory or wave function theory for the oligomers provides a useful practical model chemistry for making electronic structure calculations and simulations more affordable by improving the scaling with respect to system size.

Electrostatically Embedded Many-Body Expansion for Neutral and Charged Metalloenzyme Model Systems

“…Accurate zinc modeling requires quantum mechanical electronic structure calculations that pose challenges due to system size and the complexity of the calculations. Enabling accurate simulations on large and computationally demanding systems such as biozinc metallic coordination sites is a central focus of quantum chemistry research, and attempts have been made 9,10,11 to assess the accuracy of various QM-based strategies for Zn model systems representing biocenters and other complex environments such as nanoparticles and clusters. Fragmentation is a useful strategy for addressing these roadblocks, and various schemes have been explored in order to reduce calculation complexity.…”

“…12–24 The electrostatically embedded many-body expansion (EE-MB) method has emerged as a particularly promising approach. 10,17,25–29 As described in our previous work, 10,17,25–30 EE-MB addresses the challenge of system size by partitioning larger complexes into a series of fragments, embedding fragment energies in a field of point charges, and running calculations in parallel.…”

An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins

“…Although computer technology has made impressive progress in the past few decades, QM calculation for large molecules still presents a grand challenge. Over the past decade, a range of fragment-based QM method for large systems have been proposed, including the fragment molecular orbital (FMO) method, [24][25][26] molecular tailing approach (MTA), [27][28][29][30] systematic fragmentation method (SFM), [31][32][33][34] adjustable density matrix assembler (ADMA) [35][36][37] approach, electrostatically embedded many-body (EE-MB) [38][39][40] expansion approach, the generalized energy-based fragmentation (GEBF) [41][42][43] method, and the molecular fractionation with conjugate caps (MFCC) method. [44][45][46][47][48][49][50] Detailed introduction of the fragmentation methods can be found in a recent review.…”

Linear scaling explicitly correlated MP2-F12 and ONIOM methods for the long-range interactions of the nanoscale clusters in methanol aqueous solutions

“…49,50 In the recent years, we have developed an energybased fragmentation (EBF) approach, 51 and a subsequent generalized energy-based fragmentation (GEBF) approach, [52][53][54] for the calculations of large systems. Other closed fragmentation methods have also been developed by other groups, [55][56][57][58][59][60][61][62][63][64] which including systematic molecular fragmentation by Deev and co-workers, [55][56][57] molecular tailoring approach by Gadre and co-workers, [58][59][60] a fragmentation method by Bettens and co-workers, 61,62 electrostatically embedded many-body expansion method by Sorkin, Dahlke, and Truhlar, 63 and molecules-in-molecules method by Mayhall and Raghavachari, 64 more fragmentation approaches can be found in recent review by Gordon et al 65 The basic idea of the GEBF approach is that the energy and properties of a target system can be approximately obtained from the conventional calculations of a series of subsystems, which are embedded in the field of background point charges generated by all atoms outside this subsystem, 52 and can be constructed automatically. 53 The GEBF approach has been implemented for the energy, dipole moments, and static polarizability calculations, 52 geometry optimizations and vibrational frequencies, 66 vibrational circular dichroism spectroscopies, 67 combined quantum mechanics and molecular mechanics (QM/MM) calculations, 68,69 of large systems at various levels of quantum chemistry methods, including Hartree-Fock (HF), DFT, MP2, and coupled cluster (CC) singles and doubles (CCSD) methods.…”