Geometry Optimizations and Vibrational Spectra of Large Molecules from a Generalized Energy-Based Fragmentation Approach

Abstract

The generalized energy-based fragmentation (GEBF) approach (Li, W.; Li, S.; Jiang, Y. J. Phys. Chem. A 2007, 111, 2193) is extended for geometry optimizations and vibrational spectra calculations of general large molecules or clusters. In this approach, the total energy and its derivatives, and some molecular properties, of a target system are obtained from conventional calculations on a series of subsystems derived from the target system. Each subsystem is electronically embedded in the background point charges generated by all other atoms outside the subsystem so that the long-range interactions and polarization effects between remote fragments are approximately taken into account. The approach computationally scales linearly with the system size and can be easily implemented for large-scale parallelization. By comparing the results from the conventional and GEBF calculations for several test molecules including a polypeptide and a water cluster, we demonstrate that the GEBF approach is able to provide quite reliable predictions for molecular geometries, vibrational frequencies, and thermochemistry data and satisfactory descriptions for vibrational intensities, for general molecules with polar or charged groups.

Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method

“…[26][27][28] Some fragment based approaches [29][30][31][32][33][34][35][36][37][38][39][40] feature analytic second derivatives. [41][42][43][44][45][46] The fragment molecular orbital (FMO) method [47][48][49][50][51] is a fragment-based approach. In the FMO method, the system is divided into a set of fragments (also called monomers).…”

Theoretical study of interactions between human adult hemoglobin and acetate ion by polarizable force field and fragmentation quantum chemistry methods

“…The generalized energy-based fragmentation (GEBF) QM calculation [11][12][13][14][15][16] follows several steps: (i) The macromolecule (Hb-α and its complex with CH 3 COO − ) is divided into fragments by every two successive residues. (ii) Closed-shell subsystems are built by capping each fragment with its neighboring fragments.…”

“…First of all, we take eight fractions (containing 210-347 atoms with 1860-2992 basis functions at the level of B3LYP/6-31G(d), as shown in Figure 2) of Hb-α to test the performance of GEBF [11][12][13][14][15][16] approach instead. Each fraction is calculated by the GEBF approach and the conventional quantum chemistry method at B3LYP/6-31G(d) level, respectively.…”

“…However, it is difficult to treat such a large system with more than 2000 atoms by conventional quantum chemistry methods. As a result, a hierarchy of theoretical approaches, including conventional FF03 [9] , FF03-based polarization model [10] , and energy-based fragmentation quantum mechanism (QM) [11][12][13][14][15][16][17][18][19] , are employed here. On the basis of our calculations, FF03-based polarization models give the order of interaction energies of Arg92 > Lys127 > Lys90 > Lys16.…”

The role of the exchange in the embedding electrostatic potential for the fragment molecular orbital method

“…Recently, a large number of fragment-based methods [1][2][3][4][5][6][7][8][9][10] have been suggested in order to facilitate computing large systems with quantum-mechanical methods. The fragment molecular orbital ͑FMO͒ [11][12][13] method is based on dividing the system into pieces ͑fragments͒ and performing ab initio calculations on fragments, their pairs, and, optionally, triples.…”