Efficient and Accurate Fragmentation Methods

Abstract

Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecular orbital (FMO) method can be combined with any electronic structure method to perform accurate calculations on large molecular species with no reliance on capping atoms or empirical parameters. The FMO method is highly scalable and can take advantage of massively parallel computer systems. For example, the method has been shown to scale nearly linearly on up to 131 000 processor cores for calculations on large water clusters. There have been many applications of the FMO method to large molecular clusters, to biomolecules (e.g., proteins), and to materials that are used as heterogeneous catalysts. The effective fragment potential (EFP) method is a model potential approach that is fully derived from first principles and has no empirically fitted parameters. Consequently, an EFP can be generated for any molecule by a simple preparatory GAMESS calculation. The EFP method provides accurate descriptions of all types of intermolecular interactions, including Coulombic interactions, polarization/induction, exchange repulsion, dispersion, and charge transfer. The EFP method has been applied successfully to the study of liquid water, π-stacking in substituted benzenes and in DNA base pairs, solvent effects on positive and negative ions, electronic spectra and dynamics, non-adiabatic phenomena in electronic excited states, and nonlinear excited state properties. The effective fragment molecular orbital (EFMO) method is a merger of the FMO and EFP methods, in which interfragment interactions are described by the EFP potential, rather than the less accurate electrostatic potential. The use of EFP in this manner facilitates the use of a smaller value for the distance cutoff (Rcut). Rcut determines the distance at which EFP interactions replace fully quantum mechanical calculations on fragment-fragment (dimer) interactions. The EFMO method is both more accurate and more computationally efficient than the most commonly used FMO implementation (FMO2), in which all dimers are explicitly included in the calculation. While the FMO2 method itself does not incorporate three-body interactions, such interactions are included in the EFMO method via the EFP self-consistent induction term. Several applications (ranging from clusters to proteins) of the three methods are discussed to demonstrate their efficacy. The EFMO method will be especially exciting once the analytic gradients have been completed, because this will allow geometry optimizations, the prediction of vibrational spectra, reaction path following, and molecular dynamics simulations using the method. Disciplines Chemistry CommentsReprinted (adapted) CONSPECTUS: Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecu...

Extension of the Effective Fragment Potential Method to Macromolecules

“…For modeling intermolecular interactions, similar strategies based on multipolar expansion have been utilized. [39][40][41] Recently, EFP was combined with fragment molecular orbital (FMO) method 42 giving rise to the EFMO method capable of describing both molecular aggregates and large molecules 43,44 (however, EFMO method has not yet been extended to excited states). Detailed reviews of various flavors of fragment-based methods can be found in Refs.…”

Silanol-Assisted Carbinolamine Formation in an Amine-Functionalized Mesoporous Silica Surface: Theoretical Investigation by Fragmentation Methods

“…The FMO method is particularly appealing in this regard since the code is highly scalable and is therefore able to make efficient use of massively parallel computer systems. 33,65,66 …”

Breaking a bottleneck: Accurate extrapolation to “gold standard” CCSD(T) energies for large open shell organic radicals at reduced computational cost

“…Over the years, a number of fragment‐based methods have been devised to accurately compute energies of larger molecules . These methods incorporate a general approach, where the large system is described by smaller fragments that are treated at the same geometry that they have in the target molecule.…”

“…Over the years, a number of fragment-based methods have been devised to accurately compute energies of larger molecules. [24][25][26][27][28][29][30][31][32][33][34][35][36][37] These methods incorporate a general approach, where the large system is described by smaller fragments that are treated at the same geometry that they have in the target molecule. The total energy of the large system is obtained directly from the energies of smaller (typically overlapping) frag-ments that contain only their local interactions.…”

“…The total energy of the large system is obtained directly from the energies of smaller (typically overlapping) frag-ments that contain only their local interactions. While these methods have been highly successful on closed shell organic and bio-organic systems and water clusters, [27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42] only a few of them have been extended for organic open shell radicals. [43,44] The open shell radicals have unpaired electrons, which are most commonly treated starting from an unrestricted Hartree-Fock (UHF) wave function that can suffer from spin contamination effects.…”