Mapping Enzymatic Catalysis using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be $18.3\pm 3.5$ kcal mol$^{-1}$ for MP2/cc-pVDZ and $19.3\pm 3.6$ for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively.Comment: SI not attache

Empirical corrections and pair interaction energies in the fragment molecular orbital method

The energy and analytic gradient are developed for FMO combined with the Hartree-Fock method augmented with three empirical corrections (HF-3c). The auxiliary basis set approach to FMO is extended to perform pair interaction energy decomposition analysis. The FMO accuracy is evaluated for several typical systems including 3 proteins. Pair interaction energies computed with different approaches in FMO are compared for a water cluster and protein-ligand complexes.Comment: Revised version accepted in Chemical Physics Letter

Hybrid RHF/MP2 geometry optimizations with the Effective Fragment Molecular Orbital Method

The frozen domain effective fragment molecular orbital method is extended to allow for the treatment of a single fragment at the MP2 level of theory. The approach is applied to the conversion of chorismate to prephenate by chorismate mutase, where the substrate is treated at the MP2 level of theory while the rest of the system is treated at the RHF level. MP2 geometry optimization is found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations and ONIOM energy refinement and leads to a smoother convergence with respect to the basis set for the reaction profile. For double zeta basis sets the increase in CPU time relative to RHF is roughly a factor of two.Comment: 11 pages, 3 figure

Multicomponent Strongly Interacting Few-Fermion Systems in One Dimension

The paper examines a trapped one-dimensional system of multicomponent spinless fermions that interact with a zero-range two-body potential. We show that when the repulsion between particles is very large the system can be approached analytically. To illustrate this analytical approach we consider a simple system of three distinguishable particles, which can be addressed experimentally. For this system we show that for infinite repulsion the energy spectrum is sixfold degenerate. We also show that this degeneracy is partially lifted for finitely large repulsion for which we find and describe corresponding wave functions.Comment: Paper in connection with the 22nd European Conference on Few-Body Problems in Physics, Krakow, Poland, 9-13 September 201

Geometry Optimizations of Open-Shell Systems with the Fragment Molecular Orbital Method

The ability to perform geometry optimizations on large molecular systems is desirable for both closed- and open-shell species. In this work, the restricted open-shell Hartree–Fock (ROHF) gradients for the fragment molecular orbital (FMO) method are presented. The accuracy of the gradients is tested, and the ability of the method to reproduce adiabatic excitation energies is also investigated. Timing comparisons between the FMO method and full ab initio calculations are also performed, demonstrating the efficiency of the FMO method in modeling large open-shell systems