title: Constructing an Interpolated Potential Energy Surface of a Large Molecule: A Case Study with Bacteriochlorophyll a Model in the Fenna-Matthews-Olson Complex.
abstract: Constructing a reliable potential energy surface (PES) is a key step toward computationally studying the chemical dynamics of any molecular system. The interpolation scheme is a useful tool that can closely follow the accuracy of quantum chemical means at a dramatically reduced computational cost. However, applying interpolation to building a PES of a large molecule is not a straightforward black-box approach, as it frequently encounters practical difficulties associated with its large dimensionality. Here, we present detailed courses of applying interpolation toward building a PES of a large chromophore molecule. We take the example of S0and S1electronic states of bacteriochlorophyll a (BChla) molecules in the Fenna-Matthews-Olson light harvesting complex. With a reduced model molecule that bears BChla's main π-conjugated ring, various practical approaches are designed for improving the PES quality in a stable manner and for fine-tuning the final surface such that the surface can be adopted for long time molecular dynamics simulations. Combined with parallel implementation, we show that interpolated mechanics/molecular mechanics (IM/MM) simulations of the entire complex in the nanosecond time scale can be conducted readily without any practical issues. With 1500 interpolation data points for each chromophore unit, the PES error relative to the reference quantum chemical calculation is found to be ∼0.15 eV in the thermally accessible region of the conformational space, together with ∼0.01 eV error in S0- S1transition energies. The performance issue related to the use of a large interpolation database within the framework of our parallel routines is also discussed.
authors.affiliation: Center for Self-assembly and Complexity, Institute for Basic Science (IBS) , Pohang 37673, Korea.|Department of Chemistry, Pohang University of Science and Technology (POSTECH) , Pohang 37673, Korea.
authors.forename: Chang Woo
authors.initials: CW
authors.lastname: Kim
authors.affiliation: Center for Self-assembly and Complexity, Institute for Basic Science (IBS) , Pohang 37673, Korea.|Department of Chemistry, Pohang University of Science and Technology (POSTECH) , Pohang 37673, Korea.
authors.forename: Young Min
authors.initials: YM
authors.lastname: Rhee
mesh_terms: D025541:Bacteriochlorophyll A / Q000737:chemistry* / Q000378:metabolism; D001499:Bayes Theorem; D045342:Light-Harvesting Protein Complexes / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D025541:Bacteriochlorophyll A; D045342:Light-Harvesting Protein Complexes