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 S and S electronic 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 S - S transition energies. The performance issue related to the use of a large interpolation database within the framework of our parallel routines is also discussed.

Site-Dependent Fluctuations Optimize Electronic Energy Transfer in the Fenna–Matthews–Olson Protein

“…17 Kim and Rhee have also constructed an interpolated potential energy function of BChl a pigment using 1500 data points. 19,20 In this study, by further developing an accurate and efficient method for the calculation of excitonic couplings, we enable to Comparison of the calculated site energies at 300 K (red) with the result fitted to experimental data (green). The calculated site energies correspond to the maxima of the site energy distributions.…”

Multiscale QM/MM molecular dynamics simulations of the trimeric major light-harvesting complex II

“…Furthermore, Coker and co-workers suggested an alternative formalism to accurately describe the intramolecular part of spectral densities 38 . Although, both approaches provide an impressive agreement between the theoretical and experimental spectral densities taking into account the size of the studied system, they suffer from high numerical costs required to construct the PES 39 or to determine the normal mode analysis while calculating the intra-molecular contribution at a high level of accuracy 40 . A reliable ground state QM/MM MD dynamics followed by excitation calculations using a high level QM method would be an ideal choice to accurately describe the dynamics of the energy gap for pigment molecules.…”

Time-dependent atomistic simulations of the CP29 light-harvesting complex

“…The inconsistency in geometry between the ground and excited state is commonly known as the "geometry mismatch" problem. 49 Some recent methods to determine the intramolecular vibrational modes accurately are based on normal mode analyses 47,50 or ground state dynamics on pre-calculated quantum mechanical potential energy surfaces 51,52 and have been employed in calculations of spectral densities. In spite of providing impressive agreements compared to experimental results, these aforementioned schemes are computationally still demanding.…”

“…In spite of providing impressive agreements compared to experimental results, these aforementioned schemes are computationally still demanding. 51,53 A sophisticated quantum-mechanics/molecular mechanics (QM/MM) MD with an accurate description of the vibrational properties of the pigments would be an alternative way; however, semi-empirical schemes have a limited accuracy, 54 while DFT-based calculations are numerically expensive for pigments in LH systems. 55 To this end, we recently proposed a scheme using QM/MM MD dynamics employing the numerically efficient density functional-based tight binding (DFTB) approach 56 and have shown to be able to obtain a good agreement between the spectral densities obtained in such a manner and their experimental counterparts.…”