Young Min Rhee

Two modifications of the perturbative doubles correction to configuration interaction with single substitutions (CIS(D)) are suggested, which are excited state analogues of ground state scaled second-order Møller-Plesset (MP2) methods. The first approach employs two parameters to scale the two spin components of the direct term of CIS(D), starting from the two-parameter spin-component scaled (SCS) MP2 ground state, and is termed SCS-CIS(D). An efficient resolution-of-the-identity (RI) implementa

There are many unresolved questions regarding the role of water in protein folding. Does water merely induce hydrophobic forces, or does the discrete nature of water play a structural role in folding? Are the nonadditive aspects of water important in determining the folding mechanism? To help to address these questions, we have performed simulations of the folding of a model protein (BBA5) in explicit solvent. Starting 10,000 independent trajectories from a fully unfolded conformation, we have o

The species responsible for the broad extended red emission (ERE), discovered in 1975 and now known to be widespread throughout the Galaxy, still is unidentified. Spanning the range from approximately 540 to 900 nm, the ERE is a photoluminescent process associated with a wide variety of different interstellar environments. Over the years, a number of plausible candidates have been suggested, but subsequent observations ruled them out. The objects that present the ERE also emit the infrared featu

The recently developed narrow-band blue-emitting organoboron chromophores based on the multiple-resonance (MR) effect have now become one of the most important components for constructing efficient organic light emitting diodes (OLEDs). While they basically emit through fluorescence, they are also known for showing substantial thermally activated delayed fluorescence (TADF) even with a relatively large singlet-triplet gap (Δ<i>E</i> _ST). Indeed, understanding the reverse intersystem c

Computationally predicting reverse intersystem crossing (RISC) rates is important for designing new thermally activated delayed fluorescence (TADF) materials. We report a method that can quantitatively predict RISC rates by explicitly considering the spin-vibronic coupling mechanism. The coupling element of the spin-vibronic Hamiltonian is obtained by expanding the spin-orbit and the non-Born-Oppenheimer terms to second order and is then brought into the Golden Rule rate under the Condon approxi

In general, finding a one-dimensional representation of the kinetics of a high-dimensional system is a great simplification for the study of complex systems. Here, we propose a method to obtain a reaction coordinate whose potential of the mean force can reproduce the commitment probability distribution from the multidimensional surface. We prove that such a relevant one-dimensional representation can be readily calculated from the equilibrium distribution of commitment probabilities, which can b

One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the hetero

We analyze the environment-induced fluctuation of pigment excitation energies in the Fenna-Matthews-Olson (FMO) complex from various perspectives, by employing an interpolation-based all-atom potential energy model for describing realistic pigment vibrations. We conduct molecular dynamics simulations on a 100 ns timescale, which is an extent that can enclose the effect of static disorder, and demonstrate its timescale separation from fast dynamic disorder. We extract the spectral densities of th

An improved algorithm to construct molecular potential energy surfaces for polyatomic reactions is presented. The method uses the energies, gradients, and Hessians, which can be obtained from ab initio quantum chemical calculations. The surface is constructed by interpolating the local quadratic surfaces with reaction path weights. The method is tested with a five-atom reaction system for which an analytic potential energy surface has been reported together with classical trajectory results. An

Solvent viscosity has been frequently adopted as an adjustable parameter in various computational studies (e.g., protein folding simulations) with implicit solvent models. A common approach is to use low viscosities to expedite simulations. While using viscosities lower than that of aqueous is unphysical, such treatment is based on observations that the viscosity affects the kinetics (rates) in a well-defined manner as described by Kramers' theory. Here, we investigate the effect of viscosity on

A modified method to construct an accurate potential energy surface by interpolation is presented. The modification is based on the use of Cartesian coordinates in the weighting function. The translational and rotational invariance of the potential is incorporated by a proper definition of the distance between two Cartesian configurations. A numerical algorithm to find the distance is developed. It is shown that the present method is more exact in describing a planar system compared to the previ

Abstract Construction of force field parameters of the oxyluciferin molecule on its electronic ground and excited states is presented. Several new approaches are introduced for more reliable parameterization: argon‐scanning, Hessian matching, and constrained‐group parameterization. The Ar‐scanning approach is for fitting Lennard‐Jones parameters so that the constructed force field can mimic the changes in ab initio energy of oxyluciferin‐argon pair at various argon positions. The Hessian matchin

A method for the mode-specific energy analysis in a classical trajectory calculation is developed. The pure rotational energy is evaluated by invoking the Eckart condition. To evaluate the vibrational energy in each normal mode, the vibrational velocity is divided into two parts, the angular motion part and the angular motion free part, and the latter is analyzed with the Cartesian and internal coordinate systems. The potential energy of each normal mode is also evaluated in the two coordinate s