Hui Li Publications

Excited state geometry of photoactive yellow protein chromophore: A combined conductorlike polarizable continuum model and time-dependent density functional study

Yali Wang et al. — Fri, 06 Apr 2012 10:29:28 PDT

Analytic gradient of the combined conductorlike polarizable continuum model (CPCM) and time-dependent density functional theory method is derived and implemented. Due to the use of the fixed points with variable areas tessellation scheme, the excited state potential energy surfaces (PESs) are rigorously continuous and smooth. The CPCM/TD-B3LYP method is used to study an analog of the photoactive yellow protein chromophore, anionic thiomethyl p-coumaric acid (TMpCA⁻). Although CPCM/TD-B3LYP method may not be accurate in predicting solvent effect on vertical excitation of TMpCA⁻, it may be used to predict redshiftings of emission maxima relative to absorption maxima with an accuracy of ~0.1 eV. We also found that the excited trans-TMpCA⁻ tends to form a single bond twisted structure in the gas phase but a double bond twisted structure in aqueous solution. The TD-B3LYP minimum energy isomerization pathway shows a barrier of 3.6 kcal/mol in aqueous solution and 5.2 kcal/mol in the gas phase. The gas phase double bond twisted structure is trapped in a well of the excited state PES, with a depth of ~20 kcal/mol (0.88 eV), in good agreement with an experimental value of ~1 eV.

Analytic energy gradients in combined second order Møller-Plesset perturbation theory and conductorlike polarizable continuum model calculation

Dejun Si et al. — Fri, 06 Apr 2012 10:24:20 PDT

The analytic energy gradients in combined second order Møller-Plesset perturbation theory and conductor-like polarizable continuum model calculations are derived and implemented for spin-restricted closed shell (RMP2), Z-averaged spin-restricted open shell (ZAPT2), and spin-unrestricted open shell (UMP2) cases. Using these methods, the geometries of the S0 ground state and the T₁ state of three nucleobase pairs (guanine-cytosine, adenine-thymine, and adenine-uracil) in the gas phase and aqueous solution phase are optimized. It is found that in both the gas phase and the aqueous solution phase the hydrogen bonds in the T₁ state pairs are weakened by ∼1 kcal/mol as compared to those in the S₀ state pairs.

Smooth potential energy surface for cavitation, dispersion, and repulsion free energies in polarizable continuum model

Yali Wang et al. — Fri, 06 Apr 2012 10:20:16 PDT

The fixed points with variable areas [FIXPVA] tessellation scheme is used to obtain smooth potential energy surfaces for the cavitation G_cav, dispersion G_dis, and repulsion G_rep free energies in the polarizable continuum model (PCM). It is shown that FIXPVA can reproduce the standard GEPOL results to within 1 kcal/mol.