Hui Li PublicationsCopyright (c) 2015 University of Nebraska - Lincoln All rights reserved.
http://digitalcommons.unl.edu/chemistryli
Recent documents in Hui Li Publicationsen-usFri, 11 Dec 2015 01:35:38 PST3600Energy Gradients in Combined Fragment Molecular
Orbital and Polarizable Continuum Model
(FMO/PCM) Calculation
http://digitalcommons.unl.edu/chemistryli/4
http://digitalcommons.unl.edu/chemistryli/4Wed, 09 Dec 2015 13:45:21 PST
The analytic energy gradients for the combined fragment molecular orbital and polarizable continuum model (FMO/PCM) method are derived and implemented. Applications of FMO/PCM geometry optimization to polyalanine show that the structures obtained with the FMO/PCM method are very close to those obtained with the corresponding full ab initio PCM methods. FMO/PCM (RHF/6-31G* level) is used to optimize the solution structure of the 304-atom Trp-cage miniprotein and the result is in agreement with NMR experiments. The key factors determining the relative stability of the a-helix, b-turn and the extended form in solution are elucidated for polyalanine.
]]>
Hui Li et al.Excited state geometry of photoactive yellow protein chromophore:
A combined conductorlike polarizable continuum model and
time-dependent density functional study
http://digitalcommons.unl.edu/chemistryli/3
http://digitalcommons.unl.edu/chemistryli/3Fri, 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.
]]>
Yali Wang et al.Analytic energy gradients in combined second order Møller-Plesset perturbation theory and conductorlike polarizable continuum
model calculation
http://digitalcommons.unl.edu/chemistryli/2
http://digitalcommons.unl.edu/chemistryli/2Fri, 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 T_{1} 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 T_{1} state pairs are weakened by ∼1 kcal/mol as compared to those in the S_{0} state pairs.
]]>
Dejun Si et al.Smooth potential energy surface for cavitation, dispersion, and repulsion
free energies in polarizable continuum model
http://digitalcommons.unl.edu/chemistryli/1
http://digitalcommons.unl.edu/chemistryli/1Fri, 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.
]]>
Yali Wang et al.