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Molecular properties of excited electronic state: Formalism, implementation, and applications of analytical second energy derivatives within the framework of the time-dependent density functional theory/molecular mechanics
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10.1063/1.4863563
    + View Affiliations - Hide Affiliations
    Affiliations:
    1 State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Province Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
    2 Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei 230026, People's Republic of China
    a) Electronic mail: liangwz@xmu.edu.cn
    J. Chem. Phys. 140, 18A506 (2014); http://dx.doi.org/10.1063/1.4863563
/content/aip/journal/jcp/140/18/10.1063/1.4863563
http://aip.metastore.ingenta.com/content/aip/journal/jcp/140/18/10.1063/1.4863563

Figures

Image of FIG. 1.
FIG. 1.

The optimized hydrogen bond lengths in the complexes, Acetone+2HO, Acetamide+2HO, and Aniline+methanol, by full QM and QM/MM approaches, respectively. The numbers above the hydrogen bond denote the hydrogen bond length in S and numbers below the bond denote those in . The data in parentheses denote the bond lengths yielded by QM/MM approaches.

Image of FIG. 2.
FIG. 2.

The geometries and three different QM/MM partitions in 1-propyl-thymine (left of top panels) and in 1-propyl-cytosine (right of top panels). The electron density distributions of HOMO-1, HOMO, and LUMO in 1-propyl-thymine (middle panels), as well as those of HOMO and LUMO in 1-propyl-cytosine (bottom panels).

Image of FIG. 3.
FIG. 3.

The geometries and QM/MM partitions in dT and dA. The electron density distributions of HOMO−1, HOMO, and LUMO in dT (middle panel), as well as those in dA (bottom panel).

Image of FIG. 4.
FIG. 4.

The chromophore of RFP with part of its protein environment. The numbers above the line indicate the specific bond lengths in ground state while the numbers below the line indicate the specific bond lengths in state. The numbers alone and in parentheses are bond lengths from full QM and QM/MM optimal geometries of PC with its environment, respectively. The numbers in brackets and braces are bond lengths from QM/MM optimal geometries of PC with its neutralized MM environment and DPC with its environment, respectively.

Tables

Generic image for table
Table I.

The adiabatic excitation energies Δ (in unit of eV) with zero point energy correction, bond lengths (in Å), harmonic vibrational frequencies (in cm−1), and IR intensities (in km/mol) of selected vibration modes in isolated molecules and the solute-solvent complexes, Acetone+2HO, Acetamide+2HO, and Aniline+methanol, respectively.

Generic image for table
Table II.

MAD/RMSD of geometrical parameters of Acetone+2HO, Acetamide+2HO, and Aniline+MEOH complexes (neglecting H atoms) by QM/MM calculations compared with full QM results.

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Table III.

MAD/RMSD of geometrical parameters of 1-propyl-thymine and 1-propyl-cytosine by QM/MM calculations.

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Table IV.

Selected properties for the 1-propyl-thymine and 1-propyl-cytosine in different partitions.

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Table V.

MAD/RMSD of geometrical parameters of dT and dA (neglecting H atoms) by QM/MM calculations.

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Table VI.

Selected properties for dT and dA systems.

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Table VII.

The calculated vibrational frequencies of states for a number of systems by the current analytical approach of the excited-state Hessian in TD-B3LYP/MM and the numerical differentiation of analytical energy gradient.

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Table VIII.

CPU timings (in units of hour) for the total and major steps, including SCF, CPSCF, and CP-TDDFT, in the calculations of harmonic vibrational frequencies of Acetone and Acetone+2HO.

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Table IX.

CPU timings (in units of hour) for the total and major steps, including SCF, CPSCF, and CP-TDDFT, in the calculations of harmonic vibrational frequencies of 1-propyl-thymine in full QM and QM/MM with different partitions.

Generic image for table
Table X.

RMSD of the frequencies and IR intensities of Acetamide+89HO with the approximation (in different threshold values of 5.0, 4.0, or 0.0 Å by atoms or molecules) applying to the CPSCF and CP-TDDFT equations by reference to the results without the approximation. (Threshold value of 0.0 Å means the QM/MM results with the uncoupled approximation for all the water molecules.)

Generic image for table
Table XI.

The adiabatic and vertical excitation energies of the isolated PC, and two QM/MM model systems. Here, AE denotes adiabatic excitation energies, VE and EE denote the vertical excitation energies at the S and S optimal geometries, respectively. The data in parentheses denote the AE with zero point energy correction. “env” means the nearby environment of RFP chromophore. “nevn” means the MM environment is neutralized by a sodium ion.

Generic image for table
Table XII.

The vibrational frequencies and IR intensities of the selected bonds in the isolated RFP chromophore, and two QM/MM model systems.

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2014-02-05
2014-04-17
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Molecular properties of excited electronic state: Formalism, implementation, and applications of analytical second energy derivatives within the framework of the time-dependent density functional theory/molecular mechanics
http://aip.metastore.ingenta.com/content/aip/journal/jcp/140/18/10.1063/1.4863563
10.1063/1.4863563
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