Nonempirically Tuned Range-Separated DFT Accurately Predicts Both Fundamental and Excitation Gaps in DNA and RNA Nucleobases

Overview

Journal J Chem Theory Comput

Publisher American Chemical Society

Specialties Biochemistry
Chemistry

Date 2012 Aug 21

PMID 22904693

Citations 25

Authors

Michael E Foster

Bryan M Wong

Affiliations

Soon will be listed here.

Abstract

Using a nonempirically tuned range-separated DFT approach, we study both the quasiparticle properties (HOMO-LUMO fundamental gaps) and excitation energies of DNA and RNA nucleobases (adenine, thymine, cytosine, guanine, and uracil). Our calculations demonstrate that a physically motivated, first-principles tuned DFT approach accurately reproduces results from both experimental benchmarks and more computationally intensive techniques such as many-body GW theory. Furthermore, in the same set of nucleobases, we show that the nonempirical range-separated procedure also leads to significantly improved results for excitation energies compared to conventional DFT methods. The present results emphasize the importance of a nonempirically tuned range-separation approach for accurately predicting both fundamental and excitation gaps in DNA and RNA nucleobases.

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References

Izmaylov A, Scuseria G . Why are time-dependent density functional theory excitations in solids equal to band structure energy gaps for semilocal functionals, and how does nonlocal Hartree-Fock-type exchange introduce excitonic effects?. J Chem Phys. 2008; 129(3):034101. DOI: 10.1063/1.2953701. View

Tawada Y, Tsuneda T, Yanagisawa S, Yanai T, Hirao K . A long-range-corrected time-dependent density functional theory. J Chem Phys. 2004; 120(18):8425-33. DOI: 10.1063/1.1688752. View

Nguyen K, Day P, Pachter R . The performance and relationship among range-separated schemes for density functional theory. J Chem Phys. 2011; 135(7):074109. DOI: 10.1063/1.3624889. View

Srebro M, Autschbach J . Does a Molecule-Specific Density Functional Give an Accurate Electron Density? The Challenging Case of the CuCl Electric Field Gradient. J Phys Chem Lett. 2015; 3(5):576-81. DOI: 10.1021/jz201685r. View

Katan C, Blanchard-Desce M, Tretiak S . Position Isomerism on One and Two Photon Absorption in Multibranched Chromophores: A TDDFT Investigation. J Chem Theory Comput. 2015; 6(11):3410-26. DOI: 10.1021/ct1004406. View

Stein T, Kronik L, Baer R . Prediction of charge-transfer excitations in coumarin-based dyes using a range-separated functional tuned from first principles. J Chem Phys. 2010; 131(24):244119. DOI: 10.1063/1.3269029. View

Stein T, Kronik L, Baer R . Reliable prediction of charge transfer excitations in molecular complexes using time-dependent density functional theory. J Am Chem Soc. 2009; 131(8):2818-20. DOI: 10.1021/ja8087482. View

Wong B, Cordaro J . Coumarin dyes for dye-sensitized solar cells: A long-range-corrected density functional study. J Chem Phys. 2008; 129(21):214703. DOI: 10.1063/1.3025924. View

Hybertsen , Louie . Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies. Phys Rev B Condens Matter. 1986; 34(8):5390-5413. DOI: 10.1103/physrevb.34.5390. View

10.

Peach M, Benfield P, Helgaker T, Tozer D . Excitation energies in density functional theory: an evaluation and a diagnostic test. J Chem Phys. 2008; 128(4):044118. DOI: 10.1063/1.2831900. View

11.

Kronik L, Stein T, Refaely-Abramson S, Baer R . Excitation Gaps of Finite-Sized Systems from Optimally Tuned Range-Separated Hybrid Functionals. J Chem Theory Comput. 2015; 8(5):1515-31. DOI: 10.1021/ct2009363. View

12.

Srebro M, Autschbach J . Tuned Range-Separated Time-Dependent Density Functional Theory Applied to Optical Rotation. J Chem Theory Comput. 2015; 8(1):245-56. DOI: 10.1021/ct200764g. View

13.

Kornobis K, Kumar N, Wong B, Lodowski P, Jaworska M, Andruniow T . Electronically excited states of vitamin B12: benchmark calculations including time-dependent density functional theory and correlated ab initio methods. J Phys Chem A. 2011; 115(7):1280-92. DOI: 10.1021/jp110914y. View

14.

Bravaya K, Kostko O, Ahmed M, Krylov A . The effect of pi-stacking, H-bonding, and electrostatic interactions on the ionization energies of nucleic acid bases: adenine-adenine, thymine-thymine and adenine-thymine dimers. Phys Chem Chem Phys. 2010; 12(10):2292-307. DOI: 10.1039/b919930f. View

15.

Wong B . Optoelectronic Properties of Carbon Nanorings: Excitonic Effects from Time-Dependent Density Functional Theory. J Phys Chem C Nanomater Interfaces. 2012; 113(52):21921-21927. PMC: 3317592. DOI: 10.1021/jp9074674. View

16.

Wong B, Hsieh T . Optoelectronic and Excitonic Properties of Oligoacenes: Substantial Improvements from Range-Separated Time-Dependent Density Functional Theory. J Chem Theory Comput. 2010; 6(12):3704-3712. PMC: 3002181. DOI: 10.1021/ct100529s. View

17.

Wong B, Piacenza M, Della Sala F . Absorption and fluorescence properties of oligothiophene biomarkers from long-range-corrected time-dependent density functional theory. Phys Chem Chem Phys. 2009; 11(22):4498-508. DOI: 10.1039/b901743g. View

18.

Bravaya K, Kostko O, Dolgikh S, Landau A, Ahmed M, Krylov A . Electronic structure and spectroscopy of nucleic acid bases: ionization energies, ionization-induced structural changes, and photoelectron spectra. J Phys Chem A. 2010; 114(46):12305-17. DOI: 10.1021/jp1063726. View