### Abstract

A theoretical description of the vibrational excitons in DNA is presented by using the vibrational basis mode theory developed in Papers I and II. The parameters obtained from the density functional theory calculations, such as vibrational coupling constants and basis mode frequencies, are used to numerically simulate two-dimensional (2D) IR spectra of dG_{n}: dC _{n} and dA_{n}: dT_{n} double helices with n varying from 1 to 10. From the molecular dynamics simulations of dG_{5}C _{5} and dA_{5}T_{5} double helices in D_{2}O solution, it is found that the thermally driven internal motions of these systems in an aqueous solution do not induce strong fluctuations of basis mode frequencies nor vibrational couplings. In order to construct the two-exciton Hamiltonian, the vibrational anharmonicities of eight basis modes are obtained by carrying out B3LYP/6-31G* calculations for the nine basis modes. The simulated 2D IR spectra of dG_{n}: dC_{n} double helix in D _{2}O solution are directly compared with closely related experimental results. The 2D IR spectra of dG_{n}: dC_{n} and dA _{n}: dT_{n} are found to be weakly dependent on the number of base pairs. The present work demonstrates that the computational procedure combining quantum chemistry calculation and molecular dynamics simulation methods can be of use to predict 2D IR spectra of nucleic acids in solutions.

Original language | English |
---|---|

Article number | 114510 |

Journal | Journal of Chemical Physics |

Volume | 125 |

Issue number | 11 |

DOIs | |

Publication status | Published - 2006 Oct 3 |

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### ASJC Scopus subject areas

- Atomic and Molecular Physics, and Optics

### Cite this

*Journal of Chemical Physics*,

*125*(11), [114510]. https://doi.org/10.1063/1.2213259

**Vibrational dynamics of DNA. III. Molecular dynamics simulations of DNA in water and theoretical calculations of the two-dimensional vibrational spectra.** / Lee, Chewook; Park, Kwang Hee; Kim, Jin A.; Hahn, Seungsoo; Cho, Minhaeng.

Research output: Contribution to journal › Article

*Journal of Chemical Physics*, vol. 125, no. 11, 114510. https://doi.org/10.1063/1.2213259

}

TY - JOUR

T1 - Vibrational dynamics of DNA. III. Molecular dynamics simulations of DNA in water and theoretical calculations of the two-dimensional vibrational spectra

AU - Lee, Chewook

AU - Park, Kwang Hee

AU - Kim, Jin A.

AU - Hahn, Seungsoo

AU - Cho, Minhaeng

PY - 2006/10/3

Y1 - 2006/10/3

N2 - A theoretical description of the vibrational excitons in DNA is presented by using the vibrational basis mode theory developed in Papers I and II. The parameters obtained from the density functional theory calculations, such as vibrational coupling constants and basis mode frequencies, are used to numerically simulate two-dimensional (2D) IR spectra of dGn: dC n and dAn: dTn double helices with n varying from 1 to 10. From the molecular dynamics simulations of dG5C 5 and dA5T5 double helices in D2O solution, it is found that the thermally driven internal motions of these systems in an aqueous solution do not induce strong fluctuations of basis mode frequencies nor vibrational couplings. In order to construct the two-exciton Hamiltonian, the vibrational anharmonicities of eight basis modes are obtained by carrying out B3LYP/6-31G* calculations for the nine basis modes. The simulated 2D IR spectra of dGn: dCn double helix in D 2O solution are directly compared with closely related experimental results. The 2D IR spectra of dGn: dCn and dA n: dTn are found to be weakly dependent on the number of base pairs. The present work demonstrates that the computational procedure combining quantum chemistry calculation and molecular dynamics simulation methods can be of use to predict 2D IR spectra of nucleic acids in solutions.

AB - A theoretical description of the vibrational excitons in DNA is presented by using the vibrational basis mode theory developed in Papers I and II. The parameters obtained from the density functional theory calculations, such as vibrational coupling constants and basis mode frequencies, are used to numerically simulate two-dimensional (2D) IR spectra of dGn: dC n and dAn: dTn double helices with n varying from 1 to 10. From the molecular dynamics simulations of dG5C 5 and dA5T5 double helices in D2O solution, it is found that the thermally driven internal motions of these systems in an aqueous solution do not induce strong fluctuations of basis mode frequencies nor vibrational couplings. In order to construct the two-exciton Hamiltonian, the vibrational anharmonicities of eight basis modes are obtained by carrying out B3LYP/6-31G* calculations for the nine basis modes. The simulated 2D IR spectra of dGn: dCn double helix in D 2O solution are directly compared with closely related experimental results. The 2D IR spectra of dGn: dCn and dA n: dTn are found to be weakly dependent on the number of base pairs. The present work demonstrates that the computational procedure combining quantum chemistry calculation and molecular dynamics simulation methods can be of use to predict 2D IR spectra of nucleic acids in solutions.

UR - http://www.scopus.com/inward/record.url?scp=33749051616&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33749051616&partnerID=8YFLogxK

U2 - 10.1063/1.2213259

DO - 10.1063/1.2213259

M3 - Article

C2 - 16999493

AN - SCOPUS:33749051616

VL - 125

JO - Journal of Chemical Physics

JF - Journal of Chemical Physics

SN - 0021-9606

IS - 11

M1 - 114510

ER -