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Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory.

ABSTRACT: We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag + -mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peaks in the measured ECD spectra within a 20 nm range. However, a spurious positive peak is present in the CAM-B3LYP ECD spectra. We trace the origins of this spurious peak and find that is likely due to the sensitivity of silver atoms to the amount of Hartree?Fock exchange in the exchange-correlation functional. Our presented approach provides guidance for future computational investigations of other Ag + -mediated DNA species.

SUBMITTER: Makkonen E

PROVIDER: S-EPMC6122091 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory.

Makkonen Esko E Rinke Patrick P Lopez-Acevedo Olga O Chen Xi X

International journal of molecular sciences 20180809 8

We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag + -mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peak ...[more]

PMID: 30096923

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Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory.

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Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory.

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