Intermediate neglect of differential overlap for spectroscopy

The restricted excitation subspace approximation is explored as a basis to reduce the memory storage required in linear response time-dependent density functional theory (TDDFT) calculations within the Tamm-Dancoff approximation. It is shown that excluding the core orbitals and up to 70% of the virtual orbitals in the construction of the excitation subspace does not result in significant changes in computed UV/vis spectra for large molecules. The reduced size of the excitation subspace greatly reduces the size of the subspace vectors that need to be stored when using the Davidson procedure to determine the eigenvalues of the TDDFT equations. Furthermore, additional screening of the twoelectron integrals in combination with a reduction in the size of the numerical integration grid used in the TDDFT calculation leads to significant computational savings. The use of these approximations represents a simple approach to extend TDDFT to the study of large systems and make the calculations increasingly tractable using modest computing resources.

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“…The -+G* basis set is used, and the percentage error in the oscillator strength of the most intense transition is shown. (8) where…”

Section: Resultsmentioning

confidence: 99%

“…Other time-dependent semi-empirical approaches have been developed [7][8][9]. The low lying excited states of large systems have been studied with pseudo spectral TDDFT [10,11] which leads to a significant speedup in the calculations.…”

Section: Introductionmentioning

confidence: 99%

Assessment of time-dependent density functional theory with the restricted excitation space approximation for excited state calculations of large systems

2018

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“…Carrying out a targeted reparameterization can partly make up for this deficiency -for example, ZINDO/S was especially parameterized to reproduce electronic spectra [108]. An alternative is to include orthogonalization corrections into the semiempirical Fock matrix as done in the OMx methods.…”

Section: Semiempirical Methodsmentioning

confidence: 99%

Computational Modeling of Photoexcitation in DNA Single and Double Strands

Lü

Lan

Thiel

2014

Topics in Current Chemistry

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The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.

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“…The electronic interactions between the SWNT and the wrapped DNA were studied using the semi-empirical quantum chemical modeling method INDO/s [64,65], as implemented in the program CNDO [66]. The INDO/s method has been used in the past to calculate the electronic properties of DNA, as well as those of carbon nanotubes [50,[67][68][69][70][71][72], and showed accuracy comparable to that of higher-level quantum calculations [65,73,74].…”

Section: Theory and Simulationsmentioning

confidence: 99%

Two-color spectroscopy of UV excited ssDNA complex with a single-wall nanotube photoluminescence probe: Fast relaxation by nucleobase autoionization mechanism

et al. 2016

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SWNT ssDNADNA is capable to recover after absorbing ultraviolet (UV) radiation, for example, by autoionization (AI). Singlewall carbon nanotube (SWNT) two-color photoluminescence spectroscopy was combined with quantum mechanical calculations to explain the AI in self-assembled complexes of DNA wrapped around SWNT. DNA autoionization is a fundamental process wherein UV-photoexcited nucleobases dissipate energy by charge transfer to the environment without undergoing chemical damage. Here, single-wall carbon nanotubes (SWNT) are explored as a photoluminescent reporter for studying the mechanism and rates of DNA autoionization. Two-color photoluminescence spectroscopy allows separate photoexcitation of the DNA and the SWNTs in the UV and visible range, respectively. A strong SWNT photoluminescence quenching is observed when the UV pump is resonant with the DNA absorption, consistent with charge transfer from the excited states of the DNA to the SWNT. Semiempirical calculations of the DNA-SWNT electronic structure, combined with a Green's function theory for charge transfer, show a 20 fs autoionization rate, dominated by the hole transfer. Rate-equation analysis of the spectroscopy data confirms that the quenching rate is limited by the thermalization of the free charge carriers transferred to the nanotube reservoir. The developed approach has a great potential for monitoring DNA excitation, autoionization, and chemical damage both in vivo and in vitro arXiv:1512.00710v1 [cond-mat.mes-hall] 2 Dec 2015 2

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Intermediate neglect of differential overlap for spectroscopy

Cited by 28 publications

References 131 publications

Assessment of time-dependent density functional theory with the restricted excitation space approximation for excited state calculations of large systems

Assessment of time-dependent density functional theory with the restricted excitation space approximation for excited state calculations of large systems

Computational Modeling of Photoexcitation in DNA Single and Double Strands

Two-color spectroscopy of UV excited ssDNA complex with a single-wall nanotube photoluminescence probe: Fast relaxation by nucleobase autoionization mechanism

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