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

2018 ◽  
Vol 19 (8) ◽  
pp. 2346 ◽  
Author(s):  
Esko Makkonen ◽  
Patrick Rinke ◽  
Olga Lopez-Acevedo ◽  
Xi Chen
Keyword(s):  
Molecular Dynamics ◽  
Density Functional ◽  
Time Dependent ◽  
Basis Set ◽  
Dna Nanostructures ◽  
Exchange Correlation ◽  
Hartree Fock ◽  
Spurious Peak ◽  
20 Nm ◽  
Dependent Density

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.

Benchmark of Simplified Time-Dependent Density Functional Theory for UV-Vis Spectral Properties of Porphyrinoids

2019 ◽  
Author(s):  
Kamal Batra ◽  
Stefan Zahn ◽  
Thomas Heine
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Large Scale ◽  
Absolute Error ◽  
Time Dependent ◽  
Basis Set ◽  
Basis Sets ◽  
Functional Theory ◽  
Framework Materials ◽  
Dependent Density

<p>We thoroughly benchmark time-dependent density- functional theory for the predictive calculation of UV/Vis spectra of porphyrin derivatives. With the aim to provide an approach that is computationally feasible for large-scale applications such as biological systems or molecular framework materials, albeit performing with high accuracy for the Q-bands, we compare the results given by various computational protocols, including basis sets, density-functionals (including gradient corrected local functionals, hybrids, double hybrids and range-separated functionals), and various variants of time-dependent density-functional theory, including the simplified Tamm-Dancoff approximation. An excellent choice for these calculations is the range-separated functional CAM-B3LYP in combination with the simplified Tamm-Dancoff approximation and a basis set of double-ζ quality def2-SVP (mean absolute error [MAE] of ~0.05 eV). This is not surpassed by more expensive approaches, not even by double hybrid functionals, and solely systematic excitation energy scaling slightly improves the results (MAE ~0.04 eV). </p>

Impact of vibronic coupling effects on light-driven charge transfer in pyrene-functionalized middle and large-sized Metalloid Gold Nanoclusters from Ehrenfest dynamics.

2021 ◽  
Author(s):  
Adrian Dominguez-Castro ◽  
Thomas Frauenheim
Keyword(s):  
Molecular Dynamics ◽  
Charge Transfer ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Gold Nanoclusters ◽  
Tight Binding ◽  
Time Dependent ◽  
Effective Strategy ◽  
Dynamics Simulations ◽  
Dependent Density

Theoretical calculations are an effective strategy to comple- ment and understand experimental results in atomistic detail. Ehrenfest molecular dynamics simulations based on the real-time time-dependent density functional tight-binding (RT-TDDFTB) approach...

EXCHANGE–CORRELATION KERNEL IN TIME-DEPENDENT DENSITY FUNCTIONAL THEORY DERIVED FROM MANY-BODY THEORY

2004 ◽  
Vol 18 (07) ◽  
pp. 1055-1067 ◽  
Author(s):  
K. KARLSSON ◽  
F. ARYASETIAWAN
Keyword(s):  
Density Functional Theory ◽  
Optical Absorption ◽  
Density Functional ◽  
Time Dependent ◽  
Many Body ◽  
Functional Theory ◽  
Correlation Kernel ◽  
Exchange Correlation ◽  
Many Body Theory ◽  
Dependent Density

We derive a simplified Bethe–Salpeter equation for calculating optical absorption based on the assumption of a local electron–hole interaction. The original four-point equation for the kernel is reduced to a two-point one. A connection to the exchange–correlation kernel in time-dependent density functional theory can be established. The resulting fxc is found to be -W/2 where W contains only the short-range (local) part of the Coulomb screened interaction. This simple approximation was successfully applied to optical absorption spectra of some excitonic crystals, reproducing not only the continuum excitons but also the bound ones.

Excitation Spectra in the Time-Dependent Density-Functional Theory with Gradient Correction

1999 ◽  
Vol 579 ◽  
Author(s):  
Naoto Uimezawa ◽  
Susumu Saito
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Local Density ◽  
Oscillator Strengths ◽  
Time Dependent ◽  
Basis Set ◽  
Excitation Spectra ◽  
Functional Theory ◽  
Gradient Correction ◽  
Dependent Density

ABSTRACTWe study tile optical absorption spectra of Na clusters using the time-dependent density-functional theory with gradient correction. A jellium-sphere background model, which is free from basis-set incompleteness error and is suitable for the comparison of various theoretical methods, is adopted. For energies of surface-plasinon excitations governing profiles of photoabsorption spectra with huge oscillator strengths., the gradient correction by van Leeiiwen and Baerends with correct asymptotic behavior of the effective potential is found to show considerable improvement over the time-dependent local-density approximation.

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