Theory of time-dependent nonequilibrium transport through a single molecule in a nonorthogonal basis set

2016 ◽  
Vol 117 (1) ◽  
pp. 57-73 ◽  
Author(s):  
Miloš S. Dražić ◽  
Viktor Cerovski ◽  
Radomir Zikic
Keyword(s):  
Single Molecule ◽  
Time Dependent ◽  
Basis Set ◽  
Nonequilibrium Transport

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>

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.

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.

EGF signaling in bowel carcinoma cells utilizes higher order architectures of EGFR and HER2

2020 ◽  
Author(s):  
Adam J. M. Wollman ◽  
Charlotte Fournier ◽  
Isabel Llorente-Garcia ◽  
Oliver Harriman ◽  
Alex L. Hargreaves ◽  
...  
Keyword(s):  
Single Molecule ◽  
Normal Cell ◽  
Egf Receptor ◽  
Carcinoma Cells ◽  
Time Dependent ◽  
Negative Cooperativity ◽  
Kinetics Modelling ◽  
Preferential Binding ◽  
Epidermal Growth ◽  
Egf Signaling

AbstractEpidermal growth factor (EGF) signaling regulates normal cell development, however EGF receptor (EGFR) overexpression is reported in several carcinomas. Despite structural and biochemical evidence that EGF-EGFR ligation activates signaling through monomer-dimer transitions, live cell mechanistic details remain contentious. We report single-molecule multispectral TIRF of human epithelial carcinoma cells transfected with fluorescent EGFR, and of CHO-K1 cells containing fluorescent EGFR and HER2, enabling super-resolved localization to quantify receptor architectures and spatiotemporal dynamics upon EGF ligation. Using inhibitors that block binding to EGFR, and time-dependent kinetics modelling, we find that pre-activated EGFR consist predominantly of preformed clusters that contain a mixture of EGFR and HER2, whose stoichiometry increases following EGF activation. Although complicated by EGFR internalization and recycling, our observation of an EGFR:EGF stoichiometry >1 for plasma membrane colocalized EGFR/EGF foci soon after activation may indicate preferential binding of EGF ligand to EGFR monomers, negative cooperativity and preferential ligated-unligated dimerization of monomers.

scholarly journals Universal scaling of nonequilibrium transport in the Kondo regime of single molecule devices

2009 ◽  
Vol 79 (16) ◽  
Author(s):  
G. D. Scott ◽  
Z. K. Keane ◽  
J. W. Ciszek ◽  
J. M. Tour ◽  
D. Natelson
Keyword(s):  
Single Molecule ◽  
Nonequilibrium Transport ◽  
Universal Scaling

A density functional theory approach to the magnetic properties of a coupled single-molecule magnet (Mn7)2 complex — An entangled qubit pair candidate

2013 ◽  
Vol 91 (9) ◽  
pp. 866-871 ◽  
Author(s):  
Silvia Gómez-Coca ◽  
Eliseo Ruiz
Keyword(s):  
Density Functional Theory ◽  
Single Molecule ◽  
Exchange Coupling ◽  
Density Functional ◽  
Relative Strength ◽  
Coupling Constants ◽  
Basis Set ◽  
Theory Approach ◽  
Functional Theory ◽  
Spin Configuration

The exchange coupling constants of a Mn14 complex constituted by two weakly coupled Mn7 moieties were calculated using two different density functional theory (DFT) approaches: the Perdew–Burke–Ernzerhof (PBE) functional with a numerical basis set and the hybrid Becke, three-parameter Lee–Yang–Parr (B3LYP) functional employed with a Gaussian basis set. The sign and relative strength of the exchange coupling constants calculated with both methods were consistent; as expected, the values calculated with the PBE functional were slightly overestimated, as corroborated by comparison with the experimental magnetic susceptibility curve. Both methods gave a ground spin configuration of S = 3/2 for the Mn7 moiety, which was weakly antiferromagnetically coupled with the other Mn7 fragment, leading to an S = 0 ground spin configuration for the entire Mn14 complex.

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