scholarly journals Large-Scale Density Functional Theory Transition State Searching in Enzymes

2014 ◽  
Vol 5 (21) ◽  
pp. 3614-3619 ◽  
Author(s):  
Greg Lever ◽  
Daniel J. Cole ◽  
Richard Lonsdale ◽  
Kara E. Ranaghan ◽  
David J. Wales ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Transition State ◽  
Density Functional ◽  
Large Scale ◽  
Functional Theory

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>

scholarly journals Tensor-structured algorithm for reduced-order scaling large-scale Kohn–Sham density functional theory calculations

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Chih-Chuen Lin ◽  
Phani Motamarri ◽  
Vikram Gavini
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Large Scale ◽  
Density Functional Theory Calculations ◽  
System Size ◽  
Real Space ◽  
Functional Theory ◽  
Reduced Order ◽  
Separable Approximation ◽  
Tensor Basis

AbstractWe present a tensor-structured algorithm for efficient large-scale density functional theory (DFT) calculations by constructing a Tucker tensor basis that is adapted to the Kohn–Sham Hamiltonian and localized in real-space. The proposed approach uses an additive separable approximation to the Kohn–Sham Hamiltonian and an L1 localization technique to generate the 1-D localized functions that constitute the Tucker tensor basis. Numerical results show that the resulting Tucker tensor basis exhibits exponential convergence in the ground-state energy with increasing Tucker rank. Further, the proposed tensor-structured algorithm demonstrated sub-quadratic scaling with system-size for both systems with and without a gap, and involving many thousands of atoms. This reduced-order scaling has also resulted in the proposed approach outperforming plane-wave DFT implementation for systems beyond 2000 electrons.

A novel mechanism of spin-orientation dependence of O2 reactivity from first principles methods

2017 ◽  
Vol 7 (5) ◽  
pp. 1040-1044 ◽  
Author(s):  
M. C. S. Escaño ◽  
H. Kasai
Keyword(s):  
Density Functional Theory ◽  
Charge Transfer ◽  
Transition State ◽  
First Principles ◽  
Density Functional ◽  
Orientation Dependence ◽  
Coupling Mechanism ◽  
Spin Moment ◽  
Spin Orientation ◽  
Functional Theory

A novel mechanism of oxygen reaction on a metal surface beyond the present charge transfer or hybridization mechanism, spin-orientation dependence via a coupling mechanism due to the finite spin moment of O2 at the transition state, is obtained using a combination of spin density functional theory (SDFT) and constrained DFT.

scholarly journals Are boat transition states likely to occur in Cope rearrangements? A DFT study of the biogenesis of germacranes

2017 ◽  
Vol 13 ◽  
pp. 1969-1976 ◽  
Author(s):  
José Enrique Barquera-Lozada ◽  
Gabriel Cuevas
Keyword(s):  
Density Functional Theory ◽  
Transition State ◽  
Density Functional ◽  
Chair Conformation ◽  
High Energy ◽  
Functional Theory ◽  
Sigmatropic Rearrangements ◽  
The Density Functional Theory ◽  
Reaction Proceeds ◽  
Cope Rearrangements

It has been proposed that elemanes are biogenetically formed from germacranes by Cope sigmatropic rearrangements. Normally, this reaction proceeds through a transition state with a chair conformation. However, the transformation of schkuhriolide (germacrane) into elemanschkuhriolide (elemane) may occur through a boat transition state due to the final configuration of the elemanschkuhriolide, but this transition state is questionable due to its high energy. The possible mechanisms of this transformation were studied in the density functional theory frame. The mechanistic differences between the transformation of (Z,E)-germacranes and (E,E)-germacranes were also studied. We found that (Z,E)-germacranolides are significantly more stable than (E,E)-germacranolides and elemanolides. In the specific case of schkuhriolide, even when the boat transition state is not energetically favored, a previous hemiacetalization lowers enough the energetic barrier to allow the formation of a very stable elemanolide that is even more stable than its (Z,E)-germacrane.

Plasmonic resonances of nanoparticles from large-scale quantum mechanical simulations

2017 ◽  
Vol 31 (24) ◽  
pp. 1740003 ◽  
Author(s):  
Xu Zhang ◽  
Hongping Xiang ◽  
Mingliang Zhang ◽  
Gang Lu
Keyword(s):  
Density Functional Theory ◽  
Metallic Nanoparticles ◽  
Density Functional ◽  
Large Scale ◽  
Incident Light ◽  
Time Dependent ◽  
Coherent Motion ◽  
Quantum Mechanical ◽  
Functional Theory ◽  
Conduction Electrons

Plasmonic resonance of metallic nanoparticles results from coherent motion of its conduction electrons, driven by incident light. For the nanoparticles less than 10 nm in diameter, localized surface plasmonic resonances become sensitive to the quantum nature of the conduction electrons. Unfortunately, quantum mechanical simulations based on time-dependent Kohn–Sham density functional theory are computationally too expensive to tackle metal particles larger than 2 nm. Herein, we introduce the recently developed time-dependent orbital-free density functional theory (TD-OFDFT) approach which enables large-scale quantum mechanical simulations of plasmonic responses of metallic nanostructures. Using TD-OFDFT, we have performed quantum mechanical simulations to understand size-dependent plasmonic response of Na nanoparticles and plasmonic responses in Na nanoparticle dimers and trimers. An outlook of future development of the TD-OFDFT method is also presented.

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