Computation of large systems with an economic basis set: Structures and reactivity indices of nucleic acid base pairs from density functional theory

2007 ◽  
Vol 28 (5) ◽  
pp. 967-974 ◽  
Author(s):  
W. J. Fan ◽  
R. Q. Zhang ◽  
Shubin Liu
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Basis Set ◽  
Acid Base ◽  
Base Pairs ◽  
Functional Theory ◽  
Reactivity Indices ◽  
Economic Basis ◽  
Nucleic Acid Base ◽  
Large Systems

Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment

2001 ◽  
Vol 114 (12) ◽  
pp. 5149-5155 ◽  
Author(s):  
Marcus Elstner ◽  
Pavel Hobza ◽  
Thomas Frauenheim ◽  
Sándor Suhai ◽  
Efthimios Kaxiras
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bonding ◽  
Nucleic Acid ◽  
Density Functional ◽  
Stacking Interactions ◽  
Acid Base ◽  
Base Pairs ◽  
Functional Theory ◽  
Nucleic Acid Base

COMPUTATION OF LARGE SYSTEMS WITH AN ECONOMIC BASIS SET: AB INITIO CALCULATIONS OF BIOLOGICAL NUCLEIC ACID BASE PAIRS

2006 ◽  
Vol 05 (spec01) ◽  
pp. 411-420 ◽  
Author(s):  
WENJIE FAN ◽  
RUIQIN ZHANG
Keyword(s):  
Nucleic Acid ◽  
Single Point ◽  
Basis Set ◽  
Basis Sets ◽  
Mulliken Charge ◽  
Acid Base ◽  
Base Pairs ◽  
Point Energy ◽  
Economic Basis ◽  
Nucleic Acid Base

We show that an economic basis set, in which the polarization functions are considered only for oxygen and nitrogen atoms of strong electronegativity, can be used to determine reliable structures of nucleic acid base pairs. Mulliken charge analysis and the HOMO-LUMO gap in single-point energy calculations using standard basis sets on the geometric structures optimized with the economic basis set found reasonable agreements with the ones of standard calculations. This study is expected to provide a general guideline for basis set selection in the computation of large biological systems being performed with considerable high accuracy, using a low cost computation resource.

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>

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