Basis Set Effects in Density Functional Theory Calculation of Muoniated Cytosine Nucleobase

2020 ◽  
Vol 860 ◽  
pp. 282-287
Author(s):  
Wan Nurfadhilah Zaharim ◽  
Shukri Sulaiman ◽  
Saidah Sakinah Mohd Tajudin ◽  
Siti Nuramira Abu Bakar ◽  
Nur Eliana Ismail ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Total Energy ◽  
Density Functional ◽  
Density Functional Theory Calculation ◽  
Geometry Optimization ◽  
Density Functional Theory Method ◽  
Basis Set ◽  
Basis Sets ◽  
Functional Theory ◽  
Muonium Hyperfine

The Density Functional Theory method was employed to investigate the electronic structure and muonium hyperfine interaction of muonium trapped near carbon atom labelled as '5' in cytosine nucleobase. Eighteen different basis sets in combination with B3LYP functional were examined in geometry optimization calculations on the muoniated radical. There are significant quantitative differences in the calculated total energy. The employment of basis set that does not include polarization function produces an optimized structure with high total energy. The 6-311++G(d,p) basis set yielded the lowest total energy as compared to other basis sets. The bond order of muonium trapped at C5 atom is in the range of 0.841 to 0.862. The 6-31G basis set produced the muonium Fermi contact coupling constant that is the closest to the experimental value.

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>

Wechselwirkungen in Molekülkristallen, 166 [1, 2]. Polyiod-Moleküle I2C=CI2, (IC)4S, (IC)4NH, (IC)4N-CH3 und HCI3: Strukturbestimmung nach Kristallzüchtung oder durch Dichtefunktionaltheorie-Berechnung / Interaction in Molecular Crystals, 166 [1, 2], Polyiodo Molecules I2C=CI2, (IC)4S, (IC)4 NH, (IC)4N-CH and HCI3: Structure Determination Following Crystallization or by Density Functional Theory Calculation

2001 ◽  
Vol 56 (1) ◽  
pp. 13-24 ◽  
Author(s):  
Hans Bock ◽  
Sven Holl ◽  
Volker Krenzel
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Crystal Packing ◽  
Density Functional Theory Calculation ◽  
Density Functional Theory Calculations ◽  
Structural Data ◽  
Basis Sets ◽  
Functional Theory ◽  
Donor Acceptor ◽  
Density Functional Theory Optimization

Abstract The structures of tri-and tetraiodo-substituted carbon compounds are determined either expe­rimentally by X-Ray Structure Analysis or, because crystallization of tetraiodothiophene could not be achieved, approximated by Density Functional Theory optimization of structural data from a donor/acceptor complex. The structures show noteworthy details such as a second po­lymorph of tetraiodoethene crystallized by sublimation or herringbone crystal packing patterns of tetraiodopyrrole derivatives. All molecular geometries are discussed and compared based on relativistic density functional theory calculations with 6 -31G* basis sets including iodine pseudopotentials. They reproduce even finer structural details due to van der Waals repulsion of the bulky iodo substituents. Natural Bond Orbital (NBO) charge distributions suggest positive partial charges at all iodine centers with the strongest polarization Cδ㊀ → Iδ㊉ in HCI3, which contains well over 97% iodine.

Fast computation of DFT nuclear gradient with multiresolution*This article is dedicated to Dr. Russell J. Boyd for his distinguished career in chemical research.

2011 ◽  
Vol 89 (6) ◽  
pp. 657-662 ◽  
Author(s):  
Nicholas J. Russ ◽  
Chun-min Chang ◽  
Jing Kong
Keyword(s):  
Density Functional Theory ◽  
Electron Density ◽  
Density Functional ◽  
Density Functional Theory Calculation ◽  
Computational Cost ◽  
Basis Sets ◽  
Local Spin Density Approximation ◽  
Functional Theory ◽  
Exchange Correlation ◽  
The Impact

We present an efficient algorithm for evaluating the exchange-correlation contribution to the nuclear gradients of density-functional theory calculation within the local spin-density approximation. The algorithm is an extension of the multiresolution exchange-correlation (mrXC) method, which treats smooth and compact parts of the electron density separately. The nuclear gradient of the smooth density is calculated on the even-spaced grid while the compact part of the density is handled on the normal atom-centered grid (ACG). The overall formulism is still formally based on the ACG, and thus does not change the results of the existing ACG-based algorithms for all-electron density-functional theory (DFT) calculations. The variation of the positions and weights of ACG owing to the nuclear perturbation is also handled rigorously. Benchmark calculations with different basis sets and sizes of ACG show that mrXC reduces the computational cost by several times without loss of accuracy. It also lessens the impact on the CPU time when the size of the ACG is increased.

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>

A density functional theory study of the free radicals NH2, NF2, NCl2, PH2, PF2, and PCl2

1994 ◽  
Vol 72 (3) ◽  
pp. 695-704 ◽  
Author(s):  
Maggie A. Austen ◽  
Leif A. Eriksson ◽  
Russell J. Boyd
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Local Density ◽  
Basis Set ◽  
Basis Sets ◽  
Functional Theory ◽  
Unpaired Spin ◽  
Non Local ◽  
Local Potentials ◽  
Spin Densities

The linear combination of Gaussian-type orbitals–density functional theory (LCGTO–DFT) approach is used to study geometries and hyperfine structures of a set of neutral radicals. Each of the title molecules is investigated by means of local density approximation calculations, and using the Becke–Perdew and Perdew–Wang–Perdew corrections to the exchange and correlation functionals. The effects of local vs. non-local potentials and of various basis sets are investigated. Total densities and unpaired spin densities are compared. The isotropic couplings are found to be very dependent on the type of exchange functional used, whereas the anisotropic couplings are relatively insensitive to the choice of basis set and functional. In most cases, the Perdew–Wang exchange corrections provide isotropic couplings in satisfactory agreement with experiment.

Ammonia Dissociation on Graphene Oxide: An Ab Initio Density Functional Theory Calculation

2015 ◽  
Vol 229 (7-8) ◽  
Author(s):  
Liangliang Huang ◽  
Keith E. Gubbins
Keyword(s):  
Density Functional Theory ◽  
Graphene Oxide ◽  
Ab Initio ◽  
Functional Groups ◽  
Density Functional ◽  
Density Functional Theory Calculation ◽  
Exothermic Reaction ◽  
Density Functional Theory Method ◽  
Hydroxyl Groups ◽  
Functional Theory

AbstractInteractions of ammonia and water with the oxygen-containing functional groups of graphite oxide have been studied by ab initio density functional theory method. The results show that ammonia can dissociate on the carboxyl, epoxy and hydroxyl groups. The dissociation on the epoxy group is an exothermic reaction with a small activation energy barrier. Water is found to form a hydrogen bond with the carboxyl, epoxy and hydroxyl groups, and thus will block ammonia from interacting with those functional groups. The results in this work provide a fundamental understand of previous experiments about ammonia adsorption on graphene oxide materials.

scholarly journals Vibrational spectra of aniline in gas phase: An ab-initio study

2010 ◽  
Vol 7 (2) ◽  
pp. 449-455
Author(s):  
S. D. S. Chauhan ◽  
A.K. Sharma ◽  
R. Kumar ◽  
D. Kulshreshtha ◽  
R. Gupta ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Basis Set ◽  
Basis Sets ◽  
Ab Initio Study ◽  
Functional Theory ◽  
Hartree Fock ◽  
Modes Of Vibration ◽  
Experimental Findings

Vibrational frequencies of aniline in gas phase have been calculated and each of their modes of vibration assigned properly at RHF and DFT with 6-31G(d) basis set. In the present study, it has been observed that the 6-31G(d) basis set at both RHF and DFT levels of calculations provides better agreement to the experimental findings as compared to other basis sets. Simultaneously, Density functional theory is found to be superior to its counterpart Hartree Fock method.

scholarly journals Ultrasound Assisted Synthesis, Molecular Structure,UV-Visible Assignments, MEP and Mulliken Charges Study of (E)-3-(4-chlorophenyl)-1-(4-methoxyphenyl) prop-2-en-1-one: Experimental and DFT Correlational

2021 ◽  
Vol 18 (1) ◽  
pp. 86-96
Author(s):  
Rohit S. Shinde
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Density Functional Theory Method ◽  
Atomic Charge ◽  
Dft Method ◽  
Basis Set ◽  
Geometrical Parameters ◽  
Functional Theory ◽  
Vibrational Assignments ◽  
Uv Visible

Present investigation deals with the synthesis and density functional theory study (DFT) of a chalcone derivative; (E)-3-(4-chlorophenyl)-1-(4-methoxyphenyl)prop-2-en-1-one (CPMPP). The synthesis of a CPMPP has been carried out by the reaction of 4-methoxyacetophenone and 4-chlorobenzalehyde in ethanol at 30 ℃ under ultrasound irradiation. The structure of a synthesized chalcone is affirmed on the basis of FT-IT, 1H NMR and 13C NMR. The geometry of a CPMPP is optimized by using the density functional theory method at the B3LYP/6-31G(d,p) basis set. The optimized geometrical parameters like bond length and bond angles have been computed. The absorption energies, oscillator strength, and electronic transitions have been derived at the TD-DFT method at the B3LYP/6-31G(d,p) level of theory for B3LYP/6-31G(d p) optimized geometries. The effect of polarity on the absorption energies is discussed by computing UV-visible results in dichloromethane (DCM). Since theoretically obtained wavenumbers are typically higher than experimental wavenumbers, computed wavenumbers were scaled with a scaling factor, and vibrational assignments were made by comparing experimental wavenumbers to scaled theoretical wavenumbers. Quantum chemical parameters have been determined and examined. Molecular electrostatic potential (MEP) surface plot analysis has been carried out at the same level of theory. Mulliken atomic charge study is also discussed in the present study.

scholarly journals Raman Spectroscopy Of Fullerene-Like Molecules Of Silicon Dioxide (SiO2)N(H2O)N/2

2016 ◽  
Vol 17 (3) ◽  
pp. 401-406
Author(s):  
O.V. Filonenko
Keyword(s):  
Density Functional Theory ◽  
Raman Spectroscopy ◽  
Silicon Dioxide ◽  
Density Functional ◽  
Density Functional Theory Method ◽  
Basis Set ◽  
Theory Method ◽  
Cyclic Structure ◽  
Functional Theory ◽  
Exchange Correlation

The Raman spectra of monosilicic, disilicic acid molecules, tetra- and pentasilicic acid molecules with cyclic structure, cage-like okta- and dekasilicic asid molecules, and of fullerene-like molecule (SiO2)N(H2O)N/2 have been calculated using density functional theory method (exchange-correlation functional B3LYP and basis set 6-31G (d, p)) and assignment of frequencies in conformity with the shape fluctuations have been executed.

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