Basis set dependence using DFT/B3LYP calculations to model the Raman spectrum of thymine

2016 ◽  
Vol 14 (01) ◽  
pp. 1650002 ◽  
Author(s):  
Jakub Bielecki ◽  
Ewelina Lipiec
Keyword(s):  
Raman Spectroscopy ◽  
Ionizing Radiation ◽  
Raman Spectra ◽  
Density Functional ◽  
Surface Enhanced Raman Spectroscopy ◽  
Basis Set ◽  
Basis Sets ◽  
Hydrogen Atoms ◽  
Additional Layer ◽  
Tip Enhanced Raman Spectroscopy

Raman spectroscopy (including surface enhanced Raman spectroscopy (SERS) and tip enhanced Raman spectroscopy (TERS)) is a highly promising experimental method for investigations of biomolecule damage induced by ionizing radiation. However, proper interpretation of changes in experimental spectra for complex systems is often difficult or impossible, thus Raman spectra calculations based on density functional theory (DFT) provide an invaluable tool as an additional layer of understanding of underlying processes. There are many works that address the problem of basis set dependence for energy and bond length consideration, nevertheless there is still lack of consistent research on basis set influence on Raman spectra intensities for biomolecules. This study fills this gap by investigating of the influence of basis set choice for the interpretation of Raman spectra of the thymine molecule calculated using the DFT/B3LYP framework and comparing these results with experimental spectra. Among 19 selected Pople’s basis sets, the best agreement was achieved using 6-31[Formula: see text](d,p), 6-31[Formula: see text](d,p) and 6-11[Formula: see text]G(d,p) sets. Adding diffuse functions or polarized functions for small basis set or use of a medium or large basis set without diffuse or polarized functions is not sufficient to reproduce Raman intensities correctly. The introduction of the diffuse functions ([Formula: see text]) on hydrogen atoms is not necessary for gas phase calculations. This work serves as a benchmark for further research on the interaction of ionizing radiation with DNA molecules by means of ab initio calculations and Raman spectroscopy. Moreover, this work provides a set of new scaling factors for Raman spectra calculation in the framework of DFT/B3LYP method.

Kinetic Isotope and Collision Energy Effects in the Dissociation of Chloride and Bromide Adducts of Aliphatic Alcohols, Benzaldehyde, and 2,4-Pentanedione

2003 ◽  
Vol 56 (5) ◽  
pp. 415 ◽  
Author(s):  
Rodinei Augusti ◽  
Xubin Zheng ◽  
M. Turowski ◽  
R. Graham Cooks
Keyword(s):  
Density Functional ◽  
Collision Energy ◽  
Basis Set ◽  
Cluster Ions ◽  
Basis Sets ◽  
Stable Form ◽  
Triple Quadrupole Mass Spectrometer ◽  
Hydrogen Atoms ◽  
Hartree Fock ◽  
Chloride Adduct

A tandem-in-space triple quadrupole mass spectrometer was used to measure kinetic isotopic effects (KIEs) for the dissociation of chloride and bromide adducts of several compounds that bind halide anions via either hydrogen bonds or by nucleophilic attachment. Two isotopomers of each adduct were simultaneously mass-selected in the first quadrupole and dissociated by collision with argon in the second quadrupole. The KIEs were measured by comparing the extents of dissociation of the lighter versus the heavier isotopomeric adducts. In most cases, lower collision energies and multiple collision conditions favoured larger KIE values, an expected feature of easily dissociated cluster ions considering zero-point energies (ZPEs). The larger chloride adduct of cyclohexanol gave greater KIEs compared with the smaller alcohols, a consequence of slower dissociation due to the larger number of degrees of freedom. Dissociation of the chloride adducts gave greater KIEs than the corresponding bromide adducts, a result that is also consistent with expectations based on ZPEs. Both the chloride and bromide adducts of 2,4-pentanedione, when dissociated at 6 eV collision energy under single-collision conditions, displayed normal KIEs (1.0460 ± 0.0012 and 1.0092 ± 0.0035 respectively). These and the alcohol results were correctly predicted by the ZPEs calculated using commonly applied ab initio Hartree–Fock (HF) and B3LYP density functional theory (DFT) methods with large basis sets (6–311 containing both polarization and diffuse functions). Geometry optimization calculations for the 2,4-pentanedione chloride adduct using either the Restricted Hartree–Fock (RHF) method with a 6–31G* basis set or using the more accurate 6–31++G** method showed that, in the most stable form, the chloride is bonded at multiple sites by a molecule of 2,4-pentanedione. In this structure, chloride binds weakly to both the methylene and the methyl hydrogen atoms. Collision-induced dissociation furnishes chloride and 2,4-pentanedione anion ([M – H]–) as competitive negatively charged products, which is consistent with the proposed structure. It is interesting that the intermolecular KIEs in this study tend to be normal, while intramolecular isotope effects in halides, notably of the type M1Cl+M2 are inverse, as a consequence of the lower ZPEs associated with the heavier isotopomers. The difference in the two systems is that the stronger bonds are found in the products in the case of M1Cl+M2 dissociation but in the reactants in the case of MCl– dissociation.

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>

AlN Nanotubes: A DFT Study of Al-27 and N-14 Electric Field Gradient Tensors

2007 ◽  
Vol 62 (12) ◽  
pp. 711-715 ◽  
Author(s):  
Ahmad Seif ◽  
Mahmoud Mirzaei ◽  
Mehran Aghaie ◽  
Asadollah Boshra
Keyword(s):  
Electric Field ◽  
Electric Field Gradient ◽  
Field Gradient ◽  
Density Functional ◽  
Quadrupole Coupling Constant ◽  
Basis Set ◽  
Basis Sets ◽  
B3lyp Method ◽  
Package Program ◽  
Nqr Parameters

Density functional theory (DFT) calculations were performed to calculate the electric field gradient (EFG) tensors at the sites of aliminium (27Al) and nitrogen (14N) nuclei in an 1 nm of length (6,0) single-walled aliminium nitride nanotube (AlNNT) in three forms of the tubes, i. e. hydrogencapped, aliminium-terminated and nitrogen-terminated as representatives of zigzag AlNNTs. At first, each form was optimized at the level of the Becke3,Lee-Yang-Parr (B3LYP) method, 6-311G∗∗ basis set. After, the EFG tensors were calculated at the level of the B3LYP method, 6-311++G∗∗ and individual gauge for localized orbitals (IGLO-II and IGLO-III) types of basis sets in each of the three optimized forms and were converted to experimentally measurable nuclear quadrupole resonance (NQR) parameters, i. e. quadrupole coupling constant (qcc) and asymmetry parameter (ηQ). The evaluated NQR parameters revealed that the considered model of AlNNT can be divided into four equivalent layers with similar electrostatic properties.With the exception of Al-1, all of the three other Al layers have almost the same properties, however, N layers show significant differences in the magnitudes of the NQR parameters in the length of the nanotube. Furthermore, the evaluated NQR parameters of Al-1 in the Al-terminated form and N-1 in the N-terminated form revealed the different roles of Al (base agent) and of N (acid agent) in AlNNT. All the calculations were carried out using the GAUSSIAN 98 package program.

scholarly journals Theoretical Study of Solvent Effects on the Electronic and Thermodynamic Properties of Tetrathiafulvalene (TTF) Molecule Based on DFT

2021 ◽  
pp. 42-54
Author(s):  
Rabiu Nuhu Muhammad ◽  
N. M. Mahraz ◽  
A. S Gidado ◽  
A. Musa
Keyword(s):  
Thermodynamic Properties ◽  
Bond Length ◽  
Density Functional ◽  
Theoretical Study ◽  
Energy Gap ◽  
Basis Set ◽  
Basis Sets ◽  
Frontier Molecular Orbital ◽  
Orbital Energy ◽  
Chemical Hardness

Tetrathiafulvalene () is an organosulfur compound used in the production of molecular devices such as switches, sensors, nonlinear optical devices and rectifiers. In this work, a theoretical study on the effects of solvent on TTF molecule was investigated and reported based on Density Functional Theory (DFT) as implemented in Gaussian 03 package using B3LYP/6-31++G(d,p) basis set. Different solvents were introduced as a bridge to investigate their effects on the electronic structure. The HUMO, LUMO, energy gap, global chemical index, thermodynamic properties, NLO and DOS analysis of the TTF molecule in order to determine the reactivity and stability of the molecule were obtained. The results obtained showed that the solvents have effects on the electronic and non-linear-optical properties of the molecule. The optimized bond length revealed that the molecule has strong bond in gas phase with smallest bond length of about 1.0834Å than in the rest of the solvents. It was observed that the molecule is more stable in acetonitrile with HOMO-LUMO gap and chemical hardness of 3.6373eV and 1.8187eV respectively. This indicates that the energy gap and chemical hardness of TTF molecule increases with the increase in polarity and dielectric constant of the solvents. The computed results agreed with the results in the literature. The thermodynamics and NLO properties calculation also indicated that TTF molecule has highest value of specific heat capacity (Cv), total dipole moment () and first order hyperpolarizability () in acetonitrile, while acetone has the highest value of entropy and toluene has a slightly higher value of zero point vibrational energy (ZPVE) than the rest of the solvents. The results show that careful selection of the solvents and basis sets can tune the frontier molecular orbital energy gap of the molecule and can be used for molecular device applications.

scholarly journals C2: An Asymmetric Specie ?

2020 ◽  
Author(s):  
Robson de Farias
Keyword(s):  
Chemical Bond ◽  
Raman Spectra ◽  
Density Functional ◽  
Functional Approach ◽  
Ir And Raman Spectra ◽  
Basis Set ◽  
Ir And Raman

<p> The present work is another contribution to a better understanding of the chemical bond in C<sub>2</sub>. Several density functional approach/basis set provided calculated IR and Raman spectra with simultaneous active bands. Hence, the hypothesis of electronic asymmetry in C<sub>2</sub> [1] was reinforced. </p>

A density functional approach toward structural features and properties of C20…N2X2 (X = H, F, Cl, Br, Me) molecules

2014 ◽  
Vol 13 (04) ◽  
pp. 1450023 ◽  
Author(s):  
Reza Ghiasi ◽  
Morteza Zaman Fashami ◽  
Amir Hossein Hakimioun
Keyword(s):  
Density Functional ◽  
Chemical Shifts ◽  
Geometry Optimization ◽  
Structural Features ◽  
Nbo Analysis ◽  
Basis Set ◽  
Basis Sets ◽  
Basis Set Superposition Error ◽  
Homo And Lumo ◽  
Lowest Unoccupied Molecular Orbitals

In this work, the interaction of C 20 with N 2 X 2 ( X = H , F , Cl , Br , Me ) molecules has been explored using the B3LYP, M062x methods and 6-311G(d,p) and 6-311+G(d,p) basis sets. The interaction energies (IEs) obtained with standard method were corrected by basis set superposition error (BSSE) during the geometry optimization for all molecules at the same levels of theory. It was found C 20… N 2 H 2 interaction is stronger than the interaction of other N 2 X 2 ( X = F , Cl , Br , Me ) with C 20. Highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO, respectively) levels are illustrated by density of states spectra (DOS). The nucleus-independent chemical shifts (NICSs) confirm that C 20… N 2 X 2 molecules exhibit aromatic characteristics. Geometries obtained from DFT calculations were used to perform NBO analysis. Also, 14 N NQR parameters of the C 20… N 2 X 2 molecules are predicted.

scholarly journals Double-Hybrid DFT Functionals for the Condensed Phase: Gaussian and Plane Waves Implementation and Evaluation

Molecules ◽  
2020 ◽  
Vol 25 (21) ◽  
pp. 5174
Author(s):  
Frederick Stein ◽  
Jürg Hutter ◽  
Vladimir V. Rybkin
Keyword(s):  
Condensed Phase ◽  
Density Functional ◽  
Plane Waves ◽  
Basis Set ◽  
Basis Sets ◽  
Density Functionals ◽  
Basis Set Superposition Error ◽  
Super Cell ◽  
Long Range Interactions ◽  
Function Correlation

Intermolecular interactions play an important role for the understanding of catalysis, biochemistry and pharmacy. Double-hybrid density functionals (DHDFs) combine the proper treatment of short-range interactions of common density functionals with the correct description of long-range interactions of wave-function correlation methods. Up to now, there are only a few benchmark studies available examining the performance of DHDFs in condensed phase. We studied the performance of a small but diverse selection of DHDFs implemented within Gaussian and plane waves formalism on cohesive energies of four representative dispersion interaction dominated crystal structures. We found that the PWRB95 and ωB97X-2 functionals provide an excellent description of long-ranged interactions in solids. In addition, we identified numerical issues due to the extreme grid dependence of the underlying density functional for PWRB95. The basis set superposition error (BSSE) and convergence with respect to the super cell size are discussed for two different large basis sets.

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