DFT computations on vibrational spectra: Scaling procedures to improve the wavenumbers

2018 ◽  
Vol 3 (6) ◽  
Author(s):  
M. Alcolea Palafox
Keyword(s):  
Density Functional ◽  
Dft Method ◽  
Basis Sets ◽  
Linear Scaling ◽  
Dft Methods ◽  
Functional Theory ◽  
Scale Factors ◽  
Scaling Equation ◽  
B3lyp Method ◽  
Vibrational Wavenumbers

Abstract The performance of ab initio and density functional theory (DFT) methods in calculating the vibrational wavenumbers in the isolated state was analyzed. To correct the calculated values, several scaling procedures were described in detail. The two linear scaling equation (TLSE) procedure leads to the lowest error and it is recommended for scaling. A comprehensive compendium of the main scale factors and scaling equations available to date for a good accurate prediction of the wavenumbers was also shown. Examples of each case were presented, with special attention to the benzene and uracil molecules and to some of their derivatives. Several DFT methods and basis sets were used. After scaling, the X3LYP/DFT method leads to the lowest error in these molecules. The B3LYP method appears closely in accuracy, and it is also recommended to be used. The accuracy of the results in the solid state was shown and several additional corrections are presented.

scholarly journals Experimental and Density Functional Theory Characteristics of Ibrutinib, a Bruton’s Kinase Inhibitor Approved for Leukemia Treatment

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Ali I. Ismail
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Kinase Inhibitor ◽  
Theoretical Calculations ◽  
Dft Method ◽  
Vibrational Frequencies ◽  
Basis Sets ◽  
Electronic Transitions ◽  
Functional Theory ◽  
Leukemia Treatment

Ibrutinib, a Bruton’s tyrosine kinase that plays an essential role in the B-cell development and cancer cells, has been recently approved to treat chronic, lymphocytic, and other types of leukemia. This study focused on investigating ibrutinib by its electronic transitions, vibrational frequencies, and electrospray mass spectra. The experimental peaks for electronic spectrum were found at 248.0 and 281.0 nm, whereas the νC = 0 stretching frequency was found at 1652.4 and 1639.19 cm−1. These experimental properties were compared with the corresponding theoretical calculations in which density functional theory was applied. The optimized structure was obtained with the calculations using a hybrid function (B3LYP) and high-level basis sets [6-311G++(d,p)]. Most of the calculated vibrational frequencies showed a relatively good agreement with the experimental ones. The electronic transitions of ibrutinib calculated using time-dependent DFT method were performed at two different solvation methods: PCM and SMD. The mass spectrum of ibrutinib, its fragments, and its isotopic pattern agreed well with the expected spectra.

Comparison of different theory models and basis sets for the calculation of FbC-M10Iso-Bn geometry and geometries of chlorin-imide and chlorin-isoimide isomeric pairs

2013 ◽  
Vol 17 (05) ◽  
pp. 376-383 ◽  
Author(s):  
Jong-Kil Park ◽  
Sang Joon Choe
Keyword(s):  
Density Functional ◽  
Molecular Geometry ◽  
Basis Sets ◽  
Normal Coordinate ◽  
Dft Methods ◽  
Functional Theory ◽  
X Ray ◽  
Bond Lengths ◽  
X Ray Crystallography ◽  
Isomeric Pairs

Various density functional theory (DFT) methods with different basis sets to predict the molecular geometry of FbC-M10Iso-Bn macrocycle, a chlorin-isoimide, are compared in this study. DFT methods, including M06-2X, B3LYP, LSDA, B3PW91, PBEPBE, and BPV86, are examined. Different basis sets, such as 6-31G*, 6-31+G (d, p), 6-311+G (d, p), 6-311++G (d, p), cc-PVDZ, cc-PVTZ, and cc-PVQZ are also considered. The examined hybrid DFT methods are in agreement with the geometry of X-ray crystallography available for comparison. B3LYP/cc-PVDZ level is particularly consistent with available X-ray crystallography in terms of predicting the geometries of FbC-M10Iso-Bn. Geometries of chlorin-imide and chlorin-isoimide isomeric pairs are described through B3LYP/cc-PVDZ method. The bond lengths of chlorin-isoimide, specifically C13–C14, C14–C15, and C2–C3, increase as bond overlap index decreases because of charge transfer. β-β bond lengths (C2–C3 bond lengths) with a three-substituent benzylcarbamoyl group also increase as bond overlap index decreases compared with other molecules. The bond lengths of chlorin-imide are smaller than those of chlorin-isoimide. Angles with β-β bond lengths, specifically C2–C3–C4 in ring A, also decrease with a three-substituent benzylcarbamoyl group; however, the angles in C1–C2–C3 increase. Potential energy on the surfaces of the chlorin-imide and chlorin-isoimide isomeric pairs is optimized by calculating the total and relative energies at B3LYP/cc-PVDZ level. Results indicate that chlorin-imides are more stable than chlorin-isoimides. Normal-coordinate structural decomposition shows that chlorin-imides exhibit greater deformation than chlorin-isoimides except for FbC-M10Iso-Ph.

scholarly journals Theoretically nanoscale study on ionization of muscimol nano drug in aqueous solution

2015 ◽  
Vol 51 (1) ◽  
pp. 213-219 ◽  
Author(s):  
Farhoush Kiani ◽  
Mehran Abbaszadeh ◽  
Mohammad Pousti ◽  
Fardad Koohyar
Keyword(s):  
Density Functional ◽  
Dft Method ◽  
Acid Dissociation ◽  
Basis Sets ◽  
Acid Dissociation Constant ◽  
Functional Theory ◽  
Hydrogen Bond Formation ◽  
Pka Values ◽  
The Density Functional Theory ◽  
Good Agreement

In the present work, acid dissociation constant (pKa) values of muscimol derivatives were calculated using the Density Functional Theory (DFT) method. In this regard, free energy values of neutral, protonated and deprotonated species of muscimol were calculated in water at the B3LYP/6-31G(d) basis sets. The hydrogen bond formation of all species had been analyzed using the Tomasi's method. It was revealed that the theoretically calculated pKa values were in a good agreement with the existing experimental pKa values, which were determined from capillary electrophoresis, potentiometric titration and UV-visible spectrophotometric measurements.

scholarly journals Coordination Behavior of Ni2+, Cu2+, and Zn2+ in Tetrahedral 1-Methylimidazole Complexes: A DFT/CSD Study

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
Samuel Tetteh
Keyword(s):  
Density Functional ◽  
Population Analysis ◽  
Substantial Reduction ◽  
Nbo Analysis ◽  
Basis Sets ◽  
Dft Methods ◽  
Functional Theory ◽  
Formal Charge ◽  
Coordination Behavior ◽  
The Stability

The interaction between nickel (Ni2+), copper (Cu2+), and zinc (Zn2+) ions and 1-methylimidazole has been studied by exploring the geometries of eleven crystal structures in the Cambridge Structural Database (CSD). The coordination behavior of the respective ions was further investigated by means of density functional theory (DFT) methods. The gas-phase complexes were fully optimized using B3LYP/GENECP functionals with 6-31G∗ and LANL2DZ basis sets. The Ni2+ and Cu2+ complexes show distorted tetrahedral geometries around the central ions, with Zn2+ being a perfect tetrahedron. Natural bond orbital (NBO) analysis and natural population analysis (NPA) show substantial reduction in the formal charge on the respective ions. The interaction between metal d-orbitals (donor) and ligand orbitals (acceptor) was also explored using second-order perturbation of the Fock matrix. These interactions followed the order Ni2+ > Cu2+ > Zn2+ with Zn2+ having the least interaction with the ligand orbitals. Examination of the frontier orbitals shows the stability of the complexes in the order Ni2+ > Cu2+ < Zn2+ which is consistent with the Irving–Williams series.

A DFT INVESTIGATION ON BASIS SET SIZE AND HYDROGEN-BONDING EFFECTS ON 17O AND 2H NQR PARAMETERS

2013 ◽  
Vol 12 (04) ◽  
pp. 1350022 ◽  
Author(s):  
MEHDI D. ESRAFILI ◽  
NAFISEH MOHAMMADIRAD
Keyword(s):  
Density Functional ◽  
Quadrupole Coupling Constant ◽  
Basis Set ◽  
Basis Sets ◽  
Coupling Constant ◽  
Dft Methods ◽  
Functional Theory ◽  
Set Size ◽  
Quadrupole Coupling ◽  
Consistent Basis

A systematic theoretical study on various maleic acid (MA) clusters has been carried out employing density functional theory (DFT) methods. The performance of two different functionals namely B3LYP and M06 in the prediction of geometries, 17 O and 2 H nuclei quadrupole coupling constant (CQ) values of the MA clusters has been assessed comparing the results to those experimental data. For DFT calculations, several basis sets have been used, including the recently developed Jensen's polarization-consistent basis set families, pcJ-n and pcS-n (n = 0,1,2,3). Calculations at the basis set limit indicate that the value of CQ(2 H ) in monomer MA, changes by 0.01–0.04 kHz for each of the final two basis set increments, and seems reasonable to conclusion that the pcJ-3 result is within a few kHz of the basis set limit. Convergence with respect to basis set size was found to be very good, and the pcJ-1 and pcS-1 basis sets provided a good compromise between the basis set limit and computational expense. In most cases, the differences between B3LYP and M06 results for a given basis set are in a range of 1–2%. On the other hand, no systematic changes in the CQ(17 O ) or CQ(2 H ) were found for basis sets larger than double-ζ. Thus, the usual assumption that double-ζ basis set (pcJ-1 and pcS-1) results in the acceptable CQ values, seems to be valid in the case of 17 O and 2 H nuclei.

scholarly journals Density Functional Study of Structures and Electron Affinities of BrO4F/BrO4F-

2009 ◽  
Vol 10 (7) ◽  
pp. 3128-3148 ◽  
Author(s):  
Liangfa Gong ◽  
Jieming Xiong ◽  
Xinmin Wu ◽  
Chuansong Qi ◽  
Wei Li ◽  
...  
Keyword(s):  
Electron Affinity ◽  
Density Functional ◽  
Basis Sets ◽  
Functional Study ◽  
Bond Dissociation Energies ◽  
Electron Affinities ◽  
Dft Methods ◽  
Bond Dissociation ◽  
Dissociation Energies ◽  
B3lyp Method

The structures, electron affinities and bond dissociation energies of BrO4F/BrO4F− species have been investigated with five density functional theory (DFT) methods with DZP++ basis sets. The planar F-Br…O2…O2 complexes possess 3A' electronic state for neutral molecule and 4A' state for the corresponding anion. Three types of the neutral-anion energy separations are the adiabatic electron affinity (EAad), the vertical electron affinity (EAvert), and the vertical detachment energy (VDE). The EAad value predicted by B3LYP method is 4.52 eV. The bond dissociation energies De (BrO4F → BrO4-mF + Om) (m = 1-4) and De- (BrO4F- → BrO4-mF- + Om and BrO4F- → BrO4-mF + Om-) are predicted. The adiabatic electron affinities (EAad) were predicted to be 4.52 eV for F-Br…O2…O2 (3A'← 4A') (B3LYP method).

Effect on frontier molecular orbitals of substituents in 5-position of uracil base pairs in vacuum and water

2017 ◽  
Vol 16 (07) ◽  
pp. 1750066 ◽  
Author(s):  
Ayhan Üngördü ◽  
Nurten Tezer
Keyword(s):  
Density Functional ◽  
Dft Method ◽  
Molecular Orbitals ◽  
Basis Sets ◽  
Frontier Molecular Orbitals ◽  
Base Pairs ◽  
Band Theory ◽  
Functional Theory ◽  
Single Nanowires ◽  
Uracil Base

The most stable structure of 5-substituted uracil base pairs and metal-mediated-5-substituted uracil complexes are determined. Density functional theory (DFT) method is used in the calculations which are carried out both in vacuum and water. LANL2DZ and 6–311[Formula: see text]G(d,p) basis sets are used for metals and the rest atoms, respectively. Effects on frontier molecular orbitals and energy gaps of substituents in 5-position of uracil base pairs in vacuum and water are found. Conductivity of base pairs or complexes are investigated for single nanowires studied by band theory. It is expected that this study will be an example for future studies that require new nanotechnological applications.

scholarly journals Vibrational Spectroscopy Investigation Using Ab Initio and Density Functional Theory Analysis on the Structure oftert-Butyl 3a-Chloroperhydro-2,6a-epoxyoxireno[e]isoindole-5-carboxylate

2013 ◽  
Vol 2013 ◽  
pp. 1-13
Author(s):  
Hakan Arslan ◽  
Aydin Demircan ◽  
Gun Binzet ◽  
Ilhan Ozer Ilhan
Keyword(s):  
Title Compound ◽  
Density Functional ◽  
Standard Condition ◽  
Vibrational Frequencies ◽  
Basis Sets ◽  
Dft Methods ◽  
Functional Theory ◽  
Harmonic Vibrations ◽  
Infrared Intensities ◽  
Experimental Geometry

The molecular structure, vibrational frequencies, and infrared intensities of thetert-butyl 3a-chloroperhydro-2,6a-epoxyoxireno[e]isoindole-5-carboxylate were calculated by the HF and DFT (BLYP and B3LYP) methods using 6-31G(d) and 6-31G(d,p) basis sets. The FT infrared spectrum of the solid sample was measured under standard condition. We obtained two stable conformers for the title compound; however Conformer 1 is approximately 0.2 kcal/mol more stable than the Conformer 2. The comparison of the theoretical and experimental geometry of the title compound shows that the X-ray parameters fairly well reproduce the geometry of Conformer 2. Comparison of the observed fundamental vibrational frequencies of the title molecule and calculated results by HF and DFT methods indicates that B3LYP is superior for molecular vibrational problems. The harmonic vibrations computed by the B3LYP/6-31G(d,p) method are in a good agreement with the observed IR spectral data. Theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions (PEDs) using VEDA 4 program.

scholarly journals Infrared and Raman Spectra of and Isotopomers: A DFT-PT2 Anharmonic Study

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Andrea Alparone
Keyword(s):  
Raman Spectra ◽  
Density Functional ◽  
Basis Set ◽  
Functional Theory ◽  
B3lyp Method ◽  
Cyclic Molecules ◽  
Out Of Plane ◽  
Stretching Vibration ◽  
Ir And Raman ◽  
Vibrational Wavenumbers

IR and Raman spectra of selenophene and of its perdeuterated isotopomer have been obtained in gas phase through density-functional theory (DFT) computations. Vibrational wavenumbers have been calculated using harmonic and anharmonic second-order perturbation theory (PT2) procedures with the B3LYP method and the 6-311 basis set. Anharmonic overtones have been determined by means of the PT2 method. The introduction of anharmonic terms decreases the harmonic wavenumbers, giving a significantly better agreement with the experimental data. The most significant anharmonic effects occur for the C–H and C–D stretching modes, the observed H/D isotopic wavenumber redshifts being satisfactorily reproduced by the PT2 computations within 6–20 cm−1(1–3%). In the spectral region between 500 cm−1and 1500 cm−1, the IR spectra are dominated by the out-of-plane C–H (C–D) bending transition, whereas the Raman spectra are mainly characterized by a strong peak mainly attributed to the C=C + C–C bonds stretching vibration with the contribution of the in-plane C–H (C–D) bending deformation. The current results confirm that the PT2 approach combined with the B3LYP/6-311 level of calculation is a satisfactory choice for predicting vibrational spectra of cyclic molecules.

Study on vibrational spectroscopy, molecular property, UV-VIS, HOMO-LUMO energies and MEP analysis of N-[2-(4-Bromo-benzoyl)-benzofuran-3-yl]-acrylamide monomer by DFT method

2021 ◽  
Vol 51 (1) ◽  
pp. 69-79
Author(s):  
Esra Barim ◽  
Feride Akman
Keyword(s):  
Density Functional ◽  
Chemical Reactivity ◽  
Atomic Orbital ◽  
Molecular Geometry ◽  
Dft Method ◽  
Polymer Science ◽  
Dft Methods ◽  
Content Type ◽  
B3lyp Method ◽  
Acrylamide Monomer

Purpose This study aimed the synthesis and theoretical/experimental characterization of novel benzofuran-based acrylamide monomer. Design/methodology/approach Novel N-substituted acrylamide monomer, i.e. N-[2–(4-Bromo-benzoyl)-benzofuran-3-yl]-acrylamide (BBFA), was synthesized by reacting (3-Amino-benzofuran-2-yl)-(4-bromophenyl) methanone with acryloylchloride at 0–5oC. Nuclear magnetic resonance (1H-NMR), infrared (FT-IR) and UV-Visible spectrophotometer were used to elucidate the chemical structure of BBFA. Computational studies were performed using the DFT (B3LYP) method on the basis of 6-31 + G (d, p) using Gaussian 09 W and Gauss View 5.0 package in addition to the VEDA program, gauge-independent atomic orbital (GIAO) and time-dependent density functional theory (TD-DFT) methods. Findings Molecular geometry and vibration assignments of the BBFA monomer were calculated. The molecular structure of the monomer was examined. Both longest and shortest bonds were determined in the structure. The nucleophilic and electrophilic regions of the monomer were determined. The theoretical spectroscopic data of the monomer were compared with the experimental data; both were consistent with each other. The chemical reactivity of the monomer was also determined. Originality/value The synthesized BBFA monomer can be evaluated in many areas; from medicine to industry (such as textiles) owing to the presence of various active functional groups. Indeed, acrylamide copolymers are remarkable materials for polymer science and industry. The data produced in this study is original and adds to the scientific community.

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