scholarly journals A simple computational approach for pKa calculation of organosulfur compounds

2020 ◽  
pp. 42-42
Author(s):  
Syed Ali ◽  
Aneesa Choudhary ◽  
Majid Khalil ◽  
Arif Zubair
Keyword(s):  
Density Functional ◽  
Dft Method ◽  
Computational Approach ◽  
Basis Set ◽  
Basis Sets ◽  
Organosulfur Compounds ◽  
Pka Values ◽  
Pka Calculation ◽  
Main Emphasis ◽  
Diffuse Function

The present work is related to predicting the pKa values of organosulfur compounds through Density Functional Theory (DFT). In this study 22 organo-sulfur compounds have been considered to calculate theoretical pKa values. Main emphasis has been given on the substitution of different groups on the Sulfur atom. The computations were performed in the presence of Dimethyl sulfoxide (DMSO) as solvent. Experimentally the order of increase of acidity is; Sulfides < < Sulfoxides < Sulfones. Our computed pKa values also follow the same order. The theoretical pKa values are computed using the DFT method B3LYP, with the basis sets 6-31G(d), 6-31+G(d,p) and IEFPCM bulk solvation model. The majority of computed pKa values are in excellent agreement with the experimental ones through the diffuse function basis set. Hence this computational approach, B3LYP/6-31+G(d,p)/IEFPCM, could be utilized to predict the pKa values of these types of organosulfur compounds.

scholarly journals A Statistically Supported Antioxidant Activity DFT Benchmark—The Effects of Hartree–Fock Exchange and Basis Set Selection on Accuracy and Resources Uptake

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 5058
Author(s):  
Maciej Spiegel ◽  
Andrzej Gamian ◽  
Zbigniew Sroka
Keyword(s):  
Density Functional ◽  
Optimal Level ◽  
Basis Set ◽  
Basis Sets ◽  
Linear Regression Models ◽  
Functional Theory ◽  
Hartree Fock ◽  
Diffuse Function ◽  
Vertical Electron Affinity ◽  
High Level

Polyphenolic compounds are now widely studied using computational chemistry approaches, the most popular of which is Density Functional Theory. To ease this process, it is critical to identify the optimal level of theory in terms of both accuracy and resource usage—a challenge we tackle in this study. Eleven DFT functionals with varied Hartree–Fock exchange values, both global and range-separated hybrids, were combined with 14 differently augmented basis sets to calculate the reactivity indices of caffeic acid, a phenolic acid representative, and compare them to experimental data or a high-level of theory outcome. Aside from the main course, a validation of the widely used Janak’s theorem in the establishment of vertical ionization potential and vertical electron affinity was evaluated. To investigate what influences the values of the properties under consideration, linear regression models were developed and thoroughly discussed. The results were utilized to compute the scores, which let us determine the best and worst combinations and make broad suggestions on the final option. The study demonstrates that M06–2X/6–311G(d,p) is the best fit for such research, and, curiously, it is not necessarily essential to include a diffuse function to produce satisfactory results.

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.

New Chalcone Derivative: Synthesis, Characterization, Computational Studies and Antioxidant Activity

2019 ◽  
Vol 17 (1) ◽  
pp. 46-53
Author(s):  
Reşat Ustabaş ◽  
Nevin Süleymanoğlu ◽  
Namık Özdemir ◽  
Nuran Kahriman ◽  
Ersan Bektaş ◽  
...  
Keyword(s):  
Antioxidant Activity ◽  
Density Functional ◽  
Computational Study ◽  
Dft Method ◽  
Basis Set ◽  
Basis Sets ◽  
Isomeric Form ◽  
Compound I ◽  
Chalcone Derivative ◽  
Reducing Ability

A new chalcone derivative, called as 1-(4-(benzylideneamino)phenyl)-3-(furan-2-yl)prop-2- en-1-one (I), was synthezised and characterized by spectral methods (infrared (IR) and proton and carbon- 13 nuclear magnetic resonance (1H- and 13C-NMR) spectroscopy). A computational study was performed by the density functional theory (DFT) method. Spectral data of compound I optimized by using 6-311G(d,p) and 6-311++G(d,p) basis sets were obtained by 6-311++G(d,p) basis set. The E-Z isomerism for newly synthesized chalcone derivative was investigated by considering four isomeric form, E/E, E/Z, Z/E and Z/Z. The results show that, as assumed and thus named, the chalcone derivative is in the E/E form. In addition, quantum chemical parameters were calculated by using DFT method with 6-311++G(d,p) basis set. Antioxidant activity of compound I was determined by the ferric reducing ability of plasma (FRAP) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay methods. Compound I has low antioxidant activity.

scholarly journals THEORETICAL EVALUATION OF THE pKa VALUES OF 5-SUBSTITUED URACIL DERIVATIVES

2018 ◽  
Vol 55 (6A) ◽  
pp. 63
Author(s):  
Pham Le Nhan ◽  
Nguyen Tien Trung
Keyword(s):  
Density Functional ◽  
Basis Set ◽  
Basis Sets ◽  
Stable Form ◽  
Dft Methods ◽  
Theoretical Evaluation ◽  
Pka Values ◽  
Uracil Derivatives ◽  
Solvation Energies ◽  
Gaussian Basis Set

Density functional theory (DFT) calculations using numerical basis sets were employed to predict the solvation energies, Gibbs free energies and pKa values of a series of 5-substituted uracil derivatives. Obtained results show that solvation energies are not significantly different between DFT methods using the numerical (DNP) and Gaussian basis set (aug-cc-pVTZ). It is noteworthy that the independent and suitable solvation energy of proton of -258.6 kcal/mol has been proposed for the evaluation of pKa values in conjunction with the numerical basis set. In addition, the calculated pKa values suggest that the anti-conformation of 5-formyluracil is the most stable form in the aqueous solution. 

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.

Quantum-Chemical Ab Initio Calculations on Inda- and Thallabenzene (C5H5In and C5H5Tl) and their Structural Isomers η5-C5H5In and η5-C5H5Tl

2018 ◽  
Vol 71 (3) ◽  
pp. 102
Author(s):  
Emma Persoon ◽  
Yuekui Wang ◽  
Gerhard Raabe
Keyword(s):  
Ab Initio ◽  
Quantum Chemical ◽  
Density Functional ◽  
Single Point ◽  
Normal Modes ◽  
Dft Method ◽  
Basis Sets ◽  
Triplet States ◽  
Structural Isomers ◽  
Td Dft

Quantum-chemical ab initio, time-independent, as well as time-dependent density functional theory (TD-DFT) calculations were performed on the so far elusive heterocycles inda- and thallabenzene (C5H5In and C5H5Tl), employing several different methods (MP2, CISD, CCSD, CCSD(T), BD, BD(T), QCISD, QCISD(T), CASSCF, DFT/B3LYP), effective core potentials, and different basis sets. While calculations on the MP2 level predict the ground states of the title compounds to be singlets with the first triplet states between 13 and 15 kcal mol−1 higher in energy, single point calculations with the QCISD(T), CCSD(T), and BD(T) methods at CCSD-optimized structures result in energy differences between the singlet and the triplet states in the range between 0.3 and 2.1 kcal mol−1 in favour of the triplet states. According to a CASSCF(8,8) calculation the triplets are also more stable by about 2.5–2.9 kcal mol−1. Calculations were also performed for the C5v-symmetric η5 structural isomers (cyclopentadienylindium, CpIn, and cyclopentadienylthallium, CpTl, Cp = C5H5) of the title compounds. At the highest level of theory employed in this study, C5H5In is between 79 and 88 kcal mol−1 higher in energy than CpIn, while this energy difference is even larger for thallabenzene where C5H5Tl is energetically between 94 and 102 kcal mol−1 above CpTl. In addition we report on the UV/vis spectra calculated with a TD-DFT method as well as on the spectra of the normal modes of C5H5In and C5H5Tl. Both types of spectra might facilitate identification of the title compounds eventually formed in photolysis or pyrolysis experiments.

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 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.

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.

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