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 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.

THE INVESTIGATION ON ELECTRONIC PROPERTIES AND STABILITY OF POLYOXOMETALATES FUNCTIONALIZED BY ORGANOMETALLIC TITANIUM [CpTi · SiW9V3O40]4- BY DENSITY FUNCTIONAL THEORY

2009 ◽  
Vol 08 (04) ◽  
pp. 773-781 ◽  
Author(s):  
YANLING SI ◽  
WEILIN CHEN ◽  
ZHIMING ZHANG ◽  
ENBO WANG
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Molecular Orbitals ◽  
Frontier Molecular Orbitals ◽  
Functional Theory ◽  
Fragment Analysis ◽  
Keggin Type ◽  
System A ◽  
The Stability ◽  
Oxygen Atoms

The electronic structures of [ CpTi · SiW 9 V 3 O 40]4- constructed from Keggin–type polyoxometalates functionalized by CpTi 3+ group have been investigated by Density Functional Theory (DFT) methods. We discuss the relative stability affected by incorporating the CpTi 3+ group into the different sites of the [ SiW 9 V 3 O 40]7- framework on the basis of geometrical parameters, total bonding energies, fragment analysis and frontier molecular orbitals analysis. The calculated results indicated that the structure of the CpTi 3+ group coordinating to one terminal oxygen and two bridging oxygen atoms of the Keggin–type polyoxoanion (system a) is more stable than that to three bridging oxygen atoms (system b). In system a, Ti -Ob1, Ti -Ob2 and Ti - Ot1 are relatively shorter, and as result, it exhibits a more compact and nearly spherical structure of the well-known Keggin–type [ SiW 9 V 3 O 40]7-. Fragment analysis elucidates that there is deviation of ΔE B in systems a and b, which makes a significant contribution to the stability of system a. The stability of different isomeric forms of polyoxoanions appears to be a balance between the stabilizing ΔE O and ΔE E terms and the destabilizing ΔE P term. The relatively small energy differences (ΔE B = 4.26 eV ) between systems a and b arise directly from this balance. Frontier molecular orbitals analysis further confirms the stability order of systems a > b by the difference of the HOMO-LUMO energy gap.

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 Theoretical investigation of the structural and spectroscopic properties of expanded metalloporphyrin complexes

2019 ◽  
Vol 6 (1) ◽  
pp. 181199 ◽  
Author(s):  
Jie Jiang ◽  
Shengwei Guo ◽  
Xiaorong Wang ◽  
Liyan Xu ◽  
Qiang Li ◽  
...  
Keyword(s):  
Excited States ◽  
Density Functional ◽  
Dft Method ◽  
Spectroscopic Properties ◽  
Time Dependent ◽  
Frontier Molecular Orbitals ◽  
Functional Theory ◽  
Long Wavelength ◽  
The Density Functional Theory ◽  
Triplet Excited States

The frontier molecular orbitals, UV–Vis absorption spectra, charge transfer (CT) and triplet excited states of 12 expanded D–A porphyrin/benzoporphyrin complexes were investigated using the density functional theory (DFT) method and time-dependent DFT in this work. The results showed that thiophene was an effective fragment for absorption of ‘long wavelength’, while the benzoporphyrin worked on the ‘short wavelength’, which was derived from its saddle-shaped structure; this expanded D–A conjugated system had a mild CT process with anthraquinone/isoindigo as acceptors and a strong CT process with naphtoquinone as acceptor. In addition, based on the simulation of the triplet state, the theoretical phosphorescence wavelength range of this series of derivatives was between 1000 and 1200 nm. This study is expected to assist the design of conjugated porphyrin for the field of porphyrin chemistry.

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.

Molecular Structures, Rotational Barriers, and Density Functional Theory Studies on 3,5-Diamino-6-(2,3-Dichlorophenyl)-1,2,4-Triazine

2019 ◽  
Vol 892 ◽  
pp. 185-192
Author(s):  
Pek Lan Toh ◽  
Suh Miin Wang
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Molecular Orbitals ◽  
Geometrical Parameters ◽  
Atomic Charges ◽  
Frontier Molecular Orbitals ◽  
Dft Methods ◽  
Functional Theory ◽  
Rotational Barriers ◽  
Total Energies

In this report, different hybrid Density Functional Theory (DFT) methods were utilized to determine the geometries, total energies, Frontier molecular orbitals, atomic charges, and rotational barriers of 3,5-Diamino-6-(2,3-Dichlorophenyl)-1,2,4-Triazine, C9H7Cl2N5 molecular system. All optimized geometrical parameters (i.e. bond lengths, bond angles, and dihedral angles) were then compared with the experimental data, which reported by Sridhar and Ravikumar in 2009 [5]. Also, the results of electronic structures (i.e. total energies, Frontier molecular orbitals, atomic charges, and others) obtained by different DFT methods were compared and discussed.

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>

Understanding the molecular mechanism of the stereoselective conversion of N-trialkylsilyloxy nitronates into bicyclic isoxazoline derivatives

2021 ◽  
Author(s):  
Agnieszka Kącka-Zych ◽  
Radomir Jasinski
Keyword(s):  
Density Functional Theory ◽  
Molecular Mechanism ◽  
Electron Density ◽  
Density Functional ◽  
Dft Method ◽  
Functional Theory ◽  
Molecular Electron ◽  
Molecular Electron Density Theory

Conversion of N-trialkylsilyloxy nitronates into bicyclic isoxazoline derivatives has been explored using Density Functional Theory (DFT) method within the context of the Molecular Electron Density Theory (MEDT) at the B97XD(PCM)/6-311G(d,p)...

scholarly journals 1,3,5-Triaza-7-Phosphaadamantane (PTA) as a 31P NMR Probe for Organometallic Transition Metal Complexes in Solution

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1390 ◽  
Author(s):  
Ilya G. Shenderovich
Keyword(s):  
Chemical Shift ◽  
Transition Metal ◽  
Metal Complexes ◽  
Transition Metal Complexes ◽  
Density Functional ◽  
Molecular Structures ◽  
Basis Sets ◽  
Functional Theory ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Due to the rigid structure of 1,3,5-triaza-7-phosphaadamantane (PTA), its 31P chemical shift solely depends on non-covalent interactions in which the molecule is involved. The maximum range of change caused by the most common of these, hydrogen bonding, is only 6 ppm, because the active site is one of the PTA nitrogen atoms. In contrast, when the PTA phosphorus atom is coordinated to a metal, the range of change exceeds 100 ppm. This feature can be used to support or reject specific structural models of organometallic transition metal complexes in solution by comparing the experimental and Density Functional Theory (DFT) calculated values of this 31P chemical shift. This approach has been tested on a variety of the metals of groups 8–12 and molecular structures. General recommendations for appropriate basis sets are reported.

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