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 Distinctive Supramolecular Features of β-Cyclodextrin Inclusion Complexes with Antidepressants Protriptyline and Maprotiline: A Comprehensive Structural Investigation

2021 ◽  
Vol 14 (8) ◽  
pp. 812
Author(s):  
Thammarat Aree
Keyword(s):  
Inclusion Complexes ◽  
Density Functional ◽  
Water Solubility ◽  
Geometry Optimization ◽  
Binding Constants ◽  
Basis Set ◽  
Full Geometry Optimization ◽  
Basis Set Superposition Error ◽  
X Ray ◽  
Molecular Stability

Depression, a global mental illness, is worsened due to the coronavirus disease 2019 (COVID-2019) pandemic. Tricyclic antidepressants (TCAs) are efficacious for the treatment of depression, even though they have more side effects. Cyclodextrins (CDs) are powerful encapsulating agents for improving molecular stability, water solubility, and lessening the undesired effects of drugs. Because the atomic-level understanding of the β-CD–TCA inclusion complexes remains elusive, we carried out a comprehensive structural study via single-crystal X-ray diffraction and density functional theory (DFT) full-geometry optimization. Here, we focus on two complexes lining on the opposite side of the β-CD–TCA stability spectrum based on binding constants (Kas) in solution, β-CD–protriptyline (PRT) 1—most stable and β-CD–maprotiline (MPL) and 2—least stable. X-ray crystallography unveiled that in the β-CD cavity, the PRT B-ring and MPL A-ring are aligned at a nearly perfect right angle against the O4 plane and primarily maintained in position by intermolecular C–H···π interactions. The increased rigidity of the tricyclic cores is arising from the PRT -CH=CH- bridge widens, and the MPL -CH2–CH2- flexure narrows the butterfly angles, facilitating the deepest and shallower insertions of PRT B-ring (1) and MPL A-ring (2) in the distorted round β-CD cavity for better complexation. This is indicated by the DFT-derived complex stabilization energies (ΔEstbs), although the complex stability orders based on Kas and ΔEstbs are different. The dispersion and the basis set superposition error (BSSE) corrections were considered to improve the DFT results. Plus, the distinctive 3D arrangements of 1 and 2 are discussed. This work provides the first crystallographic evidence of PRT and MPL stabilized in the β-CD cavity, suggesting the potential application of CDs for efficient drug delivery.

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.

scholarly journals Structural characterization of kaempferol: a spectroscopic and computational study

2019 ◽  
Vol 38 (1) ◽  
pp. 49 ◽  
Author(s):  
Dejan Milenković ◽  
Jasmina M Dimitrić Marković ◽  
Dušan Dimić ◽  
Svetlana Jeremić ◽  
Dragan Amić ◽  
...  
Keyword(s):  
Density Functional ◽  
Computational Study ◽  
Chemical Shifts ◽  
Absolute Error ◽  
Nbo Analysis ◽  
Basis Set ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Spectroscopic Characteristics

Calculations based on the density functional theory, with the B3LYP functional and the 6-311++G(d,p) basis set, were performed with the aim of confirming the molecular structure and spectroscopic characteristics of kaempferol, a naturally occurring flavonoid molecule. The electronic structure of kaempferol was examined using NBO analysis. The assigning of the experimentally obtained IR and Raman spectra was performed after the best-fit-based comparison with theoretical spectra. The 13C and 1H NMR experimental spectra were related to the theoretically obtained values of the chemical shifts determined by the GIAO method. The correlation coefficient and the average absolute error values proved B3LYP-D3 to be an adequate method in describing the NMR parameters of kaempferol. Molecular docking analysis was carried out in order to identify the potency of inhibition of the title molecule against human procalcitonin. The inhibition activity was obtained for 10 conformations of ligand inside the protein.

A theoretical study of the 77Se NMR and vibrational spectroscopic properties of SenS8–n ring molecules

2002 ◽  
Vol 80 (11) ◽  
pp. 1435-1443 ◽  
Author(s):  
J Komulainen ◽  
R S Laitinen ◽  
R J Suontamo
Keyword(s):  
Ab Initio ◽  
Density Functional ◽  
Chemical Shifts ◽  
Atomic Orbital ◽  
Geometry Optimization ◽  
Spectroscopic Properties ◽  
Basis Sets ◽  
Orbital Method ◽  
Hybrid Functional ◽  
Ring Molecules

The structures and spectroscopic properties of SenS8–n ring molecules have been studied by the use of ab initio molecular orbital techniques and density functional techniques involving Stuttgart relativistic large core effective core potential approximation with double zeta basis sets for valence orbitals augmented by two polarization functions for both sulfur and selenium. Full geometry optimizations have been carried out for all 30 isomers at the Hartree-Fock level of theory. The optimized geometries and the calculated fundamental vibrations and Raman intensities of the SenS8–n molecules agree closely with experimental information where available. The nuclear magnetic shielding tensor calculations have been carried out by the Gauge-independent atomic orbital method at the DFT level using Becke's three-parameter hybrid functional with Perdew/Wang 91 correlation. The isotropic shielding tensors correlate well with the observed chemical shift data. The calculated chemical shifts provide a definite assignment of the observed 77Se NMR spectroscopic data and can be used in the prediction of the chemical shifts of unknown SenS8–n ring molecules.Key words: selenium sulfides, ab initio, DFT, effective core potentials, geometry optimization, energetics, fundamental vibrations, 77Se chemical shifts.

scholarly journals EXPERIMENTAL CUM THEORETICAL EVALUATION OF MOLECULAR STRUCTURE, VIBRATIONAL SPECTRA, NBO, UV, NMR, OF A BIOACTIVE COMPOUND – PHENOXYACETOHYDRAZIDE

2015 ◽  
Vol 3 (7) ◽  
pp. 103-115
Author(s):  
M. Sangeetha ◽  
R. Mathammal
Keyword(s):  
Molecular Orbital ◽  
Density Functional ◽  
Chemical Shifts ◽  
Atomic Orbital ◽  
Bioactive Compound ◽  
Nbo Analysis ◽  
Basis Set ◽  
Theoretical Evaluation ◽  
Vibrational Assignments ◽  
Key Species

Hydrazide-Hydrazone compounds are key species for a range of bioactivities. The first complete density functional theoretical study of Phenoxyacetohydrazide(PAH) is reported. The normal mode frequencies, intensities and the corresponding vibrational assignments were calculated using the GAUSSIAN 09W set of quantum chemistry codes at the DFT/B3LYP levels of theory using the 6-311++G** basis set. Stability of the molecule arising from hyperconjugative interactions has been probed using NBO analysis. 1H and 13C NMR spectra have been analysed and the chemical shifts were calculated using the gauge independent atomic orbital(GIAO) method. The theoretical UV-Vis spectrum and the electronic properties, such as HOMO(Highest occupied molecular orbital) and LUMO (Lowest unoccupied molecular orbital) were performed by time dependent density functional theory(TD-DFT) approach.

scholarly journals Quantum-chemical study of C— H bond dissociation enthalpies of various small non-aromatic organic molecules

2013 ◽  
Vol 6 (1) ◽  
pp. 64-72 ◽  
Author(s):  
Peter Poliak ◽  
Adam Vagánek
Keyword(s):  
13C Nmr ◽  
Linear Correlation ◽  
Density Functional ◽  
Chemical Shifts ◽  
Basis Set ◽  
Basis Sets ◽  
Nmr Chemical Shifts ◽  
Bond Dissociation ◽  
13C Nmr Chemical Shifts ◽  
Experimental Values

Abstract In this work, C-H bond dissociation enthalpies (BDE) and vertical ionization potentials (IP) for various hydrocarbons and ketones were calculated using four density functional approaches. Calculated BDEs and IPs were correlated with experimental data. The linearity of the corresponding dependences can be considered very good. Comparing two used functionals, B3LYP C-H BDE values are closer to experimental results than PBE0 values for both used basis sets. The 6-31G* basis set employed with both functionals, gives the C-H BDEs closer to the experimental values than the 6-311++G** basis set. Using the obtained linear dependences BDEexp = f (BDEcalc), the experimental values of C-H BDEs for some structurally related compounds can be estimated solely from calculations. As a descriptor of the C-H BDE, the IPs and 13C NMR chemical shifts have been investigated using data obtained from the B3LYP/6-31G* calculations. There is a slight indication of linear correlation between IPs and C-H BDEs in the sets of simple alkanes and alkenes/ cycloalkenes. However, for cycloalkanes and aliphatic carbonyl compounds, no linear correlation was found. In the case of the 13C NMR chemical shifts, the correlation with C-H BDEs can be found for the sets of alkanes and cycloalkanes, but for the other studied molecules, no trends were detected.

scholarly journals Comparative experimental and theoretical study on the molecular structure and spectroscopic properties of sideroxol isolated from Sideritis stricta and its electronic properties

2021 ◽  
Vol 9 (2) ◽  
pp. 94-107
Author(s):  
Akin Azizoglu ◽  
◽  
Zuleyha Ozer ◽  
Carikci Sema ◽  
Turgut Kilic ◽  
...  
Keyword(s):  
Density Functional ◽  
Theoretical Study ◽  
Chemical Shifts ◽  
Molecular Geometry ◽  
Spectroscopic Properties ◽  
Basis Set ◽  
Basis Sets ◽  
Polarization Functions ◽  
Nmr Properties ◽  
Theory And Experiments

Sideroxol, a kaurene diterpene, was obtained from the acetone extract of Sideritis stricta plant. The ground-state molecular geometry, vibrational frequencies, and NMR chemical shifts were also investigated by using various density functional theories and Pople basis sets. The computed geometries are in good conformity with the experimental data. The comparison between theory and experiments indicates that B3LYP and M06 methods with the 6-31G(d) basis set are able to provide satisfactory results for predicting vibrational and NMR properties. There seems to be no significant effect of addition of diffuse and polarization functions in the basis set used herein.

Ab initio MO Optimizations of Osmiumtetracarbonyldihydride and Metallacyclophanes with two Osmium Atoms and their Molecular Complexes with Different Guests

1998 ◽  
Vol 53 (10) ◽  
pp. 1223-1235
Author(s):  
Inge Warttmann ◽  
Günter Häfelinger
Keyword(s):  
Ab Initio ◽  
Density Functional ◽  
Cyano Group ◽  
Single Point ◽  
Molecular Complexes ◽  
Basis Set ◽  
Basis Sets ◽  
Basis Set Superposition Error ◽  
Hartree Fock ◽  
Surprising Effect

AbstractAb initio Hartree-Fock (HF) and density functional (DFT) optimizations on the test m olecule osmiumtetracarbonyldihydride (13) with various basis sets show that the lanl2mb pseudopotential basis set for osmium leads in the HF approximation to more reliable molecular geometries than the DFT calculations. This HF procedure was used for the optimizations of molecular geometries of three isomeric 4,4,4,4,17,17,17,17-octacarbonyl-4,17-diosma[7.7]ortho-, meta- and paracyclophanes 1 to 3, of which 3 was found to be predestined for formation of various host-guest complexes with possible guests benzene (4), fluorobenzene (5), 1,3,5- trifluorobenzene (6), 1,2,4,5-tetrafluorobenzene (7), hexafluorobenzene (8), fluoroanil (9), tetrafluoroethene (10), tetracyanoethene (11) and aniline (12). Results of optimized hostguest geometries are presented graphically for inclusions and associations of guest 4 to 12 with 3. Calculated lanl2mb interaction energies, after correction for basis set superposition error (BSSE), remain favourable only for inclusion of 5 and associations of 5, 10, 11 and 12. Additionally lanl2dz single point calculations for inclusion, which may not need BSSE correction because of the improved basis set, are favourable for 6 and 12. According to lanl2mb HOMO and LUMO energies, 3 may as well easily donate or accept electrons. This may be an interpretation to the surprising effect, that Mulliken total charges are positive on the electron accepting guest molecules 4 to 11. There are geometrical peculiarities in the optimized host-guest complexes for inclusion and association. Fluorine atoms of 5 to 10 and nitrogen atoms of a cyano group of 11 and the amino group of 12 like to come close to one or two carbonyl groups. Similar distances of 2.70 Å to 3.57 Å between the O atom of the carbonyl group and the F atom or N atom appear in all optimizations of inclusion and association of 5 to 12 except in the case of association of tetrafluoroethene (10).

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.

scholarly journals A Combined Experimental (FT-IR) and Computational Studies of 9-Chloroanthracene

2019 ◽  
Vol 31 (6) ◽  
pp. 1332-1342 ◽  
Author(s):  
KATTAESWAR SRIKANTH ◽  
RAMAIAH KONAKANCHI ◽  
JYOTHI PRASHANTH
Keyword(s):  
Density Functional ◽  
Minimum Energy ◽  
Nbo Analysis ◽  
Docking Studies ◽  
Basis Set ◽  
Protein Targets ◽  
Charge Delocalization ◽  
Fukui Functions ◽  
Homo And Lumo ◽  
Ft Ir

The experimental FT-IR spectral analysis of 9-chloroanthracene has worked out by using density functional theory (DFT). The optimized molecular structure and minimum energy of 9-chloroanthracene has analyzed using DFT/B3LYP functional employing 6-311++G(d,p) basis set. The vibrational frequencies along with IR intensities were computed, scaling was used for a better fit between the experimental and computed frequencies, they agreed with rms error 8.48 cm-1 for 9-chloroanthracene. The NLO behaviour of the molecule is investigated from first-order hyperpolarizability. The HOMO and LUMO energies are evaluated to demonstrate the chemical stability, reactivity of molecule. The MESP over the molecules were plotted to evaluate electron density regions and thermodynamic parameters are calculated. Hyper conjugative interactions and charge delocalization of the molecule study from NBO analysis and Fukui functions are evaluated for 9-chloroanthracene. The molecular docking studies were performed against anticancer protein targets Tyrosinase and HER2.

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