Parametrization of an Empirical Correction Term to Density Functional Theory for an Accurate Description of π-Stacking Interactions in Nucleic Acids

2007 ◽  
Vol 111 (45) ◽  
pp. 13124-13134 ◽  
Author(s):  
Jean-Marie Ducéré ◽  
Luigi Cavallo
Keyword(s):  
Density Functional Theory ◽  
Nucleic Acids ◽  
Density Functional ◽  
Correction Term ◽  
Accurate Description ◽  
Stacking Interactions ◽  
Functional Theory ◽  
Empirical Correction ◽  
Π Stacking

An Empirical Correction Term to Density Functional Theory for the Description of the TiCl4-Lewis Base Complexes

2007 ◽  
Vol 260 (1) ◽  
pp. 122-126 ◽  
Author(s):  
Luigi Cavallo ◽  
Rosalisa Fedele ◽  
Giampiero Morini ◽  
Jean-Marie Ducéré ◽  
Andrea Melchior ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Correction Term ◽  
Lewis Base ◽  
Functional Theory ◽  
Empirical Correction

6-Bromoindigo dye

2012 ◽  
Vol 68 (4) ◽  
pp. o160-o163 ◽  
Author(s):  
David J. Szalda ◽  
Keith Ramig ◽  
Olga Lavinda ◽  
Zvi C. Koren ◽  
Lou Massa
Keyword(s):  
Density Functional Theory ◽  
Quantum Theory ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Stacking Interactions ◽  
Inversion Center ◽  
Asymmetric Unit ◽  
Functional Theory ◽  
Bond Lengths ◽  
Type C

6-Bromoindigo (MBI) [systematic name: 6-bromo-2-(3-oxo-2,3-dihydro-1H-indol-2-ylidene)-2,3-dihydro-1H-indol-3-one], C16H9BrN2O2, crystallizes with one disordered molecule in the asymmetric unit about a pseudo-inversion center, as shown by the Br-atom disorder of 0.682 (3):0.318 (3). The 18 indigo ring atoms occupy two sites which are displaced by 0.34 Å from each other as a result of this packing disorder. This difference in occupancy factors results in each atom in the reported model used to represent the two disordered sites being 0.08 Å from the higher-occupancy site and 0.26 Å from the lower-occupancy site. Thus, as a result of the disorder, the C—Br bond lengths in the disordered components are 0.08 and 0.26 Å shorter than those found in 6,6′-dibromoindigo (DBI) [Süsse & Krampe (1979).Naturwissenschaften,66, 110], although the distances within the indigo ring are similar to those found in DBI. The crystals are also twinned by merohedry. Stacking interactions and hydrogen bonds are similar to those found in the structures of indigo and DBI. In MBI, an interaction of the type C—Br...C replaces the C—Br...Br interactions found in DBI. The interactions in MBI were calculated quantum mechanically using density functional theory and the quantum theory of atoms in molecules.

scholarly journals Anticancer Indole-Based Chalcones: A Structural and Theoretical Analysis

Molecules ◽  
2019 ◽  
Vol 24 (20) ◽  
pp. 3728 ◽  
Author(s):  
Farid A. Badria ◽  
Saied M. Soliman ◽  
Saleh Atef ◽  
Mohammad Shahidul Islam ◽  
Abdullah Mohammed Al-Majid ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Theoretical Analysis ◽  
Dft Calculations ◽  
Density Functional ◽  
Chemical Potential ◽  
Chemical Reactivity ◽  
Stacking Interactions ◽  
Functional Theory ◽  
Topology Analysis ◽  
Reactivity Indices

The crystal structures of five new chalcones derived from N-ethyl-3-acetylindole with different substituents were investigated: (E)-3-(4-bromophenyl)-1-(1-ethyl-1H-indol-3-yl)prop-2-en-1-one (3a); (E)-3-(3-bromophenyl)-1-(1-ethyl-1H-indol-3-yl)prop-2-en-1-one (3b); (E)-1-(1-ethyl-1H-indol-3-yl)-3-(4-methoxyphenyl)prop-2-en-1-one (3c); (E)-1-(1-ethyl-1H-indol-3-yl)-3-mesitylprop-2-en-1-one (3d); and (E)-1-(1-ethyl-1H-indol-3-yl)-3-(furan-2-yl)prop-2-en-1-one (3e). The molecular packing of the studied compounds is controlled mainly by C–H⋅⋅⋅O hydrogen bonds, C–H⋅⋅⋅π interactions, and π···π stacking interactions, which were quantitatively analyzed using Hirshfeld topology analysis. Using density functional theory (DFT) calculations, the order of polarity (3b ˂ 3d ˂ 3e ˂ 3a ˂ 3c) was determined. Several chemical reactivity indices such as the ionization potential (I), electron affinity (A), chemical potential (μ), hardness (η), electrophilicity (ω) and nucleophilicity (N) indices were calculated, and these properties are discussed and compared. In addition, the antiproliferative activity of the five new chalcones was studied.

scholarly journals Novel Cd (II) Coordination Polymers Afforded with EDTA or Trans-1,2-Cdta Chelators and Imidazole, Adenine, or 9-(2-Hydroxyethyl) Adenine Coligands

Crystals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 391
Author(s):  
Jeannette Carolina Belmont-Sánchez ◽  
María Eugenia García-Rubiño ◽  
Antonio Frontera ◽  
Antonio Matilla-Hernández ◽  
Alfonso Castiñeiras ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Coordination Polymers ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Aqua Ligand ◽  
Stacking Interactions ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Mixed Ligands

Three mixed-ligands of Cd(II) coordination polymers were unintentionally obtained: {[Cd(µ3-EDTA)(Him)·Cd(Him)(H2O)2]·H2O}n (1), {[Cd(µ4-CDTA)(Hade)·Cd(Hade)2]}n (2), and {[Cd(µ3-EDTA)(H2O)·Cd(H9heade)(H2O)]·2H2O}n (3), having imidazole (Him), adenine (Hade) or 9-(2-hydroxyethyl)adenine (9heade) as the N-heterocyclic coligands. Compounds 2 and 3 were obtained by working with an excess of corresponding N-heterocyclic coligands. The single-crystal X-ray diffraction structures and thermogravimetric analyses are reported. The chelate moieties in all three compounds exhibit hepta-coordinated Cd centers, whereas the non-chelated Cd center is five-coordinated in 1 and six-coordinated in 2 and 3. Him and Hade take part in the seven-coordinated chelate moieties in 1 and 2, respectively. In contrast, 9heade is unable to replace the aqua ligand of the chelate [Cd (EDTA) (H2O)] moiety in 3. The thermogravimetric analysis (TGA) behavior of [Cd (H2EDTA) (H2O)]·2H2O in 1 and 3 leads to a residue of CdO, whereas the N-rich compound 2 yields CdO·Cd(NO3)2 as a residue. Density functional theory (DFT) calculations along with molecular electrostatic potential (MEP) and quantum theory of atoms-in-molecules computations were performed in adenine (compound 2) and (2-hydroxyethyl)adenine (compound 3) to analyze how the strength of the H-bonding and π-stacking interactions, respectively, are affected by their coordination to the Cd-metal center.

Accurate description of hybridized local and charge-transfer excited-state in donor–acceptor molecules using density functional theory

RSC Advances ◽  
2016 ◽  
Vol 6 (110) ◽  
pp. 108404-108410 ◽  
Author(s):  
Y. Y. Pan ◽  
J. Huang ◽  
Z. M. Wang ◽  
S. T. Zhang ◽  
D. W. Yu ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Excited State ◽  
Charge Transfer ◽  
Ground State ◽  
Density Functional ◽  
Accurate Description ◽  
Functional Theory ◽  
Donor Acceptor ◽  
Acceptor Molecules

The ωB97X was the most reliable functional for the accurate description of HLCT state at ground state and excited state.

Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment

2012 ◽  
Vol 18 (39) ◽  
pp. 12372-12387 ◽  
Author(s):  
Judith M. Fonville ◽  
Marcel Swart ◽  
Zuzana Vokáčová ◽  
Vladimír Sychrovský ◽  
Judit E. Šponer ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Nucleic Acids ◽  
Density Functional ◽  
Chemical Shifts ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Comparison With Experiment
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