Multiple N—H...NC, C—H...NC and nitrile...π interactions in 4,4′-bipyridine-1,1′-diium bis(1,1,3,3-tetracyano-2-ethoxypropenide): structure determination and DFT calculations of anion...π cation interaction energies

2015 ◽  
Vol 71 (8) ◽  
pp. 658-663 ◽  
Author(s):  
Fatima Setifi ◽  
David K. Geiger ◽  
Ibrahim Abdul Razak ◽  
Zouaoui Setifi
Keyword(s):  
Density Functional ◽  
Rotation Axis ◽  
Interaction Energies ◽  
Materials Chemistry ◽  
Inversion Center ◽  
Asymmetric Unit ◽  
Functional Theory ◽  
Π Interactions ◽  
Electronic Delocalization ◽  
Sheet Structure

Polynitrile anions are important in both coordination chemistry and molecular materials chemistry, and are interesting for their extensive electronic delocalization. The title compound crystallizes with two symmetry-independent half 4,4′-bipyridine-1,1′-diium (bpyH22+) cations and two symmetry-independent 1,1,3,3-tetracyano-2-ethoxypropenide (tcnoet−) anions in the asymmetric unit. One of the bpyH22+ions is located on a crystallographic twofold rotation axis (canted pyridine rings) and the other is located on a crystallographic inversion center (coplanar pyridine rings). The ethyl group of one of the tcnoet−anions is disordered over two sites with equal populations. The extended structure exhibits two separate N—H...NC hydrogen-bonding motifs, which result in a sheet structure parallel to (010), and weak C—H...NC hydrogen bonds form joined rings. Two types of multicenter CN...π interactions are observed between the bpyH22+rings and tcnoet−anions. An additonal CN...π interaction between adjacent tcnoet−anions is observed. Using density functional theory, the calculated attractive energy between cation and anion pairs in the tcnoet−...π(bipyridinediium) interactions were found to be 557 and 612 kJ mol−1for coplanar and canted bpyH22+cations, respectively.

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.

Hydrogen bonding and π–π interactions in the cocrystal salt [Fe(bpe)2(H2O)4](TCEP)2·2(bpe) [bpe is trans-1,2-bis(pyridin-4-yl)ethene and TCEP is 1,1,3,3-tetracyano-2-ethoxypropenide]

2019 ◽  
Vol 75 (3) ◽  
pp. 348-353
Author(s):  
Abderrezak Addala ◽  
David K. Geiger ◽  
Zouaoui Setifi ◽  
Fatima Setifi
Keyword(s):  
Hydrogen Bonding ◽  
Density Functional ◽  
Complex Cation ◽  
Electron Delocalization ◽  
Coordination Geometry ◽  
Inversion Center ◽  
Functional Theory ◽  
Π Interactions ◽  
Distorted Octahedral Coordination Geometry ◽  
Distorted Octahedral

The cocrystal salt tetraaquabis[trans-1,2-bis(pyridin-4-yl)ethene-κN]iron(II) bis(1,1,3,3-tetracyano-2-ethoxypropenide)–trans-1,2-bis(pyridin-4-yl)ethene (1/2), [Fe(C12H10N2)2(H2O)4](C9H5N4O)2·2C12H10N2, is a rare example of a mononuclear FeII compound with trans-1,2-bis(pyridin-4-yl)ethane (bpe) ligands. The complex cation resides on a crystallographically imposed inversion center and exhibits a tetragonally distorted octahedral coordination geometry. Both the symmetry-independent bpe ligand and the cocrystallized bpe molecule are essentially planar. The 1,1,3,3-tetracyano-2-ethoxypropenide counter-ion is nonplanar and the bond lengths are consistant with significant electron delocalization. The extended structure exhibits an extensive O—H...N hydrogen-bonding network with layers of complex cations joined by the cocrystallized bpe. Both the coordinated and the cocrystallized bpe are involved in π–π interactions. Hirshfeld and fingerprint plots reveal the important intermolecular interactions. Density functional theory was used to estimate the strengths of the hydrogen-bonding and π–π interactions, and suggest that the O—H...N hydrogen bonds enhance the strength of the π-interactions by increasing the polarization of the pyridine rings.

Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

On the Nature of Halide-Water Interactions: Insights from Many-Body Representations and Density Functional Theory

2019 ◽  
Author(s):  
Brandon B. Bizzarro ◽  
Colin K. Egan ◽  
Francesco Paesani
Keyword(s):  
Density Functional Theory ◽  
Charge Transfer ◽  
Molecular Orbital ◽  
Density Functional ◽  
Decomposition Analysis ◽  
Orbital Energy ◽  
Energy Decomposition Analysis ◽  
Interaction Energies ◽  
Many Body ◽  
Functional Theory

<div> <div> <div> <p>Interaction energies of halide-water dimers, X<sup>-</sup>(H<sub>2</sub>O), and trimers, X<sup>-</sup>(H<sub>2</sub>O)<sub>2</sub>, with X = F, Cl, Br, and I, are investigated using various many-body models and exchange-correlation functionals selected across the hierarchy of density functional theory (DFT) approximations. Analysis of the results obtained with the many-body models demonstrates the need to capture important short-range interactions in the regime of large inter-molecular orbital overlap, such as charge transfer and charge penetration. Failure to reproduce these effects can lead to large deviations relative to reference data calculated at the coupled cluster level of theory. Decompositions of interaction energies carried out with the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA) method demonstrate that permanent and inductive electrostatic energies are accurately reproduced by all classes of XC functionals (from generalized gradient corrected (GGA) to hybrid and range-separated functionals), while significant variance is found for charge transfer energies predicted by different XC functionals. Since GGA and hybrid XC functionals predict the most and least attractive charge transfer energies, respectively, the large variance is likely due to the delocalization error. In this scenario, the hybrid XC functionals are then expected to provide the most accurate charge transfer energies. The sum of Pauli repulsion and dispersion energies are the most varied among the XC functionals, but it is found that a correspondence between the interaction energy and the ALMO EDA total frozen energy may be used to determine accurate estimates for these contributions. </p> </div> </div> </div>

Influence of the adsorption of toxic agents on the optical and electronic properties of B12N12 fullerene in the presence and absence of an external electric field

2020 ◽  
Vol 44 (34) ◽  
pp. 14513-14528
Author(s):  
Alireza Soltani ◽  
Mohammad Ramezanitaghartapeh ◽  
Masoud Bezi Javan ◽  
Mohammad T. Baei ◽  
Andrew Ng Kay Lup ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Electric Field ◽  
Dft Calculations ◽  
Electronic Properties ◽  
External Electric Field ◽  
Density Functional ◽  
Interaction Energies ◽  
Functional Theory ◽  
Toxic Agents ◽  
Optical And Electronic Properties

The interaction energies and optoelectronic properties of sarin (SF) and chlorosarin (SC) on the B12N12 with and without the presence of an electric field have been studied using density functional theory (DFT) calculations.

A theoretical study of weak interactions in phenylenediamine homodimer clusters

2016 ◽  
Vol 18 (42) ◽  
pp. 29249-29257 ◽  
Author(s):  
Chengqian Yuan ◽  
Haiming Wu ◽  
Meiye Jia ◽  
Peifeng Su ◽  
Zhixun Luo ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Dft Calculations ◽  
Intermolecular Interactions ◽  
Density Functional ◽  
Theoretical Study ◽  
Natural Bond Orbital ◽  
Weak Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Weak Intermolecular Interactions

Utilizing dispersion-corrected density functional theory (DFT) calculations, we demonstrate the weak intermolecular interactions of phenylenediamine dimer (pdd) clusters, emphasizing the local lowest energy structures and decomposition of interaction energies by natural bond orbital (NBO) and atoms in molecule (AIM) analyses.

THEORETICAL STUDY ON POTENCY AND SELECTIVITY OF NOVEL NONPEPTIDE INHIBITORS OF MATRIX METALLOPROTEINASES MMP-2 AND MMP-9

2009 ◽  
Vol 08 (03) ◽  
pp. 491-506 ◽  
Author(s):  
DAI-LIN LI ◽  
QING-CHUAN ZHENG ◽  
XUE-XUN FANG ◽  
HAI-TAO JI ◽  
JIN-GANG YANG ◽  
...  
Keyword(s):  
Inhibitory Activity ◽  
Density Functional ◽  
Theoretical Study ◽  
Zinc Binding ◽  
Hydroxyl Group ◽  
Interaction Energies ◽  
Binding Modes ◽  
Functional Theory ◽  
Total Interaction ◽  
Binding Affinity Calculations

Two novel matrix metalloproteinase (MMP) inhibitors, myricetin (m) and kaempferol (k), were found and the inhibitory activity is both in decreased order towards MMP-2 and MMP-9. To understand the mechanism during the processes when inhibitors bind to MMP-2 and MMP-9, molecular modeling, docking, and density functional theory (DFT) calculations were performed. The calculated results indicated that the hydroxyls on benzene ring of the inhibitors control the binding modes between inhibitors and MMPs, thus play an important role on the potency and selectivity. Besides coordinating with the N atoms of three His residues, Zn also interacts with a hydroxyl group of inhibitors by O – Zn distances of 2.66–2.78 Å in all of the docked complexes, so that the hydroxyl acts as a weak zinc binding group (ZBG). The DFT calculated results support the above analysis. The binding affinity calculations between inhibitors and MMPs present the total interaction energies in the m-MMP < k-MMP order and the solvation energy of myricetin is less than that of kaempferol, which reflect the experimental inhibitory activity.

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