Stacking interactions between hydrogen-bridged and aromatic rings: study of crystal structures and quantum chemical calculations

Blagojević, Jelena P.; Veljković, Dušan Ž.; Zarić, Snežana D.

doi:10.1039/c6ce02045c

Cited by 14 publications

(25 citation statements)

References 57 publications

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“…3) and the potential energy curves (Fig. 7) showed that TTF molecules form the strongest stacking interactions in parallel displaced geometries, which is typical for aromatic rings (Lee et al, 2007;Ninković et al, 2011), most of the chelate rings (Malenov & Zarić, 2018;Malenov et al, 2017) and also hydrogen-bridged rings (Blagojević et al, 2017;Blagojević & Zarić, 2015). The results of quantum chemical calculations are in very good agreement with the data found in the CSD crystal structures, which is well illustrated by similarities of the crystal structures in Fig.…”

Section: Comparing the Geometries In The Csd And Interaction Energiessupporting

confidence: 80%

“…At the 4.5 Å offset, the benzenebenzene stacking interaction energy is À2.01 kcal mol À1 and these interactions are highly dominant in crystal structures (Ninković et al, 2011). In addition, the work in our group showed substantial stacking interactions of non-aromatic moieties, such as chelate rings (Malenov & Zarić, 2018;Malenov et al, 2017), cyclohexane (Ninković et al, 2016) and hydrogen-bridged rings (Blagojević et al, 2017;Blagojević & Zarić, 2015). Stacking interactions of all these moieties are comparable in energy with stacking interactions of aromatic molecules and some of them are significantly stronger.…”

Section: Introductionmentioning

confidence: 65%

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Study of stacking interactions between two neutral tetrathiafulvalene molecules in Cambridge Structural Database crystal structures and by quantum chemical calculations

Antonijević

Malenov

Hall

et al. 2019

Acta Crystallogr Sect B

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Tetrathiafulvalene (TTF) and its derivatives are very well known as electron donors with widespread use in the field of organic conductors and superconductors. Stacking interactions between two neutral TTF fragments were studied by analysing data from Cambridge Structural Database crystal structures and by quantum chemical calculations. Analysis of the contacts found in crystal structures shows high occurrence of parallel displaced orientations of TTF molecules. In the majority of the contacts, two TTF molecules are displaced along their longer C2 axis. The most frequent geometry has the strongest TTF–TTF stacking interaction, with CCSD(T)/CBS energy of −9.96 kcal mol−1. All the other frequent geometries in crystal structures are similar to geometries of the minima on the calculated potential energy surface.

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Section: Comparing the Geometries In The Csd And Interaction Energiessupporting

confidence: 80%

Section: Introductionmentioning

confidence: 65%

Study of stacking interactions between two neutral tetrathiafulvalene molecules in Cambridge Structural Database crystal structures and by quantum chemical calculations

Antonijević

Malenov

Hall

et al. 2019

Acta Crystallogr Sect B

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“…64−68 Blagojevićand Zarićhave performed a systematic analysis to compute stacked hydrogen-bridged ring stabilization energies. 64 The stacking interactions occurred in different systems were analyzed, for example, between non-RAHB rings (particularly (i) two planar five-membered hydrogen-bridged rings 64 and (ii) planar sixmembered hydrogen-bridged rings and C 6 -aromattc rings 69 ) and RAHB rings ((iii) two six-membered RAHB rings 70 and (iv) six-membered RAHB rings and C 6 -aromatic rings 71 ). In these studies, the authors demonstrated that the stacking interactions between two six-membered RAHB rings (−4.7 kcal mol −1 ) and the stacking interaction between the sixmembered RAHB ring and C 6 -aromatic rings (−3.7 kcal mol −1 ) were more robust than the normal benzene•••benzene stacking interaction (−2.7 kcal mol −1 ).…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Crystal Packing Modulation of the Strength of Resonance-Assisted Hydrogen Bonds and the Role of Resonance-Assisted Pseudoring Stacking in Geminal Amido Esters: Study Based on Crystallography and Theoretical Calculations

Venkatesan

Thamotharan

Percino

et al. 2020

Crystal Growth & Design

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A detailed experimental and theoretical investigation of a series of substituted geminal amido esters (ethyl (2E)-3-(arylamino)-2-(arylcarbamoyl)prop-2-enoate, AME-1–8) leading to the identification of a unique angularly fused pseudotricyclic (S(6),S(6),S(6)) ring system stabilized by an intramolecular resonance-assisted hydrogen bond (RAHB) and a non-RAHB are presented in addition to weak intermolecular interactions. An analysis of X-ray and theoretical models reveals that the strength of the intramolecular RAHB (N1–H1 N ···O1) varies in a wide range (6.9–11.4 kcal mol–1) due to crystal-packing constraints arising from different aromatic ring substitutions. However, the effect is less significant and the strength differs only in a narrow range (8.2–9.9 kcal mol–1) in the case of non-RAHB. The downfield shift (δ ∼12.3) observed for the N–Haniline signal in 1H NMR spectra of AME-1–8 is due to the presence of intramolecular RAHB. A PIXEL energy analysis suggests that the molecular dimer formed by stacking of RAHB pseudorings is found to be strong (E tot = −14.4 to −17.9 kcal mol–1), and this dimer forms the basic motif in most of the structures reported herein. A detailed analysis of the isostructurality suggests that the basic motif exists in most of the structural combinations. The weak intermolecular C–H···O, C–H···Cl, and C–H···π interactions play a vital role in the stabilization of these crystal structures, as evaluated by PIXEL and Bader’s quantum theory of atoms in molecules approach (QTAIM). A lattice energy analysis suggests that the Coulombic contribution and total lattice energies are higher in the para-substituted compounds (AME-2, AME-5, and AME-8) in comparison to the other isomeric compounds. Further, the crystal packing of these compounds is analyzed on the basis of the energy frameworks. It shows that most of the crystals show similar 3D topologies, suggesting that these compounds may have similar mechanical behavior.

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“…Several studies suggested that important and strong stacking interactions can be formed between aromatic and nonaromatic molecules or fragments or between two nonaromatic moieties . Most recently, the research on amyloids, that are considered responsible for Alzheimer's disease, showed that aromatic–aliphatic interactions are of greater importance than aromatic–aromatic interactions in amyloid‐β polypeptides .…”

Section: Introductionmentioning

confidence: 99%

Influence of metal ion on chelate–aryl stacking interactions

Malenov

Hall²,

Zarić

2018

Int J of Quantum Chemistry

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CCSD(T)/CBS and DFT methods are employed to study the stacking interactions of acetylacetonate-type (acac-type) chelates of nickel, palladium, and platinum with benzene. The strongest chelate-aryl stacking interactions are formed by nickel and palladium chelate, with interaction energies of 25.75 kcal mol 21 and 25.73 kcal mol 21 , while the interaction of platinum chelate is weaker, with interaction energy of 25.36 kcal mol 21 . These interaction energies are significantly stronger than stacking of two benzenes, 22.73 kcal mol 21 . The strongest nickel and palladium chelate-aryl interactions are with benzene center above the metal area, while the strongest platinum chelate-aryl interaction is with the benzene center above the C2 atom of the acac-type chelate ring. These preferences arise from very different electrostatic potentials above the metal ions, ranging from very positive above nickel to slightly negative above platinum. While the differences in electrostatic potentials above metal atoms cause different geometries with the most stable interaction among the three metals, the dispersion (correlation energy) component is the largest contribution to the total interaction energy for all three metals.density functional theory, dispersion, electrostatic potentials, metal chelates, stacking interactions 1 | I N TR ODU C TI ON Stacking interactions play very important roles in many important chemical and biological systems. [1] They are primarily recognized as one of the most important forces responsible for the structure of DNA [2,3] and for the stability of protein structure, [4][5][6] where they are established between aromatic moieties. Therefore, most of the studies on stacking interactions have dealt with aromatic molecules. [7][8][9][10][11][12][13][14][15][16][17] Several studies suggested that important and strong stacking interactions can be formed between aromatic and nonaromatic molecules or fragments [18][19][20][21][22][23][24] or between two nonaromatic moieties. [25,26] Most recently, the research on amyloids, that are considered responsible for Alzheimer's disease, showed that aromatic-aliphatic interactions are of greater importance than aromatic-aromatic interactions in amyloid-b polypeptides. [27] Several transition metal ions have been associated with amyloid-b polypeptide neurotoxicity, [28][29][30] and are the possible targets for Alzheimer's disease therapy with ligands that can form stable chelate rings with such ions. Chelate rings are also constituents in many materials [31,32] and play important roles in crystal engineering. [33,34] Moreover, chelate rings have a tendency to stack with aromatic rings, which was shown in searches of the Cambridge Structural Database. [23,35,36] Crystallographic studies showed a preference for stacking of aromatic rings with chelate rings over stacking with other aromatic rings. [36] These findings were supported by quantum chemical calculations, which showed stronger stacking interactions between metal chelate and aromatic rings than between two aromati...

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Stacking interactions between hydrogen-bridged and aromatic rings: study of crystal structures and quantum chemical calculations

Cited by 14 publications

References 57 publications

Study of stacking interactions between two neutral tetrathiafulvalene molecules in Cambridge Structural Database crystal structures and by quantum chemical calculations

Study of stacking interactions between two neutral tetrathiafulvalene molecules in Cambridge Structural Database crystal structures and by quantum chemical calculations

Crystal Packing Modulation of the Strength of Resonance-Assisted Hydrogen Bonds and the Role of Resonance-Assisted Pseudoring Stacking in Geminal Amido Esters: Study Based on Crystallography and Theoretical Calculations

Influence of metal ion on chelate–aryl stacking interactions

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