Polar/.pi. interactions between stacked aryls in 1,8-diarylnaphthalenes

Cozzi, Franco; Cinquini, Mauro; Annunziata, Rita; Dwyer, Tammy J.; Siegel, Jay S.

doi:10.1021/ja00040a036

Cited by 323 publications

(260 citation statements)

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“…This is in contrast to interactions between benzene-substituted benzenes, which exhibit the opposite trends, i.e., electron-withdrawing substituents lead to stronger binding energies. 11,13,14,43 This reversal in trend is consistent with the opposite signs of the quadrupole moments of hexafluorobenzene and benzene, which suggests electrostatic forces play a prominent role in the interactions of the C 6 F 6 -C 6 H 5 X dimers, at least for the complex series 2. However, this does not mean the interactions are entirely due to electrostatic forces.…”

Section: A General Trend In Interaction Energiessupporting

confidence: 71%

“…43 Hunter and coworkers have also used Hammett plots to illustrate the dominance of electrostatic forces in aromatic interactions. 50, 51 Although the Hammett constants do not necessarily correlate with ground state arene π-electron density, 11, 46 it does give some information about possible correlations between the calculated binding energies (−ΔE int ) and classical substituent effects.…”

Section: A Threshold For Charge-transfer Interactionsmentioning

confidence: 99%

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Substituent Effects in C₆F₆C₆H₅X Stacking Interactions

2006

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Parallel displaced and sandwich configurations of hexafluorobenzene-substituted benzene dimers are studied by ab initio molecular orbital methods up to the MP2(full)/aug-cc-pVDZ level of theory to reveal how substituents influence π-π interactions. Two minimum energy configurations are found, one with the substituent group away from (2a-2f) and the other with the substituent group on top of the π-face of the hexafluorobenzene (3a-3f). Higher binding energies are predicted for dimers with the substituent on the π-face (3a-3f). All sandwich dimers (4a-4e) are found to be saddle points on the potential energy surfaces. A parallel displaced minimum energy configuration is also predicted for the parent complex, C 6 F 6 -C 6 H 6 , which is in contrast to predictions based on quadrupole moments of benzene and hexafuorobenzene. The preference for the parallel displaced, rather than the sandwich configuration, is rationalized based on the smaller interplanar distance in the former. The closeness of contact in the parallel displaced dimers leads to greater binding energies. The shape of the electron density isosurface of the monomers is suggested to provide a guide for the prediction of how arenes stack with one another. A large difference in binding energy between the C 6 F 6 complex of aniline (3e) and N,N-dimethylaniline (3f) is calculated and charge-transfer interactions are suggested to play a role in the latter.

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Section: A General Trend In Interaction Energiessupporting

confidence: 71%

Section: A Threshold For Charge-transfer Interactionsmentioning

confidence: 99%

Substituent Effects in C₆F₆C₆H₅X Stacking Interactions

2006

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“…This is expected to be predominant only in concentrated solutions or when the interacting groups are brought together by some other interactions such as coulombic interactions or hydrogen bonds as in the designing of devices for molecular recognition, catalysis, and development of self-replicating molecules and molecular clips (20 -24). Such interactions are facilitated when the aromatic moieties are brought close to each other, making them substituents of the same molecule (25)(26)(27)(28). In this report, we demonstrate that following this designing principle, stacked nucleotide fluorophores that are in rapid equilibrium with the stretched forms can be synthesized quite easily.…”

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confidence: 78%

Synthesis and Characterization of Stacked and Quenched Uridine Nucleotide Fluorophores

Dhar

Bhaduri

1999

Journal of Biological Chemistry

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Since the seminal work of Weber and Laurence (1) with 1-anilinonaphthalene-8-sulfonic acid, extrinsic fluorescent probes have been extensively used to monitor various aspects of protein-ligand or enzyme-substrate interactions. Among others, these probes have been used (i) to establish the degree of polarity or hydrophobicity of a particular region of a protein, (ii) to measure the distance between groups on protein surface, (iii) to measure the extent of flexibility of protein in solution, (iv) to measure the rate of very rapid conformational transitions, and (v) to measure kinetic constants of interaction between protein and ligand (2). To facilitate these studies, a variety of derivatized fluorescent ligands or substrate analogs have been synthesized over the years without any serious attention being given to their solution conformations or their transitions to new conformations on interaction with the target proteins. Such conformational transitions are often crucial steps in biological interactions as typically exemplified by NAD, the common cofactor for a very large number of dehydrogenases. The molecule exhibits reversible stacking between the adenine and pyridine moiety with both the open and the closed forms in rapid interconversionary equilibrium in aqueous solutions (3, 4). During catalysis, NAD takes a totally extended conformation on the enzyme surface; the conserved tertiary structure of the pyridine nucleotide binding site being a very characteristic feature of all these oxidoreductases (5).Etheno-ATP was originally synthesized as a fluorescent analog of ATP. It had a high quantum yield and a long fluorescence lifetime and could be used to follow ATP interactions primarily by polarization studies (6 -8). In contrast, as in case of NAD, significant population of etheno-NAD was in a folded conformation in aqueous solution as a result of aromatic interactions between the pyridine and the modified adenine moiety, leading to dynamic collisional quenching of fluorescence and short fluorescence life-time (9). This stacked and quenched fluorophore was brilliantly used to establish negative co-operativity for glyceraldehyde-3-phosphate dehydrogenase from rabbit muscle for the binding of the tetrameric apoenzyme to the coenzyme. The conformational transition of etheno-NAD from folded to stretched conformation as reflected by its enhanced fluorescence on interaction with the target protein was the monitoring parameter for this purpose (10). Although stacked fluorophore with quenched fluorescence can be of immense use in protein-ligand binding studies, as is exemplified by etheno-NAD, it is surprising to note that no deliberate effort has so far been made to design such compounds taking advantage of the potential aromatic interaction between the attached fluorophore and a suitable moiety of the desired biomolecule.The interaction between aromatic rings is of wide chemical and biological interest, because it plays important roles in vital biological processes, such as stabilization of protein and nucleic acid s...

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“…For naphthalene the samples were: (i) fully deuterated naphthalene (498% deuterated, Sigma Aldrich), (ii) hydrogenated naphthalene (purity 4 99.7%, Sigma Aldrich) and (iii) a 50 : 50 molar mixture of the two. For pyridine the samples were (i) fully deuterated pyridine (99.5% deuterated, Cambridge Isotope Laboratories), (ii) hydrogenated pyridine (anhydrous, 99% purity, Sigma Aldrich), (iii) a 50 : 50 molar mixture of the two and (iv) 15 N enriched hydrogenated pyridine (498% 15N, Cambridge Isotope Laboratories). The liquids were used as received and inserted into a flat-plate null coherent scattering titanium/zirconium cell, with 1 mm sample and wall thicknesses.…”

Section: Scattering Theorymentioning

confidence: 99%

“…1). Changes in structure and energetics in more complex aromatic interactions are then rationalised through their effect on the electrostatic potential of the ring, 14,15 for example with electron withdrawing groups reducing electrostatic repulsion. In recent years, this view has been challenged, 9 with the conclusion being that direct interactions between substituents play a significant role rather than being mediated through the p-system.…”

Section: Introductionmentioning

confidence: 99%

The structures of liquid pyridine and naphthalene: the effects of heteroatoms and core size on aromatic interactions

Headen

Cullen

Patel

et al. 2018

Phys. Chem. Chem. Phys.

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Total neutron scattering has been used in conjunction with H/D and *N/ 15 N isotopic substitution to determine the detailed liquid-state structures of pyridine and naphthalene. Analysis of the data via an empirical potential-based structure refinement method has allowed us to interrogate the full six-dimensional spatial and orientational correlation surfaces in these systems, and thereby to deduce the fundamental effects of a heteroatom and aromatic core-size on intermolecular p-p interactions. We find that the presence of a nitrogen heteroatom, and concomitant dipole moment, in pyridine induces surprisingly subtle departures from the structural correlations observed in liquid benzene: in both cases the most probable local motif is based on perpendicular (edge-to-face) intermolecular contacts, while parallel-displaced configurations give rise to a clear shoulder in the correlation surface. However, the effect of the heteroatom is revealed through detailed analysis of the intermolecular orientational correlations. This analysis shows a tendency for neighbouring pyridine molecules to direct one meta-and one para-hydrogen towards the neighbouring aromatic p-orbitals in edge-to-face configurations, while head-to-tail alignment of adjacent nitrogen atoms is favoured in faceto-face configurations. In contrast to this, increasing aromatic core size from one to only two rings has a clear and profound effect on the p-p interactions and liquid structure. Our experiments show that naphthalenenaphthalene contacts are dominated by parallel-displaced configurations, akin to those found in graphite. This marks a fundamental difference with the structure of liquid benzene, in which perpendicular geometries are favoured. Furthermore, it is remarkable to note that in the systems studied, the most favoured spatioorientational configurations observed in the liquid state are not predicted from ab initio calculations and/or solid state crystallographic studies. This highlights the need for caution when extrapolating the results of crystallographic and computational studies to aromatic interactions in liquids and disordered systems.

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Polar/.pi. interactions between stacked aryls in 1,8-diarylnaphthalenes

Cited by 323 publications

References 1 publication

Substituent Effects in C₆F₆C₆H₅X Stacking Interactions

Substituent Effects in C₆F₆C₆H₅X Stacking Interactions

Synthesis and Characterization of Stacked and Quenched Uridine Nucleotide Fluorophores

The structures of liquid pyridine and naphthalene: the effects of heteroatoms and core size on aromatic interactions

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Polar/.pi. interactions between stacked aryls in 1,8-diarylnaphthalenes

Cited by 323 publications

References 1 publication

Substituent Effects in C6F6C6H5X Stacking Interactions

Substituent Effects in C6F6C6H5X Stacking Interactions

Synthesis and Characterization of Stacked and Quenched Uridine Nucleotide Fluorophores

The structures of liquid pyridine and naphthalene: the effects of heteroatoms and core size on aromatic interactions

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Substituent Effects in C₆F₆C₆H₅X Stacking Interactions

Substituent Effects in C₆F₆C₆H₅X Stacking Interactions