Dominance of polar/.pi. over charge-transfer effects in stacked phenyl interactions

Cozzi, Franco; Cinquini, Mauro; Annuziata, Rita; Siegel, Jay S.

doi:10.1021/ja00065a069

Cited by 383 publications

(286 citation statements)

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“…17,37,57 Although we have no cases here with strongly electron donating groups, the trimethylbenzene case has the most donating substituents of those we did examine. Interestingly, we find it to be a poorer stacker than predicted by surface area.…”

Section: Discussion Factors Affecting Aromatic Stacking In Dnamentioning

confidence: 97%

Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA

et al. 2000

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We report the use of thermodynamic measurements in a self-complementary DNA duplex (5′-dXCGCGCG) 2 , where X is an unpaired natural or nonnatural deoxynucleoside, to study the forces that stabilize aqueous aromatic stacking in the context of DNA. Thermal denaturation experiments show that the core duplex (lacking X) is formed with a free energy (37 °C) of −8.1 kcal·mol −1 in a pH 7.0 buffer containing 1 M Na + . We studied the effects of adding single dangling nucleosides (X) where the aromatic "base" is adenine, guanine, thymine, cytosine, pyrrole, benzene, 4-methylindole, 5-nitroindole, trimethylbenzene, difluorotoluene, naphthalene, phenanthrene, and pyrene. Adding these dangling residues is found to stabilize the duplex by an additional −0.8 to −3.4 kcal·mol −1 . At 5 μM DNA concentration, T m values range from 41.7 °C (core sequence) to 64.1 °C (with dangling pyrene residues). For the four natural bases, the order of stacking ability is A > G ≥ T = C. The nonpolar analogues stack more strongly in general than the more polar natural bases. The stacking geometry was confirmed in two cases (X = adenine and pyrene) by 2-D NOESY experiments. Also studied is the effect of ethanol cosolvent on the stacking of natural bases and pyrene. Stacking abilities were compared to calculated values for hydrophobicity, dipole moment, polarizability, and surface area. In general, hydrophobic effects are found to be larger than other effects stabilizing stacking (electrostatic effects, dispersion forces); however, the natural DNA bases are found to be less dependent on hydrophobic effects than are the more nonpolar compounds. The results also point out strategies for the design nucleoside analogues that stack considerably more strongly than the natural bases; such compounds may be useful in stabilizing designed DNA structures and complexes.

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Section: Discussion Factors Affecting Aromatic Stacking In Dnamentioning

confidence: 97%

Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA

et al. 2000

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“…Porphyrin aggregation (1), the conformation of diarylnaphthalenes (2) and phenylacetylene macrocycles (3), and the strength of Kevlar (4) can be attributed, at least in part, to aromatic-aromatic interactions. Aromatic-aromatic interactions have been implicated in catalytic hydroformylation (5), the catalytic formation of elastomeric polypropylene (6), and the asymmetric cis dihydroxylation of olefins (7).…”

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π-Stacking Interactions

McGaughey¹,

Gagné²,

Rappé³

1998

Journal of Biological Chemistry

1,033

558

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A representative set of high resolution x-ray crystal structures of nonhomologous proteins have been examined to determine the preferred positions and orientations of noncovalent interactions between the aromatic side chains of the amino acids phenylalanine, tyrosine, histidine, and tryptophan. To study the primary interactions between aromatic amino acids, care has been taken to examine only isolated pairs (dimers) of amino acids because trimers and higher order clusters of aromatic amino acids behave differently than their dimer counterparts. We find that pairs (dimers) of aromatic side chain amino acids preferentially align their respective aromatic rings in an off-centered parallel orientation. Further, we find that this parallel-displaced structure is 0.5-0.75 kcal/mol more stable than a T-shaped structure for phenylalanine interactions and 1 kcal/mol more stable than a T-shaped structure for the full set of aromatic side chain amino acids. This experimentally determined structure and energy difference is consistent with ab initio and molecular mechanics calculations of benzene dimer, however, the results are not in agreement with previously published analyses of aromatic amino acids in proteins. The preferred orientation is referred to as parallel displaced -stacking.Attractive nonbonded interactions between aromatic rings are seen in many areas of chemistry, and hence are of interest to all realms of chemistry. Porphyrin aggregation (1), the conformation of diarylnaphthalenes (2) and phenylacetylene macrocycles (3), and the strength of Kevlar (4) can be attributed, at least in part, to aromatic-aromatic interactions. Aromatic-aromatic interactions have been implicated in catalytic hydroformylation (5), the catalytic formation of elastomeric polypropylene (6), and the asymmetric cis dihydroxylation of olefins (7). The vast majority of medicinal agents contain aromatic substituents and their differential recognition by proteins is likely dominated by aromatic-aromatic interactions (8). In biologically related areas of chemistry, aromatic-aromatic interactions are crucially involved in protein-deoxynucleic acid complexes where interactions between aromatic residues and base pairs are seen in x-ray crystal structures (9, 10).Because aromatic-aromatic interactions are so prevalent across chemistry, a large body of experimental and theoretical work has focused on determining the gas phase structure of the prototype, benzene dimer (11-14, 30). As summarized recently by Sun and Bernstein (15), the experimentally observed structure depends heavily upon the observation technique. Off-centered parallel displaced, 1p, and T-shaped, 1t, structures are the most commonly cited orientations (Structure 1).Large scale ab initio electronic structure theory suggests that the off-centered parallel displaced and T-shaped structures are nearly isoenergetic (11)(12)(13)(14)30). As reported by Sun and Bernstein (15), empirical force field studies favor either off-centered parallel displaced or T-shaped structures depending upon t...

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“…68) Therefore, we decided to use 22 The concentrations were determined in the total solution of the two-phase system. The concentrations were determined in the total solution of the two-phase system.…”

Section: Resultsmentioning

confidence: 99%

Supramolecular Complexes Formed by the Self-assembly of Hydrophobic Bis(Zn<sup>2+</sup>-cyclen) Complexes, Copper, and Di- or Triimide Units for the Hydrolysis of Phosphate Mono- and Diesters in Two-Phase Solvent Systems (Cyclen=1,4,7,10-Tetraazacyclododecane)

Hisamatsu

Miyazawa

Yoneda

et al. 2016

CHEMICAL & PHARMACEUTICAL BULLETIN

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Dominance of polar/.pi. over charge-transfer effects in stacked phenyl interactions

Cited by 383 publications

References 0 publications

Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA

Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA

π-Stacking Interactions

Supramolecular Complexes Formed by the Self-assembly of Hydrophobic Bis(Zn<sup>2+</sup>-cyclen) Complexes, Copper, and Di- or Triimide Units for the Hydrolysis of Phosphate Mono- and Diesters in Two-Phase Solvent Systems (Cyclen=1,4,7,10-Tetraazacyclododecane)

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