On the Cooperativity of Cation−π and Hydrogen Bonding Interactions

Vijay, Dolly; Zipse, Hendrik; Sastry, G. Narahari

doi:10.1021/jp804219e

Cited by 115 publications

(87 citation statements)

References 25 publications

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“…[41,49] Evidently, the interaction energies of both halogen bonding and the cation-p interaction in the triads become more negative relative to the respective dyads, that is, both interactions enhance each other in the triad, which is also evidenced by large value of the P ratio (P > 1). The ratio of the cation-p interaction ranges from 1.02 to 1.21, whereas that of halogen bonding is in the range of 1.98-5.55.…”

Section: Interplay Between Halogen Bonding and Cation-p Interactionsmentioning

confidence: 98%

“…Cation-p interactions have been investigated between cations (Li + , Na + , K + , Mg 2 + ) and p electrons in aromatic compounds such as phenol and pyrrole. [40,41] Herein, we designed the cation-p complexes of Li + and Na + with halobenzene. Figure S1 in the Supporting Information shows the optimized structures of both types of dyads at the MP2/aug-cc-pVDZ level.…”

Section: Halogen Bonding and Cation-p Interactionsmentioning

confidence: 99%

“…The interaction energies of the halogen bond and the cation-p interaction are calculated by using the equation DE ABÀC = E ABC ÀE AB ÀE C ÀDE AÀC , in which E ABC , E AB , and E C are the energies of the optimized triad ABC, dyad AB, and monomer C, respectively, while DE AÀC is the interaction energy between A and C obtained as a difference between the energy of AC in the triad and the energy sum of the monomers with all of them frozen in the geometry of the triad. [41,49] To compare the interaction energy in the triad with that in the dyad, the ratio (P) of the former to the latter is defined as P = DE(T)/DE(D), in which DE(T) and DE(D) are the interaction energies in the triad and dyad, respectively. Usually, when dealing with cooperativity in trimeric complexes consisting of molecules A, B, and C, one calculates the pairwise interactions AÀB, BÀC, and AÀC, and treats the remaining part as cooperativity.…”

Section: Halogen Bonding and Cation-p Interactionsmentioning

confidence: 99%

“…Usually, when dealing with cooperativity in trimeric complexes consisting of molecules A, B, and C, one calculates the pairwise interactions AÀB, BÀC, and AÀC, and treats the remaining part as cooperativity. [41,49] The cooperative energy is thus calculated as…”

Section: Halogen Bonding and Cation-p Interactionsmentioning

confidence: 99%

“…[34] It has been demonstrated that it is present not only in the same type of interaction, but in different types of interactions as well. [35][36][37][38][39][40][41] One prominent effect of cooperativity is the enhancement of interaction strength. Thus, we want to enhance halogen-hydride halogen bonding by combining it with another interaction.…”

Section: Introductionmentioning

confidence: 99%

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The Prominent Enhancing Effect of the Cation–π Interaction on the Halogen–Hydride Halogen Bond in M¹⋅⋅⋅C₆H₅X⋅⋅⋅HM²

Cheng

Liu

et al. 2011

ChemPhysChem

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We designed M(1)⋅⋅⋅C(6)H(5)X⋅⋅⋅HM(2) (M(1) =Li(+), Na(+); X=Cl, Br; M(2) =Li, Na, BeH, MgH) complexes to enhance halogen-hydride halogen bonding with a cation-π interaction. The interaction strength has been estimated mainly in terms of the binding distance and the interaction energy. The results show that halogen-hydride halogen bonding is strengthened greatly by a cation-π interaction. The interaction energy in the triads is two to six times as much as that in the dyads. The largest interaction energy is -8.31 kcal mol(-1) for the halogen bond in the Li(+)⋅⋅⋅C(6)H(5)Br⋅⋅⋅HNa complex. The nature of the cation, the halogen donor, and the metal hydride influence the nature of the halogen bond. The enhancement effect of Li(+) on the halogen bond is larger than that of Na(+). The halogen bond in the Cl donor has a greater enhancement than that in the Br one. The metal hydride imposes its effect in the order HBeH

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Section: Interplay Between Halogen Bonding and Cation-p Interactionsmentioning

confidence: 98%

Section: Halogen Bonding and Cation-p Interactionsmentioning

confidence: 99%

Section: Halogen Bonding and Cation-p Interactionsmentioning

confidence: 99%

Section: Halogen Bonding and Cation-p Interactionsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

The Prominent Enhancing Effect of the Cation–π Interaction on the Halogen–Hydride Halogen Bond in M¹⋅⋅⋅C₆H₅X⋅⋅⋅HM²

Cheng

Liu

et al. 2011

ChemPhysChem

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Cation–π Interactions in Graphene‐Containing Systems for Water Treatment and Beyond

2020

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was also recognized. [2] In addition to these forces, one intriguing noncovalent interaction: cation-π interaction, has emerged as an intermolecular force of great significance in chemistry, biology, and materials science. [3] The cation-π interactions basically refers to the interplay between cations and the π electron cloud of an aromatic system. It plays a great role in biological systems for molecular recognition, protein-protein interactions, and the maintenance of macromolecular structures. It also occurs in protein-ligand interactions and protein-DNA complexes. In structural biology, the positively charged amino acids interact with aromatic amino acids, which contribute to the formation of complex protein structures. The amide NHs are in close contact with the aromatic ring of another amino acid in the protein crystal structures. [4] The cation-π interactions are of great importance to protein stability. There is at least one intermolecular cation-π interaction in half of proteins and one third of homodimers, [5] making significant contributions to the tertiary and quaternary protein structures caused by protein folding. In addition, metallic cations, such as Na + , K + , Cu 2+ , Fe 2+ , Ca 2+ , exist in many enzymes. Their interactions with the π systems in protein structures cannot be ignored. In molecular neurobiology, many studies have proved that receptors bind the neurotransmitters through cation-π interactions. [6] The cation-π interaction is electrostatic in nature because the major contributions arise from the electrostatic attractions between cations and the quadrupole moment of the aromatics. [7] As a result, the strength of cation-π interactions can be the strongest among the noncovalent interactions, several times greater than others. It can also be regulated to be weak, depending on the type of cations and the nature of the π system. The adjustability of cation-π interaction offers a potential strategy to modify the neighboring environment where it is involved.Graphene, a 2D carbon network, with carbon atoms jointed together in a hexagonal honeycomb matrix, can be taken as a novel aromatic macromolecule from certain points of view. The unique structure endows it with excellent physicochemical, electronic, optical, thermal, and mechanical properties, leading to its potential applications in broad fields. [8] The interplay between cations and the delocalized polarizable π electrons of graphene, would alter the intrinsic characteristics of graphene-based structures and impart influences on the performance of graphene-based devices.Cation-π interactions are common in nature, especially in organisms. Their profound influences in chemistry, physics, and biology have been continuously investigated since they were discovered in 1981. However, the importance of cation-π interactions in materials science, regarding carbonaceous nanomaterials, has just been realized. The interplay between cations and delocalized polarizable π electrons of graphene would bring about significant changes to the intrinsic...

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Regulation of Transcription by Synthetic DNA‐Bending Agents

Bednarski¹,

Firestine²

2006

ChemBioChem

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Gene expression is regulated by a complex interplay between binding and the three-dimensional arrangement of transcription factors with RNA polymerase and DNA. Previous studies have supported a direct role for DNA bending and conformation in gene expression, which suggests that agents that induce bends in DNA might be able to control gene expression. To test this hypothesis, we examined the effect of triple-helix-forming oligonucleotide (TFO) bending agents on the transcription of luciferase in an in vitro transcriptional/translational system. We find that transcription is regulated only by a TFO that induces a bend in the DNA. Related TFOs that do not induce bends in DNA have no effect on transcription. Reporter expression can be increased by as much as 80 % or decreased by as much as 50 % depending on the phasing of the upstream bend relative to the promoter. We interpret the results as follows: when the bend is positioned such that the upstream DNA is curved toward the RNA polymerase on the same DNA face, transcription is enhanced. When the upstream DNA is curved away, transcription is attenuated. These results support the hypothesis that DNA-bending agents might have the capability to regulate gene expression, thereby opening up a previously undervalued avenue in research on the artificial control of gene expression.

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On the Cooperativity of Cation−π and Hydrogen Bonding Interactions

Cited by 115 publications

References 25 publications

The Prominent Enhancing Effect of the Cation–π Interaction on the Halogen–Hydride Halogen Bond in M¹⋅⋅⋅C₆H₅X⋅⋅⋅HM²

The Prominent Enhancing Effect of the Cation–π Interaction on the Halogen–Hydride Halogen Bond in M¹⋅⋅⋅C₆H₅X⋅⋅⋅HM²

Cation–π Interactions in Graphene‐Containing Systems for Water Treatment and Beyond

Regulation of Transcription by Synthetic DNA‐Bending Agents

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On the Cooperativity of Cation−π and Hydrogen Bonding Interactions

Cited by 115 publications

References 25 publications

The Prominent Enhancing Effect of the Cation–π Interaction on the Halogen–Hydride Halogen Bond in M1⋅⋅⋅C6H5X⋅⋅⋅HM2

The Prominent Enhancing Effect of the Cation–π Interaction on the Halogen–Hydride Halogen Bond in M1⋅⋅⋅C6H5X⋅⋅⋅HM2

Cation–π Interactions in Graphene‐Containing Systems for Water Treatment and Beyond

Regulation of Transcription by Synthetic DNA‐Bending Agents

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The Prominent Enhancing Effect of the Cation–π Interaction on the Halogen–Hydride Halogen Bond in M¹⋅⋅⋅C₆H₅X⋅⋅⋅HM²

The Prominent Enhancing Effect of the Cation–π Interaction on the Halogen–Hydride Halogen Bond in M¹⋅⋅⋅C₆H₅X⋅⋅⋅HM²