A gradient-corrected density functional study of indole self-association through N–H⋯π hydrogen bonding

Pejov, Ljupčo

doi:10.1016/s0009-2614(01)00341-4

Cited by 45 publications

(61 citation statements)

References 33 publications

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“…Two peaks are observed in these spectra, one corresponding to the free species (~3450 cm −1 ) and the other peak most likely corresponding to a dimeric species, the indole:indole π-hydrogen bond (~3400 cm−1). 39–41 This assignment is supported by control experiments demonstrating that the intensity of the peak at 3400 cm −1 is strongly concentration dependent, but that the peak position does not shift with concentration (Supporting Information Figure S5). DFT calculations suggest that a π-hydrogen bond complex between the N-H group of one indole molecule and the six-membered ring of another is the minimum energy structure of the dimer complex.…”

Section: The Vibrational Stark Effect As a Tool To Quantify Electric mentioning

confidence: 58%

Experimental Quantification of Electrostatics in X–H···π Hydrogen Bonds

2012

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Hydrogen bonds are ubiquitous in chemistry and biology. The physical forces that govern hydrogen bonding interactions have been heavily debated, with much of the discussion focused on the relative contributions of electrostatic vs. quantum mechanical effects. In principle, the vibrational Stark effect (VSE), the response of a vibrational mode to electric field, can provide an experimental method for parsing such interactions into their electrostatic and non-electrostatic components. In a previous study we showed that, in the case of relatively weak O-H···π hydrogen bonds, the O-H bond displays a linear response to electric field, and we exploited this response to demonstrate that the interactions are dominated by electrostatics (Saggu, M.; Levinson, N. M.; Boxer, S. G. J. Am. Chem. Soc. 2011, 133, 17414–17419). Here we extend this work to other X-H···π interactions. We find that the response of the X-H vibrational probe to electric field appears to become increasingly nonlinear in the order O-H

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Section: The Vibrational Stark Effect As a Tool To Quantify Electric mentioning

confidence: 58%

Experimental Quantification of Electrostatics in X–H···π Hydrogen Bonds

2012

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“…For example, the calculated interaction energy of the parallel and perpendicular thiophene dimers in vacuum was -1.71 and -3.12 kcal/mol, respectively [18]. In the case of pyrrole [19] and indole [20] dimers the T-shaped dimers actually interact through a ( )N-H … interaction rather than a conventional ··· interaction with interaction energies of -5.11 and -2.15 kcal/mol in vacuum, respectively. In contrast to the benzenebenzene T-shaped dimer, the pyrrole and indole dimmers have electrostatic and charge transfer interactions which play a significant role in stabilizing the complex.…”

Section: ··· Interactions 21 Physicochemical Properties Of ··· Intementioning

confidence: 97%

The Role and Significance of Unconventional Hydrogen Bonds in Small Molecule Recognition by Biological Receptors of Pharmaceutical Relevance

Tóth¹,

Bowers²,

Truong³

et al. 2007

CPD

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The discovery and optimization of nonbonded interactions, such as van der Waals interactions, hydrogen bonds, salt bridges and the hydrophobic effect, between small molecule ligands and their receptors is one of the main challenges in rational drug discovery. As the theory of molecular interactions advances more evidence accumulates that nonbonded interactions, such as unconventional hydrogen bonds (X-H...Y interactions, where X can be either C, N or O atom and Y can be either an aromatic ring system O or F atom), contribute to ligand recognition by biological receptors. This review provides an overview of unconventional hydrogen bonds between ligands and their receptors of pharmaceutical relevance by dissecting their structure activity relationships and 3D structural elements. Gaining an understanding of the energetic and the structural properties of unconventional hydrogen bonds in ligand-receptor interactions leads us to the elucidation of their practical significance. Ultimately, this enables us to consciously apply these interactions in hit and lead optimization in rational structure based drug design.

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“…Of the aromatic residues, the side chain of tryptophan (Trp) is unique, with its amphipathic nature enabling it to participate in both nonpolar interactions and in hydrogen bonding (11–14). NH… π (15–17) and CH… π interactions (18) and electrostatic interactions via the inherent quadrupoles of the aromatic ring (12,19,20) also make the Trp residue an important contributor, both to the process of protein folding and subsequent stabilization of the folded structures. For example, the role of Trp residues in stabilizing tertiary structure, leading to alternate folding patterns of proteins, has been emphasized in a recent study of a 20‐residue peptide (21).…”

Section: Introductionmentioning

confidence: 99%

Tryptophan‐containing peptide helices: interactions involving the indole side chain*

Mahalakshmi

Sengupta

Raghothama

et al. 2005

The Journal of Peptide Research

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Two designed peptide sequences containing Trp residues at positions i and i + 5 (Boc‐Leu‐Trp‐Val‐Ala‐Aib‐Leu‐Trp‐Val‐OMe, 1) as well as i and i + 6 (Boc‐Leu‐Trp‐Val‐Aib‐Ala‐Aib‐Leu‐Trp‐Val‐OMe, 2) containing one and two centrally positioned Aib residues, respectively, for helix nucleation, have been shown to form stable helices in chloroform solutions. Structures derived from nuclear magnetic resonance (NMR) data reveal six and seven intramolecularly hydrogen‐bonded NH groups in peptides 1 and 2, respectively. The helical conformation of octapeptide 1 has also been established in the solid state by X‐ray diffraction. The crystal structure reveals an interesting packing motif in which helical columns are stabilized by side chain–backbone hydrogen bonding involving the indole Nɛ1H of Trp(2) as donor, and an acceptor C=O group from Leu(6) of a neighboring molecule. Helical columns also associate laterally, and strong interactions are observed between the Trp(2) and Trp(7) residues on neighboring molecules. The edge‐to‐face aromatic interactions between the indoles suggest a potential C‐H…π interaction involving the Cζ3H of Trp(2). Concentration dependence of NMR chemical shifts provides evidence for peptide association in solution involving the Trp(2) Nɛ1H protons, presumably in a manner similar to that observed in the crystal.

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A gradient-corrected density functional study of indole self-association through N–H⋯π hydrogen bonding

Cited by 45 publications

References 33 publications

Experimental Quantification of Electrostatics in X–H···π Hydrogen Bonds

Experimental Quantification of Electrostatics in X–H···π Hydrogen Bonds

The Role and Significance of Unconventional Hydrogen Bonds in Small Molecule Recognition by Biological Receptors of Pharmaceutical Relevance

Tryptophan‐containing peptide helices: interactions involving the indole side chain*

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