Modelling biologically important NH...π interactions

Pozharskii, Alexander F.; Dyablo, Olga V.; Ozeryanskii, Valery A.; Pogosova, Olga G.

doi:10.1070/RCR5047

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Modelling biologically important NH^...π interactions

Alexander F. Pozharskii ¹

Alexander F. Pozharskii

0000-0003-3612-1392

,

Olga V. Dyablo ²

Olga V. Dyablo

,

Valery A. Ozeryanskii ²

Valery A. Ozeryanskii

0000-0002-3797-3805

,

Olga G. Pogosova ³

Olga G. Pogosova

¹ Department of Organic Chemistry, Southern Federal University, Rostov-on-Don, Russian Federation

² Department of Organic Chemistry, Southern Federal University, Rostov-on-Don, Russian Federation

³ Department of Organic Chemistry, Southern Federal University, Rostov-on-Don, Russian Federation

10.1070/RCR5047

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2022-07-01 , Review , RCR5047, Volume 91, Issue 7

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Pozharskii A. F. et al. [{"id":"-haqIGTSjn","type":"paragraph","data":{"text":"Modelling biologically important NH...π interactions"}}] // Russian Chemical Reviews. 2022. Vol. 91. No. 7. RCR5047

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Pozharskii A. F., Dyablo O. V., Ozeryanskii V. A., Pogosova O. G. [{"id":"-haqIGTSjn","type":"paragraph","data":{"text":"Modelling biologically important NH...π interactions"}}] // Russian Chemical Reviews. 2022. Vol. 91. No. 7. RCR5047

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TY - JOUR

DO - 10.1070/RCR5047

UR - https://rcr.colab.ws/publications/10.1070/RCR5047

TI - [{"id":"-haqIGTSjn","type":"paragraph","data":{"text":"Modelling biologically important NH...π interactions"}}]

T2 - Russian Chemical Reviews

AU - Pozharskii, Alexander F.

AU - Dyablo, Olga V.

AU - Ozeryanskii, Valery A.

AU - Pogosova, Olga G.

PY - 2022

DA - 2022/07/01

PB - ANO Editorial Board of the journal Uspekhi Khimii

SP - RCR5047

IS - 7

VL - 91

ER -

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@article{2022_Pozharskii,

author = {Alexander F. Pozharskii and Olga V. Dyablo and Valery A. Ozeryanskii and Olga G. Pogosova},

title = {[{"id":"-haqIGTSjn","type":"paragraph","data":{"text":"Modelling biologically important NH...π interactions"}}]},

journal = {Russian Chemical Reviews},

year = {2022},

volume = {91},

publisher = {ANO Editorial Board of the journal Uspekhi Khimii},

month = {Jul},

url = {https://rcr.colab.ws/publications/10.1070/RCR5047},

number = {7},

doi = {10.1070/RCR5047}

}

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Pozharskii, Alexander F., et al. “[{"id":"-haqIGTSjn","type":"paragraph","data":{"text":"Modelling biologically important NH...π interactions"}}].” Russian Chemical Reviews, vol. 91, no. 7, Jul. 2022, p. RCR5047. https://rcr.colab.ws/publications/10.1070/RCR5047.

Content Figures

Graphical abstract Keywords Abstract

Fig. 1

Fragment of polypeptide chain (primary protein structure) with amino acid residues containing different side groups R1 - R4.

Fragment of polypeptide chain (primary protein structure) with amino acid residues containing different side groups R¹ - R⁴.

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Fig. 2

Schematic representation of the two main types of secondary structure in proteins: a-helix (a), β-sheet (b).

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Fig. 3

Amino acids most often involved in NH...π and stacking interactions.

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Fig. 4

Schematic representation showing orientation of N-H vector to the aromatic ring centroid (M) and the nearest carbon atom(C_i). The figure was created by the authors using data of Ref.11.

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Fig. 5

NH^...π bond (a) and stacking (b) with participation of carboxamide group.The figurewas created by the authors using data of Refs 11,17.

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Fig. 6

Polarization of C H bonds (a) and schematic representation of quadrupole nature of the benzene ring (b). The figure was created by the authors using data of Ref. 22.

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Fig. 7

Mono-, bi- and tridentate benzene-ammonia complexes. The figure was created by the authors using data of Refs 25,26.

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Fig. 8

Mono-, bi- and tridentate benzene-ammonium ion complexes. The figurewas createdby the authors using data of Ref. 32

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Fig. 9

NH^...π Complexes of tris(pentafluorophenyl)borane-ammonia with benzene and toluene (7a,b) (a) and molecular structure of 7a with selected key distances in Å (b) (CCDC refcode UBUBAW, T=90 K). The figure was created by the authors using data of Ref. 33.

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Fig. 10

Region of stretching vibrations of N-H bonds in IR spectra (nujol) of (C6F5)3B•NH3 (a) and complex 7a (b). The figure was created by the authors using data of Ref. 33.

Region of stretching vibrations of N-H bonds in IR spectra (nujol) of (C₆F₅)₃B•NH₃(a) and complex 7a (b). The figure was created by the authors using data of Ref. 33.

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Fig. 11

NH^...π and NH^...O interactions in benzene solvate hemihydrate of amine 8 (NAJPIZ, 100 K). The figure was created by the authors using data of Ref. 34.

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Fig. 12

Theoretically optimized structures of σ-, π- and , π,σ-complexes of ammonia with benzene and its fluoro-, chloro-, difluoro- and methyl derivatives. Reproduced from Ref. 31 with permission of the American Chemical Society.

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Fig. 13

Structures suggested for complexes 4-fluorotoluene-NH3 (9a,b) and anisole-NH3 (10). The figure was created by the authors using data of Refs 38, 39.

Structures suggested for complexes 4-fluorotoluene-NH₃ (9a,b) and anisole-NH₃ (10). The figure was created by the authors using data of Refs 38, 39.

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Fig. 14

Phenylacetylene and its complexes with NH3 and MeNH2. The figure was created by the authors using data of Refs 42, 43.

Phenylacetylene and its complexes with NH₃ and MeNH₂. The figure was created by the authors using data of Refs 42, 43.

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Fig. 15

Proposed structures of isomeric 1:2 1-naphthol-NH3 complexes. The figurewas createdby the authors using data of Ref. 44.

Proposed structures of isomeric 1:2 1-naphthol-NH₃ complexes. The figurewas createdby the authors using data of Ref. 44.

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Fig. 16

Supposed structure of anthracene-NH3 complex. The figure was created by the authors using data of Ref. 45.

Supposed structure of anthracene-NH₃ complex. The figure was created by the authors using data of Ref. 45.

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Fig. 17

Fluorescent reagent 16 for the determination of 5-aminosalicylic acid (5-ASA). The figure was created by the authors using dataof Ref. 46.

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Fig. 18

Molecular structure of one of three independent molecules of 17 (FAGTAK, 283-303 K) (a) and a fragment of crystal packing of 17 (b). The figure was created by the authors using data of Ref. 53.

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Fig. 19

Fragment of the molecular structure of two H-linked molecules of amide 18 (BEFHIE, 150 K). The figure was created by the authors using data Ref. 54.

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Fig. 20

Molecular structure of 1-(1-naphthyl)-2-thiourea 19 (MOJDAS, 100 K). The figure was created by the authors using data of Ref. 55.

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Fig. 21

Molecular structure of salt 21. Selected parameters: φAB=58.7°; φAC=84.9°; ΣCNC=338.7°; NH...FBF3-=2.13 Å(YUWWOF, 100 K). The figure was created by the authors using data of Ref. 59.

Molecular structure of salt 21. Selected parameters: φ_AB=58.7°; φ_AC=84.9°; ΣCNC=338.7°; NH^...FBF₃^-=2.13 Å(YUWWOF, 100 K). The figure was created by the authors using data of Ref. 59.

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Fig. 22

Schematic representation of structures of pyrrole and indole dimers. Definition of intermolecular parameters, defining the mutual orientation of the units within the T-shaped indole dimer (24a). The figure was created by the authors using data of Refs 61, 62.

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Fig. 23

Theoretically optimized and alternative structures of complexes of benzene with pyridine, pyridinium and N-methyl pyridinium cations (E_int. in kcal mol^-1). The figure was created by the authors using data of Ref. 73.

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Fig. 24

Structural motives in complexes of 2-pyridone with benzene and fluorobenzenes. The figure was created by the authors using data of Refs 75-78.

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Fig. 25

Conformations of aniline dimer calculated for the gas phase. The figure was created by the authors using data of Ref. 79.

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Fig. 26

Fragment of aniline crystal structure (BAZGOY01, 100 K). The figure was created by the authors using data of Ref. 82.

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Fig. 27

NH...π binding in pyrrole61 (RUVQII, 103 K, a) and carbazole83 (CRBZOL04, 168 K, b) and dimer clusters of 3,6-di(4-alkoxyphenyl)carbazoles84 (UHUJUC, c, UHUJOW, 283-303 K, d) (XRD data). The figure was created by the authors using data of Refs 61, 83, 84.

NH^...π binding in pyrrole⁶¹ (RUVQII, 103 K, a) and carbazole⁸³ (CRBZOL04, 168 K, b) and dimer clusters of 3,6-di(4-alkoxyphenyl)carbazoles⁸⁴ (UHUJUC, c, UHUJOW, 283-303 K, d) (XRD data). The figure was created by the authors using data of Refs 61, 83, 84.

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Fig. 28

Self-association of indole in a co-crystal of N,N'-di-n-butyl-3,6-bis(phenylethynyl)pyromellitic diimide bis(indole) (NOCTUV, 123 K). The figure was created by the authors using data of Ref. 86.

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Fig. 29

1,8-Disubstituted naphthalenes used studying NH^...π for interactions. The figure was created by the authors using data of Ref. 20.

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Fig. 30

Molecular structures and selected geometrical parameters in tetrafluoroborates of protonated 9-dimethylaminobenzo[g]indoles 51-53 (XOBRAK, XOBREO, XOBRIS, 120 K; XRD data). The figurewas created by the authors using data of Ref. 19

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Fig. 31

Molecular structure (a) and fragment of the crystal lattice (b) of amine 48 (JUXFEQ, 120 K). The figure was created by the authors using data of Ref. 20.

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Fig. 32

Molecular structure (a) and a chain of H-bonded associates along the c axis (b) in the crystal lattice of amide 49 (JUXDUE, 120 K). The figure was created by the authors using data of Ref. 20.

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Fig. 33

Chemical shifts of the chloroform CH-proton in cyclohexane and benzene solutions. The figure was created by the authors using data of Ref. 96.

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Fig. 34

Fragments of the crystal lattice of ammonium tetraphenylborates 70 (a) and 71 (b). The figure was created by the authors using data of Refs 106, 107.

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Fig. 35

NH^...π and CH^...π contacts in salt 72. The figure was created by the authors using data of Ref. 108.

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Fig. 36

NH^...π interaction of type i → (i -- 1) for the most stable conformation of tripeptide Gly-Phe-Ala (gas-phase calculation). The figure was created by the authors using data of Ref. 127.

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Fig. 37

Selected examples of amide NH^...O=C and NH^...π hydrogen bonds in some peptide models. The figure was created by the authors using data of Refs 121, 123, 126

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Fig. 38

An example of a model pseudo peptide illustrating the possibility of structuring such compounds through NH...π interactions. The figure was created by the authors using data of Ref. 129

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Fig. 39

Schematic representation of the rigid proline-containing tripeptides as a model for studying NH^...π interactions in solution. The figure was created by the authors using data of Ref. 131.

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Fig. 40

Linear (93, 94) and diketopiperazine (95 ,96) structures of phenylalanyl-phenylalanine diastereomers. The figure was created by the authors using data of Ref. 132.

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Fig. 41

Molecular structure of DKP form of SPhe-SPhe (DUZDUX, 283-303 K). The figure was created by the authors using data of Ref. 135.

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Fig. 42

Examples of neurotransmitters (b, c) and related model compound 2-phenylethylamine (a).

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Fig. 43

Preferred conformations of protonated 1-amino- and 2-aminoindanes. The figure was created by the authors using data of Refs 140, 141.

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Fig. 44

The two most stable gauche-forms of 2-(o-fluorophenyl)ethylamine. The figure was created by the authors using data of Ref. 142.

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Fig. 45

Synthetic receptor 115 which efficiently encapsulates acetylcholine 114. The figure was created by the authors using data of Ref. 178.

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Fig. 46

Synthetic receptors for the recognition of hydrophilic and hydrophobic amino acids (a); theoretically calculated structure of the adduct of the doubly protonated receptor 129 with the tyrosine molecule lying in the potential minimum (b). Reproduced from Blasco et al.¹⁸⁵ with permission of the Royal Society of Chemistry.

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Fig. 47

Calculated energies of interaction of urea with aromatic rings that make up amino acids. Reproduced from Goyal et al.186 with permission of the American Chemical Society.

Calculated energies of interaction of urea with aromatic rings that make up amino acids. Reproduced from Goyal et al.¹⁸⁶ with permission of the American Chemical Society.

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Fig. 48

NH...π interaction in vitamin B12 coenzyme. The figure was created by the authors using data of Ref. 187.

NH^...π interaction in vitamin B₁₂ coenzyme. The figure was created by the authors using data of Ref. 187.

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Fig. 49

Macrocyclic polyamides 132a-e for studying NH^...π interactions. The figure was created by the authors using data of Ref. 189.

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Fig. 50

Schematic representation of NH^...π interaction of the neurokinin receptor with the drug CP-96345. The figure was created by the authors using data of Ref. 190.

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Fig. 51

Amino acid-based naphthocyclophane molecular rotors. The figure was created by the authors using data of Ref. 193.

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Fig. 52

Stabilizing micelle formation interaction of two amphiphilic molecules: NH^...π interaction between alanyl-based and phenylalanyl-based surfactants (134); π^...π interaction between two phenylalanyl-based surfactants (135). The figure was created by the authors using data of Ref. 194.

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Fig. 53

Molecular structure of diastereomeric salt of 1,1'-binaphthyl-2,2'-diol with dehydroabietyl amidine 138 (ATOFIB, 150 K). The figure was created by the authors using data of Ref. 196.

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Scheme 1

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Scheme 2

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Scheme 3

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Scheme 4

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Scheme 5

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Structure 8

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Structures 17 - 19

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Structures 20, 21

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Structures 25a-c

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Structures 38 - 41

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Structure 90

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Structures 136, 137

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Keywords

amino acids

carboxamides

Hydrogen bonding

non-valence forces

secondary protein structure

supramolecular structures

Abstract

The review summarizes the information accumulated to date on NH⋯π interactions, which represent an unconventional type of hydrogen bonding between the NH-donor (most often amines, carboxamides or NH heterocycles) and a proton acceptor (usually an electron-rich aromatic or heteroaromatic rings). The importance of NH⋯π interactions stems mainly from their involvement in the structuring of proteins and some other biomolecules, as well as in molecular recognition processes. The growth of knowledge on NH⋯π interactions contributes to a better understanding of complex biochemical processes, stimulates the development of new drugs and improved methods of their targeted delivery. Since the study of NH⋯π interactions on living tissues is rather difficult, their modelling on various synthetic objects has become widespread. In the review, various types of such models are systematized and compared in regard of their geometry, stereo dynamics, and NH⋯π binding energy. Examples of reactions driven by NH⋯π interaction are given, as well as examples of practical use. A rational classification of existing models is proposed, which facilitates their convenient consideration.The bibliography includes 196 references.