Five-membered heterocycles. Part III. Aromaticity of 1,3-imidazole in 5+n hetero-bicyclic molecules

Mrozek, A.; Karolak‐Wojciechowska, J.; Kieć‐Kononowicz, Katarzyna

doi:10.1016/s0022-2860(03)00282-5

Cited by 34 publications

(20 citation statements)

References 18 publications

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“…Mrozek and co-workers [24][25][26][27], in their study, on the HOMA of five-membered heterocyles using bond length from X-ray, also found that in the rHOMA index isoxazoles and oxazoles are not aromatic compounds and furans are classified as anti-aromatic compounds. From the results described in Table 5, it is possible to state that for six-membered heterocycles, there is a variation of aromaticity with the variation in number and position of nitrogen.…”

Section: Resultsmentioning

confidence: 95%

Aromaticity in heterocycles: new HOMA index parametrization

2011

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Section: Resultsmentioning

confidence: 95%

Aromaticity in heterocycles: new HOMA index parametrization

2011

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“…Among the 20 natural amino acids histidine (His, H) may be the most versatile actor in the protein architectures and bioactivities [1-4]. The versatility of histidine in molecular interactions arises from its unique molecular structure [5]. The side chain imidazole of histidine is an aromatic motif; an ionizable group with the acidic ionization constant around pK a =6.5; a coordinating ligand of metallic cations (for example, Ca 2+ and Zn 2+ ); and a hydrogen bond donor and acceptor.…”

Section: Introductionmentioning

confidence: 99%

The multiple roles of histidine in protein interactions

Liao

et al. 2013

Chemistry Central Journal

392

282

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BackgroundAmong the 20 natural amino acids histidine is the most active and versatile member that plays the multiple roles in protein interactions, often the key residue in enzyme catalytic reactions. A theoretical and comprehensive study on the structural features and interaction properties of histidine is certainly helpful.ResultsFour interaction types of histidine are quantitatively calculated, including: (1) Cation-π interactions, in which the histidine acts as the aromatic π-motif in neutral form (His), or plays the cation role in protonated form (His+); (2) π-π stacking interactions between histidine and other aromatic amino acids; (3) Hydrogen-π interactions between histidine and other aromatic amino acids; (4) Coordinate interactions between histidine and metallic cations. The energies of π-π stacking interactions and hydrogen-π interactions are calculated using CCSD/6-31+G(d,p). The energies of cation-π interactions and coordinate interactions are calculated using B3LYP/6-31+G(d,p) method and adjusted by empirical method for dispersion energy. ConclusionsThe coordinate interactions between histidine and metallic cations are the strongest one acting in broad range, followed by the cation-π, hydrogen-π, and π-π stacking interactions. When the histidine is in neutral form, the cation-π interactions are attractive; when it is protonated (His+), the interactions turn to repulsive. The two protonation forms (and pKa values) of histidine are reversibly switched by the attractive and repulsive cation-π interactions. In proteins the π-π stacking interaction between neutral histidine and aromatic amino acids (Phe, Tyr, Trp) are in the range from -3.0 to -4.0 kcal/mol, significantly larger than the van der Waals energies.

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“…The leaf that includes the amides Q and N interestingly includes H. Although H is aromatic, it is not found grouped with the other aromatic residues W, F, and Y in the red branch. There is good precedent for the finding that the histidine imidazole group may function in proteins primarily as an amide (likely due to its dual role as a hydrogen‐bond donor and acceptor), with aromaticity being of lesser importance to its role in structure . The inclusion of the other three aromatic residues in the same branch points to a group of characteristic three‐body interactions common among these aromats, despite the relatively low average I 2 value of the F residue‐matrix, which may be influenced by its participation in hydrophobic packing .…”

Section: Resultsmentioning

confidence: 99%

“…There is good precedent for the finding that the histidine imidazole group may function in proteins primarily as an amide 79 (likely due to its dual role as a hydrogen-bond donor and acceptor), with aromaticity being of lesser importance to its role in structure. 80,81 The inclusion of the other three aromatic residues in the same branch points to a group of characteristic three-body interactions common among these aromats, despite the relatively low average I 2 value of the F residue-matrix, which may be influenced by its participation in hydrophobic packing. 82-84 As hydrophobic packing is an interaction with no substantial need for directionality, 85 the SC spatial correlations of F with other hydrophobic residues will be very low.…”

Section: Figurementioning

confidence: 99%

Application of information theory to a three‐body coarse‐grained representation of proteins in the PDB: Insights into the structural and evolutionary roles of residues in protein structure

2014

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Knowledge-based methods for analyzing protein structures, such as statistical potentials, primarily consider the distances between pairs of bodies (atoms or groups of atoms). Considerations of several bodies simultaneously are generally used to characterize bonded structural elements or those in close contact with each other, but historically do not consider atoms that are not in direct contact with each other. In this report, we introduce an information-theoretic method for detecting and quantifying distance-dependent through-space multibody relationships between the sidechains of three residues. The technique introduced is capable of producing convergent and consistent results when applied to a sufficiently large database of randomly chosen, experimentally solved protein structures. The results of our study can be shown to reproduce established physico-chemical properties of residues as well as more recently discovered properties and interactions. These results offer insight into the numerous roles that residues play in protein structure, as well as relationships between residue function, protein structure, and evolution. The techniques and insights presented in this work should be useful in the future development of novel knowledge-based tools for the evaluation of protein structure.

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Five-membered heterocycles. Part III. Aromaticity of 1,3-imidazole in 5+n hetero-bicyclic molecules

Cited by 34 publications

References 18 publications

Aromaticity in heterocycles: new HOMA index parametrization

Aromaticity in heterocycles: new HOMA index parametrization

The multiple roles of histidine in protein interactions

Application of information theory to a three‐body coarse‐grained representation of proteins in the PDB: Insights into the structural and evolutionary roles of residues in protein structure

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