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We present a method to rapidly identify hydrogen-mediated interactions in proteins (e.g., hydrogen bonds, hydrogen bonds, water-mediated hydrogen bonds, salt bridges, and aromatic π-hydrogen interactions) through heavy atom geometry alone, that is, without needing to explicitly determine hydrogen atom positions using either experimental or theoretical methods. By including specific real (or virtual) partner atoms as defined by the atom type of both the donor and acceptor heavy atoms, a set of unique angles can be rapidly calculated. By comparing the distance between the donor and the acceptor and these unique angles to the statistical preferences observed in the Protein Data Bank (PDB), we were able to identify a set of conserved geometries (15 for donor atoms and 7 for acceptor atoms) for hydrogen-mediated interactions in proteins. This set of identified interactions includes every polar atom type present in the Protein Data Bank except OE1 (glutamate/glutamine sidechain) and a clear geometric preference for the methionine sulfur atom (SD) to act as a hydrogen bond acceptor. This method could be readily applied to protein design efforts.

This chapter contains sections titled: Introduction Cooperative Effect of the CH/π Hydrogen Bond CH/π Hydrogen Bonds in Supramolecular Chemistry Crystallographic Database Analyses Systematic CSD Analyses of the CH/π Hydrogen Bond Summary and Outlook Acknowledgments References

Many carbohydrate-binding proteins contain aromatic amino acid residues in their binding sites. These residues interact with carbohydrates in a stacking geometry via CH/π interactions. These interactions can be found in carbohydrate-binding proteins, including lectins, enzymes and carbohydrate transporters. Besides this, many non-protein aromatic molecules (natural as well as artificial) can bind saccharides using these interactions. Recent computational and experimental studies have shown that carbohydrate–aromatic CH/π interactions are dispersion interactions, tuned by electrostatics and partially stabilized by a hydrophobic effect in solvated systems.

This study demonstrates the presence of CH-π interaction in poly [9,9-dioctylfluorenyl-2,7-diyl] (PFO-1) due to an aggregate formation of PFO-1 in the liquid state. The absorption spectra of PFO-1 in certain solvents at low concentrations showed a single band at 390 nm. However, when using high concentrations, a new band at 437 nm appeared. This band is due to the aggregate formation of PFO-1. The aggregate formation occurs as a result of the CH interaction of the n-alkyl side chains with π-electrons in the benzene ring. The optical characteristics of another conjugated polymer of poly [9,9-di-(2-ethylhexyl)-fluorenyl-2,7-diyl] (PFO-2) were investigated to confirm the CH-π interaction. The absorption showed only one wavelength at 390 nm without any new band at the end of the spectrum, even at higher concentrations and lower temperatures. The main reason for the absence of aggregate formation in PFO-2 is the sterical hindrance caused by the branched alkyl side chains. In addition, Density Functional Theory (DFT) was used to compute the HOMO–LUMO transitions, electron charge distribution, and frontier molecular orbitals for each polymer. The Mulliken charge distribution and demonstrated a notable difference in the reactivity of the alkyl side chain, confirming the higher ability of PFO-1 to form CH-π bonds. docking model emphasized that the band at 437 nm could be attributed to the interaction between CH in the n-alkyl side chain and π bonds in the aromatic rings of PFO-1.

The SARS-CoV-2 main protease (Mpro), essential for viral replication, remains a prime target for antiviral drug design against COVID-19 and related coronaviruses. In this study, we present a systematic investigation into the molecular determinants of Mpro inhibition using an integrated approach combining large-scale data mining, cheminformatics, and quantum chemical calculations. A curated dataset comprising 963 high-resolution structures of Mpro–ligand complexes—348 covalent and 615 non-covalent inhibitors—was mined from the Protein Data Bank. Cheminformatics analysis revealed distinct physicochemical profiles for each inhibitor class: covalent inhibitors tend to exhibit higher hydrogen bonding capacity and sp3 character, while non-covalent inhibitors are enriched in aromatic rings and exhibit greater aromaticity and lipophilicity. A novel descriptor, Weighted Hydrogen Bond Count (WHBC), normalized for molecular size, revealed a notable inverse correlation with aromatic ring count, suggesting a compensatory relationship between hydrogen bonding and π-mediated interactions. To elucidate the energetic underpinnings of molecular recognition, 40 representative inhibitors (20 covalent, 20 non-covalent) were selected based on principal component analysis and aromatic ring content. Quantum mechanical calculations at the double-hybrid B2PLYP/def2-QZVP level quantified non-bonded interaction energies, revealing that covalent inhibitors derive binding strength primarily through hydrogen bonding (~63.8%), whereas non-covalent inhibitors depend predominantly on π–π stacking and CH–π interactions (~62.8%). Representative binding pocket analyses further substantiate these findings: the covalent inhibitor F2F-2020198-00X exhibited strong hydrogen bonds with residues such as Glu166 and His163, while the non-covalent inhibitor EDG-MED-10fcb19e-1 engaged in extensive π-mediated interactions with residues like His41, Met49, and Met165. The distinct interaction patterns led to the establishment of pharmacophore models, highlighting key recognition motifs for both covalent and non-covalent inhibitors. Our findings underscore the critical role of aromaticity and non-bonded π interactions in driving binding affinity, complementing or, in some cases, substituting for hydrogen bonding, and offer a robust framework for the rational design of next-generation Mpro inhibitors with improved selectivity and resistance profiles.

We report high-level ab initio calculations (CCSD(T)(full)/CBS//SCS-RI-MP2(full)/aug-cc-pwCVTZ) that demonstrate the importance of cooperativity effects when Anion–π and CH/π interactions are simultaneously established with benzene as the π-system. In fact, most of the complexes exhibit high cooperativity energies that range from 17% to 25.3% of the total interaction energy, which is indicative of the strong influence of the CH/π on the Anion–π interaction and vice versa. Moreover, the symmetry-adapted perturbation theory (SAPT) partition scheme was used to study the different energy contributions to the interaction energies and to investigate the physical nature of the interplay between both interactions. Furthermore, the Atoms in Molecules (AIM) theory and the Non-Covalent Interaction (NCI) approach were used to analyze the two interactions further. Finally, a few examples from the Protein Data Bank (PDB) are shown. All results stress that the concurrent formation of both interactions may play an important role in biological systems due to the ubiquity of CH bonds, phenyl rings, and anions in biomolecules.

Organic pigments are prone to aggregate, resulting in decreasing of their properties. Therefore, pigment dispersants are demanded to have both high adsorption capacity and aggregation inhibiting property for pigment particles. In the present study, the suitability of cellulose nanofibers (CNFs) as a dispersant for quinacridone, a common red–violet organic pigment, was investigated. Quinacridone particles were well adsorbed on the CNFs. Scanning electron microscopy images of the quinacridone–CNF mixtures showed that the quinacridone primary particles were stacked along the cellulose fibers, and the aggregations were inhibited. In addition, the size of the quinacridone particles had an effect on their color. The interactions of quinacridone and cellulose were investigated by Fourier transform infrared (FTIR) and solution-state nuclear magnetic resonance (NMR) spectroscopies. FTIR spectra of the quinacridone–CNF mixtures indicated the intermolecular interactions between quinacridone and cellulose. Because quinacridone and CNFs were insoluble in the NMR solvents, gel-state NMR spectroscopy, which has been used for the whole plant cell wall analysis, was conducted on them. Consequently, whole signals arising from quinacridone and cellulose were enabled to be assigned, and the coupling constant of quinacridone has reported for the first time. The nuclear Overhauser effect spectroscopy (NOESY)-NMR spectrum of the quinacridone–CNF mixture revealed both NH group and aromatic moiety of quinacridone were interacted with glucose unit. The former was considered to be related to hydrogen bonding, and the latter to CH–π interactions. These specific interactions might contribute to achieve the high adsorption capacity of CNFs for quinacridone.Graphic abstract

Polymer-assisted liquid exfoliation of graphite is a promising technique for the scale production of defect-free graphene. In this paper, graphene nanosheets (less than 5 layers, with lateral size about 500–1500 nm) were successfully produced by directly exfoliating graphite in low boiling point chloroform, in the presence of hydrocarbon polymers such as linear paraffin wax and hyperbranched polyethylene. The effect of polymer topological structure, molecular weight, initial graphite concentration, the ratio of polymer and graphite on the exfoliation has been investigated in detail. CH-π interaction between the hydrocarbon polymers and aromatic structure in graphite, together with the steric repulsion and solubility of absorbed polymer, facilitating the exfoliation and stabilization of graphene sheets. C–H bond involved in CH-π interaction was mainly originated from methylene (-CH2-) group, which has been revealed by nuclear magnetic resonance technique. This work is of practical importance for the understanding of mechanism in polymer-assisted liquid exfoliation of graphite.

Human cytochrome P450 1A2 (CYP1A2) is one of the key CYPs that activate aflatoxin B1 (AFB1), a notorious mycotoxin, into carcinogenic exo-8,9-epoxides (AFBO) in the liver. Although the structure of CYP1A2 is available, the mechanism of CYP1A2-specific binding to AFB1 has not been fully clarified. In this study, we used calculation biology to predict a model of CYP1A2 with AFB1, where Thr-124, Phe-125, Phe-226, and Phe-260 possibly participate in the specific binding. Site-directed mutagenesis was performed to construct mutants T124A, F125A, F226A, and F260A. Escherichia coli-expressed recombinant proteins T124A, F226A, and F260A had active structures, while F125A did not. This was evidenced by Fe2+∙Carbon monoxide (CO)-reduced difference spectra and circular dichroism spectroscopy. Mutant F125A was expressed in HEK293T cells. Steady kinetic assays showed that T124A had enhanced activity towards AFB1, while F125A, F226A, and F260A were significantly reduced in their ability to activate AFB1, implying that hydrogen bonds between Thr-124 and AFB1 were not important for substrate-specific binding, whereas Phe-125, Phe-226, and Phe-260 were essential for the process. The computation simulation and experimental results showed that the three key CH/π interactions between Phe-125, Phe-226, or Phe-260 and AFB1 collectively maintained the stable binding of AFB1 in the active cavity of CYP1A2.

When crystallized from ethanol, 7,7-dimethyl-2-pyridin-4-yl-6,7-dihydro-1,2,4-triazolo[1,5-a][1,3,5]triazin-5-amine forms crystals which have monoclinic (P21/n) symmetry with unit cell dimensions a = 7.3326(5) Å, b = 19.4897(14) Å, c = 8.6586(6) Å, α = 90°, β = 106.069(2)°, γ = 90°, V = 1189.06(14) Å3, Z = 4. The triazine ring in the molecule has a flattened boat conformation with gem-dimethyl groups as flagpole and bowsprit at the bow. The puckering parameters for the ring are: Q = 0.2996(14) Å, θ = 111.7(3)° and φ = 124.1(3)°. In the crystal, molecules are arranged in the three types of chains generated by the intermolecular NH···N hydrogen bonds. The extended chains with the C(11) graph-set motif running along a [010] axis are formed by the amino group hydrogen atom and the pyridine nitrogen atom of another molecule. The C(4)C(6) chains with the R22(8) binary graph-set motif running along a [101] direction are formed by linking the amino group hydrogen atom and the hydrogen atom at the triazine nitrogen atom with the triazole and triazine nitrogen atoms of another molecule, respectively. The centrosymmetric inverted dimers are formed via the C-H···π interactions between the methyl group hydrogen and the pyridine ring of the pair molecule.