Carbon-Centered Hydrogen Bonds in Proteins

Pharmacological and computational analysis of the involvement of the 5-HT4 receptor in the antidepressant-like effect of N-(3-(phenylselanyl)prop-2-yn-1-yl)benzamide in mice

The serotonin type 4 receptor (5-HT4R)shows promise as a target for treating major depressive disorder (MDD). Studies have demonstrated that 5-HT4R agonists have a faster antidepressant-like effect compared to conventional medications. Developing drugs that modulate this receptor could lead to faster and more effective MDD treatments. The compound N-(3-(phenylselanyl)prop-2-yn-1-yl)benzamide (SePB) induces an antidepressant-like effect in mice. The present study explored if the 5-HT4R mediates SePB's antidepressant effect. For this, male Swiss mice were treated with GR113808 (0.1 mg/kg, intraperitoneally - i.p.), a 5-HT4R antagonist, and SePB (10 mg/kg, intragastrically - i.g), and then subjected to the tail-suspension test (TST) and open-field test (OFT). In silico tests were conducted to analyze SePB's binding affinity to the 5-HT4R and identify participating amino acid residues. The administration of GR113808 blocked the antidepressant-like effect of SePB in the TST without changing locomotor activity in the OFT. Moreover, SePB exhibited a high binding affinity between the 5-HT4R (-7.9 kcal/mol) and the amino acid residues Leu298, Asp100, Thr97, Arg96, Glu80, Leu81, Cys184, Val185, and Phe186 seem to be important for this interaction. The involvement of the 5-HT4R in the antidepressant-like effect of SePB suggests potential for novel therapies in MDD.

Exploiting the (-C-H···C-) Interaction to Design Cage-Functionalized Organic Superbases and Hyperbases: A Computational Study

A set of carbon center-based P-ylidesubstituting bases have been exploited computationally with pentacyclo[5.4.0.02,6.03,10.05.9]undecane (PCU) and pentacyclo [6.4.0.02,7.03,11.06,10] dodecane (PCD) scaffolds using the B3LYP-D3/6-311+G(d,p) level of theory. The proton affinities calculated in the gas phase are in the range of superbases and hyperbases. The Atomsin-Molecules and Natural Bond Orbital calculations reveal that the -C-H···C- interaction plays a substantial role in improving the basicity, and tuning the -C-H···C- interaction can enhance the basicity of such systems. The free activation energy for proton exchange for PCD and PCU scaffolds substituted with P-ylide is substantially low. The computed results reveal the strength and nature of such - C-H···C- interactions compared to the -N-H···N- hydrogen bonds. The isodesmic reactions suggest that the superbasicity achieved using these frameworks arises from a combination of several factors, such as the ring strain of the bases in their unprotonated form, steric repulsion, and the intramolecular -C-H···C- interaction.

Alkali metal⋯methyl short contacts in aluminates: more than agostic interactions

Knowing the nature and strength of noncovalent interactions is key to enhancing the synthetic methods and catalytic processes in which they are involved. We present herein the synthesis and characterization of a novel aluminium sodium oximate compound, followed by a comprehensive computational study of the sodium⋯methyl interaction that appears in its crystal structure. Our experimental results have been compared to a large set of structural data retrieved from the Cambridge Structural Database in order to assess the main geometrical preferences of these interactions. Moreover, representative model systems have been studied at the DFT level and the topology of their electron density analysed by means of QTAIM. Although alkali metal⋯methyl short contacts have been traditionally considered as agostic interactions, we have demonstrated here that the physical origin of the attraction relies on the electron-rich carbon atom bound to aluminium and its interaction with the cation.

Stabilizing σ-hole Dimethyl Interactions

Methyl groups bound to electronegative atoms, such as N or O, are recognized to participate in tetrel bonding as Lewis acids. On the other hand, the capability of methyl groups bound to electropositive atoms, such as B or Al, to act as Lewis bases has been recently reported. Herein, we analyze the combination of these two behaviors to establish attractive methyl···methyl interactions. We have explored the Cambridge Structural Database to find experimental examples of these dimethyl-bound systems, finding a significant degree of directionality in the relative disposition of the two methyl groups. Moreover, we have carried out a comprehensive computational analysis at the DFT level of the dimethyl interactions, including the natural bond orbital, energy decomposition analysis, and topological analysis of the electron density (QTAIM and NCI). The dimethyl interaction is characterized as weak yet attractive and based on electrostatics, with a non-negligible contribution from orbital charge transfer and polarization.

Probing the Effect of Photovoltaic Material on Voc in Ternary Polymer Solar Cells with Non-Fullerene Acceptors by Machine Learning

The power conversion efficiency (PCE) of ternary polymer solar cells (PSCs) with non-fullerene has a phenomenal increase in recent years. However, improving the open circuit voltage (V_oc) of ternary PSCs with non-fullerene still remains a challenge. Therefore, in this work, machine learning (ML) algorithms are employed, including eXtreme gradient boosting, K-nearest neighbor and random forest, to quantitatively analyze the impact mechanism of V_oc in ternary PSCs with the double acceptors from the two aspects of photovoltaic materials. In one aspect of photovoltaic materials, the doping concentration has the greatest impact on V_oc in ternary PSCs. Furthermore, the addition of the third component affects the energy offset between the donor and acceptor for increasing V_oc in ternary PSCs. More importantly, to obtain the maximum V_oc in ternary PSCs with the double acceptors, the HOMO and LUMO energy levels of the third component should be around (-5.7 ± 0.1) eV and (-3.6 ± 0.1) eV, respectively. In the other aspect of molecular descriptors and molecular fingerprints in the third component of ternary PSCs with the double acceptors, the hydrogen bond strength and aromatic ring structure of the third component have high impact on the V_oc of ternary PSCs. In partial dependence plot, it is clear that when the number of methyl groups is four and the number of carbonyl groups is two in the third component of acceptor, the V_oc of ternary PSCs with the double acceptors can be maximized. All of these findings provide valuable insights into the development of materials with high V_oc in ternary PSCs for saving time and cost.

Halogen Bond Induced Structural and Photophysical Properties Modification in Organic-Inorganic Hybrid Manganese Halides

The role of halogen bonding in organic-inorganic hybrid (OIH) halides was seldom investigated despite its potential to enhance the stability of the compound. In this context, we have synthesized (2-methylbenzimidazolium)MnCl₃(H₂O)·H₂O (compound 1) crystallizing in a monoclinic space group P2₁/c with a 1D infinite chain of edge shared Mn octahedra. In contrast, the chloro-substituted derivative (5-chloro-2-methylbenzimidazolium)₂MnCl₄ (compound 2) exhibits 0D Mn tetrahedra with a triclinic P1̅ structure. This structural modification from 1D Mn octahedra to 0D Mn tetrahedra involves a unique type-II halogen bonding between organic chlorine (C-Cl) and inorganic chloride (Cl-Mn) ions. Compound 1 exhibits red emission, whereas compound 2 demonstrates dual-band emission, resulting from energy transfer from the organic amine to Mn centers. To rationalize this interesting modulation in structure and photophysical properties, the role of halogen bonding is explored in terms of quantitative electron density analysis and intermolecular interaction energies.

In vivo surface-enhanced Raman scattering nanosensor for the real-time monitoring of multiple stress signalling molecules in plants

When under stress, plants release molecules to activate their defense system. Detecting these stress-related molecules offers the possibility to address stress conditions and prevent the development of diseases. However, detecting endogenous signalling molecules in living plants remains challenging due to low concentrations of these analytes and interference with other compounds; additionally, many methods currently used are invasive and labour-intensive. Here we show a non-destructive surface-enhanced Raman scattering (SERS)-based nanoprobe for the real-time detection of multiple stress-related endogenous molecules in living plants. The nanoprobe, which is placed in the intercellular space, is optically active in the near-infrared region (785 nm) to avoid interferences from plant autofluorescence. It consists of a Si nanosphere surrounded by a corrugated Ag shell modified by a water-soluble cationic polymer poly(diallyldimethylammonium chloride), which can interact with multiple plant signalling molecules. We measure a SERS enhancement factor of 2.9 × 10⁷ and a signal-to-noise ratio of up to 64 with an acquisition time of ~100 ms. To show quantitative multiplex detection, we adopted a binding model to interpret the SERS intensities of two different analytes bound to the SERS hot spot of the nanoprobe. Under either abiotic or biotic stress, our optical nanosensors can successfully monitor salicylic acid, extracellular adenosine triphosphate, cruciferous phytoalexin and glutathione in Nasturtium officinale, Triticum aestivum L. and Hordeum vulgare L.-all stress-related molecules indicating the possible onset of a plant disease. We believe that plasmonic nanosensor platforms can enable the early diagnosis of stress, contributing to a timely disease management of plants.

Effect of Delta and Omicron Mutations on the RBD-SD1 Domain of the Spike Protein in SARS-CoV-2 and the Omicron Mutations on RBD-ACE2 Interface Complex

The receptor-binding domain (RBD) is the essential part in the Spike-protein (S-protein) of SARS-CoV-2 virus that directly binds to the human ACE2 receptor, making it a key target for many vaccines and therapies. Therefore, any mutations at this domain could affect the efficacy of these treatments as well as the viral-cell entry mechanism. We introduce ab initio DFT-based computational study that mainly focuses on two parts: (1) Mutations effects of both Delta and Omicron variants in the RBD-SD1 domain. (2) Impact of Omicron RBD mutations on the structure and properties of the RBD-ACE2 interface system. The in-depth analysis is based on the novel concept of amino acid-amino acid bond pair units (AABPU) that reveal the differences between the Delta and/or Omicron mutations and its corresponding wild-type strain in terms of the role played by non-local amino acid interactions, their 3D shapes and sizes, as well as contribution to hydrogen bonding and partial charge distributions. Our results also show that the interaction of Omicron RBD with ACE2 significantly increased its bonding between amino acids at the interface providing information on the implications of penetration of S-protein into ACE2, and thus offering a possible explanation for its high infectivity. Our findings enable us to present, in more conspicuous atomic level detail, the effect of specific mutations that may help in predicting and/or mitigating the next variant of concern.

Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking

Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.

Hydrogen Bonding with Polonium

Hydrogen bonding (H-bonding) with heavier chalcogens such as polonium and tellurium is almost unexplored owing to their lower electronegativities, providing us an opportunity to delve into the uncharted territory of...

Enhancement of tetrel bond involving tetrazole-TtR3 (Tt = C, Si; R = H, F). Promotion of SiR3 transfer by a triel bond

The combination of a CR3 (R = H, F) with a tetrazole can result in a moderate carbon bond, which can be further strengthened by a triel bond. On the other hand, SiR3 group is half transferred between the two N atoms in these conditions.