Analyzing the cation-aromatic interactions in proteins: Cation-aromatic database V2.0

The cation-aromatic database (CAD) is a comprehensive repository of cation-aromatic motifs found in experimentally determined protein structures, first reported in 2007 [Proteins, 2007, 67, 1179]. The present article is an update of CAD that contains information of approximately 27.26 million cation-aromatic motifs. CAD uses three distance parameters (r, d1, and d2) to determine the position of the cation relative to the centroid of the aromatic residue and classifies the motifs as cation-π or cation-σ interactions. As of June 2023, about 193 936 protein structures were retrieved from Protein Data Bank, and this resulted in the identification of an impressive number of 27 255 817 cation-aromatic motifs. Among these motifs, spherical motifs constituted 94.09%, while cylindrical motifs made up the remaining 5.91%. When considering the interaction of metal ions with aromatic residues, 965 564 motifs are identified. Remarkably, 82.08% of these motifs involved the binding of metal ions to the amino acid HIS. Moreover, the analysis of binding preferences between cations and aromatic residues revealed that the HIS-HIS, PHE-ARG, and TRP-ARG pairs exhibited a preferential geometry. The motif pair HIS-HIS was the most prevalent, accounting for 19.87% of the total, closely followed by TYR-LYS at 10.17%. Conversely, the motif pair TRP-HIS had the lowest occurrence, representing only 4.20% of the total. The data generated help in revealing the characteristics and biological functions of cation-aromatic interactions in biological molecules. The updated version of CAD (Cation-Aromatic Database V2.0) can be accessed at https://acds.neist.res.in/cadv2.

The borderless world of chemical bonding across the van der Waals crust and the valence region

The definition of the van der Waals crust as the spherical section between the atomic radius and the van der Waals radius of an element is discussed and a survey of the application of the penetration index between two interacting atoms in a wide variety of covalent, polar, coordinative or noncovalent bonding situations is presented. It is shown that this newly defined parameter permits the comparison of bonding between pairs of atoms in structural and computational studies independently of the atom sizes.

Revisiting conventional noncovalent interactions towards a complete understanding: from tetrel to pnicogen, chalcogen, and halogen bond

Typical noncovalent interactions, including tetrel (TtB), pnicogen (PniB), chalcogen (ChalB), and halogen bonds (HalB), were systematically re-investigated by modeling the N⋯Z interactions (Z = Si, P, S, Cl) between NH3 - as a nucleophilic, and SiF4, PF3, SF2, and ClF - as electrophilic components, employing highly reliable ab initio methods. The characteristics of N⋯Z interactions when Z goes from Si to Cl, were examined through their changes in stability, vibrational spectroscopy, electron density, and natural orbital analyses. The binding energies of these complexes at CCSD(T)/CBS indicate that NH3 tends to hold tightly most with ClF (-34.7 kJ mol-1) and SiF4 (-23.7 kJ mol-1) to form N⋯Cl HalB and N⋯Si TtB, respectively. Remarkably, the interaction energies obtained from various approaches imply that the strength of these noncovalent interactions follows the order: N⋯Si TtB > N⋯Cl HalB > N⋯S ChalB > N⋯P PniB, that differs the order of their corresponding complex stability. The conventional N⋯Z noncovalent interactions are characterized by the local vibrational frequencies of 351, 126, 167, and 261 cm-1 for TtB, PniB, ChalB, and HalB, respectively. The SAPT2+(3)dMP2 calculations demonstrate that the primary force controlling their strength retains the electrostatic term. Accompanied by the stronger strength of N⋯Si TtB and N⋯Cl HalB, the AIM and NBO results state that they are partly covalent in nature with amounts of 18.57% and 27.53%, respectively. Among various analysis approaches, the force constant of the local N⋯Z stretching vibration is shown to be most accurate in describing the noncovalent interactions.

Unified classification of non-covalent bonds formed by main group elements: a bridge to chemical bonding

Using correlation plots of binding energy and electron density at the bond critical point, we investigated the nature of intermolecular non-covalent bonds (D-X⋯A, where D = O/S/F/Cl/Br/H, mostly, X = main group elements (except noble gases), A = H2O, NH3, H2S, PH3, HCHO, C2H4, HCN, CO, CH3OH, and CH3OCH3). The binding energies were calculated at the MP2 level of theory, followed by Atoms in Molecules (AIM) analysis of the ab initio wave functions to obtain the electron density at the bond critical point (BCP). For each non-covalent bond, the slopes of the binding energy versus electron density plot have been determined. Based on their slopes, non-covalent bonds are classified as non-covalent bond closed-shell (NCB-C) or non-covalent bond shared-shell (NCB-S). Intriguingly, extrapolating the slopes of the NCB-C and NCB-S cases leads to intramolecular "ionic" and "covalent" bonding regimes, establishing a link between such intermolecular non-covalent and intramolecular chemical bonds. With this new classification, hydrogen bonds and other non-covalent bonds formed by a main-group atom in a covalent molecule are classified as NCB-S. Atoms found in ionic molecules generally form NCB-C type bonds, with the exception of carbon which also forms NCB-C type bonds. Molecules with a tetravalent carbon do behave like ions in ionic molecules such as NaCl and interact with other molecules through NCB-C type bonds. As with the chemical bonds, there are some non-covalent bonds that are intermediate cases.

Tracing the transition from covalent to non-covalent functionalization of pyrene through C-, N-, and O-based ionic and radical substrates using quantum mechanical calculations

Pyrene is one of the widely investigated aromatic hydrocarbons given its unique optical and electronic properties. Modulating inherent characteristics of pyrene via covalent or non-covalent functionalization has been attractive for a wide variety of advanced biomedical and other device applications. In this study, we have reported the functionalization of pyrene via C, N, and O based ionic and radical substrates, and emphasized the transition of covalent to non-covalent functionalization through making the modulation in the substrate. As expected, strong interactions were observed for cationic substrates, however, anionic substrates also exhibited a competitive binding strength. For instance, methyl and phenyl substituted CH₃ complexes exhibited IEs in the range of -17 kcal mol^-1 to -127 kcal mol^-1 and -14 kcal mol^-1 to -95 kcal mol^-1 and for cationic and anionic substrates, respectively. The analysis of topological parameters showed that un-substituted cationic, anionic, and radical substrates interact with pyrene via covalent interactions, and further become non-covalent upon methylation and phenylation of the substrates. In cationic complexes, the polarisation component is observed to be dominating the interactions, whereas highly competitive contributions from polarization and exchange components were observed in anionic and radical complexes. The contribution of the dispersion component increases with an increase in the degree of methylation and phenylation of the substrate, and starts dominating once the interactions become non-covalent in nature.

Modeling of magnesium-decorated graphene quantum dot nanostructure for trapping AsH3, PH3 and NH3 gases

A magnesium-decorated graphene quantum dot (C₂₄H₁₂-Mg) surface has been examined theoretically using density functional theory (DFT) computations at the ωB97XD/6-311++G(2p,2d) level of theory to determine its sensing capability toward XH₃ gases, where X = As, N and P, in four different phases: gas, benzene solvent, ethanol solvent and water. This research was carried out in different phases in order to predict the best possible phase for the adsorption of the toxic gases. Analysis of the electronic properties shows that in the different phases the energy gap follows the order NH₃@C₂₄H₁₂-Mg < PH₃@C₂₄H₁₂-Mg < AsH₃@C₂₄H₁₂-Mg. The results obtained from the adsorption studies show that all the calculated adsorption energies are negative, indicating that the nature of the adsorption is chemisorption. The adsorption energies can be arranged in an increasing trend of NH₃@C₂₄H₁₂-Mg < PH₃@C₂₄H₁₂-Mg < AsH₃@C₂₄H₁₂-Mg. The best adsorption performance was noted in the gas phase compared to the other studied counterparts. The interaction between the adsorbed gases and the surfaces shows a non-covalent interaction nature, as confirmed by the quantum theory of atoms-in-molecules (QTAIM) and non-covalent interactions (NCI) analysis. The overall results suggest that we can infer that the surface of the magnesium-decorated graphene quantum dot C₂₄H₁₂-Mg is more efficient for sensing the gas AsH₃ than PH₃ and NH₃.

Experimental and theoretical analyses and investigation of intermolecular interactions and antibacterial activity of a novel proton transfer compound:8-hydroxyquinolinium oxalate monohydrate

A novel proton transfer compound, 8-hydroxyquinolinium oxalate monohydrate was synthesised by solid state grinding of 8-hydroxyquinoline and oxalic acid. The resulting compound is characterised by single crystal X-ray diffraction (SXRD), FT-IR, UV-Visible, TG/DTG, DTA and DSC analyses. The compound crystallizes in monoclinic crystal system with space group P21/n. The carboxylate oxygen O₂ which acts as a tetrafurcated acceptor of four hydrogen bonds is the main feature of the crystal structure. The molecules are linked together by O-H⋯O, N-H⋯O and C-H⋯O hydrogen bonds. Carbonyl-carbonyl interactions play a crucial role in stabilising the crystal packing. Hirshfeld surface analysis and the associated finger print plots facilitates the comparison of intermolecular interactions. The nature of charge density distribution and topological parameters of the proton transfer region N₁-H_1A⋯O₂ hydrogen bond reveals that the bond has considerable covalent character. Natural Bond Orbital (NBO) has been extended to analyse the nature and strength of intermolecular interactions. Topology analysis using ELF and LOL reveals electron localisation and depletion regions. ADMET analysis reveals that the compound satisfies Lipinski's rule of five and drug likeness. Antibacterial activity was screened against 3 g positive - Bacillus subtilis, Enterococcus faecalis, Staphylococcus aureus and 2 g negative strains- Klebsiella pneumonia and Salmonella typhi by employing disc diffusion method.

Binding propensity and selectivity of cationic, anionic, and neutral guests with model hydrophobic hosts: A first principles study

Computations play a critical role in deciphering the nature of host-guest interactions both at qualitative and quantitative levels. Reliable quantum chemical computations were employed to assess the nature, binding strength, and selectivity of ionic, and neutral guests with benzenoid hosts. Optimized complex structures reveal that alkali and ammonium ions are found to be in the hydrophobic cavity, while halide ions are outside, while both complexes elicit substantial binding energy. The origin of the selectivity of host toward the guest has been traced to the interaction and deformation energies, and the nature of associated interactions is quantified using energy decomposition and the Quantum Theory of Atoms in Molecules analyses. While the larger hosts lead to loosely bound complexes, as assessed by the longer intermolecular distances, the binding strengths are proportional to the size of the host systems. The binding of cationic complexes is electrostatic or polarization driven while exchange term dominates the anionic complexes. In contrast, dispersion contribution is a key in neutral complexes and plays a pivotal role in stabilizing the polyatomic complexes.

Hydrogen-Bond-Assisted Adsorption of Nitric Oxide on Various Metal-Loaded ZSM-5 Zeolites

Understanding the characteristics of nitric oxide (NO) adsorption on metal-loaded zeolites is a prerequisite for developing efficient catalysts for NO abatement reactions. In this study, we probed the effect of the hydrogen bond that exists between adsorbed NO and Brønsted acid sites (BAS) in various metal-loaded ZSM-5 zeolites (M-ZSM-5, wherein M = Fe, Co, Ni, Cu, Zn, Pd, Ag, and Au) by using density functional theory calculations. The presence of a hydrogen bond has altered the NO adsorption energies significantly; appreciable stabilization via hydrogen bonding is noted for NO complexes of Zn, Fe, and Co, and reasonable stabilization is obtained for Ni and Cu complexes, whereas an anomalous effect of a hydrogen bond is identified in Ag, Pd, and Au species. Moderate weakening of the N-O bond in all NO-adsorbed complexes primarily due to a hydrogen bond has been realized in terms of Mayer bond order and quantum theory of atoms in molecules topological analyses; N-O bond activation follows the order Ag < Pd < Au < Ni < Cu < Co < Fe < Zn. We obtained a good correlation between hydrogen bond distance and molecular electrostatic potential at the O atom (V_O) of NO adsorbed on BAS-free M-ZSM-5; which suggests that V_O can be considered as a key descriptor to infer the strength of a hydrogen bond between the adsorbed NO and M-ZSM-5 with BAS. Finally, the energy decomposition analysis in combination with natural orbitals for chemical valence has provided the qualitative aspects of electron back-donation from the metal to the antibonding molecular orbital of NO; this back-donation is quite impressive in hydrogen-bond-assisted NO adsorption. We expect that the findings of this study will open up the possibility of the design of BAS-containing metal-loaded zeolites for the catalytic mitigation of NO.

Non-covalent interactions from a Quantum Chemical Topology perspective

About half a century after its little-known beginnings, the quantum topological approach called QTAIM has grown into a widespread, but still not mainstream, methodology of interpretational quantum chemistry. Although often confused in textbooks with yet another population analysis, be it perhaps an elegant but somewhat esoteric one, QTAIM has been enriched with about a dozen other research areas sharing its main mathematical language, such as Interacting Quantum Atoms (IQA) or Electron Localisation Function (ELF), to form an overarching approach called Quantum Chemical Topology (QCT). Instead of reviewing the latter’s role in understanding non-covalent interactions, we propose a number of ideas emerging from the full consequences of the space-filling nature of topological atoms, and discuss how they (will) impact on interatomic interactions, including non-covalent ones. The architecture of a force field called FFLUX, which is based on these ideas, is outlined. A new method called Relative Energy Gradient (REG) is put forward, which is able, by computation, to detect which fragments of a given molecular assembly govern the energetic behaviour of this whole assembly. This method can offer insight into the typical balance of competing atomic energies both in covalent and non-covalent case studies. A brief discussion on so-called bond critical points is given, highlighting concerns about their meaning, mainly in the arena of non-covalent interactions.

A Review of Transition Metal Dichalcogenides-Based Biosensors

Transition metal dichalcogenides (TMDCs) are widely used in biosensing applications due to their excellent physical and chemical properties. Due to the properties of biomaterial targets, the biggest challenge that biosensors face now is how to improve the sensitivity and stability. A lot of materials had been used to enhance the target signal. Among them, TMDCs show excellent performance in enhancing biosensing signals because of their metallic and semi-conducting electrical capabilities, tunable band gap, large specific surface area and so on. Here, we review different functionalization methods and research progress of TMDCs-based biosensors. The modification methods of TMDCs for biosensor fabrication mainly include two strategies: non-covalent and covalent interaction. The article summarizes the advantages and disadvantages of different modification strategies and their effects on biosensing performance. The authors present the challenges and issues that TMDCs need to be addressed in biosensor applications. Finally, the review expresses the positive application prospects of TMDCs-based biosensors in the future.

Applying polypharmacology approach for drug repurposing for SARS-CoV2

Exploring the new therapeutic indications of known drugs for treating COVID-19, popularly known as drug repurposing, is emerging as a pragmatic approach especially owing to the mounting pressure to control the pandemic. Targeting multiple targets with a single drug by employing drug repurposing known as the polypharmacology approach may be an optimised strategy for the development of effective therapeutics. In this study, virtual screening has been carried out on seven popular SARS-CoV-2 targets (3CL^pro, PL^pro, RdRp (NSP12), NSP13, NSP14, NSP15, and NSP16). A total of 4015 approved drugs were screened against these targets. Four drugs namely venetoclax, tirilazad, acetyldigitoxin, and ledipasvir have been selected based on the docking score, ability to interact with four or more targets and having a reasonably good number of interactions with key residues in the targets. The MD simulations and MM-PBSA studies showed reasonable stability of protein-drug complexes and sustainability of key interactions between the drugs with their respective targets throughout the course of MD simulations. The identified four drug molecules were also compared with the known drugs namely elbasvir and nafamostat. While the study has provided a detailed account of the chosen protein-drug complexes, it has explored the nature of seven important targets of SARS-CoV-2 by evaluating the protein-drug complexation process in great detail.

Can second-order perturbation theory accurately predict electron density of open-shell molecules? The importance of self-consistency

Electron density plays an essential role in predicting molecular properties.

Fate of Sc-Ion Interaction With Water: A Computational Study to Address Splitting Water Versus Solvating Sc Ion

An exhaustive study of Sc-ion interaction with water molecules in all its possible oxidation and spin states has been carried out to delineate the relative propensity of Sc ions toward solvation and water splitting. Potential energy surface analysis of the Sc-ion reaction with water molecules, topological analysis of bonds, and the effect of sequential solvation up to 6 water molecules have been examined. Calculated values showed good agreement with the available experimental results. Close-shell systems such as singlet mono- and tricationic Sc ions prefer to split the water molecules. In contrast, the open-shell systems such as triplet mono- and doublet dicationic Sc ions prefer to get solvated than split the water molecule. Topological analysis of electron density predicted the Sc^+/2+–water bond as a noncovalent bond while Sc³⁺–OH₂, Sc²⁺–OH, and Sc⁺–H bonds as partially covalent in nature. Energy decomposition analysis revealed that Sc ion–water interactions are driven by electrostatic energy followed by polarization energy. The current study reveals that transition metal catalysis can be one of the most effective tools to employ in water splitting, by properly tuning the electrons, spin, and ligands around the catalytic center.

Evidence of C-F···H-C Attractive Interaction: Enforced Coplanarity of a Tetrafluorophenylene-Ethynylene-Linked Porphyrin Dimer

The formation of C-F···H-C "hydrogen bonds" has been a controversial subject because, in principle, fluorine is hardly an acceptor for less acidic protons contrasting to the C-F···H-O and C-F···H-N hydrogen bonds. Nevertheless, the interaction is emerging as a powerful implement for confining the torsional rotation in the design of fully coplanar π-conjugated polymers. Heretofore, no evidence of the C-F···H-C interaction has been observed in solutions. We herein disclose comprehensive evidence that the C-F···H-C interaction produces an attractive force. A ¹⁹F-¹H heteronuclear Overhauser effect experiment elucidated the close proximity of the F and H atoms in the doubly edge-facing C-F···H-C interactions of a meso-tetrafluorophenylene-ethynylene-conjugated porphyrin dimer (1). Extensive electronic and photophysical property investigations confirmed that all the aromatic units were torsionally restricted by the C-F···H-C interactions. Moreover, the enforced coplanarity invoked a markedly high π-staking propensity. Thus, we have firmly established the formation of a C-F···H-C interaction that produces a hydrogen-bond-like attractive force in solution.