Noncovalent Contacts Research Articles

Structural Analyses of a GABARAP~ATG3 Conjugate Uncover a Novel Non-covalent Ubl-E2 Backside Interaction.

Members of the ATG8 family of ubiquitin-like proteins (Ubls) are conjugated to phosphatidylethanolamine (PE) in the autophagosomal membrane, where they recruit degradation substrates and facilitate membrane biogenesis. Despite this well-characterized function, the mechanisms underlying the lipidation process, including the action of the E2 enzyme ATG3, remain incompletely understood. Here, we report the crystal structure of human ATG3 conjugated to the mammalian ATG8 protein GABARAP via an isopeptide bond, mimicking the Ubl~E2 thioester intermediate. In this structure, the GABARAP~ATG3 conjugate adopts an open configuration with minimal contacts between the two proteins. Notably, the crystal lattice reveals non-covalent contacts between GABARAP and the backside of ATG3's E2 catalytic center, resulting in the formation of a helical filament of the GABARAP~ATG3 conjugate. While similar filament formations have been observed with canonical Ub~E2 conjugates, the E2 backside-binding interface of GABARAP is distinct from those of Ub/Ubl proteins and overlaps with the binding site for LC3 interacting region (LIR) peptides. NMR analysis confirms the presence of this non-covalent interaction in solution, and mutagenesis experiments demonstrate the involvement of the E2 backside in PE conjugation. These findings highlight the critical role of the E2 backside in the lipidation process and suggest evolutionary adaptations in the unique E2 enzyme ATG3.

Vibrational Energy Landscapes and Energy Flow in GPCRs.

We construct and analyze disconnectivity graphs to provide the first graphical representation of the vibrational energy landscape of a protein, in this study β2AR, a G-protein coupled receptor (GPCR), in active and inactive states. The graphs, which indicate the relative free energy of each residue and the minimum free energy barriers for energy transfer between them, reveal important composition, structural and dynamic properties that mediate the flow of energy. Prolines and glycines, which contribute to GPCR plasticity and function, are identified as bottlenecks to energy transport along the backbone from which alternative pathways for energy transport via nearby noncovalent contacts emerge, seen also in the analysis of first passage time (FPT) distributions presented here. Striking differences between the disconnectivity graphs and FPT distributions for the inactive and active states of β2AR are found where structural and dynamic changes occur upon activation, contributing to allosteric regulation.

DFT studies on N-(1-(2-bromobenzoyl)-4-cyano-1H-pyrazol-5-yl)

In this work, molecular descriptors of N-(1-(2-bromobenzoyl)-4-cyano-1H-pyrazol-5-yl) halogenated benzamides (1a-h) have been computed using a quantum chemical technique through DFT. Prior work involved the synthesis of compounds (1a-h) and the assessment of their anticancer activity on breast, colon, and liver tumors: MCF-7, HCT-116, and HepG-2 cell lines respectively. Since 1a, 1b, and 1d showed the most potential anticancer impact, their ability to inhibit EGFRWT was investigated. Based on the biological data, 1b inhibited EGFRWT the most. According to the docking evaluation, an H-bond with the threonine residue was one of the main non-covalent contacts between 1b and the EGFRWT active site residues. PES, MESP, HOMOs, LUMOs, energy band gap, global reactivity indices [electron affinity (A), ionization energies (I), electrophilicity index (ω), nucleophilicity index (ε), chemical potential (μ), electronegativity (χ), hardness (η), and softness (S)], condensed Fukui functions, NBO, and NCIs are the molecular descriptors of 1a-h that were computed using DFT technique. According to the theoretical investigation results, compounds (1a-h) might have anticancer effects; these findings are consistent with the biological findings from our previous research. Compound 1b had the lowest binding energy, according to an assessment of the binding energies between the threonine and the three most active compounds (1a, 1b, and 1d). This is consistent with the outcomes of the docking study and the biological examination of the influence of 1a, 1b, and 1d on EGFRWT.

Supramolecular assemblies involving unusual N(nitrile)∙∙∙π(fum) and nitrile-nitrile non-covalent contacts in fumarato and succinato bridged polymers of Co(II) and Ni(II): Experimental and theoretical studies

Two new Co(II) and Ni(II) coordination polymers viz. [Co(H2O)2(μ-fum)(3-CNpy)2]n (1) and {[Ni(H2O)2(μ-succ)(4-CNpy)2]·2H2O}n (2) (where, fum= fumarate, CNpy = cyanopyridine, succ = succinate) have been synthesized and characterized using single crystal XRD, elemental analysis, spectroscopic (IR and electronic) techniques and TGA. Compound 1 crystallizes as a fumarato bridged Co(II) polymer; whereas, compound 2 is a succinato bridged Ni(II) polymer. The presence of various non-covalent interactions in the compounds stabilizes the layered assemblies of the compounds. Antiparallel nitrile∙∙∙nitrile interactions are observed in both the crystal structures involving the nitrile moieties of coordinated CNpy which provide rigidity to the compounds. Further analysis reveals that the N-atom of –CN group of 3-CNpy in 1 is involved in unusual N(nitrile)∙∙∙π(fum) interactions with the π-electrons of the C=C bond of fum. Enclathrated (H2O)2 cores within the supramolecular host cavity of compound 2 provides additional reinforcement to the crystal structure. We have also carried out theoretical studies to analyze the π-stacking and H-bonding interactions present in the crystal structure of compound 1 using quantum theory of atoms-in-molecules (QTAIM), non-covalent interaction plot (NCI plot) and molecular electrostatic potential (MEP) surface analysis. The MEP value at the N-atom of the cyano group of 1 is negative and the value is neutral over the double bond of the fum; indicating the possibilities of formation of N(nitrile)∙∙∙π(fum) interactions. Energetic analysis suggests that antiparallel π-stacking observed between the 3-CNpy moieties in 1 is the most dominating force followed by N(nitrile)∙∙∙π(fum) interaction and finally the H-bonds.

Eight anhydrous organic salt forms of 2-amino-4,6-dimethoxypyrimidine and organic acids: Preparation, structure, characterizations, synthons diversity, and hirshfeld surface analysis

The intricate part of the non-covalent associates in numerous realms covering from chemistry, biology, catalysis, material science, to medicinal chemistry inspires a continuous motivation towards the discovery of new synthons that stabilize the supramolecular systems. In this work the co-crystallization between 2-amino-4,6-dimethoxypyrimidine (admpym) and eight organic acids resulted in the manufacturing of eight new crystalline salts, which were further fully characterized via the single crystal X-ray diffraction (SCXRD), spectroscopic (FT-IR) and elemental analysis methods. Their melting points were also measured. All the fabricated salts exhibited the identical stoichiometry regarding the number of the acidic unit and the admpym, namely with the 1:1 ratio at the monacids and 2 : 1 ratio in the diacids.Among the eight crystals, the H-shift from the acid to pyrimidine ring N atom has occurred, yet the NH2 group was not protonated ever. In all the crystals, the respective molecular fragments are permanently tethered to each other via the energetic H-bonds as the Npyrimidinium-Ophenolate/carboxylate type. The various weaker intermolecular linkages, embodying CH···O/CH3···O, CH···CH, CH3···N, CH···Br, CH3···CH, CH3···Cl, Cl···O, CH···π/CH3···π, C···π, O···π and π···π also contributed to the stabilization of the crystal structures in the respective conglomerates. The percentage contribution of the significant non-covalent contacts were calculated via the Hirshfeld surface analysis. The R22(8) graph was enclosed in all the systems when an acid pairs with an admpym. The job ensures that there engender both principle contact modes between the admpym and the acids, which appear in the relative higher frequency, linear heterotetramer (LHT), and cyclic heterotetramer (CHT). LHT is dominant as it appears in 5 cases, CHT in 2 ones, with the rest one structure building a rare heterodimer. The heterotrimer (HT) was never occurred here.

Structural determinants of odorant-binding proteins affecting their ability to form amyloid fibrils

The formation of amyloid fibrils is associated with many severe pathologies as well as the execution of essential physiological functions by proteins. Despite the diversity, all amyloids share a similar morphology and consist of stacked β-strands, suggesting high amyloidogenicity of native proteins enriched with β-structure. Such proteins include those with a β-barrel-like structure with β-strands arranged into a cylindrical β-sheet. However, the mechanisms responsible for destabilization of the native state and triggering fibrillogenesis have not thoroughly explored yet. Here we analyze the structural determinants of fibrillogenesis in proteins with β-barrel structures on the example of odorant-binding protein (OBP), whose amyloidogenicity was recently demonstrated in vitro. We reveal a crucial role in the fibrillogenesis of OBPs for the “open” conformation of the molecule. This conformation is achieved by disrupting the interaction between the β-barrel and the C-terminus of protein monomers or dimers, which exposes “sticky” amyloidogenic sites for interaction. The data suggest that the “open” conformation of OBPs can be induced by destabilizing the native β-barrel structure through the disruption of: 1) intramolecular disulfide cross-linking and non-covalent contacts between the C-terminal fragment and β-barrel in the protein's monomeric form, or 2) intermolecular contacts involved in domain swapping in the protein's dimeric form.

Synthesis and crystal structure of the adduct between 2-pyridyl-selenyl chloride and isobutyro-nitrile.

The reaction between 2-pyridyl-selenenyl chloride and isobutyro-nitrile results in the formation of the corresponding cationic pyridinium-fused 1,2,4-seleno-diazole, namely, 3-(propan-2-yl)-1,2,4-[1,2,4]selena-diazolo[4,5-a]pyridin-4-ylium chloride, C9H11N2Se+·Cl-, in high yield (89%). The structure of the compound, established by means of single-crystal X-ray analysis at 100 K, has monoclinic (P21/c) symmetry and revealed the presence of bifurcated chalcogen-hydrogen bonding Se⋯Cl-⋯H-Cl, and these non-covalent contacts were analysed by DFT calculations followed by a topological analysis of the electron-density distribution (ωB97XD/6-311++G** level of theory).

Preparation and characterization of whey protein isolate-dextran-proanthocyanidins ternary complexes: Formation mechanism, physicochemical stability

The present study aimed to improve the stability and antioxidant properties of whey protein isolate (WPI) in food emulsion systems. A whey protein isolate-dextran (D) binary complex (GF) was prepared using wet Melad reaction. Based on this, a ternary complex (GF-PC) system of whey protein isolate-dextran-proanthocyanidins (PC) was constructed. The interaction mechanism and functional properties of this ternary system were investigated by turbidity, Fourier infrared, and fluorescence spectroscopy, as well as DPPH radical scavenging ability. Results showed that a novel ternary composite system was successfully constructed. The maximum encapsulation efficiency of PC was 93.09% when using the GF-0.4 PC complex (the mass ratio of GF to PC was 1:0.4). Turbidity, fluorescence spectroscopy, and FTIR spectroscopy analyses showed that PC was successfully encapsulated by GF and formed the ternary complex. SDS-PAGE and interaction forces showed that the noncovalent contacts increased significantly, while covalent interactions remained the main interaction between WPI, D, and PC. The GF-PC ternary complexes significantly improved emulsification properties and free radical scavenging ability compared to single WPI and GF conjugates. This study suggested that GF-PC could be used as a delivery system for functional active ingredients with enhanced emulsifying activity and antioxidant capacity.

From 'halogen' to 'tetrel' bonds: matrix isolation IR spectroscopic and quantum mechanical studies of the effect of central atom substitution in donor tetrahalogens on binary complex formation with formic acid.

Binary complex formation between silicon tetrachloride (SiCl4) and formic acid (FA) has been observed in an argon matrix environment. Such complex formation manifests as spectral shifts in signature vibrations of the latter, namely the νCO, νC-O and νO-H vibrations. Quantum chemical calculations reveal that the most stable conformers of the complex involve predominantly the tetrel bond, which has been defined in existing literature as a variant of the "σ-hole" interactions. Here, regions of positive electrostatic potential on the tetrahedral face of SiCl4 act as electrophilic centers (σ-hole) to which the nucleophilic carbonyl group of FA is able to bind. Atoms-in-molecules analysis predicts a bond critical point along the non-covalent contact between the tetrel atom Si and the carbonyl oxygen on FA, corroborating the presence of the tetrel bond. The hyperconjugative interaction parameters at the binding interface obtained from Natural Bond Orbital (NBO) analysis are also consistent with such observations. Although apparently similar to SiCl4, there are noticeable differences in the binding preferences of the lower homologue carbon tetrachloride (CCl4). The binary complexes of the latter with the same FA acceptor molecule have been previously shown to involve halogen bonded, rather than tetrel bonded interactions (Banerjee and Bhattacharya, Spectrochim. Acta Mol. and Biomol. Spectrosc., 2021, 250, 119355). Such variations in the nature of non-covalent interactions of these tetrahalogens are attributed to differences in the distribution of electronic charge density surrounding the central tetrel atom, as obtained from mappings of their electrostatic potential surfaces. Our combined experimental and theoretical findings therefore provide direct evidence of the growing propensity of tetrel atoms to engage in tetrel bonding as we move lower down Group 14, and re-assert the reluctance of the smaller and more electronegative carbon atom to serve as a tetrel bond participant.

Manganese matere bonds in biological systems: PDB inspection and DFT calculations.

A Protein Data Bank (PDB) survey has revealed noncovalent contacts involving Mn centres and protein residues. Their geometrical features are in line with the interaction between low electron density sites located along the Mn-O/N coordination bonds (σ-holes) and the lone pairs belonging to TYR, SER or HIS residues, known as a matere bond (MaB). Calculations at the PBE0-D3/def2-TZVP level of theory were used to investigate the strength and shed light on the physical nature of the interaction. We expect the results presented herein will be useful for those scientists working in the fields of bioinorganic chemistry, particulary in protein-metal docking, by providing new insights into transition metal⋯Lewis base interactions as well as a retrospective point of view to further understand the structural and functional implications of this key transition metal ion.

Lest We Forget-The Importance of Heteroatom Interactions in Heterocyclic Conjugated Systems, from Synthetic Metals to Organic Semiconductors.

The field of synthetic metals is, and remains, highly influential for the development of organic semiconductor materials. Yet, with the passing of time and the rapid development of conjugated materials in recent years, the link between synthetic metals and organic semiconductors is at risk of being forgotten. This review reflectson one of the key concepts developed in synthetic metals - heteroatom interactions. The application of this strategy in recent organic semiconductor materials, small molecules and polymers, is highlighted, with analysis of X-ray crystal structures and comparisons with model systems used to determine the influence of these non-covalent short contacts. The case is made that the wide range of effective heteroatom interactions and the high performance that has been achieved in devices from organic solar cells to transistors is testament to the seeds sown by the synthetic metals research community.

Supramolecular Structure, Hirshfeld Surface Analysis, Morphological Study and DFT Calculations of the Triphenyltetrazolium Cobalt Thiocyanate Complex

Polymorphism is a prevalent occurrence in pharmaceutical solids and demands thorough investigation during product development. This paper delves into the crystal growth and structure of a newly synthesized polymorph (TPT)2[CoII(NCS)4], (1), where TPT is triphenyl tetrazolium. The study combines experimental and theoretical approaches to elucidate the 3D framework of the crystal structure, characterized by hydrogen-bonded interactions between (TPT)+ cations and [Co(NCS)4]2− anions. Hirshfeld surface analysis, along with associated two-dimensional fingerprints, is employed to comprehensively investigate and quantify intermolecular interactions within the structure. The enrichment ratio is calculated for non-covalent contacts, providing insight into their propensity to influence crystal packing interactions. Void analysis is conducted to predict the mechanical behavior of the compound. Utilizing Bravais-Friedel, Donnay-Harker (BFDH), and growth morphology (GM) techniques, the external morphology of (TPT)2[CoII(NCS)4] is predicted. Experimental observations align well with BFDH predictions, with slight deviations from the GM model. Quantum computational calculations of the synthesized compounds is performed in the ground state using the DFT/UB3LYP level of theory. These calculations assess the molecule’s stability and chemical reactivity, including the computation of the HOMO-LUMO energy difference and other chemical descriptors. The study provides a comprehensive exploration of the newly synthesized polymorph, shedding light on its crystal structure, intermolecular interactions, mechanical behavior, and external morphology, supported by both experimental and computational analyses.

Halogen-Dependent Diversity and Weak Interactions in the Heterometallic Ni/Cd Complex Solids: Structural and Theoretical Investigation.

Three novel heterometallic Ni/Cd coordination compounds [Ni(en)3][CdCl4]∙3dmso (1), [Ni(en)2(dmf)2][CdBr4] (2), and [Ni(en)3]2[CdI4](I)2 (3) have been synthesized through the self-assembly process in a one-pot reaction of cadmium oxide, nickel salt (or nickel powder), NH4X (X = Cl, Br, I), and ethylenediamine in non-aqueous solvents dmso (for 1) or dmf (for 2 and 3). Formation of the one- (1) or three-dimensional (2 and 3) hydrogen-bonded frameworks has been observed depending on the nature of the [CdX4]2- counter-anion, as well as on the nature of the solvent. The electronic structures of [Ni(en)3]2+ and [Ni(en)2(dmf)2]2+ cations were studied at the DFT and CASSCF levels, including the ab initio ligand field theory (AILFT) calculations. The non-covalent intermolecular contacts between the cationic nickel and anionic cadmium blocks in the solid state were investigated by the QTAIM analysis. The mechanism of ligand substitution at the nickel center in [Ni(en)2(dmf)2]2+ was theoretically investigated at the ωB97X-D4/ma-def2-TZVP//DLPNO-CCSD(T)/ma-def2-TZVPP level. The results demonstrate that thermodynamic factors are structure-determining ones due to low energy barriers of the rotation of dmf ligands in [Ni(en)2(dmf)2]2+ (below 3 kcal mol-1) and the reversible transformation of [Ni(en)2(dmf)2]2+ into [Ni(en)3]2+ (below 20 kcal mol-1).

Spodium Bonds Involving Methylmercury and Ethylmercury in Proteins: Insights from X-ray Analysis and Computations.

In this study, the stability, directionality, and physical nature of Spodium bonds (SpBs, an attractive noncovalent force involving elements from group 12 and Lewis bases) between methylmercury (MeHg) and ethylmercury (EtHg) and amino acids (AAs) have been analyzed from both a structural (X-ray analysis) and theoretical (RI-MP2/def2-TZVP level of theory) point of view. More in detail, an inspection of the Protein Data Bank (PDB) reported evidence of noncovalent contacts between MeHg and EtHg molecules and electron-rich atoms (e.g., O atoms belonging to the protein backbone and S atoms from MET residues or the π-systems of aromatic AAs such as TYR or TRP). These results were rationalized through a computational study using MeHg coordinated to a thiolate group as a theoretical model and several neutral and charged electron-rich molecules (e.g., benzene, formamide, or chloride). The physical nature of the interaction was analyzed from electrostatics and orbital perspectives by performing molecular electrostatic potential (MEP) and natural bonding orbital (NBO) analyses. Lastly, the noncovalent interactions plot (NCIplot) technique was used to provide a qualitative view of the strength of the Hg SpBs and compare them to other ancillary interactions present in these systems as well as to shed light on the extension of the interaction in real space. We believe that the results derived from our study will be useful to those scientists devoted to protein engineering and bioinorganic chemistry as well as to expanding the current knowledge of SpBs among the chemical biology community.

Elucidating the Structure, Dynamics, and Interaction of a Choline Chloride and Citric Acid Based Eutectic System by Spectroscopic and Molecular Modeling Investigations.

Eutectic solvent systems are versatile solvents that have found widespread use in numerous applications. Traditional solvents are homogeneous, having only one component, and their chemistry is relatively simple, with some exceptions. On the other hand, deep eutectic solvents (DESs) comprise binary components, generally a donor and an acceptor in hydrogen bonding with varying ratios. The interaction chemistry among the donor and acceptor involved in hydrogen bonding in DESs is complicated. Although numerous research is focused on the synthesis and application of DESs, few studies are reported to elucidate the complex structure and dynamic and interaction behavior of DESs. In this study, we employed calorimetry, vibrational spectroscopy techniques including FTIR and Raman, and nuclear magnetic resonance to derive insight into the structural feature and noncovalent contact of choline chloride (ChCl) and citric acid (CA) while they formed DESs. The 1:1 ChCl/CA eutectic system showed phase transitions and melting peaks with the most pronounced peak at 156.22 °C, suggesting the DESs melting at a lower temperature than the melting temperatures of ChCl and CA. In addition to IR and Raman findings, 1H NMR investigations demonstrate hydrogen bonding intermolecular interactions between ChCl and CA, supporting the formation of 1:1 ChCl/CA DESs based on the deshielded chemical shifts of the proton for Ch. The interaction of the chloride anion with the methyl protons (H4) and methylene protons (H3) of ChCl as well as the strong hydrogen bonding interactions between the hydroxyl hydrogen (H1) of ChCl with one of CA's carbonyl oxygens both supported the formation of conformer E. In addition, molecular dynamics followed by the density functional theory (DFT) was employed to visualize the structure and interaction of DESs using the ωB97XD theory and 6-311++G (d,p) basis set. Both experimental and theoretical IR, Raman, and structural analyses provided evidence of the formation of DESs by possessing hydrogen bonds. These multifaceted experimental and computational investigations provide details of structural and intermolecular interactions of ChCl/CA DESs.

Cooperative assemblies featuring hydrogen bonding and C[sbnd]H…π interactions in 2-(methanesulfonamido)benzohydrazide derivatives: Experimental, computational and biochemical assessment

The significant involvement of noncovalent interactions in catalyst design and synthesis of materials provides a fundamental impetus to explore various synthons that produce complex frameworks. Therefore, in the present work, cooperative assemblies of two methanesulfonamide containing benzohydrazide derivatives (6 and 7) were designed and analyzed. These compounds were synthesized through a straightforward approach using hydrazide 3 and 4-methyl-2-acetylthiophene (4) and 4-methoxyacetophenone (5) in refluxing ethanol. Both compounds were characterized by FTIR, NMR, LCMS and X-ray crystallography. Noncovalent interactions such as CH…π interactions and hydrogen bonding played a crucial and dominant role in the structural design of complex molecular architectures. X-ray crystal analysis reveals the presence of an intramolecular classical NH…O strong hydrogen bond and a weaker CH…O interaction in compounds 6 and 7. The NH…O arrangement of hydrazone-hydrazone cores also facilitates a CH…π close contact between the sulfonamide methyl group and the proximal benzoyl aromatic ring. Moreover, the methoxy group in 7 is also involved in CH…O/S and CH…π interactions. Hirshfeld surface analysis further revealed the involvement of these noncovalent contacts in the stabilization of molecular topology of both compounds. The energetic features of noncovalent interactions were characterized by DFT calculations while molecular electrostatic potential (MEP), QTAIM and NCIPlot computational tools rationalized the structural assemblies found in the crystal packing of both compounds. Furthermore, the biological assessment against urease enzyme revealed 13-fold superior inhibition with an IC50 value of 1.67 ± 0.19 µM for compound 6. In vitro inhibitory data was complemented with an in silico modeling where the observed interactions between the active site amino acids and compound 6 underscored the importance of heteroaryl (thienyl) component for strong inhibitory effects. Finally, the assessment of pharmacokinetic parameters proposed compound 6 as a suitable druggable inhibitor for further evaluation.

Linking Redox Characteristics to Dissolved Organic Matter Derived from Different Biowaste Composts: A Theoretical Modeling Approach Based on FT-ICR MS Analysis.

Compost dissolved organic matter (DOM) is a complex mixture of redox-active organic molecules that impact various biogeochemical processes in soil environments. However, the impact of chemical complexity (heterogeneity and chemodiversity) on the electron accepting capacity (EAC) and electron donating capacity (EDC) of DOM molecules remains unclear, which hinders our ability to predict their environmental behavior and redox properties. In this study, the applicability of Vienna Soil Organic Matter Modeler 2 (VSOMM2) to the composting system based on the FT-ICR MS data has been validated. A molecular modeling approach using VSOMM2 and Schrödinger software was developed to quantitatively assess the redox sites and molecular interactions of compost DOM. Compost DOM molecules are categorized into three distinct groups based on their heterogeneous origins. In addition, we have developed 18 molecular models of compost DOM based on the links of molecules to EAC/EDC. Finally, Ar-OH, quinone, Ar-SH, and Ar-NH2 were identified as the redox sites; noncovalent contacts, H bonds, salt bridges, and aromatic-H bonds might be significant electronic transmission channels of compost DOM. Our findings contribute to the development of precise regulatory methods for functional molecules within compost DOM, providing the fine standards for composts matching specific ecosystem service requirements.

Application of the method for visualization of noncovalent interactions in conformational polymorphs of four organic acids.

A method for the visualization of noncovalent interactions using examples of the conformational polymorphs of four organic compounds: 2-(phenylamino)nicotinic, 2-(3-chloro-2-methylphenylamino)nicotinic, N-(3-chloro-2-methylphenyl)anthranilic and 2-(methylphenylamino)nicotinic acids is examined. The changes in noncovalent contacts are plotted against the angle between the planes of aromatic rings allowing a visual representation of conformational adjustment of molecules as well as packing features of crystal structures. According to the k-Φ criterion, the studied structures represent conformational polymorphs. Different types of hydrogen bonding are discussed within the framework of the method of visualization and molecular Voronoi-Dirichlet polyhedra. Good correlations are found between calculated and experimental data for several cases, such as the agreement between π stacking and polymorphic transition temperatures as well as between the area of a contact and the energy of conjugation. Also, an attempt has been made to assess the relative contributions of conformational and packing polymorphism in the formation of polymorphs.

In vitro interactions of two pesticides, propazine and quinoxyfen with bovine serum albumin: Spectrofluorometric and molecular docking investigations

Binding mechanisms of two selected pesticides, propazine (PRO) and quinoxyfen (QUI) with bovine serum albumin (BSA) was examined using fluorescence, absorption and molecular docking methods. Intrinsic fluorescence of BSA was quenched in the presence of both PRO and QUI. The quenching was ascertained to be conversely linked to temperature, which suggested the contribution of static quenching process in the PRO–BSA and QUI–BSA complex formations. This results were validated by the enhancement in absorption spectrum of BSA upon binding with PRO and QUI. Binding constant values (Kf = 9.55–0.60 × 10–3 M−1 for PRO–BSA system; Kf = 7.08–5.01 × 102 M−1 for QUI–BSA system) and number of binding site (n) values for the PRO–BSA and QUI–BSA systems at different temperatures affirmed a weak binding strength with a set of equivalent binding sites on BSA. Thermodynamic data obtained for both the PRO–BSA and QUI–BSA interactions predicted that the association process was spontaneous and non-covalent contacts such as hydrophobic interactions, van der Waals forces and hydrogen bonds participated in the binding reactions. This result was further supported by the molecular docking assessments. Three-dimensional spectral results revealed the microenvironmental alterations near tryptophan (Trp) and tyrosine (Tyr) residues in BSA by the addition of PRO and QUI. The docking analysis demonstrated the binding pattern for the PRO–BSA and QUI–BSA systems and disclosed the preferred binding site of both PRO and QUI as site I (subdomain IIA) of BSA.

Intriguing π-interactions involving aromatic neutrals, aromatic cations and semiconducting behavior in a pyridinium-carboxylate salt

A new pyridinium-carboxylate salt (1) has been synthesized and characterized by elemental analysis, spectroscopy, electrical studies, and single-crystal X-ray diffraction. X-ray structure of 4,4′-oxybis(benzoic acid) with 4-(Dimethylamino)pyridine is stabilized through hydrogen bonds, C‒H···π, and numerous π-interactions together with π···π, π···π+, and π+···π+stacking. The cooperativity of the weak noncovalent interactions has been explored well that plays a crucial role in building diverse extended supramolecular frameworks. The hydrogen bonds dictate the basic structural motifs representing the supramolecular association. However, the cooperativity of the weak noncovalent contacts plays a significant role in constructing the final solid-state structure. The entire assembly produces a rare combination of π···π/π···π+/π+···π+/π+···π extended network. The binding energies of the noncovalent interactions have anticipated the usage of DFT calculations. Intricate combinations of these noncovalent interactions are characterized through computational studies by using Bader's theory of “Atoms-in-Molecules” (AIM) and “noncovalent interaction” (NCI) plot index. The evaluation of topological parameters at (3, -1) BCPs ensured the ‘closed-shell’ nature of the intermolecular interactions. By employing Tauc's plot, the optical band gap was calculated from UV–Vis spectroscopy. A device was fabricated for the analysis of I-V characteristics of the compound. An impedance study was carried out and consequently, Nyquist plot was represented for the further investigation of the semiconducting behavior of the compound.