Detection of paracetamol by a montmorillonite-modified carbon paste sensor: A study combining MC simulation, DFT computation and electrochemical investigations

This study aims to develop a suitable electrochemical electrode through the incorporation of potassium montmorillonite (MMTK10)clay into the carbon matrix for the direct and sensitive determination of paracetamol (PAR) in pharmaceutical formulations. Electrochemical characterization of the electrodes involves the use of techniques such as cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and differential pulse voltammetry (DPV). The results reveal that the voltammetric response of PAR is linear over a wide concentration range (1.0-15 μM), with a low detection limit of 0.46 μM. Analytically, PAR recovery results were around 94%, indicating that the developed electrode is highly suitable for PAR detection in pharmaceutical formulation. Additionally, density functional theory (DFT) is employed to investigate the reactivity of PAR and explain the interaction process of PAR on the electrode surface at different pH values. A Monte Carlo simulations model is developed to provide a deeper understanding of the adsorption mechanism, particularly to comprehend molecular interactions and preferential orientations of PAR with MMT fractions at the electrode surface. Reduced Density Gradient is calculated and discussed using techniques such as Multiwfn and Visualization of Molecular Dynamics. The developed CPE-MMTK10 sensor provided a simple preparation method, rapid response, high sensitivity, reproducibility, strong selectivity, and extended stability. Moreover, there is a good correlation between most parameters calculated by DFT and experimental results, thereby reinforcing the validity of the theoretical approach in this study.

Structural modification of A-C-A configured X-PCIC acceptor molecule for efficient photovoltaic properties with low energy loss in organic solar cells

Modification of terminal acceptors of non-fullerene organic solar cell molecule with different terminal acceptors can help in screening of molecules to develop organic photovoltaic cells with improved performance. Thus, in this work, seven new molecules with an unfused core have been designed and thoroughly investigated. DFT/TD-DFT simulations were performed on studied molecules to explore the ground and excited state characteristics. UV-Visible analysis revealed the red shift in the absorption spectrum (reaching 781 nm) owing to their smaller energy gap up to 1.94 eV. Furthermore, transition density matrix analysis demonstrated that peripheral acceptors extract the electron density from the core effectively. The effectiveness of our investigated molecules as materials for high-performing organic photovoltaic cells has been shown by an examination of their electron and hole mobilities for fast charge transfer. When combined with PTB7-Th, all molecules displayed high open circuit voltage. XP5 molecule exhibited highest open circuit voltage (1.70 eV) and lowest energy loss of 0.30 eV. All designed molecules exhibit the improved aforementioned parameters, which shows that these molecules can be used to develop competent solar devices in future.

Dynamics and Coordination of a P2N2 Ligand - from Twisted Conformation to Chelation

Based on their general spacial flexibility, their Lewis and Brønsted basicity, and ability to mimic second sphere effects the 1,5-diaza-3,7-diphosphacyclooctane ligand family and their complexes have regained substantial scientific interest. It was now possible to structurally analyze a recently reported member of this family with p-tolyl and t-butyl substituents on P and N, respectively, (P2 p-tolN2 tBu). Notably, the ligand crystallizes with a 'twisted' backbone. This compound is the very first of its kind to have been unambiguously characterized with regard to its chemical and molecular structure as being in this conformation. A temperature-dependent NMR study provides insight into the molecular dynamics of two isomers in solution, which are most likely also both twisted, as judged by the observed limited reactivity. Despite the in principle unfavorable conformation of the free ligand, it was successfully chelated to tungsten and molybdenum centers in mononuclear carbonyl complexes. The ligand, a derivative thereof and four new complexes were comprehensively characterized and analyzed in comparison. This includes single crystal XRD molecular structures of P2 p-tolN2 tBu and all four complexes. P2 p-tolN2 tBu, regardless of its twisted conformation, is able to coordinate to metal centers given that enough energy (heat) for a conformational change is provided.

Self-supporting noncovalent Choline Alginate/Tannic acid/Ag antibacterial films for strawberry preservation

Packaging materials with peculiar antibacterial properties can shield off and inhibit microorganism proliferation, thus achieving packaging goals such as fresh-keeping, good hygiene, and biosafety. Especially, antibacterial films made of biocompatible substances have received wide attentions, which could effectively extend the shelf life, enhance food security, and guarantee economic benefits. Herein, a self-supporting hybrid antibacterial film was prepared based on non-covalently linked choline hydroxide (ChOH) and alginic acid (HAlg). Then tannic acid (TA) and silver ions were added to improve the mechanical and antimicrobial properties of this hybrid film. The rich hydroxyl groups from TA not only form multiple hydrogen bonds with ChAlg, but can also in situ reduce silver ions to silver nanoparticles, which were confirmed with various characterizations. In addition, the quantitative antibacterial test proved that the antibacterial rate was significantly improved after adding silver ions, reaching >60 %. In an actual storage test, we found that choline cation (Ch+) captured in antibacterial film by electrostatic interaction could achieve sustained release, i.e. sustainable bacteriostasis, and keep strawberries fresh for 48 h at room temperature. This work offers a new strategy for preparing antibacterial films via non-covalent weak interactions, explored an alternative antibacterial film for food packaging applications.

Exploring Unconventional σ-Hole Interactions: Computational Insights into the Interaction of XeO3 with Non-Aromatic Coordinating Solvents

In order to control the explosiveness and shock sensitivity of XeO3 , we have investigated its plausible interaction with various non-aromatic coordinating solvents, serving as potential Lewis base donors, through density functional theory (DFT) calculations. Out of twenty six such solvents, the top ten were thus identified and then thoroughly examined by employing various computational tools such as the mapping of the electrostatic potential surface (MESP), Wiberg bond indices (WBIs), non-covalent interaction (NCI) plots, Bader's theory of atoms-in-molecules (AIM), natural bond orbital (NBO) analysis, and the energy decomposition analysis (EDA). The amphoteric nature of XeO3 was also explored by investigating the extent of back donation from the lone pair of Xe to the antibonding orbital of the donating atom/group of the solvent molecules. The C-H…O interactions were also found to be a contributing factor in the stabilization of these adducts. Although these aerogen-bonding interactions were found to be predominantly electrostatic, significant contributions from the orbital contributions, as well as dispersion interactions, were observed. The top three non-aromatic solvents (among the twenty six studied) which form the strongest adducts with XeO3 are proposed to be hexamethylphosphoramide (HMPA), N,N'-dimethylpropyleneurea (DMPU) and tetramethylethylenediamine (TMEDA).

Difference in the complexation of cholesterol with β-cyclodextrin derivatives: A combined theoretical and experimental study

This study aimed to compare differences in interactions between cholesterol and β- cyclodextrin and its derivatives for selecting a suitable β-cyclodextrin derivative to efficiently remove cholesterol from high-melting-point foods. First, the formation of cholesterol/β-cyclodextrin derivative complexes was investigated using Fourier transform infrared spectroscopy and thermogravimetric analysis. Secondly, the conformations of β-cyclodextrin derivatives were determined from experimental and calculated 1H NMR spectra, and the weak interactions between cholesterol and β-cyclodextrin derivatives were studied by computational approach. Cholesterol/hydroxypropyl-β-cyclodextrin complex had the lowest complexation energy. Besides, two moderate hydrogen bonds were formed between cholesterol and hydroxypropyl-β-cyclodextrin and between cholesterol and sulfobutyl ether-β-cyclodextrin, while one weak hydrogen bond was formed between cholesterol and methyl-β-cyclodextrin. Finally, the efficiency of cholesterol removal by hydroxypropyl-β-cyclodextrin was 5.47% higher than that by β-cyclodextrin at their optimal temperature. This work provided a theoretical basis for selecting a competent adsorbent to effectively remove cholesterol from high-melting-point foods.

Color properties and non-covalent interactions in hydrated (Z)-4-(1-cyano-2-(2,4,5-trimethoxyphenyl)-vinyl)pyridin-1-ium chloride salt: Insights from experimental and theoretical studies

The optical charge-transfer (CT) property and the crystal structure of (Z)-4-(1-cyano-2-(2,4,5-trimethoxyphenyl)vinyl)pyridin-1-ium chloride monohydrate salt (I), which belongs to an acrylonitrile family, was studied. The title salt, I, was characterized using different spectroscopy techniques and a single-crystal X-ray diffraction study combined with quantum chemical computations. The results showed that the color properties of I are determined by the CT, changes in bandgap, optical absorption, and various non-covalent interactions. The HOMO-LUMO energy gaps are 5.41 eV and 5.23 eV for the precursor and salt, respectively. It was demonstrated that π-π stacking interactions lead to the formation of intercalated dimers and donor-acceptor interactions assisted by hydrogen bonds; the dimers and interactions are different between the precursor and the salt. The cation moiety is mainly stabilized by N(1)+-H···Cl, and the anion is predominantly stabilized by strong O(1W)- H⋯ Cl- bonds as well as the hydrogen bonds with the MeO group O(2W)-H⋯O(1) and O(2W)-H⋯O(1W). The charge transfer between cation and anion moieties in the structure is established through NBO analysis.

pH-dependent self-assembly mechanism of a single repetitive domain from a spider silk protein

Spider silk is self-assembled from full-length silk proteins, and some silk protein fragments can also form silk-like fibers in vitro. However, the mechanism underlying the silk fiber formation is not understood well. In this study, we investigated the fiber formation of a single repetitive domain (RP) from a minor ampullate silk protein (MiSp). Our findings revealed that pH and salt concentration affect not only the stability of MiSp-RP but also its self-assembly into fibers and aggregates. Using nuclear magnetic resonance (NMR) spectroscopy, we solved the three-dimensional (3D) structure of MiSp RP in aqueous solution. On the basis of the structure and mutagenesis, we revealed that charge-dipole interactions are responsible for the pH- and salt-dependent properties of MiSp-RP. Our results indicate that fiber formation is regulated by a delicate balance between intermolecular and intramolecular interactions, rather than by the protein stability alone. These findings have implications for the design of silk proteins for mass production of spider silk.

Application of carboxymethyl chitosan-based coating in fresh-cut apple preservation: Incorporation of guava leaf flavonoids and their noncovalent interaction study

Carboxymethyl chitosan (CMCS) has antibacterial activity and coating-forming ability. Under the impact of noncovalent interactions, the bioactivity and functionality of CMCS may be positively affected by the coexistence of flavonoids. This study investigated the effect of a CMCS coating incorporated with flavonoids from guava (Psidium guajava L. cv. Carmine) leaf (GLF) on the refrigeration of fresh-cut apples for preservation. Compared with the CMCS group, apples treated with the CMCS-GLF coating showed better quality (weight loss, browning index, firmness), nutritional value (ascorbic acid and total phenolic content), and microbial safety during storage. The mechanism study indicated that the hydrogen bonding, electrostatic, and hydrophobic interactions between CMCS and GLF (the carboxymethyl moiety of CMCS had the highest response priority and binding strength of the interaction with -C-O of GLF) changed the surface charge distribution and microstructure of CMCS, and increased its molecular weight, particle size, viscosity, and hydrophobicity. Thus, the CMCS-GLF coating exerted better bioactivities (antibacterial and antioxidant activity), and its film showed better mechanical and barrier properties. These results revealed that the noncovalent interaction with GLF could modify the physiochemical properties of CMCS, which was beneficial to improve its bioactivity and application value in fresh fruit preservation.

Non-covalent interactions in the monohydrated complexes of 1,2,3,4-tetrahydroisoquinoline

The eleven monohydrates of 1, 2, 3, 4-tetrahydroisoquinoline (THIQ) are analyzed through natural bond orbital (NBO) analysis and QTAIM methods employing M06-2X functional in DFT and MP2 methods. Here, the role of OH bonds as an acceptor and donor is critically analyzed. The role of lone pairs of O is critically monitored in two of the complexes, where N-H···O hydrogen bonds are present. The relative contributions of rehybridisation and hyperconjugation are compared in detail. Popelier criteria are satisfied in all the complexes barring a few exceptions involving weak hydrogen bonds. At the bond critical points (BCP), four monohydrates show higher values of electron density (ρ_C) and negative values of total electron energy density (H_C), while Laplacian [Formula: see text] remains positive. These complexes satisfy the criteria of partial covalency. All these are O-H⋅⋅⋅N-type bonds. Remaining h-bonds are weaker in nature. These are also confirmed by the smaller values of ρ_C at the respective BCP. The variation of potential energy density (V_C) among the complexes seems to be the most important factor in determining the nature of non-covalent interactions.

Making and Breaking of C-N Bonds: Applications in the Synthesis of Unsymmetric Tertiary Amines and α-Amino Carbonyl Derivatives

An operationally simple process has been developed for the synthesis of unsymmetrical amines and α-amino carbonyl derivatives in the absence of a catalyst, ligand, oxidant, or any additives. Contrary to known reductive amination methods, this protocol is amenable to substrates containing other reducible groups. This process effectively results in consecutive cleavage and formation of C-N bonds. DFT studies and Hammett analysis provide useful insight into the mechanism. The role of noncovalent interactions as a stabilizing factor have been examined in the protocol. A wide range of alkyl-bromides have been coupled efficiently with a variety of dimethyl anilines to get unsymmetric tertiary amines with yields up to 90%. This methodology was further extended to the synthesis of α-amino carbonyl derivatives with yields up to 93%.

Contrasting the Noncovalent Interactions of Aromatic Sulfonyl Fluoride and Sulfonyl Chloride Motifs via Crystallography and Hirshfeld Surfaces

A heteroaryl sulfonyl(VI) fluoride, 4-chloro-7-fluorosulfonyl-2,1,3-benzoxadiazole, was synthesized from its chloride counterpart (4-chloro-7-chlorosulfonyl-2,1,3-benzoxadiazole) and the X-ray structure analysis of these compounds and the interactions in the solid-state were thoroughly examined. Hirshfeld surface analysis is used to provide a thorough and complete picture of the changes arising from the different halides in the functional groups. Surface analysis reveals that the fluoride does not participate in any hydrogen interactions as opposed to the chloride. However, the fluorine atom is observed to form close interactions with several π bonds. For both moieties, however, the sulfonyl oxygens show comparable interactions with respect to both magnitude and interatomic distances. The Hirshfeld surface analysis is coupled with computational studies to help elucidate the observed interactions that are found from the distinct nitrogen, chlorine, and oxygen atoms present in the molecules, providing new physical insights to the correlation between their structures and properties.

Non-covalent small molecule partnership for redox-active films: Beyond polydopamine technology

HYPOTHESIS

The possibility to use hexamethylenediamine (HMDA) to impart film forming ability to natural polymers including eumelanins and plant polyphenols endowed with biological activity and functional properties has been recently explored with the aim to broaden the potential of polydopamine (PDA)-based films overcoming their inherent limitations. 5,6-dihydroxyindole-2-carboxylic acid, its methyl ester (MeDHICA) and eumelanins thereof were shown to exhibit potent reducing activity.

EXPERIMENTS

MeDHICA and HMDA were reacted in aqueous buffer, pH 9.0 in the presence of different substrates to assess the film forming ability. The effect of different reaction parameters (pH, diamine chain length) on film formation was investigated. Voltammetric and AFM /SEM methods were applied for analysis of the film redox activity and morphology. HPLC, MALDI-MS and ¹HNMR were used for chemical characterization. The film reducing activity was evaluated in comparison with PDA by chemical assays and using UV stressed human immortalized keratinocytes (HaCat) cells model.

FINDINGS

Regular and homogeneous yellowish films were obtained with moderately hydrophobic properties. Film deposition was optimal at pH 9, and specifically induced by HMDA. The film consisted of HMDA and monomeric MeDHICA accompanied by dimers/small oligomers, but no detectable MeDHICA/HMDA covalent conjugation products. Spontaneous assembly of self-organized networks held together mainly by electrostatic interactions of MeDHICA in the anion form and HMDA as the dication is proposed as film deposition mechanism. The film displayed potent reducing properties and exerted significant protective effects from oxidative stress on HaCaT.

Phenolic modification of myofibrillar protein enhanced by ultrasound: The structure of phenol matters

Phenolic modification of myofibrillar protein (MPN) is an essential technology in meat processing. This paper investigated the grafting reaction of three structurally relevant polyphenols (PPs), epigallocatechin-3-gallate (EGCG), epigallocatechin (EGC), epicatechin (EC), and MPN, in a conventional alkaline reaction and ultrasound (UT)-assisted oxidation system. EC triggered the production of more hydroxyl radicals at an equal molar concentration, resulting in a noticeable improvement of the final grafting effect. Moreover, pronounced changes in pore area on the microscopic scale was observed in MPN-EGCG, which was ascribed to the unique chemical structure of EGCG. Additionally, the antioxidant activities of the UT-assisted EGCG group were 133.89% and 103.10% higher than those of the single MPN group (PP0) and pure EGCG group, respectively. These results emphasized the importance of the chemical structure of PPs in the process of different grafting reactions.

Supramolecular glycopolymers: How carbohydrates matter in structure, dynamics, and function

Supramolecular glycopolymers exhibiting inherent dynamicity, tunability, and adaptivity allow us to arrive at a deeper understanding of multivalent carbohydrate-carbohydrate interactions and carbohydrate-protein interactions, both being essential to key biological events. The impacts of the carbohydrate segments in these supramolecular glycopolymers towards their structure, dynamics, and function as biomaterials are addressed in this minireview. Bottlenecks and challenges are discussed, and we speculate about possible future directions.

Exploring competitive inhibition of a family 10 xylanase derived from Hu sheep rumen microbiota by Oryza sativa xylanase inhibitor protein: In vitro and in silico perspectives

The catalytic domain of family GH10 xylanase, XYN-LXY_CD derived from Hu sheep rumen microbiota was expressed in Pichia pastoris X33. The special activity of reXYN-LXY_CD in the culture supernatant was 232.56 U/mg. The optima of reXYN-LXY_CD were 53 °C and pH 7.0. Recombinant Oryza sativa xylanase inhibitor protein (rePOsXIP) competitively inhibited reXYN-LXY_CD with an inhibition constant (K_i) value of 237.37 nM. The concentration of hydrolysates released from beechwood xylan by reXYN-LXY_CD reduced when rePOsXIP was added into the hydrolytic system. Fluorescence of reXYN-LXY_CD was statically quenched by rePOsXIP in a dose-dependent manner. The details in intermolecular interaction between XYN-LXY_CD and OsXIP were investigated by using molecular dynamics (MD) simulations, binding free energy computation and non-covalent interactions (NCI) analysis. Hydrogen bonding and van der Waals played indispensable roles in the XYN-LXY_CD/OsXIP interaction. The α-7 helix of OsXIP tightly occupied the catalytic pocket of XYN-LXY_CD with hydrogen bonding such as K239_OsXIP-N261/Q292/E197_{XYN-LXY_CD} (E197, the acid-base catalytic residue), D236_OsXIP-K327_{XYN-LXY_CD} and Q242_OsXIP-E211/Q212_{XYN-LXY_CD}. Based on the quantum theory of atoms in molecules (QTAIM), the Laplacian of electron density and core-valence bifurcation index of HZ3_K239-OE2_E197 were 0.1025 a.u. and 0.002218, respectively. Elucidating the mechanism underlying xylanase-inhibitor interactions might help construct XYN-LXY_CD mutants that gain resistance to XIPs and high catalytic activity, which would be more efficient in feed additives in livestock.

Decomposing compounds enables reconstruction of interaction fingerprints for structure-based drug screening

Background

Structure-based drug repositioning has emerged as a promising alternative to conventional drug development. Regardless of the many success stories reported over the past years and the novel breakthroughs on the AI-based system AlphaFold for structure prediction, the availability of structural data for protein–drug complexes remains very limited. Whereas the chemical libraries contain millions of drug compounds, the vast majority of them do not have structures to crystallized targets,and it is, therefore, impossible to characterize their binding to targets from a structural view. However, the concept of building blocks offers a novel perspective on the structural problem. A drug compound is considered a complex of small chemical blocks or fragments, which confer the relevant properties to the drug and have a high proportion of functional groups involved in protein binding. Based on this, we propose a novel approach to expand the scope of structure-based repositioning approaches by transferring the structural knowledge from a fragment to a compound level.

Results

We fragmented over 100,000 compounds in the Protein Data Bank (PDB) and characterized the structural binding mode of 153,000 fragments to their crystallized targets. Using the fragment’s data, we were able to artificially reconstruct the binding mode of over 7,800 complexes between ChEMBL compounds and their known targets, for which no structural data is available. We proved that the conserved binding tendency of fragments, when binding to the same targets, highly influences the drug’s binding specificity and carries the key information to reconstruct full drugs binding mode. Furthermore, our approach was able to reconstruct multiple compound-target pairs at optimal thresholds and high similarity to the actual binding mode.

Conclusions

Such reconstructions are of great value and benefit structure-based drug repositioning since they automatically enlarge the technique’s scope and allow exploring the so far ‘unexplored compounds’ from a structural perspective. In general, the transfer of structural information is a promising technique that could be applied to any chemical library, to any compound that has no crystal structure available in PDB, and even to transfer any other feature that may be relevant for the drug discovery process and that due to data limitations is not yet fully available. In that sense, the results of this work document the full potential of structure-based screening even beyond PDB.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13321-022-00592-w.

Data to understand the nature of non-covalent interactions in the thiophene clusters

We have reported herein the data to understand the nature and number of non-covalent interactions that stabilize the structures of the thiophene clusters. In addition, we have also provided the optimized Cartesian coordinates of all the structures of the investigated thiophene clusters. Initially, the geometries have been generated using the ABCluster code which performs a global optimization to locate local and global minima structures of molecular clusters. The located geometries have been optimized at the MP2/aug-cc-pVDZ level of theory using Gaussian 16 suite of programs. To understand the nature of non-covalent interactions, we have performed a quantum theory of atoms in molecules (QTAIM) analysis on all the structures of the thiophene dimer. Furthermore, the QTAIM analysis has been performed also on the most stable structure of the thiophene trimer and tetramer. We have used the AIMAll program to perform the QTAIM analysis. The data reported in this paper contains the critical points, the bonds paths and their related properties, for each investigated structures. Besides, the data contains the optimized Cartesian coordinates of all the investigated structures of the thiophene clusters. This can be use for any further investigations involving thiophene clusters. For further information and analysis, the reader is referred to the original related research article (Malloum and Conradie, 2022).

QTAIM analysis dataset for non-covalent interactions in furan clusters

Furan clusters are very important to understand the dynamics and properties of the furan solvent. They can be used combined with quantum cluster equilibrium theory to theoretically determine the thermodynamics properties of the furan solvent. To understand the structures of the furan clusters, one needs to understand the non-covalent interactions that hold the furan molecules together. In this paper, we have provided the data necessary to understand the non-covalent interactions in furan clusters. Firstly, the structures of the furan clusters have been generated using classical molecular dynamics as implemented in the ABCluster code. Secondly, the generated structures have been fully optimized at the MP2/aug-cc-pVDZ level of theory. The optimized Cartesian coordinates of all the investigated structures are reported in this work to enable further investigations of the furan clusters. These Cartesian coordinates will save computational time for all further investigations involving the furan clusters. Thirdly, to understand the nature of the non-covalent interactions in furan clusters, we have performed a quantum theory of atoms in molecule (QTAIM) analysis using AIMAll program. Using QTAIM, we have provided the critical points, bond paths and their related properties for all the investigated structures. These data can be used to identify and classify the non-covalent interactions in furan clusters. The reader can refer to the original article for further information and discussion of the data provided herein Malloum and Conradie (2022) [1].

DNA condensation and formation of ultrathin nanosheets via DNA assisted self-assembly of an amphiphilic fullerene derivative

DNA nanotechnology propose various assembly strategies to develop novel functional nanostructures utilizing unique interactions of DNA with small molecules, nanoparticles, polymers, and other biomolecules. Although, well defined nanostructures of DNA and amphiphilic small molecules were achieved through hybridization of covalently modified DNA, attaining precise organization of functional moieties through non-covalent interactions remain as a challenging task. Herein, we report mutually assisted assembly of an amphiphilic fullerene derivative and various DNA structures through non-covalent interactions, which leads to initial DNA condensation and subsequent assembly yielding ordered fullerene-DNA nanosheets. The molecular design of the cationic, amphiphilic fullerene derivative (FPy) ensures molecular solubility in the 10% DMSO-PBS buffer system and facile interactions with DNA through groove binding and electrostatic interactions of fullerene moiety and positively charged pyridinium moiety, respectively. The formation of FPy/DNA nanostructures were thoroughly investigated in the presence of λ-DNA, pBR322 plasmid DNA, and single and double stranded 20-mer oligonucleotides using UV-visible spectroscopy, AFM and TEM analysis. λ-DNA and pBR322 plasmid DNA readily condense in presence of FPy leading to micrometer sized few layer nanosheets with significant crystallinity due to ordered arrangement of fullerenes. Similarly, single and double stranded 20-mer oligonucleotides also interact efficiently with FPy and form highly crystalline nanosheets, signifying the role of electrostatic interaction and subsequent charge neutralization in the condensation triggered assembly. However, there is significant differences in the crystallinity and ordered arrangements of fullerenes between these two cases, where longer DNA form condensed structures and less ordered nanosheets while short oligonucleotides lead to more ordered and highly crystalline nanosheets, which could be attributed to the differential DNA condensation. Finally, we have demonstrated the addressability of the assembly using a cyanine modified single strand DNA, which also forms highly crystalline nanosheets and exhibit efficient quenching of the cyanine fluorescence upon self-assembly. These results open up new prospects in the development of functional DNA nanostructures through non-covalent interactions and hence have potential applications in the context of DNA nanotechnology.

Structures, binding energies and non-covalent interactions of furan clusters

Understanding of the furan solvent is subjected to the knowledge of the structures of the furan clusters and interactions taking place therein. Although, furan clusters can be very important to determine the dynamics and the properties of the furan solvent, there has been only a few investigations reported on furan dimer. In this work, we have explored the potential energy surfaces (PESs) of the furan clusters using two incremental levels of theory. Structures have been initially generated using classical molecular dynamics followed by full optimization at the MP2/aug-cc-pVDZ level of theory. The results show that the most stable structure of the furan dimer has a stacking configuration while that of the trimer has a cyclic configuration. We have noted that the structures of the furan tetramer have no definite configurations. In addition, we have performed a quantum theory of atoms in molecule (QTAIM) analysis to identify all possible non-covalent interactions of the furan clusters. The results show that six different types of non-covalent interactions can be identified in furan clusters. We have noted that the CH⋯C and CH⋯O hydrogen bondings are the strongest non-covalent interactions while the H⋯H bonding interaction is found to be the weakest. Furthermore, we have assessed the performance of ten DFT functionals in calculating the binding energies of the furan clusters. The ten DFT functionals (M05, M05-2X, M06, M06-2X, M08HX, PBE0, ωB97XD, PW6B95D3, APFD and MN15) have been benchmarked to DLPNO-CCSD(T)/CBS. The functionals M05-2X and M06 are recommended for further affordable investigations of the furan clusters.

Supramolecular Strategies for the Recycling of Homogeneous Catalysts

Supramolecular approaches are increasingly used in the development of homogeneous catalysts and they also provide interesting new tools for the recycling of metal-based catalysts. Various non-covalent interactions have been utilized for the immobilization homogeneous catalysts on soluble and insoluble support. By non-covalent anchoring the supported catalysts obtained can be recovered via (nano-) filtration or such catalytic materials can be used in continuous flow reactors. Specific benefits from the reversibility of catalyst immobilization by non-covalent interactions include the possibility to re-functionalize the support material and the use as "boomerang" type catalyst systems in which the catalyst is captured after a homogeneous reaction. In addition, new reactor design with implemented recycling strategies becomes possible, such as a reverse-flow adsorption reactor (RFA) that combines a homogeneous reactor with selective catalyst adsorption/desorpion. Next to these non-covalent immobilization strategies, supramolecular chemistry can also be used to generate the support, for example by generation of self-assembled gels with catalytic function. Although the stability is a challenging issue, some self-assembled gel materials have been successfully utilized as reusable heterogeneous catalysts. In addition, catalytically active coordination cages, which are frequently used to achieve specific activity or selectivity, can be bound to support by ionic interactions or can be prepared in structured solid materials. These new heterogenized cage materials also have been used successfully as recyclable catalysts.

A DFT and molecular docking study

In this research, the impact of non-covalent interactions on the FT-IR spectrum and structural, electronic, topological and vibrational properties of hybrid 4-methylbenzylammonium nitrate (4MBN) have been studied combining B3LYP/CC-PVTZ calculations with molecular docking. 4MBN was synthesized and characterized by using the FT-IR spectrum while the optimized structures in gas phase and in ethanol and aqueous solutions have evidenced monodentate coordination between the nitrate and methylbenzylammonium groups, in agreement with that experimental determined for this species by X-ray diffraction. Here, non-covalent interactions were deeply analyzed in terms of topological parameters (AIM), electron localization function (ELF), localized orbital locator (LOL), Hirshfeld surface and reduced density gradient (RDG) method. Weak interactions such as H-bonds, VDW and steric effect in 4MBN were visualized and quantified by the independent gradient density (IGM) based on the promolecular density. The hyper-conjugative and the delocalization of charge in 4MBN have been elucidated by natural bonding orbital (NBO) while its chemical reactivity was studied and discussed by using molecular electrostatic potential surface (MESP), frontier molecular orbital (FMOs), density of state (DOS) and partial density of state (PDOS). The complete vibrational assignments of 69 vibration modes expected for 4MBN are reported together with the scaled force constants while the electronic transitions were evaluated by TD-DFT calculations in ethanol solution. Thermal analysis (DTA and DSC) was also determined. Molecular docking calculations have suggested that 4MBN presents biological activity and could act as a good inhibitor against schizophrenia disease.

Density functional theory-based analyses on selective gas separation by β-PVDF-supported ionic liquid membranes

Finding proper candidates for polymer-supported ionic liquid (IL)-based gas separating membranes is a challenge. The current article elucidates the quantum chemical perspective of the selective gas adsorption efficiency, from a mixture of CO₂, CO, CH₄, and H₂, of α- and β-polyvinylidene fluoride (PVDF)-supported imidazolium- and pyridinium-based six ionic liquid membranes. Although IL-based membrane efficiency mainly depends on the gas solubility of ILs, IL/support binding and gas adsorption on the support material are also studied to describe the overall gas adsorption properties of the PVDF/IL complexes. β-PVDF exhibits better binding with the ILs, and better gas affinity, thus, qualified as a more suitable membrane component as compared to α-PVDF. Dispersion-corrected density functional calculations are performed to provide a detailed insight into the energetic interactions, nonbonding intermolecular interactions based on symmetry adapted perturbation theory (SAPT), natural bond orbitals (NBO), Bader's quantum theory of atoms in molecules (QTAIM), reduced density gradient (RDG), frontier orbital interactions, density of states (DOS), and thermochemical analyses of the gas-adsorbed systems. Gas molecules interact with the membrane components through weak hydrogen bonds and exhibit low interaction energies, indicating physisorption of the gases. Gas adsorption energies are more negative than the mutual interaction energies of the gas molecules, ensuring effective gas adsorption by the membrane components. All the β-PVDF/IL systems have shown the highest and lowest affinity for CO2 and H2, respectively, leading to effective separation of CO₂ and H₂ from the other gases.

The challenge of structural heterogeneity in the native mass spectrometry studies of the SARS-CoV-2 spike protein interactions with its host cell-surface receptor

Native mass spectrometry (MS) enjoyed tremendous success in the past two decades in a wide range of studies aiming at understanding the molecular mechanisms of physiological processes underlying a variety of pathologies and accelerating the drug discovery process. However, the success record of native MS has been surprisingly modest with respect to the most recent challenge facing the biomedical community—the novel coronavirus infection (COVID-19). The major reason for the paucity of successful studies that use native MS to target various aspects of SARS-CoV-2 interaction with its host is the extreme degree of heterogeneity of the viral protein playing a key role in the host cell invasion. Indeed, the SARS-CoV-2 spike protein (S-protein) is extensively glycosylated, presenting a formidable challenge for native MS as a means of characterizing its interactions with both the host cell–surface receptor ACE2 and the drug candidates capable of disrupting this interaction. In this work, we evaluate the utility of native MS complemented with the experimental methods using gas-phase chemistry (limited charge reduction) to obtain meaningful information on the association of the S1 domain of the S-protein with the ACE2 ectodomain, and the influence of a small synthetic heparinoid on this interaction. Native MS reveals the presence of several different S1 oligomers in solution and allows the stoichiometry of the most prominent S1/ACE2 complexes to be determined. This enables meaningful interpretation of the changes in native MS that are observed upon addition of a small synthetic heparinoid (the pentasaccharide fondaparinux) to the S1/ACE2 solution, confirming that the small polyanion destabilizes the protein/receptor binding.

Non-covalent double bond sensors for gas-phase infrared spectroscopy of unsaturated fatty acids

The position and configuration of carbon-carbon double bonds in unsaturated fatty acids is crucial for their biological functions and influences health and disease. However, double bond isomers are not routinely distinguished by classical mass spectrometry workflows. Instead, they require sophisticated analytical approaches usually based on chemical derivatization and/or instrument modification. In this work, a novel strategy to investigate fatty acid double bond isomers (18:1) without prior chemical treatment or modification of the ion source was implemented by non-covalent adduct formation in the gas phase. Fatty acid adducts with sodium, pyridinium, trimethylammonium, dimethylammonium, and ammonium cations were characterized by a combination of cryogenic gas-phase infrared spectroscopy, ion mobility-mass spectrometry, and computational modeling. The results reveal subtle differences between double bond isomers and confirm three-dimensional geometries constrained by non-covalent ion-molecule interactions. Overall, this study on fatty acid adducts in the gas phase explores new avenues for the distinction of lipid double bond isomers and paves the way for further investigations of coordinating cations to increase resolution.

Rotational spectrum and internal dynamics of the hydrogen-bonded pyrrole-pyridine aromatic pair

Non-covalent interactions determine the three-dimensional structure and activity of biological molecules. In this work, the pyrrole-pyridine complex considered as a model of the NH⋯N hydrogen-bonded Watson-Crick base pairs has been generated in a supersonic expansion and characterized by chirped pulse Fourier transform microwave spectroscopy. The analysis of the unconventional spectral pattern of the 1:1 pyrrole-pyridine adduct and its ¹³C and ¹⁵N isotopologues reveal a non-planar complex, with a bent NH⋯N hydrogen bond and large amplitude motion of the pyrrole subunit. The bent structure is likely to arise from the stablishment of the secondary CH⋯N interaction between pyridine and pyrrole moieties.

Underappreciated Chemical Interactions in Protein-Ligand Complexes

Non-covalent interactions lie at the bases of the molecular recognition process. In medicinal chemistry, understanding how bioactive molecules interact with their target can help to explain structure-activity relationships (SAR) and improve potency of lead compounds. In particular, computational analysis of protein-ligand complexes can help to unravel key interactions and guide structure-based drug design.The literature describing protein-ligand complexes is typically focused on few types of non-covalent interactions (e.g., hydrophobic contacts, hydrogen bonds, and salt bridges). Stacking interactions involving aromatic rings are also relatively well known to medicinal chemistry practitioners. Potency optimization efforts are often focused on targeting these interactions. However, a variety of underappreciated interactions were shown to have a relevant effect on the stabilization of protein-ligand complexes. This chapter aims at listing selected non-covalent interactions and discuss some examples on how they can impact drug design.

Spectroscopic and molecular modelling study of binding mechanism of bovine serum albumin with phosmet

Phosmet exerts its neurotoxicity by inhibiting acetylcholinesterase that catalyzes the degradation of acetylcholine (a neurotransmitter). Serum proteins are known to influence the biodistribution of various endogenous and exogenous compounds. In the present study, the binding interactions of phosmet with bovine serum albumin (BSA) was investigated to determine the free concentration of phosmet for its neurotoxicity. The binding mechanism was studied using fluorescence, UV-Vis absorption spectroscopy, circular dichroism (CD), and molecular docking techniques. UV-Vis absorption data showed an increase in absorbance of BSA upon binding with phosmet with a slight red-shift in the peak around 280 nm. Intrinsic fluorescence of BSA was quenched in the presence of phosmet. The quenching was observed to be inversely correlated to the temperature that indicated the formation of ground state non-fluorescent complex (static quenching). Binding constant values and n values for the binding of phosmet with BSA at three different temperatures confirmed non-covalent binding interactions with a single set of equivalent binding sites. Thermodynamic parameters ∆G (-137.40 ± 3.58 kJ mol^-1); ΔH (-16.33 ± 5.28 kJ mol^-1) and ΔS(-469 ± 12.45 kJ mol^-1) confirmed that the binding was spontaneous and non-covalent interactions like electrostatic, hydrogen bonding and van der Waals forces played an important role in the binding. The CD data indicated the conformational change in BSA upon binding with phosmet which resulted in a change in the melting temperature. Molecular docking presented the binding model for BSA-phosmet complex and displayed that non-covalent interactions played a significant role in the binding mechanism.

Assessment of interfacial interactions between starch and non-isocyanate polyurethanes in their hybrids

Manufacturing of multifunctional materials through blending is a promising route for improving performance of biopolymers including starch. Non-isocyanate polyurethanes (NIPUs) are an emerging group of green materials. Understanding the mechanism of interaction between starch and NIPU not only highlights underlying chemistry but also offers an opportunity to tailor the properties and functions of starch-NIPU hybrids. We investigated the interfacial interactions between starch and NIPU to pave the way towards development of high-performance green materials. Multiple analyses revealed that NIPU interacted effectively with starch chains via intermolecular hydrogen bonds. We showed that NIPU domains can efficiently interact with the small portion of starch skeleton at interfacial region and they are only moderately miscible. Incorporation of either component above certain ratio resulted in a phase separation. This work contributes towards understanding of interfacial chemistry between starch and NIPUs and enables tailoring the interface for facile engineering of starch-NIPU hybrids.

Synthesis of Pt(II) complexes of the type [Pt(1,10-phenanthroline)(SArFn)2] (SArFn = SC6H3-3,4-F2; SC6F4-4-H; SC6F5). Preliminary evaluation of their in vitro anticancer activity

A series of Pt(II) complexes of the type [Pt(1,10-phenanthroline)(SArF_n)₂] (SArF_n = SC₆H₃-3,4-F₂(1); SC₆F₄-4-H (2); SC₆F₅(3)) were synthesized from [Pt(1,10-phenanthroline)(Cl)₂] and [Pb(SArF_n)₂] via metathesis reactions. The complexes were fully characterized including the unambiguous determination of their molecular structures by single-crystal X-ray diffraction techniques, showing the metal centers to be into a slightly distorted square-planar environments. The in vitro cytotoxic activity of the complexes was evaluated on six cancerous cell lines, i.e: glial cells of nervous central system (U-251), prostate (PC-3), leukemia (K-562), colon (HCT-15), breast (MCF-7) and lung (SKLU-1); we also included a healthy cell line of COS-7 (African green monkey kidney) for comparative purposes. We found that complex 2 was selective for PC-3. In addition, the IC₅₀ values for the series of complexes were determined using the U-251, HCT-15 and SKLU-1 cancerous cell lines, as well as in the healthy cell line (COS-7), where complex 1 exhibited the best activity, with IC₅₀ values going from 4.56 to 4.78 μM. These studies where further complemented with DNA docking theoretical calculations and DNA affinity experiments.

An In Vitro Study of Aromatic Stacking of Drug Molecules

In this paper, drug-drug chemical interactions between two different aromatic compounds were studied by mass spectrometry. Specifically, we examined non-covalent complexes (NCX) between paclitaxel, a chemotherapeutic compound, and medications widely used in palliative care for depression, psychosis, and anxiety. It is unknown whether psychotropic medications directly interact with paclitaxel. Here, we use a simple and rapid electrospray ionization mass spectrometry in vitro assay, which has been predictive in the case of neuropeptides, to measure the relative strength of non-covalent interactions. This chemical interaction is most likely due to the overlap of aromatic rings of π-orbitals between paclitaxel and five commonly used medications: diazepam, clonozepam, sertraline, fluoxetine, and haloperidol. Molecular modeling illustrates that differences in the stability of the NCXs are likely due to the distance between the aromatic rings present in both the paclitaxel and antidepressant medications. Graphical Abstract.

New coordination compounds of citric acid and polyamines with lanthanide ions - potential application in monitoring the treatment of cancer diseases

Non-covalent interaction in the binary systems of polyamines (putrescine, spermidine, spermine) with citric acid and complex formation in the binary as well as ternary systems of lanthanide(III) ions, citric acid and polyamine have been investigated. The studies were performed in aqueous solution. The overall stability constants of the complexes were determined using the potentiometric method with computer analysis of the data. Only mononuclear type of complexes were found in the ternary systems and polyamines were located in the outer as well as inner coordination sphere. Non-covalent interaction between biogenic amines and citric acid in the binary and ternary systems were confirmed on the basis of the equilibrium constants analysis and spectroscopic studies.

Co-operativity in non-covalent interactions in ternary complexes: a comprehensive electronic structure theory based investigation

The structure and stability of various ternary complexes in which an extended aromatic system such as coronene interacts with ions/atoms/molecules on opposite faces of the π-electron cloud were investigated using ab initio calculations. By characterizing the nature of the intermolecular interactions using an energy decomposition analysis, it was shown that there is an interplay between various types of interactions and that there are co-operativity effects, particularly when different types of interactions coexist in the same system. Graphical abstract Weak OH-π, π-π and van der Waals-π ternary systems are stabilized through dispersion interactions. Cation-π ternary systems are stabilized by through-space electrostatic interactions.

Fluorescence alteration of MPA capped CdSe quantum dots by spontaneous biomarker protein adsorption

Quantum dots (QDs) have significant potentials in biomedical applications of bioimaging and biosensing. Spontaneous adsorption of proteins on QDs surface is a common phenomenon, which occurred to serum proteins in biological samples, and has been observed to enhance QDs fluorescence. In this study, fluorescence alteration of 3-mercaptopropionic acid (MPA) capped CdSe quantum dots by four individual biomarker proteins was investigated. By monitoring the fluorescence emission of QDs, the biomarker protein adsorbed spontaneously on QDs surface was recognized and quantified. When alpha fetoprotein (AFP) or heat shock protein 90 alpha (HSP90α) were present, the QDs became brighter. The presence of cytochrome C (CytoC) or lysozyme (Lyz) made the QDs dimmer first, and then brighter. Within five minutes response time all four biomarker proteins were detected individually with the estimated detection limit in the range of 1-10 ng/mL and good linear dynamic ranges. The results suggested that the fluorescence of QDs was responsive to not only serum proteins but also biomarker proteins. The fluorescence response was able to correlate quantitatively with the amount of biomarker proteins in relatively low concentrations. These results provide more information to understand QDs and support their applications in biomedical fields.

Comparative study of binding interactions between porphyrin systems and aromatic compounds of biological importance by multiple spectroscopic techniques: A review

The specific spectroscopic and redox properties of porphyrins predestine them to fulfill the role of sensors during interacting with different biologically active substances. Monitoring of binding interactions in the systems porphyrin-biologically active compound is a key question not only in the field of physiological functions of living organisms, but also in environmental protection, notably in the light of the rapidly growing drug consumption and concurrently the production of drug effluents. Not always beneficial action of drugs on natural porphyrin systems induces to further studies, with commercially available porphyrins as the model systems. Therefore the binding process between several water-soluble porphyrins and a series of biologically active compounds (e.g. caffeine, guanine, theophylline, theobromine, xanthine, uric acid) has been studied in different aqueous solutions analyzing their absorption and steady-state fluorescence spectra, the porphyrin fluorescence lifetimes and their quantum yields. The magnitude of the binding and fluorescence quenching constants values for particular quenchers decreases in a series: uric acid > guanine > caffeine > theophylline > theobromine > xanthine. In all the systems studied there are characters of static quenching, as a consequence of the π-π-stacked non-covalent and non-fluorescent complexes formation between porphyrins and interacting compounds, accompanied simultaneously by the additional specific binding interactions. The porphyrin fluorescence quenching can be explain by the photoinduced intermolecular electron transfer from aromatic compound to the center of the porphyrin molecule, playing the role of the binding site. Presented results can be valuable for designing of new fluorescent porphyrin chemosensors or monitoring of drug traces in aqueous solutions. The obtained outcomes have also the toxicological and medical importance, providing insight into the interactions of the water-soluble porphyrins with biologically active substances.

Non-covalent interactions between thio-caffeine derivatives and water-soluble porphyrin in ethanol-water environment

To determine the binding interactions and ability to form the non-covalent systems, the association process between 5,10,15,20-tetrakis[4-(trimethylammonio)phenyl]-21H,23H-porphine tetra-p-tosylate (H₂TTMePP) and a series of five structurally diverse thio-caffeine analogues has been studied in ethanol and ethanol-water solutions, analyzing its absorption and steady-state fluorescence spectra. The porphyrin fluorescence lifetimes in the systems studied were established as well. During the titration with thio-caffeine compounds the slight bathochromic effect and considerable hypochromicity of the porphyrin Soret band maximum can be noted. The fluorescence quenching effect observed for interactions in H₂TTMePP - thio-caffeine derivative systems, as well as the order of binding and fluorescence quenching constants (of 10⁵-10³mol^-1) suggest the existence of the mechanism of static quenching due to the formation of non-covalent and non-fluorescent stacking complexes. In all the systems studied the phenomenon of the fractional accessibility of the fluorophore for the quencher was observed as well. Additionally, the specific binding interactions, due to the changes in reaction environment polarity, can be observed. It was found that thio-caffeine compounds can quench the porphyrin fluorescence according to the structure of thio-substituent in caffeine molecule. The obtained results can be potentially useful from scientific, therapeutic or environmental points of view.

On the competition between weak O-H···F and C-H···F hydrogen bonds, in cooperation with C-H···O contacts, in the difluoromethane - tert-butyl alcohol cluster

The 1:1 complex of tert-butyl alcohol with difluoromethane has been characterized by means of a joint experimental-computational investigation. Its rotational spectrum has been recorded by using a pulsed-jet Fourier-Transform microwave spectrometer. The experimental work has been guided and supported by accurate quantum-chemical calculations. In particular, the computed potential energy landscape pointed out the formation of three stable isomers. However, the very low interconversion barriers explain why only one isomer, showing one O-H···F and two C-H···O weak hydrogen bonds, has been experimentally characterized. The effect of the H → tert-butyl- group substitution has been analyzed from the comparison to the difluoromethane-water adduct.

Integrating computational methods and experimental data for understanding the recognition mechanism and binding affinity of protein-protein complexes

Protein-protein interactions perform several functions inside the cell. Understanding the recognition mechanism and binding affinity of protein-protein complexes is a challenging problem in experimental and computational biology. In this review, we focus on two aspects (i) understanding the recognition mechanism and (ii) predicting the binding affinity. The first part deals with computational techniques for identifying the binding site residues and the contribution of important interactions for understanding the recognition mechanism of protein-protein complexes in comparison with experimental observations. The second part is devoted to the methods developed for discriminating high and low affinity complexes, and predicting the binding affinity of protein-protein complexes using three-dimensional structural information and just from the amino acid sequence. The overall view enhances our understanding of the integration of experimental data and computational methods, recognition mechanism of protein-protein complexes and the binding affinity.

A machine learning correction for DFT non-covalent interactions based on the S22, S66 and X40 benchmark databases

Background

Non-covalent interactions (NCIs) play critical roles in supramolecular chemistries; however, they are difficult to measure. Currently, reliable computational methods are being pursued to meet this challenge, but the accuracy of calculations based on low levels of theory is not satisfactory and calculations based on high levels of theory are often too costly. Accordingly, to reduce the cost and increase the accuracy of low-level theoretical calculations to describe NCIs, an efficient approach is proposed to correct NCI calculations based on the benchmark databases S22, S66 and X40 (Hobza in Acc Chem Rev 45: 663–672, 2012; Řezáč et al. in J Chem Theory Comput 8:4285, 2012).

Results

A novel type of NCI correction is presented for density functional theory (DFT) methods. In this approach, the general regression neural network machine learning method is used to perform the correction for DFT methods on the basis of DFT calculations. Various DFT methods, including M06-2X, B3LYP, B3LYP-D3, PBE, PBE-D3 and ωB97XD, with two small basis sets (i.e., 6-31G* and 6-31+G*) were investigated. Moreover, the conductor-like polarizable continuum model with two types of solvents (i.e., water and pentylamine, which mimics a protein environment with ε = 4.2) were considered in the DFT calculations. With the correction, the root mean square errors of all DFT calculations were improved by at least 70 %. Relative to CCSD(T)/CBS benchmark values (used as experimental NCI values because of its high accuracy), the mean absolute error of the best result was 0.33 kcal/mol, which is comparable to high-level ab initio methods or DFT methods with fairly large basis sets. Notably, this level of accuracy is achieved within a fraction of the time required by other methods. For all of the correction models based on various DFT approaches, the validation parameters according to OECD principles (i.e., the correlation coefficient R², the predictive squared correlation coefficient q² and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$q_{cv}^{2}$$\end{document}qcv2 from cross-validation) were >0.92, which suggests that the correction model has good stability, robustness and predictive power.

Conclusions

The correction can be added following DFT calculations. With the obtained molecular descriptors, the NCIs produced by DFT methods can be improved to achieve high-level accuracy. Moreover, only one parameter is introduced into the correction model, which makes it easily applicable. Overall, this work demonstrates that the correction model may be an alternative to the traditional means of correcting for NCIs.Graphical abstract

A combined crystallographic analysis and ab initio calculations to interpret the reactivity of functionalized hexavanadates and their inhibitor potency toward Na(+)/K(+)-ATPase

In vitro influence of five synthesized functionalized hexavanadates (V6) on commercial porcine cerebral cortex Na(+)/K(+)-ATPase activity has been studied. Dose dependent Na(+)/K(+)-ATPase inhibition was obtained for all investigated compounds. Calculated half maximal inhibitory concentration IC50 values, in mol/L, for Na(+)/K(+)-ATPase were 7.6×10(-5), 1.8×10(-5), 2.9×10(-5), 5.5×10(-5) for functionalized hexavanadates (V6) with tetrabutylammonium (TBA) [V6-CH3][TBA]2, [V6-NO2][TBA]2, [V6-OH][TBA]2 and [V6-C3][TBA]2 respectively. [V6-OH][Na]2 inhibited Na(+)/K(+)-ATPase activity up to 30% at maximal investigated concentration 1×10(-3)mol/L. This reactivity has been interpreted using a study of the non-covalent interactions of functionalized hexavanadate hybrids through Cambridge Structural Database (CSD) analysis. Bibliographic searching has led to 18 different structures and 99 contacts. We have observed that C-H⋯O contacts consolidate the structures. We have also performed density functional theory (DFT) calculations and have determined electrostatic potential values at the molecular surface on a series of functionalized V6. These results enlightened their chemical reactivity and their potential biological applications such as the inhibition of the ATPase.

Affinity Capillary Electrophoresis Applied to Investigation of Valinomycin Complexes with Ammonium and Alkali Metal Ions

This chapter deals with the application of affinity capillary electrophoresis (ACE) to investigation of noncovalent interactions (complexes) of valinomycin, a macrocyclic dodecadepsipeptide antibiotic ionophore, with ammonium and alkali metal ions (lithium, sodium, potassium, rubidium, and cesium). The strength of these interactions was characterized by the apparent binding (stability, association) constants (K b) of the above valinomycin complexes using the mobility shift assay mode of ACE. The study involved measurements of effective electrophoretic mobility of valinomycin at variable concentrations of ammonium or alkali metal ions in the background electrolyte (BGE). The effective electrophoretic mobilities of valinomycin measured at ambient temperature and variable ionic strength were first corrected to the reference temperature 25 °C and constant ionic strength (10 or 25 mM). Then, from the dependence of the corrected valinomycin effective mobility on the ammonium or alkali metal ion concentration in the BGE, the apparent binding constants of the valinomycin-ammonium or valinomycin-alkali metal ion complexes were determined using a nonlinear regression analysis. Logarithmic form of the binding constants (log K b) were found to be in the range of 1.50-4.63, decreasing in the order Rb(+) > K(+) > Cs(+) > > Na(+) > NH4 (+) ~ Li(+).

Unraveling the performance of dispersion-corrected functionals for the accurate description of weakly bound natural polyphenols

Long-range non-covalent interactions play a key role in the chemistry of natural polyphenols. We have previously proposed a description of supramolecular polyphenol complexes by the B3P86 density functional coupled with some corrections for dispersion. We couple here the B3P86 functional with the D3 correction for dispersion, assessing systematically the accuracy of the new B3P86-D3 model using for that the well-known S66, HB23, NCCE31, and S12L datasets for non-covalent interactions. Furthermore, the association energies of these complexes were carefully compared to those obtained by other dispersion-corrected functionals, such as B(3)LYP-D3, BP86-D3 or B3P86-NL. Finally, this set of models were also applied to a database composed of seven non-covalent polyphenol complexes of the most interest. Graphical abstract Weakly bound natural polyphenolsᅟ.

Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics

Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron-sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.

Binding of dietary polyphenols to cellulose: structural and nutritional aspects

The interactions between polyphenols and plant fibres play an important role in controlling the release of phenolic compounds from food matrices for absorption in the gastrointestinal tract. This study probed the molecular interactions of diverse polyphenols with cellulose fibres by using a pure cellulose-producing bacterial model. Alkali treatment of bacterial cellulose was an effective method for obtaining a high purity cellulose model for study of polyphenol binding. Representatives of different polyphenol classes all bound to cellulose spontaneously, rapidly, and to comparable extents (up to 60% w/w of cellulose). Langmuir binding isotherms were applied to determine quantitative aspects of the adsorption at equilibrium. The study indicated that binding was similar on a molar basis for ferulic acid, gallic acid, catechin and cyanidin-3-glucoside (but lower for chlorogenic acid), with the native charge of polyphenols a secondary factor in the interactions between polyphenols and cellulose.

Gas-phase intermolecular phosphate transfer within a phosphohistidine phosphopeptide dimer

The hydrogen bonds and electrostatic interactions that form between the protonated side chain of a basic residue and the negatively charged phosphate of a phosphopeptide can play crucial roles in governing their dissociation pathways under low-energy collision-induced dissociation (CID). Understanding how phosphoramidate (i.e. phosphohistidine, phospholysine and phosphoarginine), rather than phosphomonoester-containing peptides behave during CID is paramount in investigation of these problematic species by tandem mass spectrometry. To this end, a synthetic peptide containing either phosphohistidine (pHis) or phospholysine (pLys) was analyzed by ESI-MS using a Paul-type ion trap (AmaZon, Bruker) and by traveling wave ion mobility-mass spectrometry (Synapt G2-Si, Waters). Analysis of the products of low-energy CID demonstrated formation of a doubly 'phosphorylated' product ion arising from intermolecular gas-phase phosphate transfer within a phosphopeptide dimer. The results are explained by the formation of a homodimeric phosphohistidine (pHis) peptide non-covalent complex (NCX), likely stabilized by the electrostatic interaction between the pHis phosphate group and the protonated C-terminal lysine residue of the peptide. To the best of our knowledge this is the first report of intermolecular gas-phase phosphate transfer from one phosphopeptide to another, leading to a doubly phosphorylated peptide product ion.

Graph analysis of β2 adrenergic receptor structures: a "social network" of GPCR residues

Purpose

G protein-coupled receptors (GPCRs) are a superfamily of membrane proteins of vast pharmaceutical interest. Here, we describe a graph theory-based analysis of the structure of the β₂ adrenergic receptor (β₂ AR), a prototypical GPCR. In particular, we illustrate the network of direct and indirect interactions that link each amino acid residue to any other residue of the receptor.

Methods

Networks of interconnected amino acid residues in proteins are analogous to social networks of interconnected people. Hence, they can be studied through the same analysis tools typically employed to analyze social networks – or networks in general – to reveal patterns of connectivity, influential members, and dynamicity. We focused on the analysis of closeness-centrality, which is a measure of the overall connectivity distance of the member of a network to all other members.

Results

The residues endowed with the highest closeness-centrality are located in the middle of the seven transmembrane domains (TMs). In particular, they are mostly located in the middle of TM2, TM3, TM6 or TM7, while fewer of them are located in the middle of TM1, TM4 or TM5. At the cytosolic end of TM6, the centrality detected for the active structure is markedly lower than that detected for the corresponding residues in the inactive structures. Moreover, several residues acquire centrality when the structures are analyzed in the presence of ligands. Strikingly, there is little overlap between the residues that acquire centrality in the presence of the ligand in the blocker-bound structures and the agonist-bound structures.

Conclusions

Our results reflect the fact that the receptor resembles a bow tie, with a rather tight knot of closely interconnected residues and two ends that fan out in two opposite directions: one toward the extracellular space, which hosts the ligand binding cavity, and one toward the cytosol, which hosts the G protein binding cavity. Moreover, they underscore how interaction network is by the conformational rearrangements concomitant with the activation of the receptor and by the presence of agonists or blockers.

Electronic supplementary material

The online version of this article (doi:10.1186/2193-9616-1-16) contains supplementary material, which is available to authorized users.