Supramolecular biofunctional materials

This review discusses supramolecular biofunctional materials, a novel class of biomaterials formed by small molecules that are held together via noncovalent interactions. The complexity of biology and relevant biomedical problems not only inspire, but also demand effective molecular design for functional materials. Supramolecular biofunctional materials offer (almost) unlimited possibilities and opportunities to address challenging biomedical problems. Rational molecular design of supramolecular biofunctional materials exploit powerful and versatile noncovalent interactions, which offer many advantages, such as responsiveness, reversibility, tunability, biomimicry, modularity, predictability, and, most importantly, adaptiveness. In this review, besides elaborating on the merits of supramolecular biofunctional materials (mainly in the form of hydrogels and/or nanoscale assemblies) resulting from noncovalent interactions, we also discuss the advantages of small peptides as a prevalent molecular platform to generate a wide range of supramolecular biofunctional materials for the applications in drug delivery, tissue engineering, immunology, cancer therapy, fluorescent imaging, and stem cell regulation. This review aims to provide a brief synopsis of recent achievements at the intersection of supramolecular chemistry and biomedical science in hope of contributing to the multidisciplinary research on supramolecular biofunctional materials for a wide range of applications. We envision that supramolecular biofunctional materials will contribute to the development of new therapies that will ultimately lead to a paradigm shift for developing next generation biomaterials for medicine.

Insight into the interaction between DNA bases and defective graphenes: covalent or non-covalent

Although some metal clusters and molecules were found to more significantly bind to defective graphenes than to pristine graphenes, exhibiting chemisorptions on defective graphenes, the present investigation shows that the adsorption of DNA bases on mono- and di-vacant defective graphenes does not show much difference from that on pristine graphene, and is still dominantly driven by noncovalent interactions. In the present study the adsorptions of the nucleobases, adenine (A), cytosine (C), guanine, (G), and thymine (T) on pristine and defective graphenes, are fully optimized using a hybrid-meta GGA density functional theory (DFT), M06-2X/6-31G*, and the adsorption energies are then refined with both M06-2X and B97-D/6-311++G**. Graphene is modeled as nano-clusters of C₇₂H₂₄, C₇₁H₂₄, and C₇₀H₂₄ for pristine, mono- and di-vacant defective graphenes, respectively, supplemented by a few larger ones. The result shows that guanine has the maximum adsorption energy in all of the three adsorption systems; and the sequence of the adsorption strength is G>A>T>C on the pristine and di-vacant graphene and G>T>A>C on the mono-vacant graphene. In addition, the binding energies of the DNA bases with the pristine graphene are less than the corresponding ones with di-vacant defective graphene; however, they are greater than those of mono-vacant graphene with guanine and adenine, while it is dramatic that the binding energies of mono-vacant graphene with thymine and cytosine appear larger than those of pristine graphene.

Improved color stability of anthocyanins in the presence of ascorbic acid with the combination of rosmarinic acid and xanthan gum

This study investigated the protective effect and mechanism of action of combined use of rosmarinic acid (RA) and xanthan gum (XG) on the stability of anthocyanins (ACNs) in the presence of l-ascorbic acid (pH 3.0). The addition of RA and XG, alone and in combination, significantly enhanced the color stability of ACNs, and the combined use of RA and XG showed the best effect. FTIR, 1H NMR, AFM and computational molecular simulation analyses revealed that the improvement in ACN stability following the combined addition of RA and XG was due to intermolecular interactions such as hydrogen bonding and van der Waals forces. In the ACN-RA-XG ternary complexes, XG had stronger binding interactions with ACNs than RA. Our findings provide a valuable potential to enhance the stability of ACNs in the presence of ascorbic acid with the combined use of RA and XG.

Quantum-mechanical investigation of tetrel bond characteristics based on the point-of-charge (PoC) approach

The point-of-charge (PoC) approach was employed to investigate the characteristics of the tetrel bond from an electrostatic perspective. W-T-XYZ···B nomenclature was suggested where T is a tetrel atom, W is the atom along the σ-hole extension, B is a Lewis base, and X, Y, and Z are three atoms on the same side of the σ-hole. Quantum-mechanical calculations were carried out on F-T-F₃ systems (where T = C, Si, Ge, or Sn) at the MP2/aug-cc-pVTZ level of theory, with PP functions for Ge and Sn atoms. The tetrel bond strength was estimated via the molecular stabilization energy. Tetrel bond strength was found to increase with increasing PoC negativity (i.e., Lewis basicity) and the electronegativity of the W atom. Moreover, the effects of the T···PoC distance, the W-T···PoC angle, and the aqueous medium on the tetrel bond strength were also investigated. Correlations between tetrel bond strength and several atomic and molecular descriptors such as the natural charge on the tetrel atom, E_HOMO, and the p-orbital contribution to W-T bond hybridization were observed. Contrary to expectations, the tetrel bond strength in F-C-X₃ increased as the electronegativity of X decreased. The σ-node criteria for the studied molecules were also introduced and discussed. The ability of these molecules to simultaneously form more than one tetrel bond was examined via the σⁿ-hole test. In conclusion, the tetrel bond strength was found to be governed by the strengths of (i) the attractive electrostatic interaction of the Lewis base with the σ-hole, (ii) the attractive/repulsive interaction between the Lewis base and the X, Y, and Z atoms, and (iii) the van der Waals interaction between the Lewis base and the X, Y, and Z atoms. Graphical Abstract Characterization of tetrel bond using the Point-of-Charge (PoC) approach.

Molecular interaction study of flavonoids with human serum albumin using native mass spectrometry and molecular modeling

Noncovalent interactions between proteins and small-molecule ligands widely exist in biological bodies and play significant roles in many physiological and pathological processes. Native mass spectrometry (MS) has emerged as a new powerful tool to study noncovalent interactions by directly analyzing the ligand-protein complexes. In this work, an ultrahigh-resolution native MS method based on a 15-T SolariX XR Fourier transform ion cyclotron resonance mass spectrometer was firstly used to investigate the interaction between human serum albumin (HSA) and flavonoids. Various flavonoids with similar structure were selected to unravel the relationship between the structure of flavonoids and their binding affinity for HSA. It was found that the position of the hydroxyl groups and double bond of flavonoids could influence the noncovalent interaction. Through a competitive experiment between HSA binding site markers and apigenin, the subdomain IIA (site 1) of HSA was determined as the binding site for flavonoids. Moreover, a cooperative allosteric interaction between apigenin and ibuprofen was found from their different HSA binding sites, which was further verified by circular dichroism spectroscopy and molecular docking studies. These results show that native MS is a useful tool to investigate the molecular interaction between a protein and its ligands. Graphical abstract Unravel the relationship between the structure of flavonoids and their binding affinity to HSA by native MS.

Study of the noncovalent interactions between phenolic acid and lysozyme by cold spray ionization mass spectrometry (CSI-MS), multi-spectroscopic and molecular docking approaches

Elucidating the recognition mechanisms of the noncovalent interactions between pharmaceutical molecules and proteins is important for understanding drug delivery in vivo, and for the further rapid screening of clinical drug candidates and biomarkers. In this work, a strategy based on cold spray ionization mass spectrometry (CSI-MS), combined with fluorescence, circular dichroism (CD), Fourier transform infrared spectroscopy (FTIR), and molecular docking methods, was developed and applied to the study of the noncovalent interactions between phenolic acid and lysozyme (Lys). Based on the real characterization of noncovalent complex, the detailed binding parameters, as well as the protein conformational changes and specific binding sites could be obtained. CSI-MS and tandem mass spectrometry (MS/MS) technique were used to investigate the phenolic acid-Lys complexes and the structure-affinity relationship, and to assess their structural composition and gas phase stability. The binding affinity was obtained by direct and indirect MS methods. The fluorescence spectra showed that the intrinsic fluorescence quenching of Lys in solution was a static quenching mechanism caused by complex formation, which supported the MS results. The CD and FTIR spectra revealed that phenolic acid changed the secondary structure of Lys and increased the α-helix content, indicating an increase in the tryptophan (W) hydrophobicity near the protein binding site resulting in a conformational alteration of the protein. In addition, molecular docking studies were performed to investigate the binding sites and binding modes of phenolic acid on Lys. This strategy can more comprehensively and truly characterize the noncovalent interactions and can guide further research on the interactions of phenolic acid with other proteins.

An electrochemical biosensor based on electroactive peptide nanoprobes for the sensitive analysis of tumor cells

Peptides possess many appealing and desirable features, which have attracted increasing attention in the field of electrochemical biosensing. However, peptides hardly produce noticeable electronic signals in response to target binding events. In this work, amphipathic peptides FFFGGGGRGDS with both target recognition and self-assembly capabilities are designed to be co-assembled with the electroactive species ferrocenecarboxylic acid (FcCOOH). Furthermore, the resultant electroactive peptide nanoprobes (ePNPs) are applied for sensitive electrochemical analysis of tumor cells. Specifically, tumor cells are captured by the electrode modified with the corresponding DNA aptamers, and ePNPs can then selectively bind to integrin proteins on the cell surface, thereby accompanied by a remarkable increase of electrochemical signal. Taking the assay of MDA-MB-231 cells, the fabricated biosensor can detect cancer cells with a detection limit of 7 cells mL^-1. Moreover, the ePNPs can act as a universal probe for the detection of different cell lines. Given the merits of easy synthesis, convenient operation, and favorable analytical performance, the proposed biosensor exhibits great potential in developing peptide-based electrochemical biosensing for clinical applications.

Electrical Probing and Tuning of Molecular Physisorption on Graphene

The ability to tune the molecular interaction electronically can have profound impact on wide-ranging scientific frontiers in catalysis, chemical and biological sensor development, and the understanding of key biological processes. Despite that electrochemistry is routinely used to probe redox reactions involving loss or gain of electrons, electrical probing and tuning of the weaker noncovalent interactions, such as molecular physisorption, have been challenging, primarily due to the inability to change the work function of conventional metal electrodes. To this end, we report electrical probing and tuning of the noncovalent physisorption of polar molecules on graphene surface by using graphene nanoelectronic heterodyne sensors. Temperature-dependent molecular desorptions for six different polar molecules were measured in real-time to study the desorption kinetics and extract the binding affinities. More importantly, we demonstrate electrical tuning of molecule-graphene binding kinetics through electrostatic gating of graphene; the molecular desorption can be slowed down nearly three times within a gate voltage range of 15 V. Our results provide insight into small molecule-nanomaterial interaction dynamics and signify the ability to electrically tailor interactions, which can lead to rational designs of complex chemical processes for catalysis and drug discovery.

Development of high internal phase emulsions with noncovalent crosslink of soy protein isolate and tannic acid: Mechanism and application for 3D printing

In this study, we propose a design strategy using soy protein isolate (SPI)-tannic acid (TA) complexes crosslinked through noncovalent interactions to develop high internal phase emulsions (HIPEs) for 3D printing materials. The results of Fourier transform infrared spectroscopy, intrinsic fluorescence, and molecular docking analyses indicated that the dominant interactions occurring between the SPI and TA were mediated by hydrogen bonds and hydrophobic interactions. The secondary structure, particle size, ζ-potential, hydrophobicity and wettability of SPI was significantly altered by the addition of TA. The microstructure of HIPEs stabilized by SPI-TA complexes exhibited more regular and even polygonal shapes, thereby allowing the protein to form a dense self-supporting network structure. When the concentration of TA exceeded 50 μmol/g protein, the formed HIPEs remained stable after 45 days of storage. Rheological tests revealed that the HIPEs exhibited a typical gel-like (G' > G'') and shear-thinning behavior, which contributed to preferable 3D printing behavior.

Theoretical study on the free radical scavenging potency and mechanism of natural coumestans: Roles of substituent, noncovalent interaction and solvent

The free radical scavenging potency and mechanisms of seven representative natural coumestans were systematically evaluated using density functional theory (DFT) approach. Thermodynamic feasibility of different mechanisms was assessed by various physio-chemical descriptors involved in the double (2H⁺/2e^‒) radical-trapping processes. Energy diagram and related transition state structures of the reaction between wedelolactone (WEL) and hydroperoxyl radical were constructed to further uncover the radical-trapping details. Results showed that the studied coumestans prefer to scavenge radicals via formal hydrogen atom transfer (fHAT) mechanism in the gas phase and non-polar environment, whereas sequential proton loss electron transfer (SPLET) is favored in polar media. Moreover, the feasibility of second fHAT and SPLET processes was also revealed. Sequential double proton loss double electron transfer (SdPLdET) mechanism represents the preferred pathway in aqueous solution at physiological pH. Our findings highlight the essential role of ortho-dihydroxyl group, noncovalent interaction and solvents on radical-trapping potency. 4'-OH in D-ring was found to be the most favorable site to trap radical for most of the studied coumestans, whereas 3-OH in A-ring for lucernol (LUN).

Interaction of Cun, Agn and Aun (n = 1-4) nanoparticles with ChCl:Urea deep eutectic solvent

In this study, the interaction of noble metal nanoparticles (M_n, M = Cu, Ag, and Au; n = 1-4) with ChCl:Urea deep eutectic solvent was investigated using density functional theory (DFT) method. We find that ChCl:Urea mostly interact with the M_n nanoparticles through [Cl]^- anion ([Cl]^-…M_n) and nonconventional H-bonds of C-H⋯M_n and N-H⋯M_n. NBO, QTAIM, NCI and EDA analyses show that [Cl]^-…M_n interactions are stronger than the nonconventional H-bonds interactions. Our results indicate that the nature of [Cl]^-…M_n interactions is electrostatic, while the nonconventional H-bonds of C-H⋯M_n and N-H⋯M_n are van der Waals in nature. The negative values of enthalpy (ΔH) and free energy (ΔG) for the ChCl:Urea…M_n complexes reveal that the formation of ChCl:Urea…M_n complexes is exothermic and proceeds spontaneously. The calculation of binding energy (ΔE_b) of M_n nanoparticles with ChCl:Urea shows that the strength of interaction of Au_n nanoparticles with ChCl:Urea is more favorable than Cu_n and Ag_n, following the order ChCl:Urea…Au_n > ChCl:Urea…Cu_n > ChCl:Urea…Ag_n. Furthermore, the ΔE_b, ΔH and ΔG values enhance with increasing nanoparticle size from n = 1 to n = 4, ChCl:Urea…M₄> ChCl:Urea…M₃> ChCl:Urea…M₂> ChCl:Urea…M₁ (M = Cu, Ag, and Au).

Evaluation of the binding of natural products with thrombin binding aptamer G-quadruplex using electrospray ionization mass spectrometry and spectroscopic methods

A 15-mer thrombin-binding aptamer (TBA) was discovered with specificity for thrombin. It forms a unique G-quadruplex (G4), which is postulated to be the molecular basis for its binding specificity. Many analytical methods make use of affinity binding between the thrombin and TBA as they form a very stable complex. We develop a strategy to stabilize TBA/G4's structure by introducing G4-interactive molecules, which may enhance its ability to recognize the target. Herein, a fast screening ESI-MS assay was employed to determine potential binding of natural products molecules with the TBA/G4 complex. The experimental results showed that four investigated natural alkaloids had apparent binding affinities. One of them, jatrorrhizine (L1), has been shown to bind strongly to the TBA/G4 mainly in 1:2 M ratio. Once the working conditions were established, the interaction of the jatrorrhizine with the TBA/G4 was explored using a combination of ESI-MS and spectroscopic techniques. Ligand-induced effects on TBA/G4 structure and its stability were examined by means of circular dichroism (CD). Jatrorrhizine inducing the G4 formation seems also to be the more effective in terms of thermal stabilization under the experimental conditions used. Both results of UV and fluorescence experiments undoubtedly showed a good binding affinity with the binding constant around 10⁵ L mol^-1. The stacking interactions of jatrorrhizine with the G-tetrads in TBA/G4 were further confirmed by competition experiment. ESI-MS was carried out to determine the coexistence of 1:1 and 1:2 complexes in TBA/G4-L1 system, and showed a dynamical shift from 1:1 to 1:2 complex in minutes.

Mass Spectroscopic Study of G-Quadruplex

Mass spectrometry (MS) is an analytical tool complimentary for being sensitive, accurate, and versatile in its application, such as the identification of multistranded nucleic acid assemblies, including G-quadruplex. More specifically, electrospray ionization mass spectrometry (ESI-MS) has been successfully applied to probe various G-quadruplex formations and G-quadruplex-ligand interactions. The benefit of the ESI process is that the noncovalent interactions, which typically stabilize the multistranded motifs of G-quadruplex in solution, are preserved in the gas phase. Here we use ESI-MS to describe the structural characterization of G-quadruplex structures found in three G-rich sequences, as well as the ligand binding. Detailed structural information of G-quadruplexes and their ligand-bound complexes (such as the cation/ligand binding stoichiometry, and the number of strands and G-quartets) can be obtained from a single spectrum using this ESI-MS-based method.

Halogen bonds and other noncovalent interactions in the crystal structures of trans-1,2-diiodo alkenes: an ab initio and QTAIM study

A series of interatomic interactions interpretable as halogen bonds involving I…I, I…O, and I…C(π), as well as the noncovalent interactions I…H and O…O, were observed in the crystal structures of trans-1,2-diiodoolefins dimers according to ab initio calculations and the quantum theory of "atoms in molecules" (QTAIM) method. The interplay between each type of halogen bond and other noncovalent interactions was studied systematically in terms of bond length, electrostatic potential, and interaction energy, which are calculated via ab initio methods at the B3LYP-D3/6-311++G(d,p) and B3LYP-D3/def2-TZVP levels of theory. Characteristics and nature of the halogen bonds and other noncovalent interactions, including the topological properties of the electron density, the charge transfer, and their strengthening or weakening, were analyzed by means of both QTAIM and "natural bond order" (NBO). These computational methods provide additional insight into observed intermolecular interactions and are utilized to explain the differences seen in the crystal structures. Graphical abstract The contour map presents the regions of electronic concentration and depletion along each bond in one dimer. The blue points denote the BCPs. The blue lines denote positive Laplacian of electron density, which indicate the ionic interactions, van der Waals or intermolecular interactions, and the red lines denote negative Laplacian of electron density which indicate the covalent bonds.

Analysis of Saccharides by the Addition of Amino Acids

In this work, we present the detection sensitivity improvement of electrospray ionization (ESI) mass spectrometry of neutral saccharides in a positive ion mode by the addition of various amino acids. Saccharides of a broad molecular weight range were chosen as the model compounds in the present study. Saccharides provide strong noncovalent interactions with amino acids, and the complex formation enhances the signal intensity and simplifies the mass spectra of saccharides. Polysaccharides provide a polymer-like ESI spectrum with a basic subunit difference between multiply charged chains. The protonated spectra of saccharides are not well identified because of different charge state distributions produced by the same molecules. Depending on the solvent used and other ions or molecules present in the solution, noncovalent interactions with saccharides may occur. These interactions are affected by the addition of amino acids. Amino acids with polar side groups show a strong tendency to interact with saccharides. In particular, serine shows a high tendency to interact with saccharides and significantly improves the detection sensitivity of saccharide compounds. Graphical Abstract ᅟ.

The protonated 2-halogenated imidazolium cation as the noncovalent interaction donor: the σ-hole and π-hole interactions

The σ-hole and π-hole of the protonated 2-halogenated imidazolium cation (XC₃H₄N₂⁺; X = F, Cl, Br, I) were investigated and analyzed. The monomers of (CH₃)₃SiY(Y=F, Cl, Br, I), considered as the Lewis base, were combined with the σ-hole and π-hole of XC₃H₄N₂⁺ to form the σ-hole and π-hole interactions in the bimolecular complexes (CH₃)₃SiY · · · XC₃H₄N₂⁺ and (CH₃)₃SiY · · · C₃(X)H₄N₂⁺(X/Y=F, Cl, Br, I), respectively. For both the σ-hole and π-hole interactions, the equilibrium geometries of complexes show regular changes according to the sequence of heavy sequence of the noncovalent interaction acceptors and donors. The electrostatic energy is the main contribution in the formation of both kinds of interactions, it has linear relations with the V _S,max values of σ-hole and the V' _S,max values of π-hole. Both the σ-hole and π-hole interactions belong to the closed-shell and noncovalent interactions. The π-hole interactions are stronger than the σ-hole interactions. For the π-hole interactions, the contribution percents of the dispersion energies are somewhat greater than those of the σ-hole interactions, while it is contrary for the polarization energy. Graphical Abstract The protonated 2-halogenated imidazolium cation as the noncovalent interaction donor: the σ-hole and π-hole interactionsᅟ.

Influence of copper(II) ions on the noncovalent interactions between cytidine-5'-diphosphate or cytidine-5'-triphosphate and biogenic amines putrescine or spermidine

Potentiometric and NMR spectroscopic studies of the nucleotide (NucP)/polyamine (PA) system (where NucP = CDP, CTP, PA = putrescine or spermidine) revealed the formation of molecular complexes (NucP)(H_x+y)(PA) (where H_x+y = number of protons; x - from NucP and y - from PA). Their thermodynamic parameters were determined and the modes of their interactions were proposed. The main reaction centers were found to be the protonated amine groups of polyamine (positive centers) and phosphate groups of nucleotide (negative centers). The pH ranges in which the complex occurs correspond to those of amine protonation and -PO₃^x- group deprotonation, which unambiguously confirms the dipole-dipole type of interaction. In the pH range of total deprotonation of NH_x⁺ groups from the polyamine, the molecular complexes disappear. The equilibrium and spectroscopic studies of the ternary systems Cu(II)/NucP/PA evidenced the formation of Cu(NucP)H_x+y(PA) type coordination compounds and Cu(NucP)⋯(PA)(H_x) type molecular complexes with polyamine in the outer coordination sphere. The main sites of metal ion bonding in the latter species are the phosphate groups of the nucleotide, while in the coordination compounds - besides the phosphate groups - also the donor nitrogen atoms from the polyamines. In this paper we have also quantitatively calculated the effect of metal ions on the formation of the molecular complexes.

Influence of halogen atom substitution and neutral HCN/anion CN- Lewis base on the triel-bonding interactions

Triel-bonding interactions composed of Lewis acid TrOHH₂/TrOH₂X/TrOHX₂ (Tr = B, Al, Ga; X = F, Cl, Br) molecule and Lewis base neutral HCN or anionic CN^- molecule are of research significance in bond properties, which has been investigated at MP2/aug-cc-pVTZ theory level. It is also feasible to study the halogen atom substituent effect and influence of different Lewis bases on the formation of triel bond. AIM analyses reveal that Tr (Tr = B, Al, Ga)···N bond critical point (BCP) exists in all studied triel bond. In the formation of triel bonding, compared with Lewis base HCN molecule, Lewis base anionic CN^- can participate in a stronger triel bond. Specifically, the structural change, deformation energy, and charge transfer of CN^- complexes are all larger than that of HCN complexes. In addition, halogen atom substitution effect is also discussed. MEP value and binding energy of HCN and CN^- complexes all increase after replacing one or two hydrogen atoms by halogen atoms (F, Cl, Br) in Lewis acid. Especially, replacing two hydrogen atoms by halogen atoms in Lewis acid has more remarkable enhancement in MEP value and binding energy than that of replacing only one hydrogen atom. After replacement, binding energy can be increased by 21.77 kcal/mol. The neutral and anionic triel-bonded complexes composed by Lewis acid TrOHH₂/TrOH₂X/TrOHX₂ (Tr = B, Al, Ga; X = F, Cl, Br) with Lewis base HCN and CN^- are systematically investigated at MP2/aug-cc-pVTZ level. The neutral (HCN) triel bonding is weaker than the anionic (CN^-) triel bonding due to the smaller MEP value of the neutral HCN molecule. The replacement of hydrogens (-H) in Lewis acid by electron-withdrawing groups (-F, -Cl, -Br) has a prominent enhancement effect on the MEP value of π-hole and triel-bonding strength.

Designed inhibitors with hetero linkers for gastric proton pump H+,K+-ATPase: Steered molecular dynamics and metadynamics studies

Acid suppressant SCH28080 and its derivatives reversibly reduce acid secretion activity of the H⁺,K⁺-ATPase in a K⁺ competitive manner. The results on homologation of the SCH28080 by varying the linker chain length suggested the improvement in efficacy. However, the pharmacokinetic studies reveal that the hydrophobic nature of the CH₂ linker units may not help it to function as a better acid suppressant. We have exploited the role of linker unit to enhance the efficacy of such reversible acid suppressant drug molecules using hetero linker, i.e., disulfide and peroxy linkers. The logarithm of partition coefficient defined for a drug molecule relates to the partition coefficient, which allows the optimum solubility characteristics to reach the active site. The logarithm of partition coefficient calculated for the designed inhibitors suggests that inhibitors would possibly reach the active site in sufficient concentration like in the case of SCH28080. The steered molecular dynamics studies have revealed that the Inhibitor-1 with disulfide linker unit is more stable at the active site due to greater noncovalent interactions compared to the SCH28080. Centre of mass distance analysis suggests that the Cysteine-813 amino acid residue selectively plays an important role in the inhibition of H⁺,K⁺-ATPase for Inhibitor-1. Furthermore, the quantum chemical calculations with M11L/6-31+G(d,p) level of theory have been performed to account the noncovalent interactions responsible for the stabilization of inhibitor molecules in the active site gorge of the gastric proton pump at different time scale. The hydrogen bonding and hydrophobic interaction studies corroborate the center of mass distance analysis as well. Well-tempered metadynamics free energy surface and center of mass separation analysis for the Inhibitor-1 is in good agreement with the steered molecular dynamics results. The torsional angle of the linker units seems to be crucial for better efficacy of drug molecules. The torsional angle of linker units of SCH28080 (COCH₂C) and of Inhibitor 1 (CSSC) prefers to lie within ∼60°-90° for a longer time during the simulations, whereas, the peroxy linker (COOC) of Inhibitor 2 prefers to adopt ∼120-160°. Therefore, it appears that the smaller torsion angle of linker units can achieve better interactions with the active site residues of H⁺,K⁺-ATPase to inhibit the acid secretion activity. The reversible drug molecules with disulfide linker unit would be a promising candidate as proton pump antagonist to H⁺,K⁺-ATPase.

Exploring the noncovalent interaction between β-lactoglobulin and flavonoids under nonthermal process: Characterization, physicochemical properties, and potential for lycopene delivering

The poor structure stability and low bioavailability of lycopene (LY) hampers the wide application in food field. Thus, it is crucial to explore novel deliver carrier for LY based on protein-flavonoid complexes. In this study, the noncovalent interaction mechanism between β-lactoglobulin (β-LG) and flavonoids (apigenin (API), luteolin (LUT), myricetin (MY), apigenin-7-O-glucoside, luteolin-7-O-glucoside, and myricetrin) under ultrasound treatment was explored. Results revealed that ultrasound treatment promoted reactive groups exposure and structural unfolding of β-LG to interact with six flavonoids. The main driving force between β-LG and flavonoids was hydrophobic interaction. The docking result showed that the preferred binding site for these flavonoids was on the outer surface of β-LG. The thermal stability, surface hydrophilicity, and antioxidant properties of β-LG-API, β-LG-LUT, and β-LG-MY complexes were superior by multi-spectroscopy methods and molecular simulation analysis (P < 0.05). The ability of β-LG-API for delivering LY was the best among above three binary complexes, revealing superior environmental stability and bioavailability of the β-LG-API-LY complex. This study will help to understand the ultrasound-assisted noncovalent binding of protein-flavonoid complexes, and exhibit the potential as a novel delivery system for delivery and protection of LY.

The physical mechanism of electron excitation spectrum for photo redox device controlled by gate voltage, a first-principles study

This article uses quantum chemical methods and various wave function analysis methods to firstly analyze the optical absorption spectrum and electron migration mechanism of rhodamine 6G molecular complexes on graphene substrates during electron or hole injection. Secondly, since the light absorption properties are very important during photocatalysis, the intermolecular interaction and electronic structure in both cases were calculated and analyzed. Not only the experimental results of the previous photocatalytic devices were explained, but also the physical mechanism was promoted, and the guiding recommendations for the future catalytic device design.

Direct Through-Space Substituent-π Interactions in Noncovalent Arene-Fullerene Assemblies

The arene-arene interactions between electron-rich and deficient aromatics have been less understood. Herein, we focus on a [60]fullerene π-surface as an electron-deficient aromatics. Using a 1H signal of H2O@C60 as a magnetic probe, the presence of benzene-fullerene interactions was confirmed. To investigate substituent effects on the noncovalent arene-fullerene interactions, NMR titration experiments were carried out using an open-[60]fullerene and a series of substituted benzenes, i. e., PhX (X=NO2, CN, Cl, OMe, H, CH3, and NH2), demonstrating a 1 : 2 stoichiometry with a positive correlation between stabilization energies upon the first association (ΔG1) and Hammet constants (σm). The destabilization of the self-assembled structure for X=OMe with a σ-withdrawing nature clearly showed direct through-space substituent-π interactions describable by the Wheeler-Houk model while the second association was suggested to be considerably perturbed by the secondary effects.

Noncovalent interactions between benzochalcogenadiazoles and nitrogen bases

A theoretical study has been carried out on the intermolecular interactions between tetrafluoro-benzochalcogenadiazoles (chalcogen = S, Se, Te) and a series of nitrogen bases (FCN, ClCN, NP, trans-N₂H₂, pyridine, pyrazole, imidazole) at the B97-D3/def2-TZVP level, to obtain a better insight into the nature and strength of Ch···N chalcogen bond and secondary interaction in the binary and 1:2 ternary complexes. The dispersion force plays a prominent role on the stability of the sulfur complexes, and the electrostatic effect enhanced for the heavier chalcogen complexes. Most of intermolecular bonds display the characters of closed-shell and noncovalent interaction. For the complexes involving pyridine and imidazole, chalcogen bond is stronger than hydrogen bond, while the strength of chalcogen bond is equivalent to the secondary interaction for other complexes. With the addition of nitrogen base in the 1:2 complexes, chalcogen bond is weakened, while the secondary interaction remains unchanged. In the 1:2 complexes formed by pyridine and imidazole, stronger chalcogen bond results in larger negative cooperativity than that of other complexes.

Visualization Analysis of Covalent and Noncovalent Interactions in Real Space

Understanding the types and locations of interactions between atoms or molecules within a chemical system is a fundamental concern in chemistry. In the field of theoretical and computational chemistry, wavefunction analysis offers various methods based on functions defined in 3D real space, enabling the visual representation of both covalent and noncovalent interactions. These methods provide researchers with an intuitive understanding of molecular interactions and are gaining increasing attention. This review systematically introduces various widely adopted and distinctive visualization methods, such as the noncovalent interaction (NCI) method, the independent gradient model based on Hirshfeld partition of molecular density (IGMH), the interaction region indicator (IRI), the electrostatic potential (ESP), the electron localization function (ELF), and deformation density. Additionally, numerous application examples are provided to help readers recognize the significant practical value of these methods. Also the computer program Multiwfn, which effectively implemented all the introduced methods, is briefly mentioned.

Probing Noncovalent Interaction Strengths of Host-Guest Complexes Using Negative Ion Photoelectron Spectroscopy

Noncovalent interactions (NCIs) are crucial for the formation and stability of host-guest complexes, which have wide-ranging implications across various fields, including biology, chemistry, materials science, pharmaceuticals, and environmental science. However, since NCIs are relatively weak and sensitive to bulk perturbation, direct and accurate measurement of their absolute strength has always been a significant challenge. This concept article aims to demonstrate the gas-phase electrospray ionization (ESI)-negative ion photoelectron spectroscopy (NIPES) as a direct and precise technique to measure the absolute interaction strength, probe nature of NCIs, and reveal the electronic structural information for host-guest complexes. Our recent studies in investigating various host-guest complexes that involve various types of NCIs such as anion-π, (di)hydrogen bonding, charge-separated ionic interactions, are overviewed. Finally, a summary and outlook are provided for this field.