Intermolecular Noncovalent Bonds Research Articles

Can we quantitatively evaluate the mutual impacts of intramolecular metal-ligand bonds the same as intermolecular noncovalent bonds?

In this paper, we have reviewed several equations for calculating the cooperative energy of two chemical bonds between three fragments/species, regardless of whether they are atoms, ions or molecules, and whether the bonds between them are intra- or intermolecular. It is emphasized that two chemical bonds upon cooperation in a new compound change the bond dissociation energy of each other exactly by the same quantitative value, their cooperative energy, regardless of the nature of the bonds or whether one bond is very weak and another one is very strong. However, the final benefit/drawback of weak bonds from this cooperation can be considerably larger than that of strong bonds. The above statements are supported by a computational study on the various types of inter- and intramolecular chemical bonds.

Natural biomass-derived carbon dots as a potent solubilizer with high biocompatibility and enhanced antioxidant activity.

Numerous natural compounds exhibit low bioavailability due to suboptimal water solubility. The solubilization methods of the modern pharmaceutical industry in contemporary pharmaceutical research are restricted by low efficiency, sophisticated technological requirements, and latent adverse effects. There is a pressing need to elucidate and implement a novel solubilizer to ameliorate these challenges. This study identified natural biomass-derived carbon dots as a promising candidate. We report on natural fluorescent carbon dots derived from Aurantia Fructus Immatures (AFI-CDs), which have exhibited a remarkable solubilization effect, augmenting naringin (NA) solubility by a factor of 216.72. Subsequent analyses suggest that the solubilization mechanism is potentially contingent upon the oration of a nanostructured complex (NA-AFI-CDs) between AFI-CDs and NA, mediated by intermolecular non-covalent bonds. Concomitantly, the synthesized NA-AFI-CDs demonstrated high biocompatibility, exceptional stability, and dispersion. In addition, NA-AFI-CDs manifested superior free radical scavenging capacity. This research contributes foundational insights into the solubilization mechanism of naringin-utilizing AFI-CDs and proffers a novel strategy that circumvents the challenges associated with the low aqueous solubility of water-insoluble drugs in the field of modern pharmaceutical science.

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

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

Front Cover: Supramolecular Hydrogels: Design Strategies and Contemporary Biomedical Applications (Chem. Asian J. 9/2022)

Supramolecular hydrogels are generated when gelator molecules (or macromolecules) spontaneously self-assemble to form a 3D solid-like network via dynamic intermolecular non-covalent bonds, such as hydrogen bonding, π-π bonding, hydrophobic interactions, and van der Waals interactions. Here, the interactions that underlie the formation of supramolecular hydrogels are presented, before exemplifying their versatility by highlighting a selection of recent state-of-the-art developments and their associated biomedical applications. The applications selected include drug delivery, tissue engineering, wound healing and 3D bioprinting. More information can be found in the Review by Xian Jun Loh, Cécile A. Dreiss, Tung-Chun Lee et al.

A conserved arginine residue in a staphylococcal anti-sigma factor is required to preserve its kinase activity, structure, and stability

RsbW, σB, and RsbV, encoded by Staphylococcus aureus and related bacteria, act as an anti-sigma factor, an sigma factor, and an anti-anti-sigma factor, respectively. The interaction between RsbW and σB blocks the transcription initiation activity of the latter protein. RsbW also functions as a serine kinase and phosphorylates RsbV in the presence of ATP. Our modeling study indicates that the RsbW-RsbV complex is stabilized by twenty-four intermolecular non-covalent bonds. Of the bond-forming RsbW residues, Arg 23, and Glu 49 are conserved residues. To understand the roles of Arg 23 in RsbW, rRsbW[R23A], a recombinant S. aureus RsbW (rRsbW) harboring Arg to Ala change at position 23, was investigated using various probes. The results reveal that rRsbW[R23A], like rRsbW, exists as the dimers in the aqueous solution. However, rRsbW[R23A], unlike rRsbW, neither interacted with a chimeric RsbV (rRsbV) nor formed the phosphorylated rRsbV in the presence of ATP. Furthermore, the tertiary structure and hydrophobic surface area of rRsbW[R23A] matched little with those of rRsbW. Conversely, both rRsbW[R23A] and rRsbW showed interaction with a recombinant σB (rσB). rRsbW and rRsbW[R23A] were also unfolded via the formation of at least one intermediate in the presence of urea. However, the thermodynamic stability of rRsbW significantly differed from that of rRsbW[R23A]. Our molecular dynamics (MD) simulation study also reveals the substantial change of structure, dimension, and stability of RsbW due to the above mutation. The ways side chain of critical Arg 23 contributes to maintaining the tertiary structure, and stability of RsbW was elaborately discussed. Communicated by Ramaswamy H. Sarma

Molecular Structure Evaluation of Wheat Gluten during Frozen Storage

The effects of frozen storage (0–120 day) on the secondary structure and molecular chain conformation of hydrated gluten were investigated using Fourier transform infrared spectroscopy (FTIR) and atomic force microscopy (AFM). After frozen storage, no changes were observed in the secondary structure of the 60% hydrated gluten; spectra were consistent with a tight ordered structure with many interchain hydrogen bond interactions. For the dehydrated gluten, more complex changes took place: during frozen storage for up to 60 days, there were distinctive changes in the low-frequency region of the amide I band (1618–1633 cm−1) which were attributed to changes in the β-sheet structure. However, with the increase of frozen storage from 60 to 120 days, a band near 1614 cm−1 replaced that at 1659 cm−1 illustrate that the formation of protein aggregates during the long-time frozen storage, which along with the establishment of new intermolecular non-covalent bonds within the protein molecule or between two neighboring molecules. AFM images showed that the gluten chain formed a fibril-like branched network, and this network was weakened with increasing frozen storage time.

Creation of catalytically active particles from enzymes crosslinked with a natural bifunctional agent--homocysteine thiolactone.

The current study describes an approach to creation of catalytically active particles with increased stability from enzymes by N-homocysteinylation, a naturally presented protein modification. Enzymatic activities and properties of two globular tetrameric enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and lactate dehydrogenase (LDH) were studied before and after N-homocysteinylation. Modification of these proteins concerns the accessible lysine residues and introduces an average of 2-2,5 homocysteine residues per protein monomer. Formation of a range of aggregates was observed for both enzymes, which assemble via formation of intermolecular noncovalent bonds and by disulfide bonds. It was demonstrated that both studied enzymes retain their catalytic activities on modification and the subsequent formation of oligomeric forms. At low concentrations of homocysteine thiolactone, modification of GAPDH leads not only to prevention of spontaneous inactivation but also increases thermal stability of this enzyme on heating to 80°C. A moderate reduction of the activity of GAPDH observed in case of its crosslinking with 50-fold excess of homocysteine thiolactone per lysine is probably caused by hindered substrate diffusion. Spherical particles of 100 nm and larger diameters were observed by transmission electron microscopy and atomic force microscope techniques after modification of GAPDH with different homocysteine thiolactone concentrations. In case of LDH, branched fibril-like aggregates were observed under the same conditions. Interestingly, crosslinked samples of both proteins were found to have reversible thermal denaturation profiles, indicating that modification with homocysteine thiolactone stabilizes the spatial structure of these enzymes.

Synthesis, crystal structures, and photophysical properties of dibromo-2-(2′-pyridyl)imidazole and its corresponding boron–fluorine complex

2-(2′-Pyridyl)imidazole L1 and its corresponding boron–fluorine complex, 1, were synthesized and their crystal structures correlated with their photophysical properties. L1 forms a rigid supramolecular network through hydrogen bonds and halogen bond in the single crystal, which induces amplified spontaneous emission in crystals; it emits rather poor fluorescence in solution and powder states. Its boron chelate 1 emits intense fluorescence in solution since boron chelate is an excellent chromophore, and it exhibits large Stokes shift (136 nm in acetonitrile), due to the charge-transfer transition from the electron-donating π system to the electron-accepting boron moiety. Interestingly, 1 is also highly fluorescent in amorphous powder and crystal states; C–C rotation between pyridyl and imidazole groups is inhibited by the formation of a five-member ring containing BF2, and the formation of intermolecular non-covalent bonds is the key factor. Solid emission with large Stokes shift makes it a valuable chromophore for synthesis of functional materials.

The effect of hydrogen bond on the vibrational dynamics of genistein free and complexed with β‐cyclodextrins

AbstractInclusion, or host–guest, complexes are supramolecular assemblies in which two or more molecules hold together and organize by means of intermolecular noncovalent bonds. In the pharmaceutical field, inclusion complexation of drugs with unsubstituted and derivative β‐cyclodextrins (β‐CDs) has proven to be a successful method to improve the dissolution of water insoluble drugs. Genistein (Gen), an isoflavone constituent of Onodis spinosae radix, turned out to be a suitable guest molecule for the encapsulation into β‐CD, resulting in a significant improvement of its aqueous solubility. In the present study, the modifications of the vibrational spectrum of Gen caused by its inclusion into β‐CDs cavity have been characterized by means of Raman scattering experiments. These changes have been interpreted by comparing the experimental data with the vibrational wavenumbers and Raman intensities obtained by simulation for the free and complexed guest molecule. Following this strategy, we have obtained a deeper understanding of the host–guest interactions involved in the formation and stabilization of the complexes, with particular regard to the role played by the guest chemical groups, as well as to disentangle the effects directly related to the complexation process from those ascribed to other factors, such as formation of intra‐ and intermolecular hydrogen bonds. Copyright © 2009 John Wiley & Sons, Ltd.

Toward Main Chain Metallo‐Terpyridyl Supramolecular Polymers: “The Metal Does the Trick”

Metallo-supramolecular chemistry offers possibilities for the construction of stimuli-responsive polymeric materials where the environment can have a large impact on the reversibility and strength of interactions between the individual components. The potential of manipulating the strength of the intermolecular non-covalent bonds can result in impressive modifications of the metallo-supramolecular structure and, subsequently, produces changes in the properties of the designed material. The present feature article provides an overview on recent developments in the field of metallo-polymerization of chelating terpyridyl and analogues ligands. Synthetic strategies are described followed by a discussion regarding the characterization and the application of the reviewed metallo-supramolecular structures, mainly based on terpyridines.

The pH Threshold in the Dissolution of β-Lactoglobulin Gels and Aggregates in Alkali

The existence of a practical minimum pH for the dissolution of heat-induced whey gels in alkaline solutions has been studied using beta-lactoglobulin (betaLg) as a model protein. A sharp transition in solubility was observed between pH 11 and 12; this transition shifts to higher pHs for gels formed at higher temperatures and for longer gelling times. The breakdown reactions of heat-induced aggregates in alkali were monitored with size exclusion chromatography. The destruction of large aggregates was faster at higher pH and also showed a transition between pH 11 and 12. Using tryptophan fluorescence and near- and far-UV circular dichroism, this transition was assigned to the base-induced denaturation observed in solutions of aggregates (pK 11.53). It is suggested that the high protein repulsion caused by the large number of charges at pH > 11.5 drives the unfolding of the protein and the disruption of the intermolecular noncovalent bonds. Concentrated urea and GuHCl were found to be less effective than a pH 12 solution in destroying large aggregates. Aggregates formed for a long time (80 degrees C for 24 h) contained a larger number of intermolecular disulfide bonds that hinder the dissolution process. Gels formed at low temperatures (65 degrees C for 60 min), with fewer intermolecular noncovalent bonds, showed a similar solubility-pH profile to that observed for the base-induced denaturation of unheated beta-lactoglobulin (betaLg) (pK 10.63).

Building Blocks for Organic Heterospin, Heteromolecular Complexes as Models for Organic Molecule-Based Ferrimagnets

Magnetic properties and crystal structure of a pyridine-substituted iminonitroxide biradical, 3,5-bis(4,4,5,5,-tetramethyl-4,5-dihydro-1H-imidazol-2-yl-1-oxyl)pyridine (1), were examined. The molecular ground state of1 was found to be triplet (S=1) with a singlet-triplet energy gap of 2J/kB=7.0K. The triplet biradical serves as a building block for moleculebased magnets of S>1/2 based on intermolecular noncovalent bonds.

Electron Capture Dissociation as Structural Probe for Noncovalent Gas-Phase Protein Assemblies

Electron capture dissociation (ECD) of proteins in Fourier transform ion cyclotron resonance mass spectrometry usually leads to charge reduction and backbone-bond cleavage, thereby mostly retaining labile, intramolecular noncovalent interactions. In this report, we evaluate ECD of the 84-kDa noncovalent heptameric gp31 complex and compare this with sustained off-resonance irradiation collisionally activated dissociation (SORI-CAD) of the same protein. Unexpectedly, the 21+ charge state of the gp31 oligomer exhibits a main ECD pathway resulting in a hexamer and monomer, disrupting labile, intermolecular noncovalent bonds and leaving the backbone intact. Unexpectedly, the charge separation over the two products is highly proportional to molecular weight. This indicates that a major charge redistribution over the subunits of the complex does not take place during ECD, in contrast to the behavior observed when using SORI-CAD. We speculate that the ejected monomer retains more of its original structure in ECD, when compared to SORI-CAD. ECD of lower charge states of gp31 does not lead to dissociation of noncovalent bonds. We hypothesize that the initial gas-phase structure of the 21+ charge state is significantly different from the lower charge states. These structural differences result in the different reaction pathways when using ECD.

Pyridine-substituted nitronyl nitroxide biradicals: a triplet (S = 1) ground state lasting out N-methylation

A 3,5-pyridine-substituted biradical of nitronyl nitroxide (1) has been designed, synthesized and the magnetic properties fully characterized. The ground-state spin multiplicity of 1 has been found to be triplet (S = 1) with a singlet–triplet energy gap of 2J/kB = 40 K from magnetic susceptibility measurements on a magnetically diluted system dispersed in organic polymer films. The 3,5-substituted pyridine 1 has a hydrogen-accepting site which is more accessible to hydrogen donors than previously known biradicals with sterically hindered 2,6-pyridine frameworks. N-Methylation of 1 has yielded a stable cationic species in a trifluoromethanesulfonate salt (2+·TfO−). The ground state of the cation 2+ has been found to be triplet as well with 2J/kB = 32 K from magnetic susceptibility measurements for magnetically diluted films. The magnetic susceptibility of neat crystalline solids of 1 and 2+·TfO− has been explained by Heisenberg exchange coupling models based on their X-ray crystal structures. It is well known that the energy preference of a high-spin ground state for m-phenylene, or m-xylylene, coupling units is disturbed in such cases as the π-conjugation is affected by heteroatomic substitution, an ionic charge, or molecular conformation. The present experimental results show that the high-spin preference in 1 and 2+ is little influenced by the heterocycle or the ionic charge. Intermolecular noncovalent bonds such as hydrogen bonding and electrostatic interactions are a driving force for crystallization of open-shell molecules in a controllable manner. The ground-state triplet biradicals serve as building blocks for molecule-based magnets of S > 1/2 based on intermolecular noncovalent bonding architecture.

Comparative study of some expanding arthropod cuticles: The relation between composition, structure and function

The abdominal cuticles of the adult female ticks Argas (Persicargas) robertsi and Boophilus microplus, sp der Badumna insignis, tsetse fly Glossina morsitans morsitans, sheep ked Melophagus ovinus and locust Locusta migratoria migratorioides and of the fifth-instar larva of the bug Rhodnius prolixus stretch greatly, some of them quite rapidly, when they are feeding, laying eggs or carrying a developing larva or egg mass. During this expansion the epicuticle, which is convoluted, unfolds and the underlying endocuticle stretches. There is an increase in the volume of each of the cuticles on expansion. The fine structures of those cuticles which go through cycles of expansion and contraction do not become disrupted. Cuticles with acidic proteins have much higher chitin contents than those with basic proteins. Plasticization, i.e. breaking of intermolecular non-covalent bonds, precedes rapid expansion of cuticles but is unnecessary for slow expansion. The compositions of the cuticles and the properties of the proteins are discussed in relation to the expansions which take place in the cuticles.