Asymmetric Pd/Organoboron-Catalyzed Site-Selective Carbohydrate Functionalization with Alkoxyallenes Involving Noncovalent Stereocontrol

Herein, we demonstrate the robustness of a synergistic chiral Pd/organoboron system in tackling a challenging suite of site-, regio-, enantio- and diastereoselectivity issues across a considerable palette of biologically relevant carbohydrate polyols, when prochiral alkoxyallenes were employed as electrophiles. In view of the burgeoning role of noncovalent interactions (NCIs) in stereoselective carbohydrate synthesis, our mechanistic experiments and DFT modeling of the reaction path unexpectedly revealed that NCIs such as hydrogen bonding and CH-π interactions between the resting states of the Pd-π-allyl complex and the borinate saccharide are critically involved in the stereoselectivity control. Our strategy thus illuminates the untapped potential of harnessing NCIs in the context of transition metal catalysis to tackle stereoselectivity challenges in carbohydrate functionalization.

Halogen, Chalcogen, Pnictogen, and Tetrel Bonding in Non-Covalent Organocatalysis: An Update

The use of noncovalent interactions based on electrophilic halogen, chalcogen, pnictogen, or tetrel centers in organocatalysis has gained noticeable attention. Herein, we provide an overview on the most important developments in the last years with a clear focus on experimental studies and on catalysts which act via such non-transient interactions.

Effects of pH-varying thermal modification on sewage sludge: A focus on releasing nitrogen- and phosphorus-containing substances

Sewage sludge is promising for the recovery and utilisation of nutrient components, but its complex nature hinders the release of these components. The combination of pH and thermal modifications shows promise for the release of nutrient components from sludge. However, comprehensive studies on the full spectrum of pH levels and corresponding mechanisms of pH-varying thermal modification are lacking. In this study, the main nutrient components, physicochemical properties, molecular structure, and noncovalent interactions of sludge were comprehensively investigated through pH-varying thermal modification (within a pH range of 2.0 to 12.0 under the same thermal condition). The experimental results showed that the release of main organics, particularly nitrogen (N)-containing organics, was well-fitted, with a tick-like function (R2: 0.74-0.96). The thermal protons exhibited a notable accumulative mutagenic effect on the N-containing organics release, while the thermal hydroxyl ions had a more direct effect, as revealed by the changes in multivalent metals and molecular structures with the protonation-deprotonation of carboxyl groups. The driving force for the release of N-containing organics was identified as the fluctuation of electrostatic interactions at the solid-liquid interface of the sludge. However, the release of phosphorus (P)-containing substances exhibited a contrasting response to that of N-containing substances with varying pH, likely because the reaction sites of thermal protons and thermal hydroxyl ions for P-containing substances were different. Moreover, high concentrations of thermal protons and hydroxyl ions collapsed the Lifshitz-van der Waals interactions of sludge, resulting in a decrease in viscoelasticity and binding strength. These propositions were further confirmed through statistical analyses of the main indicators of the main nutrient components, physicochemical properties, and noncovalent interactions of sludge. These findings can provide a basis for optimising characteristic-specific methods to recovery nutrient components (N/P) from sludge.

Doping heteroatoms to form multiple hydrogen bond sites for enhanced interfacial reconstruction and separations

Interfacial challenges in unconventional oil extraction include heavy oil-water-solid multiphase separation and corrosion inhibition. Herein, a novel strategy based on interfacial hydrogen bonding reconstruction is proposed for constructing multifunctional interfacially active materials (MIAMs) to address multi-interfacial separation needs. A simple one-pot method is applied to successfully synthesize four different MIAM varieties, integrating site groups (-NH2, OSO, -COOH, and Si-O-Si) with multiple hydrogen bonds (HBs) into allyl polyether chains. The results indicate that all synthesized MIAMs excel in demulsification, detergency, and corrosion inhibition simultaneously, even at 25 °C. Their dehydration efficiency for different water-in-oil emulsions (even heavy oil emulsion) surpasses 99.9 % even at 16 °C, showing their excellent energy-saving potential for field applications. Furthermore, they demonstrate effective, nondestructive static cleaning (up to 86 %) of adhered oil from solid surfaces at 25 °C and provide corrosion inhibition effects (up to 92.09 %) on mild steel immersed in saturated brine. Mechanistic tests reveal that incorporating multiple HB sites in MIAMs dramatically enhances their effectiveness in interfacial separations. Based on these findings, an HB-dominated noncovalent interaction reconstruction strategy is tentatively proposed to develop advanced materials for low-carbon, efficient interfacial separations.

Stereoselective Entry into α,α'-C-Oxepane Scaffolds through a Chalcogen Bonding Catalyzed Strain-Release C-Septanosylation Strategy

The utility of unconventional noncovalent interactions (NCIs) such as chalcogen bonding has lately emerged as a robust platform to access synthetically difficult glycosides stereoselectively. Herein, we disclose the versatility of a phosphonochalcogenide (PCH) catalyst to facilitate access into the challenging, but biologically interesting 7-membered ring α,α'-C-disubstituted oxepane core through an α-selective strain-release C-glycosylation. Methodically, this strategy represents a switch from more common but entropically less desired macrocyclizations to a thermodynamically favored ring-expansion approach. In light of the general lack of stereoselective methods to access C-septanosides, a remarkable palette of silyl-based nucleophiles can be reliably employed in our method. This include a broad variety of useful synthons, such as easily available silyl-allyl, silyl-enol ether, silyl-ketene acetal, vinylogous silyl-ketene acetal, silyl-alkyne and silylazide reagents. Mechanistic investigations suggest that a mechanistic shift towards an intramolecular aglycone transposition involving a pentacoordinate silicon intermediate is likely responsible in steering the stereoselectivity.

Challenges for the Discovery of Non-Covalent WRN Helicase Inhibitors

The Werner Syndrome RecQ helicase (WRN) is a synthetic lethal target of interest for the treatment of cancers with microsatellite instability (MSI). Different hit finding approaches were initially tested. The identification of WRN inhibitors proved challenging due to a high propensity for artefacts via protein interference, i. e., hits inhibiting WRN enzymatic activities through multiple, unspecific mechanisms. Previously published WRN Helicase inhibitors (ML216, NSC19630 or NSC617145) were characterized in an extensive set of biochemical and biophysical assays and could be ruled out as specific WRN helicase probes. More innovative screening strategies need to be developed for successful drug discovery of non-covalent WRN helicase inhibitors.

The Scope of the Applicability of Non-relativistic DFT Calculations of NMR Chemical Shifts in Pyridine-Metal Complexes for Applied Applications

Heavy metals are toxic, but it is impossible to stop using them. Considering the variety of molecular systems in which they can be present, the multicomponent nature and disorder of the structure of such systems, one of the most effective methods for studying them is NMR spectroscopy. This determines the need to calculate NMR chemical shifts for expected model systems. For elements beyond the third row of the periodic table, corrections for relativistic effects are necessary when calculating NMR parameters. Such corrections may be necessary even for light atoms due to the shielding effect of a neighboring heavy atom. This work examines the extent to which non-relativistic DFT calculations are able to reproduce experimental 15N and 113Cd NMR chemical shift tensors in pyridine-metal coordination complexes. It is shown that while for the calculation of 15N NMR chemical shift tensors there is no real need to consider relativistic corrections, for 113Cd, on the contrary, none of the tested calculation methods could reproduce the experimentally obtained tensor to any extent correctly.

Achieving High-Temperature Phosphorescence by Organic Cocrystal Engineering

Organic phosphors offer a promising alternative in optoelectronics, but their temperature-sensitive feature has restricted their applications in high-temperature scenarios, and the attainment of high-temperature phosphorescence (HTP) is still challenging. Herein, a series of organic cocrystal phosphors are constructed by supramolecular assembly with an ultralong emission lifetime of up to 2.16 s. Intriguingly, remarkable stabilization of triplet excitons can also be realized at elevated temperature, and green phosphorescence is still exhibited in solid state even up to 150 °C. From special molecular packing within the crystal lattice, it has been observed that the orientation of isolated water cluster and well-controlled molecular organization via multiple interactions can favor the structural rigidity of cocrystals more effectively to suppress the nonradiative transition, thus resulting in efficient room-temperature phosphorescence and unprecedented survival of HTP.

Recent developments in molecular modeling tools and applications related to pharmaceutical and biomedical research

In modern pharmaceutical and biomedical research, molecular modeling represents a useful tool to explore processes and their mechanistic bases at the molecular level. Integrating experimental and virtual analysis is a fruitful approach to study ligand-receptor interaction in chemical, biochemical and biological environments. In these fields, molecular docking and molecular dynamics are considered privileged techniques for modeling (bio)macromolecules and related complexes. This review aims to present the current landscape of molecular modeling in pharmaceutical and biomedical research by examining selected representative applications published in the last years and highlighting current topics and trends of this field. Thus, a systematic compilation of all published literature has not been attempted herein. After a brief overview of the main theoretical and computational tools used to investigate mechanisms at molecular level, recent applications of molecular modeling in drug discovery, ligand binding and for studying protein conformation and function will be discussed. Furthermore, specific sections will be devoted to the application of molecular modeling for unravelling enantioselective mechanisms underlying the enantioseparation of chiral compounds of pharmaceutical and biomedical interest as well as for studying new forms of noncovalent interactivity identified in biochemical and biological environments. The general aim of this review is to provide the reader with a modern overview of the topic, highlighting advancements and outlooks as well as drawbacks and pitfalls still affecting the applicability of theoretical and computational methods in the field of pharmaceutical and biomedical research.

Blueshift in Trifurcated Hydrogen Bonds: A Tradeoff between Tetrel Bonding and Steric Repulsion

We have quantum chemically investigated the origin of the atypical blueshift of the H-C bond stretching frequency in the hydrogen-bonded complex X- •••H3 C-Y (X, Y=F, Cl, Br, I), as compared to the corresponding redshift occurring in Cl- •••H3 N and Cl- •••H3 C-H, using relativistic density functional theory (DFT) at ZORA-BLYP-D3(BJ)/QZ4P. Previously, this blueshift was attributed, among others, to the contraction of the H-C bonds as the H3 C moiety becomes less pyramidal. Herein, we provide quantitative evidence that, instead, the blueshift arises from a direct and strong X- •••C interaction of the HOMO of A- with the backside lobe on carbon of the low-lying C-Y antibonding σ* LUMO of the H3 C-Y fragment. This X- •••C bond, in essence a tetrel bond, pushes the H atoms towards a shorter H-C distance and makes the H3 C moiety more planar. The blueshift may, therefore, serve as a diagnostic for tetrel bonding.

Unraveling the role of polysaccharide-goethite associations on glyphosate' adsorption-desorption dynamics and binding mechanisms

HYPOTHESIS

Glyphosate retention at environmental interfaces is strongly governed by adsorption and desorption processes. In particular, glyphosate can react with organo-mineral associations (OMAs) in soils, sediments, and aquatic environments. We hypothesize mineral-adsorbed biomacromolecules modulate the extent and rate of glyphosate adsorption and desorption where electrostatic and noncovalent interactions with organo-mineral surfaces are favored.

EXPERIMENTS

Here we use in-situ attenuated total reflectance Fourier-transform infrared, X-ray photoelectron spectroscopy, and batch experiments to characterize glyphosate' adsorption and desorption mechanisms and kinetics at an organo-mineral interface. Model polysaccharide-goethite OMAs are prepared with a range of organic (polysaccharide, PS) surface loadings. Sequential adsorption-desorption studies are conducted by introducing glyphosate and background electrolyte solutions, respectively, to PS-goethite OMAs.

FINDINGS

We find the extent of glyphosate adsorption at PS-goethite interfaces was reduced compared to that at the goethite interface. However, increased polysaccharide surface loading resulted in lower relative glyphosate desorption. At the same time, increased PS surface loading yielded slower glyphosate adsorption and desorption kinetics compared to corresponding processes at the goethite interface. We highlight that adsorbed PS promotes the formation of weak noncovalent interactions between glyphosate and PS-goethite OMAs, including the evolution of hydrogen bonds between (i) the amino group of glyphosate and PS and (ii) the phosphonate group of glyphosate and goethite. It is also observed that glyphosate' phosphonate group preferentially forms inner-sphere monodentate complexes with goethite in PS-goethite whereas bidentate configurations are favored on goethite.

Unravelling dispersion forces in liquid-phase enantioseparation. Part I: Impact of ferrocenyl versus phenyl groups

BACKGROUND

Highly ordered chiral secondary structures as well as multiple (tunable) recognition sites are the keys to success of polysaccharide carbamate-based chiral selectors in enantioseparation science. Hydrogen bonds (HBs), dipole-dipole, and π-π interactions are classically considered the most frequent noncovalent interactions underlying enantioselective recognition with these chiral selectors. Very recently, halogen, chalcogen and π-hole bonds were also identified as interactions working in polysaccharide carbamate-based selectors to promote enantiomer distinction. On the contrary, the function of dispersion interactions in this field was not explored so far.

RESULTS

The enantioseparation of chiral ferrocenes featuring chiral axis or chiral plane as stereogenic elements was performed by comparing five polysaccharide carbamate-based chiral columns, with the aim to identify enantioseparation outcomes that could be reasonably determined by dispersion forces, making available a reliable experimental data set for future theoretical studies to confirm the heuristic hypothesis. The effects of mobile phase polarity and temperature on the enantioseparation were considered, and potential recognition sites on analytes and selectors were evaluated by electrostatic potential (V) analysis and molecular dynamics (MD). In this first part, the enantioseparation of 3,3'-dibromo-5,5'-bis-ferrocenylethynyl-4,4'-bipyridine bearing two ferrocenylethynyl units linked to an axially chiral core was performed and compared to that of the analyte featuring the same structural motif with two phenyl groups in place of the ferrocenyl moieties. The results of this study showed the superiority of the ferrocenyl compared to the phenyl group, as a structural element favouring enantiodifferentiation.

SIGNIFICANCE AND NOVELTY

Even if dispersion (London) forces have been envisaged acting in liquid-phase enantioseparations, focused studies to explore possible contributions of dispersion forces with polysaccharide carbamate-based selectors are practically missing. This study allowed us to collect experimental information that support the involvement of dispersion forces as contributors to liquid-phase enantioseparation, paving the way to a new picture in this field.

Liquid Structures and Ion Dynamics of Ionic Liquids Viewed from Intermolecular Interactions

The elucidation of the factors determining liquid structures and transport properties of ionic liquids is important for the design and development of ionic liquid electrolytes. This personal account introduces the importance of computational methods for studying ionic liquids. Molecular dynamics simulations provide detailed information on liquid structures of ionic liquid such as the structures of solvated cation complexes in equimolar mixtures of glymes and Li[TFSA] and the effects of the charges of electrode on liquid structure near the electrode. Ab initio calculations reveal that the magnitude of the attraction between ions and conformational flexibility ions play important roles in determining transport properties of ionic liquids. First principle molecular dynamics simulations elucidate why solvated cation complex is stable in the equimolar mixtures, although the Li+ -[TFSA]- interaction is greater than Li+ -glyme interaction.

A Comprehensive Review of Self-Assembled Food Protein-Derived Multicomponent Peptides: From Forming Mechanism and Structural Diversity to Applications

Food protein-derived multicomponent peptides (FPDMPs) are a natural blend of numerous peptides with various bioactivities and multiple active sites that can assume several energetically favorable conformations in solutions. The remarkable structural characteristics and functional attributes of FPDMPs make them promising codelivery carriers that can coassemble with different bioactive ingredients to induce multidimensional structures, such as fibrils, nanotubes, and nanospheres, thereby producing specific health benefits. This review offers a prospective analysis of FPDMPs-based self-assembly nanostructures, focusing on the mechanism of formation of self-assembled FPDMPs, the internal and external stimuli affecting peptide self-assembly, and their potential applications. In particular, we introduce the exciting prospect of constructing functional materials through precursor template-induced self-assembly of FPDMPs, which combine the bioactivity and self-assembly capacity of peptides and could dramatically broaden the functional utility of peptide-based materials.

Systematic elucidation of the second coordination sphere effect on the structure and properties of a blue copper protein, pseudoazurin

The rational structural and computational studies of a blue copper protein, pseudoazurin (PAz), and its Met16X (X = Phe, Leu, Val, Ile) variants gave clear functional meanings of the noncovalent interaction (NCI) through the second coordination sphere. The high-resolution X-ray crystal structures of Met16X PAz demonstrated that the active site geometry is significantly affected by the substitution of Met16, which is located within the NCI distance from the His81 imidazole ring at the copper active site. The computational chemistry calculations based on the crystal structure analyses confirmed that the NCI of S-π/CH-π (wild-type), π-π (Met16Phe), double CH-π (Met16Leu), and single CH-π (Met16Val and Met16Ile). The estimated interaction energies for the NCI demonstrated that the fine-tuning of the protein stability and Cu site properties form the second coordination sphere of PAz.

The "weak" C-H···S interaction drives enantioselectivity in cinchona alkaloid complex catalyzed thiocyanation

The great success of asymmetric organocatalysis has made it one of the most important advancements made in chemistry in the past two decades. A significant achievement in this context is the asymmetric organocatalysis of the thiocyanation reaction. In the current study, computational studies with density functional theory have been done in order to understand an interesting experimental finding: the reversal of enantioselectivity from R to S when the electrophile is changed from b-keto ester to oxindole for the thiocyanation reaction with the cinchona alkaloid complex catalyst. The calculations reveal an unusual fact - the principal reason for the reversal is the presence of the C-H···S noncovalent interaction, which is present only in the major transition states in each of the two nucleophile cases. Only recently has it been realized that the supposedly weak C-H···S noncovalent interaction has the properties of a hydrogen bond, and the fact that this interaction is the cause of enantioselectivity has relevance, because of the large number of asymmetric transformations involving the sulphur heteroatom.

Elaborating E/Z-Geometry of Alkenes via Cage-Confined Arylation Catalysis of Terminal Olefins

A visible light photosensitizing metal-organic cage is applied as an artificial supramolecular reactor to control the reaction of aryl radicals with terminal olefins under green light/solvent conditions, which facilitates selective transformation in the confined enzyme-mimicking environment to give a series of geometrically defined E/Z-alkenes. The hydrophobic cage displays good host-guest inclusion with aromatic substrates, promoting Meerwein arylation and protecting E-isomeric products during reaction; while a small amount of benzonitrile can turn on efficient E→Z isomerization. Besides π-π stacking, the hydrogen bonding and halogen bonding interactions also act as control forces for the arylation of aliphatic terminal olefins known as poor acceptors in classic Meerwein arylation. The application of this switchable cage-confined arylation catalysis has been demonstrated by the syntheses of Tapinarof and a marine natural product from the same substrate via controllable E/Z selectivity.

Fine-Tuning Redox Properties of Heteroleptic Molybdenum Complexes through Ligand-Ligand-Cooperativity

Heteroleptic molybdenum complexes bearing 1,5-diaza-3,7-diphosphacyclooctane (P2N2) and non-innocent dithiolene ligands were synthesized and electrochemically characterized. The reduction potentials of the complexes were found to be fine-tuned by a synergistic effect identified by DFT calculations as ligand-ligand cooperativity via non-covalent interactions. This finding is supported by electrochemical studies combined with UV-vis spectroscopy and temperature-dependent NMR spectroscopy. The observed behavior is reminiscent of enzymatic redox modulation using second ligand sphere effects.

A New Motif in Halogen Bonding: Cooperative Intermolecular S-Br⋅⋅⋅O, O⋅⋅⋅F, and F⋅⋅⋅F Associations in the Crystal Packing of α,ω-Di(sulfonyl bromide) Perfluoroalkanes

We recently reported the first examples of S-Cl⋅⋅⋅O halogen bonding complemented by short F⋅⋅⋅F contacts between neighboring chains that resulted in stabilized crystals of ClSO₂ (CF₂ )₄ SO₂ Cl and ClSO₂ (CF₂ )₆ SO₂ Cl. More recently, other researchers studied our crystallographic data further using an Independent Gradient Model (IGM), and they suggested if one goes beyond IUPAC's proposed 'less than the sum of the van der Waals radii' criterion that even more noncovalent interactions between fluorine atoms on neighboring chains as well as Cl⋅⋅⋅Cl, Cl⋅⋅⋅S, O⋅⋅⋅F, and O⋅⋅⋅S attractive interactions can be found. With that said, we have prepared samples of the related BrSO₂ (CF₂ )_n SO₂ Br derivatives (where n=4, 6, 8, and others), which give rise to even stronger S-Br⋅⋅⋅O halogen bonding interactions complemented minimally by O⋅⋅⋅F and F⋅⋅⋅F intermolecular interactions as shown by X-ray crystallography and computational chemistry using IGM isosurface plots. Additional spectroscopic characterization (multinuclear NMR, FT-IR, and MS) of the disulfonyl bromide derivatives BrSO₂ (CF₂ )₄ SO₂ Br, BrSO₂ (CF₂ )₆ SO₂ Br, and BrSO₂ (CF₂ )₈ SO₂ Br has also been obtained as well as some preliminary spectroscopic evidence for BrSO₂ (CF₂ )₂ SO₂ Br and BrSO₂ CF₂ O(CF₂ )₂ OCF₂ SO₂ Br. The implication of these results toward the preparation of the corresponding disulfonyl iodides is discussed.

Tuning the Solid Phase Fluorescence Emission from Long Wavelength Visible to Near-Infrared in Oxazol-5-One Derivatives: Structure-Property Relationship, Theoretical and Experimental Studies

Most of the fluorescent molecules among organic [Formula: see text]-conjugated materials show blue or green emission in the solid phase but few of them emit red-shifted visible and near-infrared light in the material science. To create molecules emitting for this feature, two π-conjugated oxazol-5-one derivatives containing donor (OCH₃) and acceptor groups (NO₂) were synthesized. Their optical and charge-transport properties were investigated through experimental and theoretical methods including the single crystal X-ray crystallography, Hirshfeld Surface Analysis, photophysical studies and Density Functional Theory (DFT), respectively. In addition, FT-IR, ¹H-NMR, ¹³C-NMR spectroscopy, cyclic voltammetry (CV) measurements were performed. According to our results, both molecules may provide the significant pathway of development of long wavelength visible and red emissive features in solid phase with the aggregation induced enhanced emission (AIEE) properties particularly in the fields of OLEDs, optical communication, defence and bioimaging.

Non-classical Non-covalent σ-Hole Interactions in Protein Structure and Function: Concepts for Potential Protein Engineering Applications

The structures and associated functions of biological molecules are driven by noncovalent interactions, which have classically been dominated by the hydrogen bond (H-bond). Introduction of the σ-hole concept to describe the anisotropic distribution of electrostatic potential of covalently bonded elements from across the periodic table has opened a broad range of nonclassical noncovalent (ncNC) interactions for applications in chemistry and biochemistry. Here, we review how halogen bonds, chalcogen bonds and tetrel bonds, as they are found naturally or introduced synthetically, affect the structures, assemblies, and potential functions of peptides and proteins. This review intentionally focuses on examples that introduce or support principles of stability, assembly and catalysis that can potentially guide the design of new functional proteins. These three types of ncNC interactions have energies that are comparable to the H-bond and, therefore, are now significant concepts in molecular recognition and design. However, the recently described H-bond enhanced X-bond shows how synergism among ncNC interactions can be exploited as potential means to broaden the range of their applications to affect protein structures and functions.

Physical mechanisms of intermolecular interactions from symmetry-adapted perturbation theory

Symmetry-adapted perturbation theory (SAPT) is a method for computational studies of noncovalent interactions between molecules. This method will be discussed here from the perspective of establishing the paradigm for understanding mechanisms of intermolecular interactions. SAPT interaction energies are obtained as sums of several contributions. Each contribution possesses a clear physical interpretation as it results from some specific physical process. It also exhibits a specific dependence on the intermolecular separation R. The four major contributions are the electrostatic, induction, dispersion, and exchange energies, each due to a different mechanism, valid at any R. In addition, at large R, SAPT interaction energies are seamlessly connected with the corresponding terms in the asymptotic multipole expansion of interaction energy in inverse powers of R. Since such expansion explicitly depends on monomers' multipole moments and polarizabilities, this connection provides additional insights by rigorously relating interaction energies to monomers' properties.

Stand up for Electrostatics: The Disiloxane Case

The basicity of the simplest silicone, disiloxane (H 3 Si-O-SiH 3 ), is strongly affected by the Si-O-Si angle (α). We use high-level ab initio MP2/aug'-cc-pVTZ calculations and the molecular electrostatic potential (MEP) to analyze the relationship between the increase in basicity and the reduction of α. Our results clearly point out that this increase can be explained through the MEP, as the interactions between oxygen from disiloxane and the acceptors are mostly electrostatic. Furthermore, the effect of α on the tetrel bond between disiloxane and several Lewis bases can again be rationalized using the MEP. Finally, we explore the cooperativity throughout α for ternary complexes where disiloxane simultaneously interacts with a Lewis acid and a Lewis base. Both non-covalent interactions remain cooperative for all α values, although the largest cooperativity effects are not always those maximizing the binding energy in the binary complexes. Overall, the MEP remains a powerful predictor for noncovalent interactions.

Chirality-Puckering correlation and intermolecular interactions in Sphingosines: Rotational spectroscopy of jaspine B3 and its monohydrate

Chirality is determinant for sphingosine biofunctions and pharmacological activity, yet the reasons for the biological chiral selection are not well understood. Here, we characterized the intra- and intermolecular interactions at the headgroup of the cytotoxic anhydrophytosphingosine jaspine B, revealing chirality-dependent correlations between the puckering of the ring core and the formation of amino-alcohol hydrogen bond networks, both in the monomer and the monohydrate. Following the specific synthesis of a shortened 3-carbon side-chain molecule, denoted jaspine B3, six different isomers were observed in a jet expansion using broadband (chirped-pulsed) rotational spectroscopy. Additionally, a single isomer of the jaspine B3 monohydrate was observed, revealing the insertion of water in between the hydroxy and amino groups and the formation of a network of O-H···N-H···O_ring hydrogen bonds. The specific jaspine B3 stereochemistry thus creates a double-faced molecule where the exposed lone-pair electrons may easily catalyze the formation of intermolecular aggregates and determine the sphingosine biological properties.

Strength and Nature of Host-Guest Interactions in Metal-Organic Frameworks from a Quantum-Chemical Perspective

Metal‐organic frameworks (MOFs) offer a convenient means for capturing, transporting, and releasing small molecules. Their rational design requires an in‐depth understanding of the underlying non‐covalent host‐guest interactions, and the ability to easily and rapidly pre‐screen candidate architectures in silico. In this work, we devised a recipe for computing the strength and analysing the nature of the host‐guest interactions in MOFs. By assessing a range of density functional theory methods across periodic and finite supramolecular cluster scale we find that appropriately constructed clusters readily reproduce the key interactions occurring in periodic models at a fraction of the computational cost. Host‐guest interaction energies can be reliably computed with dispersion‐corrected density functional theory methods; however, decoding their precise nature demands insights from energy decomposition schemes and quantum‐chemical tools for bonding analysis such as the quantum theory of atoms in molecules, the non‐covalent interactions index or the density overlap regions indicator.

Probing Anion - π interactions between fluoroarene and carboxylate anion in aqueous solutions

Despite the much progress in developing π-conjugated fluoroarene moieties based functional materials in which anion - π interactions are commonly involved, it remains challenging to quantitatively characterize the nanomechanical interaction mechanism of these anion - π systems, particularly in aqueous solutions. In this study, we reported the first experimental quantification of the nanomechanics of anion - π interactions between π-conjugated fluoroarene moieties and carboxylate anions in aqueous solutions through direct molecular force measurements, with a special focus on the impact of the anion species, concentration and of the substitution effect of aromatic side group. The results using surface forces apparatus (SFA) and single-molecule force spectroscopy (SMFS) provide complementary evidences to demonstrate that the robust and reversible adhesion measured between the fluoroarene π systems and carboxylate anions was mainly attributed to anion - π interaction. Moreover, their nanomechanical properties were also systematically scrutinized, with the interaction strength being found to be significantly determined by the contact time, the type of fluoroarene systems (PFST > DFST) and the type of anions and ion concentration (HPO₄^2- > CO₃^2- > I^- > Cl^- ≈ NO₃^- > F^-).

A rotational study of the 1:1 adduct of ethanol and 1,4-dioxane

The pure rotational spectra of the 1:1 ethanol - 1,4-dioxane complex and its OD mono-deuterated species have been measured using pulsed-jet Fourier transform microwave spectroscopy. Conformational predictions for the plausible isomers of ethanol - 1,4-dioxane have been carried out considering the spatial orientation of gauche/trans ethanol with respect to the chair/boat and twisted conformations of 1,4-dioxane. Using Helium for the supersonic expansion, the microwave spectrum has been observed for the most stable structure. In the observed isomer, the two subunits are linked together by an OH⋯O hydrogen bond with gauche ethanol acting as proton donor to dioxane in the chair conformation. The non-covalent interactions have been characterized using different computational approaches. A small inverse Ubbelohde effect was observed after H → D isotopic substitution in the OH⋯O hydrogen bond.

Docking Screens of Noncovalent Interaction Motifs of the Human Subtype-D2 Receptor-75 Schizophrenia Antipsychotic Complexes with Physicochemical Appraisal of Antipsychotics

Chemoinformatics appraisal and molecular docking were employed to investigate 225 complexes of 75 schizophrenia antipsychotics with the dopamine receptor subtypes D2R, D3R, and D4R. Considering the effective noncovalent interactions in the subtype-D2 receptor selectivity of antipsychotics, this study evaluated the possible physicochemical properties of ligands underlying the design of safer and more effective antipsychotics. The pan-assay interference compounds (PAINs) include about 25% of typical antipsychotics and 5% of atypicals. Popular antipsychotics like haloperidol, clozapine, risperidone, and aripiprazole are not PAINs. They have stronger interactions with D2R and D4R, but their interactions with D3R are slightly weaker, which is similar to the behavior of dopamine. In contrast to typical antipsychotics, atypical antipsychotics exhibit more noncovalent interactions with D4R than with D2R. These results suggest that selectivity to D2R and D4R comes from the synergy between hydrophobic and hydrogen-bonding interactions through their concomitant occurrence in the form of a hydrogen-bonding site adorned with hydrophobic contacts in antipsychotic-receptor complexes. All the antipsychotics had more synergic interactions with D2R and D4R in comparison with D3R. The atypical antipsychotics made a good distinction between the subtype D2 receptors with high selectivity to D4R. Among the popular antipsychotics, haloperidol, clozapine, and risperidone have hydrophobic-hydrogen-bonding synergy with D4R, while aripiprazole profits with D2R. The most important residue participating in the synergic interactions was threonine for D2R and cysteine for D4R. This work could be useful in informing and guiding future drug discovery and development studies aimed at receptor-specific antipsychotics.

An Insight into Non-Covalent Interactions on the Bicyclo[1.1.1]pentane Scaffold

Bicyclo[1.1.1]pentane (BCP) is studied extensively as a bioisosteric component of drugs. Not found in nature, this molecular unit approximates the distance of a para-disubstituted benzene which is replaced in medicines as a method of improving treatments. Predicting interactions of these drugs with specific active sites requires knowledge of the non-covalent interactions engaged by this subunit. Structure determinations and computational analysis (Hirshfeld analysis, 2D fingerprint plots, DFT) of seven BCP derivatives chosen to probe specific and directional interactions. X-ray analysis revealed the presence of various non-covalent interactions including I ⋅⋅⋅ I, I ⋅⋅⋅ N, N-H ⋅⋅⋅ O, C-H ⋅⋅⋅ O, and H-C ⋅⋅⋅ H-C contacts. The preference of halogen bonding (I ⋅⋅⋅ I or I ⋅⋅⋅ N) in BCP 1-4 strictly depends upon the electronic nature and angle between bridgehead substituents. The transannular distance in co-crystals 2 and 4 was longer as compared to monomers 1 and 3. Stronger N-H ⋅⋅⋅ O and weaker C-H ⋅⋅⋅ O contacts were observed for BCP 5 while the O ⋅⋅⋅ H interaction was a prominent contact for BCP 6. The presence of 3D BCP units prevented the π ⋅⋅⋅ π stacking between phenyl rings in 3, 4, and 7. The BCP skeleton was often rotationally averaged, indicating fewer interactions compared to bridgehead functional groups. Using DFT analysis, geometries were optimized and molecular electrostatic potentials were calculated on the BCP surfaces. These interaction profiles may be useful for designing BCP analogs of drugs.

Fractionation of lignin using organic solvents: A combined experimental and theoretical study

Refining of industrial lignin to produce homogeneous fractions is essential for high-value applications. However, the understanding of key interactions between a variety of solvents with lignin polymer is still uncertain. In this work, single-step fractionation of industrial hardwood kraft lignin (HKL) using organic solvents of different polarities - ethanol, acetone, diethyl ether and hexane - was investigated by combining an experimental and theoretical approach. Experimental results revealed that higher polarity solvents (ethanol and acetone) exhibited higher solubility yield compared to moderate and low polarity solvents. The chemical differences between lignin fractions were proven by pyrolysis gas chromatography mass spectrometry and near infrared spectroscopy. Density functional theory (DFT) results indicated that ethanol presented higher interaction energy followed by acetone, diethyl ether and hexane, which was consistent with experimental findings. Hydrogen bond and non-covalent interaction results from DFT demonstrated that the predominant interaction was found for high polarity of ethanol over other solvents and γ-OH in the lignin model is the key site.

Nanomechanics of π-cation-π interaction with implications for bio-inspired wet adhesion

Cation-π interactions play a vital role in modulating various biological processes, e.g., potassium-selective channel, protein folding and adhesion of marine organism. Previous studies mainly focus on binary cation-π interaction, whereas due to the complexity of biological systems and surrounding environments, a single cation is often in close proximity with more than one π-conjugated unit, which could exhibit essentially different binding behavior. Herein, the first experimental evidence of ternary π-cation-π interaction is reported through direct nanomechanical force measurement in a model π-conjugated poly(catechol) (PC) system coexisting with K⁺. Ternary π-cation-π interactions can bridge π-conjugated moieties, resulting in robust adhesion and promoting PC assembly and deposition. Particularly, these ternary complexes are discovered to transit to binary binding pairs by increasing K⁺ concentration, undermining adhesion and assembly due to lack of bridging. The π-cation-π binding strength follows the trend of NMe₄⁺ > K⁺ > Na⁺ > Li⁺. Employing the π-cation-π interaction, a deposition strategy to fabricate π-conjugated moiety based adhesive coatings on different substrates is realized. Our findings provide useful insights in engineering wet adhesives and coatings with reversible adhesion properties, and more broadly, with implications on rationalizing biological assembly.

Polypeptide-based self-healing hydrogels: Design and biomedical applications

Self-healing hydrogels can heal themselves on the damaged sites, which opens up a fascinating way for enhancing lifetimes of materials. Polypeptide/poly(amino acid) is a class of polymers in which natural amino acid monomers or derivatives are linked by amide bonds with a stable and similar secondary structure as natural proteins (α-helix or β-fold). They have the advantages of nontoxicity, biodegradability, and low immunogenicity as well as easy modification. All these properties make polypeptides extremely suitable for the preparation of self-healing hydrogels for biomedical applications. In this review, we mainly focus on the progress in the fabrication strategies of polypeptide-based self-healing hydrogels and their biomedical applications in the recent 5 years. Various crosslinking methods for the preparation of polypeptide-based self-healing hydrogels are first introduced, including host-guest interactions, hydrogen bonding, electrostatic interactions, supramolecular self-assembly of β-sheets, and reversible covalent bonds of imine and hydrazone as well as molecular multi-interactions. Some representative biomedical applications of these self-healing hydrogels such as delivery system, tissue engineering, 3D-bioprinting, antibacterial and wound healing as well as bioadhesion and hemostasis are also summarized. Current challenges and perspectives in future for these "smart" hydrogels are proposed at the end . STATEMENT OF SIGNIFICANCE: Polypeptides with the advantages of nontoxicity, biodegradability, hydrophilicity and low immunogenicity, are extremely suitable for the preparation of self-healing hydrogels in biomedical applications. Recently, the researches of polypeptide-based self-healing hydrogel have drawn the great attentions for scientists and engineers. A review to summarize the recent progress in design and biomedical applications of these polypeptide-based self-healing hydrogels is highly needed. In this review, we mainly focus on the progress in fabrication strategies of polypeptide-based self-healing hydrogels and biomedical applications in recent five years and aim to draw the increased attention to the importance of these "smart" hydrogels, facilitating the advances in biomedical applications. We believe this work would draw interest from readers of Acta Biomaterialia.

Columnar Stacking of Partially Fluorinated [4]Helicenes: C-H⋅⋅⋅F Interactions Change the Stacking Orientation

The partial fluorination of polycyclic aromatic hydrocarbons often produces a layered crystal packing, where fluorinated aromatic surfaces are stacked over nonfluorinated aromatic surfaces. Herein, we report the synthesis and crystal packing of partially fluorinated [4]helicenes with steric congestion resulting from H and F atoms in the fjord region. F₆ -[4]Helicene forms head-to-tail columnar stacks consisting of an alternate arrangement of perfluorinated and nonfluorinated naphthalene moieties. With decreasing fluorine content, aromatic stacking switched from arene-fluoroarene (Ar^H -Ar^F ) hetero-stacking to Ar^H -Ar^H /Ar^F -Ar^F homo-stacking with the help of intermolecular C-H⋅⋅⋅F contacts in the fjord region. As a result, head-to-head columnar stacks appear. Therefore, the conventional Ar^H -Ar^F stacking motif is not always applicable to F_n -[4]helicenes with twisted π-surfaces.

Noncovalent interactions between isoflurane and dimethyl ether. Spectroscopic evidence of trimer formation

The IR spectra of isoflurane + dimethyl ether mixtures dissolved in liquid Kr are registered at T ~118-160 K. The results obtained at a wide range of relative concentrations suggest the formation of complexes stabilized by non-covalent interactions of H-bond type. Large excess of DME and low temperature favor trimer formation stabilized by interactions between two DME moieties and both CH groups of isoflurane predominantly. Estimations based on ab initio calculation of spectroscopic and thermodynamic parameters confirm the experimental findings.

Controlled Formation of Thiol-Thiolate Hydrogen versus Disulfide Bonds between Two Iridium(III) Centers

Here, we report an iridium(III) coordination system with 2-aminoethanethiolate (aet), which shows the formation of S-H⋅⋅⋅S hydrogen and S-S disulfide bonds in a controlled manner. Treatment of fac-[Ir(aet)₃ ] with aqueous HBF₄ under aerobic conditions gave dinuclear [Ir₂ (aet)₄ (cysta)]²⁺ ([1]²⁺ ; cysta=cystamine) with a single S-S disulfide bond, while dimeric [Ir₂ (aet)₃ (Haet)₃ ](BF₄ )₃ ([2](BF₄ )₃ ) with a triple S-H⋅⋅⋅S hydrogen bond was formed by similar treatment under anaerobic conditions. Upon exposure to air, [2]³⁺ was converted to dinuclear [Ir₂ (aet)₂ (Haet)₂ (cysta)]⁴⁺ ([3]⁴⁺ ), in which two Ir^III centers are spanned by a double S-H⋅⋅⋅S hydrogen bond and a single S-S disulfide bond. Complex [3]⁴⁺ was interconvertible with [1]²⁺ via the removal/addition of protons on S donors, accompanied by the intermolecular exchange of the fac-[Ir(aet)₃ ] units. Complexes [1]²⁺ , [2]³⁺ , and [3]⁴⁺ , isolated as BF₄ ^- salts, were fully characterized by single-crystal X-ray crystallography.

Experimental and theoretical study of the role of CH/π interactions in the aminolysis reaction of acetyl galactoside

Molecular recognition of saccharides is a growing field, which has many implications in cancer therapy, drug discovery, and cellular communication among others. The participation of CH/π interactions in this event is well known. Nevertheless, the intrinsic role of CH/π for modulating chemical reactions is still far from being applicable. In this experimental and computational work we have evaluated the participation of CH/π interactions in the aminolysis reaction of acetyl galactoside promoted with different 6-substituted 2(1H)-pyridones. Two features have been incorporated to the promoter molecular structure, on one end the promoting pyridone group and on the other end the recognition moiety, joined together by an alkyne spacer. The small increment in the observed pseudo-first-order rate constant values (k_obs) was related to the stability of the transition state provided by noncovalent interactions, including CH/π interactions. A longer alkyne spacer was necessary to improve the molecular recognition of the galactoside substrate. The trend of the calculated activation energy values (ΔE_RTS) was in good accordance with the experimental rate constant values.

Mass Spectrometry as a Complementary Approach for Noncovalently Bound Complexes Based on Cyclodextrins

An important and well-designed solution to overcome some of the problems associated with new drugs is provided by the molecular encapsulation of the drugs in the cyclodextrins (CDs) cavity, yielding corresponding inclusion complexes (ICs). These types of non-covalent complexes are of current interest to the pharmaceutical industry, as they improve the solubility, stability and bioavailability of the guest molecules. This review highlights several methods for cyclodextrin ICs preparation and characterization, focusing mostly on the mass spectrometry (MS) studies that have been used for the detection of noncovalent interactions of CDs inclusion complexes and binding selectivity of guest molecules with CDs. Furthermore, the MS investigations of several ICs of the CD with antifungal, antioxidants or fluorescent dyes are presented in greater details, pointing out the difficulties overcome in the analysis of this type of compounds.

Modeling protic dicationic ionic liquids based on quaternary ammonium, imidazolium or pyrrolidinium cations and bis(trifluoromethanesulfonyl)imide anion: Structure and spectral characteristics

Protic dicationic ionic liquids (PDILs) have attracted growing attention owing to their applications in domains of electrochemistry, proton conducting materials and other diverse areas. In the present work protic dicationic ionic liquids (PDILs) comprising of quaternary ammonium-, imidazolium- or pyrrolidinium-dications and bis(trifluoromethanesulfonyl)imide (Tf₂N‾) anion have been modelled as the dication-(Tf₂N)₂ complexes. Electronic structure, vibrational and ¹H NMR spectra of these complexes have been derived employing the M06-2x density functional theory. Theoretical calculations have shown that the strength of cation-anion binding follows the order: methylpyrrolidinum > quaternary ammonium > butylpyrrolidinium > imidazolium, which can be attributed to number and strength of N-H---O and C-H---O interactions. The dication-(Tf₂N)₂ complexes emerge with signature in frequency up-shift of the characteristic N-H stretching in their infrared spectra. Underlying molecular interactions are unveiled through natural bond orbital analyses, Quantum theory of atoms in molecules (QTAIM) and noncovalent interaction reduced density gradient method. The calculations have shown that cation-anion binding energies increase linearly with kinetic energy density component G(r) in QTAIM analysis and proton affinities in the PDILs. A correlation between change in free energies accompanying the dication-(Tf₂N)₂ complexes and proton affinities has also been established.

Influence of hydrogen bonds on edge-to-face interactions between pyridine molecules

Edge-to-face interactions between two pyridine molecules and the influence of simultaneous hydrogen bonding of one or both of the pyridines to water on those interactions were studied by analyzing data from ab initio calculations. The results show that the edge-to-face interactions of pyridine dimers that are hydrogen bonded to water are generally stronger than those of non-H-bonded pyridine dimers, especially when the donor pyridine forms a hydrogen bond. The binding energy of the most stable edge-to-face interacting H-bonded pyridine dimer is -5.05 kcal/mol, while that for the most stable edge-to-face interacting non-H-bonded pyridine dimer is -3.64 kcal/mol. The interaction energy data obtained in this study cannot be explained solely by the differences in electrostatic potential between pyridine and the pyridine-water dimer. However, the calculated cooperative effect can be predicted using electrostatic potential maps.

Deconvoluting the Innocent vs. Non-innocent Behavior of N,N-diethylphenylazothioformamide Ligands with Copper Sources

Redox-active ligands lead to ambiguity in often clearly defined oxidation states of both the metal centre and the ligand. The arylazothioformamide (ATF) ligand class represents a redox-active ligand with three possible redox states (neutral, singly reduced, and doubly reduced). ATF-metal interactions result in strong colorimetric transitions allowing for the use of ATFs in metal detection and/or separations. While previous reports have discussed dissolution of zerovalent metals, the resulting oxidation states of coordination complexes have proved difficult to interpret through X-ray crystallographic analysis alone. This report describes the X-ray crystallographic analysis combined with computational modelling of the ATF ligand and metal complexes to deconvolute the metal and ligand oxidation state of metal-ATF complexes. Metal(ATF)2 complexes that originated from zerovalent metals were found to exist as dicationic metal centers containing two singly reduced ATF ligands. When employing Cu(I) salts instead of Cu(0) to generate copper-ATF complexes, the resulting complexes remained Cu(I) and the ATF ligand remained "innocent", existing in its neutral state. Although the use of CuX (where X = Br or I) or [Cu(NCMe)4]Y (where Y = BF4 or PF6) generated species of the type: [(ATF)Cu(μ-X)]2 and [Cu(ATF)2]Y, respectively, the ATF ligand remained in its neutral state for each species type.

Gauging the performance of some density functionals including dispersion and nonlocal corrections for relative energies of water 20-mers

Currently, development of density functional theory approximations and their benchmarking for accurately modeling different types of molecular interactions become a very active field of research. In this report, performance of the dispersion (D3) and nonlocal (NL) corrected density functionals has been compared with generalized energy-based fragmentation approach at the complete basis set limit for predicting the relative energies of 10 low-energy isomers of water nanoclusters (H₂O)₂₀ as an illustrative example of hydrogen bonded systems. Considering a variety of exchange-correlation density functionals in combination with D3 and NL corrections we find that the D3 based approximations outperform the functionals incorporating NL correction. It is also shown that the LC-ωPBE-D3 and rPW86PBE-NL functionals have the best trend from the viewpoint of the order of stabilities in water nanoclusters under study.

Electrostatic Forces as Dominant Interactions Between Proteins and Polyanions: an ESI MS Study of Fibroblast Growth Factor Binding to Heparin Oligomers

The interactions between fibroblast growth factors (FGFs) and their receptors (FGFRs) are facilitated by heparan sulfate (HS) and heparin (Hp), highly sulfated biological polyelectrolytes. The molecular basis of FGF interactions with these polyelectrolytes is highly complex due to the structural heterogeneity of HS/Hp, and many details still remain elusive, especially the significance of charge density and minimal chain length of HS/Hp in growth factor recognition and multimerization. In this work, we use electrospray ionization mass spectrometry (ESI MS) to investigate the association of relatively homogeneous oligoheparins (octamer, dp8, and decamer, dp10) with acidic fibroblast growth factor (FGF-1). This growth factor forms 1:1, 2:1, and 3:1 protein/heparinoid complexes with both dp8 and dp10, and the fraction of bound protein is highly dependent on protein/heparinoid molar ratio. Multimeric complexes are preferentially formed on the highly sulfated Hp oligomers. Although a variety of oligomers appear to be binding-competent, there is a strong correlation between the affinity and the overall level of sulfation (the highest charge density polyanions binding FGF most strongly via multivalent interactions). These results show that the interactions between FGF-1 and Hp oligomers are primarily directed by electrostatics, and also demonstrate the power of ESI MS as a tool to study multiple binding equilibria between proteins and structurally heterogeneous polyanions. Graphical Abstract ᅟ.

Influence of Alkylammonium Acetate Buffers on Protein-Ligand Noncovalent Interactions Using Native Mass Spectrometry

We investigate the influence of three volatile alkylammonium acetate buffers on binding affinities for protein-ligand interactions determined by native electrospray ionization-mass spectrometry (ESI-MS). Four different types of proteins were chosen for this study. A charge-reduction effect was observed for all the cases studied, in comparison to the ions formed in ammonium acetate solution. When increasing the collision energy, the complexes of trypsin and the ligand were found to be more stable when sprayed from alkylammonium acetate buffers than from ammonium acetate. The determined dissociation constant (K_d) also exhibited a drop (up to 40%) when ammonium acetate was replaced by alkylammonium acetate buffers for the case of lysozyme and the ligand. The prospective uses of these ammonium acetate analogs in native ESI-MS are discussed in this paper as well. Graphical Abstract ᅟ.

Microfluidics-Mass Spectrometry of Protein-Carbohydrate Interactions: Applications to the Development of Therapeutics and Biomarker Discovery

The functional interactions of carbohydrates and their protein receptors are the basis of biological events critical to the evolution of pathological states. Hence, for the past years, such interactions have become the focus of research for the development of therapeutics and discovery of novel glycan biomarkers based on their binding affinity. Due to the high sensitivity, throughput, reproducibility, and capability to ionize minor species in heterogeneous mixtures, microfluidics-mass spectrometry (MS) has recently emerged as a method of choice in protein-glycan interactomics. In this chapter, a straightforward microfluidics-based MS methodology for the assessment of protein-glycan interactions is presented. The general protocol encompasses: (1) submission of the interacting partners to a binding assay under conditions mimicking the in vivo environment; and (2) screening of the reaction products and their structural characterization by fully automated chip-nanoelectrospray (nanoESI) MS and multistage MS. The first section of the chapter is devoted to describing a method that enables the study of protein-oligosaccharide interactions by chip-nanoESI quadrupole time-of-flight (QTOF) MS and top-down complex analysis by collision-induced dissociation (CID). This section provides the protocol for the determination of the complex formed by standard β-lactoglobulin (BLG) with maltohexaose (Glc₆) and recommends as a concrete application the study of the interaction between BLG extracted from human milk with Glc₆, considered a ligand able to reduce the allergenicity of this protein. The second part is dedicated to presenting the protocols for the binding assay followed by chip-nanoESI ion trap (ITMS) and electron transfer dissociation (ETD) in combination with CID for protein-ganglioside interactions, using as an example the B subunit of cholera toxin (Ctb5) in interaction with comercially available GM1 species. The methodology described may be successfully applied to native ganglioside mixtures from human brain, in particular for discovery of biomarkers on the basis of their binding affinity.

Staying Alive: Measuring Intact Viable Microbes with Electrospray Ionization Mass Spectrometry

Mass spectrometry has traditionally been the technology of choice for small molecule analysis, making significant inroads into metabolism, clinical diagnostics, and pharmacodynamics since the 1960s. In the mid-1980s, with the discovery of electrospray ionization (ESI) for biomolecule analysis, a new door opened for applications beyond small molecules. Initially, proteins were widely examined, followed by oligonucleotides and other nonvolatile molecules. Then in 1991, three intriguing studies reported using mass spectrometry to examine noncovalent protein complexes, results that have been expanded on for the last 25 years. Those experiments also raised the questions: How soft is ESI, and can it be used to examine even more complex interactions? Our lab addressed these questions with the analyses of viruses, which were initially tested for viability following electrospray ionization and their passage through a quadrupole mass analyzer by placing them on an active medium that would allow them to propagate. This observation has been replicated on multiple different systems, including experiments on an even bigger microbe, a spore. The question of analysis was also addressed in the early 2000s with charge detection mass spectrometry. This unique technology could simultaneously measure mass-to-charge and charge, allowing for the direct determination of the mass of a virus. More recent experiments on spores and enveloped viruses have given us insight into the range of mass spectrometry's capabilities (reaching 100 trillion Da), beginning to answer fundamental questions regarding the complexity of these organisms beyond proteins and genes, and how small molecules are integral to these supramolecular living structures. Graphical Abstract ᅟ.

A method for predicting individual residue contributions to enzyme specificity and binding-site energies, and its application to MTH1

A new method for predicting the energy contributions to substrate binding and to specificity has been developed. Conventional global optimization methods do not permit the subtle effects responsible for these properties to be modeled with sufficient precision to allow confidence to be placed in the results, but by making simple alterations to the model, the precisions of the various energies involved can be improved from about ±2 kcal mol⁻¹ to ±0.1 kcal mol⁻¹. This technique was applied to the oxidized nucleotide pyrophosphohydrolase enzyme MTH1. MTH1 is unusual in that the binding and reaction sites are well separated—an advantage from a computational chemistry perspective, as it allows the energetics involved in docking to be modeled without the need to consider any issues relating to reaction mechanisms. In this study, two types of energy terms were investigated: the noncovalent interactions between the binding site and the substrate, and those responsible for discriminating between the oxidized nucleotide 8-oxo-dGTP and the normal dGTP. Both of these were investigated using the semiempirical method PM7 in the program MOPAC. The contributions of the individual residues to both the binding energy and the specificity of MTH1 were calculated by simulating the effect of mutations. Where comparisons were possible, all calculated results were in agreement with experimental observations. This technique provides fresh insight into the binding mechanism that enzymes use for discriminating between possible substrates.

Mutagenicity of heteroaromatic amines: Computational study on the influence of methyl substituents

Quantum mechanical calculations were performed to elucidate the factors determining the variations in mutagenic activity within groups of isomeric heteroaromatic amines that differ in the position of methyl substituents. Formation energies for noncovalent complexes and covalent DNA adducts were evaluated by means of high level quantum chemical methods. According to the computational results in this work, covalent adduct stability is proposed to influence the relative mutagenicities of structurally related heterocyclic amines. The stability of covalent C8-dG DNA adducts was found to be mainly determined by π-stacking interactions between the fused ring system of the heteroaromatic amines and the flanking nucleobases. Relative mutagenicity of amines of very related structure is proposed to be regulated by both nitrenium ion and covalent adduct stabilities.

Interactions of helquats with chiral acidic aromatic analytes investigated by partial-filling affinity capillary electrophoresis

Noncovalent molecular interactions between helquats, a new class of dicationic helical extended diquats, and several chiral acidic aromatic drugs and catalysts have been investigated using partial-filling affinity capillary electrophoresis (PF-ACE). Helquats dissolved at 1mM concentration in the aqueous background electrolyte (40mM Tris, 20mM acetic acid, pH 8.1) were introduced as ligand zones of variable length (0-130mm) into the hydroxypropylcellulose coated fused silica capillary whereas 0.1mM solutions of negatively charged chiral drugs or catalysts (warfarin, ibuprofen, mandelic acid, etodolac, binaphthyl phosphate and 11 other acidic aromatic compounds) were applied as a short analyte zone at the injection capillary end. After application of electric field, analyte and ligand migrated against each other and in case of their interactions, migration time of the analyte was increasing with increasing length of the ligand zone. From the tested compounds, only isomers of those exhibiting helical chirality and/or possessing conjugated aromatic systems were enantioselectively separated through their differential interactions with helquats. Some compounds with conjugated aromatic groups interacted with helquats moderately strongly but non-enantiospecifically. Small compounds with single benzene ring exhibited no or very weak non-enantiospecific interactions. PF-ACE method allowed to determine binding constants of the analyte-helquat complexes from the changes of migration times of the analytes. Binding constants of the weakest complexes of the analytes with helquats were less than 50L/mol, whereas binding constants of the strongest complexes were in the range 1 000-1 400L/mol.

Temperature-modulated noncovalent interaction controllable complex for the long-term delivery of etanercept to treat rheumatoid arthritis

The clinical applications of etanercept (Enbrel), an emerging therapeutic protein for rheumatoid arthritis (RA), are limited by its instability and low bioavailability. In this study, a long-term and efficient therapeutic nanocomplex formulation for RA treatment was developed in the form of a temperature-modulated noncovalent interaction controllable (TMN) complex based on a temperature-sensitive amphiphilic polyelectrolyte (succinylated pullulan-g-oligo(L-lactide); SPL). The TMN complexes were prepared by simply mixing the negatively charged SPL copolymer and the positively charged etanercept via electrostatic interaction at 4 °C below the polymer's clouding temperature (CT), and the resulting complex demonstrated significantly improved salt and serum stability with increased hydrophobic interactions at temperatures (physiological condition, 37.5 °C) above the CT. An in vitro study of the bioactivity of etanercept indicated that the TMN complex improves the long-term stability of etanercept in an aqueous environment because of the exposure of the functional active site and the molecular chaperone-like effect of the hydrophobic copolymer. This formulation possessed prolonged in vivo pharmacokinetic parameters. In a collagen-induced arthritis RA rat model, we verified the outstanding therapeutic effect of the TMN complexes. These results imply that this approach would be widely applied to protein and peptide delivery systems.

Polyvalent Interactions in Biological Systems: Implications for Design and Use of Multivalent Ligands and Inhibitors

Found throughout biology, polyvalent interactions are characterized by the simultaneous binding of multiple ligands on one biological entity to multiple receptors on another (top part of the illustration) and have a number of characteristics that monovalent interactions do not (bottom). In particular, polyvalent interactions can be collectively much stronger than corresponding monovalent interactions, and they can provide the basis for mechanisms of both agonizing and antagonizing biological interactions that are fundamentally different from those available in monovalent systems.