Toward a more complete understanding of noncovalent interactions involving aromatic rings

Counterion docking: a general approach to reducing energetic disorder in doped polymeric semiconductors

Molecular doping plays an important role in controlling the carrier concentration of organic semiconductors. However, the introduction of dopant counterions often results in increased energetic disorder and traps due to the molecular packing disruption and Coulomb potential wells. To date, no general strategy has been proposed to reduce the counterion-induced structural and energetic disorder. Here, we demonstrate the critical role of non-covalent interactions (NCIs) between counterions and polymers. Employing a computer-aided approach, we identified the optimal counterions and discovered that NCIs determine their docking positions, which significantly affect the counterion-induced energetic disorder. With the optimal counterions, we successfully reduced the energetic disorder to levels even lower than that of the undoped polymer. As a result, we achieved a high n-doped electrical conductivity of over 200 S cm-1 and an eight-fold increase in the thermoelectric power factor. We found that the NCIs have substantial effects on doping efficiency, polymer backbone planarity, and Coulomb potential landscape. Our work not only provides a general strategy for identifying the most suitable counterions but also deepens our understanding of the counterion effects on doped polymeric semiconductors.

Miracle in "White":Hexagonal Boron Nitride

The exploration of 2D materials has captured significant attention due to their unique performances, notably focusing on graphene and hexagonal boron nitride (h-BN). Characterized by closely resembling atomic structures arranged in a honeycomb lattice, both graphene and h-BN share comparable traits, including exceptional thermal conductivity, impressive carrier mobility, and robust pi-pi interactions with organic molecules. Notably, h-BN has been extensively examined for its exceptional electrical insulating properties, inert passivation capabilities, and provision of an ideal ultraflat surface devoid of dangling bonds. These distinct attributes, contrasting with those of h-BN, such as its conductive versus insulating behavior, active versus inert nature, and absence of dangling surface bonds versus absorbent tendencies, render it a compelling material with broad application potential. Moreover, the unity of such contradictions endows h-BN with intriguing possibilities for unique applications in specific contexts. This review aims to underscore these key attributes and elucidate the intriguing contradictions inherent in current investigations of h-BN, fostering significant insights into the understanding of material properties.

Gallic acid: design of a pyrogallol-containing hydrogel and its biomedical applications

Polyphenol hydrogels have garnered widespread attention due to their excellent adhesion, antioxidant, and antibacterial properties. Gallic acid (GA) is a typical derivative of pyrogallol that is used as a hydrogel crosslinker or bioactive additive and can be used to make multifunctional hydrogels with properties superior to those of widely studied catechol hydrogels. Furthermore, compared to polymeric tannic acid, gallic acid is more suitable for chemical modification, thus broadening its range of applications. This review focuses on multifunctional hydrogels containing GA, aiming to inspire researchers in future biomaterial design. We first revealed the interaction mechanisms between GA molecules and between GA and polymers, analyzed the characteristics GA imparts to hydrogels and compared GA hydrogels with hydrogels containing catechol. Subsequently, in this paper, various methods of integrating GA into hydrogels and the applications of GA in biomedicine are discussed, finally assessing the current limitations and future development potential of GA. In summary, GA, a natural small molecule polyphenol with excellent functionality and diverse interaction modes, has great potential in the field of biomedical hydrogels.

Exploring the Dispersion and Electrostatic Components in Arene-Arene Interactions between Ligands and G4 DNA to Develop G4-Ligands

G-Quadruplex (G4) DNA structures are important regulatory elements in central biological processes. Small molecules that selectively bind and stabilize G4 structures have therapeutic potential, and there are currently >1000 known G4 ligands. Despite this, only two G4 ligands ever made it to clinical trials. In this work, we synthesized several heterocyclic G4 ligands and studied their interactions with G4s (e.g., G4s from the c-MYC, c-KIT, and BCL-2 promoters) using biochemical assays. We further studied the effect of selected compounds on cell viability, the effect on the number of G4s in cells, and their pharmacokinetic properties. This identified potent G4 ligands with suitable properties and further revealed that the dispersion component in arene-arene interactions in combination with electron-deficient electrostatics is central for the ligand to bind with the G4 efficiently. The presented design strategy can be applied in the further development of G4-ligands with suitable properties to explore G4s as therapeutic targets.

Breaking Radial Dipole Symmetry in Planar Macrocycles Modulates Edge-to-Edge Packing and Disrupts Cofacial Stacking

Dipolar interactions are ever-present in supramolecular architectures, though their impact is typically revealed by making dipoles stronger. While it is also possible to assess the role of dipoles by altering their orientations by using synthetic design, doing so without altering the molecular shape is not straightforward. We have now done this by flipping one triazole unit in a rigid macrocycle, tricarb. The macrocycle is composed of three carbazoles (2 Debye) and three triazoles (5 Debye) defining an array of dipoles aligned radially but organized alternately in and out. These dipoles are believed to dictate edge-to-edge tiling and face-to-face stacking. We modified our synthesis to prepare isosteric macrocycles with the orientation of one triazole dipole rotated 40°. The new dipole orientation guides edge-to-edge contacts to reorder the stability of two surface-bound 2D polymorphs. The impact on dipole-enhanced π stacking, however, was unexpected. Our stacking model identified an unchanged set of short-range (3.4 Å) anti-parallel dipole contacts. Despite this situation, the reduction in self-association was attributed to long-range (~6.4 Å) dipolar repulsions between π-stacked macrocycles. This work highlights our ability to control the build-up and symmetry of macrocyclic skeletons by synthetic design, and the work needed to further our understanding of how dipoles control self-assembly.

Tunable CH/π Interactions within a Tryptophan Zipper Motif to Stabilize the Fold of Long β-Hairpin Peptides

The tryptophan zipper (Trpzip) is an iconic folding motif of β-hairpin peptides capitalizing on two pairs of cross-strand tryptophans, each stabilized by an aromatic-aromatic stacking in an edge-to-face (EtF) geometry. Yet, the origins and the contribution of this EtF packing to the unique Trpzip stability remain poorly understood. To address this question of structure-stability relationship, a library of Trpzip hairpins was developed by incorporating readily accessible nonproteinogenic tryptophans of varying electron densities. We found that each EtF geometry was, in fact, stabilized by an intricate combination of XH/π interactions. By tuning the π-electron density of Trpface rings, CH/π interactions are strengthened to gain additional stability. On the contrary, our DFT calculations support the notion that Trpedge modulations are challenging due to their simultaneous paradoxical engagement as H-bond donors in CH/π and acceptors in NH/π interactions.

The Energetic Origins of Pi-Pi Contacts in Proteins

Accurate potential energy models of proteins must describe the many different types of noncovalent interactions that contribute to a protein's stability and structure. Pi-pi contacts are ubiquitous structural motifs in all proteins, occurring between aromatic and nonaromatic residues and play a nontrivial role in protein folding and in the formation of biomolecular condensates. Guided by a geometric criterion for isolating pi-pi contacts from classical molecular dynamics simulations of proteins, we use quantum mechanical energy decomposition analysis to determine the molecular interactions that stabilize different pi-pi contact motifs. We find that neutral pi-pi interactions in proteins are dominated by Pauli repulsion and London dispersion rather than repulsive quadrupole electrostatics, which is central to the textbook Hunter-Sanders model. This results in a notable lack of variability in the interaction profiles of neutral pi-pi contacts even with extreme changes in the dielectric medium, explaining the prevalence of pi-stacked arrangements in and between proteins. We also find interactions involving pi-containing anions and cations to be extremely malleable, interacting like neutral pi-pi contacts in polar media and like typical ion-pi interactions in nonpolar environments. Like-charged pairs such as arginine-arginine contacts are particularly sensitive to the polarity of their immediate surroundings and exhibit canonical pi-pi stacking behavior only if the interaction is mediated by environmental effects, such as aqueous solvation.

Unraveling the promoter effect and the roles of counterion exchange in glycosylation reaction

The stereoselectivity of glycosidic bond formation continues to pose a noteworthy hurdle in synthesizing carbohydrates, primarily due to the simultaneous occurrence of SN1 and SN2 processes during the glycosylation reaction. Here, we applied an in-depth analysis of the glycosylation mechanism by using low-temperature nuclear magnetic resonance and statistical approaches. A pathway driven by counterion exchanges and reaction byproducts was first discovered to outline the stereocontributions of intermediates. Moreover, the relative reactivity values, acceptor nucleophilic constants, and Hammett substituent constants (σ values) provided a general index to indicate the mechanistic pathways. These results could allow building block tailoring and reaction condition optimization in carbohydrate synthesis to be greatly facilitated and simplified.

PCDD/F adsorption enhancement over nitrogen-doped biochar: A DFT-D study

Polychlorinated dibenzo-p-dioxin/furans (PCDD/F) have a great threat to the environment and human health, resulting in controlling PCDD/F emissions to regulation far important for emission source. Considering 2,3,4,7,8-pentachlorodibenzo-p-furan (PeCDF) identified as the most contributor to international toxic equivalent, 2,3,4,7,8-PeCDF can be considered as the target molecule for the adsorption of PCDD/F emission from industries. With the aim to in-depth elucidate how different types of nitrogen (N) species enhance 2,3,4,7,8-PeCDF on the biochar and guide the specific carbon materials design for industries, systematic computational investigations by density functional theory calculations were conducted. The results indicate pristine biochar intrinsically interacts with 2,3,4,7,8-PeCDF by π-π electron donor and acceptor (EDA) interaction, six-membered carbon rings of PeCDF parallel to the biochar surface as the strongest adsorption configuration. Moreover, by comparison of adsorption energy (-150.16 kJ mol-1) and interaction distance (3.593 Å) of pristine biochar, environment friendly N doping can enhance the adsorption of 2,3,4,7,8-PeCDF on biochar. Compared with graphitic N doping and pyridinic N doping, pyrrolic N doping biochar presents the strongest interaction toward 2,3,4,7,8-PeCDF molecule due to the highest adsorption energy (-155.56 kJ mol-1) and shortest interaction distance (3.532 Å). Specially, the enhancing adsorption of PeCDF over N doped biochar attributes to the enhancing π-π electron EDA interaction and electrostatic interaction. In addition, the effect of N doping species on PeCDF adsorbed on the biochar is more than that of N doping content. Specially, the adsorption capacity of N doping biochar for PCDD/F can be improved by adding pyrrolic N group most efficiently. Furthermore, pyrrolic N and pyridinic N doping result in the entropy increase, and electrons transform from pyrrolic N and pyridinic N doped biochar to 2,3,4,7,8-PeCDF molecule. A complete understanding of the research would supply crucial information for applying N-doped biochar to effectively remove PCDD/F for industries.

Interacting Quantum Atoms and Multipolar Electrostatic Study of XH···π Interactions

The interaction energies of nine XH···π (X = C, N, and O) benzene-containing van der Waals complexes were analyzed, at the atomic and fragment levels, using QTAIM multipolar electrostatics and the energy partitioning method interacting quantum atoms/fragment (IQA/IQF). These descriptors were paired with the relative energy gradient method, which solidifies the connection between quantum mechanical properties and chemical interpretation. This combination provides a precise understanding, both qualitative and quantitative, of the nature of these interactions, which are ubiquitous in biochemical systems. The formation of the OH···π and NH···π systems is electrostatically driven, with the Qzz component of the quadrupole moment of the benzene carbons interacting with the charges of X and H in XH. There is the unexpectedly intramonomeric role of X-H (X = O, N) where its electrostatic energy helps the formation of the complex and its covalent energy thwarts it. However, the CH···π interaction is governed by exchange-correlation energies, thereby establishing a covalent character, as opposed to the literature's designation as a noncovalent interaction. Moreover, dispersion energy is relevant, statically and in absolute terms, but less relevant compared to other energy components in terms of the formation of the complex. Multipolar electrostatics are similar across all systems.

π-Stacking among the Anthracenyl Groups of a Copper Complex Resulted in Doubling of Unit Cell Volume To Provide New Polymorphs

Two polymorphs of the 9-N-(3-imidazolylpropylamino)methylanthracene (Hanthraimmida) containing hydrated copper(II)-2,6-pyridinedicarboxylate complex are reported. The two polymorphs have either lamellar or Herringbone arrangements of π-stacks among the anthracenyl groups of organocation. The difference between the two polymorphs originated from having face-to-face stacking arrangements between the two anthracenyl groups of the symmetry independent cations within the unit cell in one of the polymorphs. The π-stacked anthracenyl groups in consecutive layers of the polymorphs are oriented in one direction in the polymorph designated as P1, whereas the polymorph designated as P2 has such orientations in opposite directions. The unit cell volume of the polymorph P2 (Z = 4) has approximately twice the volume of the polymorph P1 (Z = 2); it happend due to coalescence of two unit cells of P1 in the ab-crystallographic plane. A mixed methanol/water solvate of the copper complex is also reported. It has a channel-like arrangement of the cations; has the anions and the solvents within the cation embraced channel-like enclosures. This complex is unstable, once taken out from the methanol solvent, it transforms in real time to P2 by replacements of the methanol molecules by water molecules.

N-Acylsulfonamide: a valuable moiety to design new sulfa drug analogues

Sulfonamides are the oldest class of antibiotics, discovered more than 80 years ago. They are still used today despite the appearance of drug resistance phenomena that limit their prescription. Since the discovery and use of the first sulfa drugs, many analogues have been synthesized in order to obtain new active molecules able to circumvent bacterial resistance. Structurally similar to sulfonamide, the N-acylsulfonamide group arouses interest in the field of medicinal chemistry due to specific physico-chemical properties. We report here the synthesis and antibacterial/antibiofilm activities of 18 sulfa drug analogues with an N-acylsulfonamide moiety. These derivatives were obtained efficiently by sulfo-click reactions between readily available thioacid and sulfonyl azide synthons.

Stack bonding in polyaromatic hydrocarbons

Parallel displacement of π-stacked component molecules enhances the efficiency of organic semiconductors by maximizing interpenetration of the π-densities. Dimers of symmetric polyaromatic hydrocarbons coronene, hexabenzo[bc,de,gh,kl,no,qr]coronene, circumcoronene, kekulene, and circumcircumcoronene are examined using density functional theory from the stack bonding perspective which considers π-stacking interactions in terms of contributions of monomer π-orbital overlap to the character of dimer orbitals. Energetically favored parallel displaced and/or twisted dimer conformations are consistent with patterns of mixing of the monomer molecular orbitals (MOs) that maximize interpenetration of the π densities. The multiple minima found along parallel displacement (PD) coordinates coincide with the formation of dimer MOs formally antibonding between the monomers at the sandwich conformation to bonding at the PD minima. Minima identified with favorable stack bonding are consistent with polymorphs found in large polyaromatic hydrocarbons.

Resistance to Resveratrol Treatment in Experimental PTSD Is Associated with Abnormalities in Hepatic Metabolism of Glucocorticoids

Glucocorticoids are metabolized by the CYP3A isoform of cytochrome P450 and by 11-β-hydroxysteroid dehydrogenase type 1 (11β-HSD-1). Experimental data suggest that post-traumatic stress disorder (PTSD) is associated with an increase in hepatic 11β-HSD-1 activity and a concomitant decrease in hepatic CYP3A activity. Trans-resveratrol, a natural polyphenol, has been extensively studied for its antipsychiatric properties. Recently, protective effects of trans-resveratrol were found in relation to PTSD. Treatment of PTSD rats with trans-resveratrol allowed the rats to be divided into two phenotypes. The first phenotype is treatment-sensitive rats (TSR), and the second phenotype is treatment-resistant rats (TRRs). In TSR rats, trans-resveratrol ameliorated anxiety-like behavior and reversed plasma corticosterone concentration abnormalities. In contrast, in TRR rats, trans-resveratrol aggravated anxiety-like behavior and decreased plasma corticosterone concentration. In TSR rats, hepatic 11β-HSD-1 activity was suppressed, with a concomitant increase in CYP3A activity. In TRR rats, the activities of both enzymes were suppressed. Thus, the resistance of PTSD rats to trans-resveratrol treatment is associated with abnormalities in hepatic metabolism of glucocorticoids. The free energy of binding of resveratrol, cortisol, and corticosterone to the human CYP3A protein was determined using the molecular mechanics Poisson-Boltzmann surface area approach, indicating that resveratrol could affect CYP3A activity.

Soil amended with Algal Biochar Reduces Mobility of deicing salt contaminants in the environment: An atomistic insight

Soil-based filter media in green infrastructure buffers only a minor portion of deicing salt in surface water, allowing most of that to infiltrate into groundwater, thus negatively impacting drinking water and the aquatic ecosystem. The capacity of the filter medium to adsorb and fixate sodium (Na⁺) and chloride (Cl^-) ions has been shown to improve by biochar amendment. The extent of improvement, however, depends on the type and density of functional groups on the biochar surface. Here, we use density functional theory (DFT) and molecular dynamics (MD) simulations to show the merits of biochar grafted by nitrogenous functional groups to adsorb Cl^-. Our group has shown that such functional groups are abundant in biochar made from protein-rich algae feedstock. DFT is used to model algal biochar surface and its possible interactions with Cl^- through two possible mechanisms: direct adsorption and cation (Na⁺)-bridging. Our DFT calculations reveal strong adsorption of Cl^- to the biochar surface through hydrogen bonding and electrostatic attractions between the ions and active sites on biochar. MD results indicate the efficacy of algal biochar in delaying chloride diffusion. This study demonstrates the potential of amending soils with algal biochar as a dual-targeting strategy to sequestrate carbon and prevent deicing salt contaminants from leaching into water bodies.

The Impact of Solution Ionic Strength, Hardness, and pH on the Sorption Efficiency of Polychlorinated Biphenyls in Magnetic Nanocomposite Microparticle (MNM) Gels

Environmental conditions of groundwater and surface water greatly vary as a function of location. Factors such as ionic strength, water hardness, and solution pH can change the physical and chemical properties of the nanocomposites used in remediation and the pollutants of interest. In this work, magnetic nanocomposite microparticle (MNM) gels are used as sorbents for remediation of PCB 126 as model organic contaminant. Three MNM systems are used: curcumin multiacrylate MNMs (CMA MNMs), quercetin multiacrylate MNMs (QMA MNMs), and polyethylene glycol-400-dimethacrylate MNMs (PEG MNMs). The effect of ionic strength, water hardness, and pH were studied on the sorption efficiency of the MNMs for PCB 126 by performing equilibrium binding studies. It is seen that the ionic strength and water hardness have a minimal effect on the MNM gel system sorption of PCB 126. However, a decrease in binding was observed when the pH increased from 6.5 to 8.5, attributed to anion-π interactions between the buffer ions in solution and the PCB molecules as well as with the aromatic rings of the MNM gel systems. Overall, the results indicate that the developed MNM gels can be used as magnetic sorbents for polychlorinated biphenyls in groundwater and surface water remediation, provided that the solution pH is controlled.

Polycyclic Aromatic Hydrocarbons as Anode Materials in Lithium-Ion Batteries: A DFT Study

The structure and energetics of the interactive behavior of Li⁺ and Li with polycyclic aromatic hydrocarbons (PAHs) have been studied at the wB97XD/6-311G(d,p) level of DFT. The electron distribution in the PAHs, analyzed using the topology of the molecular electrostatic potential (MESP), led to the categorization of their aromatic rings into five types, viz R_s, R_n, R_d, R_b, and R_e. Among the different rings, sextet-type R_s and naphthalene-type R_n rings showed the highest interaction with Li⁺. The change in MESP at the nucleus of Li⁺ (ΔV_Li⁺) due to the formation of the complex Li⁺...PAH is found to be proportional to the adsorption energy (E₁). In Li...PAH, the spin density on Li is close to zero, suggesting the formation of Li⁺...PAH^•- due to the electron transfer from Li to PAH. The adsorption energy (E₂) for Li...PAH does not correlate with the change in MESP at the nucleus of Li, whereas the dissociation energy (E₃) of Li⁺...PAH^•- to yield Li⁺ and PAH^•- correlates well with the MESP data, ΔV_Li. The study confirms that the change in MESP at the nucleus of Li⁺ due to complex formation gives a quantitative measure of the electronic effect of the cation-π binding. The cell potential (V_cell) is predicted for the lithium ion battery (LIB) using the Li⁺...PAH and Li...PAH adsorption energies. On the basis of the V_cell data, "carbon nanoflake"-type systems, viz coronene, circumbiphenyl, C₄₂H₁₆, and C₅₀H₁₈ are suggested as good anode materials for LIBs.

Catalyst-Substrate Helical Character Matching Determines the Enantioselectivity in the Ishihara-Type Iodoarenes Catalyzed Asymmetric Kita-Dearomative Spirolactonization

Catalyst design has traditionally focused on rigid structural elements to prevent conformational flexibility. Ishihara's elegant design of conformationally flexible C₂-symmetric iodoarenes, a new class of privileged organocatalysts, for the catalytic asymmetric dearomatization (CADA) of naphthols is a notable exception. Despite the widespread use of the Ishihara catalysts for CADAs, the reaction mechanism remains the subject of debate, and the mode of asymmetric induction has not been well established. Here, we report an in-depth computational investigation of three possible mechanisms in the literature. Our results, however, reveal that this reaction is best rationalized by a fourth mechanism called "proton-transfer-coupled-dearomatization (PTCD)", which is predicted to be strongly favored over other competing pathways. The PTCD mechanism is consistent with a control experiment and further validated by applying it to rationalize the enantioselectivities. Oxidation of the flexible I(I) catalyst to catalytic active I(III) species induces a defined C₂-symmetric helical chiral environment with a delicate balance between flexibility and rigidity. A match/mismatch effect between the active catalyst and the substrate's helical shape in the dearomatization transition states was observed. The helical shape match allows the active catalyst to adapt its conformation to maximize attractive noncovalent interactions, including I(III)···O halogen bond, N-H···O hydrogen bond, and π···π stacking, to stabilize the favored transition state. A stereochemical model capable of rationalizing the effect of catalyst structural variation on the enantioselectivities is developed. The present study enriches our understanding of how flexible catalysts achieve high stereoinduction and may serve as an inspiration for the future exploration of conformational flexibility for new catalyst designs.

Discovery, implications and initial use of semi-synthetic organisms with an expanded genetic alphabet/code

Much recent interest has focused on developing proteins for human use, such as in medicine. However, natural proteins are made up of only a limited number of canonical amino acids with limited functionalities, and this makes the discovery of variants with some functions difficult. The ability to recombinantly express proteins containing non-canonical amino acids (ncAAs) with properties selected to impart the protein with desired properties is expected to dramatically improve the discovery of proteins with different functions. Perhaps the most straightforward approach to such an expansion of the genetic code is through expansion of the genetic alphabet, so that new codon/anticodon pairs can be created to assign to ncAAs. In this review, I briefly summarize more than 20 years of effort leading ultimately to the discovery of synthetic nucleotides that pair to form an unnatural base pair, which when incorporated into DNA, is stably maintained, transcribed and used to translate proteins in Escherichia coli. In addition to discussing wide ranging conceptual implications, I also describe ongoing efforts at the pharmaceutical company Sanofi to employ the resulting 'semi-synthetic organisms' or SSOs, for the production of next-generation protein therapeutics. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.

Engineering Chiral Induction in Centrally Functionalized o-Phenylenes

Work on foldamers, nonbiological oligomers that mimic the hierarchical structure of biomacromolecules, continues to yield new architectures of ever increasing complexity. o-Phenylenes, a class of helical aromatic foldamers, are well-suited to this area because of their structural simplicity and the straightforward characterization of their folding in solution. However, control of structure requires, by definition, control over folding handedness. Control over o-phenylene twist sense is currently lacking. While chiral induction from groups at o-phenylene termini has been demonstrated, it would be useful to instead direct twisting from internal positions to leave the ends free. Here, we explore chiral induction in a series of o-phenylenes with chiral imides at their centers. Conformational behavior has been studied by nuclear magnetic resonance and circular dichroism spectroscopies and density functional theory calculations. Chiral induction in otherwise unfunctionalized o-phenylenes is generally poor. However, strategic functionalization of the helix surface with trifluoromethyl or methyl groups allows it to better interact with the imide groups, greatly increasing diastereomeric excesses. The sense of chiral induction is consistent with computational models that suggest that it primarily arises from a steric effect.

Thermodynamic, Spectroscopic, and Structural Study on a Sodium Uranyl Tri-2-Methoxybenzoate Dodecahydrate Coordination Compound with Considerably Low Solubility in Acidic Conditions

A spontaneous crystallization of an uranium(VI)-organic coordination compound with sodium and 2-methoxybenzoate (2-mba) was observed in acidic solutions, and the solubility product, molecular vibrations, crystal structure, thermal stability, and emission properties of the atypically low-soluble U(VI) complex (Na[UO₂(2-mba)₃]·12H₂O(s)) were fully investigated for the first time. A long-term solubility experiment and speciation modeling gave a solubility product of log K_s,0 = -12.18 ± 0.02 (T = 25 °C and I = 0.1 M NaClO₄), and vibrational analyses confirmed the overall molecular structure of complex and the frequencies of characteristic stretching motions of uranyl moiety as well. The crystal quality of Na[UO₂(2-mba)₃]·12H₂O(s) was improved by a digestion method, and X-ray diffraction analysis of the single crystalline specimen verified that the newly studied uranyl-organic compound contains one-dimensional channels with a diameter of 20 Å along the [001] direction; the sodium and water molecules are arranged in the channel structures. In the coordination environment around uranyl, three aromatic carboxylates are symmetrically bound in the equatorial plane of uranyl coplanarily, and the unit [UO₂(2-mba)₃]^- complexes are further extended along the plane to form the layered-morphologies. The three-dimensional packing of [UO₂(2-mba)₃]^- anions is driven by the parallel-displaced π-stacking of aromatic rings with a centroid-centroid distance of 3.7 Å. Additional thermogravimetric analysis confirmed that the Na[UO₂(2-mba)₃]·12H₂O(s) is stable up to 250 °C, and dehydration and release of the organic ligand were subsequently observed beyond that temperature. Photoluminescence spectrum of the Na[UO₂(2-mba)₃]·12H₂O(s) clearly displayed the characteristic U(VI) emission, and a band spacing between the ground electronic states of U(VI) uranyl was evaluated to be 831 ± 14 cm^-1. Such detailed characterization of the unique Na[UO₂(2-mba)₃]·12H₂O(s) is advancing upon a systematic understanding of the structural effects of the aromatic model ligands on U(VI) complexation, with relevance to the environmental chemistry of U(VI) and crystal engineering for development of diverse uranyl-organic frameworks.

π-Stacking Isomerism in Polycyclic Aromatic Hydrocarbons: The 2-Naphthalenethiol Dimer

π-Stacking is a common descriptor for face-to-face attractive forces between aromatic hydrocarbons. However, the physical origin of this interaction remains debatable. Here we examined π-stacking in a model homodimer formed by two thiol-substituted naphthalene rings. Two isomers of the 2-naphthalenethiol dimer were discovered using rotational spectroscopy, sharing a parallel-displaced crossed orientation and absence of thiol-thiol hydrogen bonds. One of the isomers presents C₂ symmetry, structurally analogous to the global minimum of the naphthalene dimer. The experimental data were rationalized with molecular orbital calculations, revealing a shallow potential energy surface. Noncovalent interactions are dominated by dispersion forces according to SAPT energy decomposition. In addition, the reduced electronic density shows a diffuse and extended region of inter-ring interactions, compatible with the description of π-stacking as a competition between dispersion and Pauli repulsion forces.

Using Macrocyclic G-Quadruplex Ligands to Decipher the Interactions Between Small Molecules and G-Quadruplex DNA

This study aims to deepen the knowledge of the current state of rational G4-ligand design through the design and synthesis of a novel set of compounds based on indoles, quinolines, and benzofurans and their comparisons with well-known G4-ligands. This resulted in novel synthetic methods and G4-ligands that bind and stabilize G4 DNA with high selectivity. Furthermore, the study corroborates previous studies on the design of G4-ligands and adds deeper explanations to why a) macrocycles offer advantages in terms of G4-binding and -selectivity, b) molecular pre-organization is of key importance in the development of strong novel binders, c) an electron-deficient aromatic core is essential to engage in strong arene-arene interactions with the G4-surface, and d) aliphatic amines can strengthen interactions indirectly through changing the arene electrostatic nature of the compound. Finally, fundamental physicochemical properties of selected G4-binders are evaluated, underscoring the complexity of aligning the properties required for efficient G4 binding and stabilization with feasible pharmacokinetic properties.

Triple ionization and fragmentation of benzene trimers following ultrafast intermolecular Coulombic decay

Intermolecular interactions involving aromatic rings are ubiquitous in biochemistry and they govern the properties of many organic materials. Nevertheless, our understanding of the structures and dynamics of aromatic clusters remains incomplete, in particular for systems beyond the dimers, despite their high presence in many macromolecular systems such as DNA and proteins. Here, we study the fragmentation dynamics of benzene trimer that represents a prototype of higher-order aromatic clusters. The trimers are initially ionized by electron-collision with the creation of a deep-lying carbon 2s⁻¹ state or one outer-valence and one inner-valence vacancies at two separate molecules. The system can thus relax via ultrafast intermolecular decay mechanisms, leading to the formation of C\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${}_{6}{{{{{{{{{\rm{H}}}}}}}}}_{6}}^{+}\cdot$$\end{document}6H6+⋅C\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${}_{6}{{{{{{{{{\rm{H}}}}}}}}}_{6}}^{+}\cdot$$\end{document}6H6+⋅C\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${}_{6}{{{{{{{{{\rm{H}}}}}}}}}_{6}}^{+}$$\end{document}6H6+ trications and followed by a concerted three-body Coulomb explosion. Triple-coincidence ion momentum spectroscopy, accompanied by ab-initio calculations and further supported by strong-field laser experiments, allows us to elucidate the details on the fragmentation dynamics of benzene trimers.

Higher-order aromatic clusters are prevalent in biochemical systems, but a full understanding of their structural and dynamical properties is lacking. Here, the authors demonstrate that inner-valence ionization can induce ultrafast relaxation and further fragmentation mechanisms in benzene trimers.

Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers

It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.

Noncovalent Interactions in the Oxazaborolidine-Catalyzed Enantioselective Mukaiyama Aldol

Current models for oxazaborolidine-catalyzed transition-state structures are determined by C–H···O–B and C–H···O=S formyl hydrogen bonding between the electrophile and catalyst. However, selectivity in the oxazaborolidine-catalyzed Mukaiyama aldol cannot be fully rationalized using these models. Combined density functional theory and noncovalent interaction analyses reveal a new reaction model relying on C–H···O, C–H···π, and π–π interactions between the nucleophile, electrophile, and catalyst to induce selectivity.

Weakly Bound Complex Formation between HCN and CH3Cl: A Matrix-Isolation and Computational Study

The matrix-isolated infrared spectrum of a hydrogen cyanide-methyl chloride complex was investigated in a solid argon matrix. HCN and CH₃Cl were co-condensed onto a substrate held at 10 K with an excess of argon gas, and the infrared spectrum was measured using Fourier-transform infrared spectroscopy. Quantum chemical geometry optimization, harmonic frequency, and natural bonding orbital calculations indicate stabilized hydrogen- and halogen-bonded structures. The two resulting weakly bound complexes are both composed of one CH₃Cl molecule bound to a (HCN)₃ subunit, where the three HCN molecules are bound head-to-tail in a ring formation. Our study suggests that─in the presence of CH₃Cl─the formation of (HCN)₃ is promoted through complexation. Since HCN aggregates are an important precursor to prebiotic monomers (amino acids and nucleobases) and other life-bearing polymers, this study has astrophysical implications toward the search for life in space.

Stereocontrolled 1,3-nitrogen migration to access chiral α-amino acids

α-Amino acids are essential for life as building blocks of proteins and components of diverse natural molecules. In both industry and academia, the incorporation of unnatural amino acids is often desirable for modulating chemical, physical and pharmaceutical properties. Here we report a protocol for the economical and practical synthesis of optically active α-amino acids based on an unprecedented stereocontrolled 1,3-nitrogen shift. Our method employs abundant and easily accessible carboxylic acids as starting materials, which are first connected to a nitrogenation reagent, followed by a highly regio- and enantioselective ruthenium- or iron-catalysed C(sp3)-H amination. This straightforward method displays a very broad scope, providing rapid access to optically active α-amino acids with aryl, allyl, propargyl and alkyl side chains, and also permits stereocontrolled late-stage amination of carboxylic-acid-containing drugs and natural products.

Quantum–Classical Mechanics: Nano-Resonance in Polymethine Dyes

It is well known in quantum mechanics that the theory of quantum transitions is based on the convergence of the series of time-dependent perturbation theory. This series converges in atomic and nuclear physics. However, in molecular and chemical physics, this series converges only in the Born–Oppenheimer adiabatic approximation and due to the application of the Franck–Condon principle, and it diverges as a result of going beyond the adiabatic approximation and the Franck–Condon principle. This divergence (singularity) is associated with the incommensurability of the masses of light electrons and heavy nuclei which jointly participate in the full-fledged movement in the transient state of molecular “quantum” transitions. In a new physical theory—quantum–classical mechanics (Egorov, V.V. Heliyon Physics 2019, 5, e02579)—this singularity is damped by introducing chaos into the transient state. This transient chaos is introduced by replacing the infinitely small imaginary additive in the energy denominator of the spectral representation of the total Green’s function of the system with a finite value and is called dozy chaos. In this article, resonance at the nanoscale (nano-resonance) between electron and nuclear reorganization motions in the quantum–classical (dozy-chaos) mechanics of elementary electron transfers in condensed media and their applications to polymethine dyes and J-aggregates in solutions are reviewed. Nano-resonance explains the resonant character of the transformation of the shape of the optical absorption band in a series of polymethine dyes in which the length of the polymethine chain changes, as well as the nature of the red-shifted absorption band of the J-aggregates of polymethine dyes (J-band), which is narrow and intense. The process of dye aggregation in an aqueous solution with an increase in its concentration by the formation of J-aggregates is considered a structural tuning of the “polymethine dye + environment” system into resonance with light absorption. For J-aggregates in Langmuir films, the asymmetry of the luminescence and absorption bands, as well as the small value of their Stokes shifts, are explained. The parasitic transformation of the resonant shape of the optical absorption band of a polymethine dye in solution during the transition from one-photon to two-photon absorption is also explained, and the conditions for the restoration of this nano-resonance shape are predicted.

Unveiling a key catalytic pocket for the ruthenium NHC-catalysed asymmetric heteroarene hydrogenation

The chiral ruthenium(ii)bis-SINpEt complex is a versatile and powerful catalyst for the hydrogenation of a broad range of heteroarenes. This study aims to provide understanding of the active form of this privileged catalyst as well as the reaction mechanism, and to identify the factors which control enantioselectivity. To this end we used computational methods and in situ NMR spectroscopy to study the hydrogenation of 2-methylbenzofuran promoted by this system. The high flexibility and conformational freedom of the carbene ligands in this complex lead to the formation of a chiral pocket interacting with the substrate in a "lock-and-key" fashion. The non-covalent stabilization of the substrate in this particular pocket is an exclusive feature of the major enantiomeric pathway and is preserved throughout the mechanism. Substrate coordination leading to the minor enantiomer inside this pocket is inhibited by steric repulsion. Rather, the catalyst exhibits a "flat" interaction surface with the substrate in the minor enantiomer pathway. We probe this concept by computing transition states of the rate determining step of this reaction for a series of different substrates. Our findings open up a new approach for the rational design of chiral catalysts.

Alkaline Stability Evaluation of Polymerizable Hexyl-Tethered Ammonium Cations

One of the important challenges in designing robust alkaline anion exchange membranes is the difficulty associated with the chemical stability of covalently bound cationic units. Here, a systematic study exploring alkaline stabilities of polymerizable hexyltrimethylammonium cations is presented, where the hexyl chain is linked to a phenyl ring through a direct carbon-carbon, phenyl ether, or benzyl ether functionality. For this work, small molecule model compounds, styrenic monomer analogs, and their homopolymers are synthesized. Alkaline stabilities of the small molecule cations and their homopolymers are compared to alkaline stability of benzyltrimethylammonium (BTMA) cation and its homopolymer poly(BTMA), respectively. All the hexyl-tethered cations and their homopolymers are significantly more stable under strongly alkaline conditions (2 m KOD at 80 °C). Moreover, ether-linked cations show comparable stability to the direct carbon-carbon linked cation. Via ¹ H NMR analyses, possible degradation mechanisms are investigated for each small molecule cation. Findings of this study strongly suggest that the alkaline stability is dictated by the steric hindrance around the β-hydrogen. This study expands beyond the limits of general knowledge on alkaline stability of alkyl-tethered ammonium cations via the Hofmann elimination route, highlights important design parameters for stable ammonium cations, and demonstrates accessible directly polymerizable alkaline stable ammonium cations.

Substituent Effects on the Basicity of Patriscabrin A and Lettucenin A: Evolution Favors the Aromatic?

Basicities for derivatives of patriscabrin A and lettucenin A were calculated with density functional theory. A significant correlation is observed between the basicity and Hammett σ parameters. Protonation increases the aromatic character of the cyclic moieties of each natural product. The naturally occurring structures are predicted to be the most aromatic.

Dissection of the Polar and Non-Polar Contributions to Aromatic Stacking Interactions in Solution

Aromatic stacking interactions have been a matter of study and debate due to their crucial role in chemical and biological systems. The strong dependence on orientation and solvent together with the relatively small interaction energies have made evaluation and rationalization a challenge for experimental and theoretical chemists. We have used a supramolecular cage formed by two tris(pyridylmethyl)amines units to build chemical Double Mutant Cycles (DMC) for the experimental measurement of the free energies of π-stacking interactions. Extrapolating the substituent effects to remove the contribution due to electrostatic interactions reveals that there is a substantial contribution to the measured stacking interaction energies which is due to non-polar interactions (-3 to -6 kJ mol-1 ). The perfectly flat nature of the surface of an aromatic ring gives π-stacking an inherent advantage over non-polar interactions with alkyl groups and accounts for the wide-spread prevalence of stacking interactions in Nature.

Structural and functional stability of the sulfur-free surfactant protein B peptide mimic B-YL in synthetic surfactant lipids

BACKGROUND

Optimal functionality of synthetic lung surfactant for treatment of respiratory distress syndrome in preterm infants largely depends on the quality and quantity of the surfactant protein B (SP-B) peptide mimic and the lipid mixture. B-YL peptide is a 41-residue sulfur-free SP-B mimic with its cysteine and methionine residues replaced by tyrosine and leucine, respectively, to enhance its oxidation resistance.

AIM

Testing the structural and functional stability of the B-YL peptide in synthetic surfactant lipids after long-term storage.

METHODS

The structural and functional properties of B-YL peptide in surfactant lipids were studied using three production runs of B-YL peptides in synthetic surfactant lipids. Each run was held at 5 °C ambient temperature for three years and analyzed with structural and computational techniques, i.e., MALDI-TOF mass spectrometry, ATR-Fourier Transform Infrared Spectroscopy (ATR-FTIR), secondary homology modeling of a preliminary B-YL structure, and tertiary Molecular Dynamic simulations of B-YL in surfactant lipids, and with functional methods, i.e., captive bubble surfactometry (CBS) and retesting in vivo surface activity in surfactant-deficient young adult rabbits.

RESULTS

MALDI-TOF mass spectrometry showed no degradation of the B-YL peptide as a function of stored time. ATR-FTIR studies demonstrated that the B-YL peptide still assumed stable alpha-helical conformations in synthetic surfactant lipids. These structural findings correlated with excellent in vitro surface activity during both quasi-static and dynamic cycling on CBS after three years of cold storage and in vivo surface activity of the aged formulations with improvements in oxygenation and dynamic lung compliance approaching those of the positive control surfactant Curosurf®.

CONCLUSIONS

The structure of the B-YL peptide and the in vitro and in vivo functions of the B-YL surfactant were each maintained after three years of refrigeration storage.

Are Heavy Pnictogen-π Interactions Really "π Interactions"?

The noncovalent interactions of heavy pnictogens with π-arenes play a fundamental role in fields like crystal engineering or catalysis. The strength of such bonds is based on an interplay between dispersion and donor/acceptor interactions, and is generally attributed to the presence of π-arenes. Computational studies of the interaction between the heavy pnictogens As, Sb and Bi and cyclohexane, in comparison with previous studies on the interaction between heavy pnictogens and benzene, show that this concept probably has to be revised. A thorough analysis of all the different energetic components that play a role in these systems, carried out with state-of-the-art computational methods, sheds light on how they influence one another and the effect that their interplay has on the overall system. Furthermore, the analysis of such interactions leads us to the unexpected finding that the presence of the pnictogen compounds strongly affects the conformational equilibrium of cyclohexane, reversing the relative stability of the chair and boat-twist conformers, and thus suggesting a possible application of tuneable dispersion energy donors to stabilise the desired conformation.

Computational Evaluation of Me2 TCCP as Lewis Acid

Supramolecular adducts between dimethyl-2,2,3,3-tetracyanocyclopropane (Me2 TCCP) with 21 small (polar) molecules and 10 anions were computed with DFT (B3LYP-D3/def2-TZVP). Their optimized geometries were used to obtain interaction energies, and perform energy decomposition and 'atoms-in-molecules' analyses. A set of 38 other adducts were also evaluated for comparison purposes. Selected examples were further scrutinized by inspection of the molecular electrostatic potential maps, Noncovalent Interaction index plots, the Laplacian, the orbital interactions, and by estimating the Gibbs free energy of complexation in hexane solution. These calculations divulge the thermodynamic feasibility of Me2 TCCP adducts and show that complexation is typically driven by dispersion with less polarized partners, but by orbital interactions when more polarized or anionic guests are deployed. Most Me2 TCCP adducts are more stable than simple hydrogen bonding with water, but less stable than traditional Lewis adducts involving Me3 B, or a strong halogen bond such as with Br2 . Several bonding analyses showed that the locus of interaction is found near the electron poor sp3 -hydridized (NC)2 C-C(CN)2 carbon atoms. An empty hybrid σ*/π* orbital on Me2 TCCP was identified that can be held responsible for the stability of the most stable adducts due to donor-acceptor interactions.

On the question of steric repulsion versus noncovalent attractive interactions in chiral phosphoric acid catalyzed asymmetric reactions

The origin of enantioselectivity in asymmetric catalysis is often built around the differential steric interaction in the enantiocontrolling transition states (TSs). A closer perusal of enantiocontrolling TSs in an increasingly diverse range of reactions has revealed that the cumulative effect of weak noncovalent interactions could even outweigh the steric effects. While enunciating this balance is conspicuously important, quantification of such intramolecular forces within a TS continues to remain scarce and challenging. Herein, we demonstrate the utility of the fragment molecular orbital method in establishing the relative contributions of various attractive and repulsive contributions in the total interaction energy between the suitably chosen fragments in enantiocontrolling TSs. Three types of reactions of high contemporary importance, namely, axially chiral phosphoric acid (CPA) catalyzed kinetic resolution of rac-α-methyl-γ-hydroxy ester (reaction I), asymmetric dearomative amination of β-naphthols by dimethyl azodicarboxylate (IIa and IIb), and intramolecular desymmetrization of β,β-disubstituted methyl oxetanes (IIIa) and hydroxyl oxetane (IIIb), bearing a tethered alcohol (-OCH₂CH₂OH or -(CH₂)₂CH₂OH), are considered. In all the five reactions, the differences in the stabilizing contributions arising due to electrostatic, charge-transfer, and dispersion interactions between the catalyst and the reacting partners in the enantiocontrolling transition states are weighed against the destabilizing exchange interaction. The balancing interactions are found to be between dispersion and exchange repulsion in reaction I, a combination of charge transfer and dispersion energies offsets the repulsive energy in reaction IIb involving the electron rich anthryl groups in the catalyst, whereas the -(CF₃)₂C₆H₄ 3,3'-substituent in the catalyst (reaction IIa) leads to a trade-off between dispersion and exchange energies. In reactions IIIa and IIIb, however, electrostatic and dispersion energies help compensate the repulsive interactions. These quantitative insights on the intramolecular interactions in the stereocontrolling TSs could help in the rational design of asymmetric catalysis.

Investigation of Tribological Behavior of Lubricating Greases Composed of Different Bio-Based Polymer Thickeners

One commonly used lubricant in rolling bearings is grease, which consists of base oil, thickener and small amounts of additives. Commercial greases are mostly produced from petrochemical base oil and thickener. Recently, the development of base oils from renewable resources have been significantly focused on in the lubricant industry. However, to produce an entirely bio-based grease, the thickener must also be produced from renewable materials. Therefore, this work presents the design and evaluation of three different bio-based polymer thickener systems. Tribological tests are performed to characterize lubrication properties of developed bio-based greases. The effect of thickener type on film thickness and friction behavior of the produced bio-based greases is evaluated on a ball-on-disc tribometer. Moreover, the results are compared to a commercial petrochemical grease chosen as benchmark.

Data Science Meets Physical Organic Chemistry

ConspectusAt the heart of synthetic chemistry is the holy grail of predictable catalyst design. In particular, researchers involved in reaction development in asymmetric catalysis have pursued a variety of strategies toward this goal. This is driven by both the pragmatic need to achieve high selectivities and the inability to readily identify why a certain catalyst is effective for a given reaction. While empiricism and intuition have dominated the field of asymmetric catalysis since its inception, enantioselectivity offers a mechanistically rich platform to interrogate catalyst-structure response patterns that explain the performance of a particular catalyst or substrate.In the early stages of an asymmetric reaction development campaign, the overarching mechanism of the reaction, catalyst speciation, the turnover limiting step, and many other details are unknown or posited based on related reactions. Considering the unclear details leading to a successful reaction, initial enantioselectivity data are often used to intuitively guide the ultimate direction of optimization. However, if the conditions of the Curtin-Hammett principle are satisfied, then measured enantioselectivity can be directly connected to the ensemble of diastereomeric transition states (TSs) that lead to the enantiomeric products, and the associated free energy difference between competing TSs (ΔΔG⧧ = -RT ln[(S)/(R)], where (S) and (R) represent the concentrations of the enantiomeric products). We, and others, speculated that this important piece of information can be leveraged to guide reaction optimization in a quantitative way.Although traditional linear free energy relationships (LFERs), such as Hammett plots, have been used to illuminate important mechanistic features, we sought to develop data science derived tools to expand the power of LFERs in order to describe complex reactions frequently encountered in modern asymmetric catalysis. Specifically, we investigated whether enantioselectivity data from a reaction can be quantitatively connected to the attributes of reaction components, such as catalyst and substrate structural features, to harness data for asymmetric catalyst design.In this context, we developed a workflow to relate computationally derived features of reaction components to enantioselectivity using data science tools. The mathematical representation of molecules can incorporate many aspects of a transformation, such as molecular features from substrate, product, catalyst, and proposed transition states. Statistical models relating these features to reaction outputs can be used for various tasks, such as performance prediction of untested molecules. Perhaps most importantly, statistical models can guide the generation of mechanistic hypotheses that are embedded within complex patterns of reaction responses. Overall, merging traditional physical organic experiments with statistical modeling techniques creates a feedback loop that enables both evaluation of multiple mechanistic hypotheses and future catalyst design. In this Account, we highlight the evolution and application of this approach in the context of a collaborative program based on chiral phosphoric acid catalysts (CPAs) in asymmetric catalysis.

A Structural Model for the Ligand Binding of Pneumococcal Serotype 3 Capsular Polysaccharide-Specific Protective Antibodies

Capsular polysaccharides (CPSs) are major virulence factors that decorate the surfaces of many human bacterial pathogens. In their pure form or as glycoconjugate vaccines, CPSs are extensively used in vaccines deployed in clinical practice worldwide. However, our understanding of the structural requirements for interactions between CPSs and antibodies is limited. A longstanding model based on comprehensive observations of antibody repertoires binding to CPSs is that antibodies expressing heavy chain variable gene family 3 (VH3) predominate in these binding interactions in humans and VH3 homologs in mice. Toward understanding this highly conserved interaction, we generated a panel of mouse monoclonal antibodies (MAb) against Streptococcus pneumoniae serotype 3 CPS, determined an X-ray crystal structure of a protective MAb in complex with a hexasaccharide derived from enzymatic hydrolysis of the polysaccharide, and elucidated the structural requirements for this binding interaction. The crystal structure revealed a binding pocket containing aromatic side chains, suggesting the importance of hydrophobicity in the interaction. Through mutational analysis, we determined the amino acids that are critical in carbohydrate binding. Through elucidating the structural and functional properties of a panel of murine MAbs, we offer an explanation for the predominant use of the human VH3 gene family in antibodies against CPSs with implications in knowledge-based vaccine design.

The Crystal Structure and Intermolecular Interactions in Fenamic Acids-Acridine Complexes

In order to improve pharmaceutical properties of drugs, complexes are synthesized as combinations with other chemical substances. The complexes of fenamic acid and its derivatives, such as mefenamic-, tolfenamic- and flufenamic acid, with acridine were obtained and the X-ray structures were discussed. Formation of the crystals is determined by the presence of the intermolecular O–H^…N hydrogen bond that occur between fenamic acids and acridine. Intermolecular interactions stabilizing the crystals such as π^…π stacking, C–H^…X (X = O, Cl) intermolecular hydrogen bonds as well as C–H^…π and other dispersive interactions were analyzed by theoretical methods: the quantum theory of atoms in molecules (QTAIM) and noncovalent interaction (NCI) approaches.

Impact of Noncovalent Interactions on the Structural Chemistry of Thorium(IV)-Aquo-Chloro Complexes

Five novel tetravalent thorium (Th) compounds that consist of Th(H₂O)_xCl_y structural units were isolated from acidic aqueous solutions using a series of nitrogen-containing heterocyclic hydrogen (H) bond donors. Taken together with three previously reported phases, the compounds provide a series of monomeric Th^IV complexes wherein the effects of noncovalent interactions (and H-bond donor identity) on Th structural chemistry can be examined. Seven distinct structural units of the general formulas [Th(H₂O)_xCl_8-x]^x-4 (x = 2, 4) and [Th(H₂O)_xCl_9-x]^x-5 (x = 5-7) are described. The complexes range from chloride-deficient [Th(H₂O)₇Cl₂]²⁺ to chloride-rich [Th(H₂O)₂Cl₆]^2- species, and theory was used to understand the relative energies that separate complexes within this series via the stepwise chloride addition to an aquated Th cation. Electronic structure theory predicted the reaction energies of chloride addition and release of water through a series of transformations, generally highlighting an energetic driving force for chloride complexation. To probe the role of the counterion in the stabilization of these complexes, electrostatic potential (ESP) surfaces were calculated. The ESP surfaces indicated a dependence of the chloride distribution about the Th metal center on the pK_a of the countercation, highlighting the directing effects of noncovalent interactions (e.g., Hbonding) on Th speciation.

Self-Assembled 2,3-Dicyanopyrazino Phenanthrene Aggregates as a Visible-Light Photocatalyst

In this study, 2,3-dicyanopyrazino phenanthrene (DCPP), a commodity chemical that can be prepared at an industrial scale, was used as a photocatalyst in lieu of Ru or Ir complexes in C-X (X = C, N, and O) bond-forming reactions under visible-light irradiation. In these reactions, [DCPP]_n aggregates were formed in situ through physical π-π stacking of DCPP monomers in organic solvents. These aggregates exhibited excellent photo- and electrochemical properties, including a visible light response (430 nm), long excited-state lifetime (19.3 μs), high excited-state reduction potential (E_red([DCPP]_n*/[DCPP]_n^·-) = +2.10 V vs SCE), and good reduction stability. The applications of [DCPP]_n aggregates as a versatile visible-light photocatalyst were demonstrated in decarboxylative C-C cross-coupling, amidation, and esterification reactions.

Pyromellitic-Based Low Molecular Weight Gelators and Computational Studies of Intermolecular Interactions: A Potential Additive for Lubricant

Low molecular weight gelators (LMWG) have been extensively explored in many research fields due to their unique reversible gel-sol transformation. Intermolecular interactions between LMWG are known as the main driving force for self-assembly. During this self-assembly process, individually analyzing the contribution difference between various intermolecular interactions is crucial to understand the gel properties. Herein, we report 2,5-bis(hexadecylcarbamoyl)terephthalic acid (BHTA) as a LMWG, which could efficiently form a stable organogel with n-hexadecane, diesel, liquid paraffin, and base lubricant oil at a relatively low concentration. To investigate the contribution difference of intermolecular interactions, we first finished FT-IR spectroscopy and XRD experiments. On the basis of the d-spacing, a crude simulation model was built and then subjected to molecular dynamics (MD) simulations. Then, we knocked out the energy contribution of the H-bonding interactions and π-π stacking, respectively, to evaluate the intermolecular interactions significantly influencing the stability of the gel system. MD simulations results suggest that the self-assembly of the aggregates was mainly driven by dense H-bonding interactions between carbonyl acid and amide moieties of BHTA, which is consistent with FT-IR data. Moreover, wave function analysis at a quantum level suggested these electrostatic interactions located in the middle of the BHTA molecule were surrounded by strong dispersion attraction originating from a hydrophobic environment. Furthermore, we also confirmed that 2 wt % BHTA was able to form gel lubricant with 150BS. The coefficient of friction (COF) data show that the gel lubricant has a better tribological performance than 150BS base lubricant oil. Finally, XPS was performed and offered valuable information about the lubrication mechanism during the friction.

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.