Direct Hydrogen Bonds Research Articles

Multifunctional Biocomposite Materials from Chlorella vulgaris Microalgae.

Extrusion 3D-printing of biopolymers and natural fiber-based biocomposites enables the fabrication of complex structures, ranging from implants' scaffolds to eco-friendly structural materials. However, conventional polymer extrusion requires high energy consumption to reduce viscosity, and natural fiber reinforcement often requires harsh chemical treatments to improve adhesion. We address these challenges by introducing a sustainable framework to fabricate natural biocomposites using Chlorella vulgaris microalgae as the matrix. Through bioink optimization and process refinement, we produced lightweight, multifunctional materials with hierarchical architectures. Infrared spectroscopy analysis reveals that hydrogen bonding plays a critical role in the binding and reinforcement of Chlorella cells by hydroxyethyl cellulose (HEC). As water content decreases, the hydrogen bonding network evolves from water-mediated interactions to direct hydrogen bonds between HEC and Chlorella, enhancing the mechanical properties. A controlled dehydration process maintains continuous microalgae morphology, preventing cracking. The resulting biocomposites exhibit a bending stiffness of 1.6 GPa and isotropic heat transfer and thermal conductivity of 0.10 W/mK at room temperature, demonstrating effective thermal insulation. These characteristics make Chlorella biocomposites promising candidates for applications requiring both structural performance and thermal insulation, offering a sustainable alternative to conventional materials in response to growing environmental demands.

Self-assembled properties of water cuboids

Although liquid water and ice are characterised by predominantly tetrahedral coordination, small water clusters often exhibit a cubic structural motif. In this article, the stability of hydrogen-bonded water nanostructures in the form of n 1×n 2×n 3 cuboids is investigated. The requirement for complete hydrogen bonding imposes a strong constraint on their structure. The equations of the donor–acceptor balance are derived, from which all possible forms of completely hydrogen-bonded cuboids are deduced. The flexible non-additive AMOEBA potential is used for geometric optimisation of the set of configurations with different directions of hydrogen (H-) bonds. It has been established that the majority of completely hydrogen-bonded structures are formed by one layer of fused cubes. The lowest energy configurations of the, in fact, bilayer structures are formed by trans-configurations of transverse pairs of molecules, although some H-bonds are broken in this case. It is noted that the structure of the cuboids may result from the assembly of short nanotubes and smaller cuboids. On the other hand, unrealised H-bonds at the corners of the cuboids make it possible to assemble larger bilayer structures.

Diverse Self-Assembled Molecular Architectures Promoted by C-H···O and C-H···Cl Hydrogen Bonds in a Triad of α-Diketone, α-Ketoimine, and an Imidorhenium Complex: A Unified Analysis Based on XRD, NEDA, SAPT, QTAIM, and IBSI Studies.

X-ray structural elucidation, supramolecular self-assembly, and energetics of existential noncovalent interactions for a triad comprising α-diketone, α-ketoimine, and an imidorhenium complex are highlighted in this report. Molecular packing reveals a self-assembled 2D network stabilized by the C-H···O H-bonds for the α-diketone (benzil), and the first structural report of Brown and Sadanaga stressing on the prevalence of only the van der Waals forces seems to be an oversimplified conjecture. In the α-ketoimine, the imine nitrogen atom undergoes intramolecular N···H interaction to render itself inert toward intermolecular C-H···N interaction and exhibits two types of C-H···O H-bonds in consequence to generate a self-assembled 2D molecular architecture. The imidorhenium complex features a self-aggregated 3D packing engendered by the interplay of C-H···Cl H-bonds along with the ancillary C-H···π, C···C, and C···Cl contacts. To the best of our knowledge, in rhenium chemistry, this imidorhenium complex unravels the first example of self-associated 3D molecular packing constructed by the directional hydrogen bonds of C-H···Cl type. The presence of characteristic supramolecular synthons, viz., R2 2(12), R2 2(16), and R2 2(14), in the α-diketone, α-ketoimine, and imidorhenium complex, respectively, has prompted us to delve into the energetics of noncovalent interactions. Symmetry-adapted perturbation theory analysis has authenticated a stability order: R2 2(14) > R2 2(12) > R2 2(16) based on the interaction energy values of -25.97, -9.93, and -4.98 kcal/mol, respectively. The respective average contributions of the long-range dispersion, electrostatic, and induction forces are 58.5, 32.8, and 8.7%, respectively, for the intermolecular C-H···O interactions. The C-H···Cl interactions experience comparable contribution from the dispersion force (57.9% on average), although the electrostatic and induction forces contribute much less, 28.0 and 14.1%, respectively, on average. The natural energy decomposition analysis has further attested that the short-range, interfragment charge transfer occurring via the lp(O/Cl) → σ*(C-H) routes contributes 17-25% of the total attractive force for the C-H···O and C-H···Cl interactions. Quantum theory of atoms in molecules analysis unfolds a first-order exponential decay relation (y = 8.1043e -x/0.4095) between the electron density at the bond critical point and the distance of noncovalent interactions. The distances of noncovalent interactions in the lattices are internally governed by the individual packing patterns rather than the chemical nature of the H-bond donors and acceptors. Intrinsic bond strength index analysis shows promise to correlate the electron density at BCP with the SAPT-derived interaction energy for the noncovalent interactions. Two factors: (i) nearly half the HOMO-LUMO energy difference for the imidorhenium complex (∼30 kcal/mol) compared to the organics, and (ii) ∼60% localization of HOMO over the mer-ReCl3 moiety clearly indicate an enhanced polarizability of the complex facilitating the growth of weak C-H···Cl H-bonds.

Peptide programming of supramolecular vinylidene fluoride ferroelectric phases.

Ferroelectric structures have spontaneous macroscopic polarization that can be inverted using external electric fields and have potential applications including information storage, energy transduction, ultralow-power nanoelectronics1,2 and biomedical devices3. These functions would benefit from nanoscale control of ferroelectric structure, the ability to switch polarization with lower applied fields (low coercive field) and biocompatibility. Soft ferroelectrics based on poly(vinylidene fluoride) (PVDF)4-6 have a thermodynamically unstable ferroelectric phase in the homopolymer, complex semi-crystalline structures, and high coercive fields. Here we report on ferroelectric materials formed by water-soluble molecules containing only six VDF repeating units covalently conjugated to a tetrapeptide, with the propensity to assemble into the β-sheet structures that are ubiquitous in proteins. This led to the discovery of ribbon-shaped ferroelectric supramolecular assemblies that are thermodynamically stable with their long axes parallel to both the preferred hydrogen-bonding direction of β-sheets and the bistable polar axes of VDF hexamers. Relative to a commonly used ferroelectric copolymer, the biomolecular assemblies exhibit a coercive field that is two orders of magnitude lower, as the result of supramolecular dynamics, and a similar level of remnant polarization, despite having a peptide content of 49 wt%. Furthermore, the Curie temperature of the assemblies is about 40 °C higher than that of a copolymer containing a similar amount of VDF. This supramolecular system was created using a biologically inspired strategy that is attractive in terms of sustainability and that could lead to new functions for soft ferroelectrics.

Electric field modulated configuration and orientation of aqueous molecule chains.

Understanding how external electric fields (EFs) impact the properties of aqueous molecules is crucial for various applications in chemistry, biology, and engineering. In this paper, we present a study utilizing molecular dynamics simulation to explore how direct-current (DC) and alternative-current (AC) EFs affect hydrophobic (n-triacontane) and hydrophilic (PEG-10) oligomer chains. Through a machine learning approach, we extract a 2-dimensional free energy (FE) landscape of these molecules, revealing that electric fields modulate the FE landscape to favor stretched configurations and enhance the alignment of the chain with the electric field. Our observations indicate that DC EFs have a more prominent impact on modulation compared to AC EFs and that EFs have a stronger effect on hydrophobic chains than on hydrophilic oligomers. We analyze the orientation of water dipole moments and hydrogen bonds, finding that EFs align water molecules and induce more directional hydrogen bond networks, forming 1D water structures. This favors the stretched configuration and alignment of the studied oligomers simultaneously, as it minimizes the disruption of 1D structures. This research deepens our understanding of the mechanisms by which electric fields modulate molecular properties and could guide the broader application of EFs to control other aqueous molecules, such as proteins or biomolecules.

Prediction of Flavor Potential of Ocimum basilicum L. Side-Stream Phytoconstituents, Using Liquid Chromatography–Tandem Mass Spectrometry Analysis and In Silico Techniques

Although post-distillation side-streams of basil (Ocimum basilicum L.) pose significant economic and environmental challenges, they also bring forth new opportunities in the flavor industry. Thus, the objective of the current study was to assess the phenolic profile of basil side-stream extracts to identify key compounds and to evaluate their taste properties, using liquid chromatography–tandem mass spectrometry (LC-MS/MS) analysis, flavor prediction tools and molecular docking. In particular, 52 phytoconstituents, mainly phenolic acids, salvianolic acids, flavonoids and fatty acids derivatives, were elucidated in the side-streams of two different basil varieties (Minimum and Genovese) harvested and distilled in early and late autumn, highlighting the effect of pre-harvest factors on basil’s phenolic fingerprint. Furthermore, the results of tests undertaken using taste prediction tools showed that most of the identified compounds were very likely to taste bitter, while six of them (caffeoylferuloyltartaric acid, isoquercetin, lithospermic acid A, sagerinic acid, salvianolic acids C and F) presented a high bitterant capacity (70–90%). Moreover, according to molecular docking studies, these compounds exhibited a stronger binding affinity to the hTAS2R46 bitter receptor compared to its known agonist, strychnine. This outcome and consequently their bitterness were mainly attributed to interactions with Glu265, Thr180 and/or Trp88 through the formation of direct hydrogen bonds. Therefore, the present results provide insights into the taste profiles of basil side-streams, leading to more sustainable and innovative uses of aromatic herbs residues.

Three-dimensional alkaline earth metal-organic framework poly[[μ-aqua-aqua-bis-(μ3-carba-moyl-cyano-nitro-somethanido)barium] monohydrate] and its thermal decomposition.

In the structure of the title salt, {[Ba(μ3-C3H2N3O2)2(μ-H2O)(H2O)]·H2O} n , the barium ion and all three oxygen atoms of the water mol-ecules reside on a mirror plane. The hydrogen atoms of the bridging water and the solvate water mol-ecules are arranged across a mirror plane whereas all atoms of the monodentate aqua ligand are situated on this mirror plane. The distorted ninefold coord-ination of the Ba ions is completed with four nitroso-, two carbonyl- and three aqua-O atoms at the distances of 2.763 (3)-2.961 (4) Å and it is best described as tricapped trigonal prism. The three-dimensional framework structure is formed by face-sharing of the trigonal prisms, via μ-nitroso- and μ-aqua-O atoms, and also by the bridging coordination of the anions via carbonyl-O atoms occupying two out of the three cap positions. The solvate water mol-ecules populate the crystal channels and facilitate a set of four directional hydrogen bonds. The principal Ba-carbamoyl-cyano-nitro-somethanido linkage reveals a rare example of the inherently polar binodal six- and three-coordinated bipartite topology (three-letter notation sit). It suggests that small resonance-stabilized cyano-nitroso anions can be utilized as bridging ligands for the supra-molecular synthesis of MOF solids. Such an outcome may be anti-cipated for a broader range of hard Lewis acidic alkaline earth metal ions, which perfectly match the coordination preferences of highly nucleophilic nitroso-O atoms. Thermal analysis reveals two-stage dehydration of the title compound (383 and 473 K) followed by decomposition with release of CO2, HCN and H2O at 558 K.

Structure of an internal loop motif with three consecutive U•U mismatches from stem-loop 1 in the 3'-UTR of the SARS-CoV-2 genomic RNA.

The single-stranded RNA genome of SARS-CoV-2 is highly structured. Numerous helical stem-loop structures interrupted by mismatch motifs are present in the functionally important 5'- and 3'-UTRs. These mismatches modulate local helical geometries and feature unusual arrays of hydrogen bonding donor and acceptor groups. However, their conformational and dynamical properties cannot be directly inferred from chemical probing and are difficult to predict theoretically. A mismatch motif (SL1-motif) consisting of three consecutive U•U base pairs is located in stem-loop 1 of the 3'-UTR. We combined NMR-spectroscopy and MD-simulations to investigate its structure and dynamics. All three U•U base pairs feature two direct hydrogen bonds and are as stable as Watson-Crick A:U base pairs. Plasmodium falciparum 25S rRNA contains a triple U•U mismatch motif (Pf-motif) differing from SL1-motif only with respect to the orientation of the two closing base pairs. Interestingly, while the geometry of the outer two U•U mismatches was identical in both motifs the preferred orientation of the central U•U mismatch was different. MD simulations and potassium ion titrations revealed that the potassium ion-binding mode to the major groove is connected to the different preferred geometries of the central base pair in the two motifs.

Spectroscopic Evidence for Doubly Hydrogen-Bonded Cationic Dimers in the Solid, Liquid, and Gaseous Phases of Carboxyl-Functionalized Ionic Liquids.

Intermolecular interactions determine whether matter sticks together, gases condense into liquids, or liquids freeze into solids. The most prominent example is hydrogen bonding in water, responsible for the anomalous properties in the liquid phase and polymorphism in ice. The physical properties are also exceptional for ionic liquids (ILs), wherein a delicate balance of Coulomb interactions, hydrogen bonds, and dispersion interactions results in a broad liquid range and the vaporization of ILs as ion pairs. In this study, we show that strong, local, and directional hydrogen bonds govern the structures and arrangements in the solid, liquid, and gaseous phases of carboxyl-functionalized ILs. For that purpose, we explored the H-bonded motifs by X-ray diffraction and attenuated total reflection (ATR) infrared (IR) spectroscopy in the solid state, by ATR and transmission IR spectroscopy in the liquid phase, and by cryogenic ion vibrational predissociation spectroscopy (CIVPS) in the gaseous phase at low temperature. The analysis of the CO stretching bands reveals doubly hydrogen-bonded cationic dimers (c═c), resembling the archetype H-bond motif known for carboxylic acids. The like-charge doubly hydrogen-bonded ion pairs are present in the crystal structure of the IL, survive phase transition into the liquid state, and are still present in the gaseous phase even in (2,1) complexes wherein one counterion is removed and repulsive Coulomb interaction increased. The interpretation of the vibrational spectra is supported by quantum chemical methods. These observations have implications for the fundamental nature of the hydrogen bond between ions of like charge.

Synthon Approach in Crystal Engineering to Modulate Physicochemical Properties in Organic Salts of Chlorpropamide.

The formulation of drug with improved bioavailability is always challenging and indispensable in the field of pharmaceutics. The control of intermolecular interactions via crystal engineering approach and solid-state molecular recognition results in the formation of active drug molecules with modulated pharmacological benefits. Therefore, with the aim to improve the solubility and dissolution rate of the drug chlorpropamide (CPA), the mechanochemical liquid-assisted grinding (LAG) of the drug with several pharmaceutically accepted excipients was performed. This contributed to the discovery of six novel solid phases, namely salts, salt cocrystals and salt cocrystal hydrate─the salt of CPA with 3, 4-diaminopyridine (DAP); salt and salt cocrystal (SC) polymorph (Z″=3) with 1, 4-diazabicyclo [2.2.2] octane (DABCO); a salt, SC polymorph (Z″=9), and a SC hydrate (Z″=9) with piperazine (PIP). The formation of these salts and salt cocrystals are mainly guided by the strong hydrogen bonds with tunable strength having high electrostatic contribution. This attractive interaction brings the donor and the acceptor atoms close to each other for a facile proton transfer. Furthermore, the conformational constraints on the drug molecules, provided by the excipients via strong and directional hydrogen bonds, are quite impressive as this leads to the identification and characterization of "new conformational isomers" for the CPA molecules. The new crystalline phases exhibit enhanced intrinsic dissolution rate in comparison to that of the pure drug, the magnitude being 7, 131, and 120 folds for CPADAP, CPADABCO_II, and CPAPIP_III, respectively. Furthermore, it is interesting to note that the order of solubility is enhanced by 2.7-, 3-, and 7-fold, respectively, for the abovementioned salts. This also mirrors the trends in the magnitude of the binding energy, the higher magnitude being reflected in the lower solubility. Additionally, the in vivo experiments performed in SD rats results in the enhancement of the magnitude of the pharmacokinetic properties, when compared to the pristine drug. The concentration of the drug in CPADABCO_II and CPAPIP_III formulations exhibits 6- and 4-fold increments, respectively. Indeed, these results corroborate to the trends observed in the structural characterization, intermolecular energy calculations, solubility, and in vitro dissolution assessments.

Structural Insights into Partial Activation of the Prototypic G Protein-Coupled Adenosine A2A Receptor.

The adenosine A2A receptor (A2AAR) belongs to the rhodopsin-like G protein-coupled receptor (GPCR) family, which constitutes the largest class of GPCRs. Partial agonists show reduced efficacy as compared to physiological agonists and can even act as antagonists in the presence of a full agonist. Here, we determined an X-ray crystal structure of the partial A2AAR agonist 2-amino-6-[(1H-imidazol-2-ylmethyl)sulfanyl]-4-p-hydroxyphenyl-3,5-pyridinedicarbonitrile (LUF5834) in complex with the A2AAR construct A2A-PSB2-bRIL, stabilized in its inactive conformation and being devoid of any mutations in the ligand binding pocket. The determined high-resolution structure (2.43 Å) resolved water networks and crucial binding pocket interactions. A direct hydrogen bond of the p-hydroxy group of LUF5834 with T883.36 was observed, an amino acid that was mutated to alanine in the most frequently used A2AAR crystallization constructs thus preventing the discovery of its interactions in most of the previous A2AAR co-crystal structures. G protein dissociation studies confirmed partial agonistic activity of LUF5834 as compared to that of the full agonist N-ethylcarboxamidoadenosine (NECA). In contrast to NECA, the partial agonist was still able to bind to the receptor construct locked in its inactive conformation by an S913.39K mutation, although with an affinity lower than that at the native receptor. This could explain the compound's partial agonistic activity: while full A2AAR agonists bind exclusively to the active conformation, likely following conformational selection, partial agonists bind to active as well as inactive conformations, showing higher affinity for the active conformation. This might be a general mechanism of partial agonism also applicable to other GPCRs.

Interfacial Glucose to Regulate Hydrated Lipid Bilayer Properties: Influence of Concentrations.

A series of atomistic molecular dynamics (MD) simulations were carried out with a hydrated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer with the variation of glucose concentrations from 0 to 30 wt % in the presence of 0.3 M NaCl. The study suggested that although the thickness of the lipid bilayer dropped significantly with the increase in glucose concentration, it expanded laterally at high glucose levels due to the intercalation of glucose between the headgroups of adjacent lipids. We adopted the surface assessment via the grid evaluation method to compute the deviation of the bilayer's key structural features for the different amounts of glucose present. This suggested that the accumulation of glucose molecules near the headgroups influences the local lipid bilayer undulation and crimping of the lipid tails. We find that the area compressibility modulus increases with the glucose level, causing enhanced bilayer rigidity arising from the slow lateral diffusion of lipids. The restricted lipid motion at high glucose concentrations controls the sustainability of the curved bilayer surface. Calculations revealed that certain orientations of of interfacial glucose with the of lipid headgroups are preferred, which helps the glucose to form direct hydrogen bonds (HBs) with the lipid headgroups. Such lipid-glucose (LG) HBs relax slowly at low glucose concentrations and exhibit a higher lifetime, whereas fast structural relaxation of LG HBs with a shorter lifetime was noticed at a higher glucose level. In contrast, lipid-water (LW) HBs exhibited a higher lifetime at a higher glucose level, which gradually decreased with the glucose level lowering. The study interprets that the glucose concentration-driven LW and LG interactions are mutually inclusive. Our detailed analysis will exemplify small saccharide concentration-driven membrane stabilizing efficiency, which is, in general, helpful for drug delivery study.

Synthesis and Crystal Structures of Two Crystalline Silicic Acids: Hydrated H-Apophyllite, H16Si16O40 • 8–10 H2O and H-Carletonite, H32Si64O144

Hydrated H-Apophyllite (HH-Apo) and H-carletonite (H-Car) were synthesized at 0 °C by leaching an apophyllite and a carletonite single crystal in a large surplus of 1.2 molar hydrochloric acid. The XRD powder patterns of HH-Apo and H-Car were indexed with space group symmetries of P4/ncc and I4/mcm and lattice parameters of a = 8.4872(2) Å, c = 16.8684(8) Å and a = 13.8972(3) Å, c = 20.4677(21) Å, respectively. The crystal structures were solved based on model building of the structures of the precursors and a physico-chemical characterization. Rietveld structure refinements confirmed the structure models. HH-Apo and H-Car are among the very few crystalline silicic acids whose structures have been determined and confirmed based on a structure refinement. The structure of HH-Apo contains thin silicate monolayers that can be regarded as constructed by rings of interconnected [SiO3OH] tetrahedra which form a puckered silicate layer. A sheet of water molecules is intercalated between the silicate layers. There are no direct hydrogen bonds between the silanol groups, but there are hydrogen bonds of different strengths between the terminal O atoms of the silicate layers and the intercalated water molecules. The 1H MAS NMR spectrum presents a strong signal at 4.9 ppm related to the aforementioned bonds and interactions between the water molecules, as well as a small signal at 22.5 ppm corresponding to an extremely strong hydrogen bond with d(O...O) ≈ 2.2 Å. The structure of H-Car is free of structural water and consists exclusively of microporous silicate double-layers with 4-connected [SiO4] and 3-connected [SiO3OH] tetrahedra in a ratio of 1:1 and a thickness of 9.2 Å. Neighboring layers are connected to each other by medium–strong hydrogen bonds with O...O distances of 2.56 Å. The structure of HH-Apo decays within several hours while H-Car is stable. A topotactic condensation reaction applied to H-Car forms an irregularly condensed silicate which still contains the layers in a distorted form as building blocks.

Dispersion Control over Molecule Cohesion: Exploiting and Dissecting the Tipping Power of Aromatic Rings.

ConspectusWe have learned over the past years how London dispersion forces can be effectively used to influence or even qualitatively tip the structure of aggregates and the conformation of single molecules. This happens despite the fact that single dispersion contacts are much weaker than competing polar forces. It is a classical case of strength by numbers, with the importance of London dispersion forces scaling with the system size. Knowledge about the tipping points, however difficult to attain, is necessary for a rational design of intermolecular forces. One requires a careful assessment of the competing interactions, either by sensitive spectroscopic techniques for the study of the isolated molecules and aggregates or by theoretical approaches. Of particular interest are the systems close to the tipping point, when dispersion interactions barely outweigh or approach the strength of the other interactions. Such subtle cases are important milestones for a scale-up to realistic multi-interaction situations encountered in the fields of life and materials science. In searching for examples that provide ideal competing interactions in complexes and small clusters, aromatic systems can offer a diverse set of molecules with a variation of dispersion and electrostatic forces that control the dominant and peripheral interactions. Our combined spectroscopic and theoretical investigations provide valuable insights into the balance of intermolecular forces because they typically allow us to switch the aromatic substituent on and off. High-resolution rotational spectroscopy serves as a benchmark for molecular structures, as correct calculations should be based on correct geometries. When discussing the competition with other noncovalent interactions, obvious competitors are directional hydrogen bonds. As a second counterweight to aryl interactions, we will discuss aurophilic/metallophilic interactions, which also have a strong stabilization with a small number of atoms involved. Vibrational spectroscopy is most sensitive to interactions of light atoms, and the competition of OH hydrogen bonds with dispersion forces in a molecular aggregate can be judged well by the OH stretching frequency. Experiments in the gas phase are ideal for gauging the accuracy of quantum chemical predictions free of solvent forces. A tight collaboration utilizing these three methods allows experiment vs experiment vs theory benchmarking of the overall influence of dispersion in molecular structures and energetics.

Liquid Structure of Ionic Liquids with [NTf2]- Anions, Derived from Neutron Scattering.

The liquid structure of three common ionic liquids (ILs) was investigated by neutron scattering for the first time. The ILs were based on the bis(trifluoromethanesulfonyl)imide anion, abbreviated in the literature as [NTf2]- or [TFSI]-, and on the following cations: 1-ethyl-3-methylimidazolium, [C2mim]+; 1-decyl-3-methylimidazolium, [C10mim]+; and trihexyl(tetradecyl)phosphonium, [P666,14]+. Comparative analysis of the three ILs confirmed increased size of nonpolar nanodomains with increasing bulk of alkyl chains. It also sheds light on the cation-anion interactions, providing experimental insight into strength, directionality, and angle of hydrogen bonds between protons on the imidazolium ring, as well as H-C-P protons in [P666,14]+, to oxygen and nitrogen atoms in the [NTf2]-. The new Dissolve data analysis package enabled, for the first time, the analysis of neutron scattering data of ILs with long alkyl chains, in particular, of [P666,14][NTf2]. Results generated with Dissolve were validated by comparing outputs from three different models, starting from three different sets of cation charges, for each of the three ILs, which gave convergent outcomes. Finally, a modified method for the synthesis of perdeuterated [P666,14][NTf2] has been reported, with the aim of reporting a complete set of synthetic and data processing approaches, laying robust foundations that enable the study of the phosphonium ILs family by neutron scattering.

SERS-Based Hydrogen Bonding Induction Strategy for Gaseous Acetic Acid Capture and Detection.

Surface-enhanced Raman scattering (SERS) can overcome the existing technological limitations, such as complex processes and harsh conditions in gaseous small-molecule detection, and advance the development of real-time gas sensing at room temperature. In this study, a SERS-based hydrogen bonding induction strategy for capturing and sensing gaseous acetic acid is proposed for the detection demands of gaseous acetic acid. This addresses the challenges of low adsorption of gaseous small molecules on SERS substrates and small Raman scattering cross sections and enables the first SERS-based detection of gaseous acetic acid by a portable Raman spectrometer. To provide abundant hydrogen bond donors and acceptors, 4-mercaptobenzoic acid (4-MBA) was used as a ligand molecule modified on the SERS substrate. Furthermore, a sensing chip with a low relative standard deviation (RSD) of 4.15% was constructed, ensuring highly sensitive and reliable detection. The hydrogen bond-induced acetic acid trapping was confirmed by experimental spectroscopy and density functional theory (DFT). In addition, to achieve superior accuracy compared to conventional methods, an innovative analytical method based on direct response hydrogen bond formation (IO-H/Iref) was proposed, enabling the detection of gaseous acetic acid at concentrations as low as 60 ppb. The strategy demonstrated a superior anti-interference capability in simulated breath and wine detection systems. Moreover, the high reusability of the chip highlights the significant potential for real-time sensing of gaseous acetic acid.

Extractive separation of citral and limonene with quaternary Ammonium/Alkanediol deep eutectic Solvents: An experimental and mechanistic study

As an aldehyde derivative of monoterpene, citral is the main oxyterpene in various botanical essential oils which has been widely applied in food, cosmetics and medicines. The separation of oxyterpenes from terpenes (deterpenation) improves its stability and quality, which is an essential step for production of citral with high market value. Herein, the extractive separation of citral and limonene using deep eutectic solvents (DESs) of quaternary ammonium/alkanediol was explored. Influence of DESs components, including different quaternary ammonium salts as hydrogen bond acceptors (HBAs), various alkanediols as hydrogen bond donors (HBDs) and the changing of HBA to HBD ratios on citral extraction were studied. Distribution coefficient, selectivity and extraction yield of the citral of these DESs were experimentally evaluated. Among the HBAs investigated, tetrabutylammonium bromide (TBABr) was determined to be the suitable one, since halide Br- was better than Cl-, and quaternary ammonium cations with longer alkyl chain length was preferable. Meanwhile, 1,2-propanediol (1,2-PDO) outperformed other alkanediols, and higher HBD contents in DESs facilitated the separation. TBABr/1,2-PDO (molar ratio 1:10) exhibited the best performance, with citral distribution coefficient 1.28, selectivity 13.65 and extraction yield 64.26%. The type and strength of molecular interactions between citral solute and DESs were identified by employing quantum chemistry calculation and molecular dynamic simulations. The performance difference of these DESs can be ascribed to the difference of the direct hydrogen bond between the α-OH of alkanediols and the O from citral carbonyl group during extraction. The mechanisms exploration provides insights for rational fine-tuning the novel DESs with better deterpenation performance.

Structure of Amyloid Peptide Ribbons Characterized by Electron Microscopy, Atomic Force Microscopy, and Solid-State Nuclear Magnetic Resonance.

Polypeptides often self-assemble to form amyloid fibrils, which contain cross-β structural motifs and are typically 5-15 nm in width and micrometers in length. In many cases, short segments of longer amyloid-forming protein or peptide sequences also form cross-β assemblies but with distinctive ribbon-like morphologies that are characterized by a well-defined thickness (on the order of 5 nm) in one lateral dimension and a variable width (typically 10-100 nm) in the other. Here, we use a novel combination of data from solid-state nuclear magnetic resonance (ssNMR), dark-field transmission electron microscopy (TEM), atomic force microscopy (AFM), and cryogenic electron microscopy (cryoEM) to investigate the structures within amyloid ribbons formed by residues 14-23 and residues 11-25 of the Alzheimer's disease-associated amyloid-β peptide (Aβ14-23 and Aβ11-25). The ssNMR data indicate antiparallel β-sheets with specific registries of intermolecular hydrogen bonds. Mass-per-area values are derived from dark-field TEM data. The ribbon thickness is determined from AFM images. For Aβ14-23 ribbons, averaged cryoEM images show a periodic spacing of β-sheets. The combined data support structures in which the amyloid ribbon growth direction is the direction of intermolecular hydrogen bonds between β-strands, the ribbon thickness corresponds to the width of one β-sheet (i.e., approximately the length of one molecule), and the variable ribbon width is a variable multiple of the thickness of one β-sheet (i.e., a multiple of the repeat distance in a stack of β-sheets). This architecture for a cross-β assembly may generally exist within amyloid ribbons.

Electrostatic coupling and water bridging in adsorption hierarchy of biomolecules at water–clay interfaces

Clay minerals are implicated in the retention of biomolecules within organic matter in many soil environments. Spectroscopic studies have proposed several mechanisms for biomolecule adsorption on clays. Here, we employ molecular dynamics simulations to investigate these mechanisms in hydrated adsorbate conformations of montmorillonite, a smectite-type clay, with ten biomolecules of varying chemistry and structure, including sugars related to cellulose and hemicellulose, lignin-related phenolic acid, and amino acids with different functional groups. Our molecular modeling captures biomolecule-clay and biomolecule-biomolecule interactions that dictate selectivity and competition in adsorption retention and interlayer nanopore trapping, which we determine experimentally by NMR and X-ray diffraction, respectively. Specific adsorbate structures are important in facilitating the electrostatic attraction and Van der Waals energies underlying the hierarchy in biomolecule adsorption. Stabilized by a network of direct and water-bridged hydrogen bonds, favorable electrostatic interactions drive this hierarchy whereby amino acids with positively charged side chains are preferentially adsorbed on the negatively charged clay surface compared to the sugars and carboxylate-rich aromatics and amino acids. With divalent metal cations, our model adsorbate conformations illustrate hydrated metal cation bridging of carboxylate-containing biomolecules to the clay surface, thus explaining divalent cation-promoted adsorption from our experimental data. Adsorption experiments with a mixture of biomolecules reveal selective inhibition in biomolecule adsorption, which our molecular modeling attributes to electrostatic biomolecule-biomolecule pairing that is more energetically favorable than the biomolecule-clay complex. In sum, our findings highlight chemical and structural features that can inform hypotheses for predicting biomolecule adsorption at water-clay interfaces.

Hydration Waters Make Up for the Missing Third Hydrogen Bond in the A·T Base Pair.

Base pairing complementarity is central to DNA function. G·C and A·T pair specificity is thought to originate from the different number of hydrogen bonds the pairs make. Quantifying how many hydrogen bonds exist can be difficult because water molecules in the surrounding can make up for or disrupt direct hydrogen bonds, and the hydration structures around A·T and G·C pairs on duplex DNA are distinct. Large-scale computer simulations have been used here to create a detailed map for the hydration structure on A·T and G·C base pairs in water. The contributions of specific hydration waters to the free energy of each of the hydrogen bonds in the A·T and G·C pairs were computed. Using the equilibrium fractions of hydrated versus unhydrated states from the hydration profiles, the impact of specific bound waters on each hydrogen bond can be uniquely quantified using a thermodynamic construction. The findings suggest that hydration water in the minor groove of an A·T pair can provide up to about 2 kcal/mol of free energy advantage, effectively making up for the missing third hydrogen bond in the A·T pair compared to G·C, rendering the intrinsic thermodynamic stability of the A·T pair almost synonymous with G·C.