Hydrogen-bonded Structure Research Articles

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.

Heterochiral coupling to bilateral β-turn structured azapeptides bearing two remote chiral centers

Enantioselective synthesis governed by chiral catalysts has been extensively developed, but that without any chiral auxiliaries or chiral catalysts is rare, particularly when remote stereogenic centers are involved. Here we report an enantioselectivity of heterochiral coupling in the one-pot reaction of racemic hydrazides with achiral 1,4-bis(isothiocyanine)benzene, yielding preferentially the heterochiral bilateral azapeptides over the homochiral ones. Despite bearing two hydrogen-bonded β-turn structures that allow intramolecular chiral transfer, the bilateral azapeptide products have two chiral centers separated by 14 atoms or 15 bonds, which prevent the direct intramolecular asymmetric communication between the two chiral centers. Interestingly, the heterochiral azapeptides feature intermolecular hydrogen bonding stacking between homochiral β-turns to form a superstructure of alternative M- and P-helices in the crystals. In contrast, the homochiral azapeptide counterparts adopt a β-sheet-like structure, which is less favorable compared to the helical-like superstructure from heterochiral azapeptides, accounting for the favored heterochiral coupling of the one-pot reaction. This work demonstrates enantioselective synthesis involving distant chiral centers through the formation of biomimetic superstructures, opening up new possibilities for the regulation of enantioselectivity.

Self-aggregation and microhydration mechanisms of monoethanolamine: Far-infrared identification of large-amplitude hydrogen bond libration.

The strong tendency for self-aggregation together with an intriguing mechanism for the microhydration of monoethanolamine (MEA) have been explored by low-temperature far-infrared cluster spectroscopy in doped neon "quantum" matrices at 4K complemented by high-level quantum chemical modeling. In addition to the assignment of new mid-infrared perturbed intramolecular transitions, a distinct far-infrared transition is unambiguously assigned to the concerted large-amplitude hydrogen bond librational motion of the MEA homodimer. This observation confirms a global "head-to-head" intermolecular potential energy minimum associated with the formation of a compact doubly intermolecular OH⋯N hydrogen-bonded cyclic structure, where both monomeric intramolecular OH⋯N hydrogen bonds are broken upon complexation. By means of relative mixing ratio dependencies, dedicated annealing procedures, and selective complexation between MEA and isotopic H216O and H218O samples, distinct far-infrared transitions associated with large-amplitude intra-molecular hindered OH torsional motion and inter-molecular H2O librational (hindered c-type overall rotational) motion of the MEA monohydrate are furthermore assigned unambiguously for the first time. These spectroscopic observations reveal an intriguing metastable conformation, where H2O acts as a OH⋯O hydrogen bond donor to the hydroxy group instead of the amino group of MEA upon microhydration in the cryogenic neon environment, where the microhydration strengthens the intramolecular OH⋯N hydrogen bond of MEA due to hydrogen bond cooperativity.

Molecular Association and Reactivity of the Pyridine Dimer Cation.

A recent experimental report has identified the formation of the C-N hemibonded pyridine dimer cation following vacuum ultraviolet near-threshold photoionization [J. Phys. Chem. Lett., 2021, 12, 4936-4943]. Herein, the dynamics and consequent reactivity of the pyridine dimer cation were investigated employing Born-Oppenheimer molecular dynamics (BOMD) simulations. An antiparallel π-stacked pyridine dimer in the neutral ground state is transformed into a noncovalently interacting C-H···N hydrogen-bonded structure which can lead to proton transfer in the cationic state. Additionally, C-N- and N-N-bonded adducts were formed in the cationic state. Further, metastable C-H···H-C-bonded cationic species was observed, which rearranged to an N-N bonded adduct. In contrast to the experimental observation, migration of the proton to the α position was not observed in the C-N bonded adduct owing to a high barrier of about 2 eV. The observed trends in the molecular association, proton transfer, and the formation of C-N and N-N bonded adducts are a consequence of the roaming dynamics of one pyridine moiety over the other in the cationic state.

Molecular Dynamics Study of Hydrogen Bond Structure and Tensile Strength for Hydrated Amorphous Cellulose.

Molecular dynamics (MD) simulations were conducted to investigate the hydrogen-bond (H-bond) structure and its impact on the tensile strength of hydrated amorphous cellulose. The study identifies a stable intramolecular H-bond between the hydroxyl group at position 3 and the ether oxygen at position 5 (OH3···O5). Intermolecularly, the hydroxyl groups at positions 2 (OH2) and 6 (OH6) form stable H-bonds. Young's modulus, maximum tensile strength, and corresponding strain were calculated as functions of moisture content, while the H-bond network, water cluster formation, and cellulose chain orientation during tensile simulations were analyzed to elucidate mechanical properties. The substitution effect of cellulose on Young's modulus is also examined, revealing that the substitution of OH3 for a hydrophobic group minimally affects Young's modulus, but substitutions at OH2 and OH6 significantly reduce tensile strength due to their roles as key intermolecular H-bond donor sites.

Fast Collective Hydrogen-Bond Dynamics in HexafluoroisopropanolRelated to its Chemical Activity.

Using fluorinated mono-alcohols, in particular hexafluoro-isopropanol (HFIP), as a solvent can enhance chemical reaction rates in a spectacular manner. Previous work has shown evidence that this enhancement is related to the hydrogen-bond structure of these liquids. Here, we investigate the hydrogen-bond dynamics of HFIP and compare it to thatof its non-fluorinated analog, isopropanol. Ultrafast infrared spectroscopy show that the dynamics of individual hydrogen-bonds is about twice as slow in HFIP as in isopropanol. Surprisingly, from dielectric spectroscopy we find the opposite behavior for the dynamics of hydrogen-bonded clusters: collective rearrangements are3 times faster in HFIP than in isopropanol. This difference indicates that the hydrogen-bonded clusters in HFIP are smaller than in isopropanol. The differences in cluster size can be traced to changes in the hydrogen-bond donor and acceptor strengths upon fluorination. The smaller cluster size canboostreaction rates in HFIP by increasing the concentration of reactive, terminal OH-groups of the clusters, whereas the fast collective dynamics can increase the rate of formation of hydrogen bonds with the reactants. The longer lifetime of the individual hydrogen bonds in HFIP can enhance the stability of the hydrogen-bonded clusters, and so increase the probability of reactant-solvent hydrogen bonding.

Constrained nuclear-electronic orbital QM/MM approach for simulating complex systems with quantum nuclear delocalization effects incorporated

The hybrid quantum mechanics/molecular mechanics (QM/MM) approach, which combines the accuracy of QM methods with the efficiency of MM methods, is widely used in the study of complex systems. However, past QM/MM implementations often neglect or face challenges in addressing nuclear quantum effects, despite their crucial role in many key chemical and biological processes. Recently, our group developed the constrained nuclear-electronic orbital (CNEO) theory, a cost-efficient approach that accurately addresses nuclear quantum effects, especially quantum nuclear delocalization effects. In this work, we integrate CNEO with the QM/MM approach through the electrostatic embedding scheme and apply the resulting CNEO QM/MM to two hydrogen-bonded complexes. We find that both solvation effects and nuclear quantum effects significantly impact hydrogen bond structures and dynamics. Notably, in the glutamic acid–glutamate complex, which mimics a common low barrier hydrogen bond in biological systems, CNEO QM/MM accurately predicts nearly equal proton sharing between the two residues. With an accurate description of both quantum nuclear delocalization effects and environmental effects, CNEO QM/MM is a promising new approach for simulating complex chemical and biological systems.

Temperature-Driven Stopped-Flow Experiments for Investigating the Initial Aggregation of the α-Synuclein Amyloid Protein, Focusing on Active and Inactive Phases.

The primary objective of this research is to further examine the events occurring during the active or burst phase by focusing on the aggregation of the Syn amyloid protein. Regarding this aspect, it was initially conducted rapid temperature variations using stopped-flow spectrometry and tyrosyl group fluorescence emission detection, within the initial 500 milliseconds in buffered Syn solutions at pH 7, exploring various temperature ranges to investigate protein aggregation. The results obtained were contrasted with results obtained for the Nα-acetyl-L-tyrosinamide (NAYA) parent compound in the same conditions. The utilization of the NAYA compound is suitable as it mimics the peptide bonds in proteins and contains a tyrosyl group resembling the four tyrosyl groups found in the Syn protein structure (the protein has no tryptophan residues). Furthermore, the NAYA compound adopts an intramolecularly hydrogen-bonded structure even in an aqueous solution, similar to the interactions seen in the hydrophilic face of β-sheets. Additionally, the Syn protein system can exhibit the presence of β-sheets as a result of the existence of very low abundant Syn amyloid precursor forms or nuclei during the initial stages of the protein aggregation. Thus, a relationship is present between the molecular processes in the NAYA and Syn protein systems, making the NAYA's application crucial in this research. Moreover, to aid in understanding the results, it was also compared the events during the quiescent or inactive phase (30-500 milliseconds) with those in the burst phase (up to 10 milliseconds) using stopped-flow spectrometry conditions. Steady-state measurements were beneficial in comprehending the occurrences in both the quiescent and burst phases examined. Although protein aggregation and disaggregation were observed during the quiescent phase, determining these processes in the burst phase was more challenging. In the latter case, the aggregation of the Syn protein is actually initiated by the interaction of the intrinsically disordered Syn monomers. In the quiescent phase, first-order rate constants were measured and analysis showed that Syn protein aggregation and disaggregation occur simultaneously. At lower temperatures, early protein disaggregation outweighs protein aggregation whereas at higher temperatures protein disaggregation and aggregation are rather similar. It is also need to highlight that the burst phase, while distinct from the quiescent phase, can be considered as a possible structural phase for obtaining details about the aggregation of this specific disordered protein in solution on a very short timescale.

Hydration level dependent dynamics of supercooled water confined in water harvester metal organic framework-303

Crystallization of bulk water cannot be avoided in the temperature range 150–235 K, which is known as no man’s land in the literature focused on the dynamics of the supercooled water. Dynamics of the supercooled water in this temperature range can be accessed by confining water in the nanopores. In the present study, we have investigated dynamics of the supercooled water confined in the pore network of a water harvester metal organic framework (MOF-303) at two different hydration levels (63.4 and 37.0 %). The framework was chosen as a confining host, because the hydrogen bonded–structure of the confined water molecules during adsorption–desorption (i.e. at different hydration levels) is explicitly known. All the relaxation processes observed in the supercooled region are comparatively slower than the bulk–like water dynamics due to the modified hydrogen-bonded structure and the interactions with the pore walls. The confined water, not directly interacting with the pore walls, undergoes a liquid-to-liquid transition (Ts) at ∼186 K followed by its glassy freezing with glass transition temperature Tg ∼ 108 K which is consistent with high density liquid phase of amorphous ice. Both Ts as well as Tg are observed to increase with the decrease in hydration level. It confirmed that the evolved hydrogen-bonded network and the interactions with the pore walls play deterministic roles in the glassy freezing of the confined water. No crystallization as well as the glassy freezing of the water molecules directly interacting with the pore walls through the hydrogen bonding is observed at both the hydration level. The observed relaxation processes corresponding to these molecules in the supercooled region can be attributed to rearrangement of their hydrogen-bonded structure.

Molecular dynamics simulations of hydrogen-bonded network structures of polybenzoxazines in the gas phase and aqueous solution

The crucial role of the amine functional group at the Mannich bridge of polybenzoxazines (PBZs) has been reported to be responsible for their hydrogen-bonded network structures. However, they have not been thoroughly studied in an aqueous solution and at the atomistic level. In this study, molecular dynamics simulations were applied to investigate the formation of hydrogen bond interactions of PBZs prepared from bisphenol A/methylamine (m-PBZ), bisphenol A/aniline-based (a-PBZ), and bisphenol A/2-(methylamino)ethylamine (e-PBZ). Based on the simulation results, the hydrogen-bonded network structures of the PBZs interfered with water molecules, leading to less compaction of the PBZ structure in the aqueous solution. The hydrogen bonding species of the m-PBZ and a-PBZ structures consisted of the –OH...N(Mannich) and –OH...O intramolecular interactions. However, for e-PBZ, the –OH...O species was not present, but the 2-(ethylamino)ethylamine substituent formed more hydrogen bonding species than those of m-PBZ and a-PBZ. Additionally, the intermolecular hydrogen bond interactions of the PBZs and water molecules were not detected in any of the aqueous solution simulations.

X-ray diffraction and quasielastic neutron scattering studies of the structure and dynamic properties of water confined in ordered microporous carbon pores

The structure and dynamic properties of capillary-condensed water confined in ordered microporous carbon (OMC) of pores diameter 18.7 Å are investigated over a temperature range of 200–300 K by adsorption/desorption isotherms, X-ray diffraction (XRD), and quasielastic neutron scattering (QENS). The nitrogen adsorption/desorption isotherm of OMC pores at 77 K exhibits an I-type pattern. The water adsorption/desorption isotherm of OMC pores at 298 K is of type V. The XRD data on water confined in OMC reveal that the tetrahedral network structure of water is perturbed from the bulk water structure, but not to such an extent as found for water confined in MCM-41 and Ph-PMO previously reported. With decreasing the temperature, the ∼2.8 Å peak shifts to shorter distances, while the second-neighbor H2O– H2O interaction distances gradually increase from 3.95 Å and 4.49 Å to 4.43 Å and 4.84 Å, indicating a tendency to form a more tetrahedral-like hydrogen-bonded water structure at subzero temperatures. Below 230 K, the hexagonal ice Ih was partially formed in OMC pores. The QENS spectra were analyzed using a jump-diffusion model to translate water molecules. The translational diffusion of water molecules in OMC pores is comparable to that of bulk water at 300 K and higher than that in MCM-41, and the mobility slows as the temperature decreases. The elastic incoherent structure factor (EISF) analysis found evidence for immobile and mobile fractions of confined water. The mobile fraction exhibited jump diffusion, with a jump length consistent with a sphere of confinement radius of 4–8 Å. The results obtained in the present work are compared with those reported for MCM-41 with a hydrophilic interface and Ph-PMO with an amphiphilic interface, and the influence of interface effect on local structure and dynamic properties of confined water is discussed.

Rapid formation of carbon dioxide hydrate governed by the natural nano-clay for effective carbon dioxide capture

Gas hydrate can separate and capture enormous carbon dioxide (CO2) only using water cages. Capturing CO2 in hydrate form is viewed as a green and effective technology to reduce the global CO2 emission. However, the sluggish kinetics and high cost of kinetics promotors of CO2 hydrate formation limited the application of hydrate-based CO2 capture technology. Here, we used the nano-clay prepared by cheap natural clay to promote the formation kinetics of CO2 hydrate. At the low concentration range, the formation period of CO2 hydrate in the two-dimensional nano-clay dispersion was significantly shorter than that of the one-dimensional nano-clay dispersion. The induction time (5 min) obtained in vermiculite nanoflakes dispersion was shorter than most solid promotors of CO2 hydrate formation kinetics in reported works. Besides, we found that the water molecules near the negatively charged two-dimensional nano-clay surface were more likely to form the cage-like structure than those around the one-dimensional nano-clay surface. The similar hydrogen-bonded structure of the cage-like water with CO2 hydrate made them favorable for the CO2 hydrate formation. These results shed light on the design of the effective kinetics promotors of CO2 hydrate and contribute to develop the hydrate-based CO2 capture technologies.

High proton conductivity of sulfonate-amine ionic HOFs and enhancement of SPEEK composite membranes.

Hydrogen-bonded organic frameworks (HOFs) are crystalline materials assembled by intermolecular hydrogen-bonding interactions, and their hydrogen-bonding structures are effective pathways for proton transport. Herein, we synthesize iHOF-45 using 4,4'-diaminodiphenylmethane and 1,3,6,8-pyrenetetrasulfonicacid sodium salt with 2D hydrogen-bonding networks. The introduction of ionic bond based on the weak hydrogen-bonding force was employed to enhance the stability of ionic HOFs (iHOFs). Thermal analyses demonstrated that iHOF-45 exhibited excellent thermal stability up to 332 °C. The proton conductivity of iHOF-45 was evaluated, demonstrating a notable increase with rising temperature and RH. At 100 °C and 98% RH, the conductivity reached 5.25 × 10-3 S cm-1. The activation energy (Ea) of iHOF-45 was calculated to be 0.281 eV for 98% RH, and the proton conduction was attributed to the Grotthuss mechanism, whereby the protons were transported in 2D hydrogen-bonding networks. Moreover, iHOF-45 was doped into SPEEK to prepare composite membranes, the proton conductivity of the 15%-iHOF-45/SPEEK membrane reached 9.52 × 10-2 S cm-1 at 80 °C and 98% RH, representing a 45.1% increase over that of the SPEEK. This suggests that doping enhances the proton conductivity of SPEEK and providing a reference for the development of high proton conductivity materials.

Magnetic field modulation of confined water structure and transport in nanochannel

As a simple model of aquaporins, one-dimensional confined water in nanochannels, especially carbon nanotubes (CNTs), has attracted much attention due to its unique structure and rapid transport. The influence of external fields such as pressure, heat, electric field, and terahertz electromagnetic wave on confined water in CNTs has been widely studied. Magnetic field plays an important role in the regulation of water transport, but its research is limited at present. Therefore, in order to fill this gap, the effects of magnetic field with different strengths and directions on the structure and transport property of confined water in CNT were studied by molecular dynamics simulation. Simulation results showed that the magnetic field increased the number of hydrogen bonds by 1.10 % and accelerated the turnover frequency of the confined water (i.e. flipping interval decreased by 36.84 %), finally leading to a decrease in the water flow rate by 16.83 %. The effect of adjusting the magnetic field strength and direction on the hydrogen bond structure of confined water was more obvious. The results will help to understand the effect of magnetic field on confined water and provide guidance for the design of magnetic field regulation in water transport.

Molecular insights into the formation of carbon dioxide hydrates on the external surface of sodium montmorillonite in the presence of various types of organic matters

To address the urgent challenge of global climate change due to the greenhouse effect resulting from increasing carbon dioxide (CO2) emissions, viable technologies for geological CO2 storage must be developed. Of such technologies, CO2 hydrates holds significant promise for CO2 storage in seabed sediments, which typically contain clay minerals and organic matter (OM). Thus, investigating the structure of clay mineral interfaces and their interactions with OM is crucial for understanding the nucleation and growth of CO2 hydrate in seabed sediments. In this study, molecular dynamics simulations were used to investigate CO2 hydrate formation on the external surface of sodium montmorillonite (Na-Mnt) in the presence of various types of OM. The results show that the Na-Mnt surface adsorbed certain numbers of sodium ions (Na+) and OM molecules. The hydration of Na + disrupted of the hydrogen bond structure of CO2 hydrates, while hydrogen bonds that formed between OM and H2O molecules hindered CO2 hydrate formation. Consequently, CO2 hydrates predominantly formed in the bulk-like solution away from the Na-Mnt. However, the electrostatic interaction between the carboxyl groups of OM and Na+ mitigated the inhibitory effect of Na+ on CO2 hydrate formation. Over all, these findings can serve as a fundamental theoretical basis for understanding the formation and occurrence characteristics of CO2 hydrates in seabed sediments with a rich Mnt content. Such understanding will help to advance the development of CO2 storage technologies utilizing CO2 hydrates in seabed sediments.

An effective strategy to enhance phosphoric acid retention and proton conductivity stability: Construction of proton transfer channels with starch rather than H3PO4

To enhance the phosphoric acid (PA) retention as well as maintain high proton conductivity of phosphoric acid doped proton exchange membranes at high temperature, we successfully design a series of phosphoric acid doped biobased composite membranes by incorporation of starch and graphene oxide (GO) into poly arylene ether ketones (PAEK). Proton transfer channels should be mainly built through dense hydrogen bonds formed from massive oxygen-containing groups of starch mainchain, which is confirmed by Molecular dynamics (MD) simulation, FT-IR and XRD analysis. The dense hydrogen-bond structure could construct fast proton transfer channels with extreme low doping level (0.00484 molH3PO4). The excellent PA retention properties with almost unchanged proton conductivity at high temperature (200 °C) for 600 min indicates that PA molecules are firmly fixed into membranes. Thus, in this study, we suggest a novel strategy for stablizing proton conductivity at high temperature and improving PA retention properties of PA doped membranes, which is building dense hydrogen-bond structure with low PA doping level.Based on the results in this study and the Grotthuss proton transfer mechanism, dense hydrogen-bonds from oxygen-containing groups in polymer backbones should be more stable than hydrogen-bonds from massive H3PO4 molecules with high acid doping levels to promote proton conduction.

Effects of hydrophilic groups of polymer on change in hydrogen-bonding structure of water in hydrogels during dehydration

To investigate the effects of polymer hydrophilicity on hydrogen-bonding structures of water in hydrogels, differential scanning calorimetry and X-ray diffraction measurements were performed. The results show that the amount of intermediate water in polyacrylamide (PAA) hydrogel is about 12% smaller than that in poly-N,N’-dimethylacrylamide (PDMAA) hydrogel. Furthermore, it was found that the bound water in PAA hydrogel primarily exists around the surface of the polymer bundles, whereas that in PDMAA hydrogel acts as a crosslinker between polymer chains. These results suggest that the polymer hydrophilicity is an important factor for dehydration and water absorption in hydrogels.

A polyurea capturing both high strength and rapid self-healing tailored for intelligent barrier anti-corrosion system

The long-term repair of organic coatings in underwater environments is hindered by microcracks and their poor healing performance. In this study, a high-strength and rapidly self-healing polyurea (PU3) coating that combines asymmetric dense stacking of supramolecular units with mismatched rigid and flexible polymer chains was developed. By exploiting the interaction between a 2D sheet-like Ti3C2TX MXene and finely tailored hydrogen-bonded structures of PU3, a smart biomimetic anticorrosion composite coating (PU3-1.0 wt% MXene) was produced. This coating achieved rapid (15 s), specific, and repeatable in situ repair underwater when exposed to near infrared laser light. Electrochemical tests confirmed its excellent anticorrosion capability.

Switched symmetric vibration SRS of −CxH2 by hydrogen bonding regulating conformations of aqueous NPA solution

Molecular conformation is an important characteristic feature of chemistry and physics, which exists in organic molecules. Based on the hydrogen bonding (HB) regulating conformations, we proposed a scheme to switch the stimulated Raman scattering peak from the symmetric vibration mode of −CαH2 (2878 cm−1) to that of −CβH2 (2937 cm−1) of n-propanol (NPA) aqueous solution with a volume fraction of 0.55. The dominant association structure can be converted from NPA–NPA to NPA–H2O by the HB network between H2O and NPA, and the HB structures were investigated through density functional theory calculations. The changes in intramolecular vibrational modes have effect on the relative abundances of NPA molecules by intermolecular HBs. This study can be extended to explore other organic molecular conformations in mixing solutions.

Quasi-one-dimensional hydrogen bonding in nanoconfined ice

The Bernal-Fowler ice rules stipulate that each water molecule in an ice crystal should form four hydrogen bonds. However, in extreme or constrained conditions, the arrangement of water molecules deviates from conventional ice rules, resulting in properties significantly different from bulk water. In this study, we employ machine learning-driven first-principles simulations to identify a new stabilization mechanism in nanoconfined ice phases. Instead of forming four hydrogen bonds, nanoconfined crystalline ice can form a quasi-one-dimensional hydrogen-bonded structure that exhibits only two hydrogen bonds per water molecule. These structures consist of strongly hydrogen-bonded linear chains of water molecules that zig-zag along one dimension, stabilized by van der Waals interactions that stack these chains along the other dimension. The unusual interplay of hydrogen bonding and van der Waals interactions in nanoconfined ice results in atypical proton behavior such as potential ferroelectric behavior, low dielectric response, and long-range proton dynamics.