Orientation Of Hydrogen Bonds Research Articles

Taming Molecular Folding: Anion-Templated Foldamers with Tunable Quaternary Structures.

Higher-order foldamers represent a unique class of supramolecules at the forefront of molecular design. Herein we control quaternary folding using a novel approach that combines halogen bonding (XBing) and hydrogen bonding (HBing). We present the first anion-templated double helices induced by halogen bonds (XBs) and stabilized by "hydrogen bond enhanced halogen bonds" (HBeXBs). Our findings demonstrate that the number and orientation of hydrogen bond (HB) and XB donors significantly affect the quaternary structure and guest selectivity of two similar oligomers. This research offers new design elements to engineer foldamers and tailor their quaternary structure for specific guest binding.

Study on the Selectivity of Molecular Imprinting Materials Determined through Hydrogen Bonding on Template Molecular Structures of Flavonoids.

Molecular imprinting technology is widely used for the specific identification of compounds, but the selective recognition mechanisms of the same compounds still need to be further studied. Based on differences in hydrogen bond size and orientation, molecularly imprinted polymers (MIPs) were designed to adsorb flavonols with the same parent core and different hydroxyl groups. A surface-imprinted material was designed with silicon dioxide as the carrier, myricetin as the template molecule, and methacrylic acid (MAA) as the functional monomer. Scanning electron microscopy (SEM), Brunauer-Emmett-Teller surface area (BET) analyses, Fourier-transform infrared spectroscopy (FT-IR), and other characterization experiments were carried out. The intrinsic mechanism of the MIPs was also explored. The MIPs showed good adsorption of myricetin and other flavonoids through hydrogen bonding and steric hindrance. The adsorption capacity was 3.12-9.04 mg/g, and the imprinting factor was 1.78-3.37. Flavonoids with different hydroxyl groups in different numbers and directions had different hydrogen bond strengths with functional monomers. R2, R4, and R1 on 2-phenylchromogenone had stronger electronegativity, and the hydroxyl group was also more likely to form and have stronger hydrogen bonds. The hydroxyl negativity and the degree of steric hindrance of flavonoids played a major role in the recognition of molecularly imprinted materials. This study is of great significance for the synthesis of and selection of templates for analogous molecular imprinting materials.

Quantum dipole interactions and transient hydrogen bond orientation order in cells, cellular membranes and myelin sheath: Implications for MRI signal relaxation, anisotropy, and T1 magnetic field dependence.

Despite significant impact on the study of human brain, MRI lacks a theory of signal formation that integrates quantum interactions involving proton dipoles (a primary MRI signal source) with brain intricate cellular environment. The purpose of the present study is developing such a theory. We introduce the Transient Hydrogen Bond (THB) model, where THB-mediated quantum dipole interactions between water and protons of hydrophilic heads of amphipathic biomolecules forming cells, cellular membranes and myelin sheath serve as a major source of MR signal relaxation. The THB theory predicts the existence of a hydrogen-bond-driven structural order of dipole-dipole connections within THBs as a primary factor for the anisotropy observed in MRI signal relaxation. We have also demonstrated that the conventional Lorentzian spectral density function decreases too fast at high frequencies to adequately capture the field dependence of brain MRI signal relaxation. To bridge this gap, we introduced a stretched spectral density function that surpasses the limitations of Lorentzian dispersion. In human brain, our findings reveal that at any time point only about 4% to 7% of water protons are engaged in quantum encounters within THBs. These ultra-short (2 to 3 ns), but frequent quantum spin exchanges lead to gradual recovery of magnetization toward thermodynamic equilibrium, that is, relaxation of MRI signal. By incorporating quantum proton interactions involved in brain imaging, the THB approach introduces new insights on the complex relationship between brain tissue cellular structure and MRI measurements, thus offering a promising new tool for better understanding of brain microstructure in health and disease.

Unlocking the potential of solvent polarity in directing ESIPT pathways of HHMB with dual hydrogen bond acceptors: a DFT/TD-DFT study

The excited-state intramolecular proton transfer (ESIPT) process involving dual hydrogen bond acceptors (HBAs) is of great interest in research and has significant potential for applications due to its flexible adjustability. In this work, the solvent polarity-dependent changes in structures, photophysical properties and ESIPT processes of 2-(2-hydroxy-3-hydroxyiminomethyl-5-methylphenyl)-benzimidazole (HHMB) with two asymmetric HBAs are investigated. Firstly, the orientation of intramolecular hydrogen bond (IHB) under different solvent polarities are explored. The computational results indicate that in non-polar solvents, the central hydroxyl group predominantly forms an IHB with the imine of the oxime group, resulting in large Stokes and near-infrared emission peaks. Conversely, in polar solvents, the central hydroxyl group links the imidazole group to form a stronger IHB with improved fluorescence efficiency. Additionally, the quantum chemical calculations are used to simulate the absorption–emission spectra and plot the frontier molecular orbitals, as well as the potential energy curves about ESIPT in different solvents. In conclusion, we elucidate the rationale behind the preferential formation of the biased IHBs and examine its impact on the ESIPT process by manipulating the solvent polarity. Theoretical studies on the dual HBAs molecule, exhibiting specific selectivity, pave the way for the development of higher-performance fluorescence probes and luminescent materials.

Perturbation of Hydrogen Bonding Network Plays an Important Role in Determining Antifreeze Activity

In order to develop new antifreeze agents, it is crucial to understand the antifreeze activity. The adsorption-inhibition mechanism has been widely accepted, and most previous studies focus on ice-binding affinity of additive molecules but rarely discuss their influence on the hydrogen bonding network of ice. Herein, we investigate the ice recrystallization inhibition (IRI) activity of two structurally similar molecules, histidine (His) and phenylalanine (Phe). It is verified by experiment that Phe has excellent IRI activity, while His does not. Molecular dynamics simulation is conducted to study the process of ice growth with amino acids and to explore the origin of the difference between His and Phe. We find that His is prone to be swallowed up by ice and thus no longer hinders its growth, whereas Phe can remain unswallowed on the ice surface for a long period, which is attributed to their different abilities to perturb the hydrogen bonding network. Based on a statistical analysis of oxygen–hydrogen bond orientations, we propose a method to evaluate the order of the hydrogen bonding network. With this method, the IRI activity of His and Phe can be well interpreted, and the influence of different groups on the hydrogen bonding network can be quantified. This study takes the structural integrity of ice into consideration and provides a possibility to investigate the influence of different additive molecules on hydrogen bonding network, which is expected to improve the understanding of antifreeze mechanism.

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.

Turning ON/OFF the fluorescence of the ESIPT state by changing the hydrogen bond distance and orientation in quinoline–pyrazole derivatives

• Targeted modifications to the HB structure can induce different ESIPT activities. • The ISC process is responsible for the fluorescence quenching in QP1 and QP3. • The dark state of ESIPT was successfully lighted up in fused HB six-membered ring QP2. The excited-state intramolecular proton transfer (ESIPT) process is sometimes non-fluorescent owing to interference from other non-radiative processes. Thus, effectively lighting up the “invisible” ESIPT state is crucial. In this work, quinoline–pyrazole (QP) derivatives containing fused and non-fused aromatic frameworks (QP1, QP2, and QP3) were used as model compounds to explore the effects of hydrogen bond (HB) distance and orientation on ESIPT. Analysis of the electronic structures and HB interactions revealed that the HB in fused six-membered ring QP2 was significantly enhanced upon photoexcitation, which making the ESIPT process occur more readily. In contrast, the ESIPT process was less favorable for the more flexible non-fused six-membered ring in QP3 owing to HB weakening in the S 1 state. Furthermore, analysis of the potential energy curves indicated that the ESIPT fluorescence of QP1 and QP3 was quenched by intersystem crossing. Remarkably, the dark ESIPT state was successfully illuminated in QP2. Our findings demonstrate that targeted modifications to the molecular structure in the region of HBs can serve as a control knob to effectively regulate the ESIPT fluorescence, providing a route toward potential photoelectric applications.

Hydrogen bonds dominated frictional stick-slip of cellulose nanocrystals

Crystalline cellulose, the most abundant natural polymer on earth, features exceptional physical and mechanical properties. Using atomistic simulation, this study reports the mechanical behavior of cellulose-cellulose nanocrystal hydrophilic interface and systematically examines the impact of loading direction, interfacial moisture, misalignment and surface types. The density, orientation or distribution of interfacial hydrogen bonds are shown to explain the series of findings presented here, including stick-slip behavior, stiffness recovery after an irreversible slip, direction-dependent behavior and weakening induced by hydration or misalignment. Correlation analysis shows that, regardless of the various loading conditions, the interfacial stress, shear velocity and interaction energy are strongly correlated with the density of interfacial hydrogen bonds, which quantitatively supports the central role of hydrogen bonding. Based on this correlation, the friction force rendered by a single hydrogen bond is inferred to be fHB ∼1.3 E-10 N under a shearing speed of 1 m s−1.

Dense Hydrogen-Bonding Network Boosts Ionic Conductive Hydrogels with Extremely High Toughness, Rapid Self-Recovery, and Autonomous Adhesion for Human-Motion Detection.

The construction of ionic conductive hydrogels with high transparency, excellent mechanical robustness, high toughness, and rapid self-recovery is highly desired yet challenging. Herein, a hydrogen-bonding network densification strategy is presented for preparing a highly stretchable and transparent poly(ionic liquid) hydrogel (PAM-r-MVIC) from the perspective of random copolymerization of 1-methyl-3-(4-vinylbenzyl) imidazolium chloride and acrylamide in water. Ascribing to the formation of a dense hydrogen-bonding network, the resultant PAM-r-MVIC exhibited an intrinsically high stretchability (>1000%) and compressibility (90%), fast self-recovery with high toughness (2950 kJ m−3), and excellent fatigue resistance with no deviation for 100 cycles. Dissipative particle dynamics simulations revealed that the orientation of hydrogen bonds along the stretching direction boosted mechanical strength and toughness, which were further proved by the restriction of molecular chain movements ascribing to the formation of a dense hydrogen-bonding network from mean square displacement calculations. Combining with high ionic conductivity over a wide temperature range and autonomous adhesion on various surfaces with tailored adhesive strength, the PAM-r-MVIC can readily work as a highly stretchable and healable ionic conductor for a capacitive/resistive bimodal sensor with self-adhesion, high sensitivity, excellent linearity, and great durability. This study might provide a new path of designing and fabricating ionic conductive hydrogels with high mechanical elasticity, high toughness, and excellent fatigue resilience for skin-inspired ionic sensors in detecting complex human motions.

Chemically Stable Black Phase CsPbI3 Inorganic Perovskites for High-Efficiency Photovoltaics.

Research on chemically stable inorganic perovskites has achieved rapid progress in terms of high efficiency exceeding 19% and high thermal stabilities, making it one of the most promising candidates for thermodynamically stable and high-efficiency perovskite solar cells. Among those inorganic perovskites, CsPbI3 with good chemical components stability possesses the suitable bandgap (≈1.7eV) for single-junction and tandem solar cells. Comparing to the anisotropic organic cations, the isotropic cesium cation without hydrogen bond and cation orientation renders CsPbI3 exhibit unique optoelectronic properties. However, the unideal tolerance factor of CsPbI3 induces the challenges of different crystal phase competition and room temperature phase stability. Herein, the latest important developments regarding understanding of the crystal structure and phase of CsPbI3 perovskite are presented. The development of various solution chemistry approaches for depositing high-quality phase-pure CsPbI3 perovskite is summarized. Furthermore, some important phase stabilization strategies for black phase CsPbI3 are discussed. The latest experimental and theoretical studies on the fundamental physical properties of photoactive phase CsPbI3 have deepened the understanding of inorganic perovskites. The future development and research directions toward achieving highly stable CsPbI3 materials will further advance inorganic perovskite for highly stable and efficient photovoltaics.

Effect of H3O+ on the Structure and Dynamics of Water at the Interface with Phospholipid Bilayers.

This study investigates the effect of hydronium ions (H3O+) on the structure and dynamics of water at the interface of a phospholipid bilayer using molecular dynamics simulations of a POPC bilayer in the presence and absence of H3O+ ions. From these simulations, the survival probability, hydrogen bond lifetimes, orientation relaxation, and angular distribution of interfacial water, at increasing distances from the membrane surface, were calculated. Simulations of POPC in the absence of H3O+ ions reproduce previously reported deviations of interfacial water from the properties of bulk water. Our results show that in the presence of H3O+, these deviations are even more pronounced with the strongest effects seen in the survival probability and orientation relaxation. To further investigate the effect of the H3O+-induced reduction of area per lipid on interfacial water, we carried out simulations where H3O+ ions were removed, but the area per lipid was fixed to the values seen in the presence of H3O+. The combined findings from our study suggest that the presence of H3O+ ions affects the properties of interfacial water, accentuates the deviation from bulk properties, and extends the long-range effect of these deviations further away from the membrane surface.

Interfacial structure in the liquid-liquid extraction of rare earth elements by phosphoric acid ligands: a molecular dynamics study.

Solvent extraction (SX), wherein two immiscible liquids, one containing the extractant molecules and the other containing the solute to be extracted are brought in contact to effect the phase transfer of the solute, underpins metal extraction and recovery processes. The interfacial region is of utmost importance in the SX process, since besides thermodynamics, the physical and chemical heterogeneity at the interface governs the kinetics of the process. Yet, a fundamental understanding of this heterogeneity and its implications for the extraction mechanism are currently lacking. We use molecular dynamics (MD) simulations to study the liquid-liquid interface under conditions relevant to the SX of Rare Earth Elements (REEs) by a phosphoric acid ligand. Simulations revealed that the extractant molecules and varying amounts of acid and metal ions partitioned to the interface. The presence of these species had a significant effect on the interfacial thickness, hydrogen bond life times and orientations of the water molecules at the interface. Deprotonation of the ligands was essential for the adsorption of the metal ions at the interface, with these ions forming a number of different complexes at the interface involving one to three extractant molecules and four to eight water molecules. Although the interface itself was rough, no obvious 'finger-like' water protrusions penetrating the organic phase were seen in our simulations. While the results of our work help us gain fundamental insights into the sequence of events leading to the formation of a variety of interfacial complexes, they also emphasize the need to carry out a more detailed atomic level study to understand the full mechanism of extraction of REEs from the aqueous to organic phases by phosphoric acid ligands.

Subtle changes in hydrogen bond orientation result in glassification of carbon capture solvents.

Water-lean CO2 capture solvents show promise for more efficient and cost-effective CO2 capture, although their long-term behavior in operation has yet to be well studied. New observations of extended structure solvent behavior show that some solvent formulations transform into a glass-like phase upon aging at operating temperatures after contact with CO2. The glassification of a solvent would be detrimental to a carbon-capture process due to plugging of infrastructure, introducing a critical need to decipher the underlying principles of this phenomenon to prevent it from happening. We present the first integrated theoretical and experimental study to characterize the nano-structure of metastable and glassy states of an archetypal single-component alkanolguanidine carbon-capture solvent and assess how minute changes in atomic-level interactions convert the solvent between metastable and glass-like states. Small-angle neutron scattering and neutron diffraction coupled with small- and wide-angle X-ray scattering analysis demonstrate that minute structural changes in solution precipitae reversible aggregation of zwitterionic alkylcarbonate clusters in solution. Our findings indicate that our test system, an alkanolguanidine, exhibits a first-order phase transition, similar to a glass transition, at approximately 40 °C-close to the operating absorption temperature for post-combustion CO2 capture processes. We anticipate that these phenomena are not specific to this system, but are present in other classes of colvents as well. We discuss how molecular-level interactions can have vast implications for solvent-based carbon-capture technologies, concluding that fortunately in this case, glassification of water-lean solvents can be avoided as long as the solvent is run above its glass transition temperature.

Effect of Hydrogen Bonds on the Dielectric Properties of Interfacial Water.

The dielectric constant for water is reduced under confinement. Although this phenomenon is well known, the underlying physical mechanism for the reduction is still in debate. In this work, we investigate the effect of the orientation of hydrogen bonds on the dielectric properties of confined water using molecular dynamics simulations. We find a reduced rotational diffusion coefficient for water molecules close to the solid surface. The reduced rotational diffusion arises due to the hindered rotation away from the plane parallel to the channel walls. The suppressed rotation in turn affects the orientational polarization of water, leading to a low value for the dielectric constant at the interface. We attribute the constrained out-of-plane rotation to originate from a higher density of planar hydrogen bonds formed by the interfacial water molecules.

Molecular Dynamics Study on the Effect of Surface Hydroxyl Groups on Three-Phase Wettability in Oil-Water-Graphite Systems.

In this paper, a hydroxylated graphite surface is generated as a hydrophilic oleophobic material for the application of oil-water separation, and the effects of hydroxyl density on the three-phase wettability are studied in oil-water-graphite systems. We analyze the adsorption of water molecules on the hydroxylated surfaces and obtain the relationship between water-oil-solid interfacial properties and the hydroxyl density, which results from the synthetic effects of the orientation of molecules and hydrogen bonds. With the increase of hydroxyl density, the water-solid contact angle first decreases rapidly, and then remains constant. The density of the hydrogen bond formed between hydroxyls and water molecules in the adsorption layer can explain the regularity of the three-phase wettability. The orientation of the water molecules in the adsorption layer shows insignificant variation, owing to the hydrogen bond network formed between the water molecules; thus, little change is observed in the hydrogen bond density in the adsorption layer.

Compressibility and reversible amorphization of thaumasite Ca3Si(OH)6(CO3)(SO4)·12H2O pressurized in methanol–ethanol–H2O up to 5 GPa

The elastic and structure behavior of natural thaumasite compressed in methanol–ethanol–H2O up to 5 GPa was studied by synchrotron powder diffraction with a diamond anvil cell. In the pressure range between 0.0001 and 4.5 GPa, the compression is regular and slightly anisotropic, with a more rigid ab-plane coinciding with the orientation of hydrogen bonds and S–O, C–O bonds in anion groups. The corresponding bulk moduli derived from the third-order Birch–Murnaghan EoS fit are K a = 43(2), K c = 35(2), K T = 39(2) GPa. Rietveld refinements reveal some general features of the structure evolution of thaumasite, which are consistent with the observed elastic anisotropy. The compression within the ab-plane proceeds mainly at the expense of shortening of hydrogen bonds and much lesser decrease of C–O and S–O bonds. In the range of 0.0001–3 GPa the Ca–O polyhedra contract more rapidly along the c-axis as compared to the ab-plane. At about 5 GPa, thaumasite undergoes a reversible transformation to an amorphous phase. The observed behavior differs drastically with that studied previously using helium as the pressure medium, which suggests the effect of He penetration increasing the structure stiffness. Without helium support, the thaumasite structure is preserved only up to 4.5 GPa.

Reinventing Design Principles for Developing Low-Viscosity Carbon Dioxide-Binding Organic Liquids for Flue Gas Clean Up.

Anthropogenic CO2 emissions from point sources (e.g., coal fired-power plants) account for the majority of the greenhouse gases in the atmosphere. Water-lean solvent systems such as CO2 -binding organic liquids (CO2 BOLs) are being developed to reduce the energy requirement for CO2 capture. Many water-lean solvents such as CO2 BOLs are currently limited by the high viscosities of concentrated electrolyte solvents, thus many of these solvents have yet to move toward commercialization. Conventional standard trial-and-error approaches for viscosity reduction, while effective, are time consuming and economically expensive. We rethink the metrics and design principles of low-viscosity CO2 -capture solvents using a combined synthesis and computational modeling approach. We critically study the effects of viscosity reducing factors such as orientation of hydrogen bonding, introduction of higher degrees of freedom, and cation or anion charge solvation, and assess whether or how each factor affects viscosity of CO2 BOL CO2 capture solvents. Ultimately, we found that hydrogen bond orientation and strength is the predominant factor influencing the viscosity in CO2 BOL solvents. With this knowledge, a new CO2 BOL variant, 1-MEIPADM-2-BOL, was synthesized and tested, resulting in a solvent that is approximately 60 % less viscous at 25 mol % CO2 loading than our base compound 1-IPADM-2-BOL. The insights gained from the current study redefine the fundamental concepts and understanding of what influences viscosity in concentrated organic CO2 -capture solvents.

Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli.

The respiratory cytochrome bo3 ubiquinol oxidase from Escherichia coli has a high-affinity ubiquinone binding site that stabilizes the one-electron reduced ubisemiquinone (SQH), which is a transient intermediate during the electron-mediated reduction of O2 to water. It is known that SQH is stabilized by two strong hydrogen bonds from R71 and D75 to ubiquinone carbonyl oxygen O1 and weak hydrogen bonds from H98 and Q101 to O4. In this work, SQH was investigated with orientation-selective Q-band (∼34 GHz) pulsed 1H electron-nuclear double resonance (ENDOR) spectroscopy on fully deuterated cytochrome (cyt) bo3 in a H2O solvent so that only exchangeable protons contribute to the observed ENDOR spectra. Simulations of the experimental ENDOR spectra provided the principal values and directions of the hyperfine (hfi) tensors for the two strongly coupled H-bond protons (H1 and H2). For H1, the largest principal component of the proton anisotropic hfi tensor Tz' = 11.8 MHz, whereas for H2, Tz' = 8.6 MHz. Remarkably, the data show that the direction of the H1 H-bond is nearly perpendicular to the quinone plane (∼70° out of plane). The orientation of the second strong hydrogen bond, H2, is out of plane by ∼25°. Equilibrium molecular dynamics simulations on a membrane-embedded model of the cyt bo3 QH site show that these H-bond orientations are plausible but do not distinguish which H-bond, from R71 or D75, is nearly perpendicular to the quinone ring. Density functional theory calculations support the idea that the distances and geometries of the H-bonds to the ubiquinone carbonyl oxygens, along with the measured proton anisotropic hfi couplings, are most compatible with an anionic (deprotonated) ubisemiquinone.

Viscosity of Water under Electric Field: Anisotropy Induced by Redistribution of Hydrogen Bonds.

The viscosity of water under an external electric field of 0.00-0.90 V/nm was studied using both molecular dynamics simulations and atomistic modeling accounting for intermolecular potentials. For all temperatures investigated, the water viscosity becomes anisotropic under an electric field: the viscosity component parallel to the field increases monotonically with the field strength, E, while the viscosity perpendicular to the field first decreases and then increases with E. This anisotropy is believed to be mainly caused by the redistribution of hydrogen bonds under the electric field. The preferred orientation of hydrogen bonds along the field direction leads to an increase of the energy barrier of a water molecule to its neighboring site, and hence increases the viscosity in that direction. However, the probability of hydrogen bonds perpendicular to the electric field decreases with E, together with the increase of the average number of hydrogen bonds per molecule, causing the perpendicular component of water viscosity to first decrease and then increase with the electric field.

High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction

The matrix 2 (M2) protein from influenza A virus is a proton channel that uses His37 as a selectivity filter. Here we report high-resolution (1.10 Å) cryogenic crystallographic structures of the transmembrane domain of M2 at low and high pH. These structures reveal that waters within the pore form hydrogen-bonded networks or "water wires" spanning 17 Å from the channel entrance to His37. Pore-lining carbonyl groups are well situated to stabilize hydronium via second-shell interactions involving bridging water molecules. In addition, room temperature crystallographic structures indicate that water becomes increasingly fluid with increasing temperature and decreasing pH, despite the higher electrostatic field. Complementary molecular dynamics simulations reveal a collective switch of hydrogen bond orientations that can contribute to the directionality of proton flux as His37 is dynamically protonated and deprotonated in the conduction cycle.