Hydrogen Bond Exchange Research Articles

Shape Memory and Self-Healing Properties of Poly(acrylate amide) Elastomers Reinforced with Polyhedral Oligomeric Silsesquioxanes

The organic–inorganic nanocomposite elastomers were synthesized via the random copolymerization of 5-acetylaminopentyl acrylate (AA) with 3-methacryloxypropyl heptaphenyl polyhedral oligomeric silsesquioxane (MAPOSS). The morphological results showed that the random copolymers were microphase-separated and the POSS structural units were aggregated into the nanodomains that were composed of tens of silsesquioxane cages. Compared to neat PAA, the organic–inorganic copolymers possessed enhanced glass transition temperatures and improved mechanical strengths. Most importantly, the organic–inorganic copolymers simultaneously had shape memory and self-healing properties. The shape memory properties can be attributed to the formation of physical cross-linking in the random copolymers; in the physically cross-linked network, the POSS nanodomains constituted the net points. The self-healing properties are responsible for the dynamic exchange of the intramolecular hydrogen bonds among acrylate amide groups in spite...

Highly efficient removal of ceftiofur sodium using a superior hydroxyl group functionalized ionic liquid-modified polymer

The occurrence of cephalosporin antibiotics in water resources has caused increasing concerns about their potential effects on ecosystem and human health. However, reports on the efficient removal of these antibiotics are limited. In this work, a superior hydroxyl-functionalized ionic liquid based polymer (PS-[Hemim][Cl]) was prepared for highly efficient removal of ceftiofur sodium (CFS) antibiotic from aqueous solutions, and the effect of various factors on the adsorption was investigated. It was found that the PS-[Hemim][Cl] exhibited a super-high adsorption capacity of 1260.5 mg/g for CFS within 60 min and kept high removal efficiency in a wide range of antibiotic concentrations from 5 ppb level to 1000 mg/L. Even the concentration of common inorganic ions was 1000 times higher than that of CFS, the adsorption efficiency remained above 93%. At the same time, the PS-[Hemim][Cl] showed excellent adsorption performance for the antibiotics with similar structure to CFS. Compared with commercially available adsorbents, the adsorption capacity of PS-[Hemim][Cl] for CFS was 4–468 times higher under the same experimental conditions. The application of PS-[Hemim][Cl] to real wastewater containing different concentrations of CFS was investigated and promising results were reported. Additionally, preliminary mechanism studies suggested that electrostatic attraction, hydrogen bond and ion exchange synergistically contributed to the highly efficient adsorption of CFS.

Coupled jump rotational dynamics in aqueous nitrate solutions.

A nitrate ion (NO3-) with its trigonal planar geometry and charges distributed among nitrogen and oxygen atoms can couple to the extensive hydrogen bond network of water to give rise to unique dynamical characteristics. We carry out detailed atomistic simulations and theoretical analyses to investigate these aspects and report certain interesting findings. We find that the nitrate ions in aqueous potassium nitrate solution exhibit large amplitude rotational jump motions that are coupled to the hydrogen bond rearrangement dynamics of the surrounding water molecules. The jump motion of nitrate ions bears certain similarities to the Laage-Hynes mechanism of rotational jump motions of tagged water molecules in neat liquid water. We perform a detailed atomic-level investigation of hydrogen bond rearrangement dynamics of water in aqueous KNO3 solution to unearth two distinct mechanisms of hydrogen bond exchange that are instrumental to promote these jump motions of nitrate ions. As observed in an earlier study by Xie et al., in the first mechanism, after breaking a hydrogen bond with nitrate ion, water forms a new hydrogen bond with a water molecule, whereas the second mechanism involves just a switching of hydrogen bond between the two oxygen atoms of the same nitrate ion (W. J. Xie et al., J. Chem. Phys. 143, 224504 (2015)). The magnitude as well as nature of the reorientational jump of nitrate ion for the two mechanisms is different. In the first mechanism, nitrate ion predominantly undergoes out-of-plane rotation, while in the second mechanism, in-plane reorientation of NO3- is favourable. These have been deduced by computing the torque on the nitrate ion during the hydrogen bond switching event. We have defined and computed the time correlation function for coupled reorientational jump of nitrate and water and obtained the associated relaxation time which is also different for the two mechanisms. These results provide insight into the relation between the coupled reorientational jump dynamics of solute and solvent molecules.

Molecular dynamics simulation study on the structure and the dynamic properties of nano-confined alcohols between graphene surfaces

Molecular dynamics simulation was conducted to study the structure and dynamics of hydrogen bonds in alcohols (methanol, ethanol, and 1-propanol) confined within graphene nanopores at a constant parallel component of pressure, 101.3 kPa, and at constant temperatures, ranging from 260 to 340 K. The results indicated that, while confined alcohol molecules orient themselves with the hydrophobic methyl groups exposing to the two plates, the polar hydroxyl groups stand away from surface to preserve a hydrogen-bonding with adjacent layer. Contrary to confined water, the average of hydrogen-bond values of confined alcohol molecules is found to be the same as bulk. Decreasing diffusion coefficient, increasing the relaxation time and, accordingly, decreasing hydrogen bond exchange dynamics occur by increasing the size of alkyl group in alcohol molecules in bulk and confined fluids. Our findings in this work indicate that the effect of confining surfaces on the confined fluid increase at lower temperatures compared to the higher temperatures.

Cosolvent Effects on Solute-Solvent Hydrogen-Bond Dynamics: Ultrafast 2D IR Investigations.

Cosolvents strongly influence the solute-solvent interactions of biomolecules in aqueous environments and have profound effects on the stability and activity of several proteins and enzymes. Experimental studies have previously reported on the hydrogen-bond dynamics of water molecules in the presence of a cosolvent, but understanding the effects from a solute's perspective could provide greater insight into protein stability. Because carbonyl groups are abundant in biomolecules, the current study used 2D IR spectroscopy and molecular dynamics simulations to compare the hydrogen-bond dynamics of the solute's carbonyl group in aqueous solution, with and without the presence of DMSO as a cosolvent. 2D IR spectroscopy was used to quantitatively estimate the time scales of the hydrogen-bond dynamics of the carbonyl group in neat water and 1:1 DMSO/water solution. The 2D IR results show spectral signatures of a chemical exchange process: The presence of the cosolvent was found to lower the hydrogen-bond exchange rate by a factor of 5. The measured exchange rates were 7.50 × 10(11) and 1.48 × 10(11) s(-1) in neat water and 1:1 DMSO/water, respectively. Molecular dynamics simulations predict a significantly shorter carbonyl hydrogen-bond lifetime in neat water than in 1:1 DMSO/water and provide molecular insights into the exchange mechanism. The binding of the cosolvent to the solute was found to be accompanied by the release of hydrogen-bonded water molecules to the bulk. The widely different hydrogen-bond lifetimes and exchange rates with and without DMSO indicate a significant change in the ultrafast hydrogen-bond dynamics in the presence of a cosolvent, which, in turn, might play an important role in the stability and activity of biomolecules.

Retardation of Water Reorientation at the Oil/Water Interface

Molecular dynamics simulations reveal the retardation of water reorientation at the oil/water interface, which is mainly contributed by the slow reorienting interfacial water molecules with hydrogen bonds donated to other interfacial water. On the basis of the extended jump model, the retardation of water reorientation is explained to be mainly caused by the slowed hydrogen bond exchange, with a minor contribution of the slowed frame reorientation. The excluded volume effect due to the space occupied by the hydrophobic phase predicts a retardation factor higher than that observed. It is deduced that the increased transition state density for hydrogen bond exchanges at the interface compensates this effect to some extent. Water reorientation dynamics at the oil/water interface exhibits differences as compared to those reported around hydrophobic groups, next to a hydrophobic solid surface and at the air/water interface. Free dangling OH bonds at the interface have little influence on overall water reorient...

Characterization of the Local Structure in Liquid Water by Various Order Parameters.

A wide range of geometric order parameters have been suggested to characterize the local structure of liquid water and its tetrahedral arrangement, but their respective merits have remained elusive. Here, we consider a series of popular order parameters and analyze molecular dynamics simulations of water, in the bulk and in the hydration shell of a hydrophobic solute, at 298 and 260 K. We show that these parameters are weakly correlated and probe different distortions, for example the angular versus radial disorders. We first combine these complementary descriptions to analyze the structural rearrangements leading to the density maximum in liquid water. Our results reveal no sign of a heterogeneous mixture and show that the density maximum arises from the depletion in interstitial water molecules upon cooling. In the hydration shell of the hydrophobic moiety of propanol, the order parameters suggest that the water local structure is similar to that in the bulk, with only a very weak depletion in ordered configurations, thus confirming the absence of any iceberg-type structure. Finally, we show that the main structural fluctuations that affect water reorientation dynamics in the bulk are angular distortions, which we explain by the jump hydrogen-bond exchange mechanism.

Hydrogen bond dynamics in bulk alcohols.

Hydrogen-bonded liquids play a significant role in numerous chemical and biological phenomena. In the past decade, impressive developments in multidimensional vibrational spectroscopy and combined molecular dynamics-quantum mechanical simulation have established many intriguing features of hydrogen bond dynamics in one of the fundamental solvents in nature, water. The next class of a hydrogen-bonded liquid--alcohols--has attracted much less attention. This is surprising given such important differences between water and alcohols as the imbalance between the number of hydrogen bonds, each molecule can accept (two) and donate (one) and the very presence of the hydrophobic group in alcohols. Here, we use polarization-resolved pump-probe and 2D infrared spectroscopy supported by extensive theoretical modeling to investigate hydrogen bond dynamics in methanol, ethanol, and isopropanol employing the OH stretching mode as a reporter. The sub-ps dynamics in alcohols are similar to those in water as they are determined by similar librational and hydrogen-bond stretch motions. However, lower density of hydrogen bond acceptors and donors in alcohols leads to the appearance of slow diffusion-controlled hydrogen bond exchange dynamics, which are essentially absent in water. We anticipate that the findings herein would have a potential impact on fundamental chemistry and biology as many processes in nature involve the interplay of hydrophobic and hydrophilic groups.

Origins of the non-exponential reorientation dynamics of nanoconfined water.

The dynamics of water are dramatically modified upon confinement in nanoscale hydrophilic silica pores. In particular, the OH reorientation dynamics of the interfacial water are non-exponential and dramatically slowed relative to the bulk liquid. A detailed analysis of molecular dynamics simulations is carried out to elucidate the microscopic origins of this behavior. The results are analyzed in the context of the extended jump model for water that describes the reorientation as a combination of hydrogen-bond exchanges, or jumps, and rotation of intact hydrogen bonds, with the former representing the dominant contribution. Within this model, the roles of surface and dynamical heterogeneities are considered by spatially resolving the hydrogen-bond jump dynamics into individual sites on the silica pore surface. For each site the dynamics is nearly mono-exponential, indicating that dynamical heterogeneity is at most a minor influence, while the distribution of these individual site jump times is broad. The non-exponential dynamics can also not be attributed to enthalpic contributions to the barriers to hydrogen-bond exchanges. Two entropic effects related to the surface roughness are found to explain the retarded and diverse dynamics: those associated with the approach of a new hydrogen-bond acceptor and with the breaking of the initial hydrogen-bond.

CNN pincer ruthenium catalysts for hydrogenation and transfer hydrogenation of ketones: experimental and computational studies.

Reaction of [RuCl(CNN)(dppb)] (1-Cl) (HCNN=2-aminomethyl-6-(4-methylphenyl)pyridine; dppb=Ph2 P(CH2 )4 PPh2 ) with NaOCH2 CF3 leads to the amine-alkoxide [Ru(CNN)(OCH2 CF3 )(dppb)] (1-OCH2 CF3 ), whose neutron diffraction study reveals a short RuO⋅⋅⋅HN bond length. Treatment of 1-Cl with NaOEt and EtOH affords the alkoxide [Ru(CNN)(OEt)(dppb)]⋅(EtOH)n (1-OEt⋅n EtOH), which equilibrates with the hydride [RuH(CNN)(dppb)] (1-H) and acetaldehyde. Compound 1-OEt⋅n EtOH reacts reversibly with H2 leading to 1-H and EtOH through dihydrogen splitting. NMR spectroscopic studies on 1-OEt⋅n EtOH and 1-H reveal hydrogen bond interactions and exchange processes. The chloride 1-Cl catalyzes the hydrogenation (5 atm of H2 ) of ketones to alcohols (turnover frequency (TOF) up to 6.5×10(4) h(-1) , 40 °C). DFT calculations were performed on the reaction of [RuH(CNN')(dmpb)] (2-H) (HCNN'=2-aminomethyl-6-(phenyl)pyridine; dmpb=Me2 P(CH2 )4 PMe2 ) with acetone and with one molecule of 2-propanol, in alcohol, with the alkoxide complex being the most stable species. In the first step, the Ru-hydride transfers one hydrogen atom to the carbon of the ketone, whereas the second hydrogen transfer from NH2 is mediated by the alcohol and leads to the key "amide" intermediate. Regeneration of the hydride complex may occur by reaction with 2-propanol or with H2 ; both pathways have low barriers and are alcohol assisted.

Mechanistic Insight into Asymmetric N–H Insertion Cooperatively Catalyzed by a Dirhodium Compound and a Spiro Chiral Phosphoric Acid

The insertion of a carbenoid into an N–H bond of an amine cooperatively catalyzed by a dirhodium catalyst and a spiro chiral phosphoric acid has been investigated in detail using density functional theory methods. Calculations indicate that the reaction begins with the nucleophilic amine attacking at the carbenoid, forming a metal-associated ammonium ylide first followed by a rapid proton transfer to afford a metal-associated enamine intermediate. Subsequently, the enamine intermediate dissociates from the metal and yield a more stable seven-membered-ring conformation via an intramolecular hydrogen-bond exchange. Formation of the enamine intermediate requires an overall barrier of 5.7 kcal/mol and is exergonic by 5.1 kcal/mol. Calculations demonstrated that, although the conversion of the achiral enamine into the N–H insertion product can be facilitated efficiently by the dirhodium catalyst through a two-step process, it can be compressed to a large extent. This is due to the more competitive decompositio...

Distributions of single-molecule properties as tools for the study of dynamical heterogeneities in nanoconfined water

The explicit trend of the distribution functions of single-molecule rotational relaxation constants and atomic mean-square displacement are used to study the dynamical heterogeneities in nanoconfined water. The trend of the single-molecule properties distributions is related to the dynamic heterogeneities, and to the dynamic crossovers found in water clusters of different shapes and sizes and confined in a variety of zeolites. This was true in all the cases that were considered, in spite of the various shapes and sizes of the clusters. It is confirmed that the high temperature dynamical crossover occurring in the temperature range 200–230 K can be interpreted at a molecular level as the formation of almost translationally rigid clusters, characterized by some rotational freedom, hydrogen bond exchange and translational jumps as cage-to-cage processes. We also suggest a mechanism for the low temperature dynamical crossover (LTDC), falling in the temperature range 150–185 K, through which the adsorbed water clusters are made of nearly rigid sub-clusters, slightly mismatched, and thus permitting a relatively free librational motion at their borders. It appears that the condition required for LTDC to occur is the presence of highly heterogeneous environments for the adsorbed molecules, with some dangling hydrogen bonds or weaker than water–water hydrogen bonds. Under these conditions some dynamics are permitted at very low temperature, although most rotational motion is frozen. Therefore, it is unlikely, though not entirely excluded, that LTDC will be found in supercooled bulk water where no heterogeneous interface is present.

Energetic and Molecular Water Permeation Mechanisms of the Human Red Blood Cell Urea Transporter B

Urea transporter B (UT-B) is a passive membrane channel that facilitates highly efficient permeation of urea. In red blood cells (RBC), while the major function of UT-B is to transport urea, it is assumed that this protein is able to conduct water. Here, we have revisited this last issue by studying RBCs and ghosts from human variants with defects of aquaporin 1 (AQP1) or UT-B. We found that UT-B's osmotic water unit permeability (pfunit) is similar to that of AQP1. The determination of diffusional permeability coefficient (Pd) allowed the calculation of the Pf/Pd ratio, which is consistent with a single-file water transport. Molecular dynamic simulations of water conduction through human UT-B confirmed the experimental finding. From these results, we propose an atomistic description of water–protein interactions involved in this permeation. Inside the UT-B pore, five water molecules were found to form a single-file and move rapidly along a channel by hydrogen bond exchange involving two critical threonines. We further show that the energy barrier for water located in the central region coincides with a water dipole reorientation, which can be related to the proton exclusion observed experimentally. In conclusion, our results indicate that UT-B should be considered as a new member of the water channel family.

Dipyridyl‐immobilized ionic liquid type hybrid silica monolith for hydrophilic interaction electrochromatography

A pyridinium-based immobilized ionic liquid type multifunctional hybrid silica monolith was prepared by the in situ polymerization of 3-chloropropyl-silica matrix and 4,4'-dipyridyl for hydrophilic interaction CEC. The obtained hybrid monolith possessed of high stable skeletal microstructures with obviously hydrophilic retention mechanism under ACN content >50% in the mobile phase. Strong and stable anodic EOF could be observed under a broad pH range from pH 3.0 to 9.0. Due to the immobilized dipyridyl groups bonded to the silica matrix surface, the resulting hydrophilic hybrid monolith possessed multiple separation interactions including hydrogen bond, π-π, and anion exchange. Excellent separations of various polar analytes including electroneutral phenols, charged acid nucleotides, and basic analytes were successfully achieved. The highest column efficiencies up to 120,000, 164,000, and 106,000 plates/m were obtained for nucleotides, nucleic acid bases, and nucleosides and nicotines, respectively. These results demonstrated that the dipyridyl-immobilized ionic liquid functionalized hybrid monolith possessed highly mechanical stability and good chromatographic performance for hydrophilic interaction electrochromatography.

A TT Dinucleotide with a Nonionic Silyl Backbone: Impact on Conformation and H-Bond Mediated Base Pairing as Studied by Low-Temperature NMR

Abstract A TSiT dinucleotide linked through a nonionic diisopropylsilyl backbone has been synthesized and studied for its self-association through base–base recognition together with a free thymidine nucleoside. To characterize hydrogen-bonded associates in more detail, NMR measurements were performed in a freonic solvent at temperatures as low as 113 K in the slow hydrogen bond exchange regime. For the thymidine, TT base pairs with both the 2- and 4-carbonyl engaged in hydrogen bonds to the imino proton were observed. Whereas hydrogen bonds to the O4 acceptor are stronger as evidenced by a more deshielded proton in the hydrogen bridge when compared to hydrogen bonds to the O2 acceptor, the latter is nevertheless slightly favored over O4 in the H-bond formation of TT base pairs. The diisopropylsilyl linkage of the TSiT dinucleotide has no significant impact on the geometry and strength of formed NH–O2 and NH–O4 hydrogen bonds indicating, that the silyl backbone does not compromise the alignment of bases and does not pose any restrictions to the cyclic hydrogen bond formation between thymidines of the two strands. However, NMR results point to an exclusive formation of TSiT duplexes with an antiparallel strand orientation.

Low-Temperature NMR Studies on the Geometry of Base Pairs Involving 5-Substituted Uracil Derivatives

Uridine (U) imino proton chemical shifts, measured in the slow hydrogen-bond exchange regime at low temperatures in a freonic solution, show that electron-withdrawing 5-bromo and 5-fluoro substituents on the uracil base strengthen NHN hydrogen bonds in (X)U·A base pairs formed by the free nucleosides. Whereas the halogens do not alter the preferential formation of Watson-Crick geometries, self-associates of the halouracils point to a more favorable engagement of the 2-carbonyl as proton acceptor in the cyclic hydrogen bonds, suggesting increased formation of reverse geometries and wobble base pairs with guanine when compared to the thymine base. Employing (15)N-labeled 5-bromouridine, no noticeable population of minor enol tautomers is found in the freonic mixture at 113 K.

Partial crystalline transformation of solvated cellulose IIII crystals, reproduced by theoretical calculations

In hot-water molecular dynamics simulation at 370 K, four cellulose IIII crystal models, with different lattice planes and dimensions, exhibited partial crystalline transformations of (1 −1 0) chain sheets, in which hydroxymethyl groups were irreversibly rotated from gt into tg conformations, accompanied by hydrogen-bond exchange from the original O3–O6 to cellulose-I-like O2–O6 bonds. The final hydrogen-bond exchange ratio was about 95 % for some of the crystal models after 50 ns simulation. The corrugated (1 −1 0) chain sheet was converted to a cellulose-I-like flat chain sheet with a slightly right-handed twist. The 3D structures of the three types of isolated chain sheet models were optimized using density functional theory calculations to compare their stabilities without crystal packing forces. The cellulose Iβ (1 0 0) models were more stable than the cellulose IIII (1 −1 0) models. The optimized structure of cellulose IIII (1 0 0) models deviated largely from the initial sheet form. It was proposed to the crystalline transformation from cellulose IIII to Iβ that conversion of the chain sheet structure first take place, followed by sliding of the chain sheet along the fiber axis.

Molecular Recognition in Different Environments: β-Cyclodextrin Dimer Formation in Organic Solvents

Electrostatic and van der Waals interactions as well as entropy contribute to the energetics governing macromolecular complexation in biomolecules. Hydrogen bonds play a particularly important role in such interactions. Here we use molecular dynamics (MD) simulations to investigate the hydrogen bond (HB) orientations of free beta-cyclodextrin (β-CD) and head-to-head dimerization of β-CD monomers with and without guest molecules in different environments, namely, in 10 different solvents covering a wide range of polarity. Potentials of mean force for the dimer dissociation are derived from umbrella sampling simulations, allowing determination of the binding affinity between monomers. The HB orientations are in good agreement with available experimental data in water and dimethyl sulfoxide, yielding confidence in the force field used. HB exchanges at the secondary rim of β-CD are observed with a fast rate in water and with a low rate or even no exchange in other solvents. Orientational preferences of interglucopyranose HBs and their effects on the β-CD structure in these solvents are discussed in detail. Polar solvents with stronger HB accepting abilities can interrupt intermolecular HBs more easily, resulting in a less stable dimer. Guest molecules included in the channel-type cavity strengthen the binding affinity between two monomers to some extent, particularly in polar solvents. Formation of the head-to-head dimer is therefore solvent-dependent and guest-modulated. There is only limited correlation between the dimer binding energies and solvent properties like the dielectric constant. This implies that implicit solvent models will not be capable of predicting important properties like binding energy for other solvents than water without a complete reparameterization. This work provides a deeper comprehension on the properties of β-CD, and implications for the application of cyclodextrins in aqueous and nonaqueous media are discussed.

Statics and Dynamics of Free and Hydrogen-Bonded OH Groups at the Air/Water Interface

We use classical atomistic molecular dynamics simulations of two water models (SPC/E and TIP4P/2005) to investigate the orientation and reorientation dynamics of two subpopulations of OH groups belonging to water molecules at the air/water interface at 300 K: those OH groups that donate a hydrogen bond (called "bonded") and those that do not (called "free"). Free interfacial OH groups reorient in two distinct regimes: a fast regime from 0 to 1 ps and a slow regime thereafter. Qualitatively similar behavior was reported by others for free OH groups near extended hydrophobic surfaces. In contrast, the net reorientation of bonded OH groups occurs at a rate similar to that of bulk water. This similarity in reorientation rate results from compensation of two effects: decreasing frequency of hydrogen-bond breaking/formation (i.e., hydrogen-bond exchange) and faster rotation of intact hydrogen bonds. Both changes result from the decrease in density at the air/water interface relative to the bulk. Interestingly, because of the presence of capillary waves, the slowdown of hydrogen-bond exchange is significantly smaller than that reported for water near extended hydrophobic surfaces, but it is almost identical to that reported for water near small hydrophobic solutes. In this sense water at the air/water interface has characteristics of water of hydration of both small and extended hydrophobic solutes.

Hydration and Mobility of Trehalose in Aqueous Solution

The disaccharide trehalose stabilizes proteins against unfolding, but the underlying mechanism is not well understood. Because trehalose is preferentially excluded from the protein surface, it is of interest to examine how trehalose modifies the structure and dynamics of the solvent. From the spin relaxation rates of deuterated trehalose and (17)O-enriched water, we obtain the rotational dynamics of trehalose and water in solutions over wide ranges of concentration (0.025-1.5 M) and temperature (236-293 K). The results reveal direct solute-solute interactions at all concentrations, consistent with transient trehalose clusters. Similar to other organic solutes, the trehalose perturbation of water rotation (and hydrogen-bond exchange) is modest: a factor 1.6 (at 298 K) on average for the 47 water molecules in the first hydration layer. The deviation of the solute tumbling time from the Stokes-Einstein-Debye relation is partly caused by a dynamic solvent effect that is often modeled by incorporating "bound water" in the hydrodynamic volume. By comparing the measured temperature dependences of trehalose and water dynamics, we demonstrate that a more realistic local viscosity model accounts for this second-order dynamic coupling.