IR investigation of hydrogen bonds in weakly hydrated films of poly(vinyl alcohol)

A system of hydrogen bonds in weakly hydrated PVA films containing up to ≤8.5 wt % water is investigated via IR spectroscopy. It is shown that water molecules bind to only part of the hydroxyl groups of the polymer that are available for hydration and form the first hydrating layer. In a completely dehydrated film, practically every hydroxyl group of PVA forms hydrogen bonds with two other hydroxyl groups and serves as both a proton donor and a proton acceptor. In the hydrated film, one to three water molecules directly bind with one hydroxyl group of PVA.     

Ultrafast Vibrational Dynamics and Local Interactions of Hydrated DNA

Biochemical processes occur mainly in aqueous environments, where interactions with water molecules play a key role for both the structure and function of biomolecules. Deoxyribonucleic acid (DNA), the basic carrier of genetic information, is characterized by an equilibrium double helix structure which is held together by intermolecular hydrogen bonds between base pairs and hydrated by an environment of water molecules with fluctuating hydrogen bonds. Basic vibrational motions of hydrated DNA and the fastest changes in the DNA–water interactions and hydration geometries occur in less than 1 ps. These processes can be accessed by mapping the vibrational dynamics of DNA and water in a time‐resolved way by nonlinear ultrafast vibrational spectroscopy. Recent studies provide a detailed understanding of DNA vibrations and their dynamics, and give insight into nonequilibrium properties and structures of hydrated DNA.     

Adsorption, diffusion, dewetting, and entrapment of acetone on Ni(111), surface-modified silicon, and amorphous solid water studied by time-of-flight secondary ion mass spectrometry and temperature programmed desorption

Interactions of acetone with the silicon surfaces terminated with hydrogen, hydroxyl, and perfluorocarbon are investigated; results are compared to those on amorphous solid water (ASW) to gain insights into the roles of hydrogen bonds in surface diffusion and hydration of acetone adspecies. The surface mobility of acetone occurs at ～60 K irrespective of the surface functional groups. Cooperative diffusion of adspecies results in a 2D liquid phase on the H- and perfluorocarbon-terminated surfaces, whereas cooperativity tends to be quenched via hydrogen bonding on the OH-terminated surface, thereby forming residues that diffuse slowly on the surface after evaporation of the physisorbed species (i.e., 2D liquid). The interaction of acetone adspecies on the non-porous ASW surface resembles that on the OH-terminated Si surface, but the acetone molecules tend to be hydrated on the porous ASW film, as evidenced by their desorption during the glass-liquid transition and crystallization of water. The roles of micropores in hydration of acetone molecules are discussed from comparison with the results using mesoporous Si substrates.     

Synthesis of functionalized linear poly(divinylbenzene). II. Synthesis of poly(divinylbenzene) with hydroxyl pendants and/or endgroups

Poly(divinylbenzene) [poly(DVB)] derivatives having hydroxyl terminals and/or pendants were synthesized by chemical modifications (hydration and hydroxylation) of unsaturated linear poly(DVB) ( I ), which was prepared by the polymerization of DVB catalyzed by acetyl perchlorate. Hydroboration of both terminal and in-chain carbon–carbon double bonds in I with BH₃.THF complex yielded a fully hydrated poly(DVB) II , in which hydrophilic and hydrophobic groups are placed alternately. Selective hydroboration of the vinyl endgroups in I with 9-borabicyclo[3.3.1]nonane led to an α,ω-dihydroxy-poly(DVB) ( III ). Reaction of I with m-chloroperbenzoic acid gave fully epoxidated poly(DVB) IV , which was subsequently hydrated to yield polymer V consisting of glycol repeat units and terminals. The physical properties and reactions (chain extension and crosslinking) of these polymers were also studied.     

Infrared spectroscopic study of the interactions of nylon‐6 with water

We studied the interactions of nylon‐6 with water by following the Fourier transform infrared spectra of a hydrated thin film during dehydration. Very small changes in the spectra caused by the interactions were clearly revealed by the application of spectral subtraction. The water was found to interact with amide groups to form hydrogen bonds with non‐hydrogen‐bonded or free C?O and NH groups in the amorphous portion in the first hydration sphere. This was deduced from an analysis of minus and plus peaks appearing around the absorptions of the NH stretching, amide I band, and amide II bands in the difference spectra between the spectra during dehydration and the one at the most dehydration. The interactions of the amide groups with water were significantly stronger than the hydrogen bond between CO and NH in the crystalline portion, according to the magnitude of the frequency shift of relevant bands. Water, as the interacting counterpart, showed a distorted OH stretching absorption with two close peaks at about 3450 cm^?1. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1722–1729, 2003     

Binding strength of sodium ions in cellulose for different water contents

The interaction strength of sodium ions (Na(+)) with cellulose is investigated from first principles for varying degrees of water content. We find that the interaction of water molecules and Na(+) can be studied independently at the various OH groups in cellulose which we categorize as two different types. In the absence of water, Na(+) forms strong ionic bonds with the OH groups of cellulose. When water molecules are anchored to the OH groups via hydrogen bonds, Na(+) can eventually no longer bind to the OH groups, but will instead interact with the oxygen atoms of the water molecules. Due to the rather weak attachment of the latter to the OH groups, Na(+) becomes effectively more mobile in the fully hydrated cellulose framework. The present study thus represents a significant step toward a first-principles understanding of the experimentally observed dependence of ionic conductivity on the level of hydration in cellulose network.     

Solvation free energies and hydration structure of N-methyl-p-nitroaniline

Solvation Gibbs energies of N-methyl-p-nitroaniline (MNA) in water and 1-octanol are calculated using the expanded ensemble molecular dynamics method with a force field taken from the literature. The accuracy of the free energy calculations is verified with the experimental Gibbs free energy data and found to reproduce the experimental 1-octanol∕water partition coefficient to within ±0.1 in log unit. To investigate the hydration structure around N-methyl-p-nitroaniline, an independent NVT molecular dynamics simulation was performed at ambient conditions. The local organization of water molecules around the solute MNA molecule was investigated using the radial distribution function (RDF), the coordination number, and the extent of hydrogen bonding. The spatial distribution functions (SDFs) show that the water molecules are distributed above and below the nitrogen atoms parallel to the plane of aromatic ring for both the methylamino and nitro functional groups. It is found that these groups have a significant effect on the hydration of MNA with water molecules forming two weak hydrogen bonds with both the methylamino and nitro groups. The hydration structures around the functional groups in MNA in water are different from those that have been found for methylamine, nitrobenzene, and benzene in aqueous solutions, and these differences together with weak hydrogen bonds explain the lower solubility of MNA in water. The RDFs together with SDFs provide a tool for the understanding the hydration of MNA (and other molecules) and therefore their solubility.     

Picosecond relaxations in hydrated polyamide-6 observed by millimeter-wave spectroscopy

Absorption measurements at millimeter-wave frequencies (50–151 GHz) are reported for dried and hydrated polyamide-6. The measurements were extended over the temperature range from liquid helium to room temperature using the oversized-cavity technique. For dried polyamide-6 (water content ≤ 0.5% w/w), a nearly linear increase with frequency and an exponential increase with temperature of the absorption coefficient is found between 50 and 300 K. This frequency and temperature dependence is described by relaxation processes in asymmetric double-well potentials. The observed relaxation times are on a picosecond time scale, thus suggesting an assignment to the NH…OC hydrogen bonds and the adjacent peptide unit (O?C? N? H). Hydration results in an increase of the absorption over the whole temperature and frequency range. This is attributed to the fact that the water of hydration is adsorbed in the neighborhood of the hydrogen bonds and changes their dynamical properties. This interpretation is supported by IR-spectroscopic measurements of the shift of amide I and amide II after hydration.     

Water-induced folding of 1,7-diammoniumheptane

Effects of hydration on the gaseous structures of diprotonated 1,7-diaminoheptane and protonated heptylamine are investigated by infrared photodissociation (IRPD) spectroscopy and computational chemistry. IRPD spectra in the hydrogen bond stretching region (2800-3900 cm(-1)) indicate that 1,7-diammoniumheptane is linear and that hydration occurs predominantly by alternate solvation of the two protonated amine groups for clusters with up to 10 water molecules. The relative intensities of bonded versus free hydroxyl (OH) stretches are greater in the spectra of 1,7-diammoniumheptane with more than 12 water molecules attached than the corresponding reference spectra of heptylammonium. This indicates that in the larger clusters, 1,7-diammoniumheptane adopts a more folded conformation in which the two protonated amine groups are solvated by a single water nanodrop. These results are supported by molecular dynamics simulations which show more hydrogen bonds in representative folded structures of hydrated 1,7-diammoniumheptane versus those with linear structures. These results indicate that the increase in Coulomb energy as a result of bringing the two positive charges closer together in the folded structures is compensated for by the additional hydrogen bonds that are possible when a single nanodrop solvates both protonated amine groups.     

Structure and dynamics of methanol in water: a quantum mechanical charge field molecular dynamics study

An ab initio quantum mechanical charge field molecular dynamics simulation was carried out for one methanol molecule in water to analyze the structure and dynamics of hydrophobic and hydrophilic groups. It is found that water molecules around the methyl group form a cage-like structure whereas the hydroxyl group acts as both hydrogen bond donor and acceptor, thus forming several hydrogen bonds with water molecules. The dynamic analyses correlate well with the structural data, evaluated by means of radial distribution functions, angular distribution functions, and coordination number distributions. The overall ligand mean residence time, τ identifies the methanol molecule as structure maker. The relative dynamics data of hydrogen bonds between hydroxyl of methanol and water molecules prove the existence of both strong and weak hydrogen bonds. The results obtained from the simulation are in excellent agreement with the experimental results for dilute solution of CH(3)OH in water. The overall hydration shell of methanol consists in average of 18 water molecules out of which three are hydrogen bonded.     

Solvation structure of hydroxyl radical by Car-Parrinello molecular dynamics

Car-Parrinello molecular dynamics simulations of a hydroxyl radical in liquid water have been performed. Structural and dynamical properties of the solvated structure have been studied in details. The partial atom-atom radial distribution functions for the hydrated hydroxyl do not show drastic differences with the radial distribution functions for liquid water. The OH is found to be a more active hydrogen bond donor and acceptor than the water molecule, but the accepted hydrogen bonds are much weaker than for the hydroxide OH- ion. The first solvation shell of the OH is less structured than the water's one and contains a considerable fraction of water molecules that are not hydrogen bonded to the hydroxyl. Part of them are found to come closer to the solvated radical than the hydrogen bonded molecules do. The lifetime of the hydrogen bonds accepted by the hydroxyl is found to be shorter than the hydrogen bond lifetime in water. A hydrogen transfer between a water molecule and the OH radical has been observed, though it is a much rarer event than a proton transfer between water and an OH- ion. The velocity autocorrelation power spectrum of the hydroxyl hydrogen shows the properties both of the OH radical in clusters and of the OH- ion in liquid.     

Competition between hydrogen and halogen bonding in halogenated 1‐methyluracil: Water systems

The competition between hydrogen‐ and halogen‐bonding interactions in complexes of 5‐halogenated 1‐methyluracil (XmU; X = F, Cl, Br, I, or At) with one or two water molecules in the binding region between C5‐X and C4?O4 is investigated with M06‐2X/6‐31+G(d). In the singly‐hydrated systems, the water molecule forms a hydrogen bond with C4?O4 for all halogens, whereas structures with a halogen bond between the water oxygen and C5‐X exist only for X = Br, I, and At. Structures with two waters forming a bridge between C4?O and C5‐X (through hydrogen‐ and halogen‐bonding interactions) exist for all halogens except F. The absence of a halogen‐bonded structure in singly‐hydrated ClmU is therefore attributed to the competing hydrogen‐bonding interaction with C4?O4. The halogen‐bond angle in the doubly‐hydrated structures (150–160°) is far from the expected linearity of halogen bonds, indicating that significantly non‐linear halogen bonds may exist in complex environments with competing interactions. © 2016 Wiley Periodicals, Inc.     

Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide

The vibrational spectrum of the Ala-Leu-Ala-Leu peptide in solution, computed from first-principles simulations, shows a prominent band in the amide I region that is assigned to stretching of carbonyl groups. Close inspection reveals combined but slightly different contributions by the three carbonyl groups of the peptide. The shift in their exact vibrational signature is in agreement with the different probabilities of these groups to form hydrogen bonds with the solvent. The central carbonyl group has a hydrogen bond probability intermediate to the other two groups due to interchanges between different hydrogen-bonded states. Analysis of the interaction energies of individual water molecules with that group shows that shifts in its frequency are directly related to the interactions with the water molecules in the first hydration shell. The interaction strength is well correlated with the hydrogen bond distance and hydrogen bond angle, though there is no perfect match, allowing geometrical criteria for hydrogen bonds to be used as long as the sampling is sufficient to consider averages. The hydrogen bond state of a carbonyl group can therefore serve as an indicator of the solvent’s effect on the vibrational frequency.     

Hydration, swelling, interlayer structure, and hydrogen bonding in organolayered double hydroxides: insights from molecular dynamics simulation of citrate-intercalated hydrotalcite

Molecular dynamics (MD) simulation of the Mg/Al (3:1) layered double hydroxide (LDH), hydrotalcite (HT), containing citrate, C6H5O7(3-), as the charge balancing interlayer anion provides new molecular scale insight into the interlayer structure, hydrogen bonding, and energetics of the hydration and consequent swelling of LDH compounds containing organic and biomolecules. Citrate-HT exhibits affinity for water up to very high hydration levels, in contrast to the preferred low hydration states of most LDHs intercalated with small, inorganic anions. This result is consistent with the recent experimental observation of the delamination of lactate-HT. The high water affinity is rationalized in terms of the preference of citrate ion for hydrogen bonds (H-bonds) donated from water molecules rather than from the hydroxyl groups of the metal hydroxide layer and the need to develop an integrated interlayer H-bond network among the citrate ions, water, and -OH groups of the hydroxide layers. The changes in the orientation of citrate molecules with progressive hydration are also intimately related to its preference to accept hydrogen bonds from water.     

Conformational analysis of cellulose acetate in the dense amorphous state

Atomistic simulations of cellulose acetates (CAs) differing in their degree of substitution have been performed and analyzed in terms of conformation and interaction schemes. The stabilization of the structure of these cellulose derivatives is understood as a subtle balance between hydrogen bonds and the dipolar acetate-acetate interactions that are associated with important changes in the macromolecular conformation. On the one hand, cellulose and cellulose triacetate (CTA) are characterized by a single stabilization process (H-bonds and dipolar interactions respectively), showing a similar structure in their melt phase together with similar radii of gyration. On the other hand partially acetylated CAs combine both the conformational properties of cellulose and CTA but present an unexpected conformational domain, named C2, which induces a local hydrophobic pocket. These CAs are also further stabilized by hydrogen bonds between the hydroxyl and acetyl groups. Although idealized, the proposed models are realistic since they are in good agreement with literature experimental results.     

Carbohydrate intramolecular hydrogen bonding cooperativity and its effect on water structure

Molecular dynamics (MD) simulations combined with water-water H-bond angle analysis and calculation of solvent accessible surface area and approximate free energy of solvation were used to determine the influence of hydroxyl orientation on solute hydration and surrounding water structure for a group of chemically identical solutes-the aldohexopyranose sugars. Intramolecular hydrogen bond cooperativity was closely associated with changes in water structure surrounding the aldohexopyranose stereoisomers. The OH-4 group played a pivotal role in hydration as it was able to participate in a number of hydrogen bond networks utilizing the OH-6 group. Networks that terminated within the molecule (OH-4 --> OH-6 --> O-5) had relatively more nonpolar-like hydration than those that ended in a free hydroxyl group (OH-6 --> OH-4 --> OH-3). The OH-2 group modulated the strength of OH-4 networks through syndiaxial OH-2/4 intramolecular hydrogen bonding, which stabilized and induced directionality in the network. Other syndiaxial interactions, such as the one between OH-1 and OH-3, only indirectly affected water structure. Water structure surrounding hydrogen bond networks is discussed in terms of water-water hydrogen bond populations. The impact of syndiaxial versus vicinal hydrogen bonds is also reviewed. The results suggest that biological events such as protein-carbohydrate recognition and cryoprotection by carbohydrates may be driven by intramolecular hydrogen bond cooperativity.     

Combined Monte Carlo and molecular dynamics simulation of hydrated 18:0 sphingomyelin-cholesterol lipid bilayers

We have carried out atomic level molecular dynamics and Monte Carlo simulations of hydrated 18:0 sphingomyelin (SM)-cholesterol (CHOL) bilayers at temperatures of 20 and 50 degrees C. The simulated systems each contained 266 SM, 122 CHOL, and 11861 water molecules. Each simulation was run for 10 ns under semi-isotropic pressure boundary conditions. The particle-mesh Ewald method was used for long-range electrostatic interactions. Properties of the systems were calculated over the final 3 ns. We compare the properties of 20 and 50 degrees C bilayer systems with each other, with experimental data, and with experimental and simulated properties of pure SM bilayers and dipalmitoyl phospatidyl choline (DPPC)-CHOL bilayers. The simulations reveal an overall similarity of both systems, despite the 30 degrees C temperature difference which brackets the pure SM main phase transition. The area per molecule, lipid chain order parameter profiles, atom distributions, and electron density profiles are all very similar for the two simulated systems. Consistent with simulations from our lab and others, we find strong intramolecular hydrogen bonding in SM molecules between the phosphate ester oxygen and the hydroxyl hydrogen atoms. We also find that cholesterol hydroxyl groups tend to form hydrogen bonds primarily with SM carbonyl, methyl, and amide moieties and to a lesser extent methyl and hydroxyl oxygens.     

Solvation free energy of amino acids and side-chain analogues

The solvation free energies of amino acids and their side-chain analogues in water and cyclohexane are calculated by using Monte Carlo simulation. The molecular interactions are described by the OPLS-AA force field for the amino acids and the TIP4P model for water, and the free energies are determined by using the Bennett acceptance method. Results for the side-chain analogues in cyclohexane and in water are used to evaluate the performance of the force field for the van der Waals and the electrostatic interactions, respectively. Comparison of the calculated hydration free energies for the amino acid analogues and the full amino acids allows assessment of the additivity of the side chain contributions on the number of hydrating water molecules. The hydration free energies of neutral amino acids can be reasonably approximated by adding the contributions of their side chains to that of the hydration of glycine. However, significant nonadditivity in the free energy is found for the zwitterionic form of amino acids with polar side chains. In serine and threonine, intramolecular hydrogen bonds are formed between the polar side chains and backbone groups, leading to weaker solvation than for glycine. In contrast, such nonadditivity is not observed in tyrosine, in which the hydroxyl group is farther separated from, and therefore cannot form an intramolecular hydrogen bond with, the backbone. For histidine we find that a water molecule can form a bridge when the intramolecular hydrogen bond between the polar group and the backbone is broken.     

Two modes of O—H...O hydrogen bonding utilized in dimorphs of racemic 6‐O‐acryloyl‐2‐O‐benzoyl‐myo‐inositol 1,3,5‐orthoformate

The title compound, C₁₇H₁₆O₈, yields conformational dimorphs [forms (I) and (II)] at room temperature, separately or concomitantly, depending on the solvent of crystallization. The yield of crystals of form (I) is always much more than that of crystals of form (II). The molecule has one donor –OH group that can make intermolecular O—H...O hydrogen bonds with one of the two acceptor C=O groups, as well as with the hydroxyl O atom; interestingly, each of the options is utilized separately in the dimorphs. The crystal structure of form (I) contains one molecule in the asymmetric unit and is organized as a planar sheet of centrosymmetric dimers via O—H...O hydrogen bonds involving the OH group and the carbonyl O atom of the acryloyl group. In the crystal structure of form (II), which contains two independent molecules in the asymmetric unit, two different O—H...O hydrogen bonds, viz. hydroxyl–hydroxyl and hydroxyl–carbonyl (benzoyl), connect the molecules in a layered arrangement. Another notable feature is the transformation of form (II) to form (I) via melt crystallization upon heating to 411 K. The higher yield of form (I) during crystallization and the thermal transition of form (II) to form (I) suggest that the association in form (I) is more highly favoured than that in form (II), which is valuable in understanding the priorities of molecular aggregation during nucleation of various polymorphs.     

Molecular recognition in cyclodextrin complexes of amino acid derivatives. 1. Crystallographic studies of beta-cyclodextrin complexes with N-acetyl-L-phenylalanine methyl ester and N-acetyl-L-phenylalanine amide pseudopeptides

Cyclodextrins (CDs) are widely utilized in studies of chiral and molecular recognition. By changing the functionality of the guest molecule, the effect of such changes on recognition by the host CD molecule can be examined. We report crystal structure determinations for two nearly isomorphous complexes of phenylalanine derivatives: beta-CD/N-acetyl-L-phenylalanine methyl ester and beta-CD/N-acetyl-L-phenylalanine amide. The complexes crystallize as hydrated head-to-head host dimers with two included guest molecules in space group P1. The crystal packing is such that it presents a nonconstraining hydrophobic pocket adjacent to a hydrophilic region, where potential hydrogen-bonding interactions with hydroxyl groups of neighboring cyclodextrin molecules and waters of hydration can occur. The two host molecules display very similar conformations; only a few of the primary hydroxyl groups are conformationally disordered. There are a number of changes in the location of water of hydration molecules, some of which are the result of different hydrogen-bonding interactions. For the different guest molecules, similar modes of penetration are observed in the CD torus; however, there is a 0.985-A shift in the position of the guest molecules in the host torus, which takes place without changing the hydrophobic interactions displayed by the phenyl side chains. This observation and the thermal motion of the guest molecules in the ester complex are taken as evidence that complex binding forces are weak. The pseudopeptides experience a significant degree of flexibility in the crystalline environment provided by CD dimers. Conformational differences of the pseudopeptide backbones and the presence of disordered water molecules in the host-guest interface provide examples of different hydrogen-bonding schemes of similar potential energy. The crystal system presents an opportunity to establish a database of molecular interactions for small peptides and peptide analogues with waters of hydration and functional groups in nonconstraining binding environments.