A guest-induced reversible switching of a self-assembled H-bonded supramolecular framework

A new class of organic crystalline 2,2'-biphenol-based H-bonded material displaying 1D-channels encapsulating solvent molecules is described. A reversible guest-induced crystal-to-crystal conversion between the solvated H-bonded phase and a compact H-bonded non-solvated phase was observed. The energy competition between intramolecular H-bonds formation and solvation of organic pores has been characterized using PACHA calculations.     

Solvation of calcium ions in methanol-water mixtures: molecular dynamics simulation

Molecular dynamics simulations of CaCl2 solutions in water and methanol-water mixtures, with methanol concentrations of 5, 10, 50, and 90 mol %, at room temperature, have been performed. The methanol and water molecules have been modeled as flexible three-site bodies. Solvation of the calcium ions has been discussed on the basis of the radial and angular distribution functions, the orientation of the solvent molecules, and their geometrical arrangement in the coordination shells. Analysis of the H-bonds of the solvent molecules coordinated by Ca2+ has been done. Residence time of the solvent molecules in the coordination shell has been calculated. The preferential hydration of the calcium ions has been found over the whole range of the mixture composition. The water concentration in the first and second coordination shells of Ca2+ significantly exceeds the water content in the solution, despite the very similar interaction energy of the calcium ion with water and methanol. In aqueous solution and methanol-water mixtures, the first coordination shell of Ca2+ is irregular and long-living. The solvent molecules prefer the anti-dipole arrangement, but, in aqueous solutions and water-rich mixtures, the water molecules in the primary shell have only one H-bonded neighbor.     

Transition from patchlike to clusterlike inhomogeneity arising from hydrogen bonding in water

Assembling of water molecules via hydrogen bonding has been studied by molecular dynamics simulations using flexible potential model. The relationship between the number of H-bonds per molecule, n(HB), the size of H-bonded nets, k, and the size of patches of four-bonded molecules, k(4), has been examined for several thermodynamic states of water ranging from ambient to supercritical conditions. Two kinds of structural inhomogeneity have been found: the patchlike associated with the mean n(HB)> 2.0 and the clusterlike for n(HB)< 1.9. In compressed water up to ~473 K patches coexist with less ordered nets, both constituting the gel-like H-bonded network. The size of patches steeply decreases with the increasing temperature and the decreasing density of water. The inhomogeneity resulting from the presence of patches disappears above 473 K. This feature is associated with the rapid increase in the fraction of unbound molecules and with the breakage of the gel-like network into a variety of H-bonded clusters leading to the clusterlike structural inhomogeneity. In contrast to the patchlike inhomogeneity an increase in temperature and a decrease in density make this kind of inhomogeneity more pronounced. A degree of connectivity of H-bonds has been characterized by a parameter P(g) defined as the total fraction of molecules belonging to the H-bonded clusters of size k ≥ 5. The simulation-derived values of P(g) agree well with the predictions of the random bond theory giving the explicit expression for P(g) as a function of the mean n(HB). Going from ambient to supercritical conditions, we have found that the patchlike inhomogeneity is connected with the very slight reduction in P(g), whereas the clusterlike inhomogeneity generates a steep linear decrease of P(g) with the decreasing mean n(HB). The self-diffusion coefficient calculated for the thermodynamic states of water showing the clusterlike inhomogeneity has occurred to be inversely proportional to the density. We have also found that the clusterlike inhomogeneity is associated with the linear correlation between P(g) and the macroscopic properties of water: the static dielectric constant, the viscosity, and the density. The provided relationships allow one to estimate the degree of connectivity of hydrogen bonds from the measured macroscopic quantities.     

Spectroscopic Signatures of Internal Hydrogen Bonds of Brønsted-Acid Sites in the Zeolite H-MFI

The location of Brønsted-acid sites (bridging OH groups, b-OH) at different crystallographic positions of zeolite catalysts influences their reactivity due to varying confinement. Selecting the most stable b-OH conformers at each of the 12 T-sites (T=Si/Al) of H-MFI, a representative set of 26 conformers is obtained which includes free b-OH groups pointing into the empty pore space and b-OH groups forming H-bonds across five- or six-membered rings of TO₄ tetrahedra. Chemically accurate coupled-cluster-quality calculations for periodic models show that the strength of internal H-bonds and, hence, the OH bond length vary substantially with the framework position. For 11 of the 19 H-bonded b-OH groups examined, our predictions fall into the full width at half maximum range of the experimental signals at 3250±175 cm⁻¹ and 7.0±1.4 ppm which supports previously debated assignments of these signals to H-bonded b-OH sites.     

How to achieve self-assembly in polar solvents based on specific interactions? Some general guidelines

In general, self-assembly in polar solutions requires a combination of several non-covalent interactions within one binding motif. Besides the combination of H-bonds and hydrophobic or aromatic stacking interactions, in the last few years H-bonded ion pairs have been proven useful in this context. Also the molecular rigidity and the extent of intra- versus intermolecular interactions within the monomer play an important role in determining the self-assembling properties of a given monomer. We present some general guidelines and illustrative examples of various approaches that have been pursued in the literature before finally concentrating on a case study from our own work, the dimerization of a guanidiniocarbonyl pyrrole carboxylate zwitterion. This zwitterion forms stable dimers with K > 10(9) M(-1) in DMSO and >10(2) M(-1) even in water and can not only be used to study the importance of various non-covalent interactions for self-assembly in polar solvents but also to construct large nanostructures.     

Molecular basis of the recognition process: hydrogen-bonding patterns in the guanine primary recognition site of ribonuclease T1

Investigation of the intrinsic H-bonding pattern of the guanine complex with a sizable segment (from Asn43 to Glu46) of the primary recognition site (PRS) in RNase T1 at the B3LYP/6-311G(d,p) level of theory enables the electronic density characteristics of the H-bonding patterns of the guanine-PRS complexes to be identified. The perfect H-bonding pattern in the guanine recognition site is achieved through the guanine complex interactions with the large segment of the PRS. Two significant short H-bonds, O epsilon 1...HN1 and O epsilon 2...HN2, have been identified. The similar short H-bond distances found in the anionic GC- base pair and in this study suggest that the short hydrogen-bond distances may be characteristic of the multiple H-bonded anionic nucleobases. The H-bonding energy distribution, the geometric analysis of the H-bonding pattern, and the electron structure characteristics of the H-bonds in the guanine PRS of RNase T1 all suggest that the O epsilon 1...HN1 and O epsilon 2...HN2 side-chain H-bonds dominate the binding at the guanine recognition site of RNase T1. Also, the geometry evidence, the electron structure characteristics, and the properties of the bond critical points of the H-bonds reveal that the side-chain H-bonding and the main-chain H-bonding are mutually intensifying. Thus the positive cooperativity between Asn43 to Tyr45 and Glu46 is proposed.     

A temperature and pH double sensitive cholesteric polymer film from a photopolymerizable chiral hydrogen-bonded assembly

In this study, a novel H-bonded cholesteric polymer film responding to temperature and pH by changing the reflection color was fabricated. The H-bonded cholesteric polymer film was achieved by UV-photopolymerizing a cholesteric liquid crystal (Ch-LC) monomers mixture containing a photopolymerizable chiral H-bonded assembly (PCHA). The cholesteric polymer film based on PCHA can be thermally switched to reflect red color from the initial green/yellow color as temperature is increased, which is due to a change in helical pitch induced by the weakening of H-bonded interaction in the polymer film. Additionally, the selective reflection band (SRB) of the cholesteric polymer film in solution with pH > 7 showed an obvious red shift with increasing pH values. While the SRB of the cholesteric polymer film in solutions with pH = 7 and pH < 7 hardly changed. This pH sensitivity in solutions with pH > 7 could be explained by the breakage of H-bonds in the cholesteric polymer film and the structure changes induced by―OH and―K + ions in the alkaline solution. In contrast, it couldn’t happen in the neutral and acidic solutions. The cholesteric polymer film in this study can be used as optical/photonic papers, optical sensors and LCs displays, etc.     

Sequence-specific, dynamic covalent crosslinking in aqueous media

This article describes an associating system that integrates the specificity of multiple hydrogen bonding and the strength of dynamic covalent interactions. Linear oligoamides that sequence-specifically pair into H-bonded duplexes in nonpolar solvents were modified with S-trityl groups, allowing the reversible formation of disulfide bonds. The disulfide-crosslinking reactions of oligoamides capable of pairing via two, four, and six intermolecular H-bonds, along with several control strands, were examined using ESI, MALDI-TOF, reverse phase HPLC, and two-dimensional NMR. Results from these studies demonstrate that this system possesses both the high fidelity of multiply H-bonded assemblies and the high stability of covalent interaction, leading to the sequence-specific crosslinking of complementary oligoamides in not only nonpolar (methylene chloride) solutions but also highly competitive (aqueous) media. Experiments were designed to systematically probe the mechanism behind the specific formation of the sequence-matched products, which revealed a thermodymically controlled process. Multiple pairs in the same solution were crosslinked in a sequence-specific fashion. In addition, a length-dependent selectivity was also observed. Thus, oligoamides with different lengths or sequences did not crosslink into mismatched products. As few as two H-bonds is sufficient to bias the specific formation of the crosslinked product in aqueous media, suggesting that associating units with tunable sizes, high stability, and high specificity can be conveniently designed. The combination of H-bonding and dynamic covalent interactions represents a new, generalizable strategy for developing highly specific molecular associating units that are stable in a wide variety of media. These associating units will greatly facilitate the construction of various structures with many applications.     

Photoluminescent color tuning in fluorene derivative/copolymer composite films based on H-bonds

Reversible addition-fragmentation chain transfer (RAFT) polymerization is used to synthesize diblock and random copolymers of poly[(2-trifluoroethyl methacrylate)-co-(methacrylic acid)]. Copolymer films doped with fluorene derivatives comprised of pyridine groups exhibit reversible photoluminescent (PL) color tuning by adjusting the location of fluorene derivatives in H-bonds or non-H-bonds environments. The composite films exhibit green and blue photoluminescence with and without effective H-bonding between the pyridine ring in the fluorene derivative and the carboxylic acid side group, respectively. At elevated temperatures, the H-bonded structure dissociates and the fluorene derivative migrates to the hydrophobic block in the diblock polymer, and they do not form H-bonds upon cooling. However, re-formation of H-bonds also occurs upon cooling random copolymers. Moreover, adjusting the annealing temperature and the solvent annealing reversibly tunes the PL color in the diblock copolymer composite films.     

Hydrogen-bonded networks in ethanol proton wires: IR spectra of (EtOH)qH+-Ln clusters (L = Ar/N2, q < or = 4, n < or = 5)

Isolated and microsolvated protonated ethanol clusters, (EtOH)qH+-Ln with L = Ar and N2, are characterized by infrared photodissociation (IRPD) spectroscopy in the 3 microm range and quantum chemical calculations. For comparison, also the spectrum of the protonated methanol dimer, (MeOH)2H+, is presented. The IRPD spectra carry the signature of H-bonded (EtOH)qH+ chain structures, in which the excess proton is either strongly localized on one or (nearly) equally shared between two EtOH molecules, corresponding to Eigen-type ion cores (EtOH2+ for q = 1, 3) or Zundel-type ion cores (EtOH-H+-HOEt for q = 2, 4), respectively. In contrast to neutral (EtOH)q clusters, no cyclic (EtOH)qH+ isomers are detected in the size range investigated (q < or = 4), indicative of the substantial impact of the excess proton on the properties of the H-bonded ethanol network. The acidity of the two terminal OH groups in the (EtOH)qH+ chains decreases with the length of the chain (q). Comparison between (ROH)qH+ with R = CH3 and C2H5 shows that the acidity of the terminal O-H groups increases with the length of the aliphatic rest (R). The most stable (EtOH)qH+-Ln clusters with n < or = 2 feature intermolecular H-bonds between the inert ligands and the two available terminal OH groups of the (EtOH)qH+ chain. Asymmetric microsolvation of (EtOH)qH+ with q = 2 and 4 promotes a switch from Zundel-type to Eigen-type cores, demonstrating that the fundamental structural motif of the (EtOH)qH+ proton wire sensitively depends on the environment. The strength of the H-bonds between L and (EtOH)qH+ is shown to provide a rather sensitive probe of the acidity of the terminal OH groups.     

The structure of H-bonded clusters in sub- and supercritical water

The structure of H-bonded complexes in sub- and supercritical water in regions close to and remote from the saturation curve was studied. The Car-Parrinello method was used to calculate water dipole moment distributions in 11 thermodynamic states. The dependence of the mean dipole moment of water molecules on the size of clusters and number of H-bonds was obtained.     

Isotope effects in liquid water by infrared spectroscopy. IV. No free OH groups in liquid water

The presence of free OH (OH not H-bonded) in bulk water is a key element for the determination of its molecular structure. The OH covalent bond infrared (IR) absorption is highly sensitive to the molecular environment. For this reason, IR spectroscopy is used for the determination of free OH. A workable definition of this is obtained with methanol (MeOH) in hexane where minute quantities of free OH are present. These absorb at 3654?cm(-1) (a 27?cm(-1) redshift from the gas position) with a full width at half height of 35?cm(-1). The IR spectrum of water between room temperature and 95?°C does not display such a band near 3650?cm(-1). This indicates that we do not see, in the IR spectra, the "free" OH group. From this we conclude that it is not present in liquid water at least down to the 1000 ppm level which is the limit of detectivity of our spectrometer. Other spectroscopic considerations of methanol and water in acetonitrile solutions indicate that weak H-bonds are also not present in liquid water.     

Matrix-isolation FT-IR study and theoretical calculations of the vibrational, tautomeric and H-bonding properties of hypoxanthine

The neutral compound hypoxanthine is investigated using the technique of matrix-isolation FT-IR spectroscopy combined with density functional theory (DFT) and ab initio methods. Two theoretical methods (RHF and DFT/B3-LYP) are compared for vibrational frequency prediction, and four methods (RHF//RHF, MP2//RHF, DFT//DFT and MP2//DFT) for prediction of the relative energies of the tautomers and the interaction energies of the complexes. All the possible tautomeric forms have been considered theoretically, and the results indicate that two oxo forms (O17 and O19) and one hydroxy form (H9-r1) are the three most stable forms. The experimental FT-IR spectra are consistent with this prediction, and nearly all the characteristic spectral features of these forms have been identified in the spectrum. A theoretical study of the H-bonded complexes of these three tautomers with water is also performed. Several structures have been found for each form and the results demonstrate that the closed complexes with two H-bonds are the most stable systems due to the H-bond cooperative effect.     

Understanding hydrogen bonding of hydroxamic acids with some amino acid side chain model molecules

The hydrogen-bonding abilities of a few amino acid side chains have been studied through aggregation of methylamine, methanol, and acetic acid (as model molecules) with formo- and thioformo- hydroxamic acids using ab initio calculations. Forty six aggregates representing all possible H-bond interactions between these amino acid side chain groups and two most stable keto and enol tautomeric forms of both hydroxamic acids have been optimized. Although participation of conventional H-bond donors and acceptors leads to significant stabilization energies, yet C–H···O, C–H···N, S–H···O, and S–H···N etc. unconventional H-bonds also contribute to stabilize interactions in many aggregates. Strength of H-bonds of the molecules with formo- and thioformo- hydroxamic acid studied follows the order acetic acid > methylamine > methanol. A comparative study of atomic charges and orbital interactions employing NBO analysis has been carried out to explore the role of bond polarizations, charge transfer, and electron delocalizations as contributors to stabilization energy.     

A Model of Hydrogen-Bonded Liquids

The orientation defect model can be used for quantitative estimates and for understanding the properties of H-bonded liquids, such as water and alcohol. The defect concentrations can be determined by vibrational spectroscopy, and the applicability of the approximation procedure derives from considering H-bonds as chemical equilibria. Possible extensions of the simple model are critically discussed.     

Hydrogen bonded bimolecular complexes of carboxylic acids in the vapor phase : Observation and characterization by low resolution microwave spectroscopy

Various carboxylic acids and amides are shown to form H-bonded bimolecules with trifluoroacetic acid in the vapor phase. These bimolecules have been observed directly by low resolution microwave spectroscopy which gives rotational constants in agreement with those calculated with the assumption of a planar, 8-membered ring geometry for the H-bonded portion of the structure. A number of combinations did not provide observable spectra, and reasons are proposed why the bimolecules probably did not form in certain of these cases. Approximate dipole moments are obtained for the H-bonded bimolecular complexes.     

Single-conformation ultraviolet and infrared spectroscopy of model synthetic foldamers: beta-peptides Ac-beta3-hPhe-beta3-hAla-NHMe and Ac-beta3-hAla-beta3-hPhe-NHMe

The conformational preferences and infrared and ultraviolet spectral signatures of two model beta-peptides, Ac-beta3-hPhe-beta3-hAla-NHMe (1) and Ac-beta3-hAla-beta3-hPhe-NHMe (2), have been explored under jet-cooled, isolated-molecule conditions. The mass-resolved, resonant two-photon ionization spectra of the two molecules were recorded in the region of the S0-S1 origin of the phenyl substituents (37,200-37,800 cm(-1)). UV-UV hole-burning spectroscopy was used to determine the ultraviolet spectral signatures of five conformational isomers of both 1 and 2. Transitions due to two conformers (labeled A and B) dominate the R2PI spectra of each molecule, while the other three are minor conformers (C-E) with transitions a factor of 3-5 smaller. Resonant ion-dip infrared spectroscopy was used to obtain single-conformation infrared spectra in the 3300-3700 cm(-1) region. The infrared spectra showed patterns of NH stretch transitions characteristic of the number and type of intramolecular H-bonds present in the beta-peptide backbone. For comparison with experiment, full optimizations of low-lying minima of both molecules were carried out at DFT B3LYP/6-31+G*, followed by single point MP2/6-31+G* and selected MP2/aug-cc-pVDZ calculations at the DFT optimized geometries. Calculated harmonic vibrational frequencies and infrared intensities for the amide NH stretch vibrations were used to determine the beta-peptide backbone structures for nine of the ten observed conformers. Conformers 1B, 1D, and 2A were assigned to double ring structures containing two C6 H-bonded rings (C6a/C6a), conformers 1A and 2B are C10 single H-bonded rings, conformers 1C and 2D are double ring structures composed of two C8 H-bonded rings (C8/C8), and conformers 1E and 2E are double ring/double acceptor structures in which two NH groups H-bond to the same C=O group, thereby weakening both H-bonds. Both 1E and 2E are tentatively assigned to C6/C8 double ring/double acceptor structures, although C8/C12 structures cannot be ruled out unequivocally. Finally, no firm conformational assignment has been made for conformer 2C whose unusual infrared spectrum contains one very strong H-bond with NH stretch frequency at 3309 cm(-1), a second H-bonded NH stretch fundamental of more typical value (3399 cm(-1)), and a third fundamental at 3440 cm(-1), below that typical of a branched-chain free NH. The single conformation spectra provide characteristic wavenumber ranges for the amide NH stretch fundamentals ascribed to C6 (3378-3415 cm(-1)), C8 (3339-3369 cm(-1)), and C10 (3381-3390 cm(-1)) H-bonded rings.     

Molecular structures, hydrogen bonding and electrostatic interactions of 3-(2-bromo-pyridinium)-propionic acid and 3-(pyridinium)-pivalic acid halides

Intra- and intermolecular interactions and the conformations of 3-(2-bromo-pyridinium)-propionic acid bromide (1) and 3-(pyridinium)-pivalic acid chloride (2) have been studied by X-ray diffraction and theoretically. In these complexes, Br⁻ and Cl⁻ anions are H-bonded to the COOH group and interact electrostatically with the positively charged nitrogen atoms of neighbouring molecules. To analyse these interactions theoretically, the structures of monomers and dimers in various configurations were optimized by PM3 and BLYP/6-31G(d,p) methods. The analysis confirmed the vital role of both the H-bonds and electrostatic interactions (intra- and intermolecular) for the molecular conformation and the ionic aggregation in the solid state.     

Influence of H-bond strength on chelate cooperativity

Intermolecular complexes formed between metalloporphyrins and pyridine ligands equipped with multiple H-bond donors and acceptors have been used to measure the free energy contributions due to intramolecular ether-phenol H-bonding in the 24 different supramolecular architectures using chemical double mutant cycles in toluene. The ether-phenol interactions are relatively weak, and there are significant populations of partially bound states where between zero and four intramolecular H-bonds are made in addition to the porphyrin-ligand coordination interaction. The complexes were analyzed as ensembles of partially bound states to determine the effective molarities for the intramolecular interactions by comparison with the corresponding intermolecular ether-phenol H-bonds. The properties of the ether-phenol interactions were compared with phosphonate diester-phenol interactions in a closely related ligand system, which has more powerful H-bond acceptor oxygens positioned at the same location on the ligand framework. This provides a comparison of the properties of weak and strong H-bonds embedded in the same 24 supramolecular architectures. When the product of the intermolecular association constant and the effective molarity KEM > 1, there is a linear increase in the free energy contribution due to H-bonding with log EM, because the intramolecular interactions contribute fully to the stability of the complex. When KEM < 1, the H-bonded state is not significantly populated, and there is no impact on the overall stability of the complex. Intermolecular phosphonate diester-phenol H-bonds are 2 orders of magnitude stronger than ether-phenol H-bonds in toluene, so for the phosphonate diester ligand system, 23 of the 24 supramolecular architectures make intramolecular H-bonds. However, only 8 of these architectures lead to detectable H-bonding in the ether ligand system. The other 15 complexes have a suitable geometry for formation of H-bonds, but the ether-phenol interaction is not strong enough to overcome the reorganization costs associated with making intramolecular contacts, i.e., KEM < 1 for the ether ligands, and KEM > 1 for the phosphonate diester ligands. The values of EM measured for two different types of H-bond acceptor are linearly correlated, which suggests that EM is a property of the supramolecular acrchitecture. However, the absolute value of EM for an intramolecular phosphonate diester H-bond is about 4 times lower than the corresponding value for an intramolecular ether-phenol interaction embedded in the same supramolecular framework, which suggests that there may be some interplay of K and EM.     

Charge-assisted intramolecular hydrogen bonds in disubstituted cyclohexane derivatives

In this paper, the N(+)-H···N, N(+)-H···O, and O-H···O(-) charge-assisted intramolecular hydrogen bonds (CAHBs) are investigated using different theoretical approaches. Monocharged cyclohexyldiamines (CHDA), aminocyclohexanols (ACHO), and cyclohexanediols (CHDO) are used as model compounds. Geometry optimizations at the MP2/aug-cc-pVDZ level are used to find the equilibrium structures for all possible H-bonded conformers. CAHBs are characterized geometrically and spectroscopically, and their energy is evaluated by means of homodesmic reactions. By comparison with the neutral forms, the presence of the charge is found to have a deep influence on the geometric and energetic H-bond parameters. In addition, these parameters are strongly dependent on the type of the groups involved as well as on their relative position in the cyclohexyl ring. For the systems under study, the H-bond energies vary from -23 to -113 kJ mol(-1), being classified from moderate to strong H-bonds. These H-bonds are also characterized by the application of the NBO and AIM theories. NBO analysis reveals that the energy corresponding to the charge transfer between the lone-pairs of the electron donor group and the antibonding orbitals of the acceptor group represents an important contribution in the H-bond stabilization. From the application of the AIM theory it is possible to see that these H-bonds possess some covalence which varies according to the type and relative position of the intervenient groups.