Hydrogen Bond Donor Molecules Research Articles

Adsorption, Dissociation, and Dehydrogenation of Water Monomer and Water Dimer on the Smallest 3D Aluminum Particle. The O-H Dissociation Barrier Disappears for the Dimer.

We present a detailed mechanistic study on the interaction and reaction of water monomer and water dimer with the smallest 3D aluminum particle (Al6) by employing density functional and explicitly correlated coupled cluster CCSD(T)-F12 theories. Water adsorption, dissociation, and dehydrogenation are considered. For the monomer reaction, where core-valence correlation and an extrapolation to the complete basis set limit is allowed for, our coupled cluster calculations predict the O-H dissociation barrier of about 2 kcal/mol. For the dimer reaction, two distinct reaction paths are identified, initiated by forming separate dimer complexes wherein (H2O)2 adsorbs mainly via the oxygen atom of the donor H2O molecule. The key O-H dissociation transition states of the dimer reaction involve a concerted migration of two H atoms resulting in the dissociation of the donor molecule and formation of the OH-water complex adsorbed on the metal cluster's surface. The most remarkable feature of both dimer reaction energy profiles is the lack of the overall energy barrier for the (rate-determining) O-H dissociation. The hydrogen bond acceptor molecule is suggested to have an extra catalytic effect on the O-H dissociation barrier of the hydrogen bond donor molecule by removing this barrier. A similar effect on the dehydrogenation step is indicated.

Experimental determination of the LLE data of systems consisting of {hexane + benzene + deep eutectic solvent} and prediction using the Conductor-like Screening Model for Real Solvents

Recently, deep eutectic solvents (DESs) have proven to be excellent extracting agents in the separation of aromatic components from their mixtures with aliphatic compounds. The tunable properties of the DESs allow to tailor-make optimal solvents for this application. In this work type III DESs, based on chloride quaternary ammonium salts (tetramethylammonium chloride, tetraethylammonium chloride, tetrabutylammonium and tetrahexylammonium chloride) as hydrogen bond acceptor molecules and polyols (ethylene glycol and glycerol) as hydrogen bond donor molecules were used. The liquid-liquid equilibrium (LLE) data of the system {hexane+benzene+DES} was measured at room temperature and atmospheric pressure. The solute distribution ratio and the selectivities were calculated and compared. The highest solute distribution ratios were obtained for salts with long alkyl chain length as hydrogen bond acceptor molecules and for ethylene glycol as hydrogen bond donor molecules.COSMO-RS was used for the prediction of the LLE data of the studied systems. It was found that both the LLE data and the solute distribution ratio of the ternary systems containing DESs can be qualitatively well predicted using this model. Moreover, the LLE data was quantitatively predicted within a root mean square error of 10wt% without the need of any experimental data. This implies that COSMO-RS is an effective screening tool for the optimization of the separation process of aromatic components from {aliphatic+aromatic} mixtures using DESs as extracting agents.

Pharmacophore modeling using site-identification by ligand competitive saturation (SILCS) with multiple probe molecules.

Receptor-based pharmacophore modeling is an efficient computer-aided drug design technique that uses the structure of the target protein to identify novel leads. However, most methods consider protein flexibility and desolvation effects in a very approximate way, which may limit their use in practice. The Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling protocol (SILCS-Pharm) was introduced recently to address these issues, as SILCS naturally takes both protein flexibility and desolvation effects into account by using full molecular dynamics simulations to determine 3D maps of the functional group-affinity patterns on a target receptor. In the present work, the SILCS-Pharm protocol is extended to use a wider range of probe molecules including benzene, propane, methanol, formamide, acetaldehyde, methylammonium, acetate and water. This approach removes the previous ambiguity brought by using water as both the hydrogen-bond donor and acceptor probe molecule. The new SILCS-Pharm protocol is shown to yield improved screening results, as compared to the previous approach based on three target proteins. Further validation of the new protocol using five additional protein targets showed improved screening compared to those using common docking methods, further indicating improvements brought by the explicit inclusion of additional feature types associated with the wider collection of probe molecules in the SILCS simulations. The advantage of using complementary features and volume constraints, based on exclusion maps of the protein defined from the SILCS simulations, is presented. In addition, reranking using SILCS-based ligand grid free energies is shown to enhance the diversity of identified ligands for the majority of targets. These results suggest that the SILCS-Pharm protocol will be of utility in rational drug design.

Pharmacophore Modeling using Site-Identification by Ligand Competitive Saturation (SILCS) Method with Multiple Probe Molecules

Receptor-based pharmacophore modeling is an efficient computer-aided drug design technique that uses the structure of the target protein to identify novel leads. However, most methods consider protein flexibility and desolvation effects in a very approximate way, which may limit their use in practice. The Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling protocol (SILCS-Pharm) was introduced recently to address these issues, as SILCS naturally takes both protein flexibility and desolvation effects into account by using full molecular dynamics simulations to determine 3D maps of the functional group-affinity patterns on a target receptor. In the present work, the SILCS-Pharm protocol is extended to use a wider range of probe molecules including benzene, propane, methanol, formamide, acetaldehyde, methylammonium, acetate and water. This approach removes the previous ambiguity brought by using water as both the hydrogen-bond donor and acceptor probe molecule. The new SILCS-Pharm protocol is shown to yield improved screening results, as compared to the previous approach based on three target proteins. Further validation of the new protocol using five additional protein targets showed improved screening compared to those using common docking methods, further indicating improvements brought by the explicit inclusion of additional feature types associated with the wider collection of probe molecules in the SILCS simulations. The advantage of using complementary features and volume constraints, based on exclusion maps of the protein defined from the SILCS simulations, is presented. In addition, reranking using SILCS-based ligand grid free energies is shown to enhance the diversity of identified ligands for the majority of targets. These results suggest that the SILCS-Pharm protocol will be of utility in rational drug design.

Biomass-Derived Platform Chemicals: Thermodynamic Studies on the Extraction of 5-Hydroxymethylfurfural from Ionic Liquids

Activity coefficients at infinite dilution, γi∞, of 13 solutes such as alkanes, alkenes, alkylbenzenes, alcohols, esters, and ethers in six 1,3-dialkylimidazolium- or tetraalkylphosphonium-based ionic liquids have been determined by gas chromatography using the ionic liquids as the stationary phase. Furthermore, the solubility of 5-hydroxymethylfurfural (HMF) in these solutes and the solubility of the solutes in 1-butyl-3-methylimidazolium methanesulfonate ([C4mim][CH3SO3]) was assessed. The combination of these data allowed for the interpretation of prevailing interactions on molecular level and resulted in the hypothesis that an ideal extracting agent must feature hydrogen bond acceptor properties to obtain high extraction efficiencies of hydrogen bond donor molecules such as HMF from this ionic liquid. Extraction data obtained using the thus proposed extracting agents demonstrated that this hypothesis was correct and can in future be transposed to other separation problems. In the case of a multifunctional molecule such as HMF, extraction efficiencies are however in general low and can only be little improved by removing other potential interaction sites from the ionic liquid’s cation: hence, in the N-ethyl-N-methylpyrrolidinium analogue [C2C1pyr][CH3SO3], π–π-interactions between cation and HMF cannot form, which increases the extraction efficiency somewhat.

Synthesis and self-assembly of halogen-bond donor–spacer–hydrogen-bond donor molecules: polymeric liquid crystals induced by combination of intermolecular halogen- and hydrogen-bonding interactions

A series of linear molecules of 4-(n-(2,3,5,6-tetrafluoro-4-iodophenoxy)alkoxy)benzoic acid (4a–d) bearing a hydrogen-bond donor on one end of the molecule and a halogen-bond donor on another end was synthesised. Compounds 4a–d formed composite halogen- and hydrogen-bonded polymeric complexes with bis(4-trans-4′-stilbazolyl)-oligo(ethylene glycol) (5a-c), as verified by Fourier transform infrared spectroscopy and differential scanning calorimetry (DSC). The degree of polymerisation of complexes 4a–d/5a–c was estimated to be in the range of 11–25 using the Flory equation, suggesting the polymeric nature of the complexes. The complexes 4a–d/5a–c showed thermotropic mesophases upon cooling, confirmed by polarised optical microscopy and DSC. The liquid crystals exhibited significantly broader mesophase temperature ranges than those induced by the halogen bond alone, indicating that the introduction of a more flexible hydrogen-bonded mesogenic core in halogen-bonded polymeric assembly likely led to a marked improvement in the stability of the mesophase by way of modulating the flexibility of the polymeric chains. The novel halogen- and hydrogen-bonded assembly of this type is thought to provide an excellent model upon which to build supramolecular polymeric liquid crystals through a precise manipulation of the two types of non-covalent interactions.

Hydrogen bonding of ethanol in supercritical mixtures with CO2 by 1H NMR spectroscopy and molecular simulation

Abstract High pressure 1 H NMR spectroscopic studies of mixtures of CO 2 and ethanol (EtOH) were conducted at a wide range of temperatures (293.15, 308.15, 323.15, and 338.15 K), pressures (5–25.5 MPa) and concentrations ( x EtOH = 0.0017–1.0 mol/mol). The relative chemical shift of the protons in the hydroxyl group was used to describe the degree of hydrogen bonding in ethanol. The dependence of the results on pressure is only weak. The quantification of hydrogen bonding was based on the assumption that the observed shift results from a superposition of the shifts of ethanol molecules differing in the way they are hydrogen bonded. Three different types were distinguished: monomer, donor and acceptor. The monomer shift was found from an extrapolation of the NMR data. Molecular dynamics simulations based on force fields from the literature were carried out for the same mixtures at the same conditions and were used to determine the distribution of differently hydrogen bonded ethanol species. Geometric cluster criteria from the literature were used for identifying the hydrogen bonding and the different types of ethanol species. Using the species distribution from the molecular simulations together with the NMR spectroscopic data, the two state independent numbers for the shifts of the hydrogen bond donor and hydrogen bond acceptor molecules were found. Even though only these two parameters are fitted the large set of experimental data is very well described. This confirms our earlier observations on the CO 2 –methanol system that molecular models of the simple Lennard–Jones plus point charge type as they are used here can describe both thermodynamic properties and the structural effects of hydrogen bonding in solutions.

The effect of intermolecular hydrogen bonding on the planarity of amides

Ab initio and density functional theory (DFT) calculations on some model systems are presented to assess the extent to which intermolecular hydrogen bonding can affect the planarity of amide groups. Formamide and urea are examined as archetypes of planar and non-planar amides, respectively. DFT optimisations suggest that appropriately disposed hydrogen-bond donor or acceptor molecules can induce non-planarity in formamide, with OCNH dihedral angles deviating by up to ca. 20° from planarity. Ab initio energy calculations demonstrate that the energy required to deform an amide molecule from the preferred geometry of the isolated molecule is more than compensated by the stabilisation due to hydrogen bonding. Similarly, the NH(2) group in urea can be made effectively planar by the presence of appropriately positioned hydrogen-bond acceptors, whereas hydrogen-bond donors increase the non-planarity of the NH(2) group. Small clusters (a dimer, two trimers and a pentamer) extracted from the crystal structure of urea indicate that the crystal field acts to force planarity of the urea molecule; however, the interaction with nearest neighbours alone is insufficient to induce the molecule to become completely planar, and longer-range effects are required. Finally, the potential for intermolecular hydrogen bonding to induce non-planarity in a model of a peptide is explored. Inter alia, the insights obtained in the present work on the extent to which the geometry of amide groups may be deformed under the influence of intermolecular hydrogen bonding provide structural guidelines that can assist the interpretation of the geometries of such groups in structure determination from powder X-ray diffraction data.

Supramolecular main-chain liquid crystalline polymers and networks with competitive hydrogen bonding: a study of flexible bis-acids and a mixture of rigid and flexible polypyridyls

A series of novel liquid crystalline supramolecular networks formed through hydrogen bonds have been synthesised. These networks are based on flexible bi-benzoic acid and two types of pyridyl species – a small rigid bipyridyl capable of forming liquid crystalline phases and polyfunctional non-mesogenic pyridyl species that can compete for available hydrogen bond donor molecules. It was found that the networks display monotropic nematic character at high concentrations of disrupting net points – up to 50% for tetrapyridyls, 40% for tripyridyls and 35% for bipyridyls. Weak smectic phases were observed in all systems in loadings up to 10% of each disrupting unit. It is believed that the reversibility of the hydrogen bond allows for the formation of the ordered mesophases in the presence of the non-liquid crystalline groups.

Ultrafast 2D IR anisotropy of water reveals reorientation during hydrogen-bond switching

Rearrangements of the hydrogen bond network of liquid water are believed to involve rapid and concerted hydrogen bond switching events, during which a hydrogen bond donor molecule undergoes large angle molecular reorientation as it exchanges hydrogen bonding partners. To test this picture of hydrogen bond dynamics, we have performed ultrafast 2D IR spectral anisotropy measurements on the OH stretching vibration of HOD in D(2)O to directly track the reorientation of water molecules as they change hydrogen bonding environments. Interpretation of the experimental data is assisted by modeling drawn from molecular dynamics simulations, and we quantify the degree of molecular rotation on changing local hydrogen bonding environment using restricted rotation models. From the inertial 2D anisotropy decay, we find that water molecules initiating from a strained configuration and relaxing to a stable configuration are characterized by a distribution of angles, with an average reorientation half-angle of 10°, implying an average reorientation for a full switch of ≥20°. These results provide evidence that water hydrogen bond network connectivity switches through concerted motions involving large angle molecular reorientation.

Supramolecular main-chain liquid crystalline polymers and networks with competitive hydrogen bonding: a study of increased flexibility on distonic mesogenic hydrogen bond acceptors with networks created from tetrakis-, tris- and bis-functionalised pyridyl networking agents

A series of novel liquid crystalline supramolecular networks formed through hydrogen bonds have been synthesised. These networks based on a bis benzoic acid and two types of pyridyl species (a distonic bis stilbazole capable of forming liquid crystalline phases and a polyfunctional non-mesogenic pyridyl species) can compete for available hydrogen bond donor molecules. It was found that the networks display monotropic nematic character at high concentrations of disrupting netpoints – up to 60% for tetrapyridyls, 50% for tripyridyls and 42.5% for bipyridyls.

Nuclear magnetic resonance parameters in water dimer

The changes in the computed nuclear magnetic resonance (NMR) parameters of the water dimer with respect to their monomer values were monitored as the geometry of the dimer was systematically varied. Nuclear magnetic shielding constants, shielding tensor anisotropies, nuclear quadrupole coupling constants and spin–spin coupling constants for the hydrogen bond donor and acceptor molecules were calculated at hybrid density-functional theory level. The dimer geometry was specified through the intermolecular oxygen–oxygen distance ROO and the hydrogen bond angle α. A grid of 120 geometries was selected by systematically varying these two parameters. The other geometrical parameters of the dimer were allowed to relax, keeping the two parameters fixed. As the dimer geometry was varied, all NMR parameters were observed to be smoothly behaving. Characteristic changes as a function of the intermolecular geometry were observed. These include, besides the well-known deshielding of the donor hydrogen shielding constant, also influences on the donor deuterium quadrupole coupling constant, as well as the shielding anisotropy of the donor and acceptor oxygens. We discuss the contributions to the total dimerisation effect from, on the one hand, the dominant direct interaction effect at a fixed geometry and, on the other hand, from the quantitatively relevant indirect, geometric effect. A fundamental ambiguity of this partitioning is demonstrated. By forging the general, smooth trends in all the studied NMR parameters into a specific geometric definition, we find our data to be in agreement with the widely used distance criterion for hydrogen bonding in water, ROO ≤ 3.5 A.

Direct Observation of Hydrogen-Bond Exchange in Small Water Clusters

The authors studied the structure and dynamics of individual water dimer and trimer on Cu(110) by using a scanning tunneling microscope (STM) and density functional theory (DFT). The dimer consists of hydrogen-bond donor and acceptor molecules, and dynamically rearranges the hydrogen bond resulting in the interchange of their roles. The large isotope effect (∼60) was founded in the interchange rate between (H2O)2 and (D2O)2, suggesting that the process involves quantum tunneling. The interchange motion was enhanced upon the excitation of an intermolecular mode that correlates with the reaction coordinate. In contrast, the water trimer was imaged as a static triangular shape. The calculation revealed that it forms a hydrogen-bond chain along the atomic row.

Water Monomer and Dimer on Cu(110) Studied Using a Scanning Tunneling Microscope

The authors studied the structure and dynamics of water monomer and dimer on Cu(110) by using a scanning tunneling microscope (STM) and density-functional theory (DFT). The monomer adsorbs on top of a Cu atom and thermally hops along the atomic row at 6 K. The hopping motion is also induced via inelastic electron tunneling process. The dimer consists of hydrogen-bond donor and acceptor molecules, that were observed to dynamically exchange their roles via hydrogen-bond rearrangement. The interchange motion was suppressed upon substitution with heavy water, suggesting that the process involves quantum tunneling. [DOI: 10.1380/ejssnt.2008.296]

Ab Initio Study of Hydrogen-Bond Formation between Cyclic Ethers and Selected Amino Acid Side Chains

Binding energies for hydrogen-bonded complexes of six cyclic ethers with five hydrogen-bond donor molecules that mimic selected amino acid side chains have been calculated at the MP2/6-31G*, MP2/6-31+G*, MP2/6-311++G**(single point), and MP2/aug-cc-pvtz levels, using geometries obtained with or without counterpoise corrections throughout the geometry optimization. The calculated basis set superposition error (BSSE) amounts to 10-20% and 5-10% of the uncorrected binding energies for the neutral and ionic species, respectively, at the MP2/aug-cc-pvtz level. The authors conclude that the O...H distances in the hydrogen bonds and binding energies for the studied systems may be determined with uncertainties of up to 0.08 A and 1-2 kcal/mol, respectively, in comparison with the MP2/aug-cc-pvtz values at a reasonable computational cost by performing standard geometry optimization at the MP2/6-31+G* level. Hydrogen-bond formation energies are more negative for cyclic ethers compared to their counterparts with a C=C double bond in the ring next to the oxygen atom. The less negative hydrogen-bonding energy and the increased O...H separation have been attributed to the reduced basicity of the ether oxygen when the lone pairs can enter conjugation with the pi-electrons of the Calpha=Cbeta double bond. The present study is the first step toward the development of an affordable computational level for estimating the binding energies of natural product, fused ring ether systems to the human estrogen receptor.

Theoretical Study of Dihydrogen Bonds between (XH)2, X = Li, Na, BeH, and MgH, and Weak Hydrogen Bond Donors (HCN, HNC, and HCCH)

The dihydrogen-bonded (DHB) complexes formed by (XH)2, with X = Li, Na, BeH, and MgH, with one, two, and four protonic molecules (HCN, HNC, and HCCH) have been studied. These complexes have been compared to those of the XH monomers with the same hydrogen bond donor molecules. The energetic results have been rationalized based on the electrostatic potential of the isolated hydridic systems. The electron density properties have been analyzed within the AIM methodology, both at the bond critical points and the integrated values at the atomic basins. Exponential relationships between several properties calculated at the bond critical points (rho,nabla2rho, lambdai, G, and V) and variation of integrated properties (energy, charge, and volume) vs the DHB distance have been obtained.

Triple Hydrogen Bonds Direct Crystal Engineering of Metal‐Assembled Complexes: The Effect of a Novel Organic–Inorganic Module on Supramolecular Structure

Novel triply hydrogen bonded suprastructures based on [M(tdpd)2(L)2]2- (H2tdpd=1,4,5,6-tetrahydro-5,6-dioxo-2,3-pyrazinedicarbonitrile, L=solvent) and melamine-analogous cations have been synthesized and characterized. The use of anions containing two AAA sets from [M(tdpd)2(L)2]2- together with cations containing one DDD set (A=hydrogen-bond acceptor, D=hydrogen-bond donor) leads to the formation of complementary triply hydrogen bonded modules in the solid state. In all cases, the building module is further extended via additional hydrogen-bonding interactions to produce a tape, and tapes are assembled into sheets. These results show that a hydrogen-bonded module consisting of different kinds of building blocks, one of which is a metal complex that includes hydrogen-bond acceptor sites and the other is a hydrogen-bond donor molecule, will be attractive for constructing metal-containing supramolecular systems by the self-assembly technique.

Photodissociation of the water dimer: Three-dimensional quantum dynamics studies on diabatic potential-energy surfaces

The results are presented of three-dimensional model studies of the photodissociation of the water dimer following excitation in the first absorption band. Diabatic potential-energy surfaces are used to investigate the photodissociation following excitation of the hydrogen bond donor molecule and of the hydrogen bond acceptor molecule. In both cases, the degrees of freedom considered are the two OH-stretch modes of the molecule being excited, and the dimer stretch vibration. The diabatic potentials are based on adiabatic potential surfaces computed with the multireference configuration-interaction method, and the dynamics of dissociation was studied using the time-dependent wave-packet method. The dynamics calculations yield a donor spectrum extending over roughly the same range of frequencies as the spectrum of the water monomer computed at the same level of theory. The acceptor spectrum has the same width as the monomer spectrum, but is shifted to the blue by 0.4-0.5 eV. The dimer spectrum obtained by averaging the donor and the acceptor spectrum is broader than the monomer spectrum, with the center of the dimer first absorption band shifted to the blue by about 0.2 eV relative to the monomer band. Our reduced dimensionality calculations do not find the red tail predicted for the dimer first absorption band by Harvey et al. [J. Chem. Phys. 109, 8747 (1998)]. This conclusion also holds if preexcitation of the dimer stretch vibration with one or two quanta is considered.

Raman and infrared studies of hydrogen-bonding in supercritical ethanol

The purpose of this paper is to present a Raman and an infrared spectroscopic study of hydrogen-bonding in supercritical ethanol (T c=516 K, P c=6.4 MPa, ϱ c = 0.276 g.cm −3). The Raman and infrared spectra of the ν OH stretching mode (in the range of 3500–3700 cm −1) have been measured at constant temperature, T=523K, in a broad pressure range (1<P<30 MPa). We observed a narrow profile cenred at about 3630 cm −1 assigned to both ethanol monomers and unbonded OH groups of ethanol oligomers. The broad band observed at about 3500 cm −1 corresponds to hydrogen-bond donor molecules. The analysis of the band shapes reveals that hydrogen bonding is still present in supercritical ethanol. An important issue concerning the respective sensitivity of Raman scattering and infrared absorption in connection with hydrogen bonding is also addressed.

Fluorescence properties of phenolate anions of coelenteramide analogues: the light-emitter structure in aequorin bioluminescence

Abstract To elucidate the ionic structure of the excited state of light-emitter coelenteramide in aequorin bioluminescence, the fluorescent properties of phenolate anions of coelenteramide analogues were investigated. Fluorescence of phenolate anion in non-polar solvents was observed by electronic excitation of a 1:1 hydrogen-bonded complex of a coelenteramide analogue with a hydrogen-bond donor molecule such as n-butylamine. In polar solvents, the phenolate anion was directly generated using a base, and its fluorescence was studied. These results confirm that the singlet-excited state of phenolate anion of coelenteramide has an intramolecular CT character, and that its fluorescence emission wavelength changes depending upon solvent polarity. The fluoro-substituent effect on the fluorescent property of phenolate anions was also clarified to help in explaining the bioluminescent property of fluorinated semi-synthetic aequorin. These results consistently support the assignment that the phenolate anion is the ionic structure of the excited light-emitter in BFP during AQ bioluminescence.