Self-complementary quadruply hydrogen-bonded duplexes based on imide and urea units

The quadruply hydrogen-bonded duplexes based on an imide-urea structure preorganized by three-center hydrogen bonds were found to associate via bifurcated hydrogen bonds. (1)H NMR dilution experiments revealed the high stability of the homodimer in apolar solvent (K(dim) > 10(5) M(-1) in CDCl(3)) and enhancement of association ability due to electron-withdrawing substituent effects. The ready synthetic availability and adjustable association affinity via electronic effects may render these association units potentially applicable in constructing supramolecular architectures.     

Stability of a new class of unnatural hydrogen-bonded molecular duplexes: A computational study

The stability of a series of hydrogen-bonded duplexes was studied using molecular mechanics method with a modified AMBER GAFF force field, in which the original atomic charges were replaced by ones that are more appropriate for non-polar solvents. The free energy change of dimerization was calculated in vacuo and good agreement with experimental data was found. It is also shown that the stability of these duplexes increases linearly with the number of hydrogen bonds, in agreement with experimental data.     

Hydrogen-bonding interactions in gas-phase polyether/ammonium ion complexes

Hydrogen bonds are among the most important interactions involved in selective complexation in host-guest chemistry. In this study a variety of hydrogen-bonded crown ether/ammonium ion complexes are generated in the gas phase by association reactions between an amine substrate and a polyether, one of which is initially protonated, and stabilized by many collisions in the chemical ionlzation source of a triple quadrupole mass spectrometer or in a quadrupole ion trap. The nature of the hydrogen-bonding interactions of the ion complexes are evaluated by comparison of their collision-activated dissociation spectra. After collisional activation, those complexes that are weakly bound dissociate to form intact protonated polyether molecules and/or ammonium ions by simple cleavages of the hydrogen-bond association interactions. In contrast, those complexes strongly bound by multiple hydrogen bonds dissociate not only to the protonated polyether and/or ammonium ions but also by extensive covalent bond cleavage of the protonated ether skeleton.This latter type of dissociation behavior suggests that the polyether/ammonium ion complexes may be sufficiently strongly bound that surpassing the high barrier to decomposition results in formation of internally excited polyether molecules that may then undergo subsequent fragmentation by skeletal cleavages. Moreover, complexes involving multiple hydrogen bonds may have slower dissociation kinetics, allowing competition from fast dissociation processes that have substantial energy barriers.     

Sequence-specific association in aqueous media by integrating hydrogen bonding and dynamic covalent interactions

Oligoamide strands that associate in a sequence-specific fashion into hydrogen-bonded duplexes in nonpolar solvents were converted into disulfide cross-linked duplexes in aqueous media. Thus, by incorporating trityl-protected thiol groups, which allows the reversible formation of disulfide bonds, into the oligoamide strands, only duplexes consisting of complementary hydrogen-bonding sequences were formed in aqueous solution as well as in methanol. The sequence-specific cross-linking of oligoamide strands was confirmed by MALDI-TOF, reverse-phase HPLC, and by isolating a cross-linked duplex. This study demonstrates that the sequence-specificity characteristic of multiply hydrogen-bonded systems can be extended into competitive media through the interplay of H-bonding and reversible covalent interactions, based on which a new class of molecular associating and ligating units that are compatible with both polar and nonpolar environments can be conveniently obtained.     

Hydrogen-bonding-mediated anthranilamide homoduplexes. Increasing stability through preorganization and iterative arrangement of a simple amide binding site

This paper describes the assembly of two new series of self-complementary duplexes by making use of amide units, the simplest assembling units of hydrogen bonding, as binding sites. All the new monomers possess a rigidified anthranilamide skeleton, which is stabilized by intramolecular hydrogen bonding. Amide units are iteratively introduced to one side of the preorganized skeletons to facilitate the formation of intermolecular hydrogen bonding. Compounds 2 and 3 bear two and three CONH(2) units, respectively, while 4, 6, and 7 are incorporated with two, three, and four AcNH units, respectively. For comparison, compound 5, which is similar to 4 but contains one AcNH and one CF(3)CONH unit, is also prepared. X-ray diffraction analysis of 2, 4, and 5 revealed homodimeric motifs in the solid state which are stabilized by two or more intermolecular hydrogen bonds. (1)H NMR investigations in CDCl(3) indicated that all the compounds form hydrogen-bonded homoduplexes. Duplexes 3.3, 6.6, and 7.7 are highly stable in CDCl(3), with a lower K(assoc) limit of 2.3 x 10(5) M(-1). The K(assoc) values of the three duplexes in more polar CDCl(3)/CD(3)CN (9:1, v/v) were determined with the (1)H NMR dilution method. The result opens the way for the development of new polymeric duplexes of well-ordered structures.     

A TD-DFT study on the hydrogen bonding of three esculetin complexes in electronically excited states: strengthening and weakening

Time-dependent density functional theory (TD-DFT) method was used to study the excited-state hydrogen bonding of three esculetin complexes formed with aprotic solvents. The geometric structures, molecular orbitals (MOs), electronic spectra and the infrared (IR) spectra of the three doubly hydrogen-bonded complexes formed by esculetin and aprotic solvents dimethylsulfoxide (DMSO), tetrahyrofuran (THF) and acetonitrile (ACN) in both ground state S(0) and the first singlet excited state S(1) were calculated by the combined DFT and TD-DFT methods with the COSMO solvation model. Two intermolecular hydrogen bonds can be formed between esculetin and the aprotic solvent in each hydrogen-bonded complex. Based on the calculated bond lengths of the hydrogen bonds and the groups involved in the formation of the intermolecular hydrogen bonds in different electronic states, it is demonstrated that one of the two hydrogen bonds formed in each hydrogen-bonded complex is strengthened while the other one is weakened upon photoexcitation. Furthermore, it is found that the strength of the intermolecular hydrogen bonds formed in the three complexes becomes weaker as the solvents change from DMSO, via THF, to ACN, which is suggested to be due to the decrease of the hydrogen bond accepting (HBA) ability of the solvents. The spectral shifts of the calculated IR spectra further confirm the strengthening and weakening of the intermolecular hydrogen bonds upon the electronic excitation. The variations of the intermolecular hydrogen bond strengths in both S(0) and S(1) states are proposed to be the main reasons for the gradual spectral shifts in the absorption and fluorescence spectra both theoretically and experimentally.     

Hydrogen bonds between hydrogen halides and unsaturated hydrocarbons

Ab initio molecular orbital theory is used to study geometrics and energies of hydrogen-bonded complexes between hydrogen fluoride, hydrogen chloride (as proton donors) and acetylene, ethylene (as proton acceptors). Symmetrical T-shaped structures are found to be equilibrium structures for all four complexes. The strengths of the hydrogen bonds are found to be less than for conventional hydrogen bonds involving lone pairs of electrons.     

Vibrational analysis of sodium α-, β- and γ-hydroxybutyrates. Inter- and intramolecular hydrogen bonds

The infrared and Raman spectra of sodium α-, β- and γ-hydroxybutyrates and their deuterated analogues are examined in the 4000-100 cm⁻¹ range and an assignment of the fundamental vibrations is given. Based on the localization of the asymmetric stretching vibrations ν_asOH and the out-of-plane vibration γOH, inter- and/or intramolecularly hydrogen-bonded forms are proposed: the low frequencies of ν_asOH (<3200 cm⁻¹) and high frequencies of γOH (≈800 cm⁻¹) argue in favour of the existence of intramolecular hydrogen bonding. Sodium α-hydroxybutyrate exhibits as a chelate ring with an intramolecular hydrogen bond between hydroxyl and carboxyl groups, whereas sodium, β-hydroxybutyrate has the two association forms with inter- and intramolecular hydrogen bonds. Sodium γ-hydroxybutyrate exists as a hydrogen-bonded polymer, with an intermolecular hydrogen bond between the hydroxyl groups and between the hydroxyl and carbonyl groups. At a crystallization temperature above 50°C, only the α- salt showed a structural change indicating the existence of intra- and intermolecular hydrogen bonds. This result is confirmed by differential scanning analysis.     

Helical molecular duplex strands: multiple hydrogen-bond-mediated assembly of self-complementary oligomeric hydrazide derivatives

Careful examination of the X-ray structure of a ditopic hydrazide derivative 7 led to the concept that with malonyl groups as interhydrazide linkers hydrogen-bonding-mediated molecular duplex strands might be obtained. Complexation studies between 7, 8, and 9 confirmed this hypothesis. Two quadruple hydrogen-bonded heterodimers formed, in which spectator repulsive secondary electrostatic interaction was found to play an important role in determining the stability of the complexes. Extensive studies on 1-4 indicated that the hydrogen-bonding mode could persist in longer oligomeric hydrazide derivatives with chain extension from monomer to tetramer. Molecular duplex strands via two to fourteen interstrand hydrogen bonds were obtained. In addition to affecting the stability of the duplex strands, spectator repulsive secondary electrostatic interaction also played an important role in determining dynamic behavior of the duplex strands as exemplified by variable temperature (1)H NMR experiments. IR studies confirmed stronger hydrogen bonding in the longer oligomers. The assemblies of 1-4 on HOPG were also studied by STM technology. Molecular mechanical calculations further revealed double-helical structures for the longer oligomers. The results provide new opportunities for development of polymeric helical duplexes with well-defined structures.     

Molecular clusters in aqueous solutions of pyridine and its methyl derivatives

Small-angle neutron scattering proved that molecules in aqueous solutions of pyridine, 2-methylpyridine and 2,6-dimethylpyridine form clusters. The clusters are dynamic aggregates consisting of hydrogen-bonded water-amine complexes. Strengthening of the hydrogen bonds between water and amine molecules due to the methyl groups in the ortho position in the pyridine ring makes the structures more stable, as was evidenced by relatively long times of the structural relaxation. The strong intermolecular forces affect the thermal expansion of the systems. No aggregates similar to those in aqueous systems are present in the methanolic ones. That points to the crucial role of water in the molecular clustering. A molecule of methanol, although capable of hydrogen bonding with the amines, cannot participate in larger structures because of the lack of protons that could form the enhanced network. Thus, even if the amine-methanol complexes occur, they are incapable of further association. It was shown that the co-operative nature of hydrogen bonds and the propensity of water to association are the main factors that determine the properties of aqueous systems.     

Tunable conformation and stability of amidourea-based hydrogen-bonded heteroduplexes

A class of multiply hydrogen-bonded heteroduplexes were constructed from readily available amidourea derivatives, and their structures and association stabilities were investigated. Although the amidourea derivatives possessed different spacers or termini, they could adjust their conformations to achieve an optimal binding module. Consequently, all the heteroduplexes adopted similar hydrogen-bonding patterns through eight intermolecular bifurcated hydrogen bonds based on the amidourea motif. Moreover, it was also found that the association stabilities of the heteroduplexes could be well tuned by varying the spacers or termini of the monomers.     

Topology of hydrogen-bonded clusters in sub- and supercritical <Emphasis Type="Italic">n</Emphasis>-buthanol. Molecular dynamics simulation

We present the study of hydrogen-bonded clusters in sub- and supercritical n-buthanol by molecular dynamics. A number of characteristics of hydrogen bonds were calculated on the basis of a geometrical criterion. It was determined that the effect of the partial reduction of the structure of condensed medium near critical point is manifested in an increase in the average number of hydrogen bonds and the first peak of the hydrogen-oxygen radial distribution function. By investigating the topology of hydrogen-bonded clusters, it was shown that this reduction is determined by an increase of the fraction of molecules bound by two hydrogen bonds, and a reduction in the fraction of unbonded ones.     

Lower Rim-Upper Rim Hydrogen-Bonded Adducts of Calix[4]arenes

An upper-rim-substituted calix[4]arene tetracarboxylic acid forms hydrogen-bonded duplexes with lower-rim-substituted tetra(4-pyridyl)- and tetra(3-pyridyl)calix[4]arenes in chloroform. The formation of these adducts was studied by extraction experiments. The association constants determined via (1)H NMR dilution experiments in CDCl(3) are 7.6 x 10(3) and 1.3 x 10(3) M(-1) for the 4-pyridyl and the 3-pyridyl derivative, respectively. IR studies in the solid state and in solution indicate that the interaction is based on hydrogen bonding and that the degree of proton transfer is negligible. VPO measurements support the formation of 1:1 adducts.     

Glycoluril ribbons tethered by complementary hydrogen bonds

Four complementary hydrogen bonds between sulfamides and ureas link adjacent hydrogen-bonded ribbons to form sheets in the solid-state; this interaction is investigated in solution using model urea and sulfamide compounds.     

Binding of small guest molecules to multivalent receptors

The complexation of phenol derivatives, aromatic carboxylic acids, and n-octylgalactopyranoside by hydrogen-bonded exo-receptors is described. The receptors are formed by self-assembly of differently functionalized calix[4]arene dimelamines with 5,5-diethyl barbiturate or butyl cyanurate. The multivalent complementary recognition site of the receptors is used very efficiently to complex multiple guests. A 1:6 binding mode was observed for phenol derivatives forming single hydrogen bonds with all six recognition sites of an ureido functionalized receptor assembly, while 1:3 complexation was observed for phenol derivatives which form two hydrogen bonds with two different ureido recognition sites of the same receptor. Aromatic carboxylic acids are complexed in a 1:6 ratio by receptors having six amino recognition sites. The complexation of n-octylgalactopyranoside by Gly-L-Ser functionalized receptors is also described, indicating that it is possible to use small peptidic fragments to complex biologically important molecules.     

Deformation of porous molecular networks induced by the exchange of guests in single crystals

A strategy for making molecular networks that are porous and deformable is revealed by the behavior of compound 1, in which groups that form hydrogen bonds are attached to a nominally tetrahedral Si core. Compound 1 crystallizes from various carboxylic acids to produce a porous hydrogen-bonded diamondoid network, with up to 65% of the volume available for including guests. Changing the guests expands or contracts the network up to 30% in one direction, and single crystals can accommodate these exchange-induced deformations without loss of crystallinity. This resilience appears to result in part from the incorporation of flexible Si nodes in an otherwise robust network maintained by multiple hydrogen bonds. In certain cases, exchange is faster than deformation of the network, allowing the isolation of metastable structures with a new guest included in an otherwise unchanged network. Such processes can provide new materials that would be difficult or impossible to obtain in other ways.     

NMR parameters and geometries of OHN and ODN hydrogen bonds of pyridine-acid complexes

In this paper, equations are proposed which relate various NMR parameters of OHN hydrogen-bonded pyridine-acid complexes to their bond valences which are in turn correlated with their hydrogen-bond geometries. As the valence bond model is strictly valid only for weak hydrogen bonds appropriate empirical correction factors are proposed which take into account anharmonic zero-point energy vibrations. The correction factors are different for OHN and ODN hydrogen bonds and depend on whether a double or a single well potential is realized in the strong hydrogen-bond regime. One correction factor was determined from the known experimental structure of a very strong OHN hydrogen bond between pentachlorophenol and 4-methylpyridine, determined by the neutron diffraction method. The remaining correction factors which allow one also to describe H/D isotope effects on the NMR parameters and geometries of OHN hydrogen bond were determined by analysing the NMR parameters of the series of protonated and deuterated pyridine- and collidine-acid complexes. The method may be used in the future to establish hydrogen-bond geometries in biologically relevant functional OHN hydrogen bonds.     

Hamilton受体与萘之间光诱导电子转移和三重态能量传递研究

将两个2,6-二氨基吡啶衍生物与异酞酸相连, 得到一个袋状巴比妥酸衍生物受体(Hamilton受体, H-receptor), 同时合成了带有萘基团的巴比妥酸衍生物(G-Np), 两者在非极性溶剂中形成氢键体系, 二氯甲烷溶剂中表观结合常数KAPP＝(4.9±0.5)×104 mol－1&#8226;L. 稳态荧光发射光谱和磷光发射光谱研究表明, 室温下H-receptor和G-Np之间主要发生单重态电子转移过程, 77 K下, H-receptor与G-Np之间发生三重态能量传递过程. 本研究为Hamilton氢键体系的理论研究提供了一个新的模型, 对理解氢键在生命体系中的作用有重要的意义.