Self-assembly of novel [3]- and [2]rotaxanes with two different ring components: donor-acceptor and hydrogen bonding interactions and molecular-shuttling behavior

Three of the first kind of hetero[3]rotaxanes, which comprise one linear component and one neutral and one tetracationic ring component, have been assembled by using the intermolecular hydrogen bonding and donor-acceptor interactions. Three neutral [2]rotaxanes and three tetracationic [2]rotaxanes have also been synthesized as intermediate products or for the sake of property comparison. The linear molecules are incorporated with two glycine subunits, for templating the formation of the neutral tetraamide cyclophane, and one or two hydroquinone subunits, for inducing the formation of the tetracationic cyclophane. Variable-temperature (1)H NMR investigation reveals that the shuttling behavior of the tetracationic ring component along the linear component is substantially influenced by the existence of the neutral ring component. The spatial repelling interaction of the neutral ring on the electron-deficient tetracationic ring simultaneously weakens the latter's "positioning" tendency at both electron-rich hydroquinone sites of the linear component. As a result, the activation energy associated with the shuttling process of the tetracationic ring between the two hydroquinone sites is remarkably reduced in comparison to that of the shuttling process of the corresponding neutral ring-free [2]rotaxanes. For the first time, the rotation of the dipyridinium subunit around the axis formed by the two methylene groups connecting them within the tetracationic cyclophane has been investigated by variable-temperature (1)H NMR spectroscopy and the associated kinetic data have also been successfully obtained. Furthermore, the UV-vis and fluorescent properties of the new [2]- and [3]rotaxanes have been studied. The results demonstrate that [3]rotaxanes with different ring components possess unique kinetic features that are not available in [3]rotaxanes with identical ring components.     

The effect of hydrogen bonding on allylic alkylation and isomerization reactions in ionic liquids

Neutral allylic alkylation reactions, in which a base is generated in situ and which hence require no external bases, can significantly be retarded when carried out in the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF(4)]). Evidence suggests that the base or base precursor enters into hydrogen bonding with the imidazolium cation and is thus made less readily available for deprotonation of pre-nucleophiles. However, the reaction proceeds well in the presence of stronger bases that are capable of deprotonation. Whilst the phenomenon of hydrogen bonding in ionic liquids can be detrimental to reactions such as allylic alkylation, it can be exploited to suppress unwanted allylic isomerization.     

On differences between hydrogen bonding and improper blue-shifting hydrogen bonding.

Twenty two hydrogen-bonded and improper blue-shifting hydrogen-bonded complexes were studied by means of the HF, MP2 and B3LYP methods using the 6-31G(d,p) and 6--311 ++G(d,p) basis sets. In contrast to the standard H bonding, the origin of the improper blue-shifting H bonding is still not fully understood. Contrary to a frequently presented idea, the electric field of the proton acceptor cannot solely explain the different behavior of the H-bonded and improper blue-shifting H-bonded complexes. Compression of the hydrogen bond due to different attractive forces-dispersion or electrostatics--makes an important contribution as well. The symmetry-adapted perturbation theory (SAPT) has been utilized to decompose the total interaction energy into physically meaningful contributions. In the red-shifting complexes, the induction energy is mostly larger than the dispersion energy while, in the case of blue-shifting complexes, the situation is opposite. Dispersion as an attractive force increases the blue shift in the blue-shifting complexes as it compresses the H bond and, therefore, it increases the Pauli repulsion. On the other hand, dispersion in the red-shifting complexes increases their red shift.     

Dynamic switching between single- and double-axial rotaxanes manipulated by charge and bulkiness of axle termini

Twin-axial [3]pseudorotaxanes, in which two multicharged axles simultaneously thread through the gamma-CD cavity, were formed for the first time in solution. The twin-axial [3]pseudorotaxane was converted exclusively to a CB [6]-stoppered [4]pseudorotaxane by the addition of CB[6] but regenerated from the [4]pseudorotaxane by the addition of spermine, implementing an unprecedented switching of single/twin-axial rotaxanation.     

Effects of hydrogen bonding on the ring stretching modes of pyridine

The effects of hydrogen bonding on the ring stretching modes (both ring breathing and triangle) of pyridine are experimentally investigated using noisy light based coherent Raman scattering spectroscopy. Three systems, pyridine/formamide, pyridine/water, and pyridine/acetic acid, provide varying degrees of strength for the diluent-pyridine hydrogen bond complex. Formamide forms a relatively weaker hydrogen bond, while acetic acid essentially fully transfers a proton to pyridine. Both dilution studies and temperature studies are performed on the three systems. Together, these provide a broad context in which a very simple model for the electronic behavior of pyridine is formulated. This model is based on a molecular orbital picture and electrostatic arguments, and it well explains the observed experimental results. Additionally, a new mechanism for the line broadening of the ring breathing mode for the pyridine-water hydrogen bonded complex is proposed.     

Residue-specific 13C' CSA tensor principal components for ubiquitin: correlation between tensor components and hydrogen bonding

The residue-specific 13C' CSA tensor principal components, sigma(11), sigma(22), sigma(33), and the tensor orientation defined by the rotation angles beta and gamma have been determined by solution NMR for uniformly labeled ubiquitin partially aligned in four different media. Spurious chemical shift deviations due to solvent effects were corrected with an offset calculated by linear regression of the residual dipolar couplings and chemical shifts at increasing alignment strengths. Analysis of this effect revealed no obvious correlation to solvent exposure. Data obtained in solution from a protein offer a better sampling of 13C' CSA for different amino acid types in a complex heterogeneous environment, thereby allowing for the evaluation of structural variables that would be challenging to achieve by other methods. The 13C' CSA principal components cluster about the average values previously determined, and experimental correlations observed between sigma(11), sigma(22) tensorial components and C'O...H(N) hydrogen bonding are discussed. The inverse association of sigma(11) and sigma(22) exemplify the calculated and solid-state NMR observed effect on the tensor components by hydrogen bonding. We also show that 13C' CSA tensors are sensitive to hydrogen-bond length but not hydrogen-bond angle. This differentiation was previously unavailable. Similarly, hydrogen bonding to the conjugated NH of the same peptide plane has no detectable effect. Importantly, the observed weak correlations signify the presence of confounding influences such as nearest-neighbor effects, side-chain conformation, electrostatics, and other long-range factors to the 13C' CSA tensor. These analyses hold future potential for exploration provided that more accurate data from a larger number of proteins and alignments become available.     

Template synthesis of [2]rotaxanes with large ring components and tris(biphenyl)methyl group as the blocking group. The relationship between the ring size and the stability of the rotaxanes

We synthesized a series of macrocyclic phenanthrolines 3a-e and a tris(biphenyl)methyl derivative 4. [2]Rotaxanes with large ring components (10a,b) were synthesized by the template method, and the stability of the rotaxanes was examined. The study revealed that the tris(biphenyl)methyl group is an effective blocking group for the rotaxanes with up to a 33-membered ring. Even a rotaxane with a 37-membered macrocyclic phenanthroline (10b) could be isolated. The dissociation of 10b occurred at 60 degrees C.     

Nonconventional hydrogen bonding between clusters of gold and hydrogen fluoride

The bonding patterns between small neutral gold Au(3 < or = n < or = 7) and hydrogen fluoride (HF)(1 < or = m < or = 4) clusters are discussed using a high-level density functional approach. Two types of interactions, anchoring Au-F and F-H...Au, govern the complexation of these clusters. The F-H...Au interaction exhibits all the characteristics of nonconventional hydrogen bonding and plays a leading role in stabilizing the lowest-energy complexes. The anchor bonding mainly activates the conventional F-H...F hydrogen bonds within HF clusters and reinforces the nonconventional F-H...Au one. The strength of the F-H...Au bonding, formed between the terminal conventional proton donor group FH and an unanchored gold atom, depends on the coordination of the involved gold atom: the less it is coordinated, the stronger its nonconventional proton acceptor ability. The strongest F-H...Au bond is formed between a HF dimer and the singly coordinated gold atom of a T-shape Au4 cluster and is accompanied by a very large red shift (1023 cm(-1)) of the nu(F-H) stretch. Estimations of the energies of formation of the F-H...Au bonds for the entire series of the studied complexes are provided.     

Synergistic effect between metal coordination and hydrogen bonding in phosphate and halide recognition

The equilibrium constant for binding of dimethyl phosphate to a Co(III) complex in water increases from 6.2 to 210 M-1 upon addition of a single hydrogen bond between the bound phosphate and the metal complex. Crystal structure reveals that the hydrogen bond distance is 1.96 A. The synergistic effect between metal coordination and hydrogen bonding can also be observed for fluoride binding but not for bromide binding.     

Interplay between anion-pi and hydrogen bonding interactions

The interplay between two important noncovalent interactions involving aromatic rings is studied by means of high level ab initio calculations. They demonstrate that synergistic effects are present in complexes where anion-pi and hydrogen bonding interactions coexist. These synergistic effects have been studied using the "atoms-in-molecules" theory and the Molecular Interaction Potential with polarization partition scheme. The present study examines how these two interactions mutually influence each other.     

The effect of hydrogen chemisorption on titanium surface bonding

The effect of hydrogen chemisorption on the strength of Ti-Ti bonds is studied byab initio configuration interaction techniques using an embedding theory to describe the electronic structure. A Ti adatom on Ti(0001) is modelled by a Ti₂₀H cluster with boundary potentials determined from the embedding treatment. Hydrogen atom chemisorption is highly exothermic for adsorption atop the adatom, a three-fold site formed by the adatom and in the interstitial site below the adatom. Compared to the planar Ti(0001) surface the adatom region binds hydrogen much more strongly. Removal of Ti from the surface is energetically much more favorable if H remains on the surface as opposed to the removal of TiH. The exchange reaction Ti₂₀+HTi₁₉H+Ti is endothermic by 0.3 eV. These results suggest high reactivity of the adatom region on Ti(0001) but not such that the surface is more easily fragmented by removal of Ti or TiH.Dedicated to Professor J. Koutecký on the occasion of his 65th birthday     

Intermolecular hydrogen bonding between N-substituted caproamides and tetrahydrofuran

The results are reported of a study of hydrogen bonding between various N-substituted caproamides and tetrahydrofuran as an O-electron donor by means of FTIR spectroscopy. The spectroscopic characteristics for N-H...O hydrogen bonded complexes are given. The B3LYP functional with 6–31G** basis set has been used to calculate the structural parameters of the studied hydrogen bonded complexes. It can be assumed that both inductive and steric effects play an important role in the stability of these hydrogen bonded complexes.     

Highly effective and reversible control of the rocking rates of rotaxanes by changes to the size of stimulus-responsive ring components

We have designed and synthesized rotaxanes whose rates of rocking motion (pendular motion) were switched reversibly through changes to the size of the ring component in response to external stimuli. The ring molecules of the rotaxanes incorporate a metaphenylene unit, which swings like a pendulum, and a dianthrylethane unit, which undergoes reversible isomerization in response to photo- and thermal stimuli and changes the size of the ring component. The rocking rates were estimated quantitatively by variable-temperature (VT) NMR spectroscopy and saturation transfer experiments, which revealed substantial changes in the rates between the open and closed forms, particularly in the case of rotaxanes with an isopropoxy group attached to a phenylene unit.     

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.