Effect of hydrogen bonding on the structure and vibrational spectra of the complementary pairs of nucleic acid bases. II. adenine-thymine

The vibrational spectra of an isolated complementary adenine-thymine pair are calculated in the B3LYP/6-311++G(d,p) approximation and analyzed. The effect of hydrogen bonds on the structure is shown along with the position of frequencies and intensities of normal vibrations of the pair in comparison with the spectra of isolated thymine and adenine molecules. A comparative analysis of the hydrogen bonding effect on the IR and Raman spectra of thymine and adenine is performed     

Borane-ammonia complexes stabilized by hydrogen bonding

Novel boron-ammonia complexes, wherein an NH(3) molecule is tightly bound through all four of its atoms, have been prepared and studied. The solid-state structure of ortho MOM-phenyllithium is reported. [reaction: see text]     

Lyotropic phases reinforced by hydrogen bonding

Amphiphilic guanidinium alkylbenzenesulfonates (GCnBS; n = number of carbons in the alkyl chain) exhibited lyotropic behavior in aqueous and organic solvents. The GCnBS compounds formed gel-like phases in certain cyclic organic solvents (e.g. p-xylene, cyclohexane) through the formation of swollen interdigitated lamellar phases reinforced by hydrogen bonding between the guanidinium ions and sulfonate moieties. This behavior was not observed for the homologous sodium alkylbenzenesulfonates, indicating that hydrogen bonding, mediated by the guanidinium (G) ion, was required for gel formation. Infrared spectroscopy unambiguously demonstrated the existence of the quasi-hexagonal hydrogen-bonded sheet typically adopted by G ions and the sulfonate groups in layered, solvent-free crystalline phases of the compounds, supporting lamellar structures in the gels. Small-angle X-ray scattering analysis of these gels revealed GCnBS lamellar phases with interlayer spacings (d) that increased with increasing temperature, consistent with increased absorption of solvent by the nonpolar regions of the gelator. At the lower gelator concentrations, the increase in d-spacing achieved at the higher temperatures exceeded the sum of the alkylbenzene chain lengths, suggesting either long-range interactions between the GS sheets or undulation stabilized lamellae, which have been reported in aqueous lamellar gels. The GCnBS compounds also formed lyotropic phases in water, but the phase behavior was more complex than that of the organogels. The rheology suggested gel-like behavior associated with entangled worm-like micelles at these higher concentrations. These lyotropic phases were reminiscent of crystalline layered and tubular architectures exhibited by various guanidinium organomonosulfonate compounds. These lyotropic phases expand the liquid crystal behavior observed for GS compounds beyond recently observed thermotropic smectic phases, adding to the portfolio of phase behavior exhibited by these materials.     

Self-complementary purines by quadruple hydrogen bonding

The first discrete, self-complementary, quadruply hydrogen-bonded complexes based on the 2,6-diaminopurine (DAP) scaffold have been prepared; regioselective urea formation at the C2 amino group of the heterocycle allows intermolecular dimerization (K(dim) approximately 1-1.6 x 10(3) M(-1) in CDCl3) through a DADA hydrogen bonding motif.     

Incommensurability induced by intermolecular hydrogen bonding

Non-symmetric dimesogens are composed of two different mesogenic units linked via a flexible spacer. In this study, a new type of non-symmetric dimesogen has been built through the self-assembly via intermolecular hydrogen bonding between appropriately designed H-bond donor (3-cholesteryloxycarbonylpentanoic acid) and acceptor (aromatic mesogen with a pyridyl group) moieties. As for covalently linked dimesogens, several types of smectic periodicities are observed for these H-bonded cholesteryl compounds depending on the length of the terminal chain of the acceptor moiety: a smectic periodicity resulting from associated dimesogens is observed for long terminal chains, while short chain homologues display an intercalated structure corresponding to half the molecular length. The competition between these two incommensurate lengths can induce an incommensurate smectic phase where the two smectic periodicities coexist at long range.     

Porphyrin nanochannels reinforced by hydrogen bonding

Carboxyl groups were introduced at the peripheral positions of dodecaphenylporphyrin to link nanochannel structures with intermolecular hydrogen bonds to make the supramolecular structures robust.     

Small molecule‐mediated glass transition of acrylic copolymers: Effect of hydrogen bonding strength on glass transition temperature

Poly(styrene‐co‐ethyl acrylate) [P(St‐co‐EA)] with different ratios of St/EA was mixed with the small molecule 4,4′‐thio‐bis(6‐tert‐butyl‐m‐methyl phenol) (AO300) to investigate the influence of hydrogen bonding strength on the glass transition behavior. The glass transition temperature (T_g) linearly increased after adding AO300, and the slope value decreased with increased St/EA ratio. All lines could be extended to 62 °C, demonstrating that T_g of the small molecule in situ detected by the polymer chain was much higher than that by small molecule itself (29 °C). Fourier transform infrared spectroscopy analysis showed that the small molecules began to be self‐associated at a concentration where the hydrogen bonded carbonyl ratio of the bulk polymer was approximately 0.5 and irrespective of the St/EA ratio. Above the critical loading, the mixture's T_g negatively deviated from the linearly extended lines because of self‐association of the small molecules. The apparent T_g of AO300 was found to strongly depend on intermolecular hydrogen bonding number and strength. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 400–408     

Self-assembly of well-defined structures by hydrogen bonding

The directionality and specificity of hydrogen bonds are invaluable tools in designing complex self-assembling structures. Hydrogen bonds have been used to construct defined structures ranging from reversible polymeric systems to cyclic arrays and capsules which reversibly bind guest molecules. Recent developments show the emergence of functionality in these structures and suggest future uses of well-defined assemblies in areas as diverse as catalysis and materials science. © 1999 Elsevier Science Ltd.     

Thermoplastic elastomers by hydrogen bonding 4. Influence of hydrogen bonding on the temperature dependence of the viscoelastic properties

The temperature dependence of the viscoelastic properties of thermoreversible polybutadiene networks based on hydrogen bond linkages is analyzed from the logarithmic shift factors loga _T . For binary hydrogen bond complexes thermorheologically simple behavior is observed. The temperature dependence of loga _T is described by the Williams-Landel-Ferry (WLF) equation. The thermoreversible linkages cause an increase in the apparent activation enthalpy of flow which is related to the number of complexing sites in the polymer. Thermorheologically complex behavior is observed in a system with more complex association.     

Topochemical transketalization reaction driven by hydrogen bonding

An unusual thermal isomerization of 1,2;3,4-di-O-isopropylidene-myo-inositol to 1,2;5,6-di-O-isopropylidene-myo-inositol was observed in the solid state. A detailed study revealed that this ketal migration is a topochemically driven one. X-ray structure revealed that strong intermolecular hydrogen bonding in the crystal preorganizes the hydroxyl and ketal carbon in a transition-state-like arrangement favorable for the reaction. The 5-OH of each molecule faces the trans ketal carbon of a neighboring molecule at a close distance and an angle of approach near to linearity, making a trigonal-bipyramidal-like arrangement in the crystal, which could facilitate the reaction. This is the first report of a topochemical transketalization reaction.     

Studies on the hydrogen bonding of aniline's derivatives by FT-IR

The hydrogen bonding of 23 aniline's derivatives in various solvents and in solid states are studied by Fourier transform infrared spectroscopy. The Infrared absorption of their amino group is greatly influenced by solvents. Compared with those data determined in hexane, the symmetric stretching frequency (nu(s)) and asymmetric stretching frequency (nu(as)) of amino group have an obvious bathochromic shift in benzene, but a relatively smaller shift in CCl4. It is also found that the concentration of these compounds has very little effect on the frequencies, the band shapes and relative absorption intensities of amino group. This indicates that the intermolecular hydrogen bonds are very weak between the aniline's derivatives in the solution. The substituent of methyl (-CH3) has different electronic effects in organic solvents with various polarities. Methyl group behaves as an electron-donating functional group in hexane, however, it shows an electron-withdrawing effect in benzene. When methoxyl (CH3O-) is ortho-substituted, v(as) of amino group increases and nu(s) almost does not change. While methoxyl (CH3O-) is meta-substituted, v(as) of amino group increases, but nu(s) decreases. The groups of chloro- (Cl-) and nitro- (-NO2) cause a hyposochromic shift of the nu(as) and nu(s) of amino group, while substituent of -NH2 makes a bathochromic shift. The solvents influence the relative intensities of nu(as) and nu(s) of amino group more greatly than the substituents do. In solid states, the amino group of aniline's derivatives has more than two absorption bands because of forming the inter- or intra-molecular hydrogen bonds.     

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.     

Transmembrane anion transport mediated by halogen bonding and hydrogen bonding triazole anionophores

Transmembrane ion transport by synthetic anionophores is typically achieved using polar hydrogen bonding anion receptors. Here we show that readily accessible halogen and hydrogen bonding 1,2,3-triazole derivatives can efficiently mediate anion transport across lipid bilayer membranes with unusual anti-Hofmeister selectivity. Importantly, the results demonstrate that the iodo-triazole systems exhibit the highest reported activity to date for halogen bonding anionophores, and enhanced transport efficiency relative to the hydrogen bonding analogues. In contrast, the analogous fluoro-triazole systems, which are unable to form intermolecular interactions with anions, are inactive. The halogen bonding anionophores also exhibit a remarkable intrinsic chloride over hydroxide selectivity, which is usually observed only in more complex anionophore designs, in contrast to the readily accessible acyclic systems reported here. This highlights the potential of iodo-triazoles as synthetically accessible and versatile motifs for developing more efficient anion transport systems. Computational studies provide further insight into the nature of the anion-triazole intermolecular interactions, examining the origins of the observed transport activity and selectivity of the systems, and revealing the role of enhanced charge delocalisation in the halogen bonding anion complexes.

Halogen and hydrogen bonding 1,2,3-triazole derivatives efficiently mediate anion transport across lipid bilayer membranes with unusual anion selectivity profiles.     

Calculation of the hydrogen binding energies of complexes between formamide and adenine-thymine pair

The hydrogen bonding of complexes formed between formamide and adenine-thymine base pair has been completely investigated in the present study. In order to gain deeper insight into structure, charge distribution, and energies of complexes, we have investigated them using density functional theory at 6–311++G(d, p), 6–31G, 6–31+G(d), and 6–31++G(d, p) level. Seven stable cyclic structures (ATF1–ATF7) being involved in the interaction has been found on the potential energy surface. In addition, for further correction of interaction energies between adenine—thymine and formamide, the basis set superposition error associated with the hydrogen bond energy has been computed via the counterpoise method using the individual bases as fragments. The infrared spectrum frequencies, IR intensities and the vibrational frequency shifts are reported.     

Anion recognition through hydrogen bonding by adamantane-dipyrromethane receptors

Adamantane-dipyrromethane (AdD) receptors [di(pyrrole-2-yl)methyladamantane (1), 2,2-di(pyrrole-2-yl)adamantane (2), 1,3-bis[di(pyrrole-2-yl)methyl]adamantane (3), 2,2,6,6-tetra(pyrrole-2-yl)adamantane (4)] form complexes with F⁻, Cl⁻, Br⁻, AcO⁻, NO₃⁻, HSO₄⁻, and H₂PO₄⁻. The association constants of the complexes were determined by ¹H NMR titrations, whereas the geometries of complexes 1·F⁻ (2:1), 2·F⁻ (2:1), 2·Cl⁻ (2:1), 2·AcO⁻ (2:1), and 4·F⁻ (1:1) were determined by X-ray structural analysis. The most stable complexes are of 2:1 stoichiometry with F⁻ and AcO⁻. The stability constants are in accordance with the anion basicity and the ability of AdD receptors to place the hydrogen bonding donor groups in a tetrahedral fashion around anions. The binding energies of the complexes between receptors 1-4 and F⁻ anion are calculated using quantum chemical methods. The calculated results show that the solvent polarity is important for the complexation of fluoride ion with AdD receptors 1-4.     

Fluorescence quenching in molecular recognition by hydrogen bonding

Steady-state fluorescence and single photon timing have been used to study the effect of the presence of hydrogen bonding on the intermolecular quenching of pyrene covalently linked to a guanine-like receptor I by an aliphatic amine (N,N-dimethylpropylamine) covalently linked to cytosine derivative II. By comparing the fluorescence quenching of I by II with that of 10methylpyrene (1-MP) by triethylamine (TEA), as a model system in which no hydrogen bonding can occur, one could possibly analyze the effect of the hydrogen bonding between receptor and substrate as a quenching as it leads to a higher local concentration of donor and acceptor. While the quenching of I by II was observed with an apparent rate constant k_q of (1.78 ± 0.10) × 10⁹ M⁻¹ s⁻¹ and (8.72 ± 0.42) × 10⁸ M⁻¹ s⁻¹ in toluene and acetonitrile, respectively, no quenching could be observed in methanol. Upon excitation of 1-MP, no quenching by II could be detected in the same concentration range as used in the quenching of I. Quenching of I and of 1-MP by TEA (⩾ 10⁻² M) in toluene leads to exciplex formation with maxima centred at 540 and 514 nm, respectively. The rate constants of exciplex formation and dissociation of I with TEA were analyzed using a global compartmental analysis. The following values were obtained for the rate constants: k₀₁ = (9.70 ± 0.01) × 10⁶ s⁻¹, k₂₁ = (1.12 ± 0.003) × 10⁹ M⁻¹ s⁻¹, k₀₂ = (5.24 ± 0.01) × 10⁷ s⁻¹ and k₁₂ = (7.74 ± 0.08) × 10⁶ s⁻¹. Quenching of I by TEA in the presence of III, a hydrogen-bonding system without an alkyl amine substituent, leads to exciplex formation centred at 538 nm. The rate constant values for the exciplex formation and dissociation of I with TEA in the presence of III were: k₀₁ = (9.32 ± 0.08) × 10⁶ s⁻¹, k₂₁ = (9.32 ± 0.003) × 10⁸ M⁻¹ s⁻¹, k₀₂ = (6.16 ± 0.03) × 10⁷ s⁻¹ and k₁₂ = (21.90 ± 0.3) × 10⁶ s⁻¹. The apparent rate constants k_q for this system was (7.26 ± 0.56) × 10⁶ M⁻¹ s⁻¹. The observed decrease in the rate of exciplex formation of I with TEA in the presence of III could suggest that the guanine-like moiety in I forms hydrogen bonds with the cytosine-like moiety and this could decrease the electron affinity of I. The rate constant of exciplex dissociation increased, indicating that the exciplex is less stable in the presence of III. Because of the single exponential decay of I in the presence and absence of II and of the agreement between steady-state and transient fluorescence measurements, the information available for quantitative analysis of the association between I and II is limited.     

Self-recognition and hydrogen bonding by polycyclic bridgehead monoalcohols

Our interest in the relationship between the hydrogen bonding motifs displayed by monoalcohols and the properties of the solids which contain these motifs has led us to determine the crystal structures of three polycyclic bridgehead monoalcohols. One C10H16O isomer crystallises in the space group P2(1)2(1)2(1) but the three molecules which comprise the asymmetric unit are related approximately by the operations of a 3(1) screw axis. They are linked by hydrogen bonds to form an infinite helix. A second C10H16O isomer forms rings containing four molecules joined by cooperative hydrogen bonds. The chiral space group P4(1)2(1)2 accommodates molecules of the S,S and R,R enantiomers in the molar ratio 92:8 (ee 84%) owing to disorder. A related C9H14O2 keto-alcohol forms infinite chains by C-OH...O = C hydrogen bonding. These hydrogen bond motifs are shown to be typical for 45 tertiary monoalcohols, CmHnOH, present in the Cambridge Structural Database. Tertiary monoalcohols display in a more pronounced form the strong preferences for trigonal and tetragonal space groups and for asymmetric units containing several molecules which are established features of the crystallochemistry of monoalcohols.     

Dependence of amide vibrations on hydrogen bonding

The effect of hydrogen bonding on the amide group vibrational spectra has traditionally been rationalized by invoking a resonance model where hydrogen bonding impacts the amide functional group by stabilizing its [(-)O-C=NH (+)] structure over the [O=C-NH] structure. However, Triggs and Valentini's UV-Raman study of solvation and hydrogen bonding effects on epsilon-caprolactum, N, N-dimethylacetamide (DMA), and N-methylacetamide (NMA) ( Triggs, N. E.; Valentini, J. J. J. Phys. Chem. 1992, 96, 6922-6931) casts doubt on the validity of this model by demonstrating that, contrary to the resonance model prediction, carbonyl hydrogen bonding does not impact the AmII' frequency of DMA. In this study, we utilize density functional theory (DFT) calculations to examine the impact of hydrogen bonding on the C=O and N-H functional groups of NMA, which is typically used as a simple model of the peptide bond. Our calculations indicate that, as expected, the hydrogen bonding frequency dependence of the AmI vibration predominantly derives from the C=O group, whereas the hydrogen bonding frequency dependence of the AmII vibration primarily derives from N-H hydrogen bonding. In contrast, the hydrogen bonding dependence of the conformation-sensitive AmIII band derives equally from both C=O and N-H groups and thus, is equally responsive to hydrogen bonding at the C=O or N-H site. Our work shows that a clear understanding of the normal mode composition of the amide vibrations is crucial for an accurate interpretation of the hydrogen bonding dependence of amide vibrational frequencies.