Hydrogen-bonding Sequences Research Articles

DL-Phenylalaninium nitrate

In the title compound, C9H12NO2+·NO3−, the phenyl­alaninium residue adopts a folded conformation. It forms a strong O—H⋯O hydrogen bond with the nitrate anion and is also involved in a zigzag head-to-tail hydrogen-bonding sequence (Z1). In the crystal packing of the title compound, the aggregation of the hydro­phobic layer about the x = 0 plane (parallel to the ab plane) is sandwiched between hydro­philic double layers at x = −½ and x = ½.

A Highly Stable, Six-Hydrogen-Bonded Molecular Duplex

This paper describes the design, synthesis, and characterization of a hydrogen-bonded molecular duplex (3·4). Two oligoamide molecular strands, 3 and 4, with the complementary hydrogen-bonding sequences ADAADA and DADDAD, respectively, were found to form an extremely stable (Ka = (1.3 ± 0.7) × 109 M-1) molecular duplex (3·4) in chloroform. Evidence from 1D and 2D 1H NMR spectroscopy, isothermal titration calorimetry, and thin-layer chromatography confirmed the formation and the high stability of the duplex. The exceptional stability is explained by positive cooperativity among the numerous hydrogen-bonding and van der Waals interactions and the preorganization of the individual strands by intramolecular hydrogen bonds. This design has opened a new avenue to supramolecular recognition units with programmable specificities and stabilities.

Molecular dynamics simulations of the unfolding of an .alpha.-helical analog of ribonuclease A S-peptide in water

Molecular dynamics simulations of the S-peptide analogue AETAAAKFLREHMDS have been conducted in aqueous solution for 300 ps at 278 K and for 500 ps in two different runs at 358 K. The results show agreement with experimental observations in that at low temperature, 5 degrees C, the helix is stable, while unfolding is observed at 85 degrees C. In the low-temperature simulation a solvent-separated ion pair was formed between Glu-2 and Arg-10, and the side chain of His-12 reoriented toward the C-terminal end of the alpha-helix. Detailed analyses of the unfolding pathways at high temperature have also revealed that the formation or disappearance of main-chain helical hydrogen bonds occurs frequently through an alpha in equilibrium with 3(10) in equilibrium with no hydrogen bond sequence.

Application of the titration method to studies on the denaturation of sodium deoxyribonucleate

AbstractA method is described whereby the difference between the irreversible forward titration curve from neutrality to pH 2.5 and the reversible back titration curve from pH 2.5 can be used to determine the extent and character of denaturation (i.e., rupture of hydrogen bonds) in various treatments of sodium deoxyribonucleate (DNA) prior to titration. On this basis, the effects of heat, ultrasonic waves, and γ‐rays are examined. Denaturation by ionization of the hydrogen‐bonded amino groups has been studied as a function of temperature and of pH. Some of the kinetic and statistical consequences of the observations are discussed in terms of a model requiring the rupture of a minimum sequence of hydrogen bonds for denaturation to occur.