Hydrogen bonds directional

Etter, M. C., Z. Urbanczyk-Lipowska, M. Zia-Ebrahimi, and T. W. Pananto. 1990. Hydrogen Bond Directed Cocrystallization and Molecular Recognition Properties of Diaryl Ureas. J. Am Chem. Soc. 112, 8415. 

Fig. 4. The molecular structure, determined by solution NMR (James et al., 1997), of Syrian hamster 90-231 (SHa90-231) prion with ball-and-stick representation of the HI domain (SHal09-122 MKHMAGAAAAGAW). Note that two short /(-chains (SI, S2) nearly stack in the hydrogen-bonding direction. If the palindromic polyalanine region was also in a /(-conformation, there would be a three-stranded /(-sheet. The structural difference between PrPc and PrPSc is in the 90-145 domain. [Model drawn using MOLSCRIPT (Kraulis, 1991)].

Fig. 10. Electron density projection along -strand direction—hydrogen-bonding direction (a-axis) horizontal, and intersheet direction (c-axis) vertical—and skeletal models of polyGln8 (Q8) and polyGln45 (Q45) assemblies. The unit cell for both peptides was monoclinic, with lattice constants a = 9.73 A, b = 7.14 A, c = 8.16 A, and y = 95.7° for Q8, and a = 9.66 A, b = 7.10 A, c = 8.33 A, and y = 94.0° for Q45. The side chains are nearly overlapped in the hydrogen-bonding direction. This difference in side chain conformation and disorder likely accounts for the differences in observed intensity between their diffraction patterns.

Scheme 48 The hydrogen-bonded directed photodimerisation of 100 yields 102 which is a good ligand for the formation of an hexa-copper cage compound... 

As the temperature continues to rise, this jumping between the two configurations, similar to melting, leads to the peak in Cp with a maximum at about 270 K (Figure 3). In summary, the model suggests that the water in direct contact with the mineral surface (hole water) is strongly bonded to the silicate layer. The second layer of water (associated water) behaves very differently because it has few if any hydrogen bonds directly to the silicate layer. 

The first step of the catalytic process is the hydrogen bond directed assembly and orientation of the reactants. In this example, the azlactone and methanol form a ternary starting complex with the organocatalyst (Fig. 1) [39]. The pseudo-Lewis acidic thiourea forms two bifurcated, nearly symmetric hydrogen bonds (2.147 A, < (0,H,N) = 155.5° and 2.146A, <(0,H,N) = 155.8°) to the carbonyl oxygen atom of the azlactone. 

The first step of the catalyhc process is the hydrogen bond directed assembly and orientation of the reactants. In this example, the azlactone and methanol form... 

Fig. 6.77. Calculations done using the statistical mechanical theory of electrolyte solutions. Probability density p(6,r) for molecular orientations of water molecules (tetrahedral symmetry) as a function of distance rfrom a neutral surface (distances are given in units of solvent diameter d = 0.28 nm) (a) 60H OH bond orientation and (b) dipolar orientation, (c) Ice-like arrangement found to dominate the liquid structure of water models at uncharged surfaces. The arrows point from oxygen to hydrogen of the same molecule. The peaks at 180 and 70° in p(0OH,r) for the contact layer correspond to the one hydrogen bond directed into the surface and the three directed to the adjacent solvent layer, respectively, in (c). (Reprinted from G. M. Tome and G. N. Patey, ElectrocNm. Acta 36 1677, copyright 1991, Figs. 1 and 2, with permission from Elsevier Science.

Fig. 8. Structure of succinamide. The NHa group form two hydrogen bonds directed at the 0 =C group linking the molecules in a two-dimensional sheet...

Hannam, J. S., Kidd, T. J., Leigh, D. A., Wilson, A. J., Magic rod rotaxanes The hydrogen bond-directed synthesis of molecular shuttles under thermodynamic control. Org. Lett. 2003, 5, 1907-1910. 

Fig. 14.26 2-Aminopyrimidine-functiona-lized anthracene (36) and the cavities formed by the hydrogen bond-directed self-assembly of this molecule (top right). These cavities...

Scheme 10.6 Self-assembly of the hydrogen bond-directed [2]catenane formation by Leigh and coworkers.

Graener H, Ye TQ, Laubereau A. Ultrafast dynamics of hydrogen bonds directly observed by time-resolved infrared spectroscopy. I Chem Phys 1989 90 3413-3416. 

Keeping in mind that all three x-rayed flavodoxins (7, 8, 9, 10, 11) exhibit C(7,8) as the only possible point of direct outer contact while all the rest of the flavin molecule is buried in the protein, we must finally admit that chemically C(8) is the reasonable site of orbital overlap between flavin and secondary heteroaromatic le -donor-acceptor molecules such as flavin itself and, above all, cytochrome. Flavodoxins represent the case of flavoproteins scheduled for le -only transfer by a hydrogen bond directed from the apoprotein towards N(5), stabilizing the radical Hp. The bond is strong enough to maintain the active protein reduced in the lower le -shuttle between Flred and Fl. 

With more than 100 elements besides carbon in the periodic table (Appendix 2), you might fear that the number of H chemical shift correlations is endless. However, except for a few specialized applications, the most important heteroatoms to which hydrogen finds itself bonded are oxygen and nitrogen. But before we discuss these two specific cases, here is a useful generalization As the electronegativity (Table 6.1) of X increases, both the acidity and chemical shift of a hydrogen bonded directly to X increase. 

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