Hydrogen-bonding geometry

Hydrogen bond geometries may be reproduced or predicted fairly weH with reasonable, but sometimes underestimated heavy atom—heavy atom distances radial dependence of the hydrogen bond may be in error. 

Cheam, T. C., and S. Krimm. 1986. Vibrational Properties of the Peptide N-H Bond as a Function of Hydrogen-Bond Geometry an Ab Initio Study. J. Mol. Struct. 146, 175-189. 

S. Sinnecker, E. Reijerse, F. Neese and W. Lubitz, Hydrogen bond geometries from paramagnetic resonance and electron-nuclear double resonance parameters Density functional study of quinone radical anion-solvent interactions, J. Am. Chem. Soc., 2004, 126, 3280. 

Modig, K., Pfrommer, B.G., and Halle, B. 2003. Temperature-dependent hydrogen-bond geometry in liquid water. Phys. Rev. Lett. 90, 075502. 

We expect the hydrogen bonded geometry Cse to be more stable than the Css or Cee conformations because substantial stabilization of the Cge conformation is already obtained in the initial fragment union, ie. OH + OH. 

FLF)- (L = H or D) anion in low temperature solutions of (C4H9)4N+ (FL)nF . The authors were able to determine zero-, one-, and two-bond, H/D isotope effects on hydrogen and fluorine NMR chemical shifts for the series n = 1 to n = 3, and to relate the observed spectra to H/D isotope effects on the hydrogen bond geometries. Isotope effects on spin-spin L-F and F-F coupling 13C constants were reported. 

A. A. Kossiakoff, M. Ultsch, S. White, C. Eigenbrot, Neutron Structure of Subtilisin BPN Effects of Chemical Environment on Hydrogen-Bonding Geometries and the Pattern of Hydrogen-Deuterium Exchange in Secondary Structure Elements , Biochemistry 1991, 30, 1211-1221. 

Criteria for hydrogen-bonding geometry in X-ray crystallographic structures have been established as follows (1) The distance between the acceptor and the hydrogen (dnA) must be less than 2.5 A (2) the distance between the... 

Fig. 2 Hydrogen bond geometry (not to scale) + and - are positions 5/2 and - 5/2, respectively. P and S are P04 core and shell is the potassium ion dotted lines indicate the contributions to C(5)...

Figure 4.2 Structure of the oxyanion hole of the active site of trypsin, complexed with a peptide inhibitor (PDB IPPE). The hydrogen atoms (in white) are only included when relevant for the hydrogen bonding geometry of the oxyanion hole. The dotted lines highlight the key interactions in the oxyanion hole.

An examination of the stereochemistry of the H+ ion is complicated by a number of factors. Because it has no electron core, hydrogen is difficult to locate using X-rays which are scattered by electrons. In earlier structure determinations its presence was often ignored because it made no contribution to the X-ray diffraction pattern and could not therefore be located. Even when H is included in the model, its position can rarely be accurately determined and in any case the centre of its electron density is usually displaced from the nucleus towards the donor anion by around 20 pm. Accurate positions of the H+ nuclei can be found using neutron diffraction which has provided sufficient information to reveal the essential characteristics of hydrogen bond geometries, but in many of the structures determined by X-ray diffraction the positions of the H cations have had to be inferred from the positions of their neighbouring anions. 

Taylor, R. and Kennard, O. (1984). Hydrogen bond geometry in organic crystals. Acc. Chem. Res. 17, 320-6. 

Figure 1.16 Various types of hydrogen bonding geometries (a) linear (b) bent (c) donating bifurcated (d) accepting bifurcated (e) trifurcated (f) three centre bifurcated.

Figure 8.53 Common hydrogen bonded geometries for alcohols, ROH.

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