Calculating Hydrogen-Bond Geometries

There are three levels of theoretical calculations which can be used to predict intra- or intermolecular hydrogen bonding and its effect on molecular geometry and association. 

Ab-initio molecular orbital calculations which use the Hartree-Fock self-consistent field theory with one-electron molecular orbitals. This method is based on the variation theorem to seek the nuclear geometry of the molecule or hydrogen-bonded complex with lowest energy [248-253]. It uses no experimental data. 

Semi-empirical molecular orbital calculations, which are based on the same or related quantum mechanical principles, but make approximations or assumptions to simplify the computations, or include some empirical parameters based on experimental data [254-259]. 

Molecular mechanical calculations which are based on classical Newtonian mechanics [260—262], but use quantum mechanical concepts to formulate empirical equations. The parameters used are based entirely on experimental data. 

Calculations by ab-initio or semi-empirical methods on isolated molecules containing hydrogen-bond donor and acceptor groups will always predict the molecular conformations which have the maximum intramolecular bonding. For a- 

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We have noted the importance of incorporating calculations of IR intensities in the analysis of spectra. This approach is certain to prove fruitful in a number of areas determination of the dependence of amide mode intensities on conformation influence of size and perfection of structure on intensities correlation of intensities with hydrogen-bond geometry (Cheam and Krimm, 1986). Just as it is possible to develop a conformational (, i/ )-frequency map (Hsu et al., 1976), it should be possible to compute a conformational (, i/ )-intensity map, which could be useful in analyzing the spectra of unordered polypeptide chain structures. Of course, nothing has yet been done on the calculation of Raman intensities of polypeptides, and this area is ripe for future development. 

Figure 6.38 (a) Hydrogen bond geometries of various molecular systems containing NHN-hydrogen bonds, (b) Barrier heights of the H-transfers calculated from the Arrhenius curves of the species in (a). The barrier heights of the transition states are set to zero. Values taken from Table 6.5. 

Klein RA, Mennucci B, TomasiJ. Ab initio calculations of 0 NMR-chemical shifts for water. The limits of PCM theory and the role of hydrogen-bond geometry and cooperativity. J Phys Chem A. 2004 108(27) 5851—5863. http //dx.doi.org/10.1021/ jp0487408. 

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