Hydrogen atom bonding

Some force fields replace the Lennard-Jones 6-12 term between hydrogen-bonding atoms by ail explicit hydrogen-bonding term, which is often described using a 10-12 Lennard-Jones potential ... 

Some force fields make special provision for hydrogen-bonded atoms A-H B, and modify the Lennard-Jones 12-6 potential to a 12-10 model ... 

Figure 3. Capsules based on other hydrogen-bonding atoms omitted) Tetraurea calixarene dimer 16-16,...

Thus, they are in rather close contact with each other. In crystals chains of hydrogen-bonded atoms may be formed. In phosphatidylethanolamine the phosphate and -NH3+ ions may alternate in these chains.132... 

Given the standard geometries of hydrogen-bonded atoms, or of helices and sheets, it is possible to apply pattern-recognition techniques to analyze the conformation of a protein. This has been done (many times) and is a useful approach to the extent that the problem is well-defined. However, in many cases helices deviate from standard geometry — especially at the ends where they can tighten up or unravel. Any investigation that requires analysis of this kind of detail is better pursued interactively. 

Hydride-transfer reactions, which formally involve two electrons and three centres, show close analogy with proton transfer reactions which comprise four electrons and three centres. Stable hydrogen-bonded complexes can be formed with the proton symmetrically or unsymmetrically spaced between the hydrogen-bonding atoms. Such structures correspond to the stable hydride bonded carbocations [8] and [9] respectively discovered by Sorensen and coworkers (Kirchen and Sorensen, 1978 Kirchen et al., 1981a) ... 

In KHFa and a few other exceptional substances the hydrogen atom is midway between the hydrogen-bonded atoms. 

Figure 10.10 Double-wdI potential I ri-pivsenting the hydrogen bond. Atom X is shown as more electronegative than atom Y I he proton wiivefimelion ijr is show In red.

The observation that in the 3 -substituted structures the hydrogen bonding atom approaches the 4 -0H trans to the 3 -substituent is verification of quantitative structure activity relationship (QSAR) data which also suggest that in vitro binding of T3 probably involves hydrogen bond donation of the 4 -OH to the 5 -side of the nuclear receptor (28). 

When the H-atom becomes dynamically disordered in the hydrogen bond, the electronic structures of the hydrogen-bonded atoms are switched over in the rhythm of the H-hopping. The electronic structure of the H-donor and acceptor atoms controls the O-H and H- O lengths as well as the R-O-H and H-O-R angles. When the H-atom becomes disordered between the H-donor and acceptor groups, the only way to preserve these dimensions is to bend the... 

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