Hydrogen Bonding in Molecular Mechanics

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

The GRID program [Goodford 1985] that is used for finding energetically favourable regions in protein binding sites uses a direction-dependent 6-4 frmction  

By no means do all force fields contain explicit hydrogen-bonding terms most rely upon electrostatic and van der Waals interactions to reproduce hydrogen bonding. 

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The literature contains a wide choice of functions and parameters for including hydrogen bonding in molecular mechanics. A selection is given in Box 4.4. All distinguish between different types of hydrogen bonds, and some are developed for particular classes of molecules. 

Lagodzinskaya GV, Yunda NG, ManeUs GB (2002) H + -catalyzed symmetric proton exchange in neat liquids with a network of N-H-N and O-H-O hydrogen bonds and molecular mechanism of Grotthus proton migration. Chem Phys 282 51-61 Lamb WJ, Brown DR, Jonas JJ (1981) Temperature and density dependence of the proton lifetime min liquid water. Phys Chem 85 2883-1887... 

Chapter 9, on entropy and molecular rotation in crystals and liquids, is concerned mostly with statistical mechanics rather than quantum mechanics, but the two appear together in SP 74. Chapter 9 contains one of Pauling s most celebrated papers, SP 73, in which he explains the experimentally measured zero-point entropy of ice as due to water-molecule orientation disorder in the tetrahedrally H-bonded ice structure with asymmetric hydrogen bonds (in which the bonding proton is not at the center of the bond). This concept has proven fully valid, and the disorder phenomenon is now known to affect greatly the physical properties of ice via the... 

There are two major experimental techniques that can be used to analyze hydrogen bonding in noncrystalline polymer systems. The first is based on thermodynamic measurements which can be related to molecular properties by using statistical mechanics. The second, and much more powerful, way to elucidate the presence and nature of hydrogen bonds in amorphous polymers is by using spectroscopy (Coleman et al., 1991). From the present repertoire of spectroscopic techniques which includes IR, Raman, electronic absorption, fluorescence, and magnetic resonance spectroscopy, the IR is by far the most sensitive to the presence of hydrogen bonds (Coleman et al., 1991). 

In molecular mechanics force fields for biological molecules, hydrogen bonds are generally modeled using an empirical 10,12-fimction (Eq. 15.8). 

The problem of transference from the hydrogen bonds in the crystal to those in a biological process is not different, in principle, from the transference of molecular structural information determined by crystal structure analysis to the interpretation of the mechanism of a chemical reaction. In Chapter 4, we discuss the differences between the geometry of hydrogen bonds in crystals and in the free molecule models that are necessarily used by the theoretical methods. 

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