Hydrogen force fields

Molecular dynamics simulations of duplex DNA or RNA in solution now yield stable structures for a duration of well over 1 ns. Different force fields, however, lead to different equilibrium stmctures. Presented are details of the equilibrium between the A and B forms of DNA by the CHARMM all-hydrogen force field for several sequences, including previously unpublished results on the d[GCGCGCG]2 and d[ATATATA]2 duplexes in solution. Comments are also included on the performance of other force fields. Based on a combination of observations a dominate role of the sugar and phosphodiester backbone moieties in the equilibrium between the A and B forms of DNA is suggested. 

Enthalpies of Hydrogenation Force Fields MM3 Molecular Mechanics Conjugated Systems,... 

Hccausc of Ihc restricted availability of corn ptilation al resources, sorn e force fields use Un itcd. torn types, fli is type of force field represeri ts implicitly all hydrogens associated with a methyl, rn elli yieti e, or rn etii in e group. Th e van der Waals param eters for united atom carbons reflect the increased si/.e because of the implicit (included) hydrogens. 

For XH bonds, where X isany heavy atom, the hydrogen electron den sity is ri ot th ough t to be cen tered at th e position of th e hydrogen n ueleus but displaced alon g th e bon d sorn ewhat, towards X. The MM+ force field reduces the XH bond length by a factor of 0.9 I 5 strictly for th e purposes of calculatin g van der Waals in teraction s with hydrogen atoms. 

I lle HIO+force field option in HyperChem hasno hydrogen bond-in g term, Th is is con sisten I with evolution andcommon useofthe CH.ARMM force field (even the 1983 paper did n ot usc a liydrogen boruiin g term in its exam pic calculation s an d men lion ed that the functional form used then was u n satisfactory and under review). 

In some force fields the interaction sites are not all situated on the atomic nuclei. For example, in the MM2, MM3 and MM4 programs, the van der Waals centres of hydrogen atoms bonded to carbon are placed not at the nuclei but are approximately 10% along the bond towards the attached atom. The rationale for this is that the electron distribution about small atoms such as oxygen, fluorine and particularly hydrogen is distinctly non-spherical. The single electron from the hydrogen is involved in the bond to the adjacent atom and there are no other electrons that can contribute to the van der Waals interactions. Some force fields also require lone pairs to be defined on particular atoms these have their own van der Waals and electrostatic parameters. 

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 ... 

I lagler A T, E Huler and S Lifson 1977. Energy Functions for Peptides and Proteins. I. Derivation of a Consistent Force Field Including the Hydrogen Bond from Amide Crystals. Journal of the American Chemical Society 96 5319-5327. 

Stretching, bond bending, torsions, electrostatic interactions, van der Waals forces, and hydrogen bonding. Force fields differ in the number of terms in the energy expression, the complexity of those terms, and the way in which the constants were obtained. Since electrons are not explicitly included, electronic processes cannot be modeled. 

The AMBER force field replaces the van der Waals by a 10-12 potential for pairs of atoms that can participate in hydrogen bonding (equation 12). The hydrogen bond potential does not contribute significantly to the hydrogen bonding attraction between two atoms rather, it is implemented to fine-tune the distances between these atoms. 

The attraction for two neutral atoms separated by more than four Angstroms is approximately zero. The depth of the potential wells is minimal. For the AMBER force field, hydrogen bonds have well depths of about 0.5 kcal/mol the magnitude of individual van der Waals well depths is usually less. 

United Atom force fields are used often for biological polymers. In these molecules, a reduced number of explicit hydrogens can have a notable effect on the speed of the calculation. Both the BlO-t and OPUS force fields are United Atom force fields. AMBER contains both a United and an All Atom force field. 

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