First-Principles-Based Multiscale, Multiparadigm Molecular Mechanics and Dynamics Methods for Describing Complex Chemical Processes - Multiscale Molecular Methods in Applied Chemistry - page 30

These were tabulated and histograms of the distribution of these valence terms,
for each unique combination of pseudo-atoms, were generated (see Fig. 15a ).
These distributions were shown to be a single-model Gaussian distribution
for the bonds and angles, and multi-modal for dihedrals. The only exception
occurred when considering the bond distribution between the phosphate (PHO)
and sugar (SUG) pseudo-atoms, which was bi-modal. This anomaly is explained
by considering that starting at the 5' end, the SUG - PHO bond length (4.4 ˚ ) >

SUG bond length (4.0 ˚ ). When constructing
the meso-model from the atomistic representation, if the backbone atoms are
alternatively labeled as PHO-SUG-PHP-SUS-PHO, this anomaly is effectively
resolved and the PHO-SUG, PHO-SUS, PHP-SUG, and PHP-SUS distributions
are uni-modal.
The parameters were obtained by performing a least squares fitting of a Gaussian
curve of the desired functional form. The fitting function is an exponential with
exponent equal to the relevant potential/2RT. For the bonds, the fitting function was
therefore y

is longer than the next PHO - >

2

a 0 e 0 : 5 k r r 0

ð Þ = 2 RT

¼ . Table 2 gives the parameters obtained for the

various bond-stretch terms.

Fig. 15 Plots of (a) adenine-sugar bond distribution from atomistic MD and (b) adenine dimer
interaction energy. This includes the binding energy of the dimer as well as the interaction with the
water molecules

Table 2 Bond parameters for pseudo-beads
k 0 (kcal mol 1 ˚ 2 ) r 0 ( ˚ )

SUG-THY 167.848 4.2136

SUG-ADE 155.974 4.6175

SUG-GUA 143.419 4.7412

SUG-CYT 193.31 4.1101

SUG-PHO 46.0059 4.0053

PHP-SUG 18.2605 4.4283