Molecular dynamics computer simulation as a tool for the analysis of solvation: A study of dilute aqueous solutions of 1,4-dioxane and 1,3-dioxane

Simple computing of the viscosity of water-dioxane mixtures, according to a fluctuating SPC/E-Ih interstitial model

In this contribution, we propose a new simple and fast computing approach to model liquid water and water-1,4 dioxane mixture, which is intermediate between molecular dynamics calculation and lattice fluid H-bonding theory in which water molecules are arranged according to a fluctuating hexagonal I_h network. It generalizes the interstitial mixture models of Samoilov and Pauling by increasing the number of spatial configurations into the space of phases due to the addition of rotations and vibrations of the molecules around their equilibrium positions. The potential energy landscape is determined by the generalization of the Madelung's approach to the molecular water network using simple point charge model (SPC/E partial charges). This approach allows useful predictions as the possibility of incorporation of a molecule of dioxane in the water I_h -network or how some cooperative dynamic jumps (site - hole) of water molecules, contribute to lower Eyring's activation energies and thus to facilitate the viscous flow. © 2017 Wiley Periodicals, Inc.

Molecular mechanics calculations of dA12.dT12 and of the curved molecule d(GCTCGAAAAA)4.d(TTTTTCGAGC)4

Using the AMBER software package (Weiner and Kollman 1981) substantially modified for electrostatic contributions, the structural energies of the double-stranded oligonucleotides dA12.dT12 and d(GCTCGAAAAA)4.d(TTTTTCGAGC)4 were minimized. Using various starting structures for the molecule dA12.dT12, one final structure is obtained which possesses the experimentally determined properties of poly(dA).poly(dT). This structure is an A-form-B-form-hybrid structure similar to that of Arnott et al. (1983). The dA-strand is similar to an A-form while the dT-strand is similar to normal B-form. This structure and separately optimized B-form sequence stretches were used to construct the double-stranded fragment d(GCTCGAAAAA)4 which again was optimized. This sequence, when imbedded in a DNA fragment as contiguous repeats, shows a gel migration anomaly which has been interpreted as stable curvature of the DNA (Diekmann 1986). The calculated structure of this sequence indeed has a curved helix axis and is discussed as a model for curved DNA. A theoretical formalism is presented which allows one to calculate the structural parameters of any nucleic acid double helix in two different geometrical representations. This formalism is used to determine the parameters of the base-pair orientations of the curved structure in terms of wedge as well as cylindrical parameters. In the structural model presented here, the curvature of the helix axis results from an alternation of two different DNA structures in which the base-pairs possess different angles with the helix axis ('cylinder tilt'). Resulting from geometric restraints, a negative cylinder tilt angle correlates strongly with the closing of the minor groove ('wedge roll'). The blocks with different structure are not exactly coincident with the dA5-blocks and the B-DNA stretches. Within the dA5 block, base-pair tilt and wedge roll adopt large values which proceed into the 3' flanking B-DNA sequence by about one base-pair. These properties of the structure calculated here are discussed in terms of different models explaining DNA curvature.