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Abstract

We describe a software tool that allows one to visualize and analyze the importance of each individual steric interaction in a molecular mechanics force field. ANLIZE is presently implemented for the Dreiding force field for use with the Cerius2 software package, but could be implemented in any molecular mechanics package with a graphical user interface. ANLIZE calculates individual interactions in the force field, sorts them by size, and displays them in several ways from a menu of choices. This allows the user to scan through selected interactions to visualize which interactions are the primary determinants of preferred conformations. The features of ANLIZE are illustrated using 18-crown-6 as an example, and the factors governing conformational preference in 18-crown-6 are demonstrated. Users of molecular mechanics packages are encouraged to demand this functionality from commercial software producers.

Congestion effect of an annulated tetracyclic thiophene-containing fragment on 18-crown-6 ether: manifestation in complex formation in solution and membrane transfer properties

“…The signals of methylene groups adjacent to phenolic oxygen atoms became slightly shifted apart, and those of H 3 and H 14 became even more shifted. Signals of two almost identical AA 0 BB 0 systems (H 5 H 6 and H 11 H 12 ) fell apart to yield two sets of signals for H 5 and H 6 and a singlet for H 11,12 , which became degenerate. The H 8,9 resonances, which were represented by a singlet in the CE 2 spectrum, became a typical AA 0 BB 0 multiplet with close chemical shifts of the protons.…”

“…Their binding properties to cations, [2][3][4] anions, 5 neutral molecules, 6,7 and ion pairs 8 are a function of both composition of heteroatoms and ring size. 9 These factors are expressed via the set of conformations [10][11][12][13] existing for a certain macrocycle.…”

“…14 Different conformations can be identified by interpreting the results of either single crystal X-ray 15 or computation experiment. [10][11][12][13] Therefore, the search for new ways to influence the conformation distribution of a crown ether system is promising as a means to control its properties. This can be done, e.g., by restricting the rotation of one or several OCH 2 CH 2 O moieties by benzannulation or annulation to another ring, 16,17 or by introduction of a diaryl spacer in place of CH 2 CH 2 group.…”

“…14 Different conformations can be identified by interpreting the results of either single crystal X-ray 15 or computation experiment. 10–13 Therefore, the search for new ways to influence the conformation distribution of a crown ether system is promising as a means to control its properties. This can be done, e.g.…”