Molecules (Mar 2025)
Direct Determination of Ratios of All Conformations and Their Lifetimes for Small Flexible Molecules from Molecular Dynamics Simulations: 1,3-Propanediol in an Aqueous Environment
Abstract
For the first time in the course of molecular dynamics modeling of a liquid, the conformations of each of the small flexible molecules present in the system were fixed at short (1 ps) time intervals. This allowed the establishment of the ratios between various individual conformations and their families and determination of the average lifetimes of both individual conformations and families. As an example, data are presented for modeling boxes with different numbers of molecules (800, 2700, and 6400) for an aqueous solution with 1 mol. % 1,3-propanediol at 298.15 K and 1 atm. The results of the conformational analysis turned out to be very close for systems with different numbers of molecules and with different choices of initial conformations. For the systems under investigation, the tTTg conformation, which does not have intramolecular hydrogen bond, predominated (37–39%), and the total fractions of all conformations in the TT family were 74–76%. Only 0.4–0.5% of 1,3-propanediol molecules had conformations with the possible formation of intramolecular hydrogen bond, although the most stable conformers of free 1,3-propanediol molecules exhibit such a bond. The average lifetimes of each individual conformation did not exceed 7 ps in simulated systems, while the maximum lifetimes reached 60 ps. The average lifetimes of the main chain vary from ~110 ps in TT family to ~12 ps in GG′ family, in which the conformations tend to have intramolecular hydrogen bonds. It was found that calculations for an individual 1,3-propanediol molecule at the MP2/aug-cc-pVDZ or MP2/aug-cc-pVTZ theoretical levels lead to 22 conformers both in vacuum and by using the PCM model for implicit aqueous solvation (at the MP2/aug-cc-pVDZ level) and that such solvation reduces the energy difference between the conformers.
Keywords
