An approach towards understanding the structure of complex molecular systems: the case of lower aliphatic alcohols

Abstract

An extensive study of liquid aliphatic alcohols methanol, ethanol, and propanol, applying reverse Monte Carlo modelling as a method of interpretation of diffraction data, is presented. The emphasis is on the evaluation of several computational strategies in view of their suitability to obtain high quality molecular models via the reverse Monte Carlo procedure. A consistent set of distances of closest approach and fixed neighbour constraints applicable to all three investigated systems was developed. An all-atom description is compared with a united-atom approach. The potentialities of employment of neutron diffraction data of completely deuterated and isotopically substituted samples, x-ray diffraction data, and results of either molecular dynamics or Monte Carlo calculations were investigated. Results show that parallel application of x-ray and neutron diffraction data, the latter being from completely deuterated samples, within an all-atom reverse Monte Carlo procedure is the most successful strategy towards attaining reliable, detailed, and well-structured molecular models, especially if the models are subsequently refined with the results of molecular dynamics simulations.

The hydrogen-bond collective dynamics in liquid methanol

“…Intramolecular bond distances were constrained to the equilibrium values (r CH  = 1.09 Å, r CO  = 1.41 Å, r OH  = 0.945 Å) by means of the SHAKE algorithm, while the remaining intramolecular motions such as bond-angle bending and rotation of the methyl group around the axis of the C-O bond were treated using a harmonic and a cosine potential, respectively, with the corresponding OPLS-AA parameters which are reported in the Supplementary Information . This model has proven to be able to reproduce in a satisfactory way the density and heat of vaporization of liquid methanol62, as well as its structure63. The equations of motion were integrated using the leapfrog algorithm with a timestep of 1 fs.…”

Investigation of the Structure of Ethanol–Water Mixtures by Molecular Dynamics Simulation I: Analyses Concerning the Hydrogen-Bonded Pairs

“…8 These approaches have been aimed at understanding the atomic level structure, including characteristics beyond pair correlations, and aggregation 7 of these materials.…”

Interplay between intramolecular and intermolecular structures of 1,1,2,2-tetrachloro-1,2-difluoroethane

“…3, 37 However, usually a careful preparation of the initial configuration is needed in order to be able to reproduce the experimental results; a preparation that if not properly done can be misleading in the case of complex molecules such as polyalcohols. 7 This problem of a strong dependence of the result on the initial choice of parameters is typical for fits with many parameters. In the case of reverse Monte Carlo, the number of degrees of freedom of the system is extremely high because the description of the data is done by molecular configurations.…”

“…Both the decoupled 5 and the coupled 6 approaches have been applied in structural modeling applications. In more complex systems, such as alcohols, 7,8 the intramolecular structure has been proven to have an effect on the intermolecular structure at short and even intermediate distances. 9 The determination of the intramolecular structure in the liquid or the solid phases is not an easy task.…”