Furan and thiophene in liquid phase: An X-ray and molecular dynamics study

The structure of liquid thiophene from total neutron scattering

The structure of pure liquid thiophene is revealed by using a combination of total neutron scattering experiments with isotopic substitution and molecular simulations via the next generation empirical potential refinement software, Dissolve. In the liquid, thiophene presents three principle local structural motifs within the first solvation shell, in plane and out of the plane of the thiophene ring. Firstly, above/below the ring plane thiophenes present a single H towards the π cloud, due to a combination of electrostatic and dispersion interactions. Secondly, around the ring plane, perpendicular thiophene molecules find 5 preferred sites driven by bifurcated C-H⋯S interactions, showing that hydrogen-sulfur bonding prevails over the charge asymmetry created by the heteroatom. Finally, parallel thiophenes sit above and below the ring, excluded from directly above the ring center and above the sulfur.

Understanding the Liquid States of Cyclic Hydrocarbons Containing N, O, and S Atoms via the 3D-RISM-KH Molecular Solvation Theory

The 3D-reference interaction site model (3D-RISM) molecular solvation theory in combination with the Kovalenko-Hirata (KH) closure is extended to seven heterocyclic liquids to understand their liquid states and to test the performance of the theory in solvation free energy (SFE) calculations of solutes in select solvents. The computed solvent site distribution profiles were compared with the all-atom molecular dynamics (MD) simulations, showing comparable performances. The computational results were compared against the structural parameters for liquids, whenever available, as well as against the experimental SFEs. The liquids are found to have local ordered structures held together via weak interactions in both the RISM and MD simulations. The 3D-RISM-KH computed SFEs are in good agreement with the benchmark values for the tetrahydrothiophene-S,S-dioxide, and showed comparatively larger deviations in the case of the SFEs in the tetrahydrofuran continuum.

Development and Validation of Quantum Mechanically Derived Force-Fields: Thermodynamic, Structural, and Vibrational Properties of Aromatic Heterocycles

A selection of several aromatic molecules, representative of the important class of heterocyclic compounds, has been considered for testing and validating an automated Force Field (FF) parametrization protocol, based only on Quantum Mechanical data. The parametrization is carried out separately for the intra- and intermolecular contributions, employing respectively the Joyce and Picky software packages, previously implemented and refined in our research group. The whole approach is here automated and integrated with a computationally effective yet accurate method, devised very recently ( J. Chem.

THEORY

Comput., 2018, 14, 543-556) to evaluate a large number of dimer interaction energies. The resulting quantum mechanically derived FFs are then used in extensive molecular dynamics simulations, in order to evaluate a number of thermodynamic, structural, and dynamic properties of the heterocycle's gas and liquid phases. The comparison with the available experimental data is good and furnishes a validation of the presented approach, which can be confidently exploited for the design of novel and more complex materials.

Parametrization and Validation of Intramolecular Force Fields Derived from DFT Calculations

The energy and its first and second geometrical derivatives obtained by DFT calculations for a number of conformations of a single molecule are used to parametrize intramolecular force fields, suitable for computer simulations. A systematic procedure is proposed to adequately treat either fully atomistic or more simplified force fields, as within the united atom approach or other coarse grained models. The proposed method is tested and validated by performing molecular dynamics simulations on several different molecules, comparing the results with literature force fields and relevant experimental data. Particular emphasis is given to the united atom approach for flexible molecules characterized by "soft" torsional potentials which are known to retain a high degree of chemical specificity.

Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data

The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first validation is achieved by successfully comparing results obtained with Joyce2.0 to literature ones, obtained for the same set of benchmark molecules. The parameterization protocol is also applied to two other larger molecules, namely nicotine and a coumarin based dye. In the former case, the parameterized force field is employed in molecular dynamics simulations of solvated nicotine, and the solute conformational distribution at room temperature is discussed. Force fields parameterized with Joyce2.0, for both the dye's ground and first excited electronic states, are validated through the calculation of absorption and emission vertical energies with molecular mechanics optimized structures. Finally, the newly implemented procedure to handle polarizable force fields is discussed and applied to the pyrimidine molecule as a test case.