Structure and dynamics of mesogens using intermolecular potentials derived from ab initio calculations

Automated Parameterization of Quantum Mechanically Derived Force Fields for Soft Materials and Complex Fluids: Development and Validation

The reliability of molecular dynamics (MD) simulations in predicting macroscopic properties of complex fluids and soft materials, such as liquid crystals, colloidal suspensions, or polymers, relies on the accuracy of the adopted force field (FF). We present an automated protocol to derive specific and accurate FFs, fully based on ab initio quantum mechanical (QM) data. The integration of the Joyce and Picky procedures, recently proposed by our group to provide an accurate description of simple liquids, is here extended to larger molecules, capable of exhibiting more complex fluid phases. While the standard Joyce protocol is employed to parameterize the intramolecular FF term, a new automated procedure is here proposed to handle the computational cost of the QM calculations required for the parameterization of the intermolecular FF term. The latter is thus obtained by integrating the old Picky procedure with a fragmentation reconstruction method (FRM) that allows for a reliable, yet computationally feasible sampling of the intermolecular energy surface at the QM level. The whole FF parameterization protocol is tested on a benchmark liquid crystal, and the performances of the resulting quantum mechanically derived (QMD) FF were compared with those delivered by a general-purpose, transferable one, and by the third, "hybrid" FF, where only the bonded terms were refined against QM data. Lengthy atomistic MD simulations are carried out with each FF on extended 5CB systems in both isotropic and nematic phases, eventually validating the proposed protocol by comparing the resulting macroscopic properties with other computational models and with experiments. The QMD-FF yields the best performances, reproducing both phases in the correct range of temperatures and well describing their structure, dynamics, and thermodynamic properties, thus providing a clear protocol that may be explored to predict such properties on other complex fluids or soft materials.

Density functional theory study of π-aromatic interaction of benzene, phenol, catechol, dopamine isolated dimers and adsorbed on graphene surface

We analyze the influence of different groups on the intermolecular energy of aromatic homodimers and on the interaction between a single aromatic molecule and a graphene surface. The analysis is performed for benzene, phenol, catechol, and dopamine. For calculating the energies, we employ density functional theory within the local density approximation (LDA-DFT). Our results show that the lowest intermolecular energies between the aromatic molecules are related to the T-shaped configurations. This lower energy results from the quadrupole interaction. In the case of the interaction between the graphene sheet and the aromatic molecules, the lowest energy configuration is the face to face. The adsorption energy of a molecule on a graphene surface involves π - π interactions that explain the face to face arrangement. These results provide insight into the manner by which substituents can be utilized in crystal engineering, supramolecular chemistry, bioinspired materials, formation of various molecular clusters, parameterization of force fields suitable for classical simulations, and design of novel sensing, drug delivery, and filters based on graphene.

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.

Intermolecular interactions in eumelanins: a computational bottom-up approach. I. small building blocks

Building eumelanin: from basic units to spectral properties.

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.

An automated approach for the parameterization of accurate intermolecular force-fields: pyridine as a case study

An automated protocol is proposed and validated, which integrates accurate quantum mechanical calculations with classical numerical simulations. Intermolecular force fields, (FF) suitable for molecular dynamics (MD) and Monte Carlo simulations, are parameterized through a novel iterative approach, fully based on quantum mechanical data, which has been automated and coded into the PICKY software, here presented. The whole procedure is tested and validated for pyridine, whose bulk phase, described through MD simulations performed with the specifically parameterized FF, is characterized by computing several of its thermodynamic, structural, and transport properties, comparing them with their experimental counterparts.

A survey of the potential energy surface for the (benzene)13 cluster

We report on a survey of the potential energy surface for the 13-molecule benzene cluster, (C(6)H(6))(13), bound by an atom-atom intermolecular potential developed from first principles. The potential, which has an anisotropic repulsion term, is found to support distinct pairs of structures of C(3), C(i), and S(6) symmetry as low-lying minima, including a C(3) global minimum. The organisation of the low-lying region of the potential energy surface suggests that one of the S(6) structures is likely to act as a kinetic trap, hindering efficient relaxation to the global minimum, in agreement with the hypothesis that two isomers coexist in this system, suggested by spectroscopic experiments.