Developing accurate molecular mechanics force fields for conjugated molecular systems

Abstract

A rapid method to parameterize the intramolecular component of classical force fields for complex conjugated molecules is proposed. The method is based on a procedure of force matching with a reference electronic structure calculation. It is particularly suitable for those applications where molecular dynamics simulations are used to generate structures that are therefore analysed with electronic structure methods, because it is possible to build force fields that are consistent with the electronic structure calculations that follow the classical simulations. Such applications are commonly encountered in organic electronics, spectroscopy of complex systems and photobiology (e.g. photosynthetic systems). We illustrate the method by parameterizing the force fields of a molecule used in molecular semiconductors (2,2-dicyanovinyl-capped S, N-heteropentacene or DCV-SN5), a polymeric semiconductor (thieno[3,2-b]thiophene-diketopyrrolopyrrole TT-DPP) and a chromophore embedded in a protein environment (15,16-Dihydrobiliverdin or DBV) where several hundreds of parameters need to be optimized in parallel.

Regimes of Exciton Transport in Molecular Crystals in the Presence of Dynamic Disorder

“…In the case of DCVSN5, a force fi eld was developed that reproduced the equilibrium structure and the forces around the equilibrium position computed at the B3LYP/6-31G** level. [ 75 ] The electrostatic intermolecular interaction was modeled by point charges (evaluated via the CHELPG procedure [ 76 ] whereas the nonbonded interactions were described by CHARMM parameters [ 77,78 ] (see the Supporting Information for further details about the force fi eld for DCVSN5). The integration time was set to 1 fs and 2050 snapshots every 50 fs were taken.…”

“…In the case of DCVSN5, we developed a force field that reproduces the equilibrium structure and the forces around the equilibrium position computed at the B3LYP/6-31G** level. [43] The electrostatic intermolecular interaction was modelled by point charges (evaluated via the CHELPG procedure [44] )…”

A Comprehensive study of the Effects of Chain Morphology on the Transport Properties of Amorphous Polymer Films

“…In that sense, adding the polymer morphology is counterproductive as it introduces several new parameters. However, although outside the scope of the authors expertise, we believe that in a real film the parameters are dependent and molecular calculations 34 could reduce the parameter space significantly. As such inter-dependencies are not available to us at present we outline the main findings below assuming the various parameters are independent: The most influential parameters on the charge carrier mobility are the energetic disorder, the average number of NN (~film’s density), the carrier delocalization (conjugation) length, and the on-chain transport.…”

Developing an effective polarizable bond method for small molecules with application to optimized molecular docking

“…In the past few decades, signicant progress has been made in the development of molecular mechanics (MM) force elds for biomolecular simulation. [54][55][56][57][58][59] However, the main drawback of standard force elds is the lack of polarization effects. In 1976, Warshel and Levitt 60 considered the protein polarization effect within the QM/MM method.…”