Developing Consistent Molecular Dynamics Force Fields for Biological Chromophores via Force Matching

Claridge, Kirsten; Troisi, Alessandro

doi:10.1021/acs.jpcb.8b10746

Cited by 25 publications

(33 citation statements)

References 69 publications

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“…It still remains a challenge to find satisfactorily accurate FFs for applications where MD is the preliminary step toward the study of electronic structure properties. [19][20][21] Most existing procedures [22][23][24][25] are general tools for constructing FFs for small organic molecules, either in the gas phase or in a continuum solvent. When applied to specific problems in condensed phases, these FFs may not be directly transferable to the systems under investigation.…”

Section: Introductionmentioning

confidence: 99%

Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene

Jiang

Rogers

Hirst

et al. 2020

J. Chem. Theory Comput.

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Utilising a force matching procedure, we parameterise new force fields systematically for large conjugated systems. We model both conjugated polymers and molecular crystals that contain diketopyrrolopyrrole, thiophene, and thieno[3,2-b]thiophene units. These systems have recently been found to have low band gaps, which exhibit high efficiency for photovoltaic devices. The equilibrium structures, forces and energies of the building block chromophores: diketopyrrolopyrrole thiophene, and thieno[3,2b]thiophene computed using our parameters are comparable to those computed using the reference electronic structure method. We assess the suitability of this new force field for electronic property calculations by comparing the electronic excitation properties computed along classical and ab initio molecular dynamics trajectories. For both trajectories, we find similar distributions of TDDFT calculated excitation energies and oscillator strengths for the building block chromophore diketopyrrolopyrrole-thieno[3,2b]thiophene. The structural, dynamical, and electronic properties of the macromolecular assemblies built upon these chromophores are characterised. For both polymers and molecular crystals, pronounced peaks around 0 o or 180 o are observed for the torsions between chromophores under ambient conditions. The high planarity in these systems can promote local ordering and π-π stacking, thereby potentially facilitating charge transport across these materials. For the model conducting polymers, we found that the fluctuations in the density of states per chain per monomer is neglegibly small and does not vary significantly with chains comprising 20 to 40 monomers. Analysis of the electron-hole distributions and the transition density matrices indicates that the delocalised length is approximately four to six monomers, which is in good agreement with other theoretical and experimental studies of different conducting polymers. For the molecular crystals, our investigation of the characteristic timescale of the fluctuation in the excitonic couplings shows that low frequency vibration below 10 cm −1 is observed for the nearest neighbors. These observations are in line with previous studies on other molecular crystals, in which low frequency vibrations are believed to be responsible for the large modulation of the excitonic coupling. Thus, our approach and the new force fields provide a direct route for studying the structure-property relations and the molecular level origins of the high-efficiency of these classes of materials.

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Section: Introductionmentioning

confidence: 99%

Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene

Jiang

Rogers

Hirst

et al. 2020

J. Chem. Theory Comput.

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“…This might introduce a further obstacle, which can be overcome by refining or fully re-parameterizing the FF, based on accurate Quantum Mechanical (QM) data, as recently reported by several groups. [44][45][46][47][48][49] Once the reliability of the classical MD trajectories has been validated, a very convenient method to compute spectra of complex and flexible systems in explicit environments is performing a Classical Ensemble Average of Vertical Excitations (CEA-VE). It essentially consists in performing a sufficiently long and accurate MD trajectory, from which a number of uncorrelated snapshots, large enough to ensure convergence, is extracted, and successively computing vertical transition energies and intensities for each frame.…”

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confidence: 99%

Accounting for Vibronic Features through a Mixed Quantum-Classical Scheme: Structure, Dynamics, and Absorption Spectra of a Perylene Diimide Dye in Solution

Segalina

Cerezo

Prampolini

et al. 2020

J. Chem. Theory Comput.

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The optical absorption spectrum of a perylene diimide (PDI) dye in acetonitrile solution is simulated using the recently developed (J. Chem. Theory Comput. 2020, 16, 1215–1231) Ad-MD|gVH method. This mixed quantum-classical (MQC) approach is based on an adiabatic (Ad) separation of soft(classical)/stiff(quantum) nuclear degrees of freedom and expresses the spectrum as a conformational average (over the soft coordinates) of vibronic spectra (for the stiff coordinates) obtained through the generalized vertical Hessian (gVH) vibronic approach. The average is performed over snapshots extracted from classical molecular dynamics (MD) runs, performed with a specifically parameterized quantum-mechanically derived force field (QMD-FF). A comprehensive assessment of the reliability of different approaches, designed to reproduce spectral shapes of flexible molecules, is here presented. First, the differences in the sampled configurational space and their consequences on the prediction of the absorption spectra are evaluated by comparing the results obtained by means of the specific QMD-FF and of a general-purpose transferable FF with those of a reference ab initio MD (AIMD) in the gas phase, in both a purely classical scheme (ensemble average) and in the Ad-MD|gVH framework. Next, classical ensemble average and MQC predictions are also obtained for the PDI dynamics in solution and compared with the results of a ″static″ approach, based on vibronic calculations carried out on a single optimized perylene diimide structure. In the classical ensemble average approach, the remarkably different samplings obtained with the two FFs lead to sizeable changes in both position and intensity of the predicted spectra, with the one computed along the QMD-FF trajectory closely matching its AIMD counterpart. Conversely, at the Ad-MD|gVH level of theory, the different samplings deliver very similar vibronic spectra, indicating that the error found in the absorption spectra obtained with the general-purpose FF mainly concerns the stiff modes. In fact, it can be effectively corrected by the quadratic extrapolation performed by gVH to locate the minima of the ground- and excited-state potential energy surfaces along such coordinates. Furthermore, in the perspective of studying the self-assembling process of PDI dyes and the vibronic spectra of large-size aggregates, the use of a molecule-specific QMD-FF also appears mandatory, considering the significant errors found in the GAFF trajectory in the flexible lateral chain populations, which dictate the supramolecular aggregation properties.

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“…From the point of view of the FFs, it can be foreseen that for accurate applications, besides the introduction of polarizable FFs to account for the mutual solute-solvent polarization already mentioned, general purpose FFs will be replaced by QMD-FFs, optimized both for the solute-solvent interactions, and also for the intramolecular motion of the solute and specific for each of its electronic states. [226][227][228][229] QMD-FFs offer the possibility to replace a QM/MM trajectory with a much faster fully MM/MM trajectory, and have been proven to be helpful to investigate solvation problems. 43 They should be particularly suited when extended sampling before photoexcitation is required, or when many initial conditions and/or long excited-state propagations are needed.…”

Section: Discussionmentioning

confidence: 99%

Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives

Santoro

Green

Martínez‐Fernández

et al. 2021

Phys. Chem. Chem. Phys.

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Developing Consistent Molecular Dynamics Force Fields for Biological Chromophores via Force Matching

Cited by 25 publications

References 69 publications

Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene

Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene

Accounting for Vibronic Features through a Mixed Quantum-Classical Scheme: Structure, Dynamics, and Absorption Spectra of a Perylene Diimide Dye in Solution

Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives

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