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Development and Testing of an All-Atom Force Field for Diketopyrrolopyrrole Polymers with Conjugated Substituents.

ABSTRACT: We develop an all-atom force field for a series of diketopyrrolopyrrole polymers with two aromatic pyridine substituents and a variable number of ?-conjugated thiophene units in the backbone (DPP2PymT), used as donor materials in organic photovoltaic devices. Available intrafragment parameterizations of the individual fragment building blocks are combined with interfragment bonded and nonbonded parameters explicitly derived from density functional theory calculations. To validate the force field, we perform classical molecular dynamics simulations of single polymer chains with m = 1, 2, 3 in good and bad solvents and of melts. We observe the expected dependence of the chain conformation on the solvent quality, with the chain collapsing in water, and swelling in chloroform. The glass-transition temperature for the polymer melts is found to be in the range of 340-370 K. Analysis of the mobility of the conjugated segments in the polymer backbone reveals two relaxation processes: a fast one with a characteristic time at room temperature on the order of 10 ps associated with nearly harmonic vibrations and a slow one on the order of 100 ns associated with temperature-activated cis-trans transitions.

SUBMITTER: Sundaram V

PROVIDER: S-EPMC7720275 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Development and Testing of an All-Atom Force Field for Diketopyrrolopyrrole Polymers with Conjugated Substituents.

Sundaram Vivek V Lyulin Alexey V AV Baumeier Björn B

The journal of physical chemistry. B 20201119 48

We develop an all-atom force field for a series of diketopyrrolopyrrole polymers with two aromatic pyridine substituents and a variable number of π-conjugated thiophene units in the backbone (DPP2Py<i>m</i>T), used as donor materials in organic photovoltaic devices. Available intrafragment parameterizations of the individual fragment building blocks are combined with interfragment bonded and nonbonded parameters explicitly derived from density functional theory calculations. To validate the forc ...[more]

PMID: 33211500

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Project description:We present an extension of the CHARMM hexopyranose monosaccharide additive all-atom force field to enable modeling of glycosidic-linked hexopyranose polysaccharides. The new force field parameters encompass 1→1, 1→2, 1→3, 1→4, and 1→6 hexopyranose glycosidic linkages, as well as O-methylation at the C(1) anomeric carbon, and are developed to be consistent with the CHARMM all-atom biomolecular force fields for proteins, nucleic acids, and lipids. The parameters are developed in a hierarchical fashion using model compounds containing the key atoms in the full carbohydrates, in particular O-methyl-tetrahydropyran and glycosidic-linked dimers consisting of two molecules of tetrahyropyran or one of tetrahydropyran and one of cyclohexane. Target data for parameter optimization include full two-dimensional energy surfaces defined by the Φ/Ψ glycosidic dihedral angles in the disaccharide analogs as determined by quantum mechanical MP2/cc-pVTZ single point energies on MP2/6-31G(d) optimized structures (MP2/cc-pVTZ//MP2/6-31G(d)). In order to achieve balanced, transferable dihedral parameters for the Φ/Ψ glycosidic dihedral angles, surfaces for all possible chiralities at the ring carbon atoms involved in the glycosidic linkages are considered, resulting in over 5000 MP2/cc-pVTZ//MP2/6-31G(d) conformational energies. Also included as target data are vibrational frequencies, pair interaction energies and distances with water molecules, and intramolecular geometries including distortion of the glycosidic valence angle as a function of the glycosidic dihedral angles. The model-compound optimized force field parameters are validated on full disaccharides through comparison of molecular dynamics results to available experimental data. Good agreement is achieved with experiment for a variety of properties including crystal cell parameters and intramolecular geometries, aqueous densities, and aqueous NMR coupling constants associated with the glycosidic linkage. The newly-developed parameters allow for the modeling of linear, branched, and cyclic hexopyranose glycosides both alone and in heterogenous systems including proteins, nucleic acids and/or lipids when combined with existing CHARMM biomolecular force fields.

Dataset Information

Development and Testing of an All-Atom Force Field for Diketopyrrolopyrrole Polymers with Conjugated Substituents.

Publications

Development and Testing of an All-Atom Force Field for Diketopyrrolopyrrole Polymers with Conjugated Substituents.

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