We describe a general scheme to obtain force-field parameters for classical molecular dynamics simulations of conjugated polymers. We identify a computationally inexpensive methodology for calculation of accurate intermonomer dihedral potentials and partial charges. Our findings indicate that the use of a two-step methodology of geometry optimization and single-point energy calculations using DFT methods produces potentials which compare favorably to high level theory calculation. We also report the effects of varying the conjugated backbone length and alkyl side-chain lengths on the dihedral profiles and partial charge distributions and determine the existence of converged lengths above which convergence is achieved in the force-field parameter sets. We thus determine which calculations are required for accurate parametrization and the scope of a given parameter set for variations to a given molecule. We perform simulations of long oligomers of dioctylfluorene and hexylthiophene in explicit solvent and find peristence lengths and end-length distributions consistent with experimental values.
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http://dx.doi.org/10.1021/acs.jctc.5b01195 | DOI Listing |
Adv Mater
January 2025
State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, 130012, China.
The design and synthesis of metal-organic frameworks (MOFs) with outstanding light-harvesting and photoexcitation for artificial photocatalytic CO reduction is an attractive but challenging task. In this work, a novel aggregation-induced emission (AIE)-active ligand, tetraphenylpyrazine (PTTBPC) is proposed and utilized for the first time to construct a Zr-MOF photocatalyst via coordination with stable Zr-oxo clusters. Zr-MOF is featured by a scu topology with a two-fold interpenetrated framework, wherein the PTTBPC ligands enable strong light-harvesting and photoexcitation, while the Zr-oxo clusters facilitate CO adsorption and activation, as well as offer potential sites for further metal modification.
View Article and Find Full Text PDFACS Nano
January 2025
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, United States.
Most traditional optical biosensors operate through molecular recognition, where ligand binding causes conformational changes that lead to optical perturbations in the emitting motif. Optical sensors developed from single-stranded DNA-functionalized single-walled carbon nanotubes (ssDNA-SWCNTs) have started to make useful contributions to biological research. However, the mechanisms underlying their function have remained poorly understood.
View Article and Find Full Text PDFSmall
January 2025
National Energy Metal Resources and New Materials Key Laboratory, Engineering Research Center of the Ministry of Education for Advanced Battery Materials, Hunan Provincial Key Laboratory of Nonferrous Value-Added Metallurgy, School of Metallurgy and Environment, Central South University, Changsha, 410083, P. R. China.
Electrochemical CO reduction (CORR) in membrane electrode assembly (MEA) represents a viable strategy for converting CO into value-added multi-carbon (C) compounds. Therefore, the microstructure of the catalyst layer (CL) affects local gas transport, charge conduction, and proton supply at three-phase interfaces, which is significantly determined by the solvent environment. However, the microenvironment of the CLs and the mechanism of the solvent effect on C selectivity remains elusive.
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
Globin X is a newly discovered member of the globin family, while its structure and function are not fully understood. In this study, we performed protein modelling studies using Alphafold3 and molecular dynamics simulations, which suggested that the protein adopts a typical globin fold, with the formation of a potential disulfide bond of Cys65 and Cys141. To elucidate the role of this unique disulfide in protein structure and stability, we constructed a double mutant of C65S/C141S by mutating the two cysteine residues to serine.
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