Impact of backbone fluorination on nanoscale morphology and excitonic coupling in polythiophenes

Fluorination represents an important strategy in developing high-performance conjugated polymers for photovoltaic applications. Here, we use regioregular poly(3-ethylhexylthiophene) (P3EHT) and poly(3-ethylhexyl-4-fluorothiophene) (F-P3EHT) as simplified model materials, using single-molecule/aggregate spectroscopy and molecular dynamic simulations, to elucidate the impacts of backbone fluorination on morphology and excitonic coupling on the molecular scale. Despite its high regioregularity, regioregular P3EHT exhibits a rather broad distribution in polymer chain conformation due to the strong steric hindrance of bulky ethylhexyl side chains. This conformational variability results in disordered interchain morphology even between a few chains, prohibiting long-range effective interchain coupling. In stark contrast, the experimental and molecular dynamic calculations reveal that backbone fluorination of F-P3EHT leads to an extended rod-like single-chain conformation and hence highly ordered interchain packing in aggregates. Surprisingly, the ordered and close interchain packing in F-P3EHT does not lead to strong excitonic coupling between the chains but rather to dominant intrachain excitonic coupling that greatly reduces the molecular energetic heterogeneity.

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Adsorption of ethanol molecules on the Al (1 1 1) surface: a molecular dynamic study

Royal Society Open Science ◽

10.1098/rsos.181189 ◽

2019 ◽

Vol 6 (1) ◽

pp. 181189 ◽

Cited By ~ 1

Author(s):

Pingan Liu ◽

Junpeng Liu ◽

Mengjun Wang

Keyword(s):

Force Field ◽

Molecular Dynamic ◽

Single Molecule ◽

Adsorption Process ◽

Hydroxyl Group ◽

Hydroxyl Groups ◽

Dynamic Simulations ◽

Adsorption Processes ◽

Different Temperatures ◽

Reaxff Force Field

The adsorption process of ethanol molecules on Al slabs was investigated by molecular dynamic simulations with a ReaxFF force field. The force field used in this paper has been validated by comparing adsorption energy results with quantum mechanical (QM) calculations. All simulations were performed under the canonical (NVT) ensemble. The single-molecule adsorption simulation shows that the hydroxyl group plays a more important role in the whole progress than the ethyl group. Besides, decomposition of hydroxyl groups was also observed during multimolecule adsorption processes. Simulations of adsorption processes of Al slab by ethanol molecules at different temperatures and pressures (controlled by the number of ethanol molecules) was also performed. System energy and radial distribution function (RDF) plots were invoked to describe adsorption processes and centro-symmetry parameter (CSP) analysis was adopted to study the surface properties with coating layers. Our results indicate that the whole adsorption process can be divided into two periods and the greater the pressure, the more ethanol molecules diffuse into the Al slab. How raising the temperature helps the adsorption processes is related to the initial number of molecules. The crystal structure of the Al surface will become amorphous under the constant impact of ethanol molecules.

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Spotting Differences in Molecular Dynamic Simulations of Influenza A M2 Protein-Ligand Complexes by Varying M2 construct, Lipid Bilayer and Force Field

10.26434/chemrxiv.11365943.v1 ◽

2019 ◽

Author(s):

Dimitrios Kolokouris ◽

Iris Kalenderoglou ◽

Panagiotis Lagarias ◽

Antonios Kolocouris

Keyword(s):

Molecular Dynamic ◽

Lipid Bilayer ◽

Influenza A ◽

Md Simulations ◽

Membrane Curvature ◽

Buffer Size ◽

M2 Protein ◽

Dynamic Simulations ◽

Amphipathic Helices ◽

Drug Protein Binding

We studied by molecular dynamic (MD) simulations systems including the inwardclosed state of influenza A M2 protein in complex with aminoadamantane drugs in membrane bilayers. We varied the M2 construct and performed MD simulations in M2TM or M2TM with amphipathic helices (M2AH). We also varied the lipid bilayer by changing either the lipid, DMPC or POPC, POPE or POPC/cholesterol (chol), or the lipids buffer size, 10x10 Å2 or 20x20 Å2. We aimed to suggest optimal system conditions for the computational description of this ion channel and related systems. Measures performed include quantities that are available experimentally and include: (a) the position of ligand, waters and chlorine anion inside the M2 pore, (b) the passage of waters from the outward Val27 gate of M2 S31N in complex with an aminoadamantane-aryl head blocker, (c) M2 orientation, (d) the AHs conformation and structure which is affected from interactions with lipids and chol and is important for membrane curvature and virus budding. In several cases we tested OPLS2005, which is routinely applied to describe drug-protein binding, and CHARMM36 which describes reliably protein conformation. We found that for the description of the ligands position inside the M2 pore, a 10x10 Å2 lipids buffer in DMPC is needed when M2TM is used but 20x20 Å2 lipids buffer of the softer POPC; when M2AH is used all 10x10 Å2 lipid buffers with any of the tested lipids can be used. For the passage of waters at least M2AH with a 10x10 Å2 lipid buffer is needed. The folding conformation of AHs which is defined from hydrogen bonding interactions with the bilayer and the complex with chol is described well with a 10x10 Å2 lipids buffer and CHARMM36.

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Antimicrobial and Cell-Penetrating Peptides: Structure, Assembly and Mechanisms of Membrane Lysis via Atomistic and Coarse-Grained Molecular Dynamic Simulations

Protein and Peptide Letters ◽

10.2174/0929866511009011313 ◽

2010 ◽

Vol 17 (11) ◽

pp. 1313-1327 ◽

Cited By ~ 30

Author(s):

Peter J. Bond ◽

Syma Khalid

Keyword(s):

Molecular Dynamic ◽

Cell Penetrating Peptides ◽

Coarse Grained ◽

Molecular Dynamic Simulations ◽

Dynamic Simulations ◽

Membrane Lysis ◽

Cell Penetrating ◽

Structure Assembly

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The localized electron: magnetic properties

10.1093/oso/9780198814597.003.0002 ◽

2018 ◽

Author(s):

Jean-Pierre Launay ◽

Michel Verdaguer

Keyword(s):

Single Molecule ◽

Model Systems ◽

Ferromagnetic Coupling ◽

Single Chain ◽

Single Molecule Magnets ◽

Magnetic Systems ◽

Orbital Interactions ◽

Prussian Blue Analogues ◽

Mononuclear Complexes

After preliminaries about electron properties, and definitions in magnetism, one treats the magnetism of mononuclear complexes, in particular spin cross-over, showing the role of cooperativity and the sensitivity to external perturbations. Orbital interactions and exchange interaction are explained in binuclear model systems, using orbital overlap and orthogonality concepts to explain antiferromagnetic or ferromagnetic coupling. The phenomenologically useful Spin Hamiltonian is defined. The concepts are then applied to extended molecular magnetic systems, leading to molecular magnetic materials of various dimensionalities exhibiting bulk ferro- or ferrimagnetism. An illustration is provided by Prussian Blue analogues. Magnetic anisotropy is introduced. It is shown that in some cases, a slow relaxation of magnetization arises and gives rise to appealing single-ion magnets, single-molecule magnets or single-chain magnets, a route to store information at the molecular level.

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Numerical Evaluation of a HVAC System Based on a High-Performance Heat Transfer Fluid

Energies ◽

10.3390/en14113298 ◽

2021 ◽

Vol 14 (11) ◽

pp. 3298

Author(s):

Gianpiero Colangelo ◽

Brenda Raho ◽

Marco Milanese ◽

Arturo de Risi

Keyword(s):

Heat Transfer ◽

High Performance ◽

Cooling System ◽

Electrical Energy ◽

Simulation Software ◽

Heat Transfer Fluid ◽

Hvac System ◽

Dynamic Simulations ◽

Heating And Cooling ◽

The University

Nanofluids have great potential to improve the heat transfer properties of liquids, as demonstrated by recent studies. This paper presents a novel idea of utilizing nanofluid. It analyzes the performance of a HVAC (Heating Ventilation Air Conditioning) system using a high-performance heat transfer fluid (water-glycol nanofluid with nanoparticles of Al2O3), in the university campus of Lecce, Italy. The work describes the dynamic model of the building and its heating and cooling system, realized through the simulation software TRNSYS 17. The use of heat transfer fluid inseminated by nanoparticles in a real HVAC system is an innovative application that is difficult to find in the scientific literature so far. This work focuses on comparing the efficiency of the system working with a traditional water-glycol mixture with the same system that uses Al2O3-nanofluid. The results obtained by means of the dynamic simulations have confirmed what theoretically assumed, indicating the working conditions of the HVAC system that lead to lower operating costs and higher COP and EER, guaranteeing the optimal conditions of thermo-hygrometric comfort inside the building. Finally, the results showed that the use of a nanofluid based on water-glycol mixture and alumina increases the efficiency about 10% and at the same time reduces the electrical energy consumption of the HVAC system.

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