Convergence of Free Energy Profile of Coumarin in Lipid Bilayer

Atomistic molecular dynamics (MD) simulations of druglike molecules embedded in lipid bilayers are of considerable interest as models for drug penetration and positioning in biological membranes. Here we analyze partitioning of coumarin in dioleoylphosphatidylcholine (DOPC) bilayer, based on both multiple, unbiased 3 μs MD simulations (total length) and free energy profiles along the bilayer normal calculated by biased MD simulations (∼7 μs in total). The convergences in time of free energy profiles calculated by both umbrella sampling and z-constraint techniques are thoroughly analyzed. Two sets of starting structures are also considered, one from unbiased MD simulation and the other from “pulling” coumarin along the bilayer normal. The structures obtained by pulling simulation contain water defects on the lipid bilayer surface, while those acquired from unbiased simulation have no membrane defects. The free energy profiles converge more rapidly when starting frames from unbiased simulations are used. In addition, z-constraint simulation leads to more rapid convergence than umbrella sampling, due to quicker relaxation of membrane defects. Furthermore, we show that the choice of RESP, PRODRG, or Mulliken charges considerably affects the resulting free energy profile of our model drug along the bilayer normal. We recommend using z-constraint biased MD simulations based on starting geometries acquired from unbiased MD simulations for efficient calculation of convergent free energy profiles of druglike molecules along bilayer normals. The calculation of free energy profile should start with an unbiased simulation, though the polar molecules might need a slow pulling afterward. Results obtained with the recommended simulation protocol agree well with available experimental data for two coumarin derivatives

Atomistic Picture of Fluorescent Probes with Hydrocarbon Tails in Lipid Bilayer Membranes: An Investigation of Selective Affinities and Fluorescent Anisotropies in Different Environmental Phases

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Carbon dots enabling parts-per-billion sensitive and ultraselective photoluminescence lifetime-based sensingof inorganic mercury

One of the UN Sustainable Development Goals is to ensure universal access to clean drinking water. Among the various types of water contaminants, mercury (Hg) is considered to be one of the most dangerous ones. It is mostly its immense toxicity and vast environmental impact that stand out. To tackle the issue of monitoring water quality, a nanosensor based on carbon dots (CDs) is developed, whose surface is functionalized with carboxylic groups. CDs show Hg2+ concentration-dependent photoluminescence (PL) lifetimes along with an ultrahigh sensitivity and selectivity. The selectivity of PL quenching by Hg2+ is rationalized by performing light-induced electron paramagnetic resonance (LEPR) spectroscopy showing significant perturbation of the CD photoexcited state upon Hg2+ binding. The experimental findings are supported by time-dependent density functional theory (TD-DFT) calculations. These unveiled the emergence of a low-lying charge transfer state involving a vacant 6s orbital of Hg2+ stabilized by relativistic effects.Web of Science112