Effect of Polymerization on the Charge-Transfer Mechanism in the One (Two)-Photon Absorption Process of D-A-Type Triphenylamine Derivatives

To investigate the effect of polymerization (n = 1, 2, 3, and 4) on the charge-transfer (CT) mechanisms in the one (two)-photon absorption (OPA and TPA) process of D-A-type triphenylamine derivatives, charge density difference is used to graphically represent the CT characteristics. A transition density matrix is utilized to reveal the direction of CT on different groups quantitatively. With the n increasing, electrons are mainly transferred between the groups in the middle position of the molecular chain during OPA and TPA processes. Simulated results show that the energy gap and excitation energy have a good linear relationship with the reciprocal of the polymerization degree. Importantly, the polymerization effect can effectively increase the electronic transmission capability, TPA performance, and second hyperpolarizability. Besides, the simplified sum over state model reveals the variation factor of the TPA cross-section and the second static hyperpolarizability. The McRae formula and Bakhshiev formula are used to estimate the difference of dipole moments, which is an important parameter of the second hyperpolarizability. The comprehensive analysis of the nonlinear optical (NLO) parameters of triphenylamine derivatives can provide some significant guidance for molecular design and improve the NLO performance of D-A molecular materials. Also, the thermodynamic parameters can provide some theoretical supports for solving practical problems.

Computational Characterization of Novel Malononitrile Variants of Laurdan with Improved Photophysical Properties for Sensing in Membranes

Fluorescent probes are powerful tools for improving our understanding of cellular membranes and other complex biological environments. Using simulations, we gain atomistic and electronic insights into the effectiveness of the probes. In the current work, we have used various computational approaches to comprehensively investigate the properties of the fluorescent probe Laurdan and two Laurdan-like probes: AADAL and ECL. In addition, we propose the development of their corresponding novel malononitrile variants, which are computationally characterized herein. For the candidate probes, electronic structure calculations were used to rationalize their optical properties, including their ability for two-photon activation, and molecular dynamics simulations were used to unravel atomistic details of their functioning within lipid bilayers. While Laurdan, AADAL, and ECL were found to have very similar optical and membrane partitioning profiles, their malononitrile variants were found to show significantly improved optical properties, especially in regard to two-photon cross sections, and they appear to retain the desired membrane characteristics of the parent Laurdan molecule.

The Secret Lives of Fluorescent Membrane Probes as Revealed by Molecular Dynamics Simulations

Fluorescent probes have been employed for more than half a century to study the structure and dynamics of model and biological membranes, using spectroscopic and/or microscopic experimental approaches. While their utilization has led to tremendous progress in our knowledge of membrane biophysics and physiology, in some respects the behavior of bilayer-inserted membrane probes has long remained inscrutable. The location, orientation and interaction of fluorophores with lipid and/or water molecules are often not well known, and they are crucial for understanding what the probe is actually reporting. Moreover, because the probe is an extraneous inclusion, it may perturb the properties of the host membrane system, altering the very properties it is supposed to measure. For these reasons, the need for independent methodologies to assess the behavior of bilayer-inserted fluorescence probes has been recognized for a long time. Because of recent improvements in computational tools, molecular dynamics (MD) simulations have become a popular means of obtaining this important information. The present review addresses MD studies of all major classes of fluorescent membrane probes, focusing in the period between 2011 and 2020, during which such work has undergone a dramatic surge in both the number of studies and the variety of probes and properties accessed.

Characterization of β-turns by electronic circular dichroism spectroscopy: a coupled molecular dynamics and time-dependent density functional theory computational study

Electronic circular dichroism is one of the most used spectroscopic techniques for peptide and protein structural characterization. However, while valuable experimental spectra exist for α-helix, β-sheet and random coil secondary structures, previous studies showed important discrepancies for β-turns, limiting their use as a reference for structural studies. In this paper, we simulated circular dichroism spectra for the best-characterized β-turns in peptides, namely types I, II, I' and II'. In particular, by combining classical molecular dynamics simulations and state-of-the-art quantum time-dependent density functional theory (with the polarizable embedding multiscale model) computations, two common electronic circular dichroism patterns were found for couples of β-turn types (namely, type I/type II' and type II/type I'), at first for a minimal di-peptide model (Ace-Ala-Ala-NHMe), but also for all sequences tested with non-aromatic residues in the central positions. On the other hand, as expected, aromatic substitution causes important perturbations to the previously found ECD patterns. Finally, by applying suitable approximations, these patterns were subsequently rationalized based on the exciton chirality rule. All these results provide useful predictions and pave the way for a possible experimental characterization of β-turns based on circular dichroism spectroscopy.

Rational Design of Nile Red Analogs for Sensing in Membranes

Development of next-generation fluorescent probes is a key element in the quest for a greater understanding of complex biological environments (e.g., membranes) by bioimaging. Such fluorescence-based techniques rely on specialized small molecules that possess excellent fluorescent properties but also do not perturb the native biological environment in which they reside. Herein we present a theoretical/computational strategy for the design of novel optical probes for sensing in membranes based on the parent chromophore Nile Red. Using a combination of time-dependent density functional theory (TD-DFT) and molecular dynamics (MD), we have studied the optical properties and accommodation in a model membrane of Nile Red and eight analogs. Special attention has been given to the design of probes with improved solvatochromism and two-photon absorption (2PA) without altering the membrane properties. Of the eight studied analogs, two probes were found to possess attractive probe features and are hence suggested to be taken forward to chemical synthesis and experimental exploration.