Controlled-advancement rigid-body optimization of nanosystems

In this study, we propose a novel optimization algorithm, with application to the refinement of molecular complexes. Particularly, we consider optimization problem as the calculation of quasi-static trajectories of rigid bodies influenced by the inverse-inertia-weighted energy gradient and introduce the concept of advancement region that guarantees displacement of a molecule strictly within a relevant region of conformational space. The advancement region helps to avoid typical energy minimization pitfalls, thus, the algorithm is suitable to work with arbitrary energy functions and arbitrary types of molecular complexes without necessary tuning of its hyper-parameters. Our method, called controlled-advancement rigid-body optimization of nanosystems (Carbon), is particularly useful for the large-scale molecular refinement, as for example, the putative binding candidates obtained with protein–protein docking pipelines. Implementation of Carbon with user-friendly interface is available in the SAMSON platform for molecular modeling at https://www.samson-connect.net . © 2019 Wiley Periodicals, Inc.     

Photodynamics of polyene-polymethine transformations and spectral fluorescent properties of merocyanine dyes

Absorption and fluorescence spectrum band moments (center of gravity, width, asymmetry, excess, and fine structure) have been determined in a wide range of solvents with different polarities for inverse solvatochromic di-, tetra-, and hexamethinemerocyanines derived from 1,3-diphenyl-2,3-dihydro-1H-benzimidazole. Juxtaposition of the quantum-chemically calculated (by the semiempirical AM1 method) charges, bond orders, and dipole moments of the merocyanine molecules in the ground and excited singlet states with the experimentally observed spectral fluorescent characteristics suggests that the molecular electronic structure in the two states can vary from a nonpolar polyene via a polymethine to a charge-separated polyene, depending on the length of the polymethine chain and the medium polarity. As shown, solvatofluorochromism gives rise to smaller spectral band shifts than those of solvatochromism. This effect is attributable to weaker intermolecular solute-solvent interactions in the fluorescent excited state due to the more equalized charges as compared to those of the ground state. A lack of mirror symmetry of the absorption and fluorescence spectra has been revealed for di- and tetramethinemerocyanines (broadened fluorescence bands) as well as for hexamethinemerocyanines (narrowed fluorescence bands); the two cases are accounted for by the different behavior of vibronic and intermolecular interactions in the course of absorption and emission. As found for merocyanines, the electronic structure of their fluorescent state approaches the cyanine limit and the ground state becomes increasingly polyene-like with lengthening of the polymethine chain. A close vicinity of the excited state to the cyanine limit causes a dramatic increase in fluorescence quantum yields and a decrease in Stokes shifts observed for higher merocyanine vinylogues.     

Solitonic waves in polyene dications and principles of charge carrier localization in π‐conjugated organic materials

The quantum‐chemical investigations by ab initio method (restricted Hartree–Fock/6‐31G**) have been performed for a series of unsubstituted, monosubstituted, and disubstituted neutral polyenes and their double charged cations. The waves of charge alternation (characterized by the difference in the electron densities at the nearest carbon atoms or Δq function) and bond length alternation (characterized by the lengths difference of the nearest carbon–carbon bonds or Δl function) are reported. Comparisons are made with the corresponding monocationic polymethine molecules. We found that ionization by two electrons results in formation of two solitonic waves of charge alternation, rather than superposition of two overlapping solitonic waves into one. These waves behave similar to two independent elastic particles, which do not penetrate into each other despite the special confinement by the length of chromophore π‐system. In monosubstituted polyene dication, Δq and Δl functions contain two waves each; however, only one wave is mobile and sensitive to a change of the chemical nature of the terminal group, whereas the second wave remains practically unchanged. The introduction of one oxymethyl or phenyl terminal groups leads to a relatively small shift of the mobile wave from the center to a direction of the terminal group. The effect of the amino or tropilium terminal groups is much more pronounced and leads to a shift of the mobile wave to the end of the molecule. In disubstituted polyene dication, both solitonic waves become mobile and shift symmetrically to both ends. The general principles of the charge localization described in this study may be used in molecular design and fine‐tuning of the charge transport properties in plastic photovoltaics and other organic semiconducting materials. © 2012 Wiley Periodicals, Inc.     

The alignment of nematic liquid crystal by the Ti layer processed by nonlinear laser lithography

It is well known that the alignment of liquid crystals (LCs) can be realised by rubbing or photoalignment technologies. Recently, nonlinear laser lithography (NLL) was introduced as a fast, relatively low-cost method for large area nano-grating fabrication based on laser-induced periodic surface structuring. In this letter for the first time, the usage of the NLL as a perspective method of the alignment of nematics was presented. By NLL, nanogrooves with about 0.92 μm period were formed on Ti layer. The nanostructured Ti layer (NSTL) was coated with oxidianiline-polyimide film with annealing of the polymer followed without any further processing. Aligning properties of NSTLs were examined with combined twist LC cell. The dependencies of the twist angle of LC cells and azimuthal anchoring energy (AE) of layers on scanning speed and power of laser beam during processing of the Ti layer were the focus of our studies as well. The maximum azimuthal AE, obtained for pure NSTL, is comparable with photoalignment technology. It was found that the deposition of polyimide film on NSTL leads to the gain effect of the azimuthal AE. Also, atomic force microscopy (AFM) study of aligning surfaces was carried out.     

Design and Photonics of Merocyanine Dyes

Merocyanines, thanks to their easily adjustable electronic structure, appear to be the most versatile and promising functional dyes. Their D–π–A framework offers ample opportunities for custom design through variations in both donor/acceptor end-groups and the π-conjugated polymethine chain, and leads to a broad range of practical properties, including noticeable solvatochromism, high polarizability/hyperpolarizabilities, and the ability to sensitize various physicochemical processes. Accordingly, merocyanines are applied and extensively studied in various fields, such as light-converting materials for optoelectronics, nonlinear optics, optical storage, solar cells, fluorescent probes, and antitumor agents in photodynamic therapy. This review encompasses both classical and novel more important publications on the structure–property relationships in merocyanines, with particular emphasis on the results by A. I. Kiprianov and his followers in Institute of Organic Chemistry in Kyiv, Ukraine.     

Stable Carbenes as Structural Components of Partially Saturated Sulfur-Containing Heterocycles

Recently, an unusual elongation of the C-S bond was observed experimentally for some sulfur-containing heterocycles. Using a superior ab initio (SCS-MP2/cc-pVTZ) level of theory, we showed that the phenomenon can be explained by a contribution of a donor–acceptor adduct of a carbene with an unsaturated ligand. One may achieve further elongation of the C-S bond, eventually turning it to a coordinate one, by increasing the stability of each part of the system as, e.g., in the utmost case of spiro adducts with Arduengo carbenes. The effect of carbene stability was quantified by employing the isodesmic reactions of carbene exchange.