LEADD: Lamarckian evolutionary algorithm for de novo drug design

Given an objective function that predicts key properties of a molecule, goal-directed de novo molecular design is a useful tool to identify molecules that maximize or minimize said objective function. Nonetheless, a common drawback of these methods is that they tend to design synthetically unfeasible molecules. In this paper we describe a Lamarckian evolutionary algorithm for de novo drug design (LEADD). LEADD attempts to strike a balance between optimization power, synthetic accessibility of designed molecules and computational efficiency. To increase the likelihood of designing synthetically accessible molecules, LEADD represents molecules as graphs of molecular fragments, and limits the bonds that can be formed between them through knowledge-based pairwise atom type compatibility rules. A reference library of drug-like molecules is used to extract fragments, fragment preferences and compatibility rules. A novel set of genetic operators that enforce these rules in a computationally efficient manner is presented. To sample chemical space more efficiently we also explore a Lamarckian evolutionary mechanism that adapts the reproductive behavior of molecules. LEADD has been compared to both standard virtual screening and a comparable evolutionary algorithm using a standardized benchmark suite and was shown to be able to identify fitter molecules more efficiently. Moreover, the designed molecules are predicted to be easier to synthesize than those designed by other evolutionary algorithms. Graphical Abstract

The Genetic Control of the Compound Leaf Patterning in Medicago truncatula

Simple and compound which are the two basic types of leaves are distinguished by the pattern of the distribution of blades on the petiole. Compared to simple leaves comprising a single blade, compound leaves have multiple blade units and exhibit more complex and diverse patterns of organ organization, and the molecular mechanisms underlying their pattern formation are receiving more and more attention in recent years. Studies in model legume Medicago truncatula have led to an improved understanding of the genetic control of the compound leaf patterning. This review is an attempt to summarize the current knowledge about the compound leaf morphogenesis of M. truncatula, with a focus on the molecular mechanisms involved in pattern formation. It also includes some comparisons of the molecular mechanisms between leaf morphogenesis of different model species and offers useful information for the molecular design of legume crops.

First theoretical probe for alkynyl bridged thiophene modified coumarin nonlinear optical materials with D-π-A and A-π-D-π-A structures

First-principles exploration is very important to molecular design. In this study, geometric structure, intramolecular charge transfer (ICT), energy levels, polar moment, and ultraviolet–visible (UV–Vis) spectroscopy of eight novel and different alkynyl bridged thiophene modified coumarin nonlinear optical molecules with [Formula: see text]-[Formula: see text]-[Formula: see text] and [Formula: see text]-[Formula: see text]-[Formula: see text]-[Formula: see text]-[Formula: see text] structures had been studied by density-functional theory (DFT) calculations within B3LYP hybrid functional using 6-31 [Formula: see text], [Formula: see text] Gaussian type molecular-orbital basis set. This has guiding significance for the design of nonlinear optical molecules and the development of coumarin-based photoelectric molecules.

Mechanisms and Critical Technologies of Transport Inhibitor Agent (TIA) throughout C-S-H Nano-Channels

The critical issue of the durability of marine concrete lies in the continuous penetration and rapid enrichment of corrosive ions. Here a new ion transfer inhibitor, as TIA, with calcium silicate hydrate (C-S-H) interfacial affinity and hydrophobicity is proposed through insights from molecular dynamics into the percolation behavior of the ion solution in C-S-H nano-channels and combined with molecular design concepts. One side of the TIA can be adsorbed on the surface of the cement matrix and can form clusters of corrosive ions to block the gel pores so as to resist the ion solution percolation process. Its other side is structured as a hydrophobic carbon chain, similar to a door hinge, which can stick to the matrix surface smoothly before the erosion solution is percolated. It can then change into a perpendicular chain shape to reduce the percolation channel’s diameter and thereby inhibit the percolation when ions meet the inhibitor. Therefore, once the erosion solution contacts TIA, it can quickly chelate with calcium ions and erosion ions at the interface to form clusters and compact pores. In addition, the water absorption, chloride migration coefficient, and chloride content of concrete samples decreased significantly after adding TIA, proving that TIA can effectively enhance the durability of cement-based materials. The structure–activity relationship of ion transfer that is proposed can provide new ideas for solving the critical problems of durability of cement-based materials and polymer molecular design.

Narrowband Deep-Blue Multi-Resonance Induced Thermally Activated Delayed Fluorescence: Insights from the Theoretical Molecular Design

Multi-resonance thermal activated delayed fluorescence (MR-TADF) has been promising with large oscillator strength and narrow full width at half maxima of luminescence, overcoming the compromise of emission intensity and energy criteria of traditional charge transfer TADF frameworks. However, there are still limited theoretical investigations on the excitation mechanism and systematic molecular manipulation of MR-TADF structures. We systematically study the highly localized excitation (LE) characteristics based on typical blue boron-nitrogen (BN) MR-TADF emitters and prove the potential triangular core with theoretical approaches. A design strategy by extending the planar π-conjugate core structure is proposed to enhance the multiple resonance effects. Moreover, several substituted groups are introduced to the designed core, achieving color-tunable functions with relatively small energy split and strong oscillator strength simultaneously. This work provides a theoretical direction for molecular design strategy and a series of potential candidates for highly efficient BN MR-TADF emitters.

Deep-Red and Near-Infrared Iridium Complexes with Fine-Tuned Emission Colors by Adjusting Trifluoromethyl Substitution on Cyclometalated Ligands Combined with Matched Ancillary Ligands for Highly Efficient Phosphorescent Organic Light-Emitting Diodes

Six novel Ir(C^N)2(L^X)-type heteroleptic iridium complexes with deep-red and near-infrared region (NIR)-emitting coverage were constructed through the cross matching of various cyclometalating (C^N) and ancillary (LX) ligands. Here, three novel C^N ligands were designed by introducing the electron-withdrawing group CF3 on the ortho (o-), meta (m-), and para (p-) positions of the phenyl ring in the 1-phenylisoquinoline (piq) group, which were combined with two electron-rich LX ligands (dipba and dipg), respectively, leading to subsequent iridium complexes with gradually changing emission colors from deep red (≈660 nm) to NIR (≈700 nm). Moreover, a series of phosphorescent organic light-emitting diodes (PhOLEDs) were fabricated by employing these phosphors as dopant emitters with two doping concentrations, 5% and 10%, respectively. They exhibited efficient electroluminescence (EL) with significantly high EQE values: >15.0% for deep red light0 (λmax = 664 nm) and >4.0% for NIR cases (λmax = 704 nm) at a high luminance level of 100 cd m−2. This work not only provides a promising approach for finely tuning the emission color of red phosphors via the easily accessible molecular design strategy, but also enables the establishment of an effective method for enriching phosphorescent-emitting molecules for practical applications, especially in the deep-red and near-infrared region (NIR).