On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.     

Exploring the Potential of Metallodrugs as Chemotherapeutics for Triple Negative Breast Cancer

This review focuses on studies of coordination and organometallic compounds as potential chemotherapeutics against triple negative breast cancer (TNBC) which has one of the poorest prognoses and worst survival rates from all breast cancer types. At present, chemotherapy is still the standard of care for TNBC since only one type of targeted therapy has been recently developed. References for metal-based compounds studied in TNBC cell lines will be listed, and those of metal-specific reviews, but a detailed overview will also be provided on compounds studied in vivo (mostly in mice models) and those compounds for which some preliminary mechanistic data was obtained (in TNBC cell lines and tumors) and/or for which bioactive ligands have been used. The main goal of this review is to highlight the most promising metal-based compounds with potential as chemotherapeutic agents in TNBC.     

Expanding the Topological Landscape by a G-Column Flip of a Parallel G-Quadruplex

Canonical G-quadruplexes can adopt a variety of different topologies depending on the arrangement of propeller, lateral, or diagonal loops connecting the four G-columns. A novel intramolecular G-quadruplex structure is derived through inversion of the last G-tract of a three-layered parallel fold, associated with the transition of a single propeller into a lateral loop. The resulting (3+1) hybrid fold features three syn⋅anti⋅anti⋅anti G-tetrads with a 3’-terminal all-syn G-column. Although the ability of forming a duplex stem-loop between G-tracts seems beneficial for a propeller-to-lateral loop rearrangement, unmodified G-rich sequences resist folding into the new (3+1) topology. However, refolding can be driven by the incorporation of syn-favoring guanosine analogues into positions of the fourth G-stretch. The presented hybrid-type G-quadruplex structure as determined by NMR spectroscopy may provide for an additional scaffold in quadruplex-based technologies.     

Waste Cleaning Waste: Combining Alginate with Biowaste-Derived Substances in Hydrogels and Films for Water Cleanup

Biowaste-derived substances isolated from green compost (BBS-GC) are environmentally friendly reactants similar to humic substances, which contain multiple functionalities, that are suitable for adsorbing different kinds of pollutants in wastewater. Herein, sodium alginate (derived from brown algae) cross-linked with both Ca²⁺ ions and BBS-GC in the form of hydrogels and dried films are proposed as green, easy-to-form, and handleable materials for tertiary water treatments. The results show that both hydrogels and films are mechanically stable and can effectively remove differently charged dyes through an adsorption mechanism that can be described by the Freundlich model. BBS-GC-containing gels always performed better than samples prepared without BBS-GC, revealing that such unconventional materials can integrate waste valorization and water decontamination, potentially providing social and environmental benefits.     

Synthesis and Coordination Behavior of a New Hybrid Bidentate Ligand with Phosphine and Silylene Donors

This work describes the synthesis and coordination behavior of a new mixed-donor ligand PhC(NtBu)₂SiC₆H₄PPh₂ ( 1 ) containing both silylene and phosphine donor sites. Ligand 1 was synthesized from a reaction of ortho-lithiated diphenylphosphinobenzene (LiC₆H₄PPh₂) with chlorosilylene (PhC(NtBu)₂SiCl). Treatment of 1 with Se and GeCl₂ resulted in Si^IV compounds 2 and 3 by selective oxidation of the silylene donor. This strong σ-donor ligand induces dissociation of CuCl and PhBCl₂ leading to formation of ionic complexes 4 and 5 respectively. The reaction of 1 with ZnCl₂ and AlCl₃ resulted in the formation of chelate complexes 5 and 7 , respectively, while treatment with EtAlCl₂ and GaCl₃ forms monodentate complexes 8 and 9 . X-ray analysis of 4 showed that the copper is in the spiro center of the two five-membered rings. Moreover, the copper(I)chloride has not been oxidized but dissociates to Cu⁺ and [CuCl₂]⁻. All the compounds are well characterized by mass spectrometry, elemental analysis, NMR spectroscopy, and single-crystal X-ray diffraction studies.     

Artificial Water Channels: Towards Biomimetic Membranes for Desalination

Natural Aquaporin (AQP) channels are efficient water translocating proteins, rejecting ions. Inspired by this masterpiece of nature, Artificial Water Channels (AWCs) with controlled functional structures, can be potentially used to mimic the AQPs to a certain extent, offering flexible avenues toward biomimetic membranes for water purification. The objective of this paper is to trace the historical development and significant advancements of current reported AWCs. Meanwhile, we attempt to reveal important structural insights and supramolecular self-assembly principles governing the selective water transport mechanisms, toward innovative AWC-based biomimetic membranes for desalination.     

Polymerization-Driven Photoluminescence in Alkanolamine-Based C-Dots

Carbonized polymer dots (CPDs), a peculiar type of carbon dots, show extremely high quantum yields, making them very attractive nanostructures for application in optics and biophotonics. The origin of the strong photoluminescence of CPDs resides in a complicated interplay of several radiative mechanisms. To understand the correlation between CPD processing and properties, the early stage formation of carbonized polymer dots has been studied. In the synthesis, citric acid monohydrate and 2-amino-2-(hydroxymethyl)propane-1,3-diol have been thermally degraded at 180 °C. The use of an oil bath instead of a more traditional hydrothermal reactor has allowed the CPD properties to be monitored at different reactions times. Transmission electron microscopy, time-resolved photoluminescence, nuclear magnetic resonance, infrared, and Raman spectroscopy have revealed the formation of polymeric species with amide and ester bonds. Quantum chemistry calculations have been employed to investigate the origin of CPD electronic transitions. At short reaction times, amorphous C-dots with 80 % quantum yield, have been obtained.