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Aggregates of organic dyes that exhibit excitonic coupling have a wide array of applications, including medical imaging, organic photovoltaics, and quantum information devices. The optical properties of a dye monomer, as a basis of dye aggregate, can be modified to strengthen excitonic coupling. Squaraine (SQ) dyes are attractive for those applications due to their strong absorbance peak in the visible range. While the effects of substituent types on the optical properties of SQ dyes have been previously examined, the effects of various substituent locations have not yet been investigated. In this study, density functional theory (DFT) and time-dependent density functional theory (TD-DFT) were used to investigate the relationships between SQ substituent location and several key properties of the performance of dye aggregate systems, namely, difference static dipole (Δd), transition dipole moment (μ), hydrophobicity, and the angle (θ) between Δd and μ. We found that attaching substituents along the long axis of the dye could increase μ while placement off the long axis was shown to increase Δd and reduce θ. The reduction in θ is largely due to a change in the direction of Δd as the direction of μ is not significantly affected by substituent position. Hydrophobicity decreases when electron-donating substituents are located close to the nitrogen of the indolenine ring. These results provide insight into the structure-property relationships of SQ dyes and guide the design of dye monomers for aggregate systems with desired properties and performance.
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http://dx.doi.org/10.3390/molecules28052163 | DOI Listing |
J Comput Chem
September 2025
Department of Chemistry, Isfahan University of Technology, Isfahan, Iran.
Precise control over DNA stability and interactions is crucial for successful gene editing technologies. To achieve this, a detailed understanding of individual hydrogen bonds within GC (Watson-Crick) and GC*/GC (Hoogsteen) base pairs is essential, particularly regarding how strategic substitution of these base pairs modulates their strength and, ultimately, DNA stability. Leveraging the atomic-resolution capabilities of interacting quantum atoms (IQA) and interacting quantum fragments (IQF) analyses, this study investigates the impact of substituent position and electronic nature on individual hydrogen bond strengths in substituted GC (WC), GC* (HG) and GC (HG) base pairs.
View Article and Find Full Text PDFJ Org Chem
September 2025
Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Buenos Aires CP 1113AAD, Argentina.
A series of 3-hydroxykynurenic acid derivatives bearing a halogen atom in different positions are synthesized by hydroamination of methyl acetylenedicarboxylate with haloanilines, in an aza-Michael type reaction. Subsequent heterocyclization with Eaton's reagent yields halo-substituted kynurenic acid (KA) methyl esters via an intramolecular Friedel-Crafts reaction. Finally, the hydroxylation is achieved by the Elbs oxidation.
View Article and Find Full Text PDFChemistry
September 2025
Chemistry Department, Taras Shevchenko National University of Kyiv, Volodymyrska 64, Kyiv, 01601, Ukraine.
5-Substituted 3-hydroxychromones (3-HCs) are challenging to synthesize but are of significant interest as fluorescent labels. This is primarily due to the pronounced modulation of their fluorescence by surrounding molecules, a consequence of the 5-substituent's proximity to the negative pole of the molecular dipole. The newly synthesized derivatives of 3-hydroxy-2-(4-methoxyphenyl)-4-oxo-4H-chromene-5-carboxylic acid exhibit unique fluorescence behaviors.
View Article and Find Full Text PDFCryst Growth Des
August 2025
Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia.
In this work, we synthesized three novel 4-iodotetrafluorophenoxy-azobenzene ethers, which contain different substituents (X = -H, -Cl, -CN) on the opposite side of the molecule in relation to the perhalogenated moiety carrying the iodine atom. To explore the halogen bond donor potential of the prepared compounds, we performed cocrystal screening with a series of nitrogen-containing acceptors: 1,4-diazabicyclo[2.2.
View Article and Find Full Text PDFCurr Med Chem
August 2025
Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, 90-363, Lodz, Poland.
Transfer RNAs (tRNAs) are ubiquitous in cells and are essential for the translation of genetic information from messenger RNA (mRNA) into proteins in all three domains of life. They act as adaptors that decode mRNA codons via their anticodons and deliver the corresponding amino acids to the growing polypeptide chain. Currently, over 100 modified nucleosides have been found in tRNA that are crucial for the integrity and functionality of this molecule.
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