Exploring the interaction of phenothiazinium dyes methylene blue, new methylene blue,azure A and azure B with tRNA Phe: spectroscopic, thermodynamic, voltammetric and molecular modeling approach

This study focuses on the understanding of the interaction of phenothiazinium dyes methylene blue (MB), new methylene blue (NMB), azure A (AZA) and azure B (AZB) with tRNAPhe with particular emphasis on deciphering the mode and energetics of the binding. Strong intercalative binding to tRNAPhe was observed for MB, NMB and AZB, bound by a partial intercalative mode. AZA has shown groove binding characteristics. From spectroscopic studies binding affinity values of the order of 105 M�1 were deduced for these dyes; the trend varied as MB 4 NMB 4 AZB 4 AZA. The binding was characterized by an increase of thermal melting temperatures and perturbation in the circular dichroism spectrum of tRNA. All the dyes acquired optical activity upon binding to tRNA. The binding was predominantly entropy driven with a favorable enthalpy term that increased with temperature in all the cases. Dissection of the Gibbs energy to polyelectrolytic and non-polyelectrolytic terms revealed a major role of the nonelectrostatic forces in the binding. The small but significant heat capacity changes and the observed enthalpy–entropy compensation phenomenon confirmed the involvement of multiple weak noncovalent forces driving the interaction. The mode of binding was confirmed from quenching, viscosity and cyclic voltammetric results. Using density functional theory, ground state optimized structures of the dyes were calculated to provide insight into theoretical docking studies to correlate the experimental approaches. The modeling results verified the binding location as well as the binding energy of complexation. The results may provide new insights into the structure–activity relationship useful in the design of effective RNA targeted therapeutic agents

Aggregation-Induced Fabrication of Fluorescent Organic Nanorings: Selective Biosensing of Cysteine and Application to Molecular Logic Gate

Self-aggregation behavior in aqueous medium of four naphthalimide derivatives has exhibited substitution-dependent, unusual, aggregation induced emission enhancement (AIEE) phenomena. Absorption, emission, and time-resolved study initially indicated the formation of J-type fluorescent organic nanoaggregates (FONs). Simultaneous applications of infrared spectroscopy, theoretical studies, and dynamic light scattering (DLS) measurements explored the underlying mechanism of such substitution-selective aggregation of a chloro-naphthalimide organic molecule. Furthermore, transmission electron microscopy (TEM) visually confirmed the formation of ring like FONs with average size of 7.5–9.5 nm. Additionally, naphthalimide FONs also exhibited selective and specific cysteine amino acid sensing property. The specific behavior of NPCl aggregation toward amino acids was also employed as a molecular logic gate in information technology (IT)

Soft-Templated Room Temperature Fabrication of Nanoscale Lanthanum Phosphate: Synthesis, Photoluminescence, and Energy-Transfer Behavior

We herein report a simple and effective soft template mediated synthesis protocol for the room temperature preparation of highly crystalline cerium (Ce³⁺) and terbium (Tb³⁺) doped lanthanum phosphate (LaPO₄) nanorods (NRs) and nanoflowers. Anionic surfactant sodium bis­(2-ethylhexyl) sulfosuccinate (AOT)/<i>n</i>-alkane soft template was chosen since it forms stable reverse micelles (RMs). Transmission electron microscopy (TEM) analysis corroborated successful formation of LaPO₄:Ce³⁺,Tb³⁺ NRs having different aspect ratios (ranging from 2.8:1 to 7.6:1) under varying reaction conditions. The crystalline nature of the nanomaterials (NMs) was ascertained by X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM), and small-area electron diffraction (SAED) studies. Energy-dispersive X-ray (EDX) and Fourier transform infrared (FTIR) spectroscopy further verified the elemental existence of the desirably synthesized nanostructures. Experimental results from thermogravimetric-differential thermal analysis (TG-DTA) revealed thermal stability of the NRs up to 800 °C. The prepared NRs exhibit strong yellowish-green photoluminescence (PL) at 544 nm (⁵D₄ → ⁷F₅) when excited at 270 nm. Furthermore, time-resolved decay analysis along with steady-state PL measurements indicated an efficient energy transfer (ET) phenomenon between Ce³⁺ and Tb³⁺ ions doped in LaPO₄ (LAP) host matrix

Explicit Spectral Response of the Geometrical Isomers of a Bio-Active Pyrazoline Derivative Encapsulated in β‑Cyclodextrin Nanocavity: A Photophysical and Quantum Chemical Analysis

The existence of two geometrical isomers (<i>cis-</i> and <i>trans-</i>) of a biologically significant pyrazoline derivative [5-(-1′-(4-bromo-phenyl)-3a′,7a′-hexahydro-1′<i>H</i>-indazol-3′-yl)-3-methyl-1-phenyl-1<i>H</i>-pyrazole-4-carbonitrile] (PZ) has been established using a combined theoretical and experimental investigation. Solvatochromic analysis of PZ revealed the existence of said <i>cis-</i> and <i>trans-</i> isomers. The unique solvatochromic response of the PZ isomers and their preferential encapsulation within β-cyclodextrin (β-CD) nanocavity clearly shows the difference in the behavioral nature of the isomers of PZ in homogeneous and heterogeneous medium. Solvent polarity, time-resolved study, and anisotropy results also reinforce in favor of the existence of the isomers. To evaluate the actual orientation of <i>cis</i> and <i>trans-</i>PZ, the ground and excited state geometry of these isomers were optimized by the DFT/LanL2DZ and CIS/LanL2DZ methods, respectively. The experimentally observed results and the theoretically calculated results are found to be in close agreement

Self-Aggregation of MEGA‑9 (<i>N</i>‑Nonanoyl‑<i>N</i>‑methyl‑d‑glucamine) in Aqueous Medium: Physicochemistry of Interfacial and Solution Behaviors with Special Reference to Formation Energetics and Micelle Microenvironment

Self-aggregation of MEGA-9 (<i>N</i>-nonanoyl-<i>N</i>-methyl-d-glucamine), a nonionic sugar-based surfactant, was studied with respect to the effect of salt (NaCl) and ionic liquid (1-butyl-3-methylimidazolium tetrafluoroborate) on its critical micelle concentration (cmc), aggregation number, hydrodynamic dimensions, energetics of micellization, and micellar microenvironment. Fluorimetry (both steady state and time resolved) was used to understand the microenvironments under the influence of additives. NaCl was found to decrease cmc, increase aggregation number (<i>N</i>), increase micellar size, and decrease enthalpy of micelle formation; the IL effect on the parameters was mostly opposite. The microscopic properties of micelles were probed using two fluorophores: one nonpolar C-153 (2,3,5,6-1<i>H</i>,4<i>H</i>-tetrahydro-8-trifluormethylquinolizino-(9,9<i>a</i>,1-<i>gh</i>)­coumarin) and the other fairly polar ANS (8-anilinonaphthalene-1-sulfonate); they delivered information on the palisade layer and the peripheral region of the micelle interface, respectively. Energy of activation and entropy of activation of the dynamics of the probes were evaluated from their decay time, lifetime, and rotational movements in the regions of residency in the micelles. Density functional theory (DFT) calculations showed that the ternary combination MEGA-9/IL/H₂O had the maximum interaction energy compared to any of the binary combinations. Thus, the ionic liquid reduced MEGA-9 self-association to a large extent

Understanding the Effect of Single Cysteine Mutations on Gold Nanoclusters as Studied by Spectroscopy and Density Functional Theory Modeling

Fluorescent metal nanoclusters have generated considerable excitement in nanobiotechnology, particularly in the applications of biolabeling, targeted delivery, and biological sensing. The present work is an experimental and computational study that aims to understand the effects of protein environment on the synthesis and electronic properties of gold nanoclusters. MPT63, a drug target of <i>Mycobacterium tuberculosis</i>, was used as the template protein to synthesize, for the first time, gold nanoclusters at a low micromolar concentration of the protein. Two single cysteine mutants of MPT63, namely, MPT63Gly20Cys (mutant I) and MPT63Gly40Cys (mutant II) were employed for this study. The experimental results show that cysteine residues positioned in two different regions of the protein induce varying electronic states of the nanoclusters depending on the surrounding amino acids. A mixture of five-atom and eight-atom clusters was generated for each mutant, and the former was found to be predominant in both cases. Computational studies, including density functional theory (DFT), frontier molecular orbital (FMO), and natural bond orbital (NBO) calculations, validated the experimental observations. The as-prepared protein-stabilized nanoclusters were found to have applications in the imaging of live cells