Molecular engineering of BODIPY-bridged fluorescent probes for lysosome imaging - a computational study

Lysosome imaging plays an important role in diagnosing many diseases and understanding various intracellular processes. Recently, B0 was reported as a fluorescent probe capable of detecting lysosomal viscosity changes. BODIPY is fused into the molecule as a bridge between the acceptor and donor components of B0, yielding nine new B molecules. Computational design and analysis of their optoelectronic properties were conducted to evaluate their effectiveness as fluorescent probes for lysosome imaging, with a specific target of HSA inside lysosomes. Optimized geometries reveal excellent π electron delocalization, resulting in nearly planar molecular structures. Frontier molecular orbital analysis suggests intramolecular charge transfer, along with π-π* transitions, from donor to bridge. TD-DFT calculations were performed to study absorption properties in the solvent phase, with B3PW91 showing good agreement with experiments. Molecular docking studies indicate that B derivatives can bind with HSA, and molecular dynamics simulations confirm their HSA targeting ability. This investigation highlights the introduction of BODIPY as a bridge for developing new probes capable of producing NIR fluorescence for bio-imaging, aiding in disease diagnosis.

Exploring nonlinear optical properties in a hybrid dihydrogen phosphate system: an experimental and theoretical approach

CONTEXT

The controlled slow evaporation process conducted at room temperature has produced a novel hybrid material denoted as (2-hydroxyethyl) trimethylammonium dihydrogen phosphate [2-HDETDHP] (C5H14NO+, H2PO4-), synthesized through the solution growth method. X-ray crystallography analysis reveals a triclinic structure with a filling rate of P and a Z value of 2. This hybrid material displays noteworthy absorption characteristics in the middle and far ultraviolet regions. UV-visible spectroscopy further establishes its transparency in the visible and near-visible ultraviolet domains. FT-IR spectroscopy examines various vibration modes, elucidating their relationships with the functional groups within the structure. Two- and three-dimensional fingerprint maps, coupled with three-dimensional crystal structures through Hirshfeld Surface Analysis, unveil the dominance of O•••H and H•••H interactions in the structure, comprising 49.40% and 50.40%, respectively. Fingerprint plots derived from the Hirshfeld surface assess the percentages of hydrogen bonding interactions, with 80.6% attributed to a fragment patch. The experiment of antimicrobial efficacy of a synthesized product, conducted in triplicate, demonstrated the synthesized product's potential antimicrobial activity.

METHODS

Hirshfeld surfaces are employed to investigate intermolecular hydrogen bonding, specifically within single phosphate groups. The molecular structure of 2-HDETDHP was refined using single-crystal X-ray analysis, while its optical characteristics were examined through UV-visible spectroscopy. FT-IR spectroscopy is employed for the assignment of molecular vibrations of functional groups in the affined structure. Quantum calculations were executed with the GAUSSIAN 09 software package at B3LYP/6-311G level of theory, to optimize the molecular geometries. The antimicrobial efficacy of a synthesized product was evaluated using the disc diffusion method against antibiotic-resistant Candida albicans, Candida tropicalis, Aspergillus niger, Staphylococcus aureus, and Escherichia coli. Microorganisms were cultured on nutrient agar, and inhibition zones were measured after incubation, with streptomycin and amphotericin as positive controls.

Photovoltaic properties of novel reactive azobenzoquinolines: experimental and theoretical investigations

In this work, synthesis, characterization, DFT, TD-DFT study of some novel reactive azobenzoquinoline dye structures to elucidate their photovoltaic properties. The azobenzoquinoline compounds were experimentally synthesized through a series of reaction routes starting from acenaphthene to obtained aminododecylnaphthalimide and finally coupled with diazonium salts to get the desired azobenzoquinoline. Azo dye synthesized differ in the number of alkyl chains designated as (AR1, AR2, AR3, and AR4) which were experimentally analyzed using FT-IR and NMR spectroscopic methods. The synthesized structures were modelled for computational investigation using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) combined with B3LYP and 6-31+G(d) basis set level of theory. The results showed that the HOMO-LUMO energy gap was steady at approximately 2.8 eV as the alkyl chain increases, which has been proven to be within the material energy gap limit for application in photovoltaic. The highest intramolecular natural bond orbital (NBO) for the studied compounds is 27.60, 55.06, 55.06, and 55.04 kcal/mol for AR1, AR2, AR3, and AR4 respectively and the donor and acceptor interacting orbitals for the highest stabilization energy (E (2)) are LP(1)N 18 and π*C 16−O 19 respectively. The photovoltaic properties in terms of light-harvesting efficiency (LHE), Short circuit current density (J SC), Gibbs free energy of injection (ΔG inj), open-circuit voltage (V OC) and Gibbs free energy of regeneration (ΔG reg) were evaluated to be within the required limit for DSSC design. Overall, the obtained theoretical photovoltaic results were compared with other experimental and computational findings, thus, are in excellent agreement for organic solar cell design.

D–A systems based on oxazolone–coumarin triazoles as solid-state emitters and inhibitors of human cervical cancer cells (HeLa)

D–A systems with solid-state emission and anticancer properties have been synthesized in three steps via the MCR-Click protocol.

Recent advances in catalytic oxidative reactions of phenols and naphthalenols

This critical review aims to provide an overview of oxidative phenol and naphthalenol transformations in nature and synthetic chemistry.

Design and engineering of a dual-mode absorption/emission molecular switch for all-optical encryption

Photochemical reactions that produce a detectable change in the spectroscopic properties of organic chromophores can be exploited to harness the principles of Boolean algebra and design molecule-based logic circuits. Moreover, the logic processing capabilities of these photoactive molecules can be directed to protect, encode, and conceal information at the molecular level. We have designed a photochemical strategy to read, write and encrypt data in the form of optical signals. We have synthesized a supramolecular system based on the known dye resazurin, and investigated a series of photochemical transformations that can be used to regulate its absorption and emission properties upon illumination with ultraviolet or visible light. We have then examined the logic behaviour of the photochemistry involved, and illustrated its potential application in data encryption.

Heterocycloalkynes Fused to a Heterocyclic Core: Searching for an Island with Optimal Stability-Reactivity Balance

In the search for fundamentally new, active, stable, and readily synthetically accessible cycloalkynes as strain-promoted azide-alkyne cycloaddition (SPAAC) reagents for bioorthogonal bioconjugation, we integrated two common approaches: the reagent destabilization by the increase of a ring strain and the transition state stabilization through electronic effects. As a result new SPAAC reagents, heterocyclononynes fused to a heterocyclic core, were created. These compounds can be obtained through a general synthetic route based on four crucial steps: the electrophile-promoted cyclization, Sonogashira coupling, Nicholas reaction, and final deprotection of Co-complexes of cycloalkynes from cobalt. Varying the natures of the heterocycle and heteroatom allows for reaching the optimal stability-reactivity balance for new strained systems. Computational and experimental studies revealed similar SPAAC reactivities for stable 9-membered isocoumarin- and benzothiophene-fused heterocycloalkynes and their unstable 8-membered homologues. We discovered that close reactivity is a result of the interplay of two electronic effects, which stabilize SPAAC transition states (πin* → σ* and π* → πin*) with structural effects such as conformational changes from eclipsed to staggered conformations in the cycloalkyne scaffold, that noticeably impact alkyne bending and reactivity. The concerted influence of a heterocycle and a heteroatom on the polarization of a triple bond in highly strained cycles along with a low HOMO-LUMO gap was assumed to be the reason for the unpredictable kinetic instability of all the cyclooctynes and the benzothiophene-fused oxacyclononyne. The applicability of stable isocoumarin-fused azacyclononyne IC9N-BDP-FL for in vitro bioconjugation was exemplified by labeling and visualization of HEK293 cells carrying azido-DNA and azido-glycans.

Synthesis, characterization, and theoretical studies of the photovoltaic properties of novel reactive azonitrobenzaldehyde derivatives

All dyes conduct but at different degrees of absorption; it is interesting to study the degree of conductivity and absorptivity of novel reactive azo-dyes in respect to dye-sensitized solar cells (DSSCs) to ascertain their viability for such applications. In this study, four novel reactive azo-dyes were experimentally synthesized from p-aminobenzaldehyde, 4-amino-3-nitrobenzaldehyde, and aniline through series of condensation and coupling reactions. The various functional groups, molecular connectivities, and molecular weight of the various fragments of the synthesized dyes were elucidated using the GC-MS, FT-IR, UV-vis, and NMR respectively. The experimentally determined structures were modeled and investigated using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) approaches to computationally compute the electronic structure properties, reactivity, absorption and solvatochromism in four different phases: gas, ethanol, acetone, and water, and the photovoltaic properties for possible applications in dye-sensitized solar cells (DSSCs). By comparing the HOMO (E H) and the LUMO (E L) energies from the results obtained demonstrates that dye D has the highest E L energy value of -2.48 eV with a relatively lowest E H energy value of -5.63 eV such that it lies underneath the conduction band edge of TiO2 which is necessary to enable charge regeneration. Pi-electron delocalization was observed from the natural bond orbital (NBO) calculations between the different aromatic rings with dye B and A having the relatively highest and least second-order stabilization energies between σ* → σ* and LP* → LP interacting orbitals respectively. It is also observed in all the solvents that the Gibbs free energy of injection (ΔG inject) is greater than 0.2 eV and hence, all the studied azo structures in the four phases provided efficient electron injection and light harvesting efficiency (LHE), however, the value of ΔG inject for dyes B and D is greatest in all the four phases and thus, provided the highest electron injection of all the dyes. From the fact-findings of quantum theory of atoms-in-molecules (QTAIM), dyes A and C have extra-stability due to their relatively high numbers of intramolecular H-bond interactions along with some additional intra-atomic bonding between atoms within the studied compounds. Hence, all the four dyes are good for DSSCs applications.

Synthesis, characterization, DFT, and TD-DFT studies of (E)-5-((4,6-dichloro-1,3,5-triazin-2-yl)amino)-4-hydroxy-3-(phenyldiazenyl)naphthalene-2,7-diylbis(hydrogen sulfite)

In this study, (E)-5-((4,6-dichloro-1,3,5-triazin-2-yl)amino)-4-hydroxy-3-(phenyldiazenyl)naphthalene-2,7-diylbis(hydrogen sulfite), a cyanurated H-acid (CHA) azo dye, was synthesized and characterized using FT-IR spectrophotometer and GC-MS spectroscopy. A density functional theory (DFT) based B3LYP and CAM-B3LYP method with 6–311 + G (d,p) basis set analysis was computed for HOMO-LUMO, natural bonding orbitals (NBO), UV-Vis absorptions and excitation interactions, in order to understand its molecular orbital excitation properties. A low Energy gap (Eg) of 2.947 eV was obtained from the molecular orbital analysis, which showed that HOMO to LUMO transition is highly feasible; hence CHA is adequate for diverse electronic and optic applications. Studies of the first five excitations (S0 → S1/S2/S3/S4/S5) of CHA revealed that S0 → S1 and S0 → S3 are π → π* type local excitations distributed around the –N=N– group; S0 → S2, a Rydberg type local excitation; S0 → S4, a highly localized π → π* excitation; while S0 → S5 is an n → π* charge transfer from a benzene ring to –N=N– group. From NBO analysis, we obtained the various donor–acceptor orbital interactions contributing to the stabilization of the studied compound. Most significantly, some strong hyper-conjugations (n → n*) within fragments, and non-bondingand anti-bonding intermolecular (n → n*/π* and π → n*/π*) interactions were observed to contribute appreciable energies. This study is valuable for understanding the molecular properties of the azo dyes compounds and for synthesizing new ones in the future.

Deep eutectic solvent assisted synthesis of dihydropyrimidinones/thiones via Biginelli reaction: theoretical investigations on their electronic and global reactivity descriptors

DES 2 (ZrOCl2·8H2O-ethylene glycol at 1 : 2 ratio) was used as a catalyst for the synthesis of dihydropyrimidinones/thiones via a Biginelli reaction.

Harnessing structurally unbiased ortho-benzoquinone monoimine for biomimetic oxidative [4+2] cycloaddition with enamines

Reported herein is the first catalytic oxidative [4+2] cycloaddition of 2-aminophenols with cyclic enamines.