Molecular Electron Distribution Research Articles

Synthesis and characterization of Azo-Azomethine derivatives bearing thiazole moiety: In vitro antimicrobial, in vitro and in vivo anti-inflammatory, and cytotoxicity assessment, accompanied by computational molecular docking, RDG, ELF, DFT, and MEP analysis

In this study, a novel series of Azo-azomethine derivatives incorporating thiazole moieties (5a-h) were synthesized and thoroughly characterized using NMR (1H and 13C), FT-IR spectroscopy, and ESI-MS methods. The synthesized compounds underwent screening for their antimicrobial, anti-inflammatory (both in vitro and in vivo), and cytotoxic activities. Notably, compound 5d exhibited significant activity against S. aureus and S. epidermidis, with minimum inhibitory concentration (MIC) values as low as 20 μg/L. Additionally, compound 5d demonstrated the most potent anti-inflammatory activity both in vitro (84.72%) and in vivo. Furthermore, molecular analyses including RDG, ELF, DFT, and MEP were conducted to investigate molecular interactions, electron distribution, electronic configuration, and electrostatic potential, thus facilitating a deeper understanding of the molecular characteristics and aiding in the refinement and design of these molecules. Moreover, the compounds' efficacy against bacterial proteins was assessed through molecular docking calculations. Utilizing the PASS and pkCSM platforms, an examination of the compounds' bioactivity regulation and physicochemical attributes was conducted, highlighting their potential as prospective novel active agents.

Construction of Binary Matrix for Efficient Room Temperature Phosphorescence Emission

AbstractDespite the extensive research on room temperature phosphorescent (RTP) materials, it remains a great challenge to further improve the photophysical properties of RTP materials. In this study, the RTP emission of guest molecule is significantly enhanced by constructing binary matrices containing cyanuric acid (CA) and amino‐containing compounds. Systematic studies show that the strong interaction between the two components of binary matrix induced variations in the guest molecular configuration and excited state electron distribution, thus facilitating the production of more triplet excitons. Furthermore, the binary matrix also exhibits stronger domain‐limiting effect compared to the CA mono‐matrix, effectively inhibits the energy loss of triplet excitons due to quenching and non‐radiative transitions. The prepared binary matrix RTP materials present ultralong phosphorescence lifetime and high phosphorescence quantum yield (up to 3.21 s and 7.31%, respectively), and even achieve bright RTP emission in a variety of organic solvents and aqueous media. Moreover, the RTP emission intensity of the best binary matrix composite can reach more than 28 times that of the CA mono‐matrix composite, and the RTP lifetime can be extended by 1.51 s.

Interpreting pH-Dependent Differential UV/VIS Absorbance Spectra to Characterize Carboxylic and Phenolic Chromophores in Natural Organic Matter

Natural organic matter (NOM) is critical for the biogeochemical cycles of energy and many elements in terrestrial and aquatic ecosystems, and protonation-active functional groups in NOM molecules, notably carboxylic and phenolic groups often mediate these critical environmental functions. Molecular heterogeneity, polydispersity and dynamic behavior of NOM complicate achieving an unambiguous description of its molecular properties and reactivity. This study demonstrates that differential ultraviolet-visible (UV/VIS) absorbance spectra (DAS) of NOM acquired at varying pH values exhibit several distinct features associated with the deprotonation of NOM molecules, independent of the environmental provenance of NOM (e.g., surface water, seawater, sediment, and wastewater). The protonation-active functionalities that contribute to the Gaussian distribution bands present in the DAS were identified here by comparing characteristic properties of the bands with the stoichiometries of NOM molecules ascertained by Ultrahigh-Resolution Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS). The protonation-active individual chromophores universally present in NOM molecules were identified by a genetic molecular network analysis. The observed DAS features were closely modeled via superimposing DAS spectra of 51 individual protonation-active chromophores. Molecular orbital theory was applied to further interpret the deprotonation of these chromophores, their molecular structure, electron distribution, and electron transitions measured using DAS. The high sensitivity and easy implementation of the DAS approach allows using it as a powerful tool to quantify the molecular properties and reactivity of NOM at environmental concentrations.

Small thiophene-based molecules with favorable properties as HTMs for perovskite solar cells or as active materials in organic solar cells

Computational investigations are carried out to design new molecules based on thiophene cores substituted in several positions using different end-capped electron-donating groups formed from triphenylamine or OMe-triphenylamine that can be used as HTMs in Perovskite Solar Cells (PSCs), or as an active layer in Organic Solar Cells. The influence of π-extension on the charge transfer process is also probed by inserting two azomethine groups between acceptor and donor (D-π-A-π-D) moieties. The designed molecules (T10,12,13,15) were compared with the two synthesized molecules (T11,14) that have been applied as HTMs in a PSC. Density functional theory (DFT) and time-dependent DFT (TD-DFT) were chosen to calculate different chemical parameters of these molecules. Different chemical parameters were calculated to make the link between geometrical parameters and the efficiency, solubility, and stability of the under-probed compounds. The results show that all molecules can be used adequately with the perovskite matrix because of their sufficient deep HOMOs levels. The optoelectronic properties of the D-A-D molecules show no competition with the light-harvesting of the perovskite layer, while D-π-A-π-D compounds show a slight overlap with the absorption band of perovskites. All molecules indicate a faster hole-transport rate and an easy electron-hole pairs dissociation into free charge carriers, which facilitates the hole transport and enhances open-circuit voltage. Adding a second thiophene unit in the central core reinforces the structure's flexibility and improves Frontier Molecular Orbital's electronic density distribution, while inserting azomethine groups is advantageous for the molecule's solubility. Their short gaps, higher radiative lifetimes, and visible light absorbance make T12,15 good candidates for their usage in organic solar cell applications. A spontaneous solvation process within dichloromethane for all the investigated molecules was proved based on the high negative free energies.

Effect of the spatial configuration of donors on the photovoltaic performance of co-adsorbent organic dyes formed by Z/E configuration

Molecular modification is an important pathway to explore the highly efficient dyes for dye sensitized solar cells (DSSCs). In this work, three co-adsorbent D-π-A dye sensitizers (L1, L2 and L3) formed by Z/E configuration were prepared by the introduction of 4-methoxyphenyl group into the olefin containing triphenylamine dyes, and their photo-physical absorption, electrochemical properties and photovoltaic performance were systematically investigated. Density functional theory (DFT) calculations have been employed to gain insight into the optimized molecular configuration and electron distribution of dyes L1, L2 and L3, which are further correlated with the experimental results. The results indicated that the 4-methoxyphenyl auxiliary donor brought a molecular Z/E configuration and more electron injection capability, which is beneficial to the prevention of π-π aggregation and good light-capturing capability. The photo-physical absorptions are obviously red-shifted from 441 nm to 451 nm for dye L1 and 462 nm–492 nm for dye L2 compared with their predecessors. Co-adsorbent dye L3 with a cyclic thiourea functionalized triphenylamine donor afforded significantly improved current density (15.83 mA cm−2) and PCE (7.96%).

Design, synthesis of triazole-based scaffolds, N-(substitutedphenyl)-2-(5-(4-methoxyphenyl)-4-phenyl-4H-1,2,4-triazol-3-ylthiol)acetamides: As potential anti-cholinesterase agents for neurodegenerative diseases

Alzheimer's disease (AD) is currently regarded as a global health concern; there are now about 50 million AD patients worldwide, and it is predicted that this number will double every five years and reach 152 million by 2050. Although there are therapies that can help with the symptoms of Alzheimer's disease, there is currently no cure for the condition. This study synthesized a series of novel triazole scaffolds 7a–k, fully characterized, and investigated to unravel their anticholinesterase potential. Density functional theory (DFT) calculations were carried out to investigate the compounds' molecular geometry and electron distribution. The significant enzymatic inhibitory potential was exhibited by compound7c against AChE (IC50 = 9.52 ± 0.25 μM) and 7g against BChE (IC50 = 31.51 ± 0.38 μM), in comparison to the standard drug eserine. Moreover, the compounds were also screened for their anti-proliferative activity against HCT-116 human cancer cell lines, with 7f demonstrating 19.2% cell viability at 25 μM and 28.4% cell viability at 50 μM. The bioactivity results were further validated through computational docking analysis.

A triad molecular conductor: simultaneous control of charge and molecular arrangements.

Molecular and charge arrangements in the solid state were controlled by a new building block: a triad molecule. Owing to the appropriate flexibilities in both molecular structure and electron distribution of the triad, the apparently simple salt exhibits an unstable metallic phase, which is promising for superconducting transitions.

Design and synthesis of heterocyclic azole based bioactive compounds: Molecular structures, quantum simulation, and mechanistic studies through docking as multi-target inhibitors of SARS-CoV-2 and cytotoxicity

Two heterocyclic azole compounds, 3-(2,3-dihydrobenzo[d]thiazol-2-yl)-4H-chromen-4-one (SVS1) and 5-(1H-indol-3-yl)-4-methyl-2,4-dihydro-3H-1,2,4-triazole-3-thione (SVS2) were obtained unexpectedly from 2-aminothiophenol and 4-oxo-4H-chromene-3-carbaldehyde (for SVS1), and (E)-2-((1H-indol-3-yl)methylene)-N-methylhydrazine-1-carbothioamide in the presence of anhydrous FeCl3 (for SVS2), respectively. The compounds were well characterized by analytical and spectroscopic tools. The molecular structures of both the compounds were determined by single crystal X-ray diffraction (XRD) study. The results obtained from density functional theory (DFT) study revealed the molecular geometry and electron distribution of the compounds, which were correlated well with the three-dimensional structures obtained from the single crystal XRD. DMol3 was used to calculate quantum chemical parameters [chemical potential (µ), global hardness (η), global softness (σ), absolute electronegativity (χ) and electrophilicity index (ω)] of SVS1 and SVS2. Molecular docking study was performed to elucidate the binding ability of SVS1 and SVS2 with SARS-CoV-2 main protease and human angiotensin-converting enzyme-2 (ACE-2) molecular targets. Interestingly, the binding efficiency of the compounds with the molecular targets was comparable with that of remdesivir (SARS-CoV-2), chloroquine and hydroxychloroquine. SVS1 showed better docking energy than SVS2. The molecular docking study was complemented by molecular dynamics simulation study of SARS-CoV-2 main protease-SVS1 complex, which further exemplified the binding ability of SVS1 with the target. In addition, SVS1, SVS2 and cisplatin were assessed for their cytotoxicity against a panel of three human cancer cells such as HepG-2 (hepatic carcinoma), T24 (bladder) and EA.hy926 (endothelial), as well as Vero (kidney epithelial cells extracted from an African green monkey) normal cells using MTT assay. The results showed that SVS2 has significant cytotoxicity against HepG-2 and EA.hy926 cells with the IC50 values of 33.8 μM (IC50 = 49.9 μM-cisplatin and 8.6 μM-doxorubicin) and 29.2 (IC50 = 26.6 μM-cisplatin and 3.8 μM-doxorubicin), respectively.

Mechanism of transition metal cluster catalysts for hydrogen evolution reaction

Studying the hydrogen evolution reaction (HER) catalyst is important for the global energy crisis. Clusters have many special characteristics due to quantum size effect and super high specific surface area, including optical performance, catalytic performance, etc. In this work, the structures of transition metal cluster TMn (TM = Co, Ni, Cu, Pd, Pt, n = 4–10) were searched and optimized by quantum chemistry methods. To search for non-precious metal catalysts, we calculated the Gibbs free energies for HER process on different clusters. Furthermore, the electronic structures of clusters before and after the reaction with H were analyzed, including the molecular surface electron distribution, the frontier molecular orbital, and the charge transfer properties, which dominated the HER processes. The results show that the Cu clusters have excellent HER catalytic properties due to its suitable surface electron distribution and HOMO/LUMO levels, especially Cu4, Cu7 and Cu9, which even comparable to Pt catalysts. These results can help us better understand the mechanism of clusters catalyze HER process.

A density functional theory and information-theoretic approach study of chiral molecules in external electric fields

The effect of external electric fields and chirality are two important chemical concepts. In this work, we combine the two and consider behaviors of chiral molecules in external electric fields. A total of 74 pairs of enantiomers with one chiral center have been examined. We unveil that substantial changes in molecular structure, electron distribution, frontier orbitals and chemical reactivity were observed. Employing density functional theory and information-theoretic approach, strong linear relationships have been obtained. This work provides new understandings about the effect of external electric fields in transforming chemical reactivity from a novel theoretical and computational perspective.

Amide Bond Bioisosteres: Strategies, Synthesis, and Successes.

The amide functional group plays a key role in the composition of biomolecules, including many clinically approved drugs. Bioisosterism is widely employed in the rational modification of lead compounds, being used to increase potency, enhance selectivity, improve pharmacokinetic properties, eliminate toxicity, and acquire novel chemical space to secure intellectual property. The introduction of a bioisostere leads to structural changes in molecular size, shape, electronic distribution, polarity, pKa, dipole or polarizability, which can be either favorable or detrimental to biological activity. This approach has opened up new avenues in drug design and development resulting in more efficient drug candidates introduced onto the market as well as in the clinical pipeline. Herein, we review the strategic decisions in selecting an amide bioisostere (the why), synthetic routes to each (the how), and success stories of each bioisostere (the implementation) to provide a comprehensive overview of this important toolbox for medicinal chemists.

Molecular structure and electron distribution of 4-nitropyridine N-oxide: Experimental and theoretical study of substituent effects

The molecular structure of 4-nitropyridine N-oxide, 4-NO2-PyO, has been determined by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and by quantum chemical calculations (DFT and MP2). Comparison of these results with those for non-substituted pyridine N-oxide and 4-methylpyridine N-oxide CH3-PyO, demonstrate strong substitution effects on structural parameters and electron density distribution. The presence of the electron-withdrawing –NO2 group in para-position of 4-NO2-PyO results in an increase of the ipso-angle and a decrease of the semipolar bond length r(N→O) in comparison to the non-substituted PyO. The presence of the electron-donating –CH3 group in 4-CH3-PyO leads to opposite structural changes. Electron density distribution in pyridine-N-oxide and its two substituted compounds are discussed in terms of natural bond orbitals (NBO) and quantum theory atoms in molecule (QTAIM).

The structural, vibrational and electronic properties of the triel-bonded complexes of boron trifluoride with some cyclic ethers – An ab initio study

The properties (molecular structures, vibrational spectra and electronic distributions) of the triel-bonded complexes of boron trifluoride with the cyclic ethers oxirane, oxetane, tetrahydrofuran and tetrahydropyran have been computed. The calculations were carried out ab initio using the Gaussian 16 program at the second order level of Møller-Plesset perturbation theory (MP2) and with Dunning’s augmented correlation-consistent polarized valence triple-zeta basis sets (aug-cc-pVTZ). The results indicate that, with the exception of the oxirane complex, the interaction energies, the bond length and angle changes and the perturbations of the BF3 fragment vibrational wavenumbers are remarkably invariant to the ring size of the base. The unique position of the oxirane complex is associated with the extent of ring strain in the monomer relative to those of the other three bases.

The influence on properties with different conjugated direction of phenoxazine and phenothiazine-based chromophores for organic nonlinear optical materials

A serial of phenoxazine and phenothiazine based organic chromophores were synthesized with facile routes. Then these chromophores were applied in organic nonlinear optical materials to study the effect of different conjugated direction, extra phenyl ring and alkyl chain on the decomposition temperature, energy level, photophysical properties through Uv–vis spectral, density functional theory calculations. The electro-optic coefficient of poled films containing these chromophores doped in amorphous polycarbonate afforded the largest values of 19 pm/V, 49 pm/V and 23 pm/V at 1310 nm for chromophores B, L1 and L2 respectively. To our regret, chromophore A is not stable enough for test. The geometries of the chromophores were optimized to gain insight into the molecular structure and electron distribution. These results showed that when the phenyl ring was added in chromophore A, B, nearly 90°of the dihedral angle between PTZ and phenyl ring unit leads to the intramolecular charge transfer transition (HOMO-LUMO) being prohibited and showed a smaller hyperpolarizability (β) value.

A DFT and TD-DFT study on electronic structures and UV-spectra properties of octaethyl-porphyrin with different central metals(Ni, V, Cu, Co)

In this work, the octaethyl-porphyrins with different central metals (M-OEP, M = Ni, VO, Cu, Co) were used to investigate the ground-state molecular structure, electron distribution and UV-spectra properties on molecular level by density functional theory (DFT). The results showed that the calculation structure parameters of metalloporphyrins agreed well with the experimental value. According to the Natural Bond Orbital (NBO) analysis, the charge distribution of different metalloporphyrins was found that the charge values of the central metal M decreased with the order of VO < Ni < Co < Cu, while the bonding strength between M and the coordinating atom N was VO > Ni > Co > Cu. At the same time, the frontier molecular orbital calculations showed that the SOMO energy of VO (OEP) molecules in the open-shell system was higher than that of Co (OEP) and Cu (OEP), which means that its UV absorption characteristic peak would be red-shifted. In addition, the IEFPCM model of Time-dependent Density functional theory (TD-DFT) was further utilized to simulate the four substance in toluene solution: Co (OEP), Ni (OEP), Cu (OEP) and VO (OEP), and the Soret band peaks were calculated respectively as: 382 nm, 383 nm, 391 nm and 401 nm. Furthermore, the quantitative simulation analysis of metalloporphyrins was combined with experimental data. It could be found that the location rules of the four kinds of metalloporphyrins calculated absorption characteristic peaks were consistent with the experimental ones, and the relative errors of each peak were within 3%. These methods used above provide a theoretical path for analyzing and identifying unknown porphyrin compounds in petroleum.

Surface Self-Assembly, Film Morphology, and Charge Transport Properties of Semiconducting Triazoloarenes.

Surface-assisted molecular self-assembly is a powerful strategy for forming molecular-scale architectures on surfaces. These molecular self-assemblies have potential applications in organic electronics, catalysis, photovoltaics, and many other technologies. Understanding the intermolecular interactions on a surface can help predict packing, stacking, and charge transport properties of films and allow for new molecular designs to be tailored for a required function. We have previously studied a molecular platform, tris( N-phenyltriazole) (TPT), that exhibits planar stacking through >20 molecular layers through donor-acceptor-type intermolecular π-π contacts between the electron-deficient tris(triazole) core and electron-rich peripheral phenyl units. Here, we investigate an expanded family of TPT-based molecules with variations made on the peripheral aryl groups to modulate the molecular electron distribution and examine the impact on molecular packing and charge transport properties. Molecular-resolution scanning tunneling microscopy was used to compare the molecular packing in the monolayer and to investigate the effects that the structural and electronic modifications have on the stacking in subsequent layers. Conductivity measurements were made using the four-point probe van der Pauw technique to demonstrate charge transport properties comparable to pentacene. Although molecular packing is clearly impacted by the chemical structure, we find that the charge transport efficiency is quite tolerant to small structural variations.

Design and Synthesis of the Candesartan Key Intermediate

This paper presents experimental data regarding the synthesis and structural characterization by: 1H-NMR, 13C-NMR, IR spectral analysis, melting point and thin layer chromatography of the candesartan key intermediate: methyl 2-[(tert-butoxycarbonyl)amino]-3-nitrobenzoate. In addition, a computational study of predicted molecular parameters, vibrational wavenumbers, frontier molecular orbitals energy diagram, molecular electrostatic potential map and other electronic distributions maps using restricted hybrid HF-DFT SCF calculation has been performed for obtaining the most stable conformer. For the most Stable conformer has been made a series of DFT calculations using the B3LYP levels using the 6-31G * basis set.

Small Molecules Derived from Thieno[3,4-c]pyrrole-4,6-dione (TPD) and Their Use in Solution Processed Organic Solar Cells.

In this work, microwave synthesis, chemical, optical and electrochemical characterization of three small organic molecules, TPA-TPD, TPA-PT-TPD and TPA-TT-TPD with donor-acceptor structure and their use in organic photovoltaic cells are reported. For the synthesis, 5-(2-ethylhexyl)-4H-thieno[3,4-c]pyrrole-4,6(5H)-dione was used as electron withdrawing fragment while the triphenylamine was used as electron donating fragment. Molecular electronic geometry and electronic distribution density were established by density functional theory (DFT) calculations and confirmed by optical and chemical characterization. These molecules were employed as electron-donors in the active layer for manufacturing bulk heterojunction organic solar cells, where [6,6]-phenyl C71 butyric acid methyl ester (PC71BM) was used as electron-acceptor. As cathode, Field′s metal (FM), an eutectic alloy (Bi/In/Sn: 32.5%, 51%, and 16.5%, respectively) with a melting point above 62 °C, was easily deposited by drop casting under vacuum-free process and at air atmosphere. Prepared devices based on TPA-TPD:PC71BM (1:4 w/w ratio) presented a large VOC = 0.97 V, with JSC = 7.9 mA/cm2, a FF = 0.34, then, a power conversion efficiency (PCE) of 2.6%.

Partial atomic multipoles for internally consistent microelectrostatic calculations

An extension of the extant microelectrostatic methodologies, based on the concept of distributed generalized polarizability matrix derived from the Coupled Perturbed Hartree-Fock (CPHF) equations, is proposed for self-consistent calculation of charge carrier and charge-transfer (CT) state electrostatic energies in molecular solids, including the doped, defected and disordered ones. The CPHF equations are solved only once and the generalized molecular polarizability they yield enables low cost iterations that mutually adjust the molecular electronic distributions and the local electric field in which the molecules are immersed. The approach offers a precise picture of molecular charge densities, accounting for atomic partial multipoles up to order 2, which allows one to reproduce the recently reported large charge-quadrupole contributions to CT state energies in low-symmetry local environments. It is particularly well suited for repetitive calculations for large clusters (up to 300,000 atoms), and may potentially be useful for describing electrostatic solvent effects. © 2017 Wiley Periodicals, Inc.

Enhanced NLO response in BODIPY-coumarin hybrids: density functional theory approach

We have thoroughly investigated the first, second and third polarizability characteristics of four hybrid chromophores by spectroscopic and computational methods. B3LYP, CAMB3LYP and BHandHLYP functionals in combination with 6-311+G(d,p) basis set were used to evaluate the polarizability and hyperpolarizability characteristics of these chromophores. Generalized Mulliken Hush analysis and frontier molecular orbital electronic distribution images of chromophores obtained from Density functional theory computation has established the charge transfer characteristics of these hybrid chromophores. On the basis of charge transfer characteristic, these red absorbing and NIR emissive chromophores possess high nonlinear optical response. Comparison of isolated units with their analogous hybrid chromophores shows that fusion of coumarin with BODIPY enhances the nonlinear optical response. JCSC-D-17-00467 SYNOPSIS The NLO properties of coumarin-fused BODIPY hybrid chromophores were studied in details. Spectroscopic method gave rough estimation of polarizability and hyperpolarizability characteristics of four hybrid chromophores while computational approaches using three different hybrid functional, B3LYP, CAM-B3LYP and BHandHLYP in combination with 6-311+G(d,p) basis set, gave comparative estimation of these values. BLA/BOA calculations for ground and excited states suggested that the cyanine-type D- $$\pi $$ -A framework produces high NLO response. The hybrid molecules are proven to be the better performing NLOphores than the isolated coumarin or BODIPY units.