Exploring the activation potential of heme for 2,4-dichlorophenol, 2,4,6-trichlorophenol, and pentachlorophenol.

The presence of chlorophenols in water poses a significant threat to human health and the environment. In response to this issue, a study was undertaken to evaluate the catalytic capabilities of chlorinated Heme towards common chlorophenols present in water, such as 2,4-dichlorophenol, 2,4,6-trichlorophenol, and pentachlorophenol. The study employed the B3LYP method, a sophisticated computational technique within density functional theory, to investigate the molecular interactions and transformations involved. It scrutinized structural parameters, Wiberg Bond Indices, which offer insights into the strength and nature of chemical bonds, along with spectroscopic data including infrared vibrational spectra, ultraviolet-visible absorption spectra, and molecular fluorescence spectra. Furthermore, the research analyzed molecular binding energies and orbital energy levels before and after the formation of complexes between Heme and the targeted chlorophenols. The findings indicate that Heme displays a notable activation characteristic towards these chlorophenols. This suggests that Heme could act as an effective catalyst in the degradation of chlorophenols in water, presenting a novel approach to water purification. The theoretical insights derived from this study are invaluable, potentially guiding the development of more efficient catalytic systems for treating chlorophenol-contaminated water, thereby reducing the environmental and health risks associated with these hazardous compounds.

N-Aromatic Complexation in Tetraphenyl Porphyrin Iron (III)-Pyridine: Evidence of Spin-Flip via Gas-Phase Electronic Spectroscopy.

There is growing interest in the electronic properties of metalloporphyrins especially in relation to their interactions with other molecular species in their local environment. Here, UV-VIS laser photodissociation spectroscopy in vacuo has been applied to an iron-centred metalloporphyrin (FeTPP+) and its N-aromatic adduct with pyridine (py) to determine the electronic effect of complexation. Both the metalloporphyrin (FeTPP+) and pyridine adduct (FeTPP+⋅py) absorb strongly across the spectral region studied (652-302 nm: 1.91-4.10 eV). Notably, a large blue shift was observed for the dominant Soret band (41 nm) upon complexation (0.47 ± 0.02 eV), indicative of strong pyridine binding. Significant differences in the profiles (i.e. number and position of bands) of the electronic spectra are evident comparing FeTPP+ and FeTPP+⋅py. Time-dependent density functional theory calculations were used to assign the spectra, revealing that the FeIII spin-state flips from S = 3/2 to S = 5/2 upon complexation with pyridine. For FeTPP+, all bright spectral transitions are found to be π-π* in character, with electron density variously distributed across the porphyrin and/or its phenyl substituents. Similar electronic excitations are observed for FeTPP+⋅py, with an additional bright transition which involves charge transfer from the porphyrin to the pyridine moiety.

Schiff Bases Derived from Pyridoxal 5'-Phosphate and 2-X-Phenylamine (X = H, OH, SH): Substituent Effects on UV-Vis Spectra and Hydrolysis Kinetics.

Schiff bases are compounds that are widely distributed in nature and have practical value for industry and biomedicine. Another important use of Schiff bases is identifying metal ions and different molecules, including proteins. Their proneness to hydrolysis limits the utilization of Schiff bases to mainly non-aqueous solutions. However, by introducing -OH and -SH substituents to aromatic amine-bearing rings, it is possible to increase the resilience of the Schiff base to destruction in water. The present paper discusses how the hydroxyl or thiol group influences the spectral properties and kinetics of the hydrolysis and formation of Schiff bases derived from pyridoxal 5'-phosphate and aniline, 2-hydroxyaniline, and 2-mercaptoaniline using quantum chemical data. The spectral variation between different imines can be explained by taking into account the geometry and frontier molecular orbital alteration induced by the substituents. The changes in the hydrolysis rate are analyzed using the computed values of local reactivity indices.

Computational Investigation about the Effects of Solvent Polarity and Chalcogen Element Electronegativity on ESIPT Behaviors for the Et2N-Substituted Flavonoid.

Inspired by the outstanding nature of flavonoid derivatives in the fields of chemistry and medicine, in this work we mainly focus on exploring the photo-induced properties of the novel Et2N-substituted flavonoid (ENF) fluorophore theoretically. Considering the potential photo-induced properties in different solvents and the chalcogen atomic electronegativity-associated photoexcitation, by time-dependent density functional theory (TDDFT) methods we primarily explore the intramolecular hydrogen bonding interactions and photo-induced charge redistribution behaviors. Via comparing geometrical data and the infrared (IR) spectral shifts-associated hydroxy moiety of ENF, we confirm that the intramolecular hydrogen bond O-H···O should be enhanced with facilitating an excited-state intramolecular proton-transfer (ESIPT) reaction. Particularly, the charge reorganization around hydrogen bonding moieties further reveals the tendency of ESIPT behavior. Combined with the construction of the potential energy surface and the search for reaction transition states, we finally confirmed the solvent-polarity-regulated behaviors as well as the chalcogen elements' electronegativity-dependent ESIPT mechanisms for the ENF fluorophore. We sincerely wish our work could accelerate the further development and applications of flavonoid derivatives.

Molecular Recognition between Carbon Dioxide and Biodegradable Hydrogel Models: A Density Functional Theory (DFT) Investigation.

In this research, we explore the potential of employing density functional theory (DFT) for the design of biodegradable hydrogels aimed at capturing carbon dioxide (CO2) and mitigating greenhouse gas emissions. We employed biodegradable hydrogel models, including polyethylene glycol, polyvinylpyrrolidone, chitosan, and poly-2-hydroxymethacrylate. The complexation process between the hydrogel and CO2 was thoroughly investigated at the ωB97X-D/6-311G(2d,p) theoretical level. Our findings reveal a strong affinity between the hydrogel models and CO2, with binding energies ranging from -4.5 to -6.5 kcal/mol, indicative of physisorption processes. The absorption order observed was as follows: chitosan > PVP > HEAC > PEG. Additionally, thermodynamic parameters substantiated this sequence and even suggested that these complexes remain stable up to 160 °C. Consequently, these polymers present a promising avenue for crafting novel materials for CO2 capture applications. Nonetheless, further research is warranted to optimize the design of these materials and assess their performance across various environmental conditions.

Cobalt-based Polymerized Porphyrinic Network for Visible-light-driven CO2 Reduction.

Visible-light-driven conversion of carbon dioxide to valuable compounds and fuels is an important but challenging task due to the inherent stability of the CO2 molecules. Herein, we report a series of cobalt-based polymerized porphyrinic network (PPN) photocatalysts for CO2 reduction with high activity. The introduction of organic groups results in the addition of more conjugated electrons to the networks, thereby altering the molecular orbital levels within the networks. This integration of functional groups effectively adjusts the levels of the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO). The PPN(Co)-NO2 exhibits outstanding performance, with a CO evolution rate of 12 268 µmol/g/h and 85.8% selectivity, surpassing most similar photocatalyst systems. The performance of PPN(Co)-NO2 is also excellent in terms of apparent quantum yield (AQY) for CO production (5.7% at 420 nm). Density functional theory (DFT) calculations, time-resolved photoluminescence (TRPL), and electrochemical tests reveal that the introduction of methyl and nitro groups leads to a narrower energy gap, facilitating a faster charge transfer. The coupling reaction in this study enables the formation of stable C-C bonds, enhancing the structural regulation, active site diversity, and stability of the catalysts for photocatalytic CO2 reduction. This work offers a facile strategy to develop reliable catalysts for efficient CO2 conversion.

Self-Assembly of Molecular Landers Equipped with Functional Moieties on the Surface: A Mini Review.

The bottom-up fabrication of supramolecular and self-assembly on various substrates has become an extremely relevant goal to achieve prospects in the development of nanodevices for electronic circuitry or sensors. One of the branches of this field is the self-assembly of functional molecular components driven through non-covalent interactions on the surfaces, such as van der Waals (vdW) interactions, hydrogen bonding (HB), electrostatic interactions, etc., allowing the controlled design of nanostructures that can satisfy the requirements of nanoengineering concepts. In this context, non-covalent interactions present opportunities that have been previously explored in several molecular systems adsorbed on surfaces, primarily due to their highly directional nature which facilitates the formation of well-ordered structures. Herein, we review a series of research works by combining STM (scanning tunneling microscopy) with theoretical calculations, to reveal the processes used in the area of self-assembly driven by molecule Landers equipped with functional groups on the metallic surfaces. Combining these processes is necessary for researchers to advance the self-assembly of supramolecular architectures driven by multiple non-covalent interactions on solid surfaces.

Complexes of Gold(III) with Hydrazones Derived from Pyridoxal: Stability, Structure, and Nature of UV-Vis Spectra.

Pyridoxal and pyridoxal 5'-phosphate are aldehyde forms of B6 vitamin that can easily be transformed into each other in the living organism. The presence of a phosphate group, however, provides the related compounds (e.g., hydrazones) with better solubility in water. In addition, the phosphate group may sometimes act as a binding center for metal ions. In particular, a phosphate group can be a strong ligand for a gold(III) ion, which is of interest for researchers for the anti-tumor and antimicrobial potential of gold(III). This paper aims to answer whether the phosphate group is involved in the complex formation between gold(III) and hydrazones derived from pyridoxal 5'-phosphate. The answer is negative, since the comparison of the stability constants determined for the gold(III) complexes with pyridoxal- and pyridoxal 5'-phosphate-derived hydrazones showed a negligible difference. In addition, quantum chemical calculations confirmed that the preferential coordination of two series of phosphorylated and non-phosphorylated hydrazones to gold(III) ion is similar. The preferential protonation modes for the gold(III) complexes were also determined using experimental and calculated data.

Quantitative Analogue Simulation of Planar Molecules.

Synthetic quantum systems provide a pathway for exploring the physics of complex quantum matter in a programmable fashion. This approach becomes particularly advantageous when it comes to systems that are thermodynamically unfavorable. By sculpting the potential landscape of Cu(111) surfaces with carbon monoxide quantum corrals in a cryogenic scanning tunneling microscope, we created analogue simulators of planar organic molecules, including antiaromatic and non-Kekulé species that are generally reactive or unstable. Spectroscopic imaging of such synthetic molecules reveals close replications of molecular orbitals obtained from ab initio calculations of the organic molecules. We further illustrate the quantitative nature of such analogue simulators by faithful extraction of bond orders and global aromaticity indices, which are otherwise technically daunting using real molecules. Our approach therefore sets the stage for new research frontiers pertaining to the quantum physics and chemistry of designer nanostructures.

Evolution of structural and electronic properties standardized description in rhenium disulfide at the bulk-monolayer transition.

The structural and electronic properties of ReS2 different forms - three-dimensional bulk and two-dimensional monolayer - were studied within density functional theory and pseudopotentials. A method for standardizing the description of bulk unit cells and "artificial" slab unit cells for DFT research has been proposed. The preference of this method for studying zone dispersion has been shown. The influence of the vacuum layer thickness on specified special high-symmetry points is discussed. Electron band dispersion in both classical 3D Brillouin zones and transition to 2D Brillouin zones in the proposed two-dimensional approach using the Niggli form of the unit cell was compared. The proposed two-dimensional approach is preferable for low-symmetry layered crystals such as ReS2. It was established that the bulk ReS2 is a direct gap semiconductor (band gap of 1.20 eV), with the direct transition lying in the X point of the first Brillouin zone, and it is in good agreement with published experimental data. The reduction in material dimension from bulk to monolayer was conducted with an increasing band gap up to 1.45 eV, with a moving direct transition towards the Brillouin zone center. The monolayer of ReS2 is a direct-gap semiconductor in a wide range of temperatures, excluding only a narrow range at low temperatures, where it comes as a quasi-direct gap semiconductor. The transition, situated directly in the Γ-point, lies 3.3 meV below the first direct transition located near this point. The electronic density of states of ReS2 in the bulk and monolayer cases of ReS2 were analyzed. The molecular orbitals were built for both types of ReS2 structures as well as the electron difference density maps. For all types of ReS2 structures, an analysis of populations according to Mulliken and Voronoi was carried out. All calculated data is discussed in the context of weak quantum confinement in the 2D case.

Computational prediction for designing novel ketonic derivatives as potential inhibitors for breast cancer: A trade-off between drug likeness and inhibition potency.

Unlike simple molecular screening, a combined hybrid computational methodology has been applied which includes quantum chemical methods, molecular docking, and molecular dynamics simulations to design some novel ketonic derivatives. The current study contains the derivatives of an experimental ligand which are designed as a trade-off between drug likeness and inhibition strength. We investigate the interaction of various newly designed ketonic compounds with the breast cancer receptor known as the Estrogen Receptor Alpha (ERα). The molecular structures of all newly designed ligands were studied quantum chemically in terms of their fully optimized structures, 3-D molecular orbital distributions, global chemical descriptors, molecular electrostatic potentials and energies of frontier molecular orbitals (FMOs). All ligands under study show good binding affinities with the ERα protein. The ligands CMR2 and CMR4 exhibit improved molecular docking interactions. The intermolecular interactions indicate that CMR4 demonstrates better hydrophobic and hydrogen bonding interactions with protein (ERα). Furthermore, molecular dynamics simulations were conducted on ligands and reference drugs interacting with the ERα protein over a time span of 120 nanoseconds. The molecular dynamics results are interpreted in terms of ligand-protein stability and flexible behaviour based on their respective values of RMSD, RMSF, H-bonds, the radius of gyration, and SASA graphs. To analyse ligand-protein interactions throughout the entire 120 ns trajectory, a more advanced MM/PBSA method is utilized, where six selected ligands (CMR1, CMR2, CMR3, CMR4, CMR5 and CMR9) illustrate promising results for inhibition of the ERα receptor as assessed through MM/BBSA analysis. The CMR9 has the highest MM/BBSA binding free energy (-14.46 kcal/mol). The ADMET analysis reveals that CMR4 has maximum intestinal absorption (6.68) and clearance rate (0.1). All the compounds are non-toxic and safe to use. These findings indicate the potential of involving different computational techniques to design the ligand structures and to study the ligand-protein interactions for better understanding and achieving more potent synthetic inhibitors for breast cancer.

Development of robust chiroptical systems through spirobifluorenes.

Chiroptical responses are valuable for the structural determination of dissymmetric molecules. However, the development of everyday applications based on chiroptical systems is yet to come. We have been earlier using axially chiral allenes for the construction of linear, cyclic, and cage-shaped molecules that present remarkable chiroptical responses. Additionally, we have developed chiral surfaces through upstanding chiral architectures. Since the goal is to obtain robust chiroptical materials, more recently we have been studying spirobifluorenes (SBFs), a well-established building block in optoelectronic applications. After theoretical and experimental demonstration, the suitability of chiral SBFs for the development of robust chiroptical systems was certified by the construction all-carbon double helices, flexible shape-persistent macrocycles, chiral frameworks for surface functionalization, and structures featuring helical or spiroconjugated molecular orbitals. Here, we give an overview of our contribution to these matters.

Molecular design of D-π-A-π-D small molecule donor materials with narrow energy gap for organic solar cells applications.

CONTEXT: Developing novel materials present a great challenge to improve the photovoltaic performance of organic solar cells (OSCs). In this paper, we designed a series of the donor-π bridge-acceptor-π bridge-donor (D-π-A-π-D) structure molecules. These molecules consist of diketopyrrolopyrrole (DPP) moiety as core, 9-hexyl-carbazole moiety as terminal groups, and different planar electron-rich aromatic groups as π-bridges. The density functional theory (DFT) and time-dependent DFT (TD-DFT) computations showed that the frontier molecular orbital (FMO) energy levels, energy gaps, electron-driving forces (ΔEL-L), open-circuit voltage (Voc), fill factor (FF), reorganization energy (λ), exciton binding energy (Eb), and absorption spectra of the designed molecules can be effectively adjusted by the introduction of different π-bridges. The designed molecules have narrow energy gap and strong absorption spectra, which are beneficial for improving the photoelectric conversion efficiency of organic solar cells. In addition, the designed molecules possess large ΔEL-L, large Voc, and FF values and low Eb when the typical fullerene derivatives are used as acceptors. The FMO energy levels of the designed molecules can provide match well with the typical fullerene acceptors PC61BM, bisPC61BM, and PC71BM. Our results suggest that the designed molecules are expected to be promising donor materials for OSCs. METHODS: All DFT and TD-DFT calculations were carried out using the Gaussian 09 code. The computational technique chosen was the hybrid functional B3LYP and the 6-31G(d,p) basis set. The benzene and chloroform solvent effects have been considered using the polarized continuum model (PCM) at the TD-DFT level. The simulated absorption spectra of designed molecules were plotted by using the GaussSum 1.0 program.

Molecular modeling of [VO(L1-4)(R)] complexes (R = bipyridine, phenanthroline): DFT study of antioxidant activity, DNA binding and evaluation of electron-donating and -withdrawing substituent groups.

A DFT (density functional theory) study was conducted with eight oxovanadium complexes (C1 - C8) of general formula [VO(L1-4)(R)] (R = bipyridine, phenanthroline; L1-4 = group of ligands derived from dithiocarbamate). The obtained geometries showed a good correlation with the experimental structures. Molecular orbital analysis revealed that the contribution of the L-ligand in the SOMO (single-occupied molecular orbital) of the complexes correlated with the experimental antioxidant activity (IC50), while the contribution of the R-ligand to the LUMO (lowest unoccupied molecular orbital) of the complexes correlated with the experimental complex-DNA interaction (Kb). It has been identified that the presence of an electron-donating substituent group (such as -NH2) in the C5 - C6 structures should enhance these complexes' antioxidant and DNA interaction activities.

Theoretical, in Vitro Antiproliferative, and in Silico Molecular Docking and Pharmacokinetics Studies of Heteroleptic Nickel(II) and Copper(II) Complexes of Thiosemicarbazone-Based Ligands and Pefloxacin.

Twelve new heteroleptic nickel(II) and copper(II) complexes of the type [M(L1-6 )(Pfx)2 ] (1-12), where L1-6 =2-benzylidenehydrazinecarbothioamide (L1 ), 2-benzylidene-N-methylhydrazinecarbothioamide (L2 ), 2-benzylidene-N-phenylhydrazinecarbothioamide (L3 ), 2-(4-methylbenzylidene)hydrazinecarbothioamide (L4 ), 2-(4-methylbenzylidene)-N-methylhydrazinecarbothioamide (L5 ) and 2-(4-methylbenzylidene)-N-phenylhydrazinecarbothioamide (L6 ), Pfx=pefloxacin and M=Ni(II) or Cu(II) have been synthesised, and their structures were confirmed by different spectral techniques. The spectral data and density functional theory (DFT) calculations supported the bonding of pefloxacin drug molecule via one of the carboxylate oxygen atoms and the pyridone oxygen atom, and the thiosemicarbazone ligand via the imine nitrogen and the thione sulfur atoms with the metal(II) ion, forming distorted octahedral geometry. In vitro antiproliferative activity of the synthesized complexes was evaluated against three human breast cancer (T47D, estrogen negative (MDA-MB-231) and estrogen positive (MCF-7)) as well as non-tumorigenic human breast epithelial (MCF-10a) cell lines, which showed the higher activity for the copper(II) complexes. The interaction of the synthesized complexes with an oncogenic protein H-ras (121 p) was explored by in silico molecular docking studies. Further, in silico pharmacokinetics and ADMET parameters were also analysed to predict the drug-likeness as well as non-toxic and non-carcinogenic behavior, and safe oral administration of the complexes.

1,3-Butadiynamides the Ethynylogous Ynamides: Synthesis, Properties and Applications in Heterocyclic Chemistry.

1,3-butadiynamides-the ethynylogous variants of ynamides-receive considerable attention as precursors of complex molecular scaffolds for organic and heterocyclic chemistry. The synthetic potential of these C4-building blocks reveals itself in sophisticated transition-metal catalyzed annulation reactions and in metal-free or silver-mediated HDDA (Hexa-dehydro-Diels-Alder) cycloadditions. 1,3-Butadiynamides also gain significance as optoelectronic materials and in less explored views on their unique helical twisted frontier molecular orbitals (Hel-FMOs). The present account summarizes different methodologies for the synthesis of 1,3-butadiynamides followed by the description of their molecular structure and electronic properties. Finally, the surprisingly rich chemistry of 1,3-butadiynamides as versatile C4-building blocks in heterocyclic chemistry is reviewed by compiling their exciting reactivity, specificity and opportunities for organic synthesis. Besides chemical transformations and use in synthesis, a focus is set on the mechanistic understanding of the chemistry of 1,3-butadiynamides-suggesting that 1,3-butadiynamides are not just simple alkynes. These ethynylogous variants of ynamides have their own molecular character and chemical reactivity and reflect a new class of remarkably useful compounds.

Molecular-Orbital Delocalization Enhances Charge Transfer in π-Conjugated Organic Semiconductors.

π-Conjugated organic semiconductors are promising materials for surface-enhanced Raman scattering (SERS)-active substrates based on the tunability of electronic structures and molecular orbitals. Herein, we investigate the effect of the temperature-mediated resonance-structure transitions of poly(3,4-ethylenedioxythiophene) (PEDOT) in poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT : PSS) films on the interactions between substrate and probe molecules, thereby affecting the SERS activity. Absorption spectroscopy and density functional theory calculations show that this effect occurs mainly due to delocalization of the electron distribution in molecular orbitals, effectively promoting the charge transfer between the semiconductor and probe molecules. In this work, we investigate for the first time the effect of electron delocalization in molecular orbitals on SERS activity, which will provide new design ideas for the development of highly sensitive SERS substrates.

Geometry and UV-Vis Spectra of Au3+ Complexes with Hydrazones Derived from Pyridoxal 5'-Phosphate: A DFT Study.

Gold(III) complexes with different ligands can provide researchers with a measure against pathogenic microorganisms with antibiotic resistance. We reported in our previous paper that the UV-Vis spectra of different protonated species of complexes formed by gold(III) and five hydrazones derived from pyridoxal 5'-phosphate are similar to each other and to the spectra of free protonated hydrazones. The present paper focuses on the reasons of the noted similarity in electron absorption spectra. The geometry of different protonated species of complexes of gold(III) and hydrazones (15 structures in total) was optimized using the density functional theory (DFT). The coordination polyhedron of gold(III) bond critical points were further studied to identify the symmetry of the gold coordination sphere and the type of interactions that hold the complex together. The UV-Vis spectra were calculated using TD DFT methods. The molecular orbitals were analyzed to interpret the calculated spectra.

Orbital Nature of Carboionic Monoradicals Made from Diradicals.

The electronic, optical, and solid state properties of a series of monoradicals, anions and cations obtained from starting neutral diradicals have been studied. Diradicals based on s-indacene and indenoacenes, with benzothiophenes fused and in different orientations, feature a varying degree of diradical character in the neutral state, which is here related with the properties of the radical redox forms. The analysis of their optical features in the polymethine monoradicals has been carried out in the framework of the molecular orbital and valence bond theories. Electronic UV-Vis-NIR absorption, X-ray solid-state diffraction and quantum chemical calculations have been carried out. Studies of the different positive-/negative-charged species, both residing in the same skeletal π-conjugated backbone, are rare for organic molecules. The key factor for the dual stabilization is the presence of the starting diradical character that enables to indistinctively accommodate a pseudo-hole and a pseudo-electron defect with certainly small reorganization energies for ambipolar charge transport.

Ca2+-Triggered Coelenterazine-Binding Protein Renilla: Expected and Unexpected Features.

Ca2+-triggered coelenterazine-binding protein (CBP) is a natural form of the luciferase substrate involved in the Renilla bioluminescence reaction. It is a stable complex of coelenterazine and apoprotein that, unlike coelenterazine, is soluble and stable in an aquatic environment and yields a significantly higher bioluminescent signal. This makes CBP a convenient substrate for luciferase-based in vitro assay. In search of a similar substrate form for the luciferase NanoLuc, a furimazine-apoCBP complex was prepared and verified against furimazine, coelenterazine, and CBP. Furimazine-apoCBP is relatively stable in solution and in a frozen or lyophilized state, but as distinct from CBP, its bioluminescence reaction with NanoLuc is independent of Ca2+. NanoLuc turned out to utilize all the four substrates under consideration. The pairs of CBP-NanoLuc and coelenterazine-NanoLuc generate bioluminescence with close efficiency. As for furimazine-apoCBP-NanoLuc pair, the efficiency with which it generates bioluminescence is almost twice lower than that of the furimazine-NanoLuc. The integral signal of the CBP-NanoLuc pair is only 22% lower than that of furimazine-NanoLuc. Thus, along with furimazine as the most effective NanoLuc substrate, CBP can also be recommended as a substrate for in vitro analytical application in view of its water solubility, stability, and Ca2+-triggering "character".