Computational Chemistry: Prediction of Compound Accessibility of Targeted Synthesized Compounds

INTRODUCTION

In the present work, a series of novel pyridine carboxamides 3(a-h) were synthesized and screened with antibacterial activity. This research explores the application of Density Functional Theory (DFT) in studying biological systems at the quantum mechanical level, particularly in the context of drug design. DFT offers a streamlined approach to quantum mechanical calculations, making it indispensable in various scientific fields, and for its exceptional accuracy, reduced computational time, and cost-effectiveness has become a pivotal tool in computational chemistry. This research work highlights the integration of DFT studies with POM analyses, which effectively identify pharmacophoric sites. Moreover, the research incorporates in silico pharmacokinetics analyses to assess the pharmacokinetic properties of synthesized compounds. The paper focused on a series of compounds previously reported, aiming to provide a comprehensive understanding of their electronic structure, pharmacophoric features, and potential as drug candidates. This study not only contributes to the evolving field of computational chemistry but also holds implications for advancing drug design processes by combining theoretical insights with practical analyses.

METHODS

The compounds 3(a-h) were subjected to Density Functional Theory (DFT) computations using the B3LYP/6-31G(d) basis set to get optimized geometric structures. GaussViewis used to display the contributions of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO). The determination of energy gaps was conducted using Gaussian 09W. The pharmacokinetic profiles were evaluated using existing techniques such as Osiris, Petra, and Molinspiration, as well as a novel platform called POM Analyse.

RESULTS

The computational studies DFT, POM and in silico pharmacokinetics studies revealed that the studied compounds are biologically active, non-toxic, non-carcinogenic in nature and may be utilized as drug candidates.

CONCLUSION

Density functional theory (DFT) investigations emphasize the exceptional stability of complex 3d, which possesses the biggest energy gap and the lowest softness. In contrast, compound 3h demonstrates poorer stability among the tested compounds, characterized by the lowest energy gap and the highest softness values. These findings are further substantiated by absolute energy calculations. The negligible energy difference in compound 3h indicates an increased transfer of electric charge within the molecule, which is associated with its enhanced biological effectiveness. The drug-likeness of the compounds is confirmed by POM and in silico pharmacokinetics investigations, with compound 3h being identified as the most biologically active among the investigated compounds.

Efficiency Conceptualization Model: A Theoretical Method for Predicting the Turnover of Catalysts

In recent times, the theoretical prediction of catalytic efficiency is of utmost urgency. With the advent of density functional theory (DFT), reliable computations can delineate a quantitative aspect of the study. To this state-of-the art approach, valuable incorporation would be a tool that can acknowledge the efficiency of a catalyst. In the current work, we developed the efficiency conceptualization model (ECM) method that utilizes the quantum mechanical tool to achieve efficiency in terms of turnover frequency (TOF). Twenty-six experimentally designed transition metal (TM) water oxidation catalysts were chosen under similar experimental conditions of temperature, pressure, and pH to execute the same. The computations conclude that the Fe based [Fe(OTf)2(Me2Pytacn)] (MWOC-17) is a highly active catalyst and, therefore, can endure for more time in the catalytic cycle. Our results conclude that the Ir-based catalysts [Cp∗Ir(κ2-N,O)X] with MWOC-23: X = Cl; and MWOC-24: X = NO3 report the highest computed turnover numbers (TONs), Γ0computed TON of 406 and 490 against the highest experimental TONs,  Γ0 experimental TON of 2000 and 1200 respectively, whereas the Co-based [Co(12-TMC)]2+ (MWOC-19) has the lowest TONs (Γ0computed TON = 19,  Γ0 experimental TON= 16) among the chosen catalysts and thereby successful in corroborating the previous experimental results.

Prediction of Feasibility of Polaronic OER on (110) Surface of Rutile TiO2

The polaronic effects at the atomic level hold paramount significance for advancing the efficacy of transition metal oxides in applications pertinent to renewable energy. The lattice-distortion mediated localization of photoexcited carriers in the form of polarons plays a pivotal role in the photocatalysis. This investigation focuses on rutile TiO2, an important material extensively explored for solar energy conversion in artificial photosynthesis, specifically targeting the generation of green H2 through photoelectrochemical (PEC) H2O splitting. By employing Hubbard-U corrected and hybrid density functional theory (DFT) methods, we systematically probe the polaronic effects in the catalysis of oxygen evolution reaction (OER) on the (110) surface of rutile TiO2. Theoretical understanding of polarons within the surface, coupled with simulations of OER at distinct titanium (Ti) and oxygen (O) active sites, reveals diverse polaron formation energies within the lattice sites with strong preference for bulk and surface bridge (Ob) oxygen sites. Moreover, we provide the evidence for the facilitative role of polarons in OER. We find that hole polarons situated at the equatorial oxygen sites near the Ti-active site, along with bridge site hole polarons distal from the Ob active site yield a small reduction in OER overpotential by ~0.06 eV and ~0.12 eV, respectively. However, subsurface, equatorial, and bridge site hole polarons significantly reduce the Ti-active site OER overpotential by ~0.4 eV through the peroxo-type oxygen pathway. We also observe that the presence of hole polarons stabilizes the *OH, *O, and *OOH intermediate species compared to the scenario without hole polarons. Overall, this study provides a detailed mechanistic insight into polaron-mediated OER, offering a promising avenue for improving the catalytic activity of transition metal oxide-based photocatalysts catering to renewable energy requisites.

Unlocking the secrets of doxepin hydrochloride's crystal structure: Insights from high-quality powder diffraction analysis

Doxepin hydrochloride, a versatile pharmaceutical compound, has been the subject of extensive research aimed at elucidating its crystal structure and solid-state characteristics. In this manuscript, we explore the significance of high-quality powder diffraction data in unveiling the intricate details of doxepin hydrochloride's crystal lattice. By examining the refined atom coordinates, density functional theory (DFT) optimization, and intermolecular interactions, we gain valuable insights into its structural conformation. This knowledge highlights the importance of precise crystallographic data in advancing our understanding of complex compounds and their pharmaceutical applications.

Understanding the surrounding effects on Raman optical activity signatures of a chiral cage system: Cryptophane-PP-111

Cryptophane molecules are cage-like structures consisting in two hemispheres, each made of three benzene rings. These hemispheres are bound together with three O(CH2)nOlinkers of various lengths giving rise to a plethora of cryptophane derivatives. Moreover, they are able to encapsulate neutral guests: CH2Cl2, CHCl3, …; and charged species: Cs+, Tl+, …. Finally, they exhibit chiroptical properties thanks to the anti arrangement of the linkers between the hemispheres. This work focuses on the Raman optical activity (ROA) signatures of Cryptophane-111 (n=1 for each linker). More specifically, we aim at simulating accurately its ROA spectra with and without a xenon atom inside its cavity. Experimental data (Buffeteau et al., 2017) have already demonstrated the effect of the encapsulation in the low-wavenumbers region. To generate the initial structures, we rely on the novel Conformer-Rotamer Ensemble Sampling Tool (CREST) program, developed by S. Grimme and co-workers. This is required due to the flexibility provided by the linkers. The CREST algorithm seems promising and has already been used to sample the potential energy surface (PES) of target systems before the simulation of their vibrational spectroscopies (Eikås et al., 2022). We observe large similarities between the two sets of conformers (one with and one without Xe encapsulated), demonstrating the robustness of the CREST algorithm. For corresponding structures, the presence of xenon pushed the two hemispheres slightly further apart. After optimization at the DFT level, only one unique conformer has a Boltzmann population ratio greater than 1%, pointing out the relative rigidity of the cage. Based on this unique conformer, our simulations are in good agreement with the experimental data. Regarding xenon encapsulation, the (experimental and theoretical) ROA signatures at low wavenumbers are impacted: slight shifts in wavenumbers are observed as well as a decrease in relative ROA intensity for bands around 150 cm-1. The wavenumber shifts were very well reproduced by our simulations, but the experimental decrease in the ROA intensity was unfortunately not reproduced.

Advancing Gold Redox Catalysis: Mechanistic Insights, Nucleophilicity-Guided Transmetalation, and Predictive Frameworks for the Oxidation of Aryl Gold(I) Complexes

Gold redox catalysis, often facilitated by hypervalent iodine(III) reagents, offers unique reactivity but its progress is mainly hindered by an incomplete mechanistic understanding. In this study, we investigated the reaction between the gold(I) complexes [(aryl)Au(PR3 )] and the hypervalent iodine(III) reagent PhICl2 , both experimentally and computationally and provided an explanation for the formation of divergent products as the ligands bonded to the gold(I) center change. We tackled this essential question by uncovering an intriguing transmetalation mechanism that takes place between gold(I) and gold(III) complexes. We found that the ease of transmetalation is governed by the nucleophilicity of the gold(I) complex, [(aryl)Au(PR3 )], with greater nucleophilicity leading to a lower activation energy barrier. Remarkably, transmetalation is mainly controlled by a single orbital - the gold dx 2 -y 2 orbital. This orbital also has a profound influence on the reactivity of the oxidative addition step. In this way, the fundamental mechanistic basis of divergent outcomes in reactions of aryl gold(I) complexes with PhICl2 was established and these observations are reconciled from first principles. The theoretical model developed in this study provides a conceptual framework for anticipating the outcomes of reactions involving [(aryl)Au(PR3 )] with PhICl2 , thereby establishing a solid foundation for further advancements in this field.

Theoretical Study on Spectrum and Luminescence Mechanism of Cy5.5 and Cy7.5 Dye Based on Density Functional Theory (DFT)

Cy5.5 and 7.5 are the most commonly used NIR 2-region fluoresceins, which have good luminescence properties and important biomedical tracer applications. In this paper, their molecular non-covalent interactions, UV-Vis absorption spectra, main bond lengths, electrostatic potential distributions, frontier molecular orbitals (HOMO and LUMO) and energy gaps were calculated by density functional theory (DFT). We found that the differences in the luminescence properties and energy gaps of Cy5.5 and Cy7.5 molecules may be caused by the length of the conjugated chains between the two aromatic rings in the molecule. By calculating the relevant molecular characteristics, this paper can provide ideas and theoretical basis for the relevant modification and application, as well as the development of new fluorescent dyes.

The performance and mechanism of tetracycline and ammonium removal by Pseudomonas sp. DX-21

To remove ammonium and tetracycline (TC) from wastewater, a new strain, DX-21, was isolated and exhibited simultaneous removal ability. The performance of DX-21 in TC removal, its removal mechanism, and the potential toxicities of the degradation products were investigated with genomics, mass spectrometry, density functional theory calculations, quantitative structure-activity relationship analyses, and Escherichia coli exposure experiments. DX-21 exhibited removal of ammonium (9.64 mg·L-1·h-1) via assimilation, and TC removal (0.85 mg·L-1·h-1) primarily occurred through cell surface bio-adsorption and biodegradation. Among the 12 identified degradation products, the majority exhibited lower toxicities than TC. Moreover, potential degradation pathways were proposed, including hydroxylation and deamination. Furthermore, DX-21 possessed TC resistance genes, various oxygenases and peroxidases that could potentially contribute to TC degradation. DX-21 colonized activated sludge and significantly enhanced the biodegradation of TC. Therefore, DX-21 showed potential for treating wastewater containing both ammonium and TC.

Insight into the role of SO2 on selenium conversion during adsorption by CaO: Theoretical calculation and experimental study

SO₂ can noticeably impact the control of high toxic selenium emissions from flue gas by CaO. Surprisingly, our experiments showed that under certain conditions, SO₂ can promote selenium capture by CaO, rather than hinder it. To elucidate the underlying mechanism, a combination of theoretical calculations and experiments was conducted. Thermodynamic equilibrium analysis revealed that gaseous SO₂ and solid Ca-S reaction products can promote SeO₂ converting to SeO/Se⁰. The Ca-S products facilitated greater SeO₂ conversion compared to SO₂. Experimental results demonstrated that selenium adsorption capacity of incompletely sulfurized CaO (CaO with pre-adsorbed SO₂) was higher than that of completely sulfurized CaO (Ca-S products), highlighting the importance of adsorption sites of CaO. Density functional theory calculations showed that the pre-adsorbed SO₂ hardly affected selenium adsorption energy on the SO₂/CaO surface, while completely sulfurized CaO had low selenium adsorption energy, explaining the experimental phenomenon and proving necessary of CaO. Additionally, SeO/Se⁰ had higher adsorption energy on CaO than SeO₂. Overall, the promotion of SO₂ on selenium adsorption was primarily affected by two factors: 1) sulfur facilitating SeO₂ conversion to SeO/Se⁰ which can be adsorbed more easily by CaO; 2) sufficient adsorption sites on CaO surface existing for SeO/Se⁰ adsorption, despite co-adsorption with sulfur.

Imidazole-amino acids. Conformational switch under tautomer and pH change

Replacement of the main chain peptide bond by imidazole ring seems to be a promising tool for the peptide-based drug design, due to the specific prototropic tautomeric as well as amphoteric properties. In this study, we present that both tautomer and pH change can cause a conformational switch of the studied residues of alanine (1-4) and dehydroalanine (5-8) with the C-terminal peptide group replaced by imidazole. The DFT methods are applied and an environment of increasing polarity is simulated. The conformational maps (Ramachandram diagrams) are presented and the stability of possible conformations is discussed. The neutral forms, tautomers τ (1) and π (2), adapt the conformations αRτ (φ, ψ = - 75°, - 114°) and C7eq (φ, ψ = - 75°, 66°), respectively. Their torsion angles ψ differ by about 180°, which results in a considerable impact on the peptide chain conformation. The cation form (3) adapts both these conformations, whereas the anion analogue (4) prefers the conformations C5 (φ, ψ = - 165°, - 178°) and β2 (φ, ψ ~ - 165°, - 3°). Dehydroamino acid analogues, the tautomers τ (5) and π (6) as well as the anion form (8), have a strong tendency toward the conformations β2 (φ, ψ = - 179°, 0°) and C5 (φ, ψ = - 180°, 180°). The preferences of the protonated imidazolium form (7) depend on the environment. The imidazole ring, acting as a donor or acceptor of the hydrogen bonds created within the studied residues, has a profound effect on the type of conformation.

Computational Studies Followed by Effect of Solvent Polarity and Salts on HOMO-LUMO Gap of 7-Hydroxy Coumarine Notabally Reflected by Absorption and Emission Spectra

7-Hydroxycoumarin's FT-IR solid phase spectra were observed at 4000-400 cm^-1. The spectra were analyzed in aspects of significant approaches. DFT was used to optimize the structure of the compound and its structural properties. The molecular properties were also determined by the HF/3-21G level. The bond lengths and bond angles were obtained by the computational study of the optimized geometry. The vibrational frequencies were determined in all these approaches, which were then matched to experimental frequencies, yielding an excellent agreement between measured and estimated frequency ranges. The UV-visible spectrum of 7HC was obtained and the electronic characteristics HOMO and LUMO energies were monitored by the time-dependent TD-DFT method. The spectral behavior of 7-Hydroxycoumarin was studied using fluorescence spectroscopy in a wide range of polar and non-polar solvents. Solvatochromic effect was observed in both the fluorescence and absorption spectra. The structural properties, energies, IR intensities, absorption wavelengths, and harmonic vibrational frequencies were compared with the obtainable experimental information of the molecule.

Substituent Orchestration in Dimethylquinoxaline Derivatives: A Tool for Fishing Out Appropriate CDK5 Inhibitors as Potential Therapeutics for Alzheimer's

A set of new heterocyclic analogs (Compounds I-IX), comprising of 6,7 dimethyl Quinoxalines were found to be active against the receptor GSK3β (Compounds IV-V) (Chem. Biodiversity 2021, 18, e2100364). In an effort to modulate effective CDK5 inhibitors herein our hypothesis underpinned to fish out an appropriate derivative from the same quinoxaline series, as these two targets GSK3β and CDK5 shared structural resemblance with each other. Aligned to the goal we have synthesized Compounds I-IX, characterized them using a combination of spectroscopic techniques and evaluated their activities against CDK5. Our analysis reflected that the adjacently located alkoxy/hydroxy functionality derivatives namely Compounds III and VI, to be the most potent (micromolar) amongst others in the series, backed by Density Functional Theory (DFT) calculations and molecular modelling studies. Also, the efficacy of the Compounds I-IX, were monitored in few other members of the CMGC family namely DYRK1A, CLK1and CK1δ that have been known to be directly involved in hyperphosphorylation of Tau. But unfortunately in none of the targets, our quinoxaline series were active. In a nut shell further optimisation of these intelligent nucleus, would not only lead to the discovery of novel pharmacophores, but also marked selectivity against a pool of kinases, thereby implementing a distinct roadmap towards the design of potential therapeutics against Alzheimer's.

Exploring electronic, structural and dynamics parameters of phenylbenzothiazole complexes with Mn2+, Cu2+ and Zn2+ for designing new magnetic resonance imaging (MRI) probes: congruence between computation and spectroscopic data

Cancer is one of the leading causes of human death worldwide, being one of the most serious problems faced by mankind. For the diagnosis, Magnetic Resonance Imaging (MRI), through effective contrast agents (Cas), has greatly helped in the diagnosis at the initial stages. However, it is necessary to include new compounds more effective and selective for cancer diagnosis. The complexes with Mn²⁺, Cu²⁺ and Zn²⁺ have received great attention due to their applications as CAs for MRI. Those materials can shorten the T₂ and T₂* transverse relaxation times. Thus, the representative structures for hyperfine coupling constants (HFCCs) were selected from docking results by frequency of occupancy calculations. From the Multivariate Analysis to obtain the PCA graphs in the choice of a representative conformations. it is possible to notice that the variable energy does not present a high correlation with the other variables, and structural factors, such as the spatial positions of the metal atoms, seem to be important in the reactivity of the complexes. Structural factors, such as the spatial positions of the metal atoms, seem to be important in the reactivity of the complexes. Theoretical findings suggest that the compounds are capable of increasing the A_iso values of the water molecules, but the complex [Zn(H₂O)(NNO)] shows a greater influence, being more sensitive to the Electron paramagnetic resonance parameters than the complexes [CuCl(H₂O)NNO] and [MnCl₂(H₂O)(NNO)] with the explicit solvent and the enzyme. MRI contrast agents have generated various problems due to their high toxicity. In this perspective, this compound may be a promising alternative for transporting the CAs into diseased tissue.Communicated by Ramaswamy H. Sarma.

Quantum Chemical Analysis of the Corrosion Inhibition Potential by Aliphatic Amines

Destructive corrosion processes lead to the loss of primary mechanical properties of metal construction materials, which generates additional costs during their maintenance connected with repairs and protection. The effectiveness of corrosion inhibitors can be determined by using many methods, in particular quantum chemical modeling. The subject of the theoretical analyses presented in this work involves the anticorrosion properties of amines with various chemical structures. Evaluation of the corrosion inhibition properties of selected amines was performed on the basis of the HOMO-LUMO energy gap, dipole moment (µ), electronegativity (χ) determined as a result of the energy of the highest occupied molecular orbital (HOMO) and the energy of the lowest unoccupied molecular orbital (LUMO). Moreover, the HSAB (Hard and Soft Acids and Bases) theory was used to explain the reactivity of the analyzed amines, while the Mulliken population analysis was used to determine their electrostatic interactions with the surface of protected metal. The obtained results indicate that the protonation reaction of aliphatic amines leads to a change in the nature of the formation of a coordination bond with the surface of the protected metal. In turn, the quantum chemical calculations showed that the protonation reaction of aliphatic amines leads to a decrease in their corrosion inhibition efficiency. Most of the analyzed parameters indicated that tertiary amines are characterized by the highest corrosion inhibition efficiency.

Nitrogen-Containing Gas Sensing Properties of 2-D Ti2N and Its Derivative Nanosheets: Electronic Structures Insight

In this work, the potentials of two-dimensional Ti2N and its derivative nanosheets Ti2NT2(T=O, F, OH) for some harmful nitrogen-containing gas (NCG) adsorption and sensing applications have been unveiled based on the quantum-mechanical Density Functional Theory calculations. It is found that the interactions between pure Ti2N and NCGs (including NO, NO2, and NH3 in this study) are very strong, in which NO and NO2 can even be dissociated, and this would poison the substrate of Ti2N monolayer and affect the stability of the sensing material. For the monolayer of Ti2NT2(T=O, F, OH) that is terminated by functional groups on surface, the adsorption energies of NCGs are greatly reduced, and a large amount of charges are transferred to the functional group, which is beneficial to the reversibility of the sensing material. The significant changes in work function imply the good sensitivity of the above mentioned materials. In addition, the fast response time further consolidates the prospect of two-dimensional Ti2NT2 as efficient NCGs' sensing materials. This theoretical study would supply physical insight into the NCGs' sensing mechanism of Ti2N based nanosheets and help experimentalists to design better 2-D materials for gas adsorption or sensing applications.

Identification of photodegradation product of organophosphorus pesticides and elucidation of transformation mechanism under simulated sunlight irradiation

Organophosphorus pesticides (OPs) are posing great threat to the environment and human health, due to their overuse and persistence in the environment. Photolysis has been established as an effective method to degrade OPs. The influence of pH value, the initial concentration of pesticides and the light source on the photolysis of two OPs, including chlorpyrifos and dimethoate, was investigated. The optimal reaction condition for OPs degradation was under pH 9, with xenon lamp as the light source, in which the photodegradation efficiencies of chlorpyrifos and dimethoate (500 mg/L) were 75.12% and 94.31%, respectively. The photodegradation products of chlorpyrifos and dimethoate were identified by GC-MS. Also, density functional theory (DFT) calculations were used to characterize the molecular properties of chlorpyrifos and dimethoate, as well as predicting potential photolysis reactions. Photodegradation mechanisms of chlorpyrifos and dimethoate were proposed, in which 3,5,6-trichloropyridinol (TCP), O,O-diethyl thiophosphate (DETP), 2,3,5-Trichloro-6-methoxypyridine (TMP) and O,O,S-trimethyl phosphorothioate were identified as the main products of chlorpyrifos degradation. Omethoate, O,O,S-trimethyl thiophosphorothioate, N-methyl-2-sulfanylacetamide, O,O,O-trimethyl thiophosphate, O,O,S-trimethylphosphorothiate, and O,O,O-trimethyl phosphoric ester as the main photodegradation products for dimethoate. The main degradation mechanisms included ring opening, cleavage, oxidation and demethylation. This work demonstrated the feasibility of combining chemical analysis with quantum chemical calculation in unraveling degradation mechanisms of OPs. Also, it is of great significance for evaluating the environmental fate of OPs in aquatic system and further environmental risk assessment.

Immobilization of unmodified aminoanthraquinone derivatives onto silica gel surface for solid-phase extraction and pre-concentration of Pb(II)

In this project, silica gel chemically bonded with derivatives of aminoanthraquinone were synthesized and characterized. Adsorbents 1,8-aminoanthraquinone-3-aminopropylsilica (SL1), 2-aminoanthraquinone-3-aminopropylsilica (SL2) and 1-aminoanthraquinone-3-aminopropylsilica (SL3) were produced and tested to adsorb heavy metal solutions including Pb(II) Cu(II) Zn(II) Cd(II) and Co(II). The concentrations of the adsorbed heavy metals solution were calculated by atomic adsorption spectrophotometry employing a batch method. The results showed that speed at 200 rpm for 30 min with pH 9 is the optimum condition for heavy metal adsorption. The result also indicated that adsorbent SL3 is the best adsorbent for Pb(II) at 82.5%, and the relative standard deviation (R.S.D.) was lower than 6%. The method detection limit was 1.1 µg L^-1 for Pb²⁺. In addition, Density Functional Theory (DFT) calculation results suggested that the adsorbent sensor formed stable complexes with Pb(II) through a large number of cation-dipole interactions. The method was also applied with satisfactory results to the pre-concentration of trace Pb(II) in environmental samples.

Roles of noble metals (M = Ag, Au, Pd, Pt and Rh) on CeO2 in enhancing activity toward soot oxidation: Active oxygen species and DFT calculations

The effects of noble metal (M = Ag, Au, Pd, Pt, and Rh) on CeO₂ in enhancing the activity toward soot oxidation were studied through experimental methods and density functional theory (DFT) calculations. Each noble metal (3 mol.%) was supported on CeO₂ (M/CeO₂) and the properties of the catalysts were verified by XRD, HRTEM, N₂ physisorption, CO chemisorption, XPS, and H₂-TPR results. The noble metal was highly dispersed over CeO₂, except for Au due to the sintering of Au, and the reducibility of the catalysts was greatly improved according to degree of the interaction between each noble metal and CeO₂. The activities of M/CeO₂ catalysts for soot oxidation were better than that of CeO₂, and followed the order Rh/CeO₂ > Ag/CeO₂ > Pt/CeO₂ > Au/CeO₂ > Pd/CeO₂ > CeO₂. Moreover, our DFT calculations showed that vacancy formation energy was gradually lowered in the following order: CeO₂ > Pd₄/CeO₂ > Pt₄/CeO₂ > Au₄/CeO₂ = Ag₄/CeO₂ > Rh₄/CeO₂, which was similar order with experimental activity. In addition, the electronic states of the p and f orbitals of CeO₂ were studied to compare with the occupied Ce 4f electrons, which affect the redox property. Rh/CeO₂ and Ag/CeO₂ showed the improved soot oxidation activity, with an enhanced ability to generate oxygen vacancy formation and oxygen adsorption and increased electron transfer. Consequently, the experimental and DFT calculation results revealed the roles of noble metals on ceria with respect to catalytic activity.

Unravelling the molecular effect of ocellatin-1, F1, K1 and S1, the frog-skin antimicrobial peptides to enhance its therapeutics-quantum and molecular mechanical approaches

Ocellatin AMPs (antimicrobial peptides) are considered to be promising alternative therapeutics to conventional antibiotics. Three-dimensional (3D) structures of ocellatin-F1 with 25 residues have been reported to be potent in terms of bacterial membrane permeability. To investigate the influence of similar ocellatin peptides with 25 residues pertaining to antimicrobial effect, ocellatin-1, K1 and S1 peptides were modelled with ocellatin-F1 as template. Comparative analyses between these peptides were carried out, using computational approaches. From the results of in silico toxicity profile, all peptides were found to be non-toxic with no haemolytic activity. Further sequence analysis, net charge, hydrophobicity and hydrophobic moment revealed the membrane permeable efficacy of ocellatin-1 peptide. Besides, the investigation of peptide electronic structures through density functional theory and quantum chemical (HOMO and LUMO) calculations predicted ocellatin-1 to be a suitable peptide, which can be used as a scaffold for therapeutics. Furthermore, the determination of structural contours such as RMSD, RMSF and Rg through trajectory analysis revealed that ocellatin-1 exhibited strong structural stability. In addition, the trajectory analysis of elements of secondary structure illustrated the alpha helical conformations to be retained in all peptides, except ocellatin-1. On the aforementioned grounds, ocellatin-1 was found to possess the important role of peptide penetration of the bacterial membrane. This study becomes significant, since it is the first time where the structural importance of ocellatin peptides were explored in detail and the therapeutic potential of ocellatin-1 as a peptide-based antimicrobial drug have been theoretically revealed.

A Theoretical Study of the Occupied and Unoccupied Electronic Structure of High- and Intermediate-Spin Transition Metal Phthalocyaninato (Pc) Complexes: VPc, CrPc, MnPc, and FePc

The structural, electronic, and spectroscopic properties of high- and intermediate-spin transition metal phthalocyaninato complexes (MPc; M = V, Cr, Mn and Fe) have been theoretically investigated to look into the origin, symmetry and strength of the M–Pc bonding. DFT calculations coupled to the Ziegler’s extended transition state method and to an advanced charge density and bond order analysis allowed us to assess that the M–Pc bonding is dominated by σ interactions, with FePc having the strongest and most covalent M–Pc bond. According to experimental evidence, the lightest MPcs (VPc and CrPc) have a high-spin ground state (GS), while the MnPc and FePc GS spin is intermediate. Insights into the MPc unoccupied electronic structure have been gained by modelling M L_2,3-edges X-ray absorption spectroscopy data from the literature through the exploitation of the current Density Functional Theory variant of the Restricted Open-Shell Configuration Interaction Singles (DFT/ROCIS) method. Besides the overall agreement between theory and experiment, the DFT/ROCIS results indicate that spectral features lying at the lowest excitation energies (EEs) are systematically generated by electronic states having the same GS spin multiplicity and involving M-based single electronic excitations; just as systematically, the L₃-edge higher EE region of all the MPcs herein considered includes electronic states generated by metal-to-ligand-charge-transfer transitions involving the lowest-lying π^* orbital (7e_g) of the phthalocyaninato ligand.

Electronic modulation of oxygen evolution on metal doped NiFe layered double hydroxides

The bottleneck of electrochemical water splitting is the sluggish kinetics of oxygen evolution reaction (OER). Layered double hydroxides (LDHs) have been proposed as active and affordable electrocatalysts in OER. It has been reported that the activity of LDHs can be effectively tuned by doping of other metals. Despite previous experimental synthesis and improved catalytic performance, the in-depth OER mechanism on metal doped LDHs remains ambiguous. In the present work, transition metals (Cr, Mn and Co) doped NiFe LDHs were designed to investigate the doping effect in OER by both experimental analysis and density functional theory calculations. Based on experimental results, the intrinsic OER activity is Cr-NiFe LDHs > Co-NiFe LDHs > Mn-NiFe LDHs > NiFe LDHs, while the enhanced catalytic performance upon doping can be attributed to the interface effect, which results in the tuning of the binding energies of the intermediate states in OER.

Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens

In this review, applications of various molecular modelling methods in the study of estrogens and xenoestrogens are summarized. Selected biomolecules that are the most commonly chosen as molecular modelling objects in this field are presented. In most of the reviewed works, ligand docking using solely force field methods was performed, employing various molecular targets involved in metabolism and action of estrogens. Other molecular modelling methods such as molecular dynamics and combined quantum mechanics with molecular mechanics have also been successfully used to predict the properties of estrogens and xenoestrogens. Among published works, a great number also focused on the application of different types of quantitative structure-activity relationship (QSAR) analyses to examine estrogen's structures and activities. Although the interactions between estrogens and xenoestrogens with various proteins are the most commonly studied, other aspects such as penetration of estrogens through lipid bilayers or their ability to adsorb on different materials are also explored using theoretical calculations. Apart from molecular mechanics and statistical methods, quantum mechanics calculations are also employed in the studies of estrogens and xenoestrogens. Their applications include computation of spectroscopic properties, both vibrational and Nuclear Magnetic Resonance (NMR), and also in quantum molecular dynamics simulations and crystal structure prediction. The main aim of this review is to present the great potential and versatility of various molecular modelling methods in the studies on estrogens and xenoestrogens.

Strategies for Achieving Balance between Detonation Performance and Crystal Stability of High-Energy-Density Materials

Performance-stability contradiction of high-energy-density materials (HEDMs) is a long-standing puzzle in the field of chemistry and material science. Bridging the gap that exists between detonation performance of new HEDMs and their stability remains a formidable challenge. Achieving optimal balance between the two contradictory factors is of a significant demand for deep-well oil and gas drilling, space exploration, and other civil and defense applications. Herein, supercomputers and latest quantitative computational strategies were employed and high-throughput quantum calculations were conducted for 67 reported HEDMs. Based on statistical analysis of large amounts of physico-chemical data, in-crystal interspecies interactions were identified to be the one that provokes the performance-stability contradiction of HEDMs. To design new HEDMs with both good detonation performance and high stability, the proposed systematic and comprehensive strategies must be satisfied, which could promote the development of crystal engineering of HEDMs to an era of theory-guided rational design of materials.

Pyrenetetrone Derivatives Tailored by Nitrogen Dopants for High-Potential Cathodes in Lithium-Ion Batteries

To overcome limited information on organic cathode materials for lithium-ion batteries, we studied the electrochemical redox properties of pyrenetetrone and its nitrogen-doped derivatives. Three primary conclusions are highlighted from this study. First, the redox potential increases as the number of electron-withdrawing nitrogen dopants increases. Second, the redox potentials of pyrenetetrone derivatives continuously decrease with the number of bound Li atoms during the discharging process owing to the decrease in the reductive ability until the compounds become cathodically deactivated exhibiting negative redox potentials. Notably, pyrenetetrone with four nitrogen dopants loses its cathodic activity after the binding of five Li atoms, indicating remarkably high performance (496 mAh/g and 913 mWh/g). Last, the redox potential is strongly correlated not only with electronic properties but also with solvation energy. This highlights that pyrenetetrone derivatives would follow two-stage transition behaviors during the discharging process, implying a crucial contribution of solvation energy to their cathodic deactivation.

Efficient Nitrogen Fixation Catalyzed by Gallium Nitride Nanowire Using Nitrogen and Water

Ammonia is one of the most important bulk chemicals in modern society. However, the highly energy-extensive contemporary industrial production of ammonia was developed in the early 20th century and requires extensive heating of highly pressurized flammable hydrogen gas, whose global production still relies heavily on non-sustainable petroleum. The development of “sustainable” nitrogen fixation process represents a grand aspirational chemical pursuit concerning our future human well-being. Herein, we report an ultra-stable nitride-based photosensitizing semiconductor that enables efficient, sustainable, and mild photochemical nitrogen fixation. The catalyst exhibits strong chemisorption of nitrogen and enables immediate electron donation from its surface vacancy to nitrogen. In addition, it was also demonstrated that the nitride-based semiconductor possesses the potential to minimize electron-hole recombination.

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Efficient photo-N₂ fixation

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Strong chemisorption of N₂

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Uses water as H source

Simultaneous Photoradiochemical Labeling of Antibodies for Immuno-Positron Emission Tomography

A method for the simultaneous (one-step) photochemical conjugation and ⁸⁹Zr-radiolabeling of antibodies is introduced. A photoactivatable chelate based on the functionalization of desferrioxamine B with an arylazide moiety (DFO-ArN₃, [1]) was synthesized. The radiolabeled complex, ⁸⁹Zr-1⁺, was produced and characterized. Density functional theory calculations were used to investigate the mechanism of arylazide photoactivation. ⁸⁹Zr-radiolabeling experiments were also used to determine the efficiency of photochemical conjugation. A standard two-step approach gave a measured conjugation efficiency of 3.5% ± 0.4%. In contrast, the one-step process gave a higher photoradiolabeling efficiency of ∼76%. Stability measurements, cellular saturation binding assays, positron emission tomographic imaging, and biodistribution studies in mice bearing SK-OV-3 tumors confirmed the biochemical viability and tumor specificity of photoradiolabeled [⁸⁹Zr]ZrDFO-azepin-trastuzumab. Experimental data support the conclusion that the combination of photochemistry and radiochemistry is a viable strategy for producing radiolabeled proteins for imaging and therapy.

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Photochemistry is combined with radiochemistry for radiosynthesis in a flash

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Simultaneous photoradiochemistry is achieved with high radiolabeling efficiency

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Photoradiochemistry produces viable ⁸⁹Zr-radiolabeled antibodies

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Density functional theory calculations elucidate the photoactivation mechanism

Synthesis of Pyridazine Derivatives by Suzuki-Miyaura Cross-Coupling Reaction and Evaluation of Their Optical and Electronic Properties through Experimental and Theoretical Studies

A series of π-conjugated molecules, based on pyridazine and thiophene heterocycles 3a–e, were synthesized using commercially, or readily available, coupling components, through a palladium catalyzed Suzuki-Miyaura cross-coupling reaction. The electron-deficient pyridazine heterocycle was functionalized by a thiophene electron-rich heterocycle at position six, and different (hetero)aromatic moieties (phenyl, thienyl, furanyl) were functionalized with electron acceptor groups at position three. Density Functional Theory (DFT) calculations were carried out to obtain information on the conformation, electronic structure, electron distribution, dipolar moment, and molecular nonlinear response of the synthesized push-pull pyridazine derivatives. Hyper-Rayleigh scattering in 1,4-dioxane solutions, using a fundamental wavelength of 1064 nm, was used to evaluate their second-order nonlinear optical properties. The thienylpyridazine functionalized with the cyano-phenyl moiety exhibited the largest first hyperpolarizability (β = 175 × 10⁻³⁰ esu, using the T convention) indicating its potential as a second harmonic generation (SHG) chromophore.

Proliferating miller indices of C20 fullerene device under DFT-NEGF regime

We present ab-initio scrutiny of electron transport through C₂₀ fullerene cleaved with gold electrodes having unique set of miller orientations. The three families of miller indices {100}, {110} and {111} are considered with four exclusive device models for elucidating electronic transport under applied potential of - 2 to +2V. Thereafter, the quantum calculations employing DFT-NEGF are performed for envisaging density of states, transmission function, energy levels, molecular orbitals, charge transfer. These electronic transfer parameters lead to the study of its two electrical parameters: current and conductance. We conclude that in molecular-devices of constituted miller family {110}, HOMO-LUMO gap are inversely proportional to extent of charge carriers. While for miller devices {100} and {111}, the situation is fully contrasting with HOMO-LUMO gap being directly proportional to its charge carriers. Another important conclusion is that the gold electrodes having miller family {100} and {111} are providing equal opportunity to fullerene molecule to imply its behavior while electrodes of miller family {110} are over shadowing the performance of fullerene molecule.

A Theoretical Study of 8-Chloro-9-Hydroxy-Aflatoxin B₁, the Conversion Product of Aflatoxin B₁ by Neutral Electrolyzed Water

Theoretical studies of 8-chloro-9-hydroxy-aflatoxin B₁ (2) were carried out by Density Functional Theory (DFT). This molecule is the reaction product of the treatment of aflatoxin B₁ (1) with hypochlorous acid, from neutral electrolyzed water. Determination of the structural, electronic and spectroscopic properties of the reaction product allowed its theoretical characterization. In order to elucidate the formation process of 2, two reaction pathways were evaluated-the first one considering only ionic species (Cl⁺ and OH(-)) and the second one taking into account the entire hypochlorous acid molecule (HOCl). Both pathways were studied theoretically in gas and solution phases. In the first suggested pathway, the reaction involves the addition of chlorenium ion to 1 forming a non-classic carbocation assisted by anchimeric effect of the nearest aromatic system, and then a nucleophilic attack to the intermediate by the hydroxide ion. In the second studied pathway, as a first step, the attack of the double bond from the furanic moiety of 1 to the hypochlorous acid is considered, accomplishing the same non-classical carbocation, and again in the second step, a nucleophilic attack by the hydroxide ion. In order to validate both reaction pathways, the atomic charges, the highest occupied molecular orbital and the lowest unoccupied molecular orbital were obtained for both substrate and product. The corresponding data imply that the C₉ atom is the more suitable site of the substrate to interact with the hydroxide ion. It was demonstrated by theoretical calculations that a vicinal and anti chlorohydrin is produced in the terminal furan ring. Data of the studied compound indicate an important reduction in the cytotoxic and genotoxic potential of the target molecule, as demonstrated previously by our research group using different in vitro assays.

Spectroscopic studies and quantum chemical investigations of (3,4-dimethoxybenzylidene) propanedinitrile

The Fourier Transform Infrared (FTIR), Ultra-Violet Visible (UV-Vis) spectroscopy and Thermogravimetric (TG) analysis of (3,4-dimethoxybenzylidene) propanedinitrile have been carried out and investigated using quantum chemical calculations. The molecular geometry, harmonic vibrational frequencies, Mulliken charges, natural atomic charges and thermodynamic properties in the ground state have been investigated by using Hartree Fock Theory (HF) and Density Functional Theory (DFT) using B3LYP functional with 6-311G(d,p) basis set. Both HF and DFT methods yield good agreement with the experimental data. Vibrational modes are assigned with the help of Vibrational Energy Distribution Analysis (VEDA) program. UV-Visible spectrum was recorded in the spectral range of 190-800nm and the results are compared with the calculated values using TD-DFT approach. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results obtained from the studies of Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) are used to calculate molecular parameters like ionization potential, electron affinity, global hardness, electron chemical potential and global electrophilicity.

Computational Study of Intramolecular Heterocyclic Ring Formation with Cyclic Phosphazenes

Polyphosphazenes, because of their unique properties, have generated many opportunities to explore a variety of applications. These applications include areas such as biomedical research (e.g. drug delivery) and material science (e.g. fire-resistant polymers). Phosphazenes potentially have more variations then benzene analogues because of different substitution patterns. Here we present A computational study of the chemical modifications to a group of cyclic phosphazenes mainly hexachlorophosphazene (PNCl₂)₃. This study focuses on the relative energies of reactivity of hexachlorophosphazene to understand their geometry and the complexes they likely form. We compare diols, amino alcohols, and diamines with a carbon linker of 1-7 atoms. These heteroatom chains are attached to a single phosphorus atom or adjoining phosphorus atoms to form ring structures of geminal, vicinal (cis), and vicinal (trans) moieties. We find that the reactivities of "heteroatom caps" are predicted to be O,O (diol) > N,O (amino alcohol) > N,N (diamine). These results can be used to predict energetics and thus the stability of new compounds for biomedical and industrial applications.

The Influence of Alkoxy Substitutions on the Properties of Diketopyrrolopyrrole-Phenyl Copolymers for Solar Cells

A previously reported diketopyrrolopyrrole (DPP)-phenyl copolymer is modified by adding methoxy or octyloxy side chains on the phenyl spacer. The influence of these alkoxy substitutions on the physical, opto-electronic properties, and photovoltaic performance were investigated. It was found that the altered physical properties correlated with an increase in chain flexibility. Well-defined oligomers were synthesized to verify the observed structure-property relationship. Surprisingly, methoxy substitution on the benzene spacer resulted in higher melting and crystallization temperatures in the synthesized oligomers. This trend is not observed in the polymers, where the improved interactions are most likely counteracted by the larger conformational possibilities in the polymer chain upon alkoxy substitution. The best photovoltaic performance was obtained for the parent polymer: fullerene blends whereas the modifications on the other two polymers result in reduced open-circuit voltage and varying current densities under similar processing conditions. The current densities could be related to different polymer: fullerene blend morphologies. These results show that supposed small structural alterations such as methoxy substitution already significantly altered the physical properties of the parent polymer and also that oligomers and polymers respond divergent to structural alterations made on a parent structure.