Introducing “UCA-FUKUI” software: reactivity-index calculations

Understanding the Enzyme (S)-Norcoclaurine Synthase Promiscuity to Aldehydes and Ketones

The (S)-norcoclaurine synthase from Thalictrum flavum (TfNCS) stereoselectively catalyzes the Pictet-Spengler reaction between dopamine and 4-hydroxyphenylacetaldehyde to give (S)-norcoclaurine. TfNCS can catalyze the Pictet-Spengler reaction with various aldehydes and ketones, leading to diverse tetrahydroisoquinolines. This substrate promiscuity positions TfNCS as a highly promising enzyme for synthesizing fine chemicals. Understanding carbonyl-containing substrates' structural and electronic signatures that influence TfNCS activity can help expand its applications in the synthesis of different compounds and aid in protein optimization strategies. In this study, we investigated the influence of the molecular properties of aldehydes and ketones on their reactivity in the TfNCS-catalyzed Pictet-Spengler reaction. Initially, we compiled a library of reactive and unreactive compounds from previous publications. We also performed enzymatic assays using nuclear magnetic resonance to identify some reactive and unreactive carbonyl compounds, which were then included in the library. Subsequently, we employed QSAR and DFT calculations to establish correlations between substrate-candidate structures and reactivity. Our findings highlight correlations of structural and stereoelectronic features, including the electrophilicity of the carbonyl group, to the reactivity of aldehydes and ketones toward the TfNCS-catalyzed Pictet-Spengler reaction. Interestingly, experimental data of seven compounds out of fifty-three did not correlate with the electrophilicity of the carbonyl group. For these seven compounds, we identified unfavorable interactions between them and the TfNCS. Our results demonstrate the applications of in silico techniques in understanding enzyme promiscuity and specificity, with a particular emphasis on machine learning methodologies, DFT electronic structure calculations, and molecular dynamic (MD) simulations.

Catalytic Antioxidant Activity of Two Diterpenoid Polyphenols of Rosemary, Carnosol, and Isorosmanol, against Lipid Oxidation in the Presence of Cysteine Thiol

Lamiaceae herbs such as rosemary have excellent antioxidant properties, and lipidic diterpenoid constituents, such as carnosol, are known as characteristic components to exhibit strong antioxidant activity. This study investigates the effect of thiol compounds on the antioxidant properties of diterpenoid polyphenols. The results concerning the antioxidant activity of polyphenols in the presence of thiol showed that two polyphenols, namely, carnosol and isorosmanol, enhanced antioxidant capacity against the radical-induced oxidation of lipids. Further examination of the mechanism revealed that both polyphenols exhibit excellent catalytic antioxidant activity by using the thiol group as a reduction source. Using density functional theory calculations, we attempted to explain why only these two polyphenols exhibit catalytic antioxidant properties. The calculation results and the assumed reaction mechanism suggested that the orthoquinones produced in the antioxidant reactions of carnosol and isorosmanol are more unstable than the others and that the regioselectivity of their reactions with thiols contributes to their catalytic antioxidant properties.

A comparative study of structural and spectroscopic properties of three structurally similar mechanically bending organic single crystals - 2-Amino-3-nitro-5-halo (halo = Cl, Br, or I) pyridine

In recent years, scientists have been very interested in single crystals of monoaromatic compounds with mechanical softness, but they are hard to find. The present work reports a comparative study of structural, spectroscopic, and quantum chemical investigations of three structurally similar mechanically bending monoaromatic compounds, namely, 2-amino-3-nitro-5-chloro pyridine (I), 2-amino-3-nitro-5-bromo pyridine (II), and 2-amino-3-nitro-5-iodo pyridine (III). The mechanical responses of the three organic crystals studied here are very intriguing due to the similarity of their chemical structures, which only differ in the presence of halogen atoms (Cl, Br, and I) at the fifth position of the pyridine ring and are explained through examining intermolecular interaction energies from energy frameworks analysis, slip layer topology, and Hirshfeld surface analysis. The crystals of all the three feature one dimensional ribbons comprising alternating NaminoH⋯Onitro and NaminoH⋯Npyridine hydrogen bonds that form R22(12) and R22(8) dimeric rings, respectively. In (III), weak I⋯I interactions link the adjacent ribbons forming a two dimensional sheet. Layer-like structures are observed in all three crystals, with no significant interactions between the adjacent architectures (ribbons or sheets). Energy framework calculations are used for estimating the bending ability of the three compounds, with the three following the order Cl ≪ Br < I. The iterative electrostatic scheme coupled with the supermolecule approach (SM) at the DFT/CAM-B3LYP/aug-cc-pVTZ level is used to calculate the third-order nonlinear susceptibility (χ3) values in a simulated crystalline environment for the static case as well as two typical electric field frequency values, (λ = 1064 nm) and (λ = 532 nm). In addition, estimates of the topological studies (localized orbital locator and electron localization function) and reactivity characteristics (global reactivity parameters, molecular electrostatic potential, and Fukui function) are made for the compounds under investigation. Docking studies done using AutoDock software with a protein target (PDB ID: 6CM4) revealed that three compounds could be used to treat Alzheimer's disease.

Experimental and theoretical investigations of the effect of bis-phenylurea-based aliphatic amine derivative as an efficient green corrosion inhibitor for carbon steel in HCl solution

A novel bis-phenylurea-based aliphatic amine (BPUA) was prepared via a facile synthetic route, and evaluated as a potential green organic corrosion inhibitor for carbon steel in 1.0 M HCl solutions. NMR spectroscopy experiments confirmed the preparation of the targeted structure. The corrosion inhibitory behavior of the prospective green compound was explored experimentally by electrochemical methods and theoretically by DFT-based quantum chemical calculations. Obtained results revealed an outstanding performance of BPUA, with efficiency of 95.1% at the inhibitor concentration of 50 mg L-1 at 25 °C. The novel compound has improved the steel resistivity and noticeably reduced the corrosion rate from 33 to 1.7 mils per year. Furthermore, the adsorption study elucidates that the mechanism of the corrosion inhibition activity obeys Langmuir isotherm with mixed physisorption/chemisorption modes for BPUA derivatives on the steel surface. Calculated Gibb's free energy of the adsorption process ranges from -35 to -37 kJ mol-1. The SEM morphology analysis validates the electrochemical measurements and substantiates the corrosion-inhibiting properties of BPUA. Additionally, the eco-toxicity assessment on human epithelial MCF-10A cells proved the environmental friendliness of the BPUA derivatives. Density functional theory (DFT) calculations correlated the inhibitor's chemical structure with the corresponding inhibitory behavior. Quantum descriptors disclosed the potentiality of BPUA adsorption onto the surface through the heteroatom-based functional groups and aromatic rings.

First-principles density functional theoretical study on the structures, reactivity and spectroscopic properties of (NH) and (OH) Tautomer's of 4-(methylsulfanyl)-3[(1Z)-1-(2-phenylhydrazinylidene) ethyl] quinoline-2(1H)-one

The tautomerizations mechanism of 4-(methylsulfanyl)-3[(1Z)-1-(2-phenylhydrazinylidene) ethyl] quinoline-2(1H)-one were inspected in the gas phase and ethanol using density function theory (DFT) M06-2X and B3LYP methods. Thermo-kinetic features of different conversion processes were estimated in temperature range 273-333 K using the Transition state theory (TST) accompanied with one dimensional Eckert tunneling correction (1D-Eck). Acidity and basicity were computed as well, and the computational results were compared against the experimental ones. Additionally, NMR, global descriptors, Fukui functions, NBO charges, and electrostatic potential (ESP) were discussed. From thermodynamics analysis, the keto form of 4-(methylsulfanyl)-3-[(1Z)-1-(2 phenylhydrazinylidene) quinoline-2(1H)-one is the most stable form in the gas phase and ethanol and the barrier heights required for tautomerization process were found to be high in the gas phase and ethanol ~ 38.80 and 37.35 kcal/mol, respectively. DFT methods were used for UV-Vis electronic spectra simulation and the time-dependent density functional theory solvation model (TDDFT-SMD) in acetonitrile compounds.

Sulfadiazine degradation by combination of hydrodynamic cavitation and Fenton-persulfate: parametric optimization and deduction of chemical mechanism

This paper reports the degradation of the sulfadiazine (SDZ) drug with a hybrid advanced oxidation process (AOP) of heterogeneous α-Fe₂O₃/persulfate coupled with hydrodynamic cavitation. The major objectives of the study are parametric optimization of the process and elucidation of the chemical mechanism of degradation. The optimum conditions for maximum SDZ degradation of 93.07 ± 1.67% were as follows: initial SDZ concentration = 20 ppm, pH = 4, α-Fe₂O₃ = 181.82 mg/L, Na₂S₂O₈ = 348.49 mg/L, H₂O₂ = 0.95 mL/L, inlet pressure = 0.81 MPa (8 atm), orifice plate configuration: hole dia. = 2 mm and number of holes = 4. Density functional theory (DFT) calculations revealed that the atoms of SDZ with a high Fukui index (f ⁰) were potentially active sites for the attack of ^•OH and [Formula: see text] radicals. Fukui index calculation revealed that atom 11 N has a higher value of f ⁰ (0.1026) for oxidation at the α-amine group of the sulfadiazine molecule. Degradation intermediates detected through LC-MS/MS analysis corroborated the results of DFT simulations. Using these results, a chemical pathway has been proposed for SDZ degradation.

Theoretical prediction on the hydrolysis rate of the new types of nerve agents: A density functional study

Although the hydrolysis mechanism of the nerve agents, which is the main decontamination pathway, has been studied experimentally and theoretically, the reliable theoretical prediction method for the hydrolysis rate is not studied yet. Furthermore, after the CWC (Chemical Warfare Agent) list is updated, Novichok candidate structures can be more than 10,000 structures, for which it is not possible to perform the experiment for all of them for synthesizing and getting the hydrolysis rate. Therefore, developing a reliable theoretical method for hydrolysis rate prediction is crucial to prepare for the forthcoming usage of new types of nerve agents. Herein, by using DFT (Density Functional Theory), we successfully developed a new method of predicting the hydrolysis rate on nerve agents by investigating the electrophilicity index (EI) of the various A-, V-, and G-series nerve agents and found a suitable correlation with the experimental hydrolysis rate. Among the several DFT methods, wb97xD predicts the EI with the lowest % deviation of the studied nerve agents. Our results show that EI can be a good indicator to predict the hydrolysis rate of the anticipated nerve agents. Based on the result, we predicted the hydrolysis rate on another type of Novichok candidates, which could be the firm basis for developing a decontaminant and antidote with much fewer experimental efforts on new types of nerve agents.

Experimental and theoretical study of the mechanism and rate constants of the sequential 5-exo-trig spirocyclization involving vinyl, aryl and N-alkoxyaminyl radicals

In this research the sequential generation and cyclization of N-alkoxyaminyl radicals to produce 1-azaspiro[4.4]nonane, a prominent scaffold in organic and medicinal chemistry, was studied. Competition experiments in benzene at 80 °C with brominated oxime ethers using Bu₃SnH as chain transfer and AIBN as the initiator generated vinyl or aryl radicals which were captured by oxime ethers, allowing approximate 5-exo-trig cyclization constants at 4.6 × 10⁸ s^-1 and 9.9 × 10⁸ s^-1 respectively to be established. Similar results were obtained by kinetic studies using the transition state theory (TST) from ab initio calculations with density functional theory (DFT) using the M06-2X, B3LYP, mPW1PW91 and TPSSh functionals in combination with the 6-311+G(d, p) basis set. Additionally, it was found that the 5-exo-trig cyclization of the N-alkoxyaminyl radical onto CC double bonds is a reversible process whose constants were determined to be in the range of 6.2 × 10⁰ s^-1 and 3.5 × 10⁶ s^-1 at 80 °C, depending on the nature of the substituents. The calculation of the radical stabilization energy (RSE) shows that the N-alkoxyaminyl radical is a very stable species and its reactivity in the addition on alkenes is governed by its nucleophilic character and the stability of the carbon-centered radical formed after cyclization. The reduction constant of the N-alkoxyaminyl radical with Bu₃SnH in the gas phase at 80 °C was also estimated to be 3.4 × 10⁰ M^-1 s^-1 through computational calculations. This information facilitates the rational planning of cascades and other methodologies applied to the construction of carbocyclic and aza-heterocyclic compounds.

Structures, Energetics, and Spectra of (NH) and (OH) Tautomers of 2-(2-Hydroxyphenyl)-1-azaazulene: A Density Functional Theory/Time-Dependent Density Functional Theory Study

Tautomerization of 2-(2-hydroxyphenyl)-1-azaazulene (2OHPhAZ) in the gas phase and ethanol has been studied using B3LYP, M06-2X, and ωB97XD density functional theory (DFT) with different basis sets. For more accurate data, energies were refined at CCSD(T)/6-311++G(2d,2p) in the gas phase. Nuclear magnetic resonance (NMR), aromaticity, Fukui functions, acidity, and basicity were also calculated and compared with experimental data. Time-dependent density functional theory (TDDFT)-solvation model based on density (TDDFT-SMD) calculations in acetonitrile have been utilized for the simulation of UV-vis electronic spectra. In addition, electronic structures of the investigated system have been discussed. The results reveal that the enol form (2OHPhAZ) is thermodynamically and kinetically stable relative to the keto tautomer (2OPhAZ) and different rotamers (2OHPhAZ-R1:R3) in the gas phase and ethanol. A comparison with the experiment illustrates a good agreement and supports the computational findings.

Meta-Hybrid Density Functional Theory Prediction of the Reactivity, Stability, and IGM of Azepane, Oxepane, Thiepane, and Halogenated Cycloheptane

The application of plain cycloalkanes and heterocyclic derivatives in the synthesis of valuable natural products and pharmacologically active intermediates has increased tremendously in recent times with much attention being paid to the lower cycloalkane members. The structural and molecular properties of higher seven-membered and nonaromatic heterocyclic derivatives are less known despite their stable nature and vast application; thus, an insight into their structural and electronic properties is still needed. Appropriate quantum chemical calculations utilizing the ab initio (MP2) method, meta-hybrid (M06-2X) functional, and long-range-separated functionals (ωB97XD) have been utilized in this work to investigate the structural reactivity, stability, and behavior of substituents on cycloheptane (CHP) and its derivatives: azepane, oxepane, thiepane, fluorocycloheptane (FCHP), bromocycloheptane (BrCHP), and chlorocycloheptane (ClCHP). Molecular global reactivity descriptors such as Fukui function, frontier molecular orbitals (FMOs), and molecular electrostatic potential were computed and compared with lower members. The results of two population methods CHELPG and Atomic Dipole Corrected Hirshfeld Charges (ADCH) were equally compared to scrutinize the charge distribution in the molecules. The susceptibility of intramolecular interactions between the substituents and cycloalkane ring is revealed by natural bond orbital analysis and intramolecular weak interactions by the independent gradient model (IGM). Other properties such as atomic density of states, intrinsic bond strength index (IBSI), and dipole moments are considered. It is acclaimed that the strain effect is a major determinant effect in the energy balance of cyclic molecules; thus, the ring strain energies and validation of spectroscopic specificities with reference to the X-ray crystallographic data are also considered.

Exploring the maximum Fukui function sites with the frontier-controlled soft-soft reactions using 1,3-dipolar cycloaddition reactions of nitrilium betaines

According to P.K. Chattaraj. J Phys Chem A 2001, 105, 511-513 "the maximum Fukui function site is the best for the frontier-controlled soft-soft reactions whereas for the charge-controlled hard-hard interactions the preferred site is associated with the maximum net charge and not necessarily the minimum Fukui function". Taking into account these outcomes in this research is explored this reactivity scheme using in first case the reaction between fulminic acid with ethylene (reference reaction), after is varying the dipolarophile in the reaction between fulminic acid with acetylene, and finally is varying the dipole in the reaction between formonitrile imine with ethylene. These results allow study parameter such as charge transfer, polarizability, covalent character on bonding, among other; also shown the preference by the sf^- / sf⁺ interactions in the transition state on the sf^- / sf^- interactions. On the other hand, these results also were justified using net electrophilicity which is defined as the electrophilic power of a system relative to its own nucleophilic power.

Bis(thiophen-2-yl-methylene) Benzene-1, 4-Diamine as Fluorescent Probe for the Detection of Fe3+ in Aqueous Samples

A Schiff base bis(thiophen-2-yl-methylene)benzene-1, 4-diamine (L) was synthesized and used for selective and sensitive detection of Fe³⁺. L exhibited enhanced fluorescence response at excitation of 365 nm and emission wavelength of 440 nm for Fe³⁺. The formation of a 1:1 complex between L and Fe³⁺ was suggested by Job's plot by fluorescence titration and from optimized structures using Density functional theory (DFT). The fluorescence intensity was directly proportional to concentration of Fe³⁺ (R² = 0.999) with the detection limit of 3.8 × 10^-7 M and the binding constant of 1.20 × 10⁴ M^-1 at pH = 6.0. The probe was used to detect Fe³⁺ in different water samples with the percentage recovery of 99.7-103%. The interference of the other cations are < 5%.

A facile approach for tuning optical and surface properties of novel biobased Alginate/POTE handleable films via solvent vapor exposure

Novel biobased films consisting of alginate blends with poly (octanoic acid 2-thiophen-3-yl-ethyl ester) (POTE), a conducting polymer, were prepared by solution casting, and their optical, morphological, thermal, and surface properties were studied. Using UV-visible spectroscopy, atomic force microscopy (AFM), and scanning electron microscopy (SEM), the effects of tetrahydrofuran solvent vapors on the optical properties and surface morphology of biobased films with different POTE contents were studied. Results indicate that morphological rearrangements of POTE take place during the process of solvent exposure. Specifically, the solvent vapor induced the formation of POTE small crystalline domains, which allows envisioning the potential of tuning UV-visible absorbance and wettability behavior of biobased films. Finally, theoretical electronic calculations (specifically frontier molecular orbitals analysis) provided consistent evidence on POTE's preferential orientation and selectivity toward the THF-vapor medium.

Carbonyl Composition and Electrophilicity in Vaping Emissions of Flavored and Unflavored E-Liquids

It has been demonstrated that propylene glycol (PG), vegetable glycerin (VG), and flavoring chemicals can thermally degrade to form carbonyls during vaping, but less is known about carbonyl emissions produced by transformation of flavoring chemicals and the interactive effects among e-liquid constituents. This study characterized carbonyl composition and levels in vaping emissions of PG-VG (e-liquid base solvents) and four e-liquid formulations flavored with trans-2-hexenol, benzyl alcohol, l-(-)-menthol, or linalool. Utilizing gas chromatography (GC)- and liquid chromatography (LC)-mass spectrometry (MS) methods, 14 carbonyls were identified and quantified. PG-VG emitted highest levels of formaldehyde, acetaldehyde, and acrolein. However, flavored e-liquids contributed to the production of a wider variety of carbonyls, with some carbonyls directly corresponding to the oxidation of alcohol moieties in flavoring compounds (e.g., trans-2-hexenol and benzyl alcohol transformed into trans-2-hexenal and benzaldehyde, respectively). Detections of formaldehyde-GSH and trans-2-hexenal-GSH adducts signify interactions of carbonyls with biological nucleophiles. The global reactivity descriptors (I, A, μ, η, and ω) and condensed Fukui parameters (fk0, fk-, fk+, and dual-descriptor) were computed to elucidate site reactivities of selected simple and α,β-unsaturated carbonyls found in vaping emissions. Overall, this study highlights carbonyl emissions and reactivities and their potential health risk effects associated with vaping.

Crystal Structure and Solid-State Packing of 4-Chloro-5H-1,2,3-dithiazol-5-one and 4-Chloro-5H-1,2,3-dithiazole-5-thione

The crystal structure and solid-state packing of 4-chloro-5H-1,2,3-dithiazol-5-one and two polymorphs of 4-chloro-5H-1,2,3-dithiazole-5-thione were analyzed and compared to structural data of similar systems. These five-membered S,N-rich heterocycles are planar with considerable bond localization. All three structures demonstrate tight solid-state packing without voids which is attributed to a rich network of short intermolecular electrostatic contacts. These include S^δ+…N^δ−, S^δ+…O^δ−, S^δ+…Cl^δ− and S^δ+…S^δ− interactions that are well within the sum of their van der Waals radii (∑_VDW). B3LYP, BLYP, M06, mPW1PW, PBE and MP2 were employed to calculate their intramolecular geometrical parameters, the Fukui condensed functions to probe their reactivity, the bond order, Bird Index and NICS(1) to establish their aromaticity.

Ziziphus joazeiro Stem Bark Extract as a Green Corrosion Inhibitor for Mild Steel in Acid Medium

The aqueous extract of Joazeiro stem bark (EJSB) and its high molecular weight fraction (HMWF) were examined as potential corrosion inhibitors of mild steel in 1 mol L−1 hydrochloric acid media, using weight-loss measurements, potentiodynamic polarization curves and an electrochemical impedance spectroscopy (EIS).Varying the concentration of the inhibitors from 100 to 800 mg L−1, the results show an increase in anticorrosive efficiency from 85.4 to 89.8 and 89.8 to 93.0% for EJSB and its HMWF, respectively, using the data of the gravimetric essay, and from 84.5 to 94.5 and 89.9 to 94.7% for EJSB and its HMWF, respectively, from the impedance data. The composition of the crude extract was chemically characterized by liquid chromatography-high resolution mass spectrometry. Additionally, scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS) were used, respectively, to morphologically and chemically characterize the surface. Considering that the saponin molecules, the main constituent from juá, are responsible for its inhibitory action, quantum chemical calculations showed that the C67, C69 and O144 atoms likely have an important role in the process of electron-donation of saponin to metal, due to the higher values of ƒk+ and %HOMO observed on these atoms.

Synthesis, identification, density functional and Hirshfeld surface studies of 2,2'-disulfanediylbis(tetrahydro-4H-cyclopenta[d][1,3,2]dioxaphosphole-2-sulfide)

The new compound 2,2'-disulfanediylbis (tetrahydro-4H-cyclo penta[d][1,3,2]dioxaphosphole 2-sulfide), the dimeric form of 2-mercaptotetrahydro-4H-cyclopenta[d] [1,3,2] dioxaphosphole 2-sulfide, has been synthesized and characterized by elemental analysis, molecular weight determination and spectral data (¹ H-NMR, ¹³ C-NMR, ³¹ P-NMR, FTIR). The molecular geometry was confirmed by single X-Ray crystallography. The ground state property was examined by PBE0 and B3LYP density functionals using aug-cc-pV(Q+d)Z basis set in the gas phase and in DMSO solution. The preference of PBE0 functional was statistically established. Thermodynamic parameters and standard heat of dissociation reaction ( Δ H R 298 K o ) have been established. The calculated equilibrium constants at different temperatures reflect the stability of the dimer over the monomers at low temperatures and vice versa. Valency and Fukui indices calculations showed that the monomer is more reactive than the dimer. 2D-fingerprint revealed that, while the H…X; [X = H, O and S] nonbonding intermolecular interactions and reciprocals play a crucial role in strengthening of molecules packing in the crystal unit cell while the S…S ones contribute negatively on it.

Electronic structure theory study of the reactivity and structural molecular properties of halo-substituted (F, Cl, Br) and heteroatom (N, O, S) doped cyclobutane

Cyclobutane and its halo-substituted derivatives and its heteroatom doped derivatives have been extensively investigated in this study because of the vast applications and interesting chemistry associated with them, the vibrational assignments, Natural Bond Orbital (NBO) analysis, Conceptual Density Functional Theory, Quantum Mechanical Descriptors and Molecular Electrostatic Potential (MEP) analysis have been explored in this study. The corresponding wavenumbers of the studied compounds have as well been assigned by Potential Energy Distribution analysis. Several inter and intramolecular hyperconjugative interactions within the studied compounds have been revealed by the NBO analysis with a confirmation of geometric hybridization and electronic occupancy. The compounds reactivity was observed to decrease down the halo group in manners such as the stability, both were observed to decrease from azetidine to thietane. The distribution of charge was observed to be affected by the ring substituent as observed from the charge population analysis; in addition, adjacent atoms are very much affected by the inherent properties of the substituted atoms. The NBO result suggests that the molecules are stabilized by lone pair delocalization of electrons from the substituted atoms and molecular electrostatic potential (MEP) studies revealed that substituted halogens and doped heteroatoms are important and most probable sites of electrostatic interactions.

Preparation of High Molecular Weight Poly(urethane-urea)s Bearing Deactivated Diamines

The synthesis of poly(urethane-urea) (PUUs) bearing deactivated diamines within the backbone polymer chain is presented. Several deactivated diamines present interesting properties for several applications in the biomaterial field due to their attractive biocompatibility. Through an activation with Chloro-(trimethyl)silane (Cl-TMS) during the polymerization reaction, the reactivity of these diamines against diisocyanates was triggered, leading to PUUs with high performance. Indeed, through this activation protocol, the obtained molecular weights and mechanical features increased considerably respect to PUUs prepared following the standard conditions. In addition, to demonstrate the feasibility and versatility of this synthetic approach, diisocyanate with different reactivity were also addressed. The experimental work is supported by calculations of the electronic parameters of diisocyanate and diamines, using quantum mechanical methods.

New insights about electronic mechanism of electrocyclic reactions: theoretical study about stereoselectivity in cyclobutenes

This work presents the study of a series of electrocyclic reactions with the main aim of obtaining new insights into the reaction process along IRCs. The energy variation of the different reaction paths as well as the different transition states have been calculated. These trends are according to the experimental data. The natural bond orbitals have been obtained and the second order perturbational theory analysis has been carried out to determine the main charge transfers due to delocalization. Bond reactivity indexes have been used to describe the reactivity mechanism in a local way. These reactivity indexes are also based on NBOs and this has made it possible to connect the results of the indexes with the previous analysis. To determine quantitatively the bond structure, we used the quantum theory of atoms in molecules and we have hereby completed the information obtained from the NBO analysis. Finally, we used the Hirshfeld population analysis as an approximation to understand how the load density changes in the different reaction pathways, and we have connected these variations with the information obtained from the bond structure.

The results has found that the reaction path with the lowest energy barrier Transition State Inward Conrotatory (TSIC) or Transition State Outward Conrotatory (TSOC) is determined by two magnitudes: the charge donations by delocalisation of the substituents (which we obtained from the Second Order Perturbational Theory Analysis of the NBOs) and in the case that these donations were very similar, the non-covalent interactions dominated (which we studied by means of the interaction energies of the Hirshfeld charges). Additionality, the most important factor influencing the lower energy reaction path was the interaction of lone pairs of the substituents with the σ∗(C–C) bond that is broken at the opening of the cycle. The alignment of these lone pairs with the C–C bond favours charge donation between them and, as can be seen in the discussion, this alignment varies depending on whether the structure is TSIC and TSOC.

Piloty's acid and its hydrazide analogue: Insights from the density functional theory and vibrational spectroscopy on the conformational stability and chemical reactivity

N-hydroxybenzenesulfonamide (commonly known as Piloty's acid) is considered a major source for nitroxyl (HNO) species which has potential biological and medicinal applications. In the present study, the conformational preferences and chemical reactivity of Piloty's acid (PA) and its hydrazide analogue (benzenesulfonylhydrazide, BSH) were studied using spectroscopic and computational tools. Six stable conformations of each molecule were theoretically identified, and their structures were fully optimized at the DFT-B3LYP and MP2 levels. Both molecules in their most stable forms adopt the anti configuration with the NH bond of the secondary amine pointing away from the terminal hydroxyl and amine moieties in the acid and hydrazide molecules, respectively. Three stable gauche states facilitated by weak intramolecular interactions of the SO⋯HO and SO⋯HN types arise due to the internal rotation about the SN linkage. Reliable assignments of the vibrational modes and the calculated reaction coordinates support a two-step mechanistic pathway of the Piloty's acid dissociation leading to the production of the nitroxyl (HNO) intermediate with moderate transition state barriers. Frontier molecular orbitals distributions, molecular electrostatic potential maps and condensed Fukui functions analysis of the molecules were employed to elucidate the agility of PA to dissociate to produce HNO and the absence of such a dissociation of BSH that would produce diazene (N₂H₂).

Flavonoid content of the Libyan Onosma Cyrenaicum: isolation, identification, electronic chemical reactivity, drug likeness, docking, and MD study

In this work, an attempt to identify the flavonoid content of the Libyan Onosma Cyrenaicum led to the isolation of three flavonoids 7,8-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one(GE-001), 5,7-dihydroxy-2-(3-hydroxy-4-methoxy phenyl)-4H-chromen-4-one (GE-002) and 5,7-dihydroxy-3-(4-hydroxyphenyl)-4H-chromen-4-one (GE-003), the isolated compounds were characterized using ¹H and ¹³C-NMR techniques. A further DFT study at ωB97-XD with 6-311++G** basis set in water was conducted to calculate the isolated compounds' global and local reactivity descriptors and Fukui indices along with their antioxidant activity. The drug-likeness and bioactivity properties of the isolated compounds were estimated and discussed. Finally, GE-001, GE-002, and GE-003 were docked into HCV NS5B polymerase active siteand this was followed by molecular dynamic simulation to certify the obtained docking result and to obtain the MM-GBSA free binding energyy of the isolated compounds. Communicated by Ramaswamy H. Sarma.

Aromaticity indices, electronic structural properties, and fuzzy atomic space investigations of naphthalene and its aza-derivatives

The aromaticity and CDFT properties of naphthalene and its aza-derivatives were theoretically investigated using density functional theory (DFT) electronic structure method. The reactivity and chemistry of Azanaphthalene (1-AN), 1, 2-diazanaphthalene (1, 2-DAN), 1, 3-diazanaphthalene (1, 3-DAN), 1, 4-diazanaphthalene (1,4-DAN), 1, 5-diazanaphthalene (1, 5-DAN), 1, 6-diazanaphthalene (1, 6-DAN), 1, 7-diazanaphthalene (1,7-DAN) and 1, 8-diazanaphthalene (1, 8-DAN) were thoroughly explored and predicted focusing more on the fuzzy atomic space analysis, quantum chemical descriptors (CDFT), natural bond orbital (NBO), and structural electronic properties. The CDFT is focused on predicting the condensed Fukui function and dual descriptors along with condensed local electrophilicity and nucleophilicity investigation. From the aromaticity computational study, 1,7-DAN gave PDI, FLU, FLU- π , PLR, HOMA, BIRD and LOLIPOP values of approximately one (1) was found to be the most aromatic in the group, and strongest π -stacking ability. The aromaticity follows the trend: 1, 7-DAN > 1, 8-DAN > 1, 5-DAN > 1, 6-DAN > 1, 4-DAN > 1, 2-DAN > 1-AN > naphthalene. The second order perturbation energy NBO analysis revealed that the 3 highest stabilization energies in the molecules are C₆-N_a to C₃-C₄ ( π ∗ - π ∗ 236.90 kcal/mol) of 1, 6-DAN, C₃-C₄ to C₁-C₂ ( π ∗ - π ∗ 236.37 kcal/mol) of 1-AN and C₇-N₁₀ to C₂-C₄ ( π ∗ - π ∗ 235 kcal/mol) of 1, 3-DAN.

Computational development and validation of a representative MDI-BDO-based polyurethane hard segment model

Segmented polyurethanes show extraordinary physicochemical properties, mainly owing to the nature and the chemistry of the hard segment domains. There are yet many inexplicable physiochemical properties of MDI-BDO-based hard polyurethane segments such as the geometry, cis-trans isomerism, electronic structure, chemical reactivity, the inter-hard-segment interactions, and the photo-response. In the present study, it was attempted to develop and validate a model system that would facilitate further research on the structural and chemical properties of the MDI-BDO hard segments. It was found that the trans isomer of urethane bond is more stable than the cis isomer, and it is argued here that thermal transformation from trans to cis not possible due to the high rotational energy barrier. The differences between the calculated IR spectra of the cis and trans isomers are proposed as a powerful differentiation tool. The calculated Fukui indices show that cis and trans isomers are different in their chemical reactivity. The findings of the present study suggest intermolecular and intramolecular pi-stacking and highly plausible two significant types of hydrogen bond types between hard segments. In the present study, a model system for MDI-BDO hard segment was developed and successfully validated via computational experiments. Further calculations done with the new model provided an indispensable understanding of the structure, cis-trans isomerism, reactivity, and intermolecular interactions of the MDI-BDO hard segments. The proposed model can be further improved in the future by incorporating suitable soft segments. In summary, the model system developed and validated in the present study has provided new opportunities to understand and further study the structural and chemical features of the hard segments of the MDI-BDO-based polyurethane.

PRIMoRDiA: A Software to Explore Reactivity and Electronic Structure in Large Biomolecules

Plenty of enzymes with structural data do not have their mechanism of catalysis elucidated. Reactivity descriptors, theoretical quantities generated from resolved electronic structure, provide a way to predict and rationalize chemical processes of such systems. In this Application Note, we present PRIMoRDiA (PRIMoRDiA Macromolecular Reactivity Descriptors Access), a software built to calculate the reactivity descriptors of large biosystems by employing an efficient and accurate treatment of the large output files produced by quantum chemistry packages. Here, we show the general implementation details and the software main features. Calculated descriptors were applied for a set of enzymatic systems in order to show their relevance for biological studies and the software potential for use in large scale. Also, we test PRIMoRDiA to aid in the interaction depiction between the SARS-CoV-2 main protease and a potential inhibitor.

Bond reactivity indices approach analysis of the [2+2] cycloaddition of jatrophane skeleton diterpenoids from Euphorbia gaditana Coss to tetracyclic gaditanone

The reaction mechanism of the intramolecular [2 + 2] cycloaddition from a jatrophane precursor to the gaditanane skeleton, an unprecedented 5/6/4/6-fused tetracyclic ring framework recently isolated from Euphorbia spp., was studied using the bond reactivity indices approach. Furthermore, six diterpenoids, including three undescribed jatrophanes isolated from E. gaditana Coss, were described. The structures of these compounds were deduced by a combination of 2D NMR spectroscopy and ECD data analysis.

Novel Porous Organic Polymer for the Concurrent and Selective Removal of Hydrogen Sulfide and Carbon Dioxide from Natural Gas Streams

Natural gas sweetening currently requires multistep, complex separation processes to remove the acid gas contaminants, carbon dioxide and hydrogen sulfide. In addition to being widely recognized as energy inefficient and cost-intensive, the effectiveness of this conventional process also suffers considerably because of limitations of the sorbent materials it employs. Herein, we report a new porous organic polymer, termed KFUPM-5, that is demonstrated to be effective in the concurrent separation of both hydrogen sulfide and carbon dioxide from a mixed gas stream at ambient conditions. To understand the ability of KFUPM-5 to selectively capture these gas molecules, we performed both pure-component thermodynamic and mixed gas kinetic adsorption studies and correlated these results with theoretical molecular simulations. Our results show that the underlying polar backbone of KFUPM-5 provides favorable adsorption sites for the selective capture of these gas molecules. The outcome of this work lends credence to the prospect that, for the first time, porous organic polymers can serve as sorbents for industrial natural gas sweetening processes.

Synthesis, Biological Evaluation and Stability Studies of Some Novel Aza-Acridine Aminoderivatives

Several new amino-substituted aza-acridine derivatives bearing a basic side chain have been designed and synthesized. The antiproliferative activity of the target compounds has been evaluated against three cancer cell lines-namely HCT-116 (colorectal), the uterine sarcoma MES-SA, and its doxorubicin-resistant variant MES-SA/Dx5. A limited number of the new acridines showed marginal cytotoxicity against the tested cell lines; nevertheless, these analogues possessed a similar substitution pattern. The moderate biological activity of these derivatives was attributed to their instability in aqueous media, which has been studied by mass spectrometry and computational chemistry experiments at the density functional level of theory (DFT).

Radiosynthesis, molecular modeling and biodistribution of 99mTc-Protoporphyrin as a preclinical model for tumor diagnosis

Porphyrins are among the most important and widely used compounds involved in a variety of chemical and biochemical applications. These molecules exhibit very special properties that encourage researchers to label many derivatives with diagnostic or therapeutic radionuclides for medical applications. This study reports the radiolabeling and biodistribution of [Formula: see text]Tc-protoporphyrin IX ([Formula: see text]Tc-PPIX) as a novel potential solid-tumor imaging agent. The factors affecting the radiolabeling process were varied to achieve maximum radiochemical yield. [Formula: see text]Tc-PPIX was obtained in high yield of 97.34 ± 0.21% and high stability in serum up to 24 h. The radiochemical yield of [Formula: see text]Tc-PPIX was assessed by a combination of a paper chromatographic technique and HPLC. A computational analysis for all the potential structures that may be formed due to the interaction between protoporphyrin IX and technetium was performed via the DFT method of calculations in gas phase to predict the most likely structure. Molecular docking was further employed to shed light on the nature of the interaction between the most stable complexes with the target protein. Finally, the in-vivo biodistribution of [Formula: see text]Tc-PPIX complex was evaluated in solid-tumor-bearing mice and high tumor/tissue ratio of 5.17 ± 0.34 at 60 min post injection was obtained. Our finding clearly suggests [Formula: see text]Tc-PPIX as a potential SPECT agent for tumor imaging.