Molecular Orbital Calculations Research Articles

Assessment of the hypoglycemic and anti-hemostasis effects of Paederia foetida (L.) in controlling diabetes and thrombophilia combining in vivo and computational analysis

Paederia foetida is valued for its folk medicinal properties. This research aimed to assess the acute toxicity, hypoglycemic and anti-hemostasis properties of the methanolic extract of P. foetida leaves (PFLE). Acute toxicity of PFLE was performed on a mice model. Hypoglycemic and anti-hemostasis properties of PFLE were investigated on normal and streptozotocin-induced mice models. Deep learning, molecular docking, density functional theory, and molecular simulation techniques were employed to understand the underlying mechanisms through in silico study. Oral administration of PFLE at a dosage of 300 µg/kg body weight (BW) showed no signs of toxicity. Treatment with PFLE (300 µg/kg/BW) for 14 days resulted in a hypoglycemic condition and a 30.47% increase in body weight. Additionally, PFLE mixed with blood exhibited a 44.6% anti-hemostasis effect. Deep learning predicted the inhibitory concentration (pIC50, nM) of Cleomiscosins against SGLT2 and FXa to be 7.478 and 6.017, respectively. Molecular docking analysis revealed strong binding interactions of Cleomiscosins with crucial residues of the target proteins, exhibiting binding energies of −8.2 kcal/mol and −7.1 kcal/mol, respectively. ADME/Tox predictions indicated favorable pharmacokinetic properties of Cleomiscosins, and DFT calculations of frontier molecular orbitals analyzed the stability and reactivity of these compounds. Molecular simulation dynamics, principal component analysis and MM-PBSA calculation demonstrated the stable, compact, and rigid nature of the protein-ligand complexes. The methanolic PFLE exhibited significant hypoglycemic and anti-hemostasis properties. Cleomiscosin may have inhibitory properties for the development of novel drugs to manage diabetes and thrombophilia in the near future.

Vibrational characterization of active drug to the treatment of chagas disease, benznidazole by using force fields and internal coordinates

Two experimental structures of benznidazole active drug used to the treatment of Chagas disease have been structurally characterized and its vibrational spectra completely assigned combining B3LYP/6-311++G** calculations with the experimental FT-IR and FT-Raman spectra and the SQMFF methodology. The most stable conformer of benznidazole found in the study of the potential energy surface is in agreement with that experimentally observed by X-ray diffraction at room temperature while the other one was observed with the heating up to 195 ºC. Both differs in the positions of CH2 groups of acetamide fragment. Their structural properties in gas phase and ethanol solution were computed by using natural bond orbital (NBO), atoms in molecules (AIM), Merz-Kollman (MK) charges, molecular electrostatic potentials (MEP) and frontier orbitals calculations by using the hybrid B3LYP method and the 6-31G* and 6-311++G** basis sets. Additional WB97XD/6-311++G** calculations show that the energy values optimized for the most stable species in both media present lower values than the obtained with the B3LYP/6-31G* method. The vibrational assignments for those two conformers in both media were obtained from their corresponding harmonic force fields together with the scaled force constants.

Quantum Chemical Studies on Possible Molecular Devices Based on Electric Field-Induced Intramolecular Charge Transfer.

We report quantum chemical studies on possible molecular devices working based on electric field-induced intramolecular charge transfer (EFIMCT). In the case of donor-acceptor (DA)-type molecular systems, intramolecular charge transfer (IMCT) can be induced by applying the external electric field to molecular systems along the charge transport direction, providing a possible switching mechanism which does not depend upon the electron-phonon coupling effect and is different from the negative differential resistance mechanism observed in the well-known NO2-substituted phenylene ethynylene oligomers. When the EFIMCT proceeds, the molecular systems have strong static electron correlation effects, where the standard nonequilibrium Green's function-density functional theory (DFT) approach cannot be applied to the molecular junction. As a first step toward practical switching devices, we do quantum chemical studies on the EFIMCT in such molecular systems as an isolated molecule, instead of using the electrode-junction-electrode open quantum system model. A prototype molecule P1 is designed as a tentative candidate molecule where the EFIMCT can proceed. The complete active space self-consistent field (CASSCF) molecular orbital calculations on P1 indicate that the EFIMCT can proceed at the external electric field intensity of 0.003 au, corresponding to about 2.25 V bias voltage. This calculated result strongly suggests that the development of this type of switching devices working at practically low bias voltage is feasible if the molecular system is properly designed. Broken symmetry unrestricted Hartree-Fock and spin-polarized Kohn-Sham DFT calculations also qualitatively reproduce the CASSCF results on P1, to some extent, indicating that these approaches can be employed for rough estimations on the EFIMCT such as the first screening of a large quantity of candidate molecules for this type of molecular devices. The possibility of molecular memory devices based on the EFIMCT is also discussed by analyzing the ground and excited potential energy surface model. Remaining challenges to develop practical molecular devices are discussed.

Structure-based lead optimization to improve potency and selectivity of a novel tetrahydroimidazo[1,2-a]pyridine-5-carboxylic acid series of heparanase-1 inhibitor

Heparanase-1 (HPSE1) is an endo-β-d-glucuronidase that is the only mammalian enzyme known to cleave heparan sulfate (HS) of heparan sulfate proteoglycans (HSPG), a key component of the glycocalyx layer of the vascular endothelium matrix. Inhibition of HPSE1 has therapeutic potential for cancer and proteinuric kidney diseases. We previously reported that 2 showed a moderate potency as an HPSE1 inhibitor and an issue of selectivity against exo-β-d-glucuronidase (GUSβ) and glucocerebrosidase (GBA) remained. A structure-based lead optimization of 2 using X-ray co-crystal structure analysis and fragment molecular orbital calculation resulted in 4e, which showed a more than 7-fold increase in HPSE1 inhibitory activity. The subsequent introduction of a methyl group into the 6-hydroxy group of 4e resulted in 18 with reduced inhibitory activities against GUSβ and GBA while maintaining the inhibitory activity against HPSE1. The inhibitory activities of 18 against serum HPSE1 in mice were significant and lasted for 4 h at doses of 3, 30, and 100 mg/kg. Compound 18 could be a novel lead compound for HPSE1 inhibitors with improved inhibitory activity against HPSE1 and increased HPSE1 selectivity over GUSβ and GBA.

Computational Approach for Molecular Design of Small Organic Molecules with High Hole Mobilities in Amorphous Phase Using Random Forest Technique and Computer Simulation Method

Abstract A molecular design system of small organic molecules was developed to realize high hole mobility in the amorphous phase by using the random forest (RF) technique and a computer simulation method. Since there was no accessible datasets of the hole mobilities in the amorphous phase, we have constructed a datasets of experimental hole mobilities for 321 organic molecules with calculated MO energies to utilize machine learning techniques for molecular design procedures. RF was applied to the machine learning technique using the constructed datasets. The optimized RF exhibited correlation coefficients of 0.885 and 0.764 for the training and testing datasets, respectively. The modified ChemTS to use optimized RF was adapted to design molecules with high hole mobilities. The successive conduction (SC) model that uses ab initio molecular orbital (MO) calculations and the Marcus theory was adapted to ensure the predicted mobilities. The generated molecules were verified to have high calculated hole mobility (the order of 10−2 cm2/Vs) owing to the highest transfer integral and lowest reorganization energy by the theoretical successive conduction (SC) model. The datasets and programs used in this work were publicly released on GitHub.

Mechanistic study of lodenafil carbonate electrochemical reduction in acid medium

The electrochemical reduction mechanism of lodenafil carbonate in acidic medium was studied using cyclic voltammetry, square wave voltammetry and chronoamperometry (sulfuric acid 0.1 mol L-1, potential controlled at -1.2 V). The formed product characterization was carried out by FT-IR spectroscopy combined with quantum calculations of the lodenafil molecular orbitals. Over the products IR spectrum, it was possible to note the presence of absorption bands corresponding to the aldehyde, amine and ethanol groups. These results, together with those obtained by electrochemical techniques and quantum calculations, allowed us to propose that the process of reducing lodenafil is dependent on protons and occurs in four irreversible steps, the first being the amide group reduction to an aldehyde and a primary amine. Then, the aldehyde is reduced to an alcohol, with the consumption of two electrons and two protons in each of these steps. Then, there is a reduction in two processes of one electron and one proton each, one of which by a radical way. In this last process, there are two possibilities: one is the sulfone group reduction and the other is the azomethine reduction adjacent to the amine group formed in the previous step.

Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 3CLpro through Structure-Based Virtual Screening and Experimental Approaches.

3CLpro is a viable target for developing antiviral therapies against the coronavirus. With the urgent need to find new possible inhibitors, a structure-based virtual screening approach was developed. This study recognized 75 pharmacologically bioactive compounds from our in-house library of 1052 natural product-based compounds that satisfied drug-likeness criteria and exhibited good bioavailability and membrane permeability. Among these compounds, three promising sulfonamide chalcones were identified by combined theoretical and experimental approaches, with SWC423 being the most suitable representative compound due to its competitive inhibition and low cytotoxicity in Vero E6 cells (EC50 = 0.89 ± 0.32 μM; CC50 = 25.54 ± 1.38 μM; SI = 28.70). The binding and stability of SWC423 in the 3CLpro active site were investigated through all-atom molecular dynamics simulation and fragment molecular orbital calculation, indicating its potential as a 3CLpro inhibitor for further SARS-CoV-2 therapeutic research. These findings suggested that inhibiting 3CLpro with a sulfonamide chalcone such as SWC423 may pave the effective way for developing COVID-19 treatments.

Low entropic cost of binding confers high selectivity on an allosteric ERK2 inhibitor

Extracellular signal-regulated kinase 2 (ERK2), a mitogen-activated protein kinase (MAPK), plays an essential role in physiological cellular processes and is a drug target for treating cancers and type 2 diabetes. A previous in silico screening study focusing on an allosteric site that plays a crucial role in substrate anchoring conferred an ERK2 inhibitor (compound 1). In this report, compound 1 was found to show high selectivity toward ERK2 compared with the nearest off-target p38α MAPK, and the crystal structure revealed that compound 1 binds to the allosteric site of ERK2. Fragment molecular orbital calculations based upon this crystal structure provided the structural basis to improve potency of compound 1 derivatives. Further computational studies uncovered that the low entropic cost of binding conferred the high selectivity of compound 1 toward ERK2 over p38α MAPK. These findings demonstrate the feasibility of developing potent and selective ERK2 inhibitors.

Relationship between the contact angle of pure Cu and its alloys owing to liquid Na and electronic states at the interface

Contact angle is an indicator of the wettability between liquid Na and pure metals. This has been evaluated using the atomic interactions obtained from the calculations of the electronic structure of the interface. This study aims to investigate the applicability of the atomic interactions of the interface to the alloys. An interface model between Cu and Na with an alloying element was constructed, and the electronic states of the interface were calculated by the molecular orbital calculation. The bond order, which indicates the strength of the covalent bonding at the interface, and ionicity, which indicates the amount of charge transfer, were obtained as theoretical parameters from the calculation. The contact angles between the Cu or Cu alloys and liquid Na were measured using a droplet of liquid Na at 423 K in a high-purity Ar atmosphere. The contact angles of the Cu alloys were evaluated using these theoretical parameters. As a result, a correlation was obtained between the ratio of the bond order between the substrate metal atoms to the bond order between the Na atom and the substrate metal atoms and the contact angle, which is consistent with previous studies. Furthermore, for the first time, the correlation between the ionicity or difference in the ionicity and contact angle was clarified. The difference in ionicity is the difference between the ionicity of Na atoms and that of the alloying element, indicating the strength of the ionic bonding. It was suggested that Cu and Cu alloys should consider covalent and ionic bonding when evaluating wettability, because Cu has an intermediate electronic state between transition and nontransition metals. Further, it became clear that the evaluation of the contact angle using the atomic interactions at the interface are applicable not only to pure metals but also to alloys.

Controllable synthesis of 3D superhydrophilic Cd(II) ion-imprinted polymer microspheres based on OV-POSS and bifunctional monomers synergy with superior selectivity for Cd(II) adsorption

Novel 3D porous Cd(II) ion-imprinted polymer (Cd(II)-IIP) microspheres based on octavinyl polyhedral oligomeric silsesquioxane (OV-POSS) were prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization technique combined with the synergistic effect of N-hydroxymethylacrylamide (NMA) and 1-vinylimidazole (1-VI) as bifunctional monomers. RAFT polymerization could achieve a controllable synthesis of polymer networks on OV-POSS. The structure, composition and properties of Cd(II)-IIP were systematically investigated by X-ray diffraction, scanning electron microscopy, transmission electron microscopy, atomic force microscope, water contact angle and thermogravimetric analysis. The results showed that the adsorbent, with a water contact angle of 0 ° and superhydrophilicity, has a high potential for application in aqueous phase systems. Different parameters influencing the sorption performance of Cd(II)-IIP, such as OV-POSS ratio, functional monomers ratio, adsorbent dosage, pH and adsorption time were optimized. Under optimal conditions, the maximum adsorption amount of Cd(II)-IIP for Cd(II) was 80.21 mg/g, and the adsorption equilibrium state could be reached within 40 min. The sorption kinetics proved that the sorption was chemisorption and the rate-limiting step was intraparticle diffusion. Thermodynamic studies showed that Cd(II) sorption was a spontaneous endothermic process. Importantly, XPS analysis, density functional theory (DFT) and frontier molecular orbital (FMO) theory calculations showed that the sorption of Cd(II)-IIP was attributed to the coordination of O and N atoms with Cd(II) on NMA and1-VI, respectively. Actual water sample analysis results indicated that Cd(II)-IIP was an adsorbent of great application potential.

First-Principles Analysis of the Effects of Covalency and Ionicity on the 4f-5d Transition Energy of Ce3+ in Garnet-Type Oxides

Abstract A blue light-emitting diode (LED) and a yellow phosphor are frequently combined to create white LEDs, with (Ce3+)-doped YAG as a common phosphor utilized in this process. Yellow light is produced when Ce3+ ions, excited by blue LEDs, are combined with direct blue light to form white light. This study investigated the effects of electronic characteristics, such as covalency and ionicity, on the 5d and 4f level energies of Ce3+ in garnet-type crystals using relativistic discrete variational-Xα (DV-Xα) molecular orbital (MO) calculations. The purpose of this study is to elucidate a detailed mechanism for the centroid shift of the 5d level energies of Ce3+ in crystals based on the MO theory. The theoretical 4f-5d transition energies agreed well with experimental ones, and electronic structure analysis revealed a high correlation between the centroid shift and the net charge of Ce3+. The primary cause of the centroid shift of the 5d level energies relative to the lowest 4f level of Ce3+ in crystals is an increase of the 4f level energies caused by a reduction of the net charge of Ce3+. These results provide a theoretical foundation for the creation of novel Ce3+-doped garnet phosphors for use in displays and solid-state lighting.

Synthesis and Characterization of Octacyano-Fe-Phthalocyanine.

Octacyano-metal-phthalocyanine MPc(CN)8 is a promising n-type stable organic semiconductor material with eight cyano groups, including a strong electron-withdrawing group at its molecular terminals. However, a thorough investigation of MPc(CN)8 has not yet been conducted. Therefore, we synthesized FePc(CN)8 and investigated its crystal structure, chemical and electronic states, electrical properties, photocatalytic activity, and magnetic properties. In this paper, we discuss the various properties of MPc(CN)8 in comparison with those of FePc. X-ray diffraction measurements indicated that the crystal structure of FePc(CN)8 was strongly influenced by the cyano groups and differed from the α- and β-forms of FePc. The space group P4/mcc structure of FePc(CN)8 was similar to that of the x-form of LiPc. The ultraviolet-visible (UV-vis) absorption spectrum of FePc(CN)8 was observed at wavelengths longer than that of FePc. Density functional theory-based molecular orbital calculations indicated that the energy gap of FePc(CN)8 is smaller than that of FePc, which can lead to the observation of the Q-band in the UV-vis absorption spectrum of FePc(CN)8 at longer wavelengths than that of FePc. Because FePc(CN)8 has a wider optical absorption band in the visible region than FePc, its photocatalytic activity is approximately four times higher than that of FePc. The conductivity of FePc(CN)8 was also higher than that of FePc, which is due to the larger overlap of π-electron clouds of the molecules in the crystal structure of FePc(CN)8. Magnetic measurements revealed that FePc(CN)8 exists in an antiferromagnetic ground state. The magnetic properties of FePc(CN)8 are specific to its crystal structure, with direct exchange interactions between Fe2+ ions and π-electron-mediated interactions. In particular, the Pauli paramagnetic behavior at high temperatures and the antiferromagnetic behavior at low temperatures (Weiss temperature θ = -4.3 ± 0.1 K) are characteristic of the π-d system.

Revaluation of copper(II)-Schiff base complex for sensing of d-penicillamine and development of a molecular logic gate: A combined approach

d-penicillamine (D-PA) being a tri-functional organic compound (thiol, amine, and carboxylic acid) is used as a chelating drug for many serious diseases like Wilson’s disease. Due to its serious adverse effects, regular monitoring of blood and urine for D-PA is required during the clinical application of the drug. The dye-containing Cu(II)-Schiff base complex is revisited for easy monitoring of D-PA and the development of a new molecular logic gate through extensive studies. Revaluation is carried out in light of extensive experimental evidence and theoretical rationalization which help to achieve the target. The synthesized Cu(II)-salicylaldehyde rhodamine B hydrazone complex is characterized through FTIR, NMR, Mass spectrometry, UV–Vis, and fluorescence titrations. The crystal structure of the complex is optimized through DFT studies and found distorted square planar. Calculations of Frontier Molecular Orbitals (FMOs) assist to understand the electronic and optical properties of the complex. The recognition of D-PA (LOD = 2.60 × 10-8 M) is executed both colorimetrically and fluorometrically through the “Turn-off” mechanism. The NAND-type molecular logic gate has been developed.

Structural and Computational Analyses of the Unique Interactions of Opicapone in the Binding Pocket of Catechol O-Methyltransferase: A Crystallographic Study and Fragment Molecular Orbital Analyses.

A third-generation inhibitor of catechol O-methyltransferase (COMT), opicapone (1), has the 3-nitrocatechol scaffold as do the second-generation inhibitors such as entacapone (2) and tolcapone (3), but only 1 can sustainably inhibit COMT activity making it suitable for a once-daily regimen. These improvements should be attributed to the optimized sidechain moiety (oxidopyridyloxadiazolyl group) of 1 substituted at the 5-position of the 3-nitrocatechol ring. We analyzed the role of the sidechain moiety by solving the crystal structures of COMT/S-adenosylmethionine (SAM)/Mg/1 and COMT/S-adenosylhomocysteine (SAH)/Mg/1 complexes. Fragment molecular orbital (FMO) calculations elucidated that the dispersion interaction between the sidechains of Leu 198 and Met 201 on the β6β7-loop and the oxidopyridine ring of 1 were unique and important in both complexes. In contrast, the catechol binding site made a remarkable difference in the sidechain conformation of Lys 144. The ε-amino group of Lys 144 was outside of the catalytic pocket and was replaced by a water molecule in the COMT/SAH/Mg/1 complex. No nitrocatechol inhibitor has ever been reported to make a complex with COMT and SAH. Thus, the conformational change of Lys 144 found in the COMT/SAH/Mg/1 complex is the first crystallographic evidence that supports the role of Lys 144 as a catalytic base to take out a proton ion from the reaction site to the outside of the enzyme. The fact that 1 generated a complex with SAH and COMT also suggests that 1 could inhibit COMT twofold, as a typical substrate mimic competitive inhibitor and as a product-inhibition enhancer.

Density Functional Theory (DFT) Study of Methyl 2-methoxycyclohex-3-ene-1-carboxylate for structure optimization, transition state, vibrational, electronic and PES scan

The current investigation is carried out to study stability of Diels-Alder adduct methyl 2-methoxycyclohex-3-ene-1 where (a) and (e) represent axial and equatorial orientation of group .The region-selective mechanism of Diels-Alder reaction between 1-methoxy 1,3butadiene (1) and methyl acrylate (2) to give methyl 2-methoxycyclohex-3-ene-1-carboxylate (3) is studied using Density Functional Theory (DFT). There are three possible stereo-chemical products possible for this reaction such as axial-axial (a,a), equatorial-equatorial (e,e) and axial-equatorial (a,e). Density Functional Theory was carried out to study the optimized molecular structure and the Potential Energy Surface (PES) Scan. The Frontier Molecular Orbital (FMO) energy calculations were carried out and HOMO LUMO energy gap was calculated to analyse the stability and reactivity. The Molecular Electrostatic Potential (MEP) study was carried out to analyse the surface of the molecule. FTIR spectra show the vibrational analysis of molecule.

Stabilizing Effect of a 4c/6e Hypervalent Bond in Dinitrodiphenyl Disulfides and Their Thermochemical Properties: Experimental and Computational Approach.

Thermochemical properties and intramolecular interactions of 2,2'-dinitrodiphenyl disulfide (2DNDPDS) and 4,4'-dinitrodiphenyl disulfide (4DNDPDS) were determined and analyzed. Their standard molar formation enthalpies in the gas phase (ΔfHm°(g)'s) were experimentally determined; theoretically, they were computed using the G4 composite method and atomization reactions. Specifically, ΔfHm°(g)'s were obtained by combining formation enthalpies in the condensed phase and enthalpies of phase change. Formation enthalpies in the condensed phase were determined experimentally through combustion energies, which in turn were found by means of a rotatory bomb combustion calorimeter. Sublimation enthalpies were derived from thermogravimetric experiments, measuring the rate of mass loss and using Langmuir and Clausius-Clapeyron equations. Fusion enthalpies and heat capacities of the solid and liquid phases were measured as functions of temperature by differential scanning calorimetry, and the heat capacities of the gas phase were calculated via molecular orbital calculations. Theoretical and experimental ΔfHm°(g)'s differed by <5.5kJ·mol-1, and isomerization enthalpies are discussed. In addition, using theoretical tools [natural bond orbitals (NBO) and quantum theory of atoms in molecules (QTAIM)], intramolecular interactions were analyzed. An uncommon hypervalent four-center six-electron interaction of type O···S-S···O was found in 2DNDPDS. This hypervalent interaction, in addition to the extent of conjugation between the aryl and NO2 moieties and the formation of intramolecular C-H···S hydrogen bonds, counteracts the repulsion caused by steric repulsions. Hydrogen bonding was confirmed through geometric parameters as well as QTAIM.

Insight into the Structural and Emissive Behavior of a Three-Dimensional Americium(III) Formate Coordination Polymer.

We report the structural, vibrational, and optical properties of americium formate (Am(CHO2 )3 ) crystals synthesized via the in situ hydrolysis of dimethylformamide (DMF). The coordination polymer features Am3+ ions linked by formate ligands into a three-dimensional network that is isomorphous to several lanthanide analogs, (e. g., Eu3+ , Nd3+ , Tb3+ ). Structure determination revealed a nine-coordinate Am3+ metal center that features a unique local C3v symmetry. The metal-ligand bonding interactions were investigated by vibrational spectroscopy, natural localized molecular orbital calculations, and the quantum theory of atoms in molecules. The results paint a predominantly ionic bond picture and suggest the metal-oxygen bonds increase in strength from Nd-O<Eu-O<Am-O. The optical properties were probed using diffuse reflectance and photoluminescence spectroscopies. Notably, the rarely reported 5 D1' →7 F0' emission band is observed and dominates the emission spectrum. This behavior is unusual and is attributed to the C3v coordination environment of the metal center.

N'-(3,4-dimethoxybenzylidene)-4-methylbenzenesulfonohydrazide derivatives: Synthesis, quantum chemical method, in silico ADMET, molecular docking and molecular dynamic simulations

A new N'-(3,4-dimethoxybenzylidene)-4-methylbenzenesulfonohydrazide derivatives were prepared from a condensation reaction between 4-methylbenzenesulfonohydrazide and 3,4-dimethoxybenzaldehyde. The structure of DMSH was elucidated using various spectral techniques including FT-IR, 1HNMR and 13CNMR. The structure of DMSH bond parameters also confirmed by single crystal XRD analysis of related derivatives and optimized bond parameters are calculated by density functional theory (DFT) method at B3LYP/6–311 G (d, p) level of theory. The optimized geometrical parameters obtained by DFT calculation are in good agreement with single crystal XRD data. The experimentally observed FT-IR bands were assigned to different normal modes of the molecule. The results show a good agreement with each other when these computed bond parameters are compared to XRD values of related compounds. The stability, chemical reactivity and charge transfer within the molecule was explained by frontier molecular orbital calculations. Atomic charges on the various atoms of DMSH obtained by Mulliken population analysis. Potential reactive sites of the DMSH compound have been identified by MEP which is mapped to the electron density surfaces. The reported molecule is used as a potential NLO material since it has a high μβ0 value. The theoretical UV–vis spectrum of the compound is used to study the visible absorption maxima (λ max). The molecular docking mechanism between DMSH ligand and COVID-19/6WCF and COVID-19/6Y84 receptors were studied to investigate the binding modes of this compound at the active sites. Molecular docking outcomes have shown that the DMSH molecule can be considered as a potential agent against COVID-19/6WCF-6Y84 receptors. In addition, the theoretical parameters of the bioactive molecules were calculated to establish their drug-likeness qualities and ADME/T analysis was carried out to examine the drug properties of the synthesized compound. Molecular dynamics simulation was performed for COVID-19 main protease (Mpro: 6WCF/6Y84) to understand the elements governing the inhibitory effect and the stability of interaction under dynamic conditions. The resultant complex structures were subjected to 100 ns simulation run to estimate their binding stabilities using GROMACS. The molecular dynamics simulation studies provided essential evidence that the systems were stable during the progression of 100 ns simulation run.

Thermal behavior of borax, Na2B4O5(OH)4·8H2O

Abstract Globally, borax is one of the most important borate minerals, both industrially and from a technological viewpoint. Despite its importance, there have been only a few reports on the structural changes of borax upon heating. In this study, we have investigated the thermal behavior and structural characteristics of borax using thermal analysis, in situ high-temperature synchrotron X-ray diffraction, in situ variable-temperature single-crystal X-ray diffraction, and quantum chemical calculations. Differential scanning calorimetry (DSC) curve showed a large endothermic peak at 349 K corresponding to the dehydration reaction of borax. X-ray diffraction (XRD) pattern remained almost unchanged up to 353 K. Above 363 K, the XRD peaks gradually became less intense until they disappeared at 403 K. The unit-cell volume continuously increased with increasing temperature and became constant just before its phase transition to tincalconite. The volumetric thermal expansion coefficient between 113 and 323 K was 7.84 × 10–5 K–1. The a and c lattice parameters exhibited a slight increase trend with increasing temperature, whereas the b lattice parameter increased significantly. Therefore, the thermal expansibilities followed the order b/b0 &amp;gt;&amp;gt; c/c0 &amp;gt; a/a0. The increasing b lattice parameter was closely related to the elongation of the O4···H7B hydrogen-bond interaction along the b-axis. Na-O bond lengths were isotropically expanded with increasing temperature, whereas the B-O bond lengths and angles remained unchanged even after the phase transition to tincalconite. Molecular orbital calculations revealed that an electron cloud shared by two borate tetrahedra led to the formation of a large electron cloud distribution over the B4O5(OH)4 cluster. The intramolecular interactions with substantial covalent character made the cluster quite rigid. The existence of borate minerals containing the B4O5(OH)4 clusters in their structure evidenced the presence of moderately acidic or alkaline water, wherein the borate minerals grew via the incorporation of B4O5(OH)4 clusters. Our results indicate that the connection geometry of the fundamental building block consisting of Bφ3 triangles and Bφ4 tetrahedra (φ: O2–, OH–) can potentially be used as a palaeoenvironmental indicator.

Degradation of atrazine by a UV-activated organic chloramines process: kinetics, degradation pathways, disinfection by-product formation, and toxicity changes

Pre-chlorination is a typical drinking water treatment process to control algae growth and degrade contaminants. However, abundant dissolved organic nitrogen in the water environment, forms organic chloramines after pre-chlorination, affecting the degradation of organic pollutants. Herein, UV radiation is used to activate organic chloramines to degrade atrazine (ATZ). Electron spin resonance (ESR) spectra showed that ATZ was effectively degraded after organic chloramines were activated to generate Cl• and HO• by UV irradiation. Combined with the analysis of Kintecus software, the reaction pH exhibited a significant effect on ATZ degradation in the UV-activated organic chloramines process. By integrating UPLC-MS/MS analysis and frontier molecular orbitals calculation, identified six major degradation intermediates of ATZ and conversion pathways were proposed. The disinfection by-products (DBPs) concentration decreased during the post-chlorination process, indicating the great potential of the UV-activated organic chloramines process in eliminating micropollutants and controlling the formation of DBPs. Acute toxic changes in zebrafish larvae during ATZ degradation and post-chlorination, combined with Toxicity Estimation Software Tool (T.E.S.T.) and Ecological Structure Activity Relationship (ECOSAR) software revealed that ATZ produced more toxic intermediates. Therefore, it is necessary to further optimize disinfection for the practical application of UV-activated organic chloramines.