Molecular Orbital Calculations Research Articles

Separation of indium and tin from ITO powders with short-chain dicarboxylic acid-ChCl deep eutectic solvents: Indium tin leaching and splitting mechanism

The substitution of corrosive mineral acids with green deep eutectic solvents (DESs) for extracting rare and precious metals from discarded electronic devices has a sustained appeal for developing clean hydrometallurgical processes. However, the dissolution mechanism of DESs on specific metals still requires an exhaustive understanding. In this work, short-chain dicarboxylic acid-choline chloride DESs were used to dissolve indium tin oxide (ITO) to achieve the separation of indium and tin. Kinetic and thermodynamic studies have shown that the leaching of indium and tin was considered a mixed control of diffusion and chemical reaction, with low activation energies (Ea(In) = 39.93 kJ/mol, Ea(Sn) = 39.52 kJ/mol). The electrospray ionization mass spectrometry (ESI-MS) analysis of the leaching solution and molecular orbital calculations revealed that tin was leached in the main form of [Sn4+(OH−)3(H2O)]+ cation as well as slight [Sn4+MA2−(Cl−)3]− anion, while the dominant ions of indium were [In3+(Cl−)4]− ligand as well as small amounts of [In3+MAH−(Cl−)4]2−, [In3+(MA2−)3]3− and [In3+MA2−(Cl−)2]−. The tin-containing species in the leaching solution can be completely precipitated in the form of cassiterite SnO2 through water dilution and hydrothermal treatment, in which amorphous indium-containing substances were mixed. Most of the indium was retained in the form of [In3+(Cl−)4]− in the liquid. After adjusting the pH of the solution, over 99% of the indium precipitated out as In(OH)3, and after calcination at 600 °C in air for 1 hour, In2O3 was obtained. This study unveiled the leaching mechanism of short-chain dicarboxylic acid-choline chloride DESs on ITO powders. It developed a green, simple, and mild process for potentially recovering ITO-based materials.

Intermolecular interactions in 4-bromoaryl derived aldimines: X-ray structure, Hirshfeld surface analysis, DFT and molecular docking studies

A convenient and facile synthesis of (E)-N-(4-bromophenyl)-1-phenylmethanimine (b), (E)-N-(4-bromophenyl)-1-(2,4-dinitrophenyl) methanimine (c) and (E)-4-(((4-bromophenyl)imino) methyl)-2-methoxyphenol (d) was accomplished by refluxing 4-bromo aniline(a) with an appropriate aldehyde in solvent methanol. X-ray crystallography, theoretical computations, and spectroscopic techniques were utilized to describe and detect interactions between and among various groups of synthesized imines (b-d). Compound b-d crystallize in monoclinic crystal systems with space groups Pnma, P21, P21/c, and P21/c, respectively, whereas compound a crystallize in orthorhombic crystal systems. To identify the intermolecular interactions, Hirshfeld surface analysis was also used, emphasizing the importance of hydrogen bonding, van der Waals forces, and the impact of substituents. Hirshfeld surface fingerprint plots were used to study crystal packing motifs. Energy frameworks examined the electrostatic energy input that stabilizes solid state structures. Additionally, studies pertaining to the optimization of the structure, frontier molecular orbital (highest occupied–lowest unoccupied) and molecular electrostatic potential calculations were conducted. Lastly, using the membrane protein of the naturally occurring fungus Candida albicans SC5314, molecular docking investigations of compounds a–d were conducted (PDB-ID 7RJE)

Novel Deliberately Sensitive and Selective Tetrahydrozoline Voltammetric Sensors Integrated with a Copper Oxide Nanoparticle/Zeolite Platform.

The present study introduced a novel disposable screen-printed carbon electrodes (SPCEs) modified with copper oxide/zeolite nanostructures for eco-friendly selective differential pulse voltammetric quantification of tetrahydrozoline (THZ) in eyedrop samples and biological fluids. Modification of the electrode matrix with copper oxide nanoparticles/zeolite nanostructures (CuONPs/ZY) with their effective and synergistic electrocatalytic activity enhanced the electrode performance against electrooxidation of THZ at 0.960 V in BR at pH 9.0 with a diffusion-controlled reaction mechanism. The tentative oxidation mechanism based on molecular orbital calculations postulates the oxidation of THZ molecules through oxidation of a nitrogen atom five-membered ring and the participation of two electrons/protons in the electrode reaction. Linear calibration curves were illustrated within a wide THZ concentration range from 0.24 to 57.2 μg mL-1 recording a limit of detection (LOD) value of 0.0799 μg mL-1. The CuONPs/ZY/SPEs exhibited improved performance compared with the sole reported THZ sensor-based gold film-plated carbon paste electrodes, in addition to their high reproducibility of fabrication and measurement and prolonged shelf lifetime. Tetrahydrozoline was successfully assayed in the presence of excipients, degradation products, and chloramphenicol. The presented voltammetric sensor can be considered as an eco-friendly and reliable analytical approach for monitoring THZ residues in eye drop samples and biological fluids with high recovery compared with the official pharmacopeial analytical protocol. The presented sensors were assessed according to an EcoScale tool and also compared with the reported THZ sensor.

Prediction of Binding Pose and Affinity of Nelfinavir, a SARS-CoV-2 Main Protease Repositioned Drug, by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations.

A novel in silico drug design procedure is described targeting the Main protease (Mpro) of the SARS-CoV-2 virus. The procedure combines molecular docking, molecular dynamics (MD), and fragment molecular orbital (FMO) calculations. The binding structure and properties of Mpro were predicted for Nelfinavir (NFV), which had been identified as a candidate compound through drug repositioning, targeting Mpro. Several poses of the Mpro and NFV complexes were generated by docking, from which four docking poses were selected by scoring with FMO energy. Then, each pose was subjected to MD simulation, 100 snapshot structures were sampled from each of the generated MD trajectories, and the structures were evaluated by FMO calculations to rank the pose based on binding energy. Several residues were found to be important in ligand recognition, including Glu47, Asp48, Glu166, Asp187, and Gln189, all of which interacted strongly with NFV. Asn142 is presumably regarded to form hydrogen bonds or CH/π interaction with NFV; however, in the present calculation, their interactions were transient. Moreover, the tert-butyl group of NFV had no interaction with Mpro. Identifying such strong and weak interactions provides candidates for maintaining and substituting ligand functional groups and important suggestions for drug discovery using drug repositioning. Besides the interaction between NFV and the amino acid residues of Mpro, the desolvation effect of the binding pocket also affected the ranking order. A similar procedure of drug design was applied to Lopinavir, and the calculated interaction energy and experimental inhibitory activity value trends were consistent. Our approach provides a new guideline for structure-based drug design starting from a candidate compound whose complex crystal structure has not been obtained.

Study of Interactions of Nucleoside Anticancer Drugs, Capecitabine and Gemcitabine, with SWNT and BNNT using Molecular and Quantum Mechanical Calculations

Abstract: Using single-wall carbon nanotubes (SWCNTs) and boron nitride nanotubes (BNNTs), this study evaluated the interactions between Capecitabine (CAP) and Gemcitabine (GEM). Molecular mechanics and quantum mechanics were used in the analysis. : The interaction between CP and GM with SWCNTs and BNNTs under various solvents was analyzed using the self-consistent reaction field (SCRF) as a model and DFT as the analytical method. Additionally, the effect of temperature on the stability of the molecule interactions during the experiment was examined. The thermodynamic properties of the title compounds were analyzed based on theoretical calculations. It included the calculation of Frontier Molecular Orbitals (FMOs) and Total Density of States (DOS). In addition to studying the ionization potential (I), we also examined the other molecular properties of the structures, such as electrophilicity (ω), electron affinity (A), chemical hardness (η), and electronic chemical potential (μ). To investigate the interaction between CAP and GEM with SWCNTs and BNNTs, molecular mechanics methods (MM) including AMBER, OPLS, CHARMM, and MM+ force fields, were employed. Monte Carlo simulation techniques were used to calculate the results at different temperatures. : The effects of the liquid phase and mixed solvent media with varying dielectric constants (Water, DMSO, Methanol, and Ethanol) on the interaction between CAP and GEM using the force fields described above were examined in this study. The correlation between data generated by Monte Carlo, Quantum Mechanics, and Molecular Mechanics was demonstrated. There was a striking similarity in the thermodynamic properties and conformer populations of all three materials.

Developing high-power Li||S batteries via transition metal/carbon nanocomposite electrocatalyst engineering.

The activity of electrocatalysts for the sulfur reduction reaction (SRR) can be represented using volcano plots, which describe specific thermodynamic trends. However, a kinetic trend that describes the SRR at high current rates is not yet available, limiting our understanding of kinetics variations and hindering the development of high-power Li||S batteries. Here, using Le Chatelier's principle as a guideline, we establish an SRR kinetic trend that correlates polysulfide concentrations with kinetic currents. Synchrotron X-ray adsorption spectroscopy measurements and molecular orbital computations reveal the role of orbital occupancy in transition metal-based catalysts in determining polysulfide concentrations and thus SRR kinetic predictions. Using the kinetic trend, we design a nanocomposite electrocatalyst that comprises a carbon material and CoZn clusters. When the electrocatalyst is used in a sulfur-based positive electrode (5 mg cm-2 of S loading), the corresponding Li||S coin cell (with an electrolyte:S mass ratio of 4.8) can be cycled for 1,000 cycles at 8 C (that is, 13.4 A gS-1, based on the mass of sulfur) and 25 °C. This cell demonstrates a discharge capacity retention of about 75% (final discharge capacity of 500 mAh gS-1) corresponding to an initial specific power of 26,120 W kgS-1 and specific energy of 1,306 Wh kgS-1.

DFT study on the effects of substituents on the structure and properties of dithiophosphate collectors

AbstractThe structures and properties of seven substituted dithiophosphate (DTP) collectors containing three types of functional groups (O2PS2, C2PS2, and N2PS2) were studied using density functional theory. The collectors studied were dibutyl dithiophosphate (DNBDTP), diisobutyl dithiophosphate (DIBDTP), dibutoxyethyl dithiophosphate (DBOEDTP), xylenol dithiophosphate (DMPDTP), diisobutyl dithiohypophosphite (3418A), diphenylamine dithiophosphate (DTADTP), and dicyclohexylamine dithiophosphate (DCADTP). The structural analysis showed that the PS bond lengths in the C2PS2 and N2PS2 types are longer than those in the O2PS2 type, indicating that the strength of the PS bond is weaker in the former two. The frontier molecular orbital studies showed that the energy differences between the highest occupied molecular orbitals (HOMO) of 3418A (C2PS2 type) and DCADTP (N2PS2 type) and the lowest unoccupied molecular orbital (LUMO) of galena are significantly lower than those of the other collectors, suggesting that C2PS2 type and N2PS2 type with cyclohexane could enhance the interaction with galena. Using the Fukui function to calculate the nucleophilicity and electrophilicity of the sulfur atom indicated that the S atom exhibits nucleophilicity, especially in DMPDTP and DTADTP, which contain benzene rings, and the S atom exhibits strong nucleophilicity without electrophilicity. However, due to the lack of contribution from S atoms to the LUMO orbitals, the S atoms in these two compounds are not participate in any LUMO reactions. The adsorption results demonstrated that 3418A (C2PS2 type) and DCADTP (N2PS2 type) exhibit the strongest adsorption on Pb2+ ions, while DMPDTP (C2PS2 type) and DTADTP (O2PS2 type) which contain benzene rings, as well as DBOEDTP (C2PS2 type) which does not contain a benzene ring, exhibit weaker interaction compared to the other compounds. These are consistent with the results of the frontier molecular orbital and electrophilic nucleophilicity calculations.

Synthesis and Antibacterial Activity of Azomethine Ligand and Their Metal Complexes: A Combined Experimental and Theoretical Study

An asymmetrical Schiff base triazole ligand (4-((3-mercapto-5-(naphthalen-1-ylmethyl)-4H-1,2,4-triazol-4-yl)imino)methyl)methoxy) (L) was used to generate novel micro complexes of Cr(III), VO(IV), and Mn(II) ions. Different spectroscopic techniques, including UV-vis spectroscopy, Fourier transform infrared spectroscopy (FTIR), flame atomic absorption, conductivity tests, CHNS elemental analysis, and magnetic susceptibility, were used to determine the structures of the Schiff base micro complexes. The density functional theory (DFT) calculation was screened to consider selected complexes. The observed data indicated their stability, and the expected chemical formula of vanadium(IV) was square pyramidal geometry in VO(L) complex formula. In contrast, the Cr(III) and Mn(II) complexes have octahedral geometry in the formulas. Frontier molecular orbitals calculations (MO) have also been performed to better understand the nature of orbitals, EHOMO, and ELUMO, allowing us to confirm the experimental finding. Pseudomonas aeruginosa and Bacillus subtilis, two types of potentially dangerous bacteria, were subjected to tests to see whether L and its metal complexes have any antibacterial activities or not. All compounds were also tested for their antifungal activity against two different types of fungi, Penicillium spp. and Aspergillus flavus. There is significant action has been noted in all cases for the complexes.

XRD/DFT, Hirshfeld surface analysis and molecular modelling simulations for unfolding reactivity of newly synthesized vanillin derivatives: excellent optical, NLO and protein binding efficiency

New vanillin derivatives, namely, ethyl (4-formyl-2-methoxyphenoxy)acetate (2a) and 2-(4-formyl-2-methoxyphenoxy)-N-phenylacetamide (2b), respectively, were synthesized and characterized by NMR (1H and 13C), IR, mass spectra and confirmed by single-crystal X-ray analysis. Hirshfeld surface (HS) analysis was performed to probe intra- and intermolecular interactions and surface reactivity. 2D fingerprint plots (FP) were used to study the nature and percentage contribution of intermolecular interactions leading to the formation of the crystal unit. Density functional theory (DFT) simulations were used to obtain the electronic structure and reactivity of the new molecules. Natural population analysis (NPA) and frontier molecular orbital (FMO) calculations reveal significant charge transfer and a reduced HOMO-LUMO gap up to 4.34 eV for 2b. Bader’s quantum theory of atoms in molecules (QTAIM) study is utilized to understand the surface topological and bonding nature of 2a and 2b. The performed molecular electrostatic potential (MESP) and density of states (DOS) study further suggest sites likely to be attractive to incoming reagents. At the same time, hyperpolarizability (βo) is used to characterize the nonlinear optical properties, and TD-DFT study shows the excitation energy and absorption behavior. In silico studies were performed, including docking, binding free energies (MMBGSA) and molecular dynamics simulations. Compounds 2a and 2b were docked with RdRp of SARS-Cov-2, and the MMBGSA for 2a and 2b were −30.70 and −28.47 kcal/mol, respectively, while MD simulation showed the stability of protein-ligand complexes. Communicated by Ramaswamy H. Sarma

Synthesis of Hybrid Porphyrin(2.1.2.1)s and Their Complexation.

Novel hybrid porphyrin(2.1.2.1)s and their boron and copper complexes were synthesized using the "toy bricks" synthetic method. Crystal data, frontier molecular orbital calculations, and electrostatic potential surface maps reveal that hybridization in the porphyrin(2.1.2.1) donor-acceptor unit controls the selective coordination of BF2.

Photochromism and Photomagnetism in Two Ni(II) Complexes Based on a Photoactive 2,4,6-Tris-2-Pyridyl-1,3,5-Triazine Ligand.

It is still challenging to construct novel photochromic and photomagnetic materials in the field of molecular materials. Herein, the 2,4,6-tris-2-pyridyl-1,3,5-triazine (TPTz) molecule was found to display photochromic properties under room temperature light irradiation. Two mononuclear structures, [Ni(H2O)(TPTz)(C2O4)]·2H2O (1; C2O42- = oxalate) [Ni(H2O)(TPTz)(C2O4)]·0.5H2O (2), and one chain compound [Ni(TPTz)(H2-HEDP)]·2H2O (3; HEDP = hydroxyethylidene diphosphonate) were obtained by assembling TPTz with polydentate O-ligands (oxalate and phosphonate) and the paramagnetic Ni2+ ions. The electron-transfer (ET)-dominated photochromism was observable in 1 and 2 after light irradiation with the photogeneration of relatively stable radicals, and the resultant photochromism was demonstrated via UV-vis, photoluminescence, X-ray photoelectron spectra, electron paramagnetic resonance spectra, and molecular orbital calculations. Due to the denser stacking interactions between the adjacent organic molecules, 2 exhibited a faster photochromic rate than 1. Compared with 1 and 2, compound 3 did not show photochromic behavior, which was deciphered by the theoretical calculations for all of the compounds. Importantly, the magnetic couplings appeared between photogenerated radicals and paramagnetic Ni2+ ions, resulting in a scarcely photomagnetic phenomenon of 1 and 2 in the Ni-based electron transfer photochromic materials. This work enriches the available kind of ligands for the design of ET photochromic materials, putting forward a method to tune the electron transfer photochromic efficiency in the molecular materials.

Enhancement of energy decomposition analysis in fragment molecular orbital calculations.

Energy decomposition analysis is one of the most attractive features of fragment molecular orbital (FMO) calculations from the point of view of practical applications. Here we report some enhancements for PIEDA in the ABINIT-MP program. One is a separation of the dispersion-type stabilization from the electron correlation energy, traditionally referred to as the "dispersion interaction" (DI). Another is an alternative evaluation of the electrostatic (ES) interaction using the restrained electrostatic potential (RESP) charges. The GA:CT stacked base pair and the Trp-Cage miniprotein were used as illustrative examples.

Optimization of First-Principles Calculation Conditions for Ce3+ in Perovskite-Type Oxides

The 4f-5d transition of Ce3+ in crystals is used in a variety of optical materials, including scintillators and phosphors. It also has the advantages that the wavelength can be controlled by the coordination environment and that Ce3+ is relatively inexpensive among rare earth elements. For the theoretical design of novel Ce3+-doped phosphors, prediction of 4f-5d transition energy by first-principles molecular orbital calculations using model clusters is effective. In general, increase of the cluster size improves the accuracy of calculations and reduces the difference between the experimental and calculated values while very large clusters have the disadvantage of requiring a huge amount of calculation time. Hence, understanding the cluster size dependence is important to determine the efficient and effective cluster size for the first-principles calculations.In this study we focused on Ce3+-doped in YAlO3, and performed first-principles calculations of the 4f-5d transition energies for model clusters with different sizes. At first, the local structures around the Y3+ site of YAlO3 were cut out from the crystal structure. Then the central Y3+ ions of these clusters were replaced by Ce3+ ions. Then the transition energy of Ce3+ in YAlO3 was calculated by the relativistic discrete-variational Xα (DV-Xα) molecular orbital calculations using the Slater's transition state method. The detailed comparison of the results showed that for clusters larger than a certain size, the error between the experimental and calculated values became negligibly small. For comparison, the lattice relaxation was also taken into account by modifying the model clusters using two different methods: the method based on the Shannon's crystal radii and the structural optimization using the CASTEP code, and the results were compared in detail.

Theoretical Analysis of Anomalous Emission of Eu2+ in Crystals By First-Principles Calculation

The 5d-4f transition energies of lanthanides are very versatile, especially the 4f65d1-4f75d0 transition energy of Eu2+ has high luminescence efficiency and is used in various luminescent materials such as phosphors like SrxCa1-xAlSiN3: Eu2+, scintillators, and solid-state lasers, etc. However, there are materials that do not undergo pure 5d-4f transitions, showing the so-called anomalous luminescence instead. The anomalous luminescence is caused by the formation of excitons due to the overlap of the 5d level of Eu2+ with the conduction band and the transition of electrons from the conduction band to the 4f level, resulting in a shift to a lower energy than the general 5d-4f transition energy. A more detailed analysis of this phenomenon is important for the development of novel luminescent materials using Eu2+.In this study, we aimed to theoretically analyze the anomalous luminescence based on first-principles electronic structure calculations. The model clusters of Eu2+-doped crystals consisting of Eu2+ at the substitution site and the surrounding ions were created. Then molecular orbital calculations were performed by the relativistic discrete-variational Xα (DV-Xα) method and subsequently multiplet calculations were performed by the relativistic discrete-variational multi-electron (DVME) method. These first-principles calculations were carried out for Eu2+-doped crystals that show anomalous luminescence and those that do not show anomalous luminescence, and the electronic states of these materials were compared in detail.

Prediction of 4f-5d Transition Energy of Ce3+ in Oxides By First-Principles Calculations and Machine Learning

A Ce3+ ion has only one electron in the 4f orbitals and its 4f-5d transition energy is strongly influenced by the width of the crystal field splitting of the 5d orbitals. In other words, the absorption and emission wavelengths of Ce3+ in crystals can be widely controlled by changing the ligand field environment. As an example of Ce3+-doped phosphor, Ce:YAG (Y3Al5O12) is widely used as an yellow phosphor for standard white LEDs. Therefore, novel phosphors with desired emission colors can be developed by adding Ce3+ to appropriate host crystals.In this work, we aimed to construct an efficient prediction model for the transition energy of Ce3+ in oxide crystals. Small clusters consisting of the substituted Ce3+ ion and the first-neighbor anions were constructed and molecular orbital calculations were performed using the relativistic discrete-variational Xα (DV-Xα) method. Then machine learning based on structural and electronic state parameters was performed to create a predictive model for the 4f-5d transition energy of Ce3+ in crystals. By creating the correlation diagrams, the influence of each parameter on the transition energy was analyzed in detail.

Synthesis and biological evaluation of 2′-hydroxychalcone derivatives as AMPK activators

A series of 2′-hydroxychalcone derivatives with various substituents on B-ring were synthesized and evaluated for AMP-activated protein kinase (AMPK) activation activity in podocyte cells. The results displayed that hydroxy, methoxy and methylenedioxy groups on B-ring could enhance the activitiy better than O-saturated alkyl, O-unsaturated alkyl or other alkoxy groups. Compounds 27 and 29 possess the highest fold change of 2.48 and 2.73, respectively, which were higher than those of reference compound (8) (1.28) and metformin (1.88). Compounds 27 and 29 were then subjected to a concentration–response study to obtain the EC50 values of 2.0 and 4.8 µM, respectively and MTT assays also showed that cell viability was not influenced by the exposure of podocytes to compounds 27 and 29 at concentrations up to 50 μM. In addition, compound 27 was proved to activate AMPK via calcium/calmodulin-dependent protein kinase kinase β (CaMKKβ)-dependent pathway without affecting intracellular calcium levels. The computational study showed that the potent compounds exhibited stronger ligand-binding strength to CaMKKβ, particularly compounds 27 (−8.4 kcal/mol) and 29 (−8.0 kcal/mol), compared to compound 8 (-7.5 kcal/mol). Fragment molecular orbital (FMO) calculation demonstrated that compound 27 was superior to compound 29 due to the presence of methyl group, which amplified the binding by hydrophobic interactions. Therefore, compound 27 would represent a promising AMPK activator for further investigation of the treatment of diabetes and diabetic nephropathy.

Synthesis, quantum chemical studies, molecular docking, molecular dynamics simulation and ADMET studies on 2-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-1, 4,5-triphenyl-1H-imidazole derivatives

A novel 2-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-1,4,5-triphenyl-1H-imidazole (DDTI) molecule was synthesised and characterised by FT-IR and NMR (1H and 13C) spectral techniques. The molecular structure was optimised using the density functional theory (DFT) method with B3LYP/6-311 G (d, p) basis set. Natural bonding orbital (NBO) analysis was used to determine the electron densities of donor (i) and acceptor (j) bonds as well as the hyperconjugative interaction energy (E ( 2) ). In highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) calculations, the smaller energy gap value was discovered. Molecular electrostatic potential has been analysed. The Mulliken atomic charges of the carbon, nitrogen and oxygen atoms were calculated at the same level of theory. The dipole moment, polarizability and first-order hyperpolarizability demonstrate the good nonlinear optical (NLO) feature of the title molecule. Molecular docking studies are implemented to analyse the binding energy of the DDTI compound against standard drugs such as the crystal structure of ADP ribose phosphatase of NSP3 from SARS-CoV-2 in complex with MES, SARS-CoV-2 main protease with an unliganded active site (2019-nCoV, corona virus disease 2019, COVID-19) and the crystal structure of COVID-19 main protease in complex with an inhibitor N3 found to be considered having better antiviral agent. Molecular dynamics simulation was performed for COVID-19 main protease (Mpro: 6WCF/6Y84/6LU7) to understand the elements governing the inhibitory effect and the stability of interactions under dynamic conditions. Virtual ADMET studies were carried out as well and a relationship between biological, electronic and physicochemical qualifications of the target compound was determined. Toxicity prediction by computational technique for the title compound was also carried out.

Quantum Chemical and Biological Properties of Coumarin Derivative Compound

This work presents the characterization of 8-t-buthyl-4-methyl-2H- chromen 2-one by quantum chemical calculations and spectral techniques. The molecular geometry, vibrational frequencies and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values of title compound in the ground state have been calculated using the density functional method (B3LYP) with the 6-31G(d) basis set. The theoretical vibrational frequencies and chemical shift values show good agreement with experimental values. In addition, DFT calculations of molecular electrostatic potentials and frontier molecular orbitals of the title were carried out at the B3LYP/6-31G(d) level of theory. The title compound was screened for antibacterial, antifungal and antioxidant activities.

Theoretical and experimental study of 5-ethoxymethylfurfural and ethyl levulinate production from cellulose

Theoretical simulations and experiments were taken to explore the mechanism of cellulose conversion into 5-ethoxymethylfurfural (EMF) and ethyl levulinate (EL) catalyzed by a mixed acid of Lewis acid and Brønsted acid. Up to 64.8 % total yield of EMF and EL can be obtained when the ratios of Lewis/Brønsted acid and water/ethanol (v/v) were 1:2 and 3:7 respectively. The results showed that Lewis acid and water could reduce the activation energy of EMF formation from 75.6 to 47.9 kJ mol−1, and mixed acids and water/ethanol system were beneficial to the accumulation of EMF. Moreover, the results of molecular dynamics (MD) simulation indicated that Lewis acid could promote the distribution of Bronsted acid around the β-1,4 glycosidic bond of cellobiose. The combination of DFT and frontier molecular orbital (FMO) calculation demonstrated that the breakage of the β-1,4 glycosidic bond was the main rate-limiting step of cellulose hydrolysis. Meanwhile, the mixed acid and water/ethanol system could accelerate the hydrolysis due to the reducing energy barrier and HOMO-LUMO gap. This study gave a deep insight into the mechanism of Lewis acid with Brønsted acid on cellulose conversion into EMF and EL.

In Silico Design of Natural Inhibitors of ApoE4 from the Plant Moringa oleifera: Molecular Docking and Ab Initio Fragment Molecular Orbital Calculations.

Alzheimer's disease (AD) is a neurological disease, and its signs and symptoms appear slowly over time. Although current Alzheimer's disease treatments can alleviate symptoms, they cannot prevent the disease from progressing. To accurately diagnose and treat Alzheimer's disease, it is therefore necessary to establish effective methods for diagnosis. Apolipoprotein E4 (ApoE4), the most frequent genetic risk factor for AD, is expressed in more than half of patients with AD, making it an attractive target for AD therapy. We used molecular docking simulations, classical molecular mechanics optimizations, and ab initio fragment molecular orbital (FMO) calculations to investigate the specific interactions between ApoE4 and the naturally occurring compounds found in the plant Moringa Oleifera. According to the FMO calculations, quercetin had the highest binding affinity to ApoE4 among the sixteen compounds because its hydroxyl groups generated strong hydrogen bonds with the ApoE4 residues Trp11, Asp12, Arg15, and Asp130. As a result, we proposed various quercetin derivatives by introducing a hydroxyl group into quercetin and studied their ApoE4 binding properties. The FMO data clearly showed that adding a hydroxyl group to quercetin improved its binding capacity to ApoE4. Furthermore, ApoE4 Trp11, Asp12, Arg15, and Asp130 residues were discovered to be required for significant interactions between ApoE4 and quercetin derivatives. They had a higher ApoE4 binding affinity than our previously proposed epicatechin derivatives. Accordingly, the current results evaluated using the ab initio FMO method will be useful for designing potent ApoE4 inhibitors that can be used as a candidate agent for AD treatment.