M06-2X Levels Research Articles

Redox-Driven Magnetic Regulation in a Series of Couplers in Bridged Nitroxide Diradicals

Redox-induced magnetic regulation in organic diradicals is distinctly attractive. In this work, taking nitroxide radicals as spin sources, we predict the magnetic properties of 9, 10-anthraquinone, 9, 10-phenaquone, 9, 10-diazanthracene and 9, 10-diazepine-bridged molecular diradical structures in which the couplers are prone to dihydrogenation reduction at positions 9 and 10. As evidenced at both the B3LYP and M06-2X levels of theory, the calculations confirm that the magnetic transitions between ferromagnetism and antiferromagnetism can take place for 9, 10-anthraquinone and 9, 10-diazanthracene-bridged diradicals after dihydrogenation. The differences in the magnetic behaviors and magnetic magnitudes of 9, 10-anthraquinone and 9, 10-diazanthracene-bridged diradicals before and after dihydrogenation could be attributed to their noticeably different spin-interacting pathways. As for 9, 10-phenaquone and 9, 10-diazepine-bridged diradicals, the calculated results indicate that the signs of their magnetic exchange coupling constants J do not change, but the magnitudes remarkably change after dihydrogenation. The connecting bond character and spin polarization are crucial in explaining the different magnetic magnitudes of these designed diradicals. In detail, shorter bonds and larger spin polarization are responsible for strong magnetic coupling. In addition, the diradical with an extensively π-conjugated structure can effectively promote magnetic coupling. The McConnell’s spin alternation rule is the key to understanding the observed ferromagnetism and antiferromagnetism of these diradicals. The work provides useful information for the rational design of redox-regulated magnetic molecular switches.

Design, synthesis, characterization, and theoretical calculations, along with in silico and in vitro antimicrobial proprieties of new isoxazole-amide conjugates

Abstract Functionalized isoxazoles provide valuable structural motifs, opening up a wide range of uses in the medicinal, pharmacological, and pharmaceutical fields. Within this scope, an efficient approach has been adopted to synthesize a novel series of functionalized isoxazole derivatives, starting from aza-aurone, providing reproducible access to the desired isoxazoles in excellent yields. All synthesized compounds were structurally elucidated through the use of various spectroscopic techniques and mass spectrometry. The derivatives generated were screened for their antimicrobial potential against the fungus Candida albicans as well as three bacterial strains. The results show that almost all of the tested isoxazole derivatives were found to be significantly potent against the fungus C. albicans. The functionalized isoxazoles were also computed using the Gaussian software package with the 6-31++G(d,p) basis set at B3LYP, HF, and M062X levels, and their chemical activities were compared. Moreover, the molecular docking studies of tested isoxazole compounds were performed against the C. albicans receptor. The results suggest that the newly synthesized compounds exhibit docking scores ranging from −10.29 to −15.08 kcal/mol, revealing a high affinity for the target enzyme (5V5Z). Lastly, drug similarity studies and ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties assessments indicate that isoxazole derivatives have favorable absorption, distribution, and metabolism properties associated with a proven lack of toxicity.

Elucidating the Advancement in the Optoelectronics Characteristics of Benzoselenadiazole-Based A2-D-A1-D-A2-Type Nonfullerene Acceptors for Efficient Organic Solar Cells.

The potential applications of nonfullerene acceptors (NFAs) such as tunable band gaps, improved charge separation, wide-range absorption, enhanced power conversion efficiency, and operational stability make them highly favorable for organic photovoltaic applications. Herein, we designed eight novel structurally modified nonfused benzoselenadiazole (BSe)-based A2-D-A1-D-A2-type NFAs for efficient organic solar cells (OSCs). These newly modeled BSe-based NFA series contain BSe as the central core. We employed strong electron-withdrawing moieties at terminal acceptor A2 to further enhance the optical, optoelectronics, and photovoltaic characteristics of OSCs. These designed molecules (HNM1-HNM8) along with the synthetic reference molecule (HNM) were thoroughly characterized by using efficient and advanced quantum chemical simulation approaches. Thus, to ascertain the enhancement of both optical and photochemical response, a thorough density functional theory (DFT) study was carried out using the M062X level in association with the 6-31G(d,p) basis set. All of the investigated molecules (HNM1-HNM8) had their excited states calculated using the time-dependent density functional theory method. The newly designed molecules (HNM1-HNM8) presented narrower band gaps, improved absorption and optoelectronics properties, and reduced excitation and binding energies. The electrostatic potential, density of states, transition density matrix, ionization potential, and electron affinity analysis of this newly designed (HNM1-HNM8) series revealed a strong coherence with those of the reference HNM molecule. Electron density difference mapping allowed us to visualize the spatial movement of electrons between the donor and acceptor molecules during excitation. This insight helps us to understand the efficiency of charge separation and recombination processes that are critical for the performance of organic photovoltaics. The reorganization energy and charge transfer analysis suggests that HNM1-HNM8 molecules could act as NFAs for organic photovoltaic applications to enhance their efficiency further. The donor: acceptor charge transfer analysis was also carried out, which revealed that the PTB7-Th:HNM2 donor:acceptor complex shows a great charge transportation process at the donor-acceptor interface. Moreover, the photovoltaic analysis shows that the designed (HNM1-HNM8) NFA series has a great potential to produce improved open-circuit voltage and fill factor values, which may be helpful in enhancing the overall PCEs of the OSCs.

Synthesis of novel thiazole derivatives containing 3-methylthiophene carbaldehyde as potent anti α-glucosidase agents: In vitro evaluation, molecular docking, dynamics, MM-GBSA, and DFT studies

Thiazole derivatives bearing thiophene carbaldehyde have been successfully prepared by refluxing 3-methylthiophene carbaldehyde with thiosemicarbazide in absolute ethanol followed by treating the obtained product with different phenacyl bromide to get thiazole products in better yields. These derivatives were confirmed using 1H-, 13C NMR, and EI-MS spectrometry techniques and finally subjected for their α-glucosidase inhibitory potential. Two compounds in the series including 2 g (IC50 = 9.00 ± 0.57 µM) and 2b (IC50 = 13.50 ± 0.20 µM) were found as the most potent α-glucosidase inhibitors better than the standard acarbose. Furthermore, the remaining five compounds attributed significantly to less activity. The studied molecules were calculated on the 6–31++g(d,p) basis set at B3LYP, HF, M062X levels with the help of the Gaussian package program, and their chemical activities were compared. Following that, the molecules' interactions with different α-glucosidase proteins (PDB IDs: 1R47 and 1UAS) were investigated, and their activities were contrasted. The binding free energy of the molecule with the best docking score is computed using MM/GBSA techniques. The comparative molecular dynamics simulations of the 2g-1UAS and 2g-1R47 complexes highlight the intricate balance of forces that govern biomolecular interactions. The findings suggest that while the 2g-1UAS complex forms more stable interactions, as indicated by lower RMSD values, the 2g-1R47 complex maintains its structural integrity through strong hydrogen bonds. Overall, the equilibrium conformations achieved by both complexes suggest they are well-suited for their roles in physiological environments.

Molecular descriptors and in silico studies of 4-((5-(decylthio)-4-methyl-4n-1,2,4-triazol-3-yl)methyl)morpholine as a potential drug for the treatment of fungal pathologies

The article explores the polypharmacological profiling of 4-((5-(decylthio)-4-methyl-4H-1,2,4-triazole-3-yl)methyl)morpholine as a potential antimicrobial agent. The study utilized 15148 electronic pharmacophore models of organisms, ranked by the Tversky index. Detailed analysis revealed classical bonding patterns with selected enzymes, identifying key amino acid residues involved in complex formation. Protein target prediction was conducted through various stages using the Galaxy web service, including ligand structure creation, pharmacophore alignment, and target ranking. The activities of the molecules against 1G6C, 2W6O, 3G7F, 3OWU, 4IVR, and 4TZT proteins were compared. Docking studies with PyMOL and Discovery Studio Visualizer revealed binding to thymidine kinase, thiamine phosphate synthase, and biotin carboxylase with promising binding affinities. These interactions suggest potential antibacterial and antiviral effects, warranting further virtual screening and in-depth studies for the development of effective antimicrobial drugs. Calculations of the molecules were made with the gaussian package program. Calculations were made on the 6-31++g** basis set at B3LYP, HF, and M062X levels with Gaussian software. Afterwards, the 0–100 ns interaction of the molecule with the highest activity was examined.

Unveiling 5-fluorouracil anti-cancer drug encapsulation within pristine and silver-doped boron, aluminum, and gallium nitride nanotubes: A DFT investigation for advancing nanomedicine

Nanomaterials represent a promising frontier in drug delivery systems for combating cancer, offering precise targeting of tumour cells. This study delves into the encapsulation capabilities of 5-fluorouracil (5-FU) on pristine armchair (6,6) single-wall boron-, aluminium-, and gallium-nitride nanotubes (BNNT, AlNNT, GaNNT), both in their natural state and doped with silver (Ag) atoms under gas phase and water solution conditions. Employing density functional theory calculations at the M06-2X level, we scrutinise the geometric stabilities, encapsulation efficiencies, and electronic interactions between 5-FU molecules and NNTs. Our results reveal that a shorter distance between the drug and nanotube cavity enhances encapsulation ability and solubility while facilitating larger charge transfers, especially within Ag-doped NNTs. The Ag doping significantly augments the reactivity of NNTs towards 5-FU molecules, with thermodynamic analyses indicating exothermic and spontaneous interactions with Ag-doped NNTs. The decapsulation of 5-FU from Ag-BNNT, Ag-AlNNT, and Ag-GaNNT necessitates recovery time 6.42E+00, 3.21E+05, and 2.19E−04 s, with corresponding adsorption energies of −38.70, −49.52, and −28.42 kcal/mol, respectively. Electronic analyses demonstrate notable changes in states’ energy gap and density post-5-FU encapsulation in Ag-doped NNTs, suggesting enhanced sensitivity. Moreover, our investigation delves into topological features, molecular stability, bond strength, and intermolecular interactions using various analytical techniques, including MEPs, ELF maps, NBO, QTAIM, Hirshfeld surface, and RDG analyses. These comprehensive findings underscore the potential of Ag-doped NNTs as promising components for drug delivery systems and biosensors in nanomedicine applications, particularly in sensing and catalytic functions for 5-FU molecule encapsulation and detection.

Mechanistic studies on an isothiourea-catalyzed reaction of an aromatic ester with an imine

Increasing attention is being paid to divergent chemical reactions as a strategy for synthesizing complex organic molecules simply by regulating and adjusting reaction conditions. However, the factors controlling this switchable transformation remain unclear. A systematic study was conducted using density functional theory (DFT) at the M06–2X level to determine the mechanism of an isothiourea-catalyzed divergent chemical reaction of an aryl acetic acid ester with an imine in different solvents (acetonitrile and ethanol). The origins of the stereoselectivity and chemoselectivity of the reaction were determined using noncovalent interaction (NCI) and electrostatic potential surface (EPS) analyses. Lactamization reaction occurs preferentially in acetonitrile, and esterification proceeds preferentially in ethanol. The reaction of an ammonium enolate intermediate with an alkynyl imine preferentially generates the SS-configured isomer. The results of this theoretical study provide insight into the general mechanism of isothiourea-catalyzed reactions in which the key intermediate is ammonium enolate.

Insights into 5-fluorouracil anti–cancer drug encapsulation within the pristine and palladium-doped carbon, silicon-carbide, and germanium-carbide nanotubes: A DFT investigation for advanced nanomedicine applications

In this study, we investigated the interaction and binding properties of 5-Fluorouracil (5-FU), an anti-cancer drug, encapsulated within pristine and palladium-doped carbon, silicon-carbide, and germanium-carbide nanotubes (CNT, SiCNT, GeCNT). Using density functional theory (DFT), we conducted a comprehensive analysis at both aqueous and gas phases. This included geometrical, structural, electrical, bonding, and thermodynamic properties, optimized geometries, adsorption energies, quantum molecular descriptors, frontier molecular orbitals, and topological parameters at the M06-2X level of theory. Our findings indicate that Pd-doping enhances the encapsulation capabilities of nanotubes, strengthening interactions with 5-FU and improving water solubility. Calculations of recovery time required for drug release suggest that Pd-doped nanotubes effectively control the release of 5-FU. Notably, the decapsulation time of 5-FU from of Pd-doped nanotubes was longer in the gas phase than in aqueous conditions. Using the quantum theory of atoms in molecules (QTAIM) method, we investigated intermolecular interactions and critical bonding points. Natural bond orbital (NBO) analysis revealed enhanced stabilization of the 5-FU molecule post-encapsulation, with charge transfer primarily directed from nanotubes to the 5-FU. Hirshfeld surface analysis highlighted that hydrogen bonds between 5-FU active sites and nanotubes are crucial in encapsulation and fixation. Reduced Density Gradient (RDG) analysis confirmed Pd-doping as a primary source of strong attractive interactions in 5-FU/Pd-doped nanotube complexes compared to pristine nanotubes.

Thermal decomposition study of 1,3-dioxolane as a representative of battery solvent

As industrial compounds and organic solvent, 1,3-dioxolane (C3H6O2) is used in lithium-ion batteries arousing extensive interest. The pyrolysis of C3H6O2 at 150 torr pressure was conducted in the temperature range of 743–1013 K. In order to quantify the major products, experimental measurements of the photoionization cross-section (PICS) and photoionization efficiency (PIE) for C3H6O2 were carried out by using synchrotron radiation photoionization mass spectrometry (SR-PIMS). Twenty-three intermediates were detected in pyrolysis of C3H6O2 including the newly observed ketene, acetaldehyde, ethenol, ethanol, dimethyl ether, diacetylene and 2-propen-1-ol which played important roles in developing mechanism. The H-abstraction of C3H6O2 by H, CH3 and OH radicals were studied via high level ab initio calculations. EStokTP code was used to find and calculate optimal geometries, vibration frequencies and intrinsic reaction coordinate (IRC) at the theory level of M06–2X/6–311+G(d,p). Conventional transition state theory (TST) was used and Rice-Ramsperger-Kassel-Marcus/Master Equation (RRKM/ME) was solved to obtain rate coefficients. For H-abstraction by H and CH3, the rates are increasing versus temperature, and rates of H-abstraction by OH show different tendency. These rate parameters were used to update the model of C3H6O2, which could well predict the ignition delay times (IDTs) in shock tube and oxidation data in jet stirred reactor (JSR) from literature. For the pyrolysis, H-abstraction reactions by H, CH3 and OH and unimolecular reactions contribute to solvent decay. Detailed pathways of C3H6O2 decomposition were also given and analyzed through this experiment and previous literature. The findings, including the experimental data and the calculations will assist to better understand pyrolysis characteristics of C3H6O2 as well.

Comparative study of experimental and DFT calculations for 3-cinnamoyl 4-hydroxycoumarin derivatives.

Computational research plays an important role in predicting the chemical and physical properties of biologically active compounds important in future structural modifications to improve or modify biological activity. This research focuses on quantum chemical and spectroscopic investigations properties of synthesized 4-hydroxycoumarin derivatives. Quantum chemical calculations were obtained using B3LYP, HF, and M06-2x level methods with the 6-31++G (d,p) basis set. Afterward, IR, 1H, 13C, UV-Visible experimentally parameters were compared with the results obtained using the B3LYP/6-31+G*(d) basis set of the molecules to be able to characterize the structures. Based on the quantum chemical calculations compound with acetamido group on the phenyl ring is the most reactive, and compound with nitro substituent is the least reactive and the the strongest electrophile among tested compounds. With the exception of compounds with dimethylamino group, all other compounds have a pronounced tautomer between OH and C = O group. The calculated and experimental values are in agreement with each other. The molecular structure in the ground state of six 3-cinnamoyl 4-hydroxycoumarin derivatives was optimized using density functional theory. The observed and computed values were compared and it can be concluded that the theoretical results were in good linear agreement with the experimental data.

Hydrazone-flavonol based oxidovanadium(V) complexes: Synthesis, characterization and antihyperglycemic activity of chloro derivative in vivo

Wet synthesis approach afforded four new heteroleptic mononuclear neutral diamagnetic oxidovanadium(V) complexes, comprising salicylaldehyde-based 2-furoic acid hydrazones and a flavonol coligand of the general composition [VO(fla)(L-ONO)]. The complexes were comprehensively characterized, including chemical analysis, conductometry, infrared, electronic, and mass spectroscopy, as well as 1D 1H and proton-decoupled 13C(1H) NMR spectroscopy, alongside extensive 2D 1H1H COSY, 1H13C HMQC, and 1H13C HMBC NMR analyses. Additionally, the quantum chemical properties of the complexes were studied using Gaussian at the B3LYP, HF, and M062X levels on the 6–31++g(d,p) basis sets. The interaction of these hydrolytically inert vanadium complexes and the BSA was investigated through spectrofluorimetric titration, synchronous fluorimetry, and FRET analysis in a temperature-dependent manner, providing valuable thermodynamic insights into van der Waals interactions and hydrogen bonding. Molecular docking was conducted to gain further understanding of the specific binding sites of the complexes to BSA. Complex 2, featuring a 5-chloro-substituted salicylaldehyde component of the hydrazone, was extensively examined for its biological activity in vivo. The effects of complex administration on biochemical and hematological parameters were evaluated in both healthy and diabetic Wistar rats, revealing antihyperglycemic activity at millimolar concentration. Furthermore, histopathological analysis and bioaccumulation studies of the complex in the brain, kidneys, and livers of healthy and diabetic rats revealed the potential for further development of vanadium(V) hydrazone complexes as antidiabetic and insulin-mimetic agents.

Peripheral (E)-2-[(4-hydroxybenzylidene)-3,4-dihydronaphthalen-1(2H)-one)]-coordinated phthalocyanines with improved enzyme inhibition properties and photophysicochemical behaviors.

In this study, (E)-4-{4-[(1-oxo-3,4-dihydronaphthalen-2(1H)-ylidene)methyl]phenoxy}phthalonitrile (4) and its phthalocyanine derivatives (5-8) were synthesized for the first time. Aggregation behaviors of the novel soluble phthalocyanines in organic solvents were investigated. In addition, the efficiency of 1O2 production of (5) and ZnPc (6) was investigated. The singlet oxygen quantum yields (ΦΔ) for 2HPc (5) and ZnPc (6) were found to be 0.58 and 0.83, respectively. Additionally, novel phthalocyanines (5-8) were investigated for their ability to inhibit enzymes. They exhibited a highly potent inhibition effect on human carbonic anhydrase I and II (hCA I and II) and α-glycosidase (α-Gly) enzymes. Ki values are in the range of 2.60 ± 9.87 to 11.53 ± 6.92 µM, 3.35 ± 0.53 to 15.47 ± 1.20 µM, and 28.60 ± 4.82 to 40.58 ± 7.37 nM, respectively. The calculations of the studied molecule at the B3LYP, HF, and M062X levels in the 6-31G basis sets were made using the Gaussian package program. Afterward, the interactions occurring in the docking calculation against a protein that is the crystal structure of hCA I (PDB ID: 2CAB), the crystal structure of hCA II (PDB ID: 5AML), and the crystal structure of α-Gly (PDB ID: 1R47), were examined. Following that, Protein-Ligand Interaction Profiler (PLIP) analysis was used to look at the interactions that occurred during the docking calculation in further detail.

Significant nuclear quantum effect of proton in the reaction of phenol and hydroxyl radical

The reaction between phenol and hydroxyl radical, leading to the formation of phenoxy radicals, is analyzed using DFT calculations at the multi-component M06-2X level that accounts for the nuclear quantum effects (NQEs) of hydrogen nuclei. The NQEs affect not only the relative energy diagram of the reaction but also the geometric parameters of the stationary point structures. In the energy minimum structures, the OH covalent bonds have lengthened, while the OH…O hydrogen bonds have shortened due to the NQEs. Furthermore, the NQEs also affect the transition state structure, where the distance between carbon and oxygen atoms is strongly influenced by the NQEs of hydrogen nuclei through a hydrogen bond network formed by surrounding water molecules. Different NQEs of hydrogen nuclei have been observed in the ipso/ortho and the para stepwise reaction pathways due to differences in the driving force of the reaction.

Phosphate Migration versus the Loss of Phosphoric Acid in Protonated Phosphopeptides: A Computational Study.

Residue-specific phosphorylation is a protein post-translational modification that regulates cellular functions. Experimental determination of the exact sites of protein phosphorylation provides an understanding of the signaling and processes at work for a given cellular state. Any experimental artifact that involves migration of the phosphate group during measurement is a concern, as the outcome can lead to erroneous conclusions that may confound studies on cellular signal transduction. Herein, we examine computationally the mechanism by which a phosphate group migrates from one serine residue to another serine in monoprotonated pentapeptides [BA-pSer-Gly-Ser-BB + H]+ → [BA-Ser-Gly-pSer-BB + H]+ (where BA and BB are different combinations of the three basic amino acids, histidine, lysine, and arginine). In addition to moving the phosphate group, the overall mechanism involves transferring a proton from the N-terminal amino acid, BA, to the C-terminal amino acid, BB. This is not a synchronous process, and there is a key high-energy intermediate, structure C, that is zwitterionic with both the basic amino acids protonated and the phosphate group attached to both serine residues and carrying a negative charge. The barriers to moving the phosphate group are calculated to be in the range of 219-274 kJ mol-1 at the B3LYP/6-31G(d) level. These barriers are systematically slightly lower and in good agreement with single-point energy calculations at both M06-2X/6-311++G(d,p) and MP2/6-31++G(d,p) levels. The competitive reaction, loss of phosphoric acid from the protonated pentapeptides, has a barrier in the range of 176-202 kJ mol-1 at the B3LYP/6-31G(d) level. Extension of the theory to M06-2X/6-311++G(d,p)//B3LYP/6-31G(d) and MP2/6-31++G(d,p)// B3LYP/6-31G(d) gives higher values for the loss of phosphoric acid, falling in the range of 196-226 kJ mol-1; these are comparable to the barriers against phosphate migration at the same levels of theory. For larger peptides His-pSer-(Gly)n-Ser-His, where n has values from 2 to 5, the barriers against the loss of phosphoric acid are higher than those against the phosphate group migration. This difference is most pronounced and significant when n = 4 and 5 (the differences are approximately 80 kJ mol-1 under the single-point energy calculations at the M06-2X and MP2 levels). Energy differences using two more recent functionals, M08-HX and MN15, on His-pSer-(Gly)n-Ser-His, where n = 1 and 5, are in good agreement with the M06-2X and MP2 calculations. These results provide the mechanistic rationale for phosphate migration versus other competing reactions in the gas phase under tandem mass spectrometry conditions.

In-situ Salen-type ligand formation-driven of a heterometallic Cu(II)-Hg(II) complex: Synthetic update, crystallographic features, DFT calculations, and unveil antimicrobial profiles

This article vividly describes the synthesis and structural characterization of one 6-Bromo-2-hydroxy-3-methoxybenzaldehyde ligand involving heteronuclear complex, [Cu(L)Hg(Cl)2]. X-ray single-crystal determined the complex crystal structure and characterized it by various physical methods, including elemental, FT-IR, Raman, PXRD, UV–vis, NMR, and SEM-EDX techniques. X-ray diffraction analysis reveals that the compound adopts a monoclinic space group Cc during crystallization. The crystal structure exhibits unique supramolecular interactions, like intermolecular C-H∙∙∙π H-bonding and X-bonding (X = Halogen) between Br(1) and Br(2) atoms. Hirshfeld surfaces (HS) and 2-D fingerprint plots confirm significant H…Cl (21.9 %) contacts. Further, dispersion energy dominates due to Br atoms' higher electron/electron cloud. The complex underwent DFT calculations based on the Gaussian software package at B3LYP, HF, and M062x levels, utilizing the lanl2dz, sdd, and def2tzvp basis sets. The HOMO-LUMO, ESP, Global reactivity, Interaction energy and energy frameworks, and Fukui function investigated the complex properties in a multidimensional spectrum. The complex showed promising NLO activity, which has broad technological applications. Fukui function calculation identifies regions prone to nucleophilic (Nu-) and electrophilic (E+) attacks. The complex and synthetic components were examined for antimicrobial function against Gram+ve and Gram-ve bacterial and fungal strains. Molecular docking (MD) and Protein-Ligand Interaction Profilers (PLIP) further support the antimicrobial findings.

Hydrogen bonding interactions between Hibiscetin and ethanol/water: DFT studies on structure and topologies

The therapeutic effects of the plant Hibiscus sabdariffa are attributed significantly to the flavonoid Hibiscetin. Water and ethanol are frequently used as solvents in the extraction of flavonoids. Hydrogen bonding interactions are highly significant in the extraction process. Density functional theory (DFT) methods were used in the present investigation to theoretically examine hydrogen bonding interactions between Hibiscetin and ethanol/water. Molecular geometries, interaction energies, topological and charge studies of the complexes were investigated using the 6–311+G(d,p) basis set at the B3LYP-GD3 and M06–2X levels of theory. Eleven Hibiscetin-CH3CH2OH and nine Hibiscetin-H2O stable complexes were obtained after thorough optimization. 8OH and 5′OH positions were found to be the ideal interaction sites. The hydrogen bonds formed by the hydroxyl hydrogen atoms were moderately strong and partially covalent by the QTAIM, NCI, and ELF analyses. The MEP and NBO analyses validated the electron and charge transport from the hydrogen bond donor to the acceptor.

Design of novel molecular switches using the C20 & C40 nanobud

A molecular switch is a molecule that can reversibly switch between two or more stable states under the influence of environmental factors such as electric current or field, presence of other ions, ligands, pH change, light, etc. Using density functional theory calculations at B3LYP, M06-2X, WB97XD and B3LYP-D3 computational level, we investigate the possibility of using C20 & C40 nanobud as a molecular switch. For this purpose, the effect of different electric fields (0, 0.002, 0025, 0.003, 0.004 and 0.006 a.u.) on structural, electrical and nonlinear optical properties was investigated. It was shown that with the increase of the electric field, the dihedral angle and the bond length of the molecule changes greatly, and a sudden change in the dihedral angle can indicate the switch become ON. Also, with the increase of the electric field, the distance between the HOMO and LUMO orbitals decreases, and this changes increased greatly in a certain range of the electric field, which indicates the change of the state of the molecular switch to ON. The effect of the field on the optical properties of the switch also showed that with the increase in the intensity of the field, the values of α, β and μ increased, and this change was in a specific range of a very strong electric field, which corresponds exactly to the change of the dihedral angle and the behavior of HLG. The M06-2X, WB97XD and B3LYP-D3 methods were used to check the accuracy of the data, and it was shown that the results of these two methods are approximately the same as the results of the calculations related to the B3LYP method.

Theoretical study of an N-heterocyclic carbene-catalyzed annulation reaction between an enal and a β-silyl enone: Mechanism and origin of stereoselectivity

In this study, the mechanism and origin of the stereoselectivity of an N-heterocyclic carbene (NHC)-catalyzed transformation reaction between an enal and a β-silyl enone are systematically investigated using density functional theory (DFT) at the M06-2X level. Multiple pathways are proposed and studied to identify the most energetically favorable mechanism for the reaction. The calculation results show that the most energetically favorable pathway comprises the following processes: nucleophilic addition of NHC to the Si-face of the enal to form a zwitterionic intermediate, two sequential CsHCO3-assisted intramolecular proton shifts to produce an enolate intermediate, Michael-type addition of the enolate intermediate to the β-silyl enone, ring closure to construct a six-membered ring intermediate, and the dissociation of NHC to release the final product. The reaction between the enolate intermediate and the β-silyl enone is identified as the stereoselectivity-determining step, preferentially generating an RS-configured product. Subsequent atoms-in-molecules (AIM) and noncovalent interaction (NCI) analyses verify that the main factor for inducing stereoselectivity is the higher number of noncovalent intermolecular interactions in the low-energy transition state.

An accurate DFT study within conformational survey of the d-form serine−alanine protected dipeptide

The conformational analysis of n-formyl-d-serine-d-alanine-NH2 dipeptide was studied using density functional theory methods at B3LYP, B3LYP‒D3, and M06‒2X levels using 6‒311 + G (d,p) basis set in the gas and water phases. 87 conformers of 243 stable ones were located and the rest of them were migrated to the more stable geometries. Migration pattern suggests the more stable dipeptide model bears serine in βL, γD, γL and the alanine in γL and γD configurations. The investigation of side‒chain‒backbone interactions revealed that the most stable conformer, γD–γL, is in the β‒turn region of Ramachandran map; therefore, serine-alanine dipeptide model should be adopted with a β‒turn conformation. Intramolecular hydrogen bonding in β‒turns consideration by QTAIM disclosed γD–γL includes three hydrogen bonds. The computed UV‒Vis spectrum alongside of NBO calculation showed the five main electronic transition bands derived of n → n* of intra‒ligand alanine moiety of dipeptide structure.

Mechanism of disproportionation of methylchlorosilanes by ZSM-5(3T)@MIL-53(Al) core–shell catalyst

ABSTRACT Dimethyldichlorosilane has been one of the most widely used monomers in the organic silicon industry chain, which can be synthesised through the methylchlorosilanes disproportionation reaction with the interchange of functional groups. In this research, the disproportionation mechanism catalysed by ZSM-5(3 T)@MIL-53(Al) and AlCl3/ZSM-5(3 T)@MIL-53(Al) core–shell catalysts were studied by using the hybrid functional method on the level of M06-2X/Def2-TZVP. The results showed that the two catalysts possessed different catalytic effect assigning to their different acidic active structures. The surface activity of ZSM-5(3 T)@MIL-53(Al) core–shell catalyst modified by AlCl3 transformed to Lewis acid center of Al–Cl bond with better disproportionation activity than before modification. Energy, frequency vibration and IRC calculations, bond level, ELF and LOL analyses were used to verify the reaction mechanism proposed in this manuscript.