Noncovalent Interactions Accompanying Encapsulation of Resorcinol within Azacalix[4]pyridine Macrocycle

Computational Study on the Conformational Flexibility-Mediated Intramolecular Oxidative Spirocyclization of Procyanidin B4

Procyanidins, found widely in foods and beverages, are prone to oxidation, yet the chemical structures of their oxidation products and the mechanisms involved remain unclear. Herein, we report that the conformation of procyanidin B4 influences its oxidation products and their stereochemistry. Eight spirocyclized oxidation products were obtained from procyanidin B4 and classified as S- or R-forms based on the configuration of the spiro carbons. The ratios of S- and R-forms derived from the compact and extended rotamers of procyanidin B4, respectively, varied with the solvent. DFT calculations suggested that the four lowest-energy conformers of procyanidin B4 are diverged by interflavan bond rotation and heterocyclic ring inversion. Conformations with an axial-oriented B-ring were estimated as reactive conformations showing proximity between reaction sites on the B- and D-rings. Moreover, the extended rotamer bearing the axially oriented B-ring showed greater stabilization by noncovalent interactions (NCIs), such as OH-π interactions, compared to the counterpart of the compact rotamer. This NCI-based stabilization accounts for a higher production of the R-form despite the predominant presence of the compact rotamer in H2O. These findings highlight the conformational effects that bias the stereoselectivity of oxidative spirocyclization in procyanidin B4, advancing our understanding of procyanidin oxidation mechanisms and product stereochemistry.

Theoretical insights into enantioselective [2 + 1] cyclopropanation reactions of diazo compounds with electron-deficient olefins

CONTEXT

The cyclopropane skeleton plays a significant role in bioactive  molecules due to its distinctive structural properties. This has sparked keen interest and in-depth exploration in the field of stereoselective synthesis of cyclopropane derivatives. In the present study, the mechanism and the origin of stereoselectivity of diastereodivergent synthesis of cyclopropane derivatives via the catalyst-free [2 + 1]-cyclopropanation reactions of 3-diazo-N-methylindole (R1) with two types of electron-deficient olefins (R2 and R3) in both aqueous and toluene media have been studied using the DFT calculations. The findings indicate that these [2 + 1] cycloaddition reactions proceed in two stages, where the first step is not only the rate-determining step but also critically dictates the stereoselectivity of the product. The calculated diastereomeric ratios are in agreement with the experimental results. Furthermore, by utilizing non-covalent interaction (NCI) analysis and energy decomposition analysis based on molecular force fields (EDA-FF), we elucidated that the electrostatic interactions between reactant fragments in the transition state TS1s for the first step are the predominant factors determining the stereoselectivity, as opposed to the experimentally hypothesized steric hindrance and π-π stacking interactions.

METHODS

The geometrical structures of all minima and transition states on the potential energy surface (PES) in solvents water and toluene were fully optimized using the DFT method at the M06-2X(D3)/SMD/6-31 + G(d,p) level of theory. Single-point energy calculations were carried out based on the optimized geometries in the solution at the M06-2X(D3)/6-311 + G(d,p) level. All the DFT calculations were performed using the Gaussian 09 software. The optimized molecular structures were visualized using CYLview software. NCI analysis was performed using the Multiwfn and VMD softwares. The Multiwfn program was also used for CDFT and EDA-FF analyses.

Heteroatoms chemical tailoring of aluminum nitrite nanotubes as biosensors for 5-hydroxyindole acetic acid (a biomarker for carcinoid tumors): insights from a computational study

This study aims to elucidate the properties of aluminum nitrite nanotubes (AlNNT) encapsulated with phosphorus (P@AlNNT), sulphur (S@AlNNT), and silicon (Si@AlNNT) heteroatoms for use as biosensors for 5-hydroxyindoleacetic acid (5HIAA).

Vibrational Spectroscopies, Global Reactivity, Molecular Docking, Thermodynamic Properties and Linear and Nonlinear Optical Parameters of Monohydrate Arsonate Salt of 4-Aminopyridine

In this work, a structural and electronic properties of a novel organic arsenate template by 4-aminopyridine, with the general formula (C₅H₇N₂)(C₅H₈N₂)[AsO₄]·H₂O ((4-APH)(4-APH₂)[AsO₄]·H₂O) have been presented. The density functional theory (DFT) along with B3LYP hybrid functional is employed. The optimized structure was found to be in well consistent with the X-ray diffraction geometry. The examination of the vibrational spectrum was correlated by DFT calculation using the unit cell parameters obtained from the experiment data. Besides, the thermodynamic functions (heat capacity, entropy, enthalpy) from spectroscopic data by statistical methods were obtained for the range of temperature 100–1000 K. In addition, the molecular orbital calculations such as Natural Bond Orbitals (NBOs), AIM approach, HOMO–LUMO energy gap, NLO characteristic and Hirshfeld surface analysis were also performed with the same level of DFT. Electronic stability of the compound arising from hyper conjugative interactions and charge delocalization were also investigated based on the natural bond orbital (NBO) analysis. Molecular docking studies were also conducted as part of this study. The theoretical results showed an excellent agreement with the experimental values.

Synthesis, Structures, and Complexation with Phenolic Guests of Acridone-Incorporated Arylene-Ethynylene Macrocyclic Compounds

Acridone units were incorporated into the arylene-ethynylene structure as polar arene units. Cyclic trimers consisting of three acridone-2,7-diyl units and three 1,3-phenylene units were synthesized by Sonogashira couplings via stepwise or direct route. X-ray analysis revealed that the trimer had a nearly planar macrocyclic framework with a cavity surrounded by three carbonyl groups. In contrast, the corresponding tetramer had a nonplanar macrocyclic framework. ¹ H NMR measurements showed that the trimer formed a 1 : 1 complex as a macrocyclic host with dihydric phenol guests, and the association constants were determined to be ca. 1.0×10³  L mol^-1 for hydroquinone or resorcinol guests in CDCl₃ at 298 K. The calculated structures of these complexes by the DFT method supported the presence of two sets of OH⋅⋅⋅O=C hydrogen bonds between the host and guest molecules. The spectroscopic data of the cyclic trimers and tetramers are compared with those of reference acridone compounds.

Cyclopropenylidene: Clustering and Interaction with Water Molecules

Cyclopropenylidene (c-C₃H₂, abbreviated CPD) is a highly reactive, planar, partially aromatic carbene discovered in the interstellar medium, and, also recently, in the outer solar system. It is demonstrated herein on cogent quantum chemical grounds that CPD which possesses an electric dipole moment of 3.4 D is capable of forming stable dimer and trimer clusters through hydrogen-bonding. These attributes of CPD are conducive to the formation of stable hydrogen-bonded conformations with one- and two-water molecules. Having determined its consistency with the second-order Møller-Plesset perturbation theory MP2, we employ the ωB97xD hybrid density functional theory in conjunction with a 6-311++G(2d,2p) basis set for a credible description of noncovalent interactions involved in clustering. Molecular electrostatic potential (MESP) and characteristic vibrational frequency shifts upon clustering are presented.

Fischer-Helferich glycosidation mechanism of glucose to methyl glycosides over Al-based catalysts in alcoholic media

The Fischer-Helferich glycosidation reaction is generally the initial step in the conversion of glucose to levulinate in alcohol media. However, the relevant molecular mechanism catalyzed by Al-based catalysts is still not well understood. In this work, the reaction mechanism of the glycosidation from glucose to methyl glycosides catalyzed by Al3+ coordinated with methanol/methoxyl was investigated through density functional theory (DFT) calculations. The whole reaction process includes ring-opening, addition, and ring-closure events. The addition of methanol to the ring-opening structure of glucose makes the electronegativity of C1 site stronger to proceed with the following ring-closure reaction. Among the 28 kinds of ways of ring-closure reaction, the most preferred way is to close the loop through the six-membered ring (O5-C1) to generate methyl glucoside (MDGP). The rate-determining step is the ring-closure and the Al3+ shows a great catalytic effect which is mainly reflected in coordinating with the solvents to transfer protons. The results would be helpful to understanding the Fischer-Helferich glycosidation mechanism catalyzed by Al-based catalysts and comprehend the conversion of glucose to high value-added chemicals.

Computational insight into the mechanism and stereoselectivity of cycloaddition between donor-acceptor spirocyclopropane and aldehyde catalyzed by Brønsted acid TsOH

The mechanism and diastereoselectivity of the cycloaddition reaction between D-A spirocyclopropane and aldehydes, catalyzed by para-toluenesulfonic acid (TsOH) in dichloromethane to produce 2,5-disubstituted tetrahydrofuran-type lignans, have been investigated by density functional theory (DFT) at the M06-2X/6-311+G(d,p)//B3LYP-D3/6-31G(d,p) level combined with the solvation SMD model. Our calculations show that the entire reaction process includes three stages: the activation of the D-A cyclopropane by Brønsted acid, TsOH, the nucleophilic attack of the aldehyde on the spirocyclopropane, and the formation of the final product, 2,5-disubstituted tetrahydrofuran. It was concluded from the conceptual density functional theory (CDFT) reactivity index analysis that aldehydes with electron-rich substituents are more nucleophilic and more favorable for the reaction to proceed. Furthermore, based on the analyses of energetics as well as the noncovalent interaction (NCI) and reduced density gradient (RDG) in the key transition states, the origin of stereoselectivity was revealed to be determined thermodynamically rather than kinetically. The present work explains the experimental phenomenon well, and provides useful theoretical information for the future design of similar reactions.

Theoretical insights into the gas/heterogeneous phase reactions of hydroxyl radicals with chlorophenols: Mechanism, kinetic and toxicity assessment

Emission of 2-chlorophenols (2-CPs) can cause serious air pollution and health problems. Here, the reaction kinetics and products of key radicals in 2-CPs photo-oxidation are explored in both gaseous and heterogeneous reactions. Quantum chemical calculations show that •OH-addition pathways are more preferable than H-abstraction pathways in gas phase, while that is opposite in heterogeneous phase. At 298 K, the overall rate coefficients of the title reactions in gas and heterogeneous phases are 3.48 × 10^-13 and 2.37 × 10^-13 cm³ molecule^-1 s^-1 with half-lives of 55.3 h and 81.2 h, respectively. The strong H-bonds between linear Si₃O₂(OH)₈ and 2-CPs change the energy barriers of initial •OH-addition and H-abstraction reactions, resulting in the competition between heterogeneous reactions and gas phase reactions. The products in heterogeneous reactions are chloroquinone and HONO, which can cause atmospheric acid deposition and eco-toxicity. In gas phase, self-cyclization of alkoxy radical (RO•) leads to formation of •HO₂ and highly‑oxygenated molecules, which cause formation of secondary organic aerosol. It is emphasized that oxidation of 2-CPs by •OH leads to formation of more toxic products for aquatic organisms. Therefore, more attention should be focused on the products originated from •OH-initiated reactions of (2-)CPs in gaseous and heterogeneous reactions.

Theoretical assessment of calix[4]arene-N-β-ketoimine (n=1-4) derivatives: Conformational studies, optoelectronic, and sensing of Cu2+cation

Herein, we have investigated the key functions of the calix[4]arene, abbreviated as CX [1], and designed its several derivatives by substitution of the functional groups. Molecular geometry provides an intuitive understanding of the effect of functional groups on various physical properties. The addition of the N-β-ketoimine (n = 1-4) ligands has a direct effect on the stretching vibration of the H-bonding interaction. The results showed that all molecules possess absorption bands at 190 nm and in the range between 200 and 300 nm assigned to π-π* and n-π* transitions. HOMO-LUMO energy gap of the CX[4]-N-β-ketoimine, one with chemical hardness of 1.62 eV, has been found to be 3.24 eV calculated at B3LYP/6-31 + G(d) level of theory. This finding explains the good kinetic stability of this compound. The large values of electrophilicity make the current molecules as a good electrophilic species. The atom in molecule (AIM) and the reduced density gradient (RDG) analyses showed the type and the strength of the interactions taking place between Cu²⁺ and the β-ketoimine ligands.

Looking for the Azeotrope: A Computational Study of (Ethanol)6-Water, (Methanol)6-Water, (Ethanol)7, and (Methanol)7 Heptamers

Considering that a molecular-level understanding of the azeotropic ethanol-water system can contribute to the search of new methodologies and/or modifications of industrial separation methods, this study tries to provide some clues to understand why azeotropes should be expected for ethanol, but not for methanol. Our exploration of the potential energy surface of (ethanol)₆-water heteroheptamers, carried out at the B3LYP-D3/6-311++G(d,p) level, shows these heteroclusters to exhibit a cyclic structure where the cooperativity effects between the OH···O HBs is a fundamental ingredient. An analysis of this cooperativity clearly indicates that ethanol-water systems will exhibit a similarly high stability as the heterocluster size approaches the azeotrope. However, a similar behavior should not be expected for the methanol-containing analogues. A comparison between (ethanol)₇, (ethanol)₆-water, (methanol)₇, and (methanol)₆-water shows the ethanol-containing systems to be significantly more stable than the methanol-containing analogues. This result is probably due to the fact that the OH···O HBs are weaker than those found between ethanol molecules. However, our atoms in molecule (AIM) and noncovalent interaction (NCI) analyses unambiguously show that important contributors to the enhanced stability of the ethanol-containing clusters are the secondary van der Waals interactions between ethyl groups, which are not observed between methyl groups. Hence, while the formation of stable azeotropes is expected for the case of ethanol, for the methanol-containing analogues, the relative stability of the clusters is significantly smaller, and its formation is accompanied by an increase of the free energy.

Computational insight into the mechanism and origin of high regioselectivity in the ring-opening cyclization of spirocyclopropanes with stabilized sulfonium ylides by the DFT

Chromanes with high bioactivity play an important role in nature, and cyclization reactions of cyclopropanes with sulfonium ylides to form chromane skeletons have attracted great attention of scientists. The mechanism as well as origins of regioselectivity and stereoselectivity for the ring-opening/cyclization reactions between cyclohexane-1,3-dione-2-spirocyclopropanes and stabilized sulfonium ylides in CH₂Cl₂ were investigated by using the density functional theory (DFT) M06-2X/6-311+G(d,p)//M06-2X/6-31G(d,p) method combined with the SMD model. The calculated results revealed that the reaction process involved two key steps: the ring-opening step and the cyclization step, with the former being the rate-determining and stereoselectivity-determining step. The regioselectivity of the ring-opening step of spirocyclopropane indicated that the tertiary carbon was more preferential than the secondary one when sulfonium ylide attacked spirocyclopropane. The theoretical results confirmed that the stereoselectivity of the reaction to form the trans-isomer product is more favorable than the cis-isomer, and the calculated trans/cis ratio is in accordance with the experiment. Moreover, the conceptual density functional theory reactivity indices suggest that the electronic effect controls the regioselectivity. What is more, the stereoselectivity analyzed by weak non-covalent interaction also shows the importance of electronic effect. Graphical Abstract.

Elucidating the origin of selectivity of [3 + 2]-cycloaddition reactions between thioketone and carbohydrate-derived nitrones by the DFT

The mechanism and origin of selectivity for [3 + 2]-cycloaddition (32CA) reactions between thioketone and carbohydrate-derived nitrones in THF were investigated by using the density functional theory (DFT) at the M06-2X/6-311+G(d,p)//M06-2X/6-31+G(d,p) level of theory combined with the solvation SMD model. The calculated results revealed that the 32CA reactions proceed through the asynchronous one-step manner. For the chemoselectivity in thioketone, the C=S bond as a dipolarophile attacking three-atom-component (TAC) nitrone in reactivity was more preferential than the C=O bond. The theoretical results also confirmed the stereoselectivity of two 32CA reactions of thioketone with carbohydrate-derived nitrones with the anti-form product being more favored than the syn-form product, and the predicted anti/syn product ratios are in agreement with the experimental ones in literature. Furthermore, the analysis of the conceptual density functional theory reactivity indices showed that the 32CA reactions have polar character. Weak noncovalent interaction and Parr function analyses are used to reveal the origin of the stereoselectivity. Graphical abstract [3 + 2]-cycloaddition reactions between thioketone and carbohydrate-derived nitrones.

Multi-point interaction-based recognition of fluoride ions by tert-butyldihomooxacalix[4]arenes bearing phenolic hydroxyls and thiourea

A series of p-tert-butyldihomooxacalix[4]arenes bearing phenolic hydroxyls and thiourea moieties were prepared to investigate their anion binding behavior.

Nature of bonding and cooperativity in linear DMSO clusters: A DFT, AIM and NCI analysis

This study aims to cast light on the nature of interactions and cooperativity that exists in linear dimethyl sulfoxide (DMSO) clusters using dispersion corrected density functional theory. In the linear DMSO, DMSO molecules in the middle of the clusters are bound strongly than at the terminal. The plot of the total binding energy of the clusters vs the cluster size and mean polarizabilities vs cluster size shows an excellent linearity demonstrating the presence of cooperativity effect. The computed incremental binding energy of the clusters remains nearly constant, implying that DMSO addition at the terminal site can happen to form an infinite chain. In the linear clusters, two σ-hole at the terminal DMSO molecules were found and the value on it was found to increase with the increase in cluster size. The quantum theory of atoms in molecules topography shows the existence of hydrogen and SO⋯S type in linear tetramer and larger clusters. In the dimer and trimer SO⋯OS type of interaction exists. In 2D non-covalent interactions plot, additional peaks in the regions which contribute to the stabilization of the clusters were observed and it splits in the trimer and intensifies in the larger clusters. In the trimer and larger clusters in addition to the blue patches due to hydrogen bonds, additional, light blue patches were seen between the hydrogen atom of the methyl groups and the sulphur atom of the nearby DMSO molecule. Thus, in addition to the strong H-bonds, strong electrostatic interactions between the sulphur atom and methyl hydrogens exists in the linear clusters.

Aerogen bonds formed between AeOF2 (Ae = Kr, Xe) and diazines: comparisons between σ-hole and π-hole complexes

The interaction between KrOF₂ or XeOF₂ and the 1,2, 1,3, and 1,4 diazines is characterized chiefly by a Kr/XeN aerogen bond, as deduced from ab initio calculations. The most stable dimers take advantage of the σ-hole on the aerogen atom, wherein the two molecules lie in the same plane. The interaction is quite strong, as much as 18 kcal mol^-1. A second class of dimer geometry utilizes the π-hole above the aerogen atom in an approximate perpendicular arrangement of the two monomers; these structures are not as strongly bound: 6-8 kcal mol^-1. Both sorts of dimers contain auxiliary CHF H-bonds which contribute to their stability, but even with their removal, the aerogen bond energy remains as high as 14 kcal mol^-1. The nature and strength of each specific interaction is confirmed and quantified by AIM, NCI, NBO, and electron density shift patterns. There is not a great deal of sensitivity to the identity of either the aerogen atom or the position of the two N atoms in the diazine.

Winged-Cone Conformation in Hexa-p-tert-butylcalix[6]arene Driven by the Unusually Strong Guest Encapsulation

Hexa-p-tert-butylcalix[6]arene (1) is believed to adopt a winged conformation in a solution, featured by four phenyl rings perpendicular to the calix basis and two others at 1,4-positions lying down. However, there is some controversy on the occurrence of this conformation because it has never been found in the solid state of calix[6]arenes, regardless of the substitution pattern at lower and upper rims. Here, we have observed the winged-cone conformation for the first time in a solvate form of 1 with dimethyl sulfoxide (DMSO), dimethylformamide, and pyridine. The DMSO molecule is strongly encapsulated into 1 through two OH···O hydrogen bonds with both flattened phenolic moieties, one lp_(S)···π and four CH···π interactions with the four perpendicular phenyl rings. This host-guest complex has energy lower by 23.4 kcal mol^-1 than the isolated species. In addition, another DMSO solvate form with 1,2,3-alternate conformation was also obtained in this study, and its structure is compared with that of the precedent one. A detailed density functional theory study has also been carried out to understand the energetic relationships among cone conformers, intramolecular hydrogen-bonding patterns, and DMSO encapsulation.