IGMPlot: A program to identify, characterize, and quantify molecular interactions

Allylboration of Ketones Catalyzed by BINOL Derivatives: Which Species Are Involved Depending on Substrate Reactivity?

Allylboration reactions of ketones catalyzed by BINOL derivatives can exhibit highly variable stereochemical courses depending on the nature and reactivity of the ketone substrate. In this Article, we put into perspective the relationship between the nature of the starting material and the active species involved in the asymmetric allyboration catalyzed by BINOL derivatives. This work, aimed at comparing different plausible mechanisms by density functional theory (DFT) at the M06-2X/6-311+G(d,p) level involving different types of allylboronates in the presence of the organocatalyst, leads to the confirmation of the hitherto accepted hypothesis of a reaction promoted by the transient cyclic allyl-1,3,2-dioxaborolane derived from BINOLs in the case of unactivated or weakly activated ketones such as indanone. A hypothetical scenario involving dimeric boronate species as chiral catalysts was also investigated.

Computational Study of the Kinetics and Mechanisms of Gas-Phase Decomposition of N-Diacetamides Using Density Functional Theory

In this research work, we examined the decomposition mechanisms of N-substituted diacetamides. We focused on the substituent effect on the nitrogen lone-pair electron delocalization, with electron-withdrawing and electron donor groups. DFT functionals used the following: B1LYP, B3PW91, CAMB3LYP, LC-BLYP, and X3LYP. Dispersion corrections (d3bj) with Becke-Johnson damping were applied when necessary to improve non-covalent interactions in the transition state. Pople basis sets with higher angular moments and def2-TZVP basis sets were also applied and were crucial for obtaining consistent thermodynamic parameters. The proposed mechanism involves a six-membered transition state with the extraction of an α hydrogen. Several conformers of N-diacetamides were used to account for the decrease in entropy in the transition state in the rate-determining state. All calculations, including natural bond orbital (NBO) analyses, were performed using the Gaussian16 computational package and its GaussView 6.0 visualizer, along with VMD and GNUPLOT software. The isosurfaces and IBSIs were calculated using MultiWFN and IGMPlot, respectively.

Selective detection of food contaminants using engineered gallium-organic frameworks with MD and metadynamics simulations

The exclusion mechanism of food contaminants such as bisphenol A (BPA), Flavonoids (FLA), and Goitrin (GOI) onto the novel gallium-metal organic framework (MOF) and functionalized MOF with oxalamide group (MOF-OX) is evaluated by utilizing molecular dynamics (MD) and Metadynamics simulations. The atoms in molecules (AIM) analysis detected different types of atomic interactions between contaminant molecules and substrates. To assess this procedure, a range of descriptors including interaction energies, root mean square displacement, radial distribution function (RDF), density, hydrogen bond count (HB), and contact numbers are examined across the simulation trajectories. The most important elements in the stability of the systems under examination are found to be stacking π-π and HB interactions. It was confirmed by a significant value of total interaction energy for BPA/MOF-OX (- 338.21 kJ mol-1) and BPA/MOF (- 389.95 kJ mol-1) complexes. Evaluation of interaction energies reveals that L-J interaction plays an essential role in the adsorption of food contaminants on the substrates. The free energy values for the stability systems of BPA/MOF and BPA/MOF-OX complexes at their global minima reached about BPA/MOF = - 254.29 kJ mol-1 and BPA/MOF-OX = - 187.62 kJ mol-1, respectively. Nevertheless, this work provides a new strategy for the preparation of a new hierarchical tree-dimensional of the Ga-MOF hybrid material for the adsorption and exclusion of food contaminates and their effect on human health.

Design, Synthesis, Anti-Cancer, Anti-inflammatory and In Silico Studies of 3-Substituted-2-Oxindole Derivatives

This study focuses on the design and synthesis of 3-substituted-2-oxindole derivatives aimed at developing dual-active molecules with anti-cancer and anti-inflammatory properties. The molecules were designed with diverse structural and functional features while adhering to Lipinski, Veber, and Leeson criteria. Physicochemical properties were assessed using SWISSADME to ensure drug-likeness and favourable pharmacokinetics. Multistep synthetic procedures were employed for molecule synthesis. In vitro evaluations confirmed the dual activity of the derivatives, with specific emphasis on the significance of dialkyl aminomethyl substitutions for potency against various cell lines. 4 a exhibited GI50 value 3.00E-05 against MDA-MB-231, 4 b has shown GI50 value 2E-05 against MDA-MB-231, 4 c has shown GI50 value 6E-05 against VERO, 4 d has shown GI50 value 8E-05 each against both the MDA-MB-231 and MCF-7 and 4 e has shown GI50 values 2E-05 and 5E-05 each against both the MCF-7 and VERO. The analysis indicates that compounds 3 c (71.19 %), 3 e (66.84 %), and 3 g (63.04 %) exhibited significant anti-inflammatory activity. Additionally, in silico binding free energy analysis and interaction studies revealed significant correlations between in vitro and computational data, identifying compounds 4 d, 4 e, 3 b, 3 i, and 3 e as promising candidates. Key residues such as Glu917, Cys919, Lys920, Glu850, Lys838, and Asp1046 were found to play critical roles in ligand binding and kinase inhibition, providing valuable insights for designing potent VEGFR2 inhibitors. The Quantum Mechanics-based Independent Gradient Model analysis further highlighted the electronic interaction landscape, showing larger attractive peaks and higher electron density gradients for compounds 4 d and 4 e compared to Sunitinib, suggesting stronger and more diverse attractive forces. These findings support the potential of these compounds for further development and optimization in anticancer drug design.

A Rotational Study of 2-tert-Butylphenol and Its 1 : 1 Argon Complex

The chirped-pulse Fourier Transform microwave spectrum of 2-tert-butylphenol, an industrial intermediate for the production of antioxidants, has been investigated in the 2-8 GHz frequency range. The spectral analysis has allowed obtaining precise structural information on the most stable conformer and its complex with argon. The conformation of the monomer reveals that the hydroxyl group is coplanar with the ring but points in the opposite direction to the tert-butyl group, reducing steric interactions. In the tert-butyl group one methyl group is coplanar and the other two are symmetrically staggered respect to the ring. The complex shows the rare gas sitting above the aromatic ring. Interestingly, neither the monomer nor the complex exhibit large-amplitude hydroxyl torsion motions, previously observed in 2,6-disubstituted phenols such as 2,6-di-tert-butylphenol or propofol. The experimental results are supported by computational calculations, validating the molecular structure. Additionally, symmetry-adapted perturbation theory has allowed determining the van der Waals intermolecular interaction energy of the complex.

Theoretical Study of Cyanidin-Resveratrol Copigmentation by the Functional Density Theory

Anthocyanins are colored water-soluble plant pigments. Upon consumption, anthocyanins are quickly absorbed and can penetrate the blood-brain barrier (BBB). Research based on population studies suggests that including anthocyanin-rich sources in the diet lowers the risk of neurodegenerative diseases. The copigmentation caused by copigments is considered an effective way to stabilize anthocyanins against adverse environmental conditions. This is attributed to the covalent and noncovalent interactions between colored forms of anthocyanins (flavylium ions and quinoidal bases) and colorless or pale-yellow organic molecules (copigments). The present work carried out a theoretical study of the copigmentation process between cyanidin and resveratrol (CINRES). We used three levels of density functional theory: M06-2x/6-31g+(d,p) (d3bj); ωB97X-D/6-31+(d,p); APFD/6-31+(d,p), implemented in the Gaussian16W package. In a vacuum, the CINRES was found at a copigmentation distance of 3.54 Å between cyanidin and resveratrol. In water, a binding free energy ∆G was calculated, rendering -3.31, -1.68, and -6.91 kcal/mol, at M06-2x/6-31g+(d,p) (d3bj), ωB97X-D/6-31+(d,p), and APFD/6-31+(d,p) levels of theory, respectively. A time-dependent density functional theory (TD-DFT) was used to calculate the UV spectra of the complexes and then compared to its parent molecules, resulting in a lower energy gap at forming complexes. Excited states' properties were analyzed with the ωB97X-D functional. Finally, Shannon aromaticity indices were calculated and isosurfaces of non-covalent interactions were evaluated.

Toward Efficient and Stereoselective Aromatic and Dearomative Cope Rearrangements: Experimental and Theoretical Investigations of α-Allyl-α'-Aromatic γ-Lactone Derivatives

The aromatic Cope rearrangement is an elusive transformation that has been the subject of a limited number of investigations compared to those seemingly close analogues, namely the Cope and aromatic Claisen rearrangement. Herein we report our investigations inspired by moderate success observed in the course of pioneering works. By careful experimental and theoretical investigations, we demonstrate that key substitutions on 1,5-hexadiene scaffold allow fruitful transformations. Especially, efficient functionalisation of the heteroaromatic rings results from the aromatic Cope rearrangement, while highly stereoselective interrupted aromatic Cope rearrangements highlight the formation of chiral compounds through a dearomative process.

An Atomic-Level Perspective on the interactions between Organic Pollutants and PET particles: A Comprehensive Computational Investigation

Microplastics (MPs) have recently attracted a lot of attention worldwide due to their abundance and potentially harmful effects on the environment and on human health. One of the factors of concern is their ability to adsorb and disperse other harmful organic pollutants in the environment. To properly assess the adsorption capacity of MP for organic pollutants in different environments, it is pivotal to understand the mechanisms of their interactions in detail at the atomic level. In this work, we studied interactions between polyethylene terephthalate (PET) MP and small organic pollutants containing different functional groups within the framework of density functional theory (DFT). Our computational outcomes show that organic pollutants mainly bind to the surface of a PET model via weak non-bonding interactions, mostly hydrogen bonds. The binding strength between pollutant molecules and PET particles strongly depends on the adsorption site while we have found that the particle size is of lesser importance. Specifically, carboxylic sites are able to form strong hydrogen bonds with pollutants containing hydrogen bond donor or acceptor groups. On the other hand, it is found that in such kind of systems π-π interactions play a minor role in adsorption on PET particles.

When, Where and Why Boron Prefers Boron to Nitrogen

Boron is the archetypal Lewis acid, and therefore it is only natural that it prefers to bind nitrogen, its usual Lewis base counterpart. To challenge this assumption, we present a computationally designed bicyclopentane molecule akin to [1.1.1]propellane, but with pyramidal B and N inner atoms bonded by an "inverted" dative bond. Unexpectedly, the dimer of this system prefers to interact via an atypical boron-boron bond over the supposedly obvious boron-nitrogen bond. A molecular orbital analysis shows that the boron in this peculiar entity acts both as an electron donor and an electron acceptor, making the dimerization an amphoteric-amphoteric interaction process.

Affinity of Telluronium Chalcogen Bond Donors for Lewis Bases in Solution: A Critical Experimental-Theoretical Joint Study

Telluronium salts [Ar2 MeTe]X were synthesized, and their Lewis acidic properties towards a number of Lewis bases were addressed in solution by physical and theoretical means. Structural X-ray diffraction analysis of 21 different salts revealed the electrophilicity of the Te centers in their interactions with anions. Telluroniums' propensity to form Lewis pairs was investigated with OPPh3 . Diffusion-ordered NMR spectroscopy suggested that telluroniums can bind up to three OPPh3 molecules. Isotherm titration calorimetry showed that the related heats of association in 1,2-dichloroethane depend on the electronic properties of the substituents of the aryl moiety and on the nature of the counterion. The enthalpies of first association of OPPh3 span -0.5 to -5 kcal mol-1 . Study of the affinity of telluroniums for OPPh3 by state-of-the-art DFT and ab-initio methods revealed the dominant Coulombic and dispersion interactions as well as an entropic effect favoring association in solution. Intermolecular orbital interactions between [Ar2 MeTe]+ cations and OPPh3 are deemed insufficient on their own to ensure the cohesion of [Ar2 MeTe ⋅ Bn ]+ complexes in solution (B=Lewis base). Comparison of Grimme's and Tkatchenko's DFT-D4/MBD-vdW thermodynamics of formation of higher [Ar2 MeTe ⋅ Bn ]+ complexes revealed significant molecular size-dependent divergence of the two methodologies, with MBD yielding better agreement with experiment.

Volatile lanthanide complexes with fluorinated heptadentate ligands

Understanding factors that influence the volatility of lanthanide complexes remains an important goal for applications such as gas-phase f-metal separations and the synthesis of lanthanide-containing thin films. Lanthanide complexes often exhibit volatility differences that depend on the ability of ligands to saturate the lanthanide coordination sphere and attenuate intermolecular bonding in the solid state. This can make it difficult to assess how electronic factors associated with differing ligand substituents influence volatility. Here we describe the synthesis, structures, and thermal properties of a series of volatile lanthanide complexes (Ln = Nd, Er, and Yb) containing N4O3 ligands decorated with different alkyl and fluoroalkyl substituents (CF3, CF2CF2CF3, Me, and tBu). These ligands completely enveloped the tested lanthanides to form monomeric complexes with 7-coordinate distorted capped octahedral coordination geometries, as determined using single-crystal X-ray diffraction. Thermogravimetric analysis and bulk sublimation studies show how metal encapsulation affords complexes with the same volatility regardless of metal size, even with lanthanide ions with significantly different radii such as Nd3+ and Yb3+. Most notably, the results show that increasing ligand fluorination, a strategy often used to increase the volatility of metal complexes, is not always beneficial and can significantly attenuate the volatility of lanthanide complexes depending on location with respect to other substituents in the ligand framework. A pair-wise model based on density functional theory shows that the net intermolecular interactions in the unit cell can still be stronger when fluorination is present. In other words, even if individual interactions between neighboring molecules are weaker, the total number of interactions in the solid arising from the nature of crystal packing is equally important to consider.

The Structure of 2,6-Di-tert-butylphenol-Argon by Rotational Spectroscopy

The molecular structure of a van der Waals-bonded complex involving 2,6-di-tert-butylphenol and a single argon atom has been determined through rotational spectroscopy. The experimentally derived structural parameters were compared to the outcomes of quantum chemical calculations that can accurately account for dispersive interactions in the cluster. The findings revealed a π-bound configuration for the complex, with the argon atom engaging the aromatic ring. The microwave spectrum reveals both fine and hyperfine tunneling components. The main spectral doubling is evident as two distinct clusters of lines, with an approximate separation of 179 MHz, attributed to the torsional motion associated with the hydroxyl group. Additionally, each component of this doublet further splits into three components, each with separations measuring less than 1 MHz. Investigation into intramolecular dynamics using a one-dimensional flexible model suggests that the main tunneling phenomenon originates from equivalent positions of the hydroxyl group. A double-minimum potential function with a barrier of 1000 (100) cm-1 effectively describes this extensive amplitude motion. However, the three-fold fine structure, potentially linked to internal motions within the tert-butyl group, requires additional scrutiny for a comprehensive understanding.

A chiral pentanidium and pyridinyl-sulphonamide ion pair as an enantioselective organocatalyst for Steglich rearrangement

Enantioselective ion pair catalysis has gained significant attention due to its ability to exert selectivity control in various reactions. Achiral counterions have been found to play crucial roles in modulating reactivity and selectivity. The modular nature of an ion pair catalyst allows rapid alterations of the achiral counterion to achieve optimal outcomes, without the need to modify the more onerous chiral component. In this study, we report the successful development of a stable chiral pentanidium pyridinyl-sulphonamide ion pair as a nucleophilic organocatalyst for asymmetric Steglich rearrangement. The ion pair catalyst demonstrated excellent performance, leading to enantioenriched products with up to 99% ee through simple alterations of the achiral anions. We conducted extensive ROESY experiments and concluded that the reactivity and enantioselectivity were correlated to the formation of a tight ion pair in solution. Further computational analyses provided greater clarity to the structure of the ion pair catalyst in solution. Our findings reveal the critical roles of NMR experiments and computational analyses in the design and optimisation of ion pair catalysts.

Molecular orbital and topological electron density study of n → π* interactions: amides and thioamides cases

The n → π* interactions were studied in amides and thioamides systems models, through the analysis of the electron density topology along with the Natural Bonding Orbital (NBO) approach. The effect of the dispersion terms was assessed using different DFT functionals. The NBO, independent gradient model (IGM), and the analysis of the reduced density gradient outcomes show that dispersion forces play a significant role in the strength of n → π* interactions. The IGM results indicate that δg height values for n → π* interactions do not extend beyond 0.025. All the methods used in this work predict that n → π* interaction between pairs of thioamides is stronger than those between amides. However, the electron density topology-based methods were not able to replicate the trends in the relative force of this interaction found in the experimental and NBO results.

Implementing Mesoporosity in Zeolitic Imidazolate Frameworks through Clip-Off Chemistry in Heterometallic Iron-Zinc ZIF-8

Bond breaking has emerged as a new tool to postsynthetically modify the pore structure in metal-organic frameworks since it allows us to obtain pore environments in structures that are inaccessible by other techniques. Here, we extend the concept of clip-off chemistry to archetypical ZIF-8, taking advantage of the different stabilities of the bonds between imidazolate and Zn and Fe metal atoms in heterometallic Fe-Zn-ZIF-8. We demonstrate that Fe centers can be removed selectively without affecting the backbone of the structure that is supported by the Zn atoms. This allows us to create mesopores within the highly stable ZIF-8 structure. The strategy presented, combined with control of the amount of iron centers incorporated into the structure, permits porosity engineering of ZIF materials and opens a new avenue for designing novel hierarchical porous frameworks.

A new approach to study semi-coordination using two 2-methyl-5-nitroimidazole copper(ii) complexes of biological interest as a model system

Two novel copper(ii) complexes [Cu(2mni)2(H2O)2](NO3)2·2H2O (1) and [Cu(2mni)2(NO3)2] (2), where 2mni is 2-methyl-5-nitroimidazole, were prepared and characterized in the solid state using single-crystal and powder X-ray diffraction analyses, EPR, electronic and vibrational spectroscopies (FTIR and Raman), and thermogravimetric methods. Both products present an elongated distorted octahedral geometry with axial Cu-O bond lengths of 2.606(14) and 2.593(15) Å, indicating semi-coordination. Density functional theory (DFT) calculations at the B3LYP/LANL2DZ theory level were used to study the electronic properties of 1 and 2. The Independent Gradient Model (IGM) was employed to determine the Intrinsic Bond Strength Index (IBSI) of the semi-coordination and to plot δg isosurfaces for the electronic sharing between the metal center and ligands. A moderate to weak antibacterial activity against Escherichia coli cultures was found for 1 with a 50% growth inhibition (GI50) value of 0.25 mmol L-1. To the best of our knowledge, this is the first time that the semi-coordination analysis using IGM was carried out for a copper(ii) complex with axial elongation, finding a good correlation between the bond length and the IBSI, and the study was extended for a series of analogous complexes described in the literature.

Halogen Bonding Involving Isomeric Isocyanide/Nitrile Groups

2,3,5,6-Tetramethyl-1,4-diisocyanobenzene (1), 1,4-diisocyanobenzene (2), and 1,4-dicyanobenzene (3) were co-crystallized with 1,3,5-triiodotrifluorobenzene (1,3,5-FIB) to give three cocrystals, 1·1,3,5-FIB, 2·2(1,3,5-FIB), and 3·2(1,3,5-FIB), which were studied by X-ray diffraction. A common feature of the three structures is the presence of I···Cisocyanide or I···Nnitrile halogen bonds (HaBs), which occurs between an iodine σ-hole and the isocyanide C-(or the nitrile N-) atom. The diisocyanide and dinitrile cocrystals 2·2(1,3,5-FIB) and 3·2(1,3,5-FIB) are isostructural, thus providing a basis for accurate comparison of the two types of noncovalent linkages of C≡N/N≡C groups in the composition of structurally similar entities and in one crystal environment. The bonding situation was studied by a set of theoretical methods. Diisocyanides are more nucleophilic than the dinitrile and they exhibit stronger binding to 1,3,5-FIB. In all structures, the HaBs are mostly determined by the electrostatic interactions, but the dispersion and induction components also provide a noticeable contribution and make the HaBs attractive. Charge transfer has a small contribution (<5%) to the HaB and it is higher for the diisocyanide than for the dinitrile systems. At the same time, diisocyanide and dinitrile structures exhibit typical electron-donor and π-acceptor properties in relation to the HaB donor.