Weak Intramolecular Interactions Research Articles

An Open-Shell Functionalization of Inorganic Benzene.

A borazine derivative functionalized by nitroxide free radicals, N,N',N″-(tris(4-Bromophenyl))-B,B',B″-tris((2,6-dimethyl-4-(N-tert-butyl-N-oxyamino)phenyl) borazine (TriBNit), was synthesized as a milestone of open-shell inorganic benzene. The crystal structure determined from X-ray diffraction on a single crystal ascertains the grafting of three nitroxide radicals. The temperature dependence of the magnetic susceptibility evidences weak intramolecular antiferromagnetic interactions between the radicals with strong intermolecular antiferromagnetic interactions between two nitroxide moieties of two neighboring molecules. EPR spectroscopy at 80 K on a frozen glassy solution evidences the coexistence of S = 1/2 and S = 3/2 ground-spin state species. This is ascribed to the nitroxide radicals having different orientations with respect to the borazine core giving rise either to antiferromagnetic interaction with a low ground-spin state S = 1/2 or to ferromagnetic interaction with a high ground-spin state S = 3/2 as supported by theoretical data. At room temperature, because of nitroxide mobility, the EPR spectrum is averaged to a ground-spin state S = 1/2.

An experimental and computational investigation of the cyclopentene-containing peptide-derived compounds: focus on pseudo-cyclic motifs via intramolecular interactions.

Conformational flexibility is one of the main disadvantages of peptide-based compounds. We focus on their molecular 'chameleonicity' related to forming pseudo-cyclic motifs via modulation of weak intramolecular interactions. It is an appealing strategy for controlling equilibrium between the polar open and the nonpolar closed conformations. Within this context, we report here the crystal structure of the (R)-(2-tert-butoxycarbonyl)amino-1-oxo-3-phenyl)propyl)-1-cyclopentene (1), synthesis of which in high yield was achieved by a facile multi-step protocol. Our Cambridge Structural Database (CSD) overview for the peptide-based crystals revealed the exclusivity of this compound from the viewpoint of the unusual pseudo-bicyclic system via C-H…O and C-O…π interactions, in which cyclopentene shields the amide bond. Notably, cyclopentene as a bioisostere of proline is an appealing scaffold in medicinal chemistry. An extensive combined experimental and computational study provided more profound insight into the supramolecular landscape of 1 with respect to similar derivatives deposited in the CSD, including the tendency of cyclopentene for the generation of pseudo-cyclic motifs through weak H-bonding and π-based intramolecular interactions. These weak interactions have been examined by either the quantum theory of 'atoms-in-molecules' (QTAIM) or complex Hirshfeld surface methodology, including enrichment ratios, molecular electrostatic potential surfaces and energy frameworks. In all analysed crystals, all types of H-bonded motifs involving cyclopentene are formed at all levels of supramolecular architecture. A library of cyclopentene-based H-bonding synthons is provided. A molecular docking study depicted vital interactions of cyclopentene with key amino acid residues inside the active sites of two prominent protein kinases, uncovering the therapeutic potential of 1 against breast cancer. To a large extent, dispersion forces have significance in stabilizing the supramolecular structure of both ligand and bio-complex ligand-protein. Finally, the satisfactory in silico bio-pharmacokinetic profile of 1 related to drug-likeness and blood-brain barrier permeation was also revealed.

DFT-aided stereo-structural and electronic structure studies of poly-hydroxyl substituted chlorophyllous molecules

Numerous chlorophyll-based derivatives have found applications in the dye and pharmaceutical industries. Here, we report the synthesis of a poly-hydroxyl substituted chlorophyll molecule (THM) and its absolute configuration determination using experimental electron circular dichroism (ECD), nuclear magnetic resonance (NMR) spectroscopy, and density functional theory (DFT) calculations. Furthermore, the photoreaction types of THM (type I and type II) were investigated through theoretical calculations and validated by biological experiments. We provide a detailed analysis of electron transfer and excitation processes in THM through theoretical calculation of hole-electron distribution, as well as study intramolecular weak interactions and conjugation effects using Reduced Density Gradient (RDG), Interaction Region Indicator (IRI), and Natural Bond Orbital Analysis (NBO). The photoreaction types (type I, type II) of THM in tumor cells have also been investigated by biological experimental measures and theoretical calculation of the single-triplet state energy gap and hole-electron distribution. Molecular electrostatic potential has also been investigated by DFT methods to give insight into the molecular structure. This study provides useful guidance for the structural and photochemical studies of the chlorophyll-derived photodynamic therapeutic drugs.

Influence of hydrogen bonds on state diagrams of cryoprotectant solutions

BACKGROUND: Transformation of state diagrams of cryoprotectant solutions under the influence of weak intramolecular interactions was considered. MATERIALS AND METHODS: Phase states of aqueous glycerol and DMSO solutions within temperature range +25???−150 °?? were studied using method of volumetric scanning tensodilatometry. Temperatures below which hydrogen bonds significantly affect crystallization-melting kinetics of such solutions were determined. RESULTS: Principles for plotting of state diagram for binary solutions with weak intermolecular interaction of the components were set up. The study demonstrates that in such solutions formation of clusters based on ice microcrystals and cryoprotectant occurs. Based on the obtained results, state diagrams for glycerol and DMSO aqueous solutions were plotted. These diagrams include area of cluster phase existence and differ fundamentally from those describing eutectic crystallization. CONCLUSION: Nanostructures occurring in cryoprotectant solutions during their cooling were analyzed. Difference between these structures and classical solid phase eutectics were demonstrated.

Regioselective amination of 4-methylene-5,7-dinitroquinazoline: a mechanistic consideration on non-conventional N-H—π interactions between amine and ethylene moiety

ABSTRACT Pi (π) interactions originating from the N-H bond of amine and ethylene moiety have been explored on the mechanism of aromatic nucleophilic substitution (ArSN) of the nitro group of 4-methylene-5,7-dinitroquinazoline with methylamine in the gas phase and solvent media within DFT framework. The free energy profiles confirmed that the amination should take place at peri-position and calculations support the one-step mechanism through a transition state with no intermediate in the reaction route. Stabilisation of peri-transition state by intramolecular weak interaction akin to hydrogen bonding N-H—CH2 = C leads to the regioselective amination at peri-position of 4-methylene-5,7-dinitroquinazoline. The intramolecular hydrogen bond interactions at N-H—CH2 = C in the peri-transition state are strongly supported by a red shift in N-H stretching vibrations in simulated IR spectra and are confirmed by studying energetics of amination of structural/electronic analogues of 4-methylene-5,7-dinitroquinazoline. The present study established that ethylene plays an important role as an efficient H-bond acceptor in fixing the regioselectivity at peri-position in the amination of 4-methylene-5,7-dinitroquinazoline. This is the first-ever report for the exploration of the role of ethylene moiety as a hydrogen bond acceptor in mediating the regioselectivity of organic reactions.

IGMH‐based research on the intramolecular weak interaction of TKX‐50

AbstractTo further comprehensively study the intramolecular weak interaction of the gaseous TKX‐50 molecule, the two conformations of the TKX‐50 molecule were analyzed via the Independent Gradient Model based on the Hirshfeld Partition (IGMH) method based on the B3LYP/6‐311 g (d,p) level for geometry optimization and for single point energy. The conclusions manifest that the weak interactions between these fragments are mainly composed of hydrogen bonds and van der Waals interactions. From the strength of inter‐fragment interactions formed by contributing atomic pairs and their percentage contributions, these H bonds, together with dispersion‐dominated weak interactions provided by non‐direct facing atomic pairs near these H bonds, dominate the inter‐fragment interaction resulting in the stability of the molecular structure. Meanwhile, the weak interactions enclosed by end‐atoms of two fragments not only include the contributions provided by inter‐fragment atomic pairs of two fragments but also include the contributions provided by intra‐fragment atomic pairs of fragment 1. For conformation II, due to the H transfer between fragments, a pair of symmetric H bonds at the corresponding regions are extremely strong to reach the level of covalent bond while the two groups −OH at the other end become looser, resulting in conformation II own lower energy. Differences in inter‐fragment interactions between two conformations were essentially brought by the stronger electron‐withdrawing ability of atom O than that of atom N.

Promoting Ruddlesden-Popper Perovskite Formation by Tailoring Spacer Intramolecular Interaction for Efficient and Stable Solar Cells.

Low-dimensional Ruddlesden-Popper phase (LDRP) perovskites are widely studied in the field of photovoltaics due to their tunable energy-band properties, enhanced photostability, and improved environmental stability compared to the 3D perovskites. However, the insulating spacers with weak intramolecular interaction used in LDRP materials limit the out-of-plane charge transport, leading to poor device performance of LDRP perovskite solar cells (PSCs). Here, a functional ligand, 3-guanidinopropanoic acid (GPA), which is capable of forming strong intramolecular hydrogen bonds through the carboxylic acid group, is employed as an organic spacer for LDRP PSCs. Owing to the strong interaction between GPA molecules, high-quality LDRP (GPA)2(MA)n-1PbnI3n+1 film with promoted formation of n = 5 phase, improved crystallinity, preferential vertical growth orientations, reduced trap-state density, and prolonged carrier lifetime is achieved using GPAI as the dimensionality regulator compared to butylamine hydroiodide (BAI). As a result, GPA-based LDRP PSC exhibits a champion power conversion efficiency of 18.16% that is much superior to the BA-based LDRP PSC (15.43%). Importantly, the optimized GPA-based LDRP PSCs without encapsulation show enhanced illumination, thermal, storage, and humidity stability compared to BA-based ones. This work provides new insights into producing high n value LDRP films and their efficient and stable PSCs.

Effects of weak intramolecular interactions and distortions from trigonal prismatic coordination on the magnetic properties of zero-field Co(ii) single-ion magnets

The change of counter anions significantly affects the environment around Co(ii) ions, leading to two zero-field single-ion magnets possessing different uniaxial anisotropies and dynamic magnetic properties.

Study on solvent effect and coordination characteristics of two different types of Cu(II) salamo-salen-salamo-hybrid complexes

Based on the condensation reaction of a containg-formyl asymmetric salamo-based ligand with ethylenediamine, a salamo-salen-salamo-hybrid multi-compartment ligand possessing both salen and salamo structural moieties was prepared, and its different types (Cu(II): H2L)2−) of copper(II) complexes, confirmed as [Cu(H2L)]2·4EtOH (1) and [Cu2(H2L)2]·2MeOH·(Me)2CO (2), have been synthesized and elucidated structurally. In the complexes, Cu(II) ion is sited at the salen's N2O2 cavity, while the salamo structural moieties do not participate in coordination. This coordination characteristic indicates that the coordination ability of salen and salamo structural moieties in salamo-salen-salamo-hybrid ligand varies, with salen having relatively stronger coordination ability, which may be due to the incorporation of more electronegative multiple O atoms on C=N bonds, resulting in a decrease in the electron cloud density on the N atoms of the multi-oxime groups and a decrease in the coordination ability. Thus, Salen structural moiety on the hybrid ligand has stronger coordination ability than salamo structural moieties. In addition, due to the solvent effect, the extension direction of the single salamo long chain is different, and the configurations of the complexes are also different. Through X-ray diffraction analysis and DFT theoretical computations of the ligand and the complexes, the weak intramolecular and intermolecular interactions of the complexes, as well as the intermolecular C-H···π & π···π interactions of the complexes, were discussed. The ligand and the copper(II) complexes were analyzed for their MESP, as well as to show the mobile regions of the molecules in the complex molecules. Due to the solvent effect, the spatial orientation of the long chain of salamo has undergone significant changes, changing the region where the complex molecules move in a specific space.

In One Fell Sweep: Modeling Exchange, Hyperfine and Dipolar Interactions from EPR Spectra of Copper(II) Spin Triangles

The weak intramolecular magnetic interactions within a series of CuII3 complexes based on the trinucleating 2,4,6-tris(di-2-pyridylamino)-1,3,5-triazine (dipyatriz) ligand were investigated via Electron Paramagnetic Resonance (EPR) spectroscopy. X- and Q-band EPR spectroscopy in powders and frozen solutions were recorded and the Q-band spectra were interpreted by a multispin Hamiltonian model comprising exchange, dipolar and hyperfine interactions. The described methodology is suitable for the elucidation of weak intramolecular interactions which are not amenable to analysis via magnetic susceptibility studies.

Solution Self-Assembly of Amphiphilic Tadpole-like Giant Molecules Constructed by Monotethering Diblock Copolymer Chain onto a Nanoparticle.

The self-assembly behavior of a tadpole-like giant molecule (TGM) constructed from a hydrophobic nanoparticle (NP) monotethered by a single amphiphilic AB diblock copolymer chain was investigated by combining self-consistent field theory and density functional theory in solution. The effects of the hydrophobicities of the B blocks and NPs (i.e., solvent properties) on the self-assembly behavior of the TGMs were investigated in the cases of weak and strong intramolecular interactions (i.e., incompatibilities) between the components of giant molecules, respectively. Besides conventional ordered aggregates (such as spheres, rings, and vesicles) with hydrophobic B-cores covered by NP shells, several aggregates with novel hierarchical structures, including vesicles with NP-inserted hydrophobic walls, bead-string-like micelles, and long cylindrical micelles with NP bumps, were obtained by tuning the solvent properties under different intramolecular interactions. Noteworthy that the simulation results show that the arrangement of the NP bumps on the long cylindrical micelles may have a certain degree of helicity, which means that these micelles may have some unique electromagnetic features such as circular dichroism. Phase diagrams as a function of the hydrophobicities of the B blocks and NPs were constructed to show the formation conditions of these novel structures. These findings can not only offer new insights into understanding of the self-assembly behavior of the TGM in solution but also provide useful guidance for simple and efficient regulation of the morphology, as well as the NP distribution and arrangement of the ordered aggregates in experiments.

Experimental and computational studies of two binuclear Co(II) and Ni(II) bis(salamo)‐like complexes

Acetate‐bridged binuclear Co(II) and Ni(II) complexes, [Co2(L)(μ‐OAc)(EtOH)] (1) and [Ni2(L)(μ‐OAc)(EtOH)] (2) were synthesized via the reaction of a new bis(salamo)‐like ligand with two different metal(II) acetates. X‐ray single crystal diffraction analyses showed that two metal(II) ions (Co or Ni) occupy two sets of N2O2 cavities, respectively. The acetate group bridges the two metals, and the ethanol oxygen atom participates in the coordination. Furthermore, UV–vis titration experiments clearly indicated that the complexation between H3L and M(II) ions leads to the 1:2 complexes [(L)M2]+ through a highly synergistic process. Bond valence sum (BVS) calculations exhibited that the Co(II) and Ni(II) ions are divalent. Secondly, the ligand H3L highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO‐LUMO) gap analysis and surface electrostatic potential were theoretically analyzed by theoretical calculation (density functional theory), and the reactivity of M(II) ions and the ligand in the complex formation process was demonstrated. Finally, the microscopic properties of the complexes were deeply understood through the calculation of the weak intramolecular interactions and the unstressed regions outside the complexes.

Molecular insights into the sensing function of an oxidized graphene flake for the adsorption of Avigan antiviral drug

The Avigan antiviral drug adsorption by an oxidized form of a graphene flake; so called Ovalene, was investigated using density functional theory calculations to provide molecular insights into the sensing functions of targeted drug delivery issues. The features and stabilized models of Ovalene and Avigan and their three interacting Avigan@Ovalene complexes were obtained. Inter-molecular and intra-molecular communications were found among the models, in which the intra-molecular communications inside Avigan were observed as a preventive factor for formations of strong complexes. Hence, the complex with a weaker intra-molecular interaction was placed at the highest adsorption strength level and that one with a stronger intra-molecular interaction was placed at the lowest level. Based on the results, Ovalene was found as an expected Avigan drug carrier with suitable recovery time and conductance rate to provide a sensing function. Consequently, Avigan@Ovalene complexes were proposed for further investigations regarding the targeted drug delivery issues.

Theoretical exploration of the mechanisms on the iron complexes catalyzed ammonia borane dehydrogenation and polyaminoborane formation

Density functional theory study was carried out to provide mechanistic insights into the bifunctional iron complex [Fe(DCPE)(PhNCH2)2 (DCPE = 1,2-bis(dicyclohexylphosphino)ethane)] catalyzed AB dehydrogenation and polyaminoborane formation with the detailed mechanistic pathways. Computational results imply a favorable scenario that complies with a proton transfer pathway between the metal center and ligand, which could further lead to a kinetically feasible transition state with low energy barrier. Subsequent polyaminoborane formation involves the generation of nucleophiles, and the NH2BH2 moiety, which is featured with a nitrogen lone pair, plays a crucial role in the chain polyaminoborane formation. Natural bond orbital analysis (NBO), and energy decomposition analysis (EDA) were utilized to study the orbital interactions and intramolecular weak interactions were revealed by the independent gradient model based on Hirshfeld partition method (IGMH).

Non-Covalent Interactions in Polymers

Non-covalent interactions are one of the key topics in modern chemical science. These inter- and intramolecular weak interactions (e.g., hydrogen, halogen, and chalcogen bonds, stacking interactions and metallophilic contacts) have a significant effect on the properties of polymers. In this Special Issue, "Non-covalent interactions in polymers", we tried to collect fundamental and applied research manuscripts (original research articles and comprehensive review papers) focused on non-covalent interactions in polymer chemistry and related fields. The scope of the Special Issue is very broad: we welcome all the contributions that deal with the synthesis, structure, functionality and properties of polymer systems involving non-covalent interactions.

Time‐Dependent Density Functional Theory, AIM Analysis, NLO, and Thermodynamic Properties of Propofol and Adsorption Effects of Propofol Drug over Carbon Nanotube (C56H16) as the Factor of Drug Delivery System

This article presents a comprehensive quantum chemical study of the Propofol molecule using the Density Functional Theory (DFT). The UV (Ultra Violet)plots, Non-Linear Optical (NLO) properties' calculations, and Density Of State (DOS) plots are studied with the help of DFT using 6–311G (d, p) as the basis set. Quantum Theory of Atoms in Molecules (QTAIM) analysis shows weak intramolecular interactions of CH….O. The NLO calculations show that the molecule is a good candidate as a future nonlinear optical material. The parameters of NLO Propofol and Propofol (CH2)n, n = 1–5 are also calculated with the same level theory. During this study, we have mainly focused on the profile of its electronic properties, the vital vibrational modes during movement in the isolated gas phase, and a better understanding of the unbound interaction between drug propofol and carbon nanotubes [C56H16].

Theoretical study on intra-molecule interactions in TKX-50.

To fully and deeply understand the weak interactions in the gaseous structure of the TKX-50 molecule, two conformations I and II of the TKX-50 molecule confirmed in a crystal cell were optimized at the B3LYP/6-311g(d,p) level in the gas state, and the single point energy of the optimized structure was calculated at the M06-2X/ma-TZVPP level. Analyzing methods for weak interactions such as the interaction region indicator (IRI), topological basin analysis, and the extended transition state-natural orbitals for chemical valence (ETS-NOCV) theory with the help of Multiwfn code were employed to reveal the corresponding intramolecular weak interactions. The results showed that there were 5 kinds of intramolecular weak interaction in both conformations. They are two types of H bond, two types of intra-ring weak interaction, and one type of O-N bond within the molecular fragment containing the bis-tetrazole ring. The combined effect of all these weak interactions holds the bis-tetrazole ring of TKX-50 retaining an almost coplanar configuration. Meanwhile, the strength of these weak interactions is significantly different in conformation I and conformation II. The most obvious difference is that conformation II has a significant H transfer between intramolecular fragments due to the mirror rotation of almost 180° of cations (NH3OH)+ perpendicular to the N-O bond axis thereof as compared to the reference conformation I. This conformational difference not only makes the weak interaction between the two conformations very different but also forms a quasi-covalent bond in conformation II with much larger bonding energy than other H bonds, thus resulting in conformation II having lower electron energy and more stable geometry. In addition, the order of breaking various H bonds in the combustion decomposition process of TKX-50 is deduced by comparing various H bonds.

Sorption of hazardous industrial organic liquids with environmentally friendly functionalized cellulosic sorbents

Abstract The performances of five cellulosic polymers with different functional groups (cellulose, cellulose acetate, cellulose phosphate, chitosan, and chitin) as sorbents of seven frequently used hazardous polar organic liquids (acrolein, butanone peroxide, epichlorohydrin, formaldehyde, furfuryl alcohol, propylene oxide, and vinyl acetate) are investigated in this study. Amongst the cellulosic sorbents, cellulose phosphate exhibited enhanced sorption properties (as high as 3.09–7.03 g/g) against all seven polar organic liquids investigated, and chitosan and chitin also demonstrated comparable sorption efficiencies (2.28–7.72 g/g and 2.55–5.86 g/g, respectively) to those of cellulose phosphate. According to our investigation, the enhanced sorption efficiency could be achieved due to low powder density of cellulose phosphate, which is caused by the weak intramolecular interaction amongst the polymer chains. In addition, cellulose phosphate, chitosan, and chitin also showed enhanced absorbed solvent recovery percents (71.4, 60.6, and 61.1%, respectively, in average) compared with that of pristine cellulose (43.8%). With excellent sorption efficiency, enhanced solvent recovery rate, and reusability after drying, these functionalized cellulosic sorbents can be excellent candidates to replace the conventional carbon and vermiculites-based sorbents, especially for liquid polar organic spill sorption.

Spectroscopic, Vibrational and Topology Analysis of (2R, 3R) - Butanediol bis (Methanesulfonate)

Objectives: To find the (2R, 3R)-Butanediol bis (methanesulfonate) (BBM) to be the most bioactive through DFT calculations and multi-spectroscopic investigations. Methods: BBM molecule was characterized by multi-spectroscopic investigations (FT-IR, FT-Raman, UV-Vis) and quantum chemical computations employing density functional theory with wB97XD and cam-B3LYP basis functional. Findings: The assignments of vibrational spectral features were made with the help of Gar2ped, which incorporates the Scaled Quantum Mechanical Force Field (SQMFF) methodology. The absolute energy gap between the frontier molecular orbitals (HOMO and LUMO) at room temperature and reactivity descriptors confirm that the molecule BBM is chemically active, to realize the charge transfer within the molecule and shows the best bioactive molecule. Moreover, the weak intramolecular interaction and evaluate the intermolecular interaction (hydrogen bonds) were revealed from quantum topological atoms in molecules and reduced density gradient plots. Novelty: BBM molecule was found to very good bioactive molecules, given the results of vibrational, topological, quantum computational methods and RDG analysis. Keywords: BBM; DNA; SQMFF; HOMO; LUMO

Syntheses, structures, and magnetic properties of acetate-bridged lanthanide complexes based on a tripodal oxygen ligand.

Four homodinuclear lanthanide complexes, Dy2 (LOEt)2(OAc)4 (1), Tb2 (LOEt)2(OAc)4 (2), Ho2(LOEt)2(OAc)4 (3), and Gd2 (LOEt)2(OAc)4 (4), have been synthesized and characterized based on a tripodal oxygen ligand Na [(η5-C5H5)Co(P(O)(OC2H5)2)3] (NaLOEt). Structural analyses show that the acetate anions bridge two symmetry-related Ln3+ ions in the μ2:η1:η1 and μ2:η1:η2 coordination patterns, and each lanthanide (III) ion owns a twisted square antiprism (SAPR) conformation. Static magnetic measurements reveal the weak intramolecular ferromagnetic interaction between dysprosium (III) ions in 1 and antiferromagnetic Ln3+···Ln3+ couplings in the other three complexes. Through the analysis of the ligand-field effect and magnetic anisotropy axis orientation, the reasons for the lack of dynamic magnetic behavior in 1 were identified.