Noncovalent Index Research Articles

Mechanism and Origin of Stereoselectivity of N-Heterocyclic Carbene (NHC)-Catalyzed Transformation Reaction of Benzaldehyde with o-QDM as Key Intermediate: A DFT Study.

N-heterocyclic carbene (NHC)-bound ortho-quinodimethane, served as a nucleophile, has occupied an important position for constructing various all-carbon or heterocyclic compounds and attracted increasing attention for the functionalization of benzylic carbon of aromatic aldehydes, whereas the mechanistic studies on the generation and transformations of dienolate intermediate are rare. In the present study, the mechanism of activation/transformation of aldehyde catalyzed by NHC was theoretically studied using the density functional theory (DFT) method. Based on the calculations, the nucleophilic addition process is the stereoselectivity-determining step with RS-configured product being generated preferentially. Furthermore, non-covalent index (NCI) and atoms-in-molecules (AIM) analyses have been performed to disclose the origin of stereoselectivity, by which the larger number and stronger weak interactions are the key for stabilizing the low-energy transition state and thus leading to the stereoselectivity inducing.

Fascinating inclusion of metal–organic complex moieties in dinuclear Mn(II) and Zn(II) compounds involving pyridinedicarboxylates and phenanthroline: Experimental and theoretical studies

In the present study, we have reported the synthesis of two new dinuclear Mn(II) and Zn(II) metal–organic compounds, [Mn(2,5-PDC)(phen)2][Mn(phen)2(H2O)2]2Cl·10H2O (1) and [Zn(phen)3][Zn(2,6-PDC)2]·11.5H2O (2) (where, 2,5-PDC = 2,5-pyridinedicarboxylate, 2,6-PDC = 2,6-pyridinedicarboxylate, phen = 1,10-phenanthroline) at room temperature which have been characterized by elemental analysis, TGA, spectroscopic (FTIR, electronic) and single crystal X-ray diffraction techniques. A fascinating chloride-water supramolecular cluster in 1 and (H2O)13 H-bonded cluster in 2 along with π-stacked assemblies stabilize the solid state structures. The most interesting aspect of the crystal structure of 1 is the inclusion of complex cationic moieties within the infinite self-assembled chloride-water cluster. Similarly the inclusion of cationic complex moieties in compound 2 inside the supramolecular cavity formed by the anionic complex provides rigidity to the crystal structure. DFT calculations, molecular electrostatic potential (MEP) surface analysis, quantum theory of atoms-in-molecules (QTAIM) and the non-covalent index plot (NCI plot) analysis were performed to investigate the supramolecular assemblies of the compounds. The studies reveal that the antiparallel π-stacking interactions are energetically significant synthons for the assemblies. However, the assemblies in 2 have been dominated mostly by Columbic attraction of the cationic and anionic complex moieties.

Cavitands based nanocapsule as smart and highly effective vehicle for 5-fluorouracil anti-cancer drug delivery: DFT insights

The nanomaterials have been widely investigated as drug delivery system for a variety of anticancer drugs to limit their adverse effects while transporting to the target site. In the current study, we report the cavitand-based nanocapsules as a drug delivery vehicle for nitrosourea (NU) and fluorouracil (FU) anti-cancer drugs. FU and NU drugs interact with the nanocapsules with the interaction energies in gas phase (solvent) −24.78 kcal/mol (–22.39 kcal/mol) and −21.58 kcal/mol (-20.45 kcal/mol), respectively. The results of Quantum theory of atoms in molecules (QTAIM) and noncovalent index (NCI) analyses indicate that the FU@Capsule and NU@Capsule complexes are mainly stabilized through hydrogen bonding and van der Waals interactions. Electron density difference (EDD) and natural bond order (NBO) analyses reveal that significant amount of charge is transferred from the nanocapsule to drug molecules. Frontier molecular orbital (FMO) analysis also reveals slight reduction in the energy gap. AIMDS analysis shows that cavitand capsules can efficiently carry the anti-cancerous drug to their target site without distorting complexes. The dipole moments and pH effect are studied to understand the drug release mechanism of considered anticancer drugs. The decrease in adsorption energy and increase in interaction distances indicate that anticancer drugs can easily be off-loaded from the carrier (nanocapsule) at the target site due to the low pH of cancerous cells compared to the normal cells. Therefore, cavitand nanocapsule can be employed as an excellent drug delivery carrier in smart targeted drug delivery.

Microhydration of small protonated polyaromatic hydrocarbons: a first principles study.

Using first principles methodology, we investigate the microsolvation of protonated benzene (BzH+), protonated coronene (CorH+) and protonated dodecabenzocoronene (DbcH+). Gas phase complexes of these small protonated polyaromatic hydrocarbons (H+PAHs) with mono-, di-, and tri-hydrated water molecules are considered. Their most stable forms are presented, where we discuss their structural, energetic aromaticity and IR and UV spectral features. In particular, we focus on the analysis of the bonding and various non-bonded interactions between these protonated aromatics and water clusters. The strength of non-bonded interactions is quantified and correlated with their electron density profiles. Furthermore, insights into the interfacial interactions and stability of these complexes were obtained through non-covalent index and symmetry-adapted perturbation theory (SAPT0) analyses. We also discuss the effects of the extension of the π aromatic cloud on the water solvation of these protonated aromatics. In particular, we extended our predictions for the S0 → S1 and S0 → T1 wavelength transitions of micro hydrated H+PAHs to deduce those of these species solvated in aqueous solution. The present findings should be useful for understanding, at the microscopic level, the effects of water interacting with H+PAHs, which are relevant for organic chemistry, astrochemistry, atmospheric chemistry, combustion and materials science.

Experimental and Theoretical Survey of Intramolecular Spodium Bonds/σ/π-Holes and Noncovalent Interactions in Trinuclear Zn(II)-Salen Type Complex with OCN- Ions: A Holistic View in Crystal Engineering.

In this work, one new centrosymmetric trinuclear Zn(II) complex 1, [{(OCN)Zn(L)}2Zn], using a salen-type ligand (H2L) in the presence of OCN- was synthesized and characterized via elemental, spectral, SEM-EDX, and single-crystal X-ray diffraction (SCXRD) study. In 1, SCXRD reveals two different stereochemical environments of zinc metal ions; one terminal Zn(II) center adopts square pyramidal geometries with the Addison parameter (τ) 0.095, and the central Zn(II) is tetracoordinated tetrahedral geometry. This article provides evidence of the significance and presence of spodium bonds (SpBs) in solid-state crystal structures involving a pseudotetrahedral environment of the central Zn-atom. X-ray structures reveal intramolecular Zn···O SpBs caused by the methoxy (-OCH3) substituent O-atom adjacent to the coordinated phenoxy O-atom. These noncovalent interactions have been thoroughly studied using density functional theory calculations at the RI-BP86[2]-D3[3]/def2-TZVP level of theory that characterizes the nature of SpBs, including the Baders quantum theory of atoms-in-molecules "QTAIM", molecular electrostatic potential (MEP) surface, and noncovalent index plot (NCI). In addition, a unique complex-isomer-based theoretical model has been vividly employed to estimate the SpBs energy in the complex. Natural bond orbital (NBO) analysis also tries to establish the differentiation between σ-hole and π-hole SpBs' natures more authentically. The complex energy frameworks were used to investigate noncovalent interactions. To better understand the different intermolecular interactions, we conducted a Hirshfeld surface, which revealed N···H (15.4%) and O···H (9.1%) contacts and Zn···O (5.1%) (SpBs).

Comparative analysis of interaction of ionic liquids with porous and non-porous electrode materials

Fascinating properties of ionic liquids such as their higher ionic conductivity, lower vapor pressure, high thermal and electrochemical stability, make them promising candidates as electrolytes for novel energy storage devices. Interaction of ionic liquids (ILs) as electrolytes with electrode is crucial for optimizing the efficiency of energy storage devices. Herein, we report the interaction mechanism of ionic liquids 1-3 dimethylimidazolium halide (1,3-DMIX) on porous covalent triazine frameworks (CTF-0) and non-porous carbon nitride (C4N) electrode materials. Molecular electrostatic potential (MEP) analysis is performed for the prediction of interacting sites on studied electrolytes and electrode materials. Significant changes in geometric and electronic parameters are observed upon interaction of ionic liquid electrolytes with C4N and CTF-0. The nature of interaction between ionic liquids and electrode surfaces is evaluated through Quantum theory of atoms in molecules (QTAIM) and non-covalent index (NCI) analyses which reveal that there exist only the non-covalent interactions (van der Waals) between them. Frontier molecular orbitals (FMO) analysis shows a significant decrease in energy gap upon interaction of ILs with CTF-0, which results in increase in electrical conductivity. Overall, porous CTF-0 electrode material displays greater interaction with the considered ILs as compared to non-porous C4N electrode material. This study will provide a way for experimentalist to explore ionic liquids and carbon nitride or covalent triazine framework as electrolyte–electrode systems which can be used further in energy storage devices like fuel cells, solar cells, ion batteries, and supercapacitors.

Formation of Eigen or Zundel Features at Protonated Water Cluster-Aromatic Interfaces.

Interfacial interactions of protonated water clusters adsorbed at aromatic surfaces play an important role in biology, and in atmospheric, chemical and materials sciences. Here, we investigate the interaction of protonated water clusters ((H+H2O)n (where n = 1 - 3)) with benzene (Bz), coronene (Cor) and dodecabenzocoronene (Dbc)). To study the structure, stability and spectral features of these complexes, computations are done using DFT-PBE0(+D3) and SAPT0 methods. These interactions are probed by AIM electron density topography and non-covalent index (NCI) analyses. We suggest that the excess proton plays a crucial role in the stability of these model interfaces through strong inductive effects and the formation of Eigen or Zundel features. Also, computations reveal that the extension of the π-aromatic system and the increase of the number of water molecules in the H-bounded water network lead to a strengthening of the interactions between the corresponding aromatic compound and protonated water molecules, except when a Zundel ion is formed. The present findings may serve to understand in-depth the role of proton localized at aqueous medium interacting with large aromatic surfaces such as graphene interacting with acidic liquid water. Besides, we give their IR and UV-Vis spectra , which may help for their identification.

Unconventional Dual Donor-Acceptor Topologies of Aromatic Rings in Amine-Based Polymeric Tetrahedral Zn(II) Compounds Involving Unusual Non-Covalent Contacts: Antiproliferative Evaluation and Theoretical Studies

Two Zn(II) coordination polymers, viz., [Zn2Cl2(H2O)2(µ-4-AmBz)2]n (1) and [ZnCl2(µ-3-AmPy)2]n (2) (4-AmBz = 4-aminobenzoate, 3-AmPy = 3-aminopyridine) have been prepared at room temperature and characterized using elemental analysis, FT-IR, electronic spectroscopy, TGA (thermogravimetric analysis) and single crystal XRD. Crystal structure analyses of the polymers unfold the presence of non-covalent anion–π, π-stacking and unusual NH2(amino)⋯π interactions which provide rigidity to the crystal structures. Unconventional Type I Cl⋯Cl interactions also play a pivotal role in the stability of compound 1. Molecular electrostatic potential (MEP) surface analysis reveals that the MEP values over the center of the aromatic rings of coordinated 4-AmBz and 3-AmPy moieties are positive on one side and negative on the other side which confirms the dual non-covalent donor-acceptor topologies of the aromatic rings and explains the concurrent formation of unusual non-covalent NH2···π and anion–π interactions. DFT (density functional theory) calculations, QTAIM (quantum theory of atoms in molecules) and NCI plot (non-covalent index) index analyses reveal that among various non-covalent contacts involved in the crystal packing of the compounds, H-bonds in compound 1 and π-interactions (NH2···π, π-π, anion–π) in compound 2 are energetically significant. We have explored in vitro cytotoxic potential of the compounds in Dalton’s lymphoma (DL) cancer cells using trypan blue and apoptosis assays. The studies show that compounds 1 and 2 can significantly exhibit cytotoxicity in DL cells with minimum cytotoxicity in healthy PBMC cells. Molecular docking studies reveal that the compounds effectively bind with the antiapoptotic target proteins; thereby establishing a structure activity relationship of the compounds.

Behavior of HF and (HF)2 inside a fullerene cage: An in silico study using different density functionals

AbstractAn in silico study on the properties of HF and its dimer inside C60 using density functional theory (DFT) based approaches is presented. For this purpose, 10 different DFT functionals following Jacob's Ladder have been chosen. The geometrical parameters such as bond length and bond angle, of the molecules and their dipole moment have been computed. Two types of orientations, namely, L‐shaped and anti‐parallel of (HF)2 inside C60 are considered, the latter with an extremely short hydrogen bond. HF bond lengths are elongated upon encapsulation in comparison to its free state analogue. The calculated value of stabilization energy of HF@C60 is found to be functional dependent, whereas, (HF)2@C60 is thermodynamically unstable for all the functionals. The kinetic stability of (HF)2@C60 is assessed using the atom‐centered density matrix propagation (ADMP) simulation at 300 K temperature. The red shift in HF stretching frequencies is noticed in all cases. Non‐covalent index (NCI) analysis revealed non‐covalent interactions between HF dimer and the C60 cage. Energy decomposition analysis (EDA) showed a high value for the repulsive ΔEpauli which makes the (HF)2@C60 system unstable except for the functional BP86‐D3 of GGA family. Furthermore, the quantum theory of atoms in molecules (QTAIM) analysis is performed and it confirmed the presence of (3, −1) bond critical point along the hydrogen bond region of the L‐shaped (HF)2@C60.

Synthesis, structural and exploration of non-covalent interactions of the palladium complex with the crystalline water molecule: A comprehensive quantum chemical approach

A Schiff base ligand, N'-((2-hydroxynaphthalen-1-yl)methylene)-3-phenylpropanehydrazide (L) and its palladium(II) complex [Pd(L)Cl] were synthesized and characterized by FT-IR, SEM, EDAX, and UV–visible and single crystal X-ray diffraction analysis.The crystal structure shows distorted square-planar, where the palladium(II) metal atom is bonded to two oxygen atoms in the equatorial position whereas a nitrogen and chlorine atom along the axial position in a tetradentate monoanionic [O1, O2, N1, Cl1] fashion resulting in the formation of five and six membered chelate rings. The crystal structure is supported by intramolecular NH…O and OH…Cl hydrogen bonds, CH…Cl, NH…O, CH…π and π…π intermolecular secondary interactions resulting in the supramolecular architectures. The 3D description of the intermolecular interactions are quantified using the Hirshfeld surface analysis. Density functional theory (DFT) calculations were performed to obtain the optimum geometry structures using the wB97XD functional. The natural bond orbital (NBO) analysis showed that the metal ion coordinates to the ligands through electron donation from lone pairs on nitrogen and oxygen atoms to the d orbitals of the metal ion. The topology analysis of the electron density by means of the natural bond orbitals (NBO), quantum theory of atoms in molecules (QTAIM), noncovalent index (NCI), and electron localization function (ELF) have revealed valuable information regarding the nature of interactions and the results are in good agreement with the structural analysis results.

Covalent Organic Framework (C6N6) as a Drug Delivery Platform for Fluorouracil to Treat Cancerous Cells: A DFT Study.

Continuous studies are being carried out to explore new methods and carrier surfaces for target drug delivery. Herein, we report the covalent triazine framework C6N6 as a drug delivery carrier for fluorouracil (FU) and nitrosourea (NU) anti-cancer drugs. FU and NU are physiosorbed on C6N6 with adsorption energies of -28.14 kcal/mol and -27.54 kcal/mol, respectively. The outcomes of the non-covalent index (NCI) and quantum theory of atoms in molecules (QTAIM) analyses reveal that the FU@C6N6 and NU@C6N6 complexes were stabilized through van der Waals interactions. Natural bond order (NBO) and electron density difference (EDD) analyses show an appreciable charge transfer from the drug and carrier. The FU@C6N6 complex had a higher charge transfer (-0.16 e-) compared to the NU@C6N6 complex (-0.02 e-). Frontier molecular orbital (FMO) analysis reveals that the adsorption of FU on C6N6 caused a more pronounced decrease in the HOMO-LUMO gap (EH-L) compared to that of NU. The results of the FMO analysis are consistent with the NBO and EDD analyses. The drug release mechanism was studied through dipole moments and pH effects. The highest decrease in adsorption energy was observed for the FU@C6N6 complex in an acidic medium, which indicates that FU can easily be off-loaded from the carrier (C6N6) to a target site because the cancerous cells have a low pH compared to a normal cell. Thus, it may be concluded that C6N6 possesses the therapeutic potential to act as a nanocarrier for FU to treat cancer. Furthermore, the current study will also provide motivation to the scientific community to explore new surfaces for drug delivery applications.

On the reliability of atoms in molecules, noncovalent index, and natural bond orbital to identify and quantify noncovalent bonds.

Atoms in molecules, noncovalent index, and natural bond orbital methods are commonly invoked to identify the presence of various noncovalent bonds and to measure their strength. However, there are numerous instances in the literature where these methods provide contradictory or apparently erroneous interpretations of the bonding. The range of reliability of these methods is assessed by calculations of a variety of systems, which include an H-bond, halogen bond, π-tetrel bond, CH··HC interaction, and a pairing of two anions. While the results appear to be meaningful for the equilibrium geometries, and those where the two subunits are progressively pulled apart, these techniques erroneously predict a progressively stronger bonding interaction as the two units are compressed and the interaction becomes clearly repulsive. The methods falsely indicate a bonding interaction in the CH··HC arrangement, and incorrectly mimic the behavior of the energy when two anions approach. These approaches are also unreliable for understanding angular deformations.

Terephthalato and succinato bridged Mn(II) and Zn(II) coordination polymers involving structure-guiding H-bonded tetrameric assemblies: Antiproliferative evaluation and theoretical studies

Two new coordination polymers of Mn(II) and Zn(II) viz. {[Mn(µ-tp)(3-Ampy)2(H2O)2]2(3-Ampy)·2(H2O)}n (1) and {[Zn(µ-succ)(3-Ampy)2]·2H2O}n (2) (tp = terephthalate, 3-Ampy = 3-aminopyridine, succ = succinate) have been synthesized and characterized using elemental and spectroscopic analyses, TGA and single crystal X-ray diffraction techniques. Uncoordinated 3-AMpy and water molecules of the polymeric co-crystal hydrate 1 are involved in the formation of cyclic tetrameric {(3-Ampy)2(H2O)2} assembly which provide rigidity to the structure. The presence of guest 3-Ampy and water molecules in the voids of supramolecular Mn(II) host tetramer in 1 provides additional reinforcement to the crystal structure. The lattice water molecules of 2 are aggregated via non-covalent interactions to form discrete cyclic {(H2O)4} tetrameric clusters in the crystal structure. Density functional theory (DFT), non-covalent index (NCI) plot and quantum theory of atoms in molecules (QTAIM) computational analyses reveal that the supramolecular H-bonded cyclic tetrameric structure-guiding synthon in 1 and the (H2O)4 cyclic water clusters in 2 have significant energetic contribution towards the stability of the polymers. In vitro anticancer activities of the compounds considering trypan blue and apoptosis assays revealed that the compounds induce concentration dependent cytotoxicity in Dalton’s lymphoma (DL) cancer cells with nominal effects in normal peripheral blood mononuclear cells (PBMC) cells. Comparative analysis reveals that compound 2 induced higher apoptosis in DL cells; which is well consistent with the trypan blue exclusion assay. Molecular docking and pharmacophore modelling studies of the compounds reveal that the compound 2 significantly interacts with the antiapoptotic proteins to establish structure activity relationship (SAR).

Adsorption of sorbitan ester surfactant on copper and Cuprous oxide surfaces: A density functional theory study

This work reports a detailed density functional theory study of the adsorption of sorbitan monoacetate (SMA) molecules -as a model of the head group of sorbitan-derived surfactants- on Cu (111) and Cu2O (111) surfaces. Our study includes the most stable adsorption configurations, considering the electron-withdrawing nature of the molecule functional groups and the electron-donating sites on the surface. When SMA adsorbs on Cu (111), van der Waals interactions emerge as the most stabilizing components. In contrast, for Cu2O (111), SMA binds through coordination bonds hydrogen bonds. Charge transfer analysis in the formed Cu-O bonds showed that molecule's oxygen atoms behave as electron withdrawers whereas Cu atoms as electron-donating entities. The non-covalent index analysis revealed that van der Waals interactions in both systems present an attractive component.The results presented help explain how span surfactants head group interacts with Copper and Cuprous oxide (111) surfaces, what type of bonds and interactions are present in the adsorption process, and how strong they are to assess its applicability in area selective deposition techniques as an easily removable Copper passivating agent. Also, the clarified interactions appearing in this metal–organic system may be of great interest for the design of sensing nanodevices.

Chalcogen Bonding in the Molecular Dimers of WCh2 (Ch = S, Se, Te): On the Basic Understanding of the Local Interfacial and Interlayer Bonding Environment in 2D Layered Tungsten Dichalcogenides.

Layered two-dimensional transition metal dichalcogenides and their heterostructures are of current interest, owing to the diversity of their applications in many areas of materials nanoscience and technologies. With this in mind, we have examined the three molecular dimers of the tungsten dichalcogenide series, (WCh2)2 (Ch = S, Se, Te), using density functional theory to provide insight into which interactions, and their specific characteristics, are responsible for the interfacial/interlayer region in the room temperature 2H phase of WCh2 crystals. Our calculations at various levels of theory suggested that the Te···Te chalcogen bonding in (WTe2)2 is weak, whereas the Se···Se and S···S bonding interactions in (WSe2)2 and (WS2)2, respectively, are of the van der Waals type. The presence and character of Ch···Ch chalcogen bonding interactions in the dimers of (WCh2)2 are examined with a number of theoretical approaches and discussed, including charge-density-based approaches, such as the quantum theory of atoms in molecules, interaction region indicator, independent gradient model, and reduced density gradient non-covalent index approaches. The charge-density-based topological features are shown to be concordant with the results that originate from the extrema of potential on the electrostatic surfaces of WCh2 monomers. A natural bond orbital analysis has enabled us to suggest a number of weak hyperconjugative charge transfer interactions between the interacting monomers that are responsible for the geometry of the (WCh2)2 dimers at equilibrium. In addition to other features, we demonstrate that there is no so-called van der Waals gap between the monolayers in two-dimensional layered transition metal tungsten dichalcogenides, which are gapless, and that the (WCh2)2 dimers may be prototypes for a basic understanding of the physical chemistry of the chemical bonding environments associated with the local interfacial/interlayer regions in layered 2H-WCh2 nanoscale systems.

Chalcogen···Chalcogen Bonding in Molybdenum Disulfide, Molybdenum Diselenide and Molybdenum Ditelluride Dimers as Prototypes for a Basic Understanding of the Local Interfacial Chemical Bonding Environment in 2D Layered Transition Metal Dichalcogenides

An attempt was made, using computational methods, to understand whether the intermolecular interactions in the dimers of molybdenum dichalcogenides MoCh2 (Ch = chalcogen, element of group 16, especially S, Se and Te) and similar mixed-chalcogenide derivatives resemble the room temperature experimentally observed interactions in the interfacial regions of molybdenites and their other mixed-chalcogen derivatives. To this end, MP2(Full)/def2-TVZPPD level electronic structure calculations on nine dimer systems, including (MoCh2)2 and (MoChCh′2)2 (Ch, Ch′ = S, Se and Te), were carried out not only to demonstrate the energetic stability of these systems in the gas phase, but also to reproduce the intermolecular geometrical properties that resemble the interfacial geometries of 2D layered MoCh2 systems reported in the crystalline phase. Among the six DFT functionals (single and double hybrids) benchmarked against MP2(full), it was found that the double hybrid functional B2PLYPD3 has some ability to reproduce the intermolecular geometries and binding energies. The intermolecular geometries and binding energies of all nine dimers are discussed, together with the charge density topological aspects of the chemical bonding interactions that emerge from the application of the quantum theory of atoms in molecules (QTAIM), the isosurface topology of the reduced density gradient noncovalent index, interaction region indicator and independent gradient model (IGM) approaches. While the electrostatic surface potential model fails to explain the origin of the S···S interaction in the (MoS2)2 dimer, we show that the intermolecular bonding interactions in all nine dimers examined are a result of hyperconjugative charge transfer delocalizations between the lone-pair on (Ch/Ch′) and/or the π-orbitals of a Mo–Ch/Ch′ bond of one monomer and the dπ* anti-bonding orbitals of the same Mo–Ch/Ch′ bond in the second monomer during dimer formation, and vice versa. The HOMO–LUMO gaps calculated with the MN12-L functional were 0.9, 1.0, and 1.1 eV for MoTe2, MoSe2 and MoS2, respectively, which match very well with the solid-state theoretical (SCAN-rVV10)/experimental band gaps of 0.75/0.88, 0.90/1.09 and 0.93/1.23 eV of the corresponding systems, respectively. We observed that the gas phase dimers examined are perhaps prototypical for a basic understanding of the interfacial/inter-layer interactions in molybdenum-based dichalcogenides and their derivatives.

Bonding Analysis of Compounds with Unusual Coordination of Carbon: Proposed Symmetric Systems with Six-Coordinate Carbon.

The possibility of carbon tetravalence in geometries other than tetrahedral and of carbon hypervalence has been taken seriously since the 1970s. Computational modeling and subsequent experimental validation have established the existence of molecules with carbon atoms with planar tetravalence and as many as six objects in carbon’s coordination sphere. In this work, we develop insight into the nature of bonding to carbon in these unusual environs as provided by Bader’s Atoms in Molecules (AIM) analysis of the electron density, along with the electron localization function (ELF) and the non-covalent index (NCI). We review several well-established systems (spiropentadiene dication, hexamethyl benzene dication, dimethanospiro[2.2]octaplane dication, and 1,8-dimethoxy-9-dimethoxyanthracene cation) and propose new D2d–symmetric variants of a hexacoordinated species.

Does Chlorine in CH3Cl Behave as a Genuine Halogen Bond Donor?

The CH3Cl molecule has been used in several studies as an example purportedly to demonstrate that while Cl is weakly negative, a positive potential can be induced on its axial surface by the electric field of a reasonably strong Lewis base (such as O=CH2). The induced positive potential then has the ability to attract the negative site of the Lewis base, thus explaining the importance of polarization leading to the formation of the H3C–Cl···O=CH2 complex. By examining the nature of the chlorine’s surface in CH3Cl using the molecular electrostatic surface potential (MESP) approach, with MP2/aug-cc-pVTZ, we show that this view is not correct. The results of our calculations demonstrate that the local potential associated with the axial surface of the Cl atom is inherently positive. Therefore, it should be able to inherently act as a halogen bond donor. This is shown to be the case by examining several halogen-bonded complexes of CH3Cl with a series of negative sites. In addition, it is also shown that the lateral portions of Cl in CH3Cl features a belt of negative electrostatic potential that can participate in forming halogen-, chalcogen-, and hydrogen-bonded interactions. The results of the theoretical models used, viz. the quantum theory of atoms in molecules; the reduced density gradient noncovalent index; the natural bond orbital analysis; and the symmetry adapted perturbation theory show that Cl-centered intermolecular bonding interactions revealed in a series of 18 binary complexes do not involve a polarization-induced potential on the Cl atom.

Chemical bonding in Period 2 homonuclear diatomic molecules: a comprehensive relook

Theoretical and experimental studies of bonding in the main group homonuclear diatomic molecules have been pursued for many years, and they possess serious challenges for scientists. Most of the early experimental work have been carried out by Herzberg.1,2 We take a relook at the bonding motifs of Period 2 homonuclear diatomic molecules (from Li2 to Ne2) using varieties of quantum chemical tools, commonly used for intermolecular bonding/interactions now. The methods employed include Atoms in Molecules (AIM), Non-covalent Index plot (NCI), Electrostatic potential (ESP), and Potential Acting on one Electron in a Molecule (PAEM). The spectroscopic constants i.e., equilibrium bond distances (re), harmonic frequencies (ω), bond dissociation energies (De) have all been evaluated using high-level ab initio methods and critically compared with the experimental results. Multi-reference calculations (CASSCF) on B2 and C2 have been carried out as they have a large number of low lying electronic states. Bonding within these homonuclear diatomic molecules show all the diversities that are encountered in inter/intra-molecular bonding in chemistry. Based on the AIM analysis, these 8 homonuclear diatomic molecules could be divided into three different groups, based on the correlation between binding energy and the electron density at the bond critical point. However, PAEM/ESP analysis allows us to analyse all eight of them as one group having a good correlation between binding energy and the PAEM/ESP at the critical point between the two atoms. Our results highlight the arbitrariness in relying on some computational tools to characterize a bond as covalent (shared) or ionic/electrostatic (closed). In contrast, they also show the usefulness of the various methods in exploring similarities and differences in bonding. We propose that from Li2 to Ne2, all homonuclear diatomic molecules are bound by ‘chemical bonds’. The Period 2 homo-nuclear diatomic ‘molecules’ from the ‘covalent Li2’ to the ‘van der Waals Ne2’ show a rich diversity of 'bonds' that one can see in all inter- and intra-molecular interactions encountered in physics, chemistry and biology. Here, we show that these display a continuum in ‘chemical bonds!’

A theoretical exploration of the intermolecular interactions between resveratrol and water: a DFT and AIM analysis.

The polyphenolic compound resveratrol, classified under stilbenes, offers a broad range of health advantages, including neuroprotection and playing a role in autophagy in the nervous system. However, resveratrol has poor water solubility and is soluble in the gel phase in liposomal membranes. The main aim of this work was to understand the nature of the interactions between resveratrol and water molecules. In the present study, we used the dispersion corrected density functional theory (DFT) method to study hydrogen bonding interactions. Eight different geometries of resveratrol-water complexes were identified by optimizing the geometries by placing water at various locations. We observed the two lowest energy structures to be isoenergetic. In most complexes, water interaction occurs with phenolic hydrogen as all the phenolic hydroxyl groups have identical Vs,max values. Energy decomposition analysis shows that the dispersion contribution was minimal in these complexes, while electrostatic and orbital contributions were larger. Complex formation between water and the resveratrol molecule results in a blue shift in the vibrational frequency, along with an increase in intensity due to the transfer of electron density. The hydrogen bonds in the resveratrol-water complexes have closed-shell interactions with a medium-to-strong bonding nature. Noncovalent index analysis of the complexes shows that, in addition to hydrogen bonding, electrostatic and van der Waal's interactions play a key role in stabilizing the complexes. Graphical abstract Noncovalent index analysis showing that, in addition to hydrogen bonding, electrostatic and van der Waal's interactions play a major role in stabilizing resveratrol-water complexes.