A Complete NCI Perspective: From New Bonds to Reactivity

Noble gas hydrides: theoretical prediction of the first group of anionic species

The first group of anionic noble-gas hydrides with the general formula HNgBeO- (Ng = Ar, Kr, Xe, Rn) is predicted through MP2, Coupled-Cluster, and Density Functional Theory computations employing correlation-consistent atomic basis sets. We derive that these species are stable with respect to the loss of H, H-, BeO, and BeO-, but unstable with respect to Ng + HBeO-. The energy barriers of the latter process are, however, high enough to suggest the conceivable existence of the heaviest HNgBeO- species as metastable in nature. Their stability arises from the interaction of the H- moiety with the positively-charged Ng atoms, particularly with the σ-hole ensuing from their ligation to BeO. This actually promotes relatively tight Ng-H bonds featuring a partially-covalent character, whose degree progressively increases when going from HArBeO- to HRnBeO-. The HNgBeO- compounds are also briefly compared with other noble-gas anions observed in the gas phase or isolated in crystal lattices.

Revealing the Role of Noncovalent Interactions on the Conformation of the Methyl Group in Tricyclic Orthoamide

Tricyclic orthoamides are valuable molecules with wide-ranging applications, including organic synthesis and molecular recognition. Their structural properties make them intriguing, particularly the eclipsed all-trans conformer, which is typically less stable than the alternated conformation and is a rare phenomenon in organic chemistry. However, it gains stability in crystalline and hydrated settings, challenging the existing theoretical explanations. This study investigates which factors make eclipsed conformers more stable using experimentally reported anhydrous (ATO) and hydrated (HTO) crystal structures. Employing the quantum theory of atoms in molecules, noncovalent interaction index, and pairwise energy decomposition analysis, we delve into the noncovalent interaction environment surrounding the molecule of interest. In ATO, dispersive interactions dominate, whereas in HTO, both dispersive and electrostatic contributions are observed due to the presence of water molecules. Anchored to the lone pairs of the nitrogen atom in the orthoamide tricycle, water molecules prompt the methyl group's eclipsing through intermolecular and intramolecular interactions. This work resolves the long-standing conflict behind why tricyclic orthoamide has an eclipsed conformation by establishing the stabilization factors. These insights have implications for crystal engineering and design, enhancing our understanding of structural behavior in both crystalline and hydrated environments.

Isomeric Effect of a π Bridge in an IDT-Based Nonfused Electron Photovoltaic Acceptor

A pair of isomers, IDT-BOF containing S⋅⋅⋅O/F⋅⋅⋅H noncovalently configurational locks and IDT-BFO containing F⋅⋅⋅H/O⋅⋅⋅H noncovalently configurational locks, with an acceptor-π-donor-π-acceptor (A-π-D-π-A) structure have been designed and synthesized by choosing 4,9-dihydro-s-indaceno[1,2-b : 5,6-b']dithiophene (IDT) as the D unit, an F/n-hexyloxy substituted phenyl ring as π bridge, and 3-(dicyanomethylidene)indan-1-one as the A unit. Owing to the S⋅⋅⋅O/F⋅⋅⋅H or F⋅⋅⋅H/O⋅⋅⋅H noncovalently configurational locks, both IDT-BOF and IDT-BFO have a completely planar structure. IDT-BOF exhibits a similar LUMO to IDT-BFO, but higher HOMO energy levels, leading to a smaller optical bandgap and red-shifted absorption. However, IDT-BOF-based bulk-heterojunction organic solar cells (BHJ-OSCs) coupled with PBDB-T, and PCE-10 as donor materials both exhibited a lower PCE than that of IDT-BFO (PBDB-T: 5.2 vs. 6.1 %; PCE-10: 1.7 vs. 3.2 %). Comprehensively comparing and investigating IDT-BOF : PBDB-T and IDT-BFO : PBDB-T OSCs suggested that the large phase separation and serious charge recombination of IDT-BOF-based OSCs contributed to its lower power conversion efficiency. Importantly, ternary solar cells based on PBDB-T : Y5 as control devices with an additional 10 % IDT-BFO exhibited a 5 % enhancement in the PCE compared to the control device (14.3 vs. 13.46 %).

Double Centrosymmetric Si···π Tetrel Bonds as New Synthons─Evidence from Crystal Structures and DFT Calculations

The crystal structure of bis((μ2-ethynylsilyloxo)-dichloro-aluminum), BEDCA, and a few related structures are characterized by the occurrence of tetrel bonds that link molecules. Particularly, centosymmetric dimers in such structures occur that are connected by two equivalent Si···π tetrel bonds. The dimer of BEDCA and dimers of other model species that similarly are linked by two equivalent Si···π tetrel bonds are analyzed theoretically. Some of the complexes calculated here are also characterized by the occurrence of triel bonds. Thus, ωB97XD/aug-cc-pVTZ calculations are performed and these DFT results are further supported by calculations with the use of other theoretical approaches: the quantum theory of atoms in molecules, QTAIM; the natural bond orbital, NBO; the energy decomposition analysis, EDA; and the noncovalent interactions method, NCI. The results show that the tetrel bonds analyzed here are rather weak, and they are not detected by the QTAIM approach; however, they are detected by other approaches, like NBO, for example. On the other hand, the triel bonds that occur in a few complexes discussed here are very strong and possess characteristics of covalent bonds.

Structural, electronic, intermolecular interaction, reactivity, vibrational spectroscopy, charge transfer, Hirshfeld surface analysis, pharmacological and hydropathy plot on 5-Bromo nicotinic acid - Antiviral study (Hepatitis A, B, and C)

The therapeutic properties of 5-Bromonicotinatic acid (5BNA) were studied for antiviral illnesses like Hepatitis A, Hepatitis B and Hepatitis C and the influence of electron-donating and electron-withdrawing properties of functional groups on the nicotinic acid was evaluated and represented in this study using the DFT approach. The molecular parameters were determined for both gases as well as for various solvent phases. The reactive areas in the compound are examined utilising Fukui analysis. The molecular interactions are accomplished by recognising the different types of bonding found in the compound using the AIM, ELF, LOL, RDG and IRI. Solvation investigations were demonstrated to have an influence on molecular orbital energy, ESP, UV-Vis and NLO analyses. Electron-hole, NBO and Hirshfeld investigations are used to investigate the transfer of charges and interactions inside the molecule. The method of vibrational spectroscopy (IR and Raman) is used to differentiate and identify the various types of vibrations displayed by the compound. The hydropathy plots for the proteins 2A4O, 6CWD and 2OC8 associated with Hepatitis A, Hepatitis B and Hepatitis C illustrate the disquiet and attraction of the amino acids towards the water.

A comparison of non-covalent interactions in the crystal structures of two σ-alkane complexes of Rh exhibiting contrasting stabilities in the solid state

Non-covalent interactions surrounding the cationic Rh σ-alkane complexes within the crystal structures of [(Cy2PCH2CH2PCy2)Rh(NBA)][BArF4], [1-NBA][BArF4] (NBA = norbornane, C7H12; ArF = 3,5-(CF3)2C6H3), and [1-propane][BArF4] are analysed using Quantum Theory of Atoms in Molecules (QTAIM) and Independent Gradient Model approaches, the latter under a Hirshfeld partitioning scheme (IGMH). In both structures the cations reside in an octahedral array of [BArF4]- anions within which the [1-NBA]+ cation system exhibits a greater number of C-H⋯F contacts to the anions. QTAIM and IGMH analyses indicate these include the strongest individual atom-atom non-covalent interactions between the cation and the anion in these systems. The IGMH approach highlights the directionality of these C-H⋯F contacts that contrasts with the more diffuse C-H⋯π interactions. The accumulative effects of the latter lead to a more significant stabilizing contribution. IGMH %δGatom plots provide a particularly useful visual tool to identify key interactions and highlight the importance of a -{C3H6}- propylene moiety that is present within both the propane and NBA ligands (the latter as a truncated -{C3H4}- unit) and the cyclohexyl rings of the phosphine substituents. The potential for this to act as a privileged motif that confers stability on the crystal structures of σ-alkane complexes in the solid-state is discussed. The greater number of C-H⋯F inter-ion interactions in the [1-NBA][BArF4] system, coupled with more significant C-H⋯π interactions are all consistent with greater non-covalent stabilisation around the [1-NBA]+ cation. This is also supported by larger computed δGatom indices as a measure of cation-anion non-covalent interaction energy.

Gas-Phase Interaction of CO, CO2, H2S, NH3, NO, NO2, and SO2 with Zn12O12 and Zn24 Atomic Clusters

Atmospheric pollutants pose a high risk to human health, and therefore it is necessary to capture and preferably remove them from ambient air. In this work, we investigate the intermolecular interaction between the pollutants such as CO, CO₂, H₂S, NH₃, NO, NO₂, and SO₂ gases with the Zn₂₄ and Zn₁₂O₁₂ atomic clusters, using the density functional theory (DFT) at the meta-hybrid functional TPSSh and LANl2Dz basis set. The adsorption energy of these gas molecules on the outer surfaces of both types of clusters has been calculated and found to have a negative value, indicating a strong molecular-cluster interaction. The largest adsorption energy has been observed between SO₂ and the Zn₂₄ cluster. In general, the Zn₂₄ cluster appears to be more effective for adsorbing SO₂, NO₂, and NO than Zn₁₂O₁₂, whereas the latter is preferable for the adsorption of CO, CO₂, H₂S, and NH₃. Frontier molecular orbital (FMO) analysis showed that Zn₂₄ exhibits higher stability upon adsorption of NH₃, NO, NO₂, and SO₂, with the adsorption energy falling within the chemisorption range. The Zn₁₂O₁₂ cluster shows a characteristic decrease in band gap upon adsorption of CO, H₂S, NO, and NO₂, suggesting an increase in electrical conductivity. Natural bond orbital (NBO) analysis also suggests the presence of strong intermolecular interactions between atomic clusters and the gases. This interaction was recognized to be strong and noncovalent, as determined by noncovalent interaction (NCI) and quantum theory of atoms in molecules (QTAIM) analyses. Overall, our results suggest that both Zn₂₄ and Zn₁₂O₁₂ clusters are good candidate species for promoting adsorption and, thus, can be employed in different materials and/or systems for enhancing interaction with CO, H₂S, NO, or NO₂.

The Nicotinic Agonist Cytisine: The Role of the NH···N Interaction

We report a detailed structural study of cytisine, an alkaloid used to help with smoking cessation, looking forward to unveiling its role as a nicotinic agonist. High-resolution rotational spectroscopy has allowed us to characterize two different conformers exhibiting axial and equatorial arrangements of the piperidinic NH group. Unexpectedly, the axial form has been found as the predominant configuration, in contrast to that observed for related molecules, such as piperidine. This anomalous behavior has been justified in terms of an intramolecular NH···N hydrogen bond. Moreover, this interaction justifies the overstabilization of the axial conformer over the equatorial one and is crucial for the mechanism of action of cytisine over the nicotinic receptor, further rationalizing its behavior as a nicotinic agonist.

Description of non-covalent interactions in benzyl chalcocyanate crystals from smoothed Cromer-Mann electron density distribution functions

A well-known method to characterize non-covalent interactions consists in the topological analysis of electron density distribution (EDD) functions, complemented by the search for minima in the reduced density gradient (RDG) distributions. Here, we characterize intermolecular interactions occurring in crystals of benzyl chalcocyanate compounds through bond critical points (BCP) of the promolecular electron density (ED) built from the crystallographic Cromer-Mann parameters, at several smoothing levelst. The trajectories formed by thet-dependent BCP locations are interpreted in terms of the intermolecular interactions occurring within the crystal arrangements. Chalcogen…nitro BCPs are clearly present in the unsmoothed EDDs but are annihilated astincreases, while chalcogen…chalcogen BCPs appear and are among the only BCPs left at the highest smoothing level. The chalcogen bonds are differentiated from the other chalcogen interactions through the linear chalcogen…BCP…nitro geometry at low smoothing level and their more negative Laplacian values. The annihilation of CPs can be followed by the apparition of a RDG minimum, associated with a very weak interaction. Along the BCP trajectories, the Laplacian shows a progressive concentration of the ED in the intermolecular space within the crystals and adopts the most negative values at the shortest atom…atom separations. At the termination point of a BCP trajectory, the drastic increase of the ellipticity value illustrates the flattening of the EDD.

Unveiling the Shape of N-Acetylgalactosamine: A Cancer-Associated Sugar Derivative

In the present work, we report the first rotational study of N-acetylgalactosamine, a cancer-associated sugar derivative, by means of high-resolution rotational spectroscopy. Two different conformers have been conclusively characterized using broadband Fourier transform microwave spectroscopy coupled with a laser ablation vaporization system. Additionally, we performed a comprehensive analysis of the intramolecular interactions that govern these structures, which allowed us to both characterize the existence of intramolecular hydrogen bond networks that drive the intrinsic conformation panorama of N-acetylgalactosamine and further rationalize the biological role of this aminosugar derivative as part of the Tn antigen.

Dispersion Interactions between Molecules in and out of Equilibrium Geometry: Visualization and Analysis

The London dispersion interactions between systems undergoing bond breaking, twisting, or compression are not well studied due to the scarcity and the high computational cost of methods being able to describe both the dynamic correlation and the multireference character of the system. Recently developed methods based on the Generalized Valence Bond wave function, such as EERPA-GVB and SAPT(GVB) (SAPT = symmetry-adapted perturbation theory), allow one to accurately compute and analyze noncovalent interactions between multireference systems. Here, we augment this analysis by introducing a local indicator for dispersion interactions inspired by Mata and Wuttke's Dispersion Interaction Density [ J. Comput. Chem. 2017, 38, 15-23] applied on top of an EERPA-GVB computation. Using a few model systems, we show what insights into the nature and evolution of the dispersion interaction during bond breaking and twisting such an approach is able to offer. The new indicator can be used at a minimal cost additional to an EERPA-GVB computation and can be complemented by an energy decomposition employing the SAPT(GVB) method. We explain the physics behind the initial increase, followed by a decrease in the interaction of linear molecules upon bond stretching. Namely, the elongation of covalent bonds leads to the enhancement of attractive dispersion interactions. For even larger bond lengths, this effect is canceled by the increase of the repulsive exchange forces resulting in a suppression of the interaction and finally leading to repulsion between monomers.

Halogen Bonding in Haspin-Halogenated Tubercidin Complexes: Molecular Dynamics and Quantum Chemical Calculations

Haspin, an atypical serine/threonine protein kinase, is a potential target for cancer therapy. 5-iodotubercidin (5-iTU), an adenosine derivative, has been identified as a potent Haspin inhibitor in vitro. In this paper, quantum chemical calculations and molecular dynamics (MD) simulations were employed to identify and quantitatively confirm the presence of halogen bonding (XB), specifically halogen∙∙∙π (aromatic) interaction between halogenated tubercidin ligands with Haspin. Consistent with previous theoretical finding, the site specificity of the XB binding over the ortho-carbon is identified in all cases. A systematic increase of the interaction energy down Group 17, based on both quantum chemical and MD results, supports the important role of halogen bonding in this series of inhibitors. The observed trend is consistent with the experimental observation of the trend of activity within the halogenated tubercidin ligands (F < Cl < Br < I). Furthermore, non-covalent interaction (NCI) plots show that cooperative non-covalent interactions, namely, hydrogen and halogen bonds, contribute to the binding of tubercidin ligands toward Haspin. The understanding of the role of halogen bonding interaction in the ligand-protein complexes may shed light on rational design of potent ligands in the future.

Noble-gas compounds: A general procedure of bonding analysis

This paper accounts for a general procedure of bonding analysis that is, expectedly, adequate to describe any type of interaction involving the noble-gas (Ng) atoms. Building on our recently proposed classification of the Ng-X bonds (X = binding partner) [New J. Chem. 44, 15536 (2020)], these contacts are first distinguished into three types, namely, A, B, or C, based on the topology of the electron energy density H(r) and on the shape of its plotted form. Bonds of type B or C are, then, further assigned as B-loose (B^l) or B-tight (B^t) and C-loose (C^l) or C-tight (C^t) depending on the sign that H(r) takes along the Ng-X bond path located from the topological analysis of ρ(r), particularly at around the bond critical point (BCP). Any bond of type A, B^l/B^t, or C^l/C^t is, finally, assayed in terms of contribution of covalency. This is accomplished by studying the maximum, minimum, and average value of H(r) over the volume enclosed by the low-density reduced density gradient (RDG) isosurface associated with the bond (typically, the RDG isosurface including the BCP) and the average ρ(r) over the same volume. The bond assignment is also corroborated by calculating the values of quantitative indices specifically defined for the various types of interactions (A, B, or C). The generality of our taken approach should encourage its wide application to the study of Ng compounds.

Mutual Influence of Pnicogen Bonds and Beryllium Bonds: Energies and Structures in the Spotlight

Pnicogen bonds, which are weak noncovalent interactions (NCIs), can be significantly modified by the presence of beryllium bonds, one of the strongest NCIs known. We demonstrate the importance of this influence by studying ternary complexes in which both NCIs are present, that is, the ternary complexes formed by a nitrogen base (NH₃, NHCH₂, and NCH), a phosphine (fluorophosphane, PH₂F) and a beryllium derivative (BeH₂, BeF₂, BeCl₂, BeCO₃, and BeSO₄). Energies, structures, and nature of the chemical bonding in these complexes are studied by means of ab initio computational methods. The pnicogen bond between the nitrogen base and the phosphine and the beryllium bond between the fluorine atom of fluorophosphane and the beryllium derivative show large cooperativity effects both on energies and geometries, with dissociation energies up to 296 kJ mol^-1 and cooperativity up to 104 kJ mol^-1 in the most strongly bound complex, CH₂HN:PH₂F:BeSO₄. In the complexes between the strongest nitrogen bases and the strongest beryllium donors, phosphorus-shared and phosphorus-transfer bonds are found.

Complexes of helium with neutral molecules: Progress toward a quantitative scale of bonding character

The complexes of helium with nearly 30 neutral molecules (M) were investigated by various techniques of bonding analysis and symmetry-adapted perturbation theory (SAPT). The main investigated function was the local electron energy density H(r), analyzed, in particular, so to estimate the degree of polarization (DoP) of He in the various He(M). As we showed recently (Borocci et al., J. Comput. Chem., 2019, 40, 2318-2328), the DoP is a quantitative index that is generally informative about the role of polarization (induction plus charge transfer [CT]) and dispersion in noncovalent noble gas complexes. As further evidence in this regard, we presently ascertained quantitative correlations between the DoP(He) of the He(M) and indices based on the electron density ρ(r), including the molecular electrostatic potential at the HeM bond critical point, as well as the percentage contributions of induction and dispersion to the SAPT binding energies. Based also on the explicit evaluation of the CT, accomplished through the study of the charge-displacement function, we derived a quantitative scale that ranks the He(M) according to their dispersive, inductive, and CT bonding character. Our taken approach could be conceivably extended to other types of noncovalent complexes.

Perspective: Found in translation: Quantum chemical tools for grasping non-covalent interactions

Today's quantum chemistry methods are extremely powerful but rely upon complex quantities such as the massively multidimensional wavefunction or even the simpler electron density. Consequently, chemical insight and a chemist's intuition are often lost in this complexity leaving the results obtained difficult to rationalize. To handle this overabundance of information, computational chemists have developed tools and methodologies that assist in composing a more intuitive picture that permits better understanding of the intricacies of chemical behavior. In particular, the fundamental comprehension of phenomena governed by non-covalent interactions is not easily achieved in terms of either the total wavefunction or the total electron density, but can be accomplished using more informative quantities. This perspective provides an overview of these tools and methods that have been specifically developed or used to analyze, identify, quantify, and visualize non-covalent interactions. These include the quantitative energy decomposition analysis schemes and the more qualitative class of approaches such as the Non-covalent Interaction index, the Density Overlap Region Indicator, or quantum theory of atoms in molecules. Aside from the enhanced knowledge gained from these schemes, their strengths, limitations, as well as a roadmap for expanding their capabilities are emphasized.

Spectroscopic Evidences for Strong Hydrogen Bonds with Selenomethionine in Proteins

Careful protein structure analysis unravels many unknown and unappreciated noncovalent interactions that control protein structure; one such unrecognized interaction in protein is selenium centered hydrogen bonds (SeCHBs). We report, for the first time, SeCHBs involving the amide proton and selenium of selenomethionine (Mse), i.e., amide-N-H···Se H-bonds discerned in proteins. Using mass selective and conformer specific high resolution vibrational spectroscopy, gold standard quantum chemical calculations at CCSD(T), and in-depth protein structure analysis, we establish that amide-N-H···Se and amide-N-H···Te H-bonds are as strong as conventional amide-NH···O and amide-NH···O═C H-bonds despite smaller electronegativity of selenium and tellurium than oxygen. It is in fact, electronegativity, atomic charge, and polarizability of the H-bond acceptor atoms are at play in deciding the strength of H-bonds. The amide-N-H···Se and amide-N-H···Te H-bonds presented here are not only new additions to the ever expanding world of noncovalent interactions, but also are of central importance to design new force-fields for better biomolecular structure simulations.