The World of Non-Covalent Interactions: 2006

On the intramolecular vibrational energy redistribution dynamics of aromatic complexes: A comparative study on C6H6-C6H5Cl, C6H6-C6H3Cl3, C6H6-C6Cl6 and C6H6-C6H5F, C6H6-C6H3F3, C6H6-C6F6

Chemical dynamics Simulation studies on benzene dimer (Bz2) and benzene-hexachlorobenzene (Bz-HCB) as performed in the past suggest that the coupling between the monomeric (intramolecular) vibrational modes and modes generated due to the association of two monomers (intermolecular) has to be neither strong nor weak for a fast dissociation of the complex. To find the optimum coupling, four complexes are taken into consideration in this work, namely, benzene-monofluorobenzene, benzene-monochlorobenzene, benzene-trifluorobenzene (Bz-TFB), and benzene-trichlorobenzene. Bz-TFB has the highest rate of dissociation among all seven complexes, including Bz2, Bz-HCB, and Bz-HFB (HFB stands for hexafluorobenzene). The set of vibrational frequencies of Bz-TFB is mainly the reason for this fast dissociation. The mass of chlorine in Bz-HCB is optimized to match its vibrational frequencies similar to those of Bz-TFB, and the dissociation of Bz-HCB becomes faster. The power spectrum of Bz-TFB, Bz-HCB, and Bz-HCB with the modified mass of chlorine is also computed to understand the extent of the said coupling in these complexes.

Cooperativity between H-bonds and tetrel bonds. Transformation of a noncovalent C⋯N tetrel bond to a covalent bond

The dimers and trimers formed by imidazole (IM) and F2TO (T = C, Si, Ge) are studied by ab initio calculations. IM can engage in either a NH⋯O H-bond with F2TO or a T⋯N tetrel bond (TB) with the π-hole above the T atom. The latter is a true noncovalent TB for T = C but is a much shorter and stronger covalent bond with F2SiO or F2GeO. When a second IM is added, the cooperativity emerging from its H-bond with the first IM makes it a stronger nucleophile, leading to two minima with F2CO. The first structure contains a long noncovalent C⋯O TB and there is a much shorter covalent bond in the other, with a small energy barrier separating them. The same sort of double minimum occurs when the two IM units are situated parallel to one another in a stacked geometry.

Amphiphilic perylene diimide-based fluorescent hemispherical aggregates as probes for metal ions

The self-assembly behaviour of a newly synthesized amphiphilic core-positioned thioester appended with carboxylic acid functionalized perylene diimide derivative is studied in different organic solvents. Fluorescent J-type hemispherical aggregates are formed in THF solution. The effect of added metal ions on these fluorescent aggregates is evaluated using spectroscopic techniques, where we found these probes bind selectively to Fe³⁺ and Ba²⁺ ions. Two equivalents of Fe³⁺ ions bind cooperatively to one equivalent of perylene diimide derivative in the hemispherical aggregates with a binding constant of 1.4×10⁷ M^-1 and the limit of detection (LOD) was calculated to be 8.66×10^-6 M. The positive cooperative binding effect of Fe³⁺ ions towards hemispherical aggregates equipped with perylene diimide derivatives leads to supramolecular polymerization. Ba²⁺ ions showed selectivity and sensitivity towards the fluorescent aggregates in THF by quenching the fluorescence intensity completely. The linear Stern-Volmer plot with a Stern-Volmer constant value of 502.6 M^-1 signifies the heavy atom effect of Ba²⁺ ions, leading to fluorescence quenching. The morphological transformation of the fluorescent J-type hemispherical aggregates in the presence of Fe³⁺ and Ba²⁺ was studied in detail using electron microscopy.

Hydrogen physisorption on the (BeO)n, B2H4(Be,Ti), and B6Ti3 metal clusters: a computational study of energies and atomic charges

The equilibrium structures of BeO clusters and Be,Ti-decorated boranes were computed with the ωB97X-D method and the 6-31G + (2d,2p) and aug-cc-pVTZ basis sets to study their intermolecular interactions with hydrogen molecules. Thermochemical and molecular properties such as the harmonic vibrational frequency, dipole and quadrupole moments, and atomic charges are employed to understand the attractive interactions that control the adsorption process. Comparison of molecular properties and atomic charges of the studied compounds before and after H₂ molecule adsorption shows that most of the interactions among the BeO clusters and boranes with H₂ molecules constitute a combination of dispersion, electrostatic, and weak charge transfer interactions. Calculated values of Hirschfeld atomic charges and ΔE_e (in parenthesis) (BeO)₄.8H₂ (0.028 e and -2.0 kcal.mol^-1), (BeO)₂.12H₂ (0.030 e and -2.8 kcal.mol^-1), B₆Ti₃.10H₂ (0.045 e and -15.4 kcal.mol^-1), and B₆Ti₃⁺.10H₂ (0.058 e and -15.3 kcal.mol^-1) show qualitative correlation between hydrogen atomic charges and electronic energy of hydrogen interaction. The ωB97X-D/6-31 + G(2d,2p) values of Gibbs free energy at 298.15 K for (BeO)₄.8H₂ B₂H₄Ti.4H₂ and B₆Ti₃.10H₂ clusters are equal to -5.0, -4.9, and -5.1 kcal.mol^-1, respectively, which are within the range of energy parameters of materials that could be employed in hydrogen storage tanks for light vehicles.

Crystal Structure and Chemical Bonds in [CuII2(Tolf)4(MeOH)2]∙2MeOH

A new coordination compound of copper(II) with a tolfenamate ligand of the paddle-wheel-like structure [Cu^II₂(Tolf)₄(MeOH)₂]∙2MeOH was obtained and structurally characterized. Chemical bonds of Cu(II)∙∙∙Cu(II) and Cu(II)-O were theoretically analyzed and compared with the results for selected similar structures from the CSD database. QTAIM analysis showed that the Cu(II)∙∙∙Cu(II) interaction has a strength comparable to a hydrogen bond, as indicated by the electron density at a critical point. The remaining QTAIM parameters indicate stability of the Cu(II)∙∙∙Cu(II) interaction. Other methods, such as NCI and NBO, also indicate a significant strength of this interaction. Thus, the Cu(II)∙∙∙Cu(II) interaction can be treated as one of the noncovalent interactions that affects the structure of the coordination compound, the packing of molecules in the crystal, and the general properties of the compound.

Unraveling the Nature of Hydrogen Bonds of "Proton Sponges" Based on Car-Parrinello and Metadynamics Approaches

The nature of intra- and intermolecular non-covalent interactions was studied in four naphthalene derivatives commonly referred to as "proton sponges". Special attention was paid to an intramolecular hydrogen bond present in the protonated form of the compounds. The unsubstituted "proton sponge" served as a reference structure to study the substituent influence on the hydrogen bond (HB) properties. We selected three compounds substituted by methoxy, amino, and nitro groups. The presence of the substituents either retained the parent symmetry or rendered the compounds asymmetric. In order to reveal the non-covalent interaction properties, the Hirshfeld surface (HS) was computed for the crystal structures of the studied compounds. Next, quantum-chemical simulations were performed in vacuo and in the crystalline phase. Car-Parrinello molecular dynamics (CPMD), Path Integral Molecular Dynamics (PIMD), and metadynamics were employed to investigate the time-evolution changes of metric parameters and free energy profile in both phases. Additionally, for selected snapshots obtained from the CPMD trajectories, non-covalent interactions and electronic structure were studied. Quantum theory of atoms in molecules (QTAIM) and the Density Overlap Regions Indicator (DORI) were applied for this purpose. It was found based on Hirshfeld surfaces that, besides intramolecular hydrogen bonds, other non-covalent interactions are present and have a strong impact on the crystal structure organization. The CPMD results obtained in both phases showed frequent proton transfer phenomena. The proton was strongly delocalized in the applied time-scale and temperature, especially in the PIMD framework. The use of metadynamics allowed for tracing the free energy profiles and confirming that the hydrogen bonds present in "proton sponges" are Low-Barrier Hydrogen Bonds (LBHBs). The electronic and topological analysis quantitatively described the temperature dependence and time-evolution changes of the electronic structure. The covalency of the hydrogen bonds was estimated based on QTAIM analysis. It was found that strong hydrogen bonds show greater covalency, which is additionally determined by the proton position in the hydrogen bridge.

Different Curcumin-Loaded Delivery Systems for Wound Healing Applications: A Comprehensive Review

Curcumin or turmeric is the active constituent of Curcuma longa L. It has marvelous medicinal applications in many diseases. When the skin integrity is compromised due to either acute or chronic wounds, the body initiates several steps leading to tissue healing and skin barrier function restoration. Curcumin has very strong antibacterial and antifungal activities with powerful wound healing ability owing to its antioxidant activity. Nevertheless, its poor oral bioavailability, low water solubility and rapid metabolism limit its medical use. Tailoring suitable drug delivery systems for carrying curcumin improves its pharmaceutical and pharmacological effects. This review summarizes the most recent reported curcumin-loaded delivery systems for wound healing purposes, chiefly hydrogels, films, wafers, and sponges. In addition, curcumin nanoformulations such as nanohydrogels, nanoparticles and nanofibers are also presented, which offer better solubility, bioavailability, and sustained release to augment curcumin wound healing effects through stimulating the different healing phases by the aid of the small carrier.

Reliability of Computing van der Waals Bond Lengths of Some Rare Gas Diatomics

When the bond lengths of 11 molecules containing van der Waals bonds are optimized by 572 methods and 20 basis sets, it is found that the best mean absolute deviations (MADs) of density-functional theory (DFT) methods are 0.005 Å (shown by APFD/6-311++G**), 0.007 Å (B2PLYPD3(Full)/aug-cc-pVQZ), and 0.010 Å (revDSDPBEP86/aug-cc-pVQZ), while the best MADs of ab initio methods are 0.008 Å (BD(T)/aug-cc-pVTZ) and 0.016 Å (MP4/aug-cc-pVQZ). Moreover, the best MADs calculated by 54 selected methods in combination with 60 other basis sets (such as 6-311++G, 6-31++G(3d'f,3p'd), and UGBS1V++) are not better. Therefore, these bond lengths can be calculated with extremely high accuracy by some special methods and basis sets, and CCSD(T) is also not as good as expected because its best MAD is only 0.023 Å (CCSD(T)/aug-cc-pVQZ).

Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers

It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.

The tetrel bonding role in supramolecular aggregation of lead(II) acetate and a thiosemicarbazide derivative

A new Pb^II coordination complex [PbL(OAc)], which was readily synthesized from a mixture of Pb(OAc)₂·3H₂O and 1-(pyridin-2-yl)benzylidene-4-phenylthiosemicarbazide (HL) is reported. The crystal structure analysis of [PbL(OAc)] showed that the Pb^II cation is N,N',S-chelated by the tridentate pincer-type ligand L and by the oxygen atoms of the acetate anion. In addition, the metal centre forms Pb...O and Pb...S tetrel bonds with an adjacent complex molecule, yielding a 1D zigzag polymeric chain, which is reinforced by N-H...O hydrogen bonds and π...π interactions. These chains are interlinked by C-H...py non-covalent interactions, realized between one of the acetate hydrogen atoms and the pyridine rings. According to the Hirshfeld surface analysis, the crystal packing is mainly characterized by intermolecular H...H, H...C and H...O contacts, followed by H...N, H...S, C...C, C...N, Pb...H, Pb...O and Pb...S contacts. The FTIR and ¹H NMR spectra of [PbL(OAc)] testify to the deprotonation of the parent ligand HL, while the acetate ligand exhibits an anisobidentate coordination mode as established by means of single-crystal X-ray diffraction and FTIR spectroscopy. Lastly, theoretical calculations at the PBE0-D3/def2-TZVP level of theory have been used to analyze and characterize the Pb...O and Pb...S tetrel bonds observed in the crystal of [PbL(OAc)], using a combination of QTAIM (Quantum Theory of Atoms in Molecules) and NCIPlot (Non-Covalent Interaction Plot) computational tools.

Organogels Fabricated from Self-Assembled Nanotubes Containing Core Substituted Perylene Diimide Derivative

Perylene-based organogels are well-known for their applications as sensors and optoelectronic materials. Among them, core-substituted perylene diimide-based organogels are rarely explored. Herein, the hierarchical self-assembly mechanism of a newly synthesized, amide-linked core-substituted perylene diimide derivative, which formed organogels in organic solvents like toluene and methyl cyclohexane (MCH), is discussed. These organogels are composed of one-dimensional molecular aggregates like nanofibers and nanotubes. Organogels composed of nanofibers are very frequent. On the contrary, for the first time, we have encountered a perylene diimide-based organogel consisting of self-assembled nanotubes. The molecular interactions, molecular packing, and rheological properties of this organogel are also discussed.

Probing halogen bonding interactions between heptafluoro-2-iodopropane and three azabenzenes with Raman spectroscopy and density functional theory

The potential formation of halogen bonded complexes between a donor, heptafluoro-2-iodopropane (HFP), and the three acceptor heterocyclic azines (azabenzenes: pyridine, pyrimidine, and pyridazine) is investigated herein through normal mode analysis via Raman spectroscopy, density functional theory, and natural electron configuration analysis. Theoretical Raman spectra of the halogen bonded complexes are in good agreement with experimental data providing insight into the Raman spectra of these complexes. The exhibited shifts in vibrational frequency of as high as 8 cm^-1 for each complex demonstrate, in conjunction with NEC analysis, significant evidence of charge transfer from the halogen bond acceptor to donor. Here, an interesting charge flow mechanism is proposed involving the donated nitrogen lone pair electrons pushing the dissociated fluorine atoms back to their respective atoms. This mechanism provides further insight into the formation and fundamental nature of halogen bonding and its effects on neighboring atoms. The present findings provide novel and deeper characterization of halogen bonding with applications in supramolecular and organometallic chemistry.

Assessing the persistence of chalcogen bonds in solution with neural network potentials

Non-covalent bonding patterns are commonly harvested as a design principle in the field of catalysis, supramolecular chemistry and functional materials to name a few. Yet, their computational description generally neglects finite temperature and environment effects, which promote competing interactions and alter their static gas-phase properties. Recently, neural network potentials (NNPs) trained on Density Functional Theory (DFT) data have become increasingly popular to simulate molecular phenomena in condensed phase with an accuracy comparable to ab initio methods. To date, most applications have centered on solid-state materials or fairly simple molecules made of a limited number of elements. Herein, we focus on the persistence and strength of chalcogen bonds involving a benzotelluradiazole in condensed phase. While the tellurium-containing heteroaromatic molecules are known to exhibit pronounced interactions with anions and lone pairs of different atoms, the relevance of competing intermolecular interactions, notably with the solvent, is complicated to monitor experimentally but also challenging to model at an accurate electronic structure level. Here, we train direct and baselined NNPs to reproduce hybrid DFT energies and forces in order to identify what are the most prevalent non-covalent interactions occurring in a solute-Cl$^-$-THF mixture. The simulations in explicit solvent highlight competition with chalcogen bonds formed with the solvent and the short-range directionality of the interaction with direct consequences for the molecular properties in the solution. The comparison with other potentials (e.g., AMOEBA, direct NNP and continuum solvent model) also demonstrates that baselined NNPs offer a reliable picture of the non-covalent interaction interplay occurring in solution.

Synthesis, spectroscopic findings and crystal engineering of Pb(ii)-Salen coordination polymers, and supramolecular architectures engineered by σ-hole/spodium/tetrel bonds: a combined experimental and theoretical investigation

Spontaneous self-assembly is one of the available synthetic routes to achieve structurally versatile and unique crystal complexes with selected metal-ligand combinations in the spirit of pseudohalides. In this endeavour, we designed a novel 1D coordination polymer (CP), [(Cd)(Pb)(L)(η¹-NCS)(η¹-SCN)] _n (1), using a compartmental Salen ligand (H₃L) in the presence of NaSCN. The characterization of the CP was accomplished using several spectroscopic techniques: MALDI-TOF, PXRD, SEM, EDX mapping, and single-crystal X-ray crystallography. The CP crystallizes in the monoclinic space group P2₁/c with Z = 4. SCXRD reveals Cd(ii) and Pb(ii) metal ions fulfilled distorted square pyramidal and hemi-directed coordination spheres. Cd(ii) is placed in the inner N₂O₂ and heavier Pb(ii) in the outer O₄ compartments of the de-protonated form of the ligand [L]^2-. Supramolecular interactions in the intricate crystal structure produced attractive molecular architectures of the compound. The flexible aliphatic -OH pendent group coordinates with the Pb(ii) ions. This unique binding further elevates the supramolecular crystal topographies. The supramolecular interactions were authenticated by Hirshfeld surface analysis (HSA). The observation of the recurring unconventional tetrel bonds was rationalized by DFT calculations and surface plots of molecular electrostatic potential (MEP). In the 1D polymeric chain in the complex, the O-atom of the -OH groups shows a tetrel bonding interaction with the Pb atom. We have found that the combination of QTAIM/NCI and QTAIM/ELF plots helps reveal the nature of these contacts. Moreover, the QTAIM/ELF plot determines the donor-acceptor interaction between the O-atom and the Pb atom, establishing the σ-hole. Agreeably, the σ-hole interaction also helps Pb(ii) serve as a Lewis acid in the complex. Finally, spodium and tetrel bonds are formed, possible thanks to a hemi-directional coordination sphere of the Pb atoms in the polymer described.

Malonaldehyde-like Systems: BeF2 Clusters—A Subtle Balance between Hydrogen Bonds, Beryllium Bonds, and Resonance

The stability of malonaldehyde is governed by intramolecular hydrogen bonds (IMHBs) as well as in malonaldehyde-like systems where oxygen is replaced by N or S at any of the basic sites. As beryllium bonds have been shown to strongly cooperate with hydrogen bonds, this work explores at the high level ab initio G4 level of theory the effect of including this non-covalent interaction in the system through its association with BeF2. Although malonaldehyde follows the expected trends, where the formation of a pseudocyclic form is favored also when IMHB and Be bonds are present, the subtle balance between both non-covalent interactions leads to some surprising results when other heteroatoms are involved, to the point that interaction energies can be much larger than expected or even cyclization is not favored. A complete analysis using different computational tools gives an answer to those cases escaping the predictable trends.

Exploring Intra- and Intermolecular Interactions in Selected N-Oxides-The Role of Hydrogen Bonds

Intra- and intermolecular interactions have been explored in selected N-oxide derivatives: 2-(N,N-dimethylamino-N-oxymethyl)-4,6-dimethylphenyl (1) and 5,5’-dibromo-3-diethylaminomethyl-2,2’-biphenol N-oxide (2). Both compounds possess intramolecular hydrogen bonding, which is classified as moderate in 1 and strong in 2, and resonance-assisted in both cases. Density Functional Theory (DFT) in its classical formulation as well as Time-Dependent extension (TD-DFT) were employed to study proton transfer phenomena. The simulations were performed in the gas phase and with implicit and explicit solvation models. The obtained structures of the studied N-oxides were compared with experimental data available. The proton reaction path was investigated using scan with an optimization method, and water molecule reorientation in the monohydrate of 1 was found upon the proton scan progress. It was found that spontaneous proton transfer phenomenon cannot occur in the electronic ground state of the compound 1. An opposite situation was noticed for the compound 2. The changes of nucleophilicity and electrophilicity upon the bridged proton migration were analyzed on the basis of Fukui functions in the case of 1. The interaction energy decomposition of dimers and microsolvation models was investigated using Symmetry-Adapted Perturbation Theory (SAPT). The simulations were performed in both phases to introduce polar environment influence on the interaction energies. The SAPT study showed rather minor role of induction in the formation of homodimers. However, it is worth noticing that the same induction term is responsible for the preference of water molecules’ interaction with N-oxide hydrogen bond acceptor atoms in the microsolvation study. The Natural Bond Orbital (NBO) analysis was performed for the complexes with water to investigate the charge flow upon the polar environment introduction. Finally, the TD-DFT was applied for isolated molecules as well as for microsolvation models showing that the presence of solvent affects excited states, especially when the N-oxide acceptor atom is microsolvated.

Computational study on noncovalent interactions between (n, n) single-walled carbon nanotubes and simple lignin model-compounds

Composites of carbon nanotubes (CNTs) and lignin are promising and potentially cheap precursors of-to this day-expensive carbon fibers. Since the control of the CNT-lignin interface is crucial to maximize fiber performance, it is imperative to understand the fundamental noncovalent interactions between lignin and CNT. In the present study a density functional theory study is conducted to investigate the fundamental noncovalent interaction strength between metallic (n, n) single-walled CNT (SWCNT) and simple lignin model molecules. In particular, the respective adsorption energies are used to gauge the strength of interaction classes (ππ interaction, CHπ hydrogen bonding and OH-related hydrogen bonding. From the data, substituent-dependent interaction trends as well as class- and curvature-dependent interaction trends are derived. Overall, we find that most of the interaction strength trends appear to be strongly influenced by geometry: flat orientation of the test molecules relative to the (n, n) SWCNT surface and small (n, n) SWCNT curvature-that is, large diameter enhances the CHπ and ππ interactions.

Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller-Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, ωB97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers' stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm-1-1700 cm-1 and 2300 cm-1-3400 cm-1 in the gas phase and 600 cm-1-1800 cm-1 and 2200 cm-1-3400 cm-1 in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm-1-1700 cm-1 and 2300 cm-1-3300 cm-1 for the gas phase and one broad absorption region in the solid state between 700 cm-1 and 3100 cm-1. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons.

Non-Covalent Forces in Naphthazarin-Cooperativity or Competition in the Light of Theoretical Approaches

Non-covalent interactions responsible for molecular features and self-assembly in Naphthazarin C polymorph were investigated on the basis of diverse theoretical approaches: Density Functional Theory (DFT), Diffusion Quantum Monte Carlo (DQMC), Symmetry-Adapted Perturbation Theory (SAPT) and Car-Parrinello Molecular Dynamics (CPMD). The proton reaction paths in the intramolecular hydrogen bridges were studied. Two potential energy minima were found indicating that the proton transfer phenomena occur in the electronic ground state. Diffusion Quantum Monte Carlo (DQMC) and other levels of theory including Coupled Cluster (CC) employment enabled an accurate inspection of Potential Energy Surface (PES) and revealed the energy barrier for the proton transfer. The structure and reactivity evolution associated with the proton transfer were investigated using Harmonic Oscillator Model of Aromaticity - HOMA index, Fukui functions and Atoms In Molecules (AIM) theory. The energy partitioning in the studied dimers was carried out based on Symmetry-Adapted Perturbation Theory (SAPT) indicating that dispersive forces are dominant in the structure stabilization. The CPMD simulations were performed at 60 K and 300 K in vacuo and in the crystalline phase. The temperature influence on the bridged protons dynamics was studied and showed that the proton transfer phenomena were not observed at 60 K, but the frequent events were noticed at 300 K in both studied phases. The spectroscopic signatures derived from the CPMD were computed using Fourier transformation of autocorrelation function of atomic velocity for the whole molecule and bridged protons. The computed gas-phase IR spectra showed two regions with OH absorption that covers frequencies from 2500 cm−1 to 2800 cm−1 at 60 K and from 2350 cm−1 to 3250 cm−1 at 300 K for both bridged protons. In comparison, the solid state computed IR spectra revealed the environmental influence on the vibrational features. For each of them absorption regions were found between 2700–3100 cm−1 and 2400–2850 cm−1 at 60 K and 2300–3300 cm−1 and 2300–3200 cm−1 at 300 K respectively. Therefore, the CPMD study results indicated that there is a cooperation of intramolecular hydrogen bonds in Naphthazarin molecule.

The Role of Non-Covalent Interactions on Cluster Formation: Pentamer, Hexamers and Heptamer of Difluoromethane

The role of non-covalent interactions (NCIs) has broadened with the inclusion of new types of interactions and a plethora of weak donor/acceptor partners. This work illustrates the potential of chirped-pulse Fourier transform microwave technique, which has revolutionized the field of rotational spectroscopy. In particular, it has been exploited to reveal the role of NCIs' in the molecular self-aggregation of difluoromethane where a pentamer, two hexamers and a heptamer were detected. The development of a new automated assignment program and a sophisticated computational screening protocol was essential for identifying the homoclusters in conditions of spectral congestion. The major role of dispersion forces leads to less directional interactions and more distorted structures than those found in polar clusters, although a detailed analysis demonstrates that the dominant interaction energy is the pairwise interaction. The tetramer cluster is identified as a structural unit in larger clusters, representing the maximum expression of bond between dimers.

Unimolecular Dissociation of C6H6-C6Cl6 Complex and Effect of Mode-Mode Coupling

The unimolecular dissociation dynamics of the C₆H₆-C₆Cl₆ (Bz-HCB) complex is studied with initial excitation of all vibrational modes for a temperature range of 1000-2000 K and with mode-specific excitations at 1500 K. The results are compared with those of the C₆H₆-C₆F₆ [Bz- HFB] complex. When all modes of Bz-HCB are initially excited, the rate of dissociation is slower with respect to Bz-HFB. However, the rate of dissociation is faster when simulations with nonrandom excitation of the specific vibrational modes are performed. The rate of dissociation of Bz-HCB is found to become slower when a few intramolecular modes are excited along with all inter-fragment modes compared to the simulation when only inter-fragment modes of the same complex are excited. Such an energy-transfer dynamics is absent if both intramolecular and inter-fragment modes are not initially excited. Thus, a "stimulated" resonance energy-transfer dynamics is observed in Bz-HCB dissociation dynamics.

Supramolecular structures of NiII and CuII with the sterically demanding Schiff base dyes driven by cooperative action of preagostic and other non-covalent interactions

This work reports on synthesis and extensive experimental and theoretical investigations on photophysical, structural and thermal properties of the NiII and CuII discrete mononuclear homoleptic complexes [Ni(L I,II)2] and [Cu(L I,II)2] fabricated from the Schiff base dyes o-HOC6H4-CH=N-cyclo-C6H11 (HL I) and o-HOC10H6-CH=N-cyclo-C6H11 (HL II), containing the sterically crowding cyclo-hexyl units. The six-membered metallocycles adopt a clearly defined envelope conformation in [Ni(L II)2], while they are much more planar in the structures of [Ni(L I)2] and [Cu(L I,II)2]. It has been demonstrated by in-depth bonding analyses based on the ETS-NOCV and Interacting Quantum Atoms energy-decomposition schemes that application of the bulky substituents, containing several C-H groups, has led to the formation of a set of classical and unintuitive intra- and inter-molecular interactions. All together they are responsible for the high stability of [Ni(L I,II)2] and [Cu(L I,II)2]. More specifically, London dispersion dominated intramolecular C-H⋯O, C-H⋯N and C-H⋯H-C hydrogen bonds are recognized and, importantly, the attractive, chiefly the Coulomb driven, preagostic (not repulsive anagostic) C-H⋯Ni/Cu interactions have been discovered despite their relatively long distances (∼2.8-3.1 Å). All the complexes are further stabilized by the extremely efficient intermolecular C-H⋯π(benzene) and C-H⋯π(chelate) interactions, where both the charge-delocalization and London dispersion constituents appear to be crucial for the crystal packing of the obtained complexes. All the complexes were found to be photoluminescent in CH2Cl2, with [Cu(L II)2] exhibiting the most pronounced emission - the time-dependent density-functional-theory computations revealed that it is mostly caused by metal-to-ligand charge-transfer transitions.

O-H stretching frequency red shifts do not correlate with the dissociation energies in the dimethylether and dimethylsulfide complexes of phenol derivatives

In this perspective, we present a comprehensive report on the spectroscopic and computational investigations of the hydrogen bonded (H-bonded) complexes of Me2O and Me2S with seven para-substituted H-bond donor phenols. The salient finding was that although the dissociation energies, D0, of the Me2O complexes were consistently higher than those of the analogous Me2S complexes, the red-shifts in phenolic O-H frequencies, Δν(O-H), showed the exactly opposite trend. This is in contravention of the general perception that the red shift in the X-H stretching frequency in the X-HY hydrogen bonded complexes is a reliable indicator of H-bond strength (D0), a concept popularly known as the Badger-Bauer rule. This is also in contrast to the trend reported for the H-bonded complexes of H2S/H2O with several para substituted phenols of different pKa values wherein the oxygen centered hydrogen bonded (OCHB) complexes consistently showed higher Δν(O-H) and D0 compared to those of the analogous sulfur centered hydrogen bonded (SCHB) complexes. Our effort was to understand these intriguing observations based on the spectroscopic investigations of 1 : 1 complexes in combination with a variety of high level quantum chemical calculations. Ab initio calculations at the MP2 level and the DFT calculations using various dispersion corrected density functionals (including DFT-D3) were performed on counterpoise corrected surfaces to compute the dissociation energy, D0, of the H-bonded complexes. The importance of anharmonic frequency computations is underscored as they were able to correctly reproduce the observed trend in the relative OH frequency shifts unlike the harmonic frequency computations. We have attempted to find a unified correlation that would globally fit the observed red shifts in the O-H frequency with the H-bonding strength for the four bases, namely, H2S, H2O, Me2O, and Me2S, in this set of H-bond donors. It was found that the proton affinity normalized Δν(O-H) values scale very well with the H-bond strength.

Quantum chemical benchmark databases of gold-standard dimer interaction energies

Advances in computational chemistry create an ongoing need for larger and higher-quality datasets that characterize noncovalent molecular interactions. We present three benchmark collections of quantum mechanical data, covering approximately 3,700 distinct types of interacting molecule pairs. The first collection, which we refer to as DES370K, contains interaction energies for more than 370,000 dimer geometries. These were computed using the coupled-cluster method with single, double, and perturbative triple excitations [CCSD(T)], which is widely regarded as the gold-standard method in electronic structure theory. Our second benchmark collection, a core representative subset of DES370K called DES15K, is intended for more computationally demanding applications of the data. Finally, DES5M, our third collection, comprises interaction energies for nearly 5,000,000 dimer geometries; these were calculated using SNS-MP2, a machine learning approach that provides results with accuracy comparable to that of our coupled-cluster training data. These datasets may prove useful in the development of density functionals, empirically corrected wavefunction-based approaches, semi-empirical methods, force fields, and models trained using machine learning methods.

Tetrel Bonding and Other Non-Covalent Interactions Assisted Supramolecular Aggregation in a New Pb(II) Complex of an Isonicotinohydrazide

A new supramolecular Pb(II) complex [PbL(NO₂)]_n was synthesized from Pb(NO₃)₂, N’-(1-(pyridin-2-yl)ethylidene)isonicotinohydrazide (HL) and NaNO₂. [PbL(NO₂)]_n is constructed from discrete [PbL(NO₂)] units with an almost ideal N₂O₃ square pyramidal coordination environment around Pb(II). The ligand L⁻ is coordinated through the 2-pyridyl N-atom, one aza N-atom, and the carbonyl O-atom. The nitrite ligand binds in a κ²-O,O coordination mode through both O-atoms. The Pb(II) center exhibits a hemidirected coordination geometry with a pronounced coordination gap, which allows a close approach of two additional N-atoms arising from the N=C(O) N-atom of an adjacent molecule and from the 4-pyridyl N-atom from the another adjacent molecule, yielding a N₄O₃ coordination, constructed from two Pb–N and three Pb–O covalent bonds, and two Pb⋯N tetrel bonds. Dimeric units in the structure of [PbL(NO₂)]_n are formed by the Pb⋯N=C(O) tetrel bonds and intermolecular electrostatically enforced π⁺⋯π⁻ stacking interactions between the 2- and 4-pyridyl rings and further stabilized by C–H⋯π intermolecular interactions, formed by one of the methyl H-atoms and the 4-pyridyl ring. These dimers are embedded in a 2D network representing a simplified uninodal 3-connected fes (Shubnikov plane net) topology defined by the point symbol (4∙8²). The Hirshfeld surface analysis of [PbL(NO₂)] revealed that the intermolecular H⋯X (X = H, C, N, O) contacts occupy an overwhelming majority of the molecular surface of the [PbL(NO₂)] coordination unit. Furthermore, the structure is characterized by intermolecular C⋯C and C⋯N interactions, corresponding to the intermolecular π⋯π stacking interactions. Notably, intermolecular Pb⋯N and, most interestingly, Pb⋯H interactions are remarkable contributors to the molecular surface of [PbL(NO₂)]. While the former contacts are due to the Pb⋯N tetrel bonds, the latter contacts are mainly due to the interaction with the methyl H-atoms in the π⋯π stacked [PbL(NO₂)] molecules. Molecular electrostatic potential (MEP) surface calculations showed marked electrostatic contributions to both the Pb⋯N tetrel bonds and the dimer forming π⁺⋯π⁻ stacking interactions. Quantum theory of atoms in molecules (QTAIM) analyses underlined the tetrel bonding character of the Pb⋯N interactions. The manifold non-covalent interactions found in this supramolecular assembly are the result of the proper combination of the polyfunctional multidentate pyridine-hydrazide ligand and the small nitrito auxiliary ligand.

Automated parameterization of quantum-mechanically derived force-fields including explicit sigma holes: A pathway to energetic and structural features of halogen bonds in gas and condensed phase

In classical molecular dynamics, general purpose atomistic force-fields (FFs) often deliver inaccurate results when dealing with halogen bonds (XBs), notwithstanding their crucial role in many fields of science, ranging from material design to drug development. Given the large dimensions of the systems of interest, it would be therefore desirable to increase the FF accuracy maintaining the simplicity of the standard Lennard-Jones (LJ) plus point charge description to avoid an excessive computational cost. A simple yet effective strategy consists in introducing a number of virtual sites able to mimic the so-called "explicit σ-hole." In this work, we present an automated FF parameterization strategy based on a global optimization of both LJ and charge parameters with respect to accurate quantum mechanical data, purposely computed for the system under investigation. As a test case, we report on two homologue series, characterized either by weak or strong XBs, namely, the di-halogenated methanes and the mono-, di-, and tri-substituted acetonitriles, taking into consideration Cl, Br, and I substituents. The resulting quantum mechanically derived FFs are validated for each compound in the gas and in the condensed phase by comparing them to general purpose and specific FFs without virtual sites and to highly accurate reference quantum mechanical data. The results strongly support the adoption of the specific FFs with virtual sites, which overcome the other investigated models in representing both gas phase energetics and the structural patterns of the liquid phase structure related to the presence of XBs.

Supramolecular lead(ii) architectures engineered by tetrel bonds

The structures, including tetrel bonding, of Pb^II coordination compounds assembled from N′-(pyridin-2-ylmethylene)picolinohydrazide, N′-(pyridin-2-ylmethylene)nicotinohydrazide and N′-(1-(pyridin-2-yl)ethylidene)isonicotinohydrazide ligands are discussed.

A new spodium bond driven coordination polymer constructed from mercury(ii) azide and 1,2-bis(pyridin-2-ylmethylene)hydrazine

In this manuscript, the synthesis and X-ray characterization of a new spodium bond driven coordination polymer constructed from mercury(ii) azide and 1,2-bis(pyridin-2-ylmethylene)hydrazine are reported.

On the importance of π-hole spodium bonding in tricoordinated HgII complexes

The synthesis and X-ray characterization of two new tri-coordinated Hg complexes where the planar Hg atom participates in π-hole spodium bonding.

Structure determination of the tetracene dimer in helium nanodroplets using femtosecond strong-field ionization

Dimers of tetracene molecules are formed inside helium nanodroplets and identified through covariance analysis of the emission directions of kinetic tetracene cations stemming from femtosecond laser-induced Coulomb explosion. Next, the dimers are aligned in either one or three dimensions under field-free conditions by a nonresonant, moderately intense laser pulse. The experimental angular covariance maps of the tetracene ions are compared to calculated covariance maps for seven different dimer conformations and found to be consistent with four of these. Additional measurements of the alignment-dependent strong-field ionization yield of the dimer narrow the possible conformations down to either a slipped-parallel or parallel-slightly rotated structure. According to our quantum chemistry calculations, these are the two most stable gas-phase conformations of the dimer and one of them is favorable for singlet fission.

Tuning Optical Properties of Chalcone Derivatives: A Computational Study

The conformational feature of noncovalent complexes of two borondifluoride chalcone derivatives was assessed using DFT-D2. The corresponding optical properties were analyzed based on time-dependent density functional theory calculations. As already described in such complexes, the π-stacking interaction existing between both fragments allowed formation of a new absorption band corresponding to the S0 → S1 transition. However, this band appears very close to the most intense band corresponding the S0 → S2 transition.

Quantum chemical exploration of formaldehyde clusters (H2 CO)n (n = 2-4)

Global exploration of equilibrium structures and interconversion pathways on the quantum chemical potential energy surface (PES) is performed for (H₂ CO)n (n = 2-4) by using the Scaled Hypersphere Search-Anharmonic Downward Distortion Following (SHS-ADDF) method. Density functional theoretical (DFT) calculations with empirical dispersion corrections (D3) yielded comparable results for formaldehyde dimer in comparison with recent detailed studies at CCSD(T) levels. Based on DFT-D3 calculations, trimer and tetramer structures and their stabilities were studied. For tetramer, a highly symmetrical S₄ structure was found as the most stable form in good accordance with experimentally determined tetramer unit in the formaldehyde crystal. © 2018 Wiley Periodicals, Inc.

Characterizing the interplay of Pauli repulsion, electrostatics, dispersion and charge transfer in halogen bonding with energy decomposition analysis

Variational energy decomposition analysis establishes charge-transfer as the origin of halogen bond strength differences that go against electrostatics.