Wide spectrum of H⋯H interactions: van der Waals contacts, dihydrogen bonds and covalency

Azido-mediated intermolecular interactions of transition metal complexes

The coordinated azido ligand has a variety of ways to establish intermolecular contacts whose nature is computationally analysed in this work on dimers of the [N3-Hg(CF3)] complex with different interactions involving only N⋯N contacts, or with an additional Hg⋯N contact. The applied tools include the molecular electrostatic map of the monomer, an energy decomposition analysis (EDA), a topological AIM analysis of the electron density and the study of NCI (non-covalent interactions) isosurfaces. The interactions between two azido ligands are found to be weakly stabilizing (by 0.2 to 2.7 kcal mol-1), topology-dependent and require dispersion forces to complement orbital and electrostatic stabilization. Those interactions are supplemented by the formation of simultaneous Hg⋯N secondary interactions by about -1 kcal mol-1, and by the ability of the monomer to simultaneously interact with several neighbours in the crystal structure.

Dihydrogen Bonding-Seen through the Eyes of Vibrational Spectroscopy

In this work, we analyzed five groups of different dihydrogen bonding interactions and hydrogen clusters with an H3+ kernel utilizing the local vibrational mode theory, developed by our group, complemented with the Quantum Theory of Atoms-in-Molecules analysis to assess the strength and nature of the dihydrogen bonds in these systems. We could show that the intrinsic strength of the dihydrogen bonds investigated is primarily related to the protonic bond as opposed to the hydridic bond; thus, this should be the region of focus when designing dihydrogen bonded complexes with a particular strength. We could also show that the popular discussion of the blue/red shifts of dihydrogen bonding based on the normal mode frequencies is hampered from mode-mode coupling and that a blue/red shift discussion based on local mode frequencies is more meaningful. Based on the bond analysis of the H3+(H2)n systems, we conclude that the bond strength in these crystal-like structures makes them interesting for potential hydrogen storage applications.

A combined QTAIM/IRI topological analysis of the effect of axial/equatorial positions of NH2 and CN substituents in the [(PY5Me2)MoO]+ complex

By means of the Interaction Region Indicator (IRI) and Quantum Theory of Atoms in Molecules (QTAIM), the influence exerted by NH₂ (amino) and CN (cyano) as electron donor and electron acceptor substituent groups, respectively, located at para-positions of axial and equatorial pyridine rings of derivatized complexes coming from the [(PY₅Me₂)MoO]⁺ complex during the hydrogen molecular release in the gas phase was analyzed. In any case, a H-H covalent bond is forming at the transition state, with a strengthening of the electron density of 5.5% when the substituent group involved is NH₂ at the para-position of the axial pyridine ring. However, there was no difference between NH₂ and CN when these substituent groups are located at the para-positions of the equatorial pyridine rings. The topological properties of electron densities from the QTAIM are not perturbed by the electron donor and electron acceptor nature of the substituents, even when these substituent groups are located at the axial or equatorial pyridine rings of the Mo-based complex.

Study of Beryllium, Magnesium, and Spodium Bonds to Carbenes and Carbodiphosphoranes

The aim of this article is to present results of theoretical study on the properties of C⋯M bonds, where C is either a carbene or carbodiphosphorane carbon atom and M is an acidic center of MX2 (M = Be, Mg, Zn). Due to the rarity of theoretical data regarding the C⋯Zn bond (i.e., the zinc bond), the main focus is placed on comparing the characteristics of this interaction with C⋯Be (beryllium bond) and C⋯Mg (magnesium bond). For this purpose, theoretical studies (ωB97X-D/6-311++G(2df,2p)) have been performed for a large group of dimers formed by MX2 (X = H, F, Cl, Br, Me) and either a carbene ((NH2)2C, imidazol-2-ylidene, imidazolidin-2-ylidene, tetrahydropyrymid-2-ylidene, cyclopropenylidene) or carbodiphosphorane ((PH3)2C, (NH3)2C) molecule. The investigated dimers are characterized by a very strong charge transfer effect from either the carbene or carbodiphosphorane molecule to the MX2 one. This may even be over six times as strong as in the water dimer. According to the QTAIM and NCI method, the zinc bond is not very different than the beryllium bond, with both featuring a significant covalent contribution. However, the zinc bond should be definitely stronger if delocalization index is considered.

Observation of Dihydrogen Bonds in High-Pressure Phases of Ammonia Borane by X-ray and Neutron Diffraction Measurements

High-pressure X-ray and neutron diffraction analyses of an ambient-pressure phase (AP) and two high-pressure phases (HP1 and HP2) of ammonia borane (i.e., NH₃BH₃ and ND₃BD₃) were conducted to investigate the relationship between their crystal structures and dihydrogen bonds. It was confirmed that the hydrogen atoms in AP formed dihydrogen bonds between adjacent molecules, and the H-H distance between the hydrogen atoms forming this interaction was shorter than 2.4 Å, which was nearly 2 times larger than the van der Waals radius of hydrogen. In the case of half of the hydrogen bonds, a phase transition from AP to the first high-pressure phase (HP1) at ∼1.2 GPa resulted in an increase in the H-H distances, which suggested that the dihydrogen bonds were broken. However, when HP1 was further pressurized to ∼4 GPa, all of the H-H distances became shorter than 2.4 Å again, which implied the occurrence of pressure-induced re-formation of the dihydrogen bonds. It was speculated that the re-formation was consistent with a second-order phase transition suggested in previous studies by Raman spectroscopy and X-ray diffraction measurement. Furthermore, at ∼11 GPa, HP1 transformed to the second high-pressure phase (HP2), and its structure was determined to be P2₁ (Z = 2). In this phase transition, the inclination of the molecule axis became larger, and the number of types of dihydrogen bonds increased from 6 to 11. At 18.9 GPa, which was close to the upper pressure limit of HP2, the shortest dihydrogen bond decreased to ∼1.65 Å. Additionally, the X-ray diffraction results suggested another phase transition to the third high-pressure phase (HP3) at ∼20 GPa. The outcomes of this study confirmed experimentally for the first time that the structural change under pressure causes the breakage and re-formation of the dihydrogen bonds of NH₃BH₃.

S-H…O and O-H…O Hydrogen Bonds-Comparison of Dimers of Thiocarboxylic and Carboxylic Acids

ωB97-XD/aug-cc-pVTZ calculations were performed on dimers of selected thiocarboxylic acids and on analogous carboxylic acids. The sample of calculated thiocarboxylic acids is an extension of the Cambridge Structural Database search that contains only a few such structures. The Natural Bond Orbital (NBO) method, Symmetry-Adapted Perturbation Theory (SAPT) approach, Non-Covalent Interaction (NCI) method and Quantum Theory of Atoms in Molecules (QTAIM) were applied additionally to analyse interactions in dimers of thiocarboxylic and carboxylic acids. The insights into crystal structures as well as into results of calculations show that the formation of S-H…O hydrogen bonds between molecules of thiocarboxylic acids is steered by the same mechanisms as the formation of much stronger O-H…O hydrogen bonds in carboxylic acids. The intramolecular O-H…O and C-H…S hydrogen bonds occurring in few considered structures are also analysed.

Two faces of triel bonds in boron trihalide complexes

The N⋅⋅⋅B triel bonds in complexes of boron trihalides, BX₃ (X = F, Cl, Br, and I), with species acting as Lewis bases through the nitrogen center, NH₃ , N₂ , and HCN, are analyzed theoretically (MP2/aug-cc-pVTZ calculations). It is confirmed that stronger Lewis acid properties of the boron center are observed for the BCl₃ moiety than for the BF₃ one in complexes with the strong Lewis base (NH₃ ); while the opposite order is observed for complexes with the weak Lewis base (N₂ ). The BX₃ NCH complexes (for X = Cl, Br, and I) are characterized by two tautomeric forms and by two corresponding N⋅⋅⋅B distances, the shorter one possesses characteristics of the covalent bond. In a case of the BF₃ NCH complex one energetic minimum is observed. Ab initio calculations are supported by an analysis of molecular electrostatic potentials (EPs) and electron density distributions. The quantum theory of 'atoms in molecules' and the decomposition of the energy of interaction are applied. The aforementioned acidity orders as well as the existence of two tautomers for some of complexes result partly from the electrostatic interactions' balance; the EP distribution is different for the BF₃ species than for the other BX₃ species where X = Cl, Br, and I. © 2017 Wiley Periodicals, Inc.

Hydrogen bonds, and σ-hole and π-hole bonds – mechanisms protecting doublet and octet electron structures

For various interactions electron charge shifts try to protect the former doublet or octet electronic structure of the Lewis acid centre.

Hydrogen and Dihydrogen Bonds in the Reactions of Metal Hydrides

The dihydrogen bond-an interaction between a transition-metal or main-group hydride (M-H) and a protic hydrogen moiety (H-X)-is arguably the most intriguing type of hydrogen bond. It was discovered in the mid-1990s and has been intensively explored since then. Herein, we collate up-to-date experimental and computational studies of the structural, energetic, and spectroscopic parameters and natures of dihydrogen-bonded complexes of the form M-H···H-X, as such species are now known for a wide variety of hydrido compounds. Being a weak interaction, dihydrogen bonding entails the lengthening of the participating bonds as well as their polarization (repolarization) as a result of electron density redistribution. Thus, the formation of a dihydrogen bond allows for the activation of both the MH and XH bonds in one step, facilitating proton transfer and preparing these bonds for further transformations. The implications of dihydrogen bonding in different stoichiometric and catalytic reactions, such as hydrogen exchange, alcoholysis and aminolysis, hydrogen evolution, hydrogenation, and dehydrogenation, are discussed.

Quantitative analysis of intermolecular interactions in orthorhombic rubrene

Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ⋯Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H-H interactions. The electron density features of H-H bonding, and the interaction energy of molecular dimers connected by H-H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.

Me3N-promoted synthesis of 2,3,4,4a-tetrahydroxanthen-1-one: preparation of thiosemicarbazone derivatives, their solid state self-assembly and antimicrobial properties

Thiosemicarbazones (5a–5j) have been synthesized from 2,3,4,4a-tetrahydroxanthen-1-one, obtained in high yield through Me₃N-promoted domino Baylis–Hillman/oxa-Michael reaction. Their solid-state self-assembly and antimicrobial properties are studied.

Fundamental relation between molecular geometry and real-space topology. Combined AIM, ELI-D, and ASF analysis of hapticities and intramolecular hydrogen-hydrogen bonds in zincocene-related compounds

Despite numerous advanced and widely distributed bonding theories such as MO, VB, NBO, AIM, and ELF/ELI-D, complex modes of bonding such as M-Cp*((R)) interactions (hapticities) in asymmetrical metallocenes or weak intramolecular interactions (e.g., hydrogen-hydrogen (H···H) bonds) still remain a challenge for these theories in terms of defining whether or not an atom-atom interaction line (a "chemical bond") should be drawn. In this work the intramolecular Zn-C(Cp*(R)) (R = Me, -(CH2)2NMe2, and -(CH2)3NMe2) and H···H connectivity of a systematic set of 12 zincocene-related compounds is analyzed in terms of AIM and ELI-D topology combined with the recently introduced aspherical stockholder fragment (ASF) surfaces. This computational analysis unravels a distinct dependency of the AIM and ELI-D topology against the molecular geometry for both types of interactions, which confirms and extends earlier findings on smaller sets of compounds. According to these results the complete real-space topology including strong, medium, and weak interactions of very large compounds such as proteins may be reliably predicted by sole inspection of accurately determined molecular geometries, which would on the one hand afford new applications (e.g., accurate estimation of numbers, types, and strengths of intra- and intermolecular interactions) and on the other hand have deep implications on the significance of the method.

Bis(4-methylanilinium) and bis(4-iodoanilinium) pentamolybdates from laboratory X-ray powder data and total energy minimization

The crystal structures of poly[bis(4-methylanilinium) [tetra-μ3-oxido-hexa-μ2-oxido-hexaoxidopentamolybdenum(VI)]], {(C7H10N)2[Mo5O16]}n, (I), and poly[bis(4-iodoanilinium) [tetra-μ3-oxido-hexa-μ2-oxido-hexaoxidopentamolybdenum(VI)]], {(C6H7IN)2[Mo5O16]}n, (II), were determined from laboratory X-ray powder diffraction data using the direct-space parallel-tempering approach and refined by total energy minimization in the solid state. Both compounds adopt layered structures, in which layers of the inorganic {[Mo5O16](2-)}n polyanion alternate with layers of the organoammonium cations parallel to the (100) plane. The asymmetric units contain three Mo atoms (one situated on a twofold axis, Wyckoff position 4e), eight O atoms and one organic cation. Despite the fact that the structure determinations are based on powder diffraction data, due to the total energy minimization approach applied the Mo-O bond lengths can formally be assigned to one of the three groups, reflecting different types of O-atom placement within the polyanion. The cations form relatively strong N-H...O hydrogen bonds, anchoring one end of the organic molecules to both terminal and shared O atoms. The interactions involving the opposite end of the benzene rings are much weaker and include C-H...O and C-H...π bonds in (I) and an I...O halogen bond in (II). Mutual rotation of the benzene rings in both structures leads to the formation of a C-H...H-C dihydrogen bond, with H-atom separations of 1.95 Å in (I) and 2.12 Å in (II). Differential scanning calorimetry measurements show that the interactions between the inorganic and organic layers are stronger in (I) than in (II).

Characteristics of X-H···π interactions: ab initio and QTAIM studies

The MP2/6-311++G(d,p) calculations were performed on several hydrogen-bonded systems. Different complexes were taken into account to analyze various types of hydrogen bonds, possessing different types of proton donors and proton acceptors as well as characterized by the broad range of the interaction energy. The Quantum Theory of Atoms in Molecules is applied. The results of the hybrid variational-perturbational approach are discussed. The unique properties of hydrogen bonds, where π-electrons act as the proton acceptor (X-H···π), are analyzed, and these interactions are compared with the other types of hydrogen bonds, mainly with C-H···Y interactions. It is shown that for X-H···π systems the ellipticity at the bond critical point of the proton···acceptor interaction is much greater than for the other types of hydrogen bonds. However, both X-H···π and C-H···Y interactions are characterized by the dominance of the dispersive energy.

Theoretical analysis of the (HNO)2, (HNO···HNS), and (HNS)2 dimers — A case of red and blue shifts of N–H stretching frequency

The hydrogen-bonded interactions in the simple (HNZ)2 dimers, with Z = O and S, were investigated using quantum chemical calculations with the second-order Møller–Plesset perturbation (MP2), coupled-cluster with single, double (CCSD), and triple excitations (CCSD(T)) methods in conjunction with the 6-311++G(2d,2p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets. Six-membered cyclic structures were found to be stable complexes for the dimers (HNO)2, (HNS)2, and (HNO–HNS). The pair (HNS)2 has the largest complexation energy (–11 kJ/mol), and (HNO)2 the smallest one (–9 kJ/mol). A bond length contraction and a frequency blue shift of the N–H bond simultaneously occur upon hydrogen bond formation of the N–H···S type, which has rarely been observed before. The stronger the intramolecular hyperconjugation and the lower the polarization of the X–H bond involved as proton donor in the hydrogen bond, the more predominant is the formation of a blue-shifting hydrogen bond.