Charge-inverted hydrogen bond vs. other interactions possessing a hydridic hydrogen atom

Hydrogen bond types which do not fit accepted definitions

There are various interactions that either partially fit or do not fit the currently accepted definitions of the hydrogen bond. However, they possess characteristics of this interaction. It seems that it is partly connected to the fact that these definitions are not precise. The typical 3c-4e (three centres - four electrons) A-H⋯B hydrogen bond is characterized by the single-atom A and B centres that are highly electronegative. On the other hand, non-typical interactions that do not fit the hydrogen bond definitions well are characterised by uncommon proton donors and/or proton acceptors. The cases of multi-centre proton acceptors, π-electron or σ-electron systems are well known - such interactions are designated as A-H⋯π and A-H⋯σ hydrogen bonds, respectively. However, the cases of interactions with the multi-centre proton donors and proton acceptors do not fit the majority of definitions of hydrogen bond. The π⋯H+⋯π system in the proton-bound homodimer of acetylene is an example. This system can be classified as a hydrogen bond according to the two-sites hydrogen bond, 2sHB, definition. There are various types of interactions discussed in this review; among them, those that are undoubtedly unclassified as hydrogen bonds, i.e., hydride bonds, and charge inverted hydrogen bonds, CIHBs. Special emphasis is also put here on the proton sponges and other systems such as the [FHF]- anion or [NgHNg]+ cation (Ng is the noble gas centre).

Small-pore hydridic frameworks store densely packed hydrogen

Nanoporous materials have attracted great attention for gas storage, but achieving high volumetric storage capacity remains a challenge. Here, by using neutron powder diffraction, volumetric gas adsorption, inelastic neutron scattering and first-principles calculations, we investigate a magnesium borohydride framework that has small pores and a partially negatively charged non-flat interior for hydrogen and nitrogen uptake. Hydrogen and nitrogen occupy distinctly different adsorption sites in the pores, with very different limiting capacities of 2.33 H2 and 0.66 N2 per Mg(BH4)2. Molecular hydrogen is packed extremely densely, with about twice the density of liquid hydrogen (144 g H2 per litre of pore volume). We found a penta-dihydrogen cluster where H2 molecules in one position have rotational freedom, whereas H2 molecules in another position have a well-defined orientation and a directional interaction with the framework. This study reveals that densely packed hydrogen can be stabilized in small-pore materials at ambient pressures.

Theoretical Insights into Bifurcated Intramolecular Dihydrogen Bonds

Two-ring intramolecular π-electron delocalization assisted dihydrogen bonds existing in (1Z,4Z)-1,4-dipentene-3-bora-1,5-diol and its symmetrically substituted derivatives have been analysed here since the MP2/6-311++G(d,p) calculations on these systems were performed. The influence of the coexistence of two intramolecular dihydrogen bonded rings in these molecular structures on properties of intramolecular dihydrogen bonds as well as on the π-electron delocalization within these rings was investigated. The comparison with corresponding structures of typical two-ring, so-called resonance-assisted, RAHB, systems was performed. The results of calculations show that such rings' coexistence leads to the weakening of dihydrogen bonds, similarly as for the typical two-ring RAHB systems. The Quantum Theory of ''Atoms in Molecules'' (QTAIM) was also applied here to get more details about the nature of dihydrogen bonds. Correlations between dihydrogen bond strength measures and other energetic, geometrical and topological parameters were also analysed. It was found that characteristics of bond critical points as well as of ring critical points are useful to estimate the strength of intramolecular dihydrogen bonds in two-ring dihydrogen bonded systems discussed here. The Natural Bond Orbital, NBO, approach parameters are also discussed as useful ones to describe properties of dihydrogen bonded systems.

Si-H···Se Chalcogen-Hydride Bond Quantified by Diffraction and Topological Analyses

The Si-H···Se contact in 1-mesitylselanyl-8-(dimethylsilyl)naphthalene (1), which exhibits the spatial arrangement of a δ-agostic interaction from geometric considerations, was investigated. Is this just enforced by close 1,8-proximity or is this a favorable interaction? Charge density studies are best suited to investigate the exact origin of the interaction and to quantify the properties. Hence, they are most elucidating. High-resolution X-ray diffraction data of 1 were collected, and a multipole refinement followed by a topological analysis using Bader's quantum theory of atoms in molecules was employed. The resulting bond properties were set in relation to high-level computational parameters. The comparison to Si-H···[M] agostics, hydride bonding, chalcogen bonds, and charge-inverted hydrogen bonds qualified the Si-H···Se noncovalent interaction to be best classified as a chalcogen-hydride bond.

Charge-Inverted Hydrogen-Bridged Bond in HCa(μ-H)3E (E = Si, Ge, and Sn): Matrix Isolation Infrared Spectroscopic and Theoretical Studies

Matrix isolation infrared spectroscopy combined with quantum-chemical calculations were employed to study the reactions of calcium atoms with silane, germane, and stannane in a 4 K argon matrix. The ion pairs [HCa]⁺ and [EH₃]^- (E = Si, Ge, and Sn) in both the classical structure HCaEH₃ and the bridged structure HCa(μ-H)₃E were identified based on the H/D isotopic substitution experiments and quantum-chemical calculations. The results show that the reaction between ground-state Ca and EH₄ proceeds inefficiently, and only after the photolytic activation of Ca atoms to the Ca(¹P:4s4p) state does insertion occur to give HCaEH₃, which rearranges to HCa(μ-H)₃E upon photolysis. Topological analysis of the electronic structure suggests that the nonclassical structure HCa(μ-H)₃E is formed by the electrostatic interaction with charge-inverted hydrogen bridge bond, while HCaEH₃ is dominated by (HCa)⁺(EH₃)^- ion pair interactions.

Microsolvation of Histidine—A Theoretical Study of Intermolecular Interactions Based on AIM and SAPT Approaches

Histidine is unique among amino acids because of its rich tautomeric properties. It participates in essential enzymatic centers, such as catalytic triads. The main aim of the study is the modeling of the change of molecular properties between the gas phase and solution using microsolvation models. We investigate histidine in its three protonation states, microsolvated with 1:6 water molecules. These clusters are studied computationally, in the gas phase and with water as a solvent (Polarizable Continuum Model, PCM) within the Density Functional Theory (DFT) framework. The structural analysis reveals the presence of intra- and intermolecular hydrogen bonds. The Atoms-in-Molecules (AIM) theory is employed to determine the impact of solvation on the charge flow within the histidine, with emphasis on the similarity of the two imidazole nitrogen atoms—topologically not equivalent, they are revealed as electronically similar due to the heterocyclic ring aromaticity. Finally, the Symmetry-Adapted Perturbation Theory (SAPT) is used to examine the stability of the microsolvation clusters. While electrostatic and exchange terms dominate in magnitude over polarization and dispersion, the sum of electrostatic and exchange term is close to zero. This makes polarization the factor governing the actual interaction energy. The most important finding of this study is that even with microsolvation, the polarization induced by the presence of implicit solvent is still significant. Therefore, we recommend combined approaches, mixing explicit water molecules with implicit models.

Study of the influence of intermolecular interaction on classical and reverse substituent effects in para-substituted phenylboranes

The substituent effect and the reverse substituent effect in para-substituted phenylboranes and the influence of the intermolecular interaction of H⋯B type with either silane or methylsilane on the latter of these effects are extensively studied.

Physical nature of silane⋯carbene dimers revealed by state-of-the-art ab initio calculations

Using the SAPT2 + 3(CCD)δMP2 method in complete basis set (CBS) limit, it is shown that the interactions in the recently studied silane⋯carbene dimers are mainly dispersive in nature. Consequently, slow convergence of dispersion energy also forces slow convergence of the interaction energy. Therefore, obtaining very accurate values requires extrapolation of the correlation part to the CBS limit. The most accurate values obtained at the CCSD(T)/CBS level of theory show that the studied silane⋯carbene dimers are rather weakly bound, with interaction energies ranging from about -1.9 to -1.3 kcal/mol. Comparing to CCSD(T)/CBS, it will be shown that SCS-MP2 and MP2C methods clearly underestimate and methods based on SAPT2+ and having some third-order corrections, as well as the MP2 method, overestimate values of interaction energies. Popular SAPT(DFT) method performs better than SCS-MP2 and MP2C; nevertheless, underestimation is still considerable. The underestimation is slightly quenched if third-order dispersion energy and its exchange counterpart is added to the SAPT(DFT). The closest value of CCSD(T)/CBS has been given by the SAPT2 + (3)(CCD)δMP2 method in quadruple-ζ basis set. © 2019 Wiley Periodicals, Inc.

On the Uselessness of Bond Paths Linking Distant Atoms and on the Violation of the Concept of Privileged Exchange Channels

We refer to frequently used determinants suggesting dominant interactions between distant atoms in various dimers. First of all, we show, against the still-prevailling opinion, that, in general, bond paths have nothing in common with dominant intermolecular interactions and therefore they are useless in such cases. Quite the contrary, reliable information about dominant intermolecular interactions can be obtained by means of electrostatic potential maps, which very convincingly explain mutual orientation of molecules in a dimer. For the first time, numerous examples of interactions that violate both the concept of privileged exchange channels proposed by Pendás and his collaborators as well as inequalities obtained by Tognetti and Joubert for the β parameter related to secondary interactions are presented. The possible cause of this violation is suggested. We also show that the so-called counterintuitive bond paths result from quite natural behavior of the electron density gradient vector, i. e. searching for those areas of space that are characterized by large values of electron density or the most expanded its distributions.

Bond paths between distant atoms do not necessarily indicate dominant interactions

The goal of the article is to revive discussion on the interpretation of bond paths linking distant atoms, particularly tracing weak interactions in dimers. According to the Pendás' concept of privileged exchange channel, a bond path is formed between this pair of competing atoms, which is associated with larger value of the exchange energy. We point out that, due to the short-range nature of the exchange energy, bond paths linking distant atoms clearly become doubtful indicators of dominant intermolecular interactions, particularly if some other characteristics (geometric, spectroscopic, based on electrostatic parameters, etc.) indicate other intermolecular interactions as dominant. Several such cases are thoroughly investigated. We show that electrostatic parameters are much more reliable indicators of dominant intermolecular interactions than bond paths. Then, we pay attention that the presence of ("unexpected", i.e., not necessarily indicating dominant intermolecular interactions) bond paths between pairs of atoms featuring highly expanded charge distributions can be easily explained by visual exploration of isodensity contour plots. As always pointing in the direction of the steepest increase, the gradient vector of the electron density favors areas of its high values gaining higher exchange energy, yet being blind to highly electron deficient areas nearby, which, however, can quite often be involved in dominant intermolecular interactions as strongly suggested by many other bonding analysis. We also suggest that an interatomic component of Hellmann-Feynman force would most likely be the most reliable indicator of attractive or repulsive character of individual interatomic interaction. © 2018 Wiley Periodicals, Inc.

Hydride-Triel Bonds

In this article, we present the results of our comprehensive studies of 72 dimers of the R3XXH⋯YR3Y type (X = Si, Ge; Y = B, Al, Ga; R^X  = H, Cl, Me; R^Y  = H, F, Cl, Me) and featuring hydride-triel bonds (i.e., charge-inverted hydrogen bonds). Influence of X and Y atoms as well as R^X and R^Y substituents on various properties of these dimers is investigated in detail. In particular the strength of the H⋯Y hydride-triel bonds is paid a close attention and it is shown that hydride-triel bonds can be strong enough to considerably determine structure and properties of molecular systems. In addition, properties of the investigated dimers are largely governed by the charge transfer from the Lewis base to the Lewis acid, which is particularly important if more bulky and polarizable R^Y and Y atoms are present in the YR3Y molecule. Several excellent linear (R² close to 1) and exponential correlations between pairs of diverse parameters are presented. Few instances are discussed where somewhat unexpected bond paths exist between two atoms featuring partial negative charges (e.g., between hydride hydrogen and halogen and between lateral sides of two halogens) showing that in some cases a bond path prefers to link two closely spaced electron-rich atoms instead of two atoms that are expected to form a bond. © 2018 Wiley Periodicals, Inc.

Attractive PHHP interactions revealed by state-of-the-art ab initio calculations

We report in this work a combined structural and state-of-the-art computational study of homopolar P-HH-P intermolecular contacts. Database surveys have shown the abundance of such surprisingly unexplored contacts, which are usually accompanied by other weak interactions in the solid state. By means of a detailed theoretical study utilizing SAPT(DFT), MP2, SCS-MP2, MP2C and CCSD(T) methods and both aug-cc-pVXZ and aug-cc-pCVXZ (X = D, T, Q, 5) basis sets as well as extrapolation to the CBS limit, we have shown that P-HH-P contacts are indeed attractive and considerably strong. SAPT(DFT) calculations have revealed the dispersive nature of the P-HH-P interaction with only minor contribution of the inductive term, whereas the first-order electrostatic term is clearly overbalanced by the first-order exchange energy. In general the computed interaction energies follow the trend: E ≈ E < E < E. Our results have also shown that the aug-cc-pVDZ (or aug-cc-pCVDZ) basis set is not yet well balanced and that the second-order dispersion energy term is the slowest converging among all SAPT(DFT) energy components. Compared to aug-cc-pVXZ basis sets, their core-correlation counterparts have a modest influence on all supermolecular interaction energies and a negligible influence on both the SAPT(DFT) interaction energy and its components.

Revealing the physical nature and the strength of charge-inverted hydrogen bonds by SAPT(DFT), MP2, SCS-MP2, MP2C, and CCSD(T) methods

The physical nature of charge-inverted hydrogen bonds in H₃ XH ⋯YH₃ (X = Si, Ge; Y = Al, Ga) dimer systems is studied by means of the SAPT(DFT)-based decomposition of interaction energies and supermolecular interaction energies based on MP2, SCS-MP2, MP2C, and CCSD(T) methods utilizing dimer-centered aug-cc-pCVnZ (n = D, T, Q) basis sets as well as an extrapolation to the complete basis set limit. It is revealed that charge-inverted hydrogen bonds are inductive in nature, although dispersion is also important. Computed interaction energies form the following relation: EintSAPT<EintSCS-MP2≤EintMP2C<EintMP2≈EintCCSD(T). It is confirmed that the aug-cc-pCVDZ basis set performs poorly and that very accurate values of interaction and dispersion energies require basis sets of at least quadrupole-ζ quality. Considerably large binding energies suggest potential usefulness of charge-inverted hydrogen bonds as an important structural motif in molecular binding. Terminology applying to σ- and π-hole interactions as well as to triel and tetrel bonds is discussed. According to this new terminology the charge-inverted hydrogen bond would become the first described case of a hydride-triel bond. © 2017 Wiley Periodicals, Inc.

Planar-chiral ferrocenylphosphine-borane complexes featuring agostic-type B–H⋯E (E = Hg, Sn) interactions

Ferrocenylphosphine-borane adducts with Lewis acidic organotin and organomercury substituents inortho-position show rare agostic-type B–H⋯E (E = Sn, Hg) interactions that have been studied by single crystal XRD, multinuclear solution NMR, and computational methods.

The nature of NO-bonding in N-oxide group

The nature of the NO-bond in the N-oxide group was investigated by means of combined theoretical calculations (including QTAIM and NBO approaches) and statistical analyses of the contents of crystal structure databases. The N-O bond in the N-oxide group should be classified as the NO donating bond with an important contribution of ON back-donation (of the π-electron type, when available). The visualization of the Laplacian of electron density in the region of an oxygen valence sphere suggests the presence of two lone pairs for the imine-N-oxide group (characterized by effective ON back-donation). A detailed bonding analysis performed by means of natural resonance theory indicates that the N→O bond is of an order of magnitude clearly greater than 1. In addition, the stability of the N→O bond in various N-oxides was estimated. The analyses of the hydrogen- and halogen-bonded complexes of the N-oxides reveal strong Lewis basicity of the N-oxide group. The formation of H- and X-bonding leads to N→O bond elongation due to its structural, topological and spectroscopic characteristics. Moreover, in pyridine-N-oxide, the electron-withdrawing -NO2 group additionally stabilizes the N→O bond, whereas the opposite effect can be observed for the electron-donating-NH2 substituent. This is due to a substituent effect on the π-type ON back-donation. As a result, the oxygen atom in pyridine-N-oxide may change its availability during intermolecular interaction formation, as revealed in the interaction energy, which changes by about half of the estimated total interaction energy.

QTAIM-based comparison of agostic bonds and intramolecular charge-inverted hydrogen bonds

Using DFT-based calculations with seven exchange-correlation functionals (BP86, B3LYP, B3PW91, PBE0, TPSSh, M06-L, M06) we have performed comparative studies on α-, β-, γ-, and δ-agostic bonds (ABs) and intramolecular charge-inverted hydrogen bonds (IMCIHBs). Our detailed analysis of values of QTAIM parameters computed at bond (BCP) and ring critical points (RCP) as well as of the curvatures of bond paths tracing agostic bonds and intramolecular charge-inverted hydrogen bonds gives the opportunity to distinguish between both these types of interactions. In the case of molecules with agostic bonds, the BCP is significantly closer to the agostic hydrogen, whereas in systems with IMCIHB the BCP is, instead, somewhat closer to the metal atom. Agostic bonds are characterized by H···M bond paths being straight in the BCP···M section and then highly curved near the agostic hydrogen, whereas in the case of IMCIHB any substantial curvature of BP in the vicinity of hydrogen is not present. Quite the contrary, the significant curvature of BP near the metal atom can be obtained, instead. One can also distinguish IMCIHBs and ABs on the basis of values of bond ellipticity at BCP and the electron density at RCP which are either somewhat (PBE0) or considerably (M06) greater for the latter type of interaction. It has also been shown that, in general, the exchange-correlation functional has small influences on most of QTAIM parameters computed at BCP and RCP. More significant influences have only been obtained for Laplacian of the electron density, some its components, and the bond ellipticity.