Cooperativity in Hydrogen-Bonded Interactions: Ab Initio and “Atoms in Molecules” Analyses

Modulating of the pnicogen-bonding by a H⋯π interaction: An ab initio study

An ab initio study of the cooperativity in XH₂P⋯NCH⋯Z and XH₂P⋯CNH⋯Z complexes (X=F, Cl, Br, CN, NC; Z=C₂H₂,C₆H₆) connected by pnicogen-bonding and H⋯π interactions is carried out by means of MP2 computational method. A detailed analysis of the structures, interaction energies and bonding properties is performed on these systems. For each set of the complexes considered, a favorable cooperativity is observed, especially in X=F and CN complexes. However, for a given X or Z, the amount of cooperativity effects in XH₂P⋯CNH⋯Z complexes are more important than XH₂P⋯NCH⋯Z counterparts. Besides, the influence of a H⋯π interaction on a P⋯N (C) bond is more pronounced than that of a P⋯N (C) bond on a H⋯π bond. The quantum theory of atoms in molecules shows that ternary complexes have increased electron densities at their bond critical points relative to the corresponding binary systems. The results also indicate that the strength of the P⋯N(C) and H⋯π interactions increases in the presence of the solvent.

Theoretical aspects of the enhancement of metal binding affinity by intramolecular hydrogen bonding and modulating pKavalues

The stability balance shows that the hydrogen bond network and modulation of pK_avalues can enhance the metal binding affinity.

Conciliatory Inductive Model Explaining the Origin of Changes in the η(2)-SiH Bond Length Caused by Presence of Strongly Electronegative Atoms X (X = F, Cl) in Cp(OC)2Mn[η(2)-H(SiH3-nXn)] (n = 0-3) Complexes

Using three theoretical methods, QTAIM, IQA, and NCI, we analyze an influence of halogen atoms X (X = F, Cl) substituted at various positions in the -SiH3-nXn group on the charge density distribution within the η(2)-SiH bond and on the SiH bond energies in Cp(OC)2Mn[η(2)-H(SiH3-nXn)] complexes and isolated HSiH3-nXn molecules. It is shown that shortening of the η(2)-SiH bond in Cp(OC)2Mn[η(2)-H(SiH3-nXn)] complexes should be considered as a normal inductive result of halogenation. This η(2)-SiH bond's compression may, however, be overcome by a predominant elongation resulting from a contingent presence of a halogen atom at position trans to the η(2)-SiH bond. This trans effect is particularly large for bulky and highly polarizable chlorine. Moreover, peculiar properties of the trans chlorine atom are manifested in several ways. To explain the origin of all the observed changes in both the length and the electron charge distribution of the η(2)-SiH bond in investigated Cp(OC)2Mn[η(2)-H(SiH3-nXn)] complexes a new model, called the Conciliatory Inductive Model, is being proposed.

Nature of intramolecular interactions of vitamin C in view of interacting quantum atoms: the role of hydrogen bond cooperativity on geometry

The conformational analysis of six dihedral angles was calculated by second-order Moller-Plesset perturbation theory (MP2) with the correlation-consistent aug-cc-pVDZ basis set. The quantum theory of atoms in molecules (QTAIM) was applied to gain a description of the atoms and chemical bonds. A high content of hydroxyl groups in vitamin C's (VC) structure leads to a wide range of intramolecular interactions. The nature of these interactions within the selected VC conformers was studied in view of the interacting quantum atom (IQA) approach. Complete IQA analysis of the atomic and interatomic interaction energies indicated hydrogen bond formation was responsible for the stability of most of the local minima in the potential energy surface. In these conformers, the tandem participation of interactions was operating by way of two- or three-centered (bifurcated) cooperative networks. For the intramolecular hydrogen bond interplay in cooperativity, changes of the IQA atomic and interatomic interaction energies of the participant interactions were monitored during the formation of cooperative networks. The results of the intramolecular cooperativity were evaluated with changes of the delocalization index and bond distances.

A theoretical study of weak interactions in phenylenediamine homodimer clusters

Utilizing dispersion-corrected density functional theory (DFT) calculations, we demonstrate the weak intermolecular interactions of phenylenediamine dimer (pdd) clusters, emphasizing the local lowest energy structures and decomposition of interaction energies by natural bond orbital (NBO) and atoms in molecule (AIM) analyses.

Charge-controlled switchable methane adsorption on heteroatom-doped BNNSs

The adsorption behavior of methane (CH₄) on neutral and charged states of Al-, C-, P- and Si-doped boron nitride nanosheets (BNNSs), is investigated using the density functional theory (DFT) method.

Experimental and theoretical charge density distribution in Pigment Yellow 101

The charge density distribution in 2,2'-dihydroxy-1,1'-naphthalazine (Pigment Yellow 101; P.Y.101) has been determined using high-resolution X-ray diffraction and multipole refinement, along with density functional theory calculations. Topological analysis of the resulting densities highlights the localisation of single/double bonds in the central C=N-N=C moiety of the molecule in its ground state. The density in the N-N is examined in detail, where we show that very small differences between experiment and theory are amplified by use of the Laplacian of the density. Quantification of hydrogen bonds highlights the importance of the intramolecular N-H···O interaction, known to be vital for retention of fluorescence in the solid state, relative to the many but weak intermolecular contacts located. However, a popular method for deriving H-bond strengths from density data appears to struggle with the intramolecular N-H···O interaction. We also show that theoretical estimation of anisotropic displacements for hydrogen atoms brings little benefit overall, and degrades agreement with experiment for one intra-molecular contact.

A new strategy for hydrogen storage using BNNS: simultaneous effects of doping and charge modulation

The adsorption behavior of hydrogen molecule (H₂) on neutral and charged states of C-, Si- and P-doped boron nitride nanosheets (BNNSs), is investigated using density functional theory (DFT) method.

What causes the weakest host to act as the strongest one? A theoretical study on the host-guest chemistry of five azacryptands and fluoride anions

In this work we have attempted to computationally analyze the important parameters affecting the selectivity in host-guest systems in order to show that the solvent effect in some host-guest systems is even more important than the hole-size fitting and/or host-guest interaction energy. For this purpose, the fluoride anion selectivities of the five most studied azacryptands with different affinities, moieties, cavity sizes and degrees of preorganization, in their fully protonated forms, were studied at PBE/TZVP and B3P86/TZVP levels of theory. The factors affecting the selectivity such as hole size fitting, steric effects, electronic properties, preorganization of hosts, as well as solvent effects were investigated. The results showed that among the five studied azacryptands, one of them, which ranks fifth for selectivity according to its weak interaction energy with fluoride anions, ranks fourth due to its good preorganization. However, a surprising improvement occurs when its selectivity for fluoride anions ranks first due to the existence of less solvent hindrance. The results of the calculations were further confirmed by a good correlation between the calculated and experimental formation constants.

Supramolecular self-assembly of linear oligosilsesquioxanes on mica--AFM surface imaging and hydrophilicity studies

Linear oligomeric [2-(carboxymethylthio)ethylsilsesquioxanes] (LPSQ-COOH) adsorb spontaneously on muscovite mica and form smooth, well-ordered lamellar structures at the liquid-solid interface. Side carboxylic groups, having donor-acceptor character with regard to hydrogen bonds, are engaged both in multipoint molecule-to-substrate interactions and intermolecular cross-linking. The unique arrangement of silsesquioxane macromolecules, with COOH groups situated at the interface with air, produces highly hydrophilic surfaces of good thermal and solvolytic stability. Supramolecular assemblies of LPSQ-COOH were studied using atomic force microscopy (AFM), angle-resolved X-ray photoelectron spectroscopy (ARXPS) and attenuated total reflectance (ATR) FTIR spectroscopy. Comparative height profile analysis combined with ATR-FTIR studies of the spectral regions characteristic of carboxylic groups and C1s core level envelope by XPS confirmed specific interactions between LPSQ-COOH and mica.

Bonding Motifs of Noble-Gas Compounds As Described by the Local Electron Energy Density

The bonding situation of some exemplary noble-gas (Ng) compounds, including HNg(+), HNgF, FNgO(-), Ng-HF, and NgBeO (Ng = He-Xe) was assayed by examining their local electron energy density H(r). In general, this function partitions the space of atomic species (neutral and ionic) into inner regions of negative values and outer regions of positive values. In the formation of chemical bonds, these atomic regions combine so to form a molecular H(r), Hmol(r), whose plotted form naturally shows the "covalent" and "noncovalent" regions of the molecular species and allows also the recognition of different types of noncovalent interactions such van der Waals, hydrogen, and ionic or partially ionic bonds. The qualitative assignment of the various bonding motifs is corroborated by the topological analysis of Hmol(r), which typically includes several critical points of rank 3 and variable signature. These points are, in particular, characterized here in terms of their bond degree (BD). From a previous definition (Espinosa J. Chem. Phys. 2002, 117, 5529-5542), this quantity is taken as the ratio between the energy density calculated at the critical point of H(r), H(rc), and the corresponding electron density ρ(rc): BD = -H(rc)/ρ(rc). Thus, the BD is positive for covalent interactions (H(rc) < 0) and negative for noncovalent interactions (H(rc) > 0). For structurally related species, the BD result, in general, positively correlated with the binding energies and is, therefore, a semiquantitative index of stability. The present study suggests the general validity of the Hmol(r) to effectively assay the bonding motifs of noble-gas compounds.

Hydrogen trapping ability of the pyridine-lithium⁺ (1:1) complex

Theoretical studies have been carried out at different levels of theory to verify the hydrogen adsorption characteristics of pyridine-lithium ion (1:1) complexes. The nature of interactions associated with the bonding between pyridine and lithium as well as that between lithium and adsorbed molecular hydrogen is studied through the calculation of electron density and electron-density-based reactivity descriptors. The pyridine-lithium ion complex has been hydrogenated systematically around the lithium site, and each lithium site is found to adsorb a maximum of four hydrogen molecules with an interaction energy of ∼-4.0 kcal/mol per molecule of H2. The fate of the hydrogen adsorbed in a pyridine-lithium ion complex (corresponding to the maximum adsorption) is studied in the course of a 2 ps time evolution through ab initio molecular dynamics simulation at different temperatures. The results reveal that the complex can hold a maximum of four hydrogen molecules at a temperature of 77 K, whereas it can hold only two molecules of hydrogen at 298 K.

Complexes of the noble gases with H3O+: a theoretical investigation on Ng(H3O+) (Ng = He-Xe)

The geometries, harmonic vibrational frequencies, and binding energies (Bes) of the Ng(H(3)O(+)) complexes (Ng = He-Xe) were investigated at the coupled cluster level of theory, and their bonding situation was assayed by various methods of bonding analysis. The effects of Ng on H(3)O(+) progressively increase from He to Xe, and only He can be regarded as an essentially "innocent" ligand. The binding energies also increase in the same periodic order, and are by far dominated by the "noncovalent" ion-induced dipole interaction arising from the H(3)O(+)-induced polarization of Ng. For Ne, Ar, Kr, and Xe, this term has a larger contribution from the p orbital lying on the bond axis, and two smaller contributions from the p orbitals perpendicular to the bond axis. For the heaviest Ar(H(3)O(+)), Kr(H(3)O(+)), and Xe(H(3)O(+)), BE also has a "covalent" component, which is ascribed to the relatively-appreciable charge transfer from Ng to H(3)O(+).

Estimating the binding ability of onium ions with CO2 and π systems: a computational investigation

The impact of increasing methyl substitution on onium ions in their complexes with CO₂ and aromatic systems has been analyzed using DFT calculations.

Dynamic and static behavior of hydrogen bonds of the X–H⋯π type (X = F, Cl, Br, I, RO and RR′N; R, R′ = H or Me) in the benzene π-system, elucidated by QTAIM dual functional analysis

The nature of the X–H-*-π interactions in X–H-*-π(C₆H₆) (X = F, Cl, Br, I, HO, MeO, H₂N, MeHN and Me₂N) was elucidated by applying QTAIM dual functional analysis. The interactions were all classified by pure closed-shell interactions and characterized to have the vdW nature.

Cooperative effects in hydrogen bond and pnicogen bond: a comparative study

A comparative study of the cooperative effects of hydrogen and pnicogen bonding on open-chain clusters of (PH2CN)n=2–7 and (HCN)n=2–7 is performed at the MP2/6-311++G(d,p) level of theory. These effects are studied in terms of geometric and energetic properties, electron density analysis, and 15N chemical shielding parameters of the clusters at the MP2/6-311++G** level. The intermolecular distances observed in the (HCN)n clusters exhibit quite larger bond contractions than those found in the (PH2CN)n clusters. Our results strongly suggest that cooperative effects induced by pnicogen and hydrogen bonds are significant in both linear PH2CN and HCN clusters, respectively. They also provide some evidence that these effects seem to reach a limit for a relatively small number of monomers. The n-dependent variation in the 15N chemical shielding tensor should serve as a useful signature of cooperativity effects in the PH2CN and HCN clusters.

Theoretical study on the properties and stabilities of complexes formed between SO4(C2v) and isostructure species of CO2, CS2, and SCO

In this work ab initio calculations at MP2 level in conjugation with aug-cc-pVXZ (X=D and T) basis set were performed in order to examine complexes formed between SO4 and each of linear molecules of CO2, CS2, and SCO. The results have been discussed on real minima located on singlet potential energy surface (PES). Single-point energy calculations at the MP2/aug-cc-pVTZ level uphold results obtained at the MP2/aug-cc-pVDZ level. The atom in molecules theory (AIM) was utilized to analyze the nature of intermolecular interactions. Also, natural bond orbital (NBO) analysis has been used in order to get charge transfer quota in complexes. The results show that the atmospheric role of SO4-CS2 system is more important than those followed by SO4-SCO and SO4-CO2, respectively.

Investigation of hydrogen bonds properties in the terephthalic acid crystal, using molecular dynamics method

The aim of this study was to perform calculations using the method of Car-Parrinello molecular dynamics, leading to the optimized geometry of the molecules of 1,4-benzenedicarboxylic acid (terephthalic acid) in crystals, for the hydrogen form and three variants of substitution of deuterium atoms inside a carboxyl group. Based on the results, trajectories and dipole moments were calculated, what makes possible to simulate vibrations in different systems, and to make calculation of theoretical infrared spectra and atomic power spectra. Theoretical results were compared with the experimental spectra, which verifies the correctness of the method and also was compared with the results obtained by quantum-mechanical calculations using DFT for the isolated dimer. Comparison of the spectra of different forms, allowed for in-depth analysis of the effect of isotopic substitution on the frequency of vibrations and shapes of bands, and confirm the presence of possible coupling effects and intra- and intermolecular interactions. Comparison with the DFT results for the dimer show influence of the crystal structure on the spectra.