Cooperative and substitution effects in enhancing strengths of halogen bonds in FCl⋯CNX complexes

In this paper, the cooperative effect of halogen bond with hydrogen bond has been used to make a halogen bond in FCl-CNH dimer vary from a chlorine-shared one to an ion-pair one. The halogen bond is strengthened in FCl-CNH-CNH trimer and its maximal interaction energy equals to -76 kJ∕mol when the number of CNH in FCl-CNH-(CNH)(n) polymer approaches infinity. Once the free H atom in FCl-CNH-CNH trimer is replaced with alkali metals, the halogen bond becomes strong enough to be an ion-pair one in FCl-CNH-CNLi and FCl-CNH-CNNa trimers. An introduction of a Lewis acid in FCl-CNH dimer has a more prominent effect on the type of halogen bond. A prominent cooperative effect is found for the halogen bond and hydrogen bond in the trimers. FH-FCl-CNH-CNH and FH-FCl-CNH-CNLi tetramers have also been studied and the interaction energy of halogen bonding in FH-FCl-CNH-CNLi tetramer is about 12 times as much as that in the FCl-CNH dimer. The atoms in molecules and natural bond orbital analyses have been carried out for these complexes to understand the nature of halogen bond and the origin of the cooperativity.     

Enhancing effects of π-hole tetrel bonds on the σ-hole interactions in complexes involving F2TO (T = Si,Ge, Sn)

Structural Chemistry - The bimolecular and termolecular complexes involving F2TO (T = Si, Ge, Sn) and XCN/BrY (X = H, Br, CH3, and PH2; Y = F, CN, OH, and H)...     

A theoretical evidence for mutual influence between S···N(C) and hydrogen/lithium/halogen bonds: competition and interplay between π-hole and σ-hole interactions

Ab initio calculations were performed to investigate the cooperativity between the S···N(C) bond and the hydrogen/lithium/halogen bond interactions in O₂S···NCX···NCH and O₂S···CNX···CNH triads (X=H, Li, Cl, and Br). To understand the properties of the systems better, the corresponding dyads are also studied. It is evident that the lithium bond has a bigger influence on the chalcogen bond than vice versa. The results indicate that the enhanced interaction energies of the S···N(C) and X···N(C) interactions in the triad increase in the order NCCl < NCBr < NCH < NCLi and CNCl < CNBr < CNH < CNLi. This is the order of the increasing positive electrostatic potential V _S,max on the X atom. The nature of S···N(C) and X···N(C) interactions of the complexes is unveiled by energy decomposition analysis and natural bond orbital (NBO) theory. The cooperativity between both types of interaction is chiefly caused by the electrostatic effects.     

Noncovalent functionalization of graphene via π-hole···π and σ-hole···π interactions

Physisorption of bromopentafluorobenzene (C₆F₅Br) on graphene can occur due to the unique σ-hole and π-hole characters of C₆F₅Br and the rich π-electrons region of graphene, leading to the formation of three types of π-hole···π and σ-hole···π interactions. The π-hole···π interactions are even stronger than the σ-hole···π interactions. The property of graphene was significantly affected by such physisorption.

     

Competition and interplay between σ-hole and π-hole interactions: a computational study of 1:1 and 1:2 complexes of nitryl halides (O2NX) with ammonia

Quantum calculations at the MP2/cc-pVTZ, MP2/aug-cc-pVTZ, and CCSD(T)/cc-pVTZ levels have been used to examine 1:1 and 1:2 complexes between O(2)NX (X = Cl, Br, and I) with NH(3). The interaction of the lone pair of the ammonia with the σ-hole and π-hole of O(2)NX molecules have been considered. The 1:1 complexes can easily be differentiated using the stretching frequency of the N-X bond. Thus, those complexes with σ-hole interaction show a blue shift of the N-X bond stretching whereas a red shift is observed in the complexes along the π-hole. The SAPT-DFT methodology has been used to gain insight on the source of the interaction energy. In the 1:2 complexes, the cooperative and diminutive energetic effects have been analyzed using the many-body interaction energies. The nature of the interactions has been characterized with the atoms in molecules (AIM) and natural bond orbital (NBO) methodologies. Stabilization energies of 1:1 and 1:2 complexes including the variation of the zero point vibrational energy (ΔZPVE) are in the ranges 7-26 and 14-46 kJ mol(-1), respectively.     

Comparison of σ-hole and π-hole tetrel bonds in complexes of borazine with TH3F and F2TO/H2TO (T = C,Si, Ge)

The complexes between borazine and TH₃F/F₂TO/H₂TO (T = C, Si, Ge) are investigated with high-level quantum chemical calculations. Borazine has three sites of negative electrostatic potential: the N atom, the ring center, and the H atom of the B H bond, whereas TH₃F and F₂TO/H₂TO provide the σ-hole and π-hole, respectively, for the tetrel bond. The N atom of borazine is the favored site for both the σ and π-hole tetrel bonds. Less-stable dimers include a σ-tetrel bond to the borazine ring center and to the BH proton. The π-hole tetrel-bonded complexes are more strongly bound than are their σ-hole counterparts. Due to the coexistence of both T···N tetrel and B···O triel bonding, the complexes of borazine with F₂TO/H₂TO (T = Si and Ge) are very stable, with interaction energies up to −108 kcal/mol. The strongly bonded complexes are accompanied by substantial net charge transfer from F₂TO/H₂TO to borazine.     

Probing internal electric fields of π- and σ-hole bonds

π- and σ-holes are nonnuclear molecular regions of positive electric potential, which make non-covalent interactions with negative sites, for example, lone pairs of molecules containing nitrogen or oxygen, the so called π- and σ-hole bonds. We investigate these bonds locally using a probe programmed as a virtual molecule. Unlike the hydrogen bond, electric fields are detected having strengths that are different from the sum of the separated parts, meaning that molecular electrostatic potential surfaces analysis of the different parts are not enough to analyze the bonds. Based on an application of the Hellmann-Feynman theorem, which states that intermolecular bonds are fully described by Coulombian interactions (electrostatic plus polarization), we connect the electric field strength with the bond strength measured in experiments, so that it can be considered as a quantifier for the bonds.     

Thermodynamic and aromaticity studies for the assessment of the halogen⋯cyano interactions on Iodobenzonitrile

The standard (p° = 0.1 MPa) molar enthalpies of formation, in the gaseous phase, of the 2-, 3- and 4-iodobenzonitrile isomers were derived from the combination of the corresponding standard molar enthalpies of formation, in the condensed phase, at T = 298.15 K, and the standard molar enthalpies of sublimation, at the same temperature, calculated respectively from the standard molar energies of combustion in oxygen, measured by rotating-bomb calorimetry, and from the vapour-pressure study of the referred compounds, measured by mass-loss Knudsen effusion technique. The strength of the halogen-halogen and the halogen-cyano intermolecular interactions, in the crystal, are evaluated by the enthalpies and entropies of phase transition of the iodobenzonitrile derived from mass-loss Knudsen technique and differential scanning calorimetry measurements and compared with those reported to fluorobenzonitrile and bromobenzonitrile isomers. The computational calculations complement the experimental work, using different aromaticity criteria (HOMA, NICS, Shannom Aromaticity, PDI and ATI) for the analysis of the electronic behaviour of each iodobenzonitrile isomer.     

Intramolecular MLOH/π and MLNH/π interactions in crystal structures of metal complexes

Intramolecular metal-ligand OH/π (MLOH/π) and metal-ligand NH/π (MLNH/π) interactions in transition metal complexes between aqua or ammine ligand and ligand containing a C6-aromatic ring were investigated in crystal structures deposited in the Cambridge Structural Database (CSD). These intramolecular interactions appear in 38 structures with aqua ligand as the hydrogen atom donor and in 10 structures with ammine ligand as the hydrogen atom donor. Among all these complexes only one is negatively charged, 14 are positively charged and 33 are neutral indicating that the overall charge of the molecule has an influence on the XH/π (X = O or N) interactions. Energy estimated by DFT calculations is approximately 19 kJ mol⁻¹ for the MLOH/π interactions and approximately 15 kJ mol⁻¹ for the MLNH/π interactions. Dedicated to Professor Milan Melník on the occasion of his 70th birthday     

Effects of transition metal ion identity and π-cation interactions in metal-bis(peptide) complexes containing phenylalanine

Electrospray ionization-tandem mass spectrometry was used to study the effects of the metal ion identity and π-cation interactions on the dissociation pathways of metal-bis(peptide) complexes, where the metal is either Mn(2+), Co(2+), Ni(2+), Cu(2+), or Zn(2+); and the peptide is either FGGF, GGGG, GF, or GG, where G is glycine and F is phenylalanine. The [(FGGF)(FGGF-H) + M(2+)](+) and [(GGGG)(GGGG-H) + M(2+)](+) complexes dissociated by losing one FGGF or GGGG, respectively. Relative binding affinities were measured using the crossover points, where the parent and product ions were equal in ion abundance and a normalized-collision energy scale. The results indicate the relative binding affinities for FGGF and GGGG follow the same order with respect to the transition metal ion identity: Cu(2+) < Ni(2+) < Mn(2+) ≈ Zn(2+) < Co(2+), and the π-cation interactions in the FGGF complex have a measureable stabilizing effect. In contrast, the main fragmentation channels of [(GF)(GF-H) + M(2+)]+ and [(GG)(GG-H) + M(2+)](+) are loss of CO(2) and 2CO(2) with the [(GF)(GF-H) + M(2+)](+) complex also exhibiting cinnamic acid ,GF, residual glycine, cinnamate and styrene loss.     

Revisiting the effects of sequence and structure on the hydrogen bonding and π-stacking interactions in nucleic acids

Calculated electron densities from PBE0/6-31+G(d,p) were analyzed with respect to the hydrogen bonding within a nucleic acid base pair and the π-stacking between sets of base pairs. From published X-ray crystallographic data, base pairs were isolated from a total of 11 DNA and RNA duplexes, and their experimental geometry was maintained throughout the analyses. Focusing solely on Watson-Crick base pairs, from the values of the electron density between interacting nuclei (at the bond critical points), we provide quantitative data on individual weak interactions. For hydrogen bonding, in addition to quantifying the scissoring effect in GC base pairs, the origin of the controversy around the relative stability of AT and AU base pairs is identified and resolved. Thus, it is illustrated how the conclusion as to their relative stability rests on the specific choice of oligonucleotides compared. For π-stacking, sequence effects for tandem AT base pairs are captured, quantified, and explained, and the greater sensitivity of GC, over AT, sequences to the rise parameter is established. The results presented here show that, from experimental geometries and their electron densities, previously determined effects of the sequence and structure of a duplex on the stabilizing interactions can be captured, quantified, and traced back to the geometry of the base pairs.     

Fourier transform far-infrared study of the νσ vibration in hydrogen-bonded complexes involving a CH group

The far-infrared spectra (200-20 cm⁻¹) of hydrogen-bonded complexes involving chloroform, 3-chloropropine, phenylacetylene and a number of dihalonitromethanes with dimethylsulphoxide and N,N-dimethylformamide have been investigated in carbon tetrachloride solution. In all cases, broad, low intensity bands near 100 cm⁻¹ have been observed and are assigned to the intermolecular stretching vibration ν_σ. The force constants K_σ have been calculated in diatomic approximation.     

Transformation of white phosphorus in the coordination sphere of nickel complexes with σ-donating ligands

Oxidation of white phosphorus in the coordination sphere of the nickel(ii) complex with 1,1,1-tris(diphenylphosphinomethyl)ethane and 1,1",5,5"-bis[methylenedi(p-phenylene)]di(3,7-diphenyl-1,5-diaza-3,7-diphosphacyclooctane) was shown to be possible and accompanied by the transformation of P₄ into the -P₃ ligand. The change in the nickel state was monitored by cyclic voltammetry, ³¹P NMR spectroscopy, ESR, and IR spectroscopy.     

Novel lanthanide complexes of 5-nitroisophthalic acid containing two kinds of π–π stacking interactions

The novel two-dimensional coordination polymers [Ln(5-nip)(5-Hnip)(H₂O)₂](H₂O)₂ (Ln?=?Sm (1), Gd (2), Dy (3); 5-nipH₂?=?5-nitroisophthalic acid) were prepared using hydrothermal methods. Their isomrphous structures were characterized by single-crystal X-ray diffraction analyses. Two-dimensional layer-like structures are constructed by lanthanide ions bridged by 5-nip^2? ligands with the layers packing in 3D motifs through two kinds of π–π stacking interactions and hydrogen bonds. The complexes are thermally stable, aside from loss of water, to ca 350°C.     

Study of correlation effects on stretching force constants of the H3N⋯LiF lithium-bonded and H3N⋯HF hydrogen-bonded complexes

All quadratic, cubic and quartic force constants associated with high and low vibrational modes of the H₃N⋯HF hydrogen-bonded and H₃N⋯LiF lithium-bonded complexes have been calculated employing the Møller—Plesset perturbation theory to the second order (MP2) with the 4-31G** basis set.     

Synthesis,spectroscopic and thermal structural investigations of the charge-transfer complexes formed in the reaction of 1-methylpiperidine with σ- and π-acceptors

The reactions of the electron donor 1-methylpiperidine (1MP) with the π-acceptors 7,7,8,8-tetracyanoquinodimethane (TCNQ), tetracyanoethylene (TCNE), 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ), 2,3,5,6-tetrachloro-1,4-benzoquinone (chloranil = CHL) and iodine (I₂) were studied spectrophotometrically in chloroform at room temperature. The electronic and infrared spectra of the formed molecular charge-transfer (CT) complexes were recorded. The obtained results showed that the stoichiometries of the reactions are not fixed and depend on the nature of the acceptor. Based on the obtained data, the formed charge-transfer complexes were formulated as [(1MP)(TCNE)₂], [(1MP)(DDQ)]·H₂O, [(1MP)(CHL)] and [(1MP)I]I₃, while in the case of 1MP–TCNQ reaction, a short-lived CT complex is formed followed by rapid N-substitution by TCNQ forming the final reaction products 7,7,8-tricyano-8-piperidinylquinodimethane (TCPQDM). The five solids products were isolated and have been characterized by electronic spectra, infrared spectra, elemental analysis and thermal analysis.     

Substituent effects in synthetic lectins--exploring the role of CH-π interactions in carbohydrate recognition

Contacts between aromatic surfaces and saccharide CH groups are common motifs in natural carbohydrate recognition. These CH-π interactions are modeled in "synthetic lectins" which employ oligophenyl units as apolar surfaces. Here we report the synthesis and study of new synthetic lectins with fluoro- and hydroxy-substituted biphenyl units, designed to explore the role of π-electron density in carbohydrate CH-π interactions. We find evidence that recognition can be moderated through electronic effects but that other factors such as cavity hydration are also important and sometimes predominant in determining binding strengths.     

Exploring the interactions between buffers and cyclodextrin complexes—formation of regular inclusion or atypical non-inclusion complexes

Journal of Inclusion Phenomena and Macrocyclic Chemistry - The aim of this study was for the first time to determine the effect of 11 buffers on a γ-cyclodextrin complex, and use these and...