Energetic and geometrical evidence of nonbonding character of some intramolecular halogen···oxygen and other Y···Y interactions

We present high-level ab initio calculations for representative group of molecules possessing the intramolecular interaction of the X···O type (X = F, Cl, Br, and I). Few examples of molecules with intramolecular O···O and F···F interactions are also investigated. We show that, although most often investigated as bonding, all these interactions are nonbonding or repulsive, as indicated by positive values of interaction energies obtained by means of a few estimating methods, by thorough studies of geometrical changes that take place during the X···O contact formation and by the lateral contact of electron density isosurfaces of X and O atoms, which both are characterized by negative values of electrostatic potential. The presented conclusion about the repulsive nature of the intramolecular X···O and similar interactions is in opposition to the proclamation of the quantum theory of atoms in molecules of Bader that the presence of a bond path and a corresponding bond critical point is always to indicate the bonding, thus, stabilizing interaction.     

Novel type of mixed O–H···N/O–H···π hydrogen bonds: monohydrate of pyridine

Investigation of characteristics of hydrogen bonding between pyridine and water by MP2/aug-cc-pvdz method reveals that these two molecules may form three types of hydrogen bonds depending on nature of proton withdrawal site of pyridine. Change of orientation of water with respect to plane of aromatic ring leads to transformation of the O–H···N bond to O–H···π bond via wide region of the potential energy surface where both lone pair of the nitrogen atom and π-system make significant contribution into hydrogen bonding. Hydrogen bond in this intermediate region may be considered as mixed O–H···N/O–H···π bond representing new type of H bonds.     

A theoretical exploration of unexpected amine···π interactions

Counterintuitive amine lone pair···π interactions are computationally revealed by MP2 and CCSD(T) methods, attractive lone pair···π interactions are observed when the lone pair of nitrogen points toward the π system. Symmetry adapted perturbation theory (SAPT) calculations and atoms in molecules (AIM) analyses were performed and the origin of the calculated attractive interaction between nitrogen lone pairs and π rings is discussed. Dispersion effects were revealed to play a crucial role in the attractive lone pair···π interaction.     

Effect of microhydration on the guanidinium···benzene interaction

The effect of microhydration on the interaction of guanidinium cation with benzene has been studied by employing ab initio calculations. Four different structural arrangements were considered for the guanidinium···benzene interaction to which up to six water molecules were added. T-shaped structures are usually the most stable, but as water molecules are included the energy differences with the parallel structures decrease, reaching a point where parallel complexes are even more stable than T-shaped ones. Therefore, the inclusion of water molecules promotes a change in the structure of the cation···π contact. The analysis reveals that these stability changes are more related with the structure of the hydrating water molecules than to a modulation of the cation···π interaction. Already with three water molecules, one water molecule in the T-shaped complex has to be located in the second solvation shell, whereas in parallel structures this occurs with four water molecules. As a consequence energy differences among structures decrease. The calculations show that the nature of the interaction is almost unaffected in T-shaped structures, whereas an important dispersion increment is observed in parallel ones, though its overall effect is small.     

Synthesis of novel O-alkylbenzochromeno-1,5-benzodiazepinones. Study of the N–H····N and CO····HN hydrogen bonding interactions with 2-aminopyridines

A series of novel 6-(O-alky)lbenzochromeno-1,5-benzodiazepin-2-ones 4a–c was prepared through the condensation between the [1]benzopyrano[4,3-c][1,5]benzodiazepin-7(8H)one 1 and a series of alkylalcohols. Scaffold 4 exhibited interesting hydrogen-bonding interaction with 2-aminopyridine derivatives. The so obtained self-assembled systems 5 were fully characterized by 1D/2D-NMR techniques and mass spectrometry. The hydrogen-bonding interaction was supported by IR and Raman spectroscopy and by ¹H NMR titration experiments, and was confirmed by an X-ray crystal structure analysis.     

Comparison of aromatic NH···π, OH···π, and CH···π interactions of alanine using MP2, CCSD, and DFT methods

A comparison of the performance of various density functional methods including long‐range corrected and dispersion corrected methods [MPW1PW91, B3LYP, B3PW91, B97‐D, B1B95, MPWB1K, M06‐2X, SVWN5, ωB97XD, long‐range correction (LC)‐ωPBE, and CAM‐B3LYP using 6‐31+G(d,p) basis set] in the study of CH···π, OH···π, and NH···π interactions were done using weak complexes of neutral (A) and cationic (A⁺) forms of alanine with benzene by taking the Møller–Plesset (MP2)/6‐31+G(d,p) results as the reference. Further, the binding energies of the neutral alanine–benzene complexes were assessed at coupled cluster (CCSD)/6‐31G(d,p) method. Analysis of the molecular geometries and interaction energies at density functional theory (DFT), MP2, CCSD methods and CCSD(T) single point level reveal that MP2 is the best overall performer for noncovalent interactions giving accuracy close to CCSD method. MPWB1K fared better in interaction energy calculations than other DFT methods. In the case of M06‐2X, SVWN5, and the dispersion corrected B97‐D, the interaction energies are significantly overrated for neutral systems compared to other methods. However, for cationic systems, B97‐D yields structures and interaction energies similar to MP2 and MPWB1K methods. Among the long‐range corrected methods, LC‐ωPBE and CAM‐B3LYP methods show close agreement with MP2 values while ωB97XD energies are notably higher than MP2 values. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010     

Physical- and Bio-Organic Chemstry of Nonbonded Selenium· · ·Oxygen Interactions

Weak nonbonded interaction between a divalent selenium and an oxygen atom (i.e., Se···O interaction) frequently plays important roles in chemical and biological functions of selenium compounds. To establish that ⁷⁷ Se NMR is an easy experimental probe to diagnose the strength of an Se···O interaction, 3 series of 2-substituted benzeneselenenyl derivatives, which have an intramolecular Se···O interaction in solution, were employed. By comparing the ⁷⁷ Se NMR chemical shifts (δ _Se ) with those observed for other series of selenium compounds, which have an intramolecular Se···Y (Y = N, O, F, Cl, or Br) interaction, approximate linear correlation was found between the δ _Se values and the strengths of the nonbonded Se···Y interactions evaluated by natural bond orbital analysis at the B3LYP level. The correlation will be useful for estimating the strength of an Se···O interaction simply from the ⁷⁷ Se NMR chemical shift. By extending the chemistry of nonbonded Se···O interactions to structural biology, analogous S···O interactions have been discovered in protein architecture. The directional features were, however, different from those of Se···O and S···O interactions of small organic compounds.     

Thermal desorption of hydrogen from ammonia borane: unexpected role of homopolar B-H···H-B interactions

The solid-state structure of ammonia borane is held together by an intricate N-H···H-B proton-hydride bonding network. These intermolecular interactions have long been considered to mediate the release of hydrogen from this material. Here we reveal the silent but important role played by B-H···H-B interactions in the thermal decomposition of this leading hydrogen storage candidate.     

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.

     

Effects of substituents upon the P···N noncovalent interaction: the limits of its strength

Previous work has documented the ability of the P atom to form a direct attractive noncovalent interaction with a N atom, based in large measure on the charge transfer from the N lone pair into the σ* antibonding orbital of the P-H that is turned away from the N atom. As the systems studied to date include only hydrides, the present work considers how substituents affect the interaction and examines whether P···N might compete with other attractive forces such as H-bonds. It is found that the addition of electron-withdrawing substituents greatly strengthens the P···N interaction to the point where it exceeds that of the majority of H-bonds. The highest interaction energy occurs in the FH(2)P···N(CH(3))(3) complex, amounting to 11 kcal/mol. A breakdown of the individual forces involved attributes the stability of the interaction to approximately equal parts electrostatic and induction energy, with a smaller contribution from dispersion.     

Infrared characterization of the HCOOH···CO2 complexes in solid argon: stabilization of the higher-energy conformer of formic acid

The complexes of formic acid (HCOOH, FA) with carbon dioxide are studied by infrared spectroscopy in an argon matrix. Two trans-FA···CO(2) and one cis-FA···CO(2) complexes are experimentally identified while the calculations at the MP2(full)/6-311++G(2d,2p) level of theory predict one more minimum for the cis-FA···CO(2) complex. The complex of the higher-energy conformer cis-FA with CO(2) is prepared by vibrational excitation of the ground-state trans-FA conformer combined with thermal annealing. The lifetime of the cis-FA···CO(2) complex in an argon matrix at 10 K is 2 orders of magnitude longer than that of the cis-FA monomer. This big difference is explained by the computational results which show a higher stabilization barrier for the complex. The solvation effects in solid argon are theoretically estimated and their contribution to the stabilization barriers of the higher-energy species is discussed. The relative barrier transmissions for hydrogen tunneling in the cis-FA···CO(2) complex and cis-FA monomer are in good agreement with the experimental decay rates.     

The art of stacking: structural folding and self-assembly of branched π-conjugation assisted by O-H···O and C-H···F hydrogen bonds

An intimate interplay of O-H···O/C-H···F hydrogen bonds and π-π stacking interactions allows a phenyleneethynylene-based dendritic molecule to fold and self-assemble into two distinctively different molecular crystals as pseudopolymorphs.     

On the nature of the stabilization of benzene···dihalogen and benzene···dinitrogen complexes: CCSD(T)/CBS and DFT-SAPT calculations

The structure and stabilization energies of benzene (and methylated benzenes)···X(2) (X=F, Cl, Br, N) complexes were investigated by performing CCSD(T)/complete basis set limit and density functional theory/symmetry-adapted perturbation theory (DFT-SAPT) calculations. The global minimum of the benzene···dihalogen complexes corresponds to the T-shaped structure, whereas that of benzene···dinitrogen corresponds to the sandwich one. The different binding motifs of these complexes arise from the different quadrupole moments of dihalogens and dinitrogen. The different sign of the quadrupole moments of these diatomics is explained based on the electrostatic potential (ESP). Whereas all dihalogens, including difluorine, possess a positive σ hole, such a positive area of the ESP is completely missing in the case of dinitrogen. Moreover, benzene···X(2) (X=Br, Cl) complexes are stronger than benzene···X(2) (X=F, N) complexes. When analyzing DFT-SAPT electrostatic, dispersion, induction, and δ(Hartree-Fock) energies, we recapitulate that the former complexes are stabilized mainly by dispersion energy, followed by electrostatic energy, whereas the latter complexes are stabilized mostly by the dispersion interaction. The charge-transfer energy of benzene···dibromine complexes, and surprisingly, also of methylated benzenes···dibromine complexes is only moderate, and thus, not responsible for their stabilization. Benzene···dichlorine and benzene···dibromine complexes can thus be characterized merely as complexes with a halogen bond rather than as charge-transfer complexes.     

Ab initio excitation spectrum of the weak H···CO interaction

The adiabatic interaction energy (IE) in the van der Waals region of the ground $ {\text{H}}\left( {{}^{2}{\text{S}}} \right) \cdots {\text{CO}}\left( {{\text{X}}^{1} \Upsigma^{ + } } \right) $ and excited $ {\text{H}}\left( {{}^{2}{\text{S}}} \right) \cdots {\text{CO}}\left( {{\text{a}}^{3} \Uppi } \right) $ electronic states of the $ {\text{H}} \cdots {\text{CO}} $ complex is studied in the framework of the supermolecule approach at the RHF-CCSD(T) level of theory. Calculations predict a minimum with β _e = 72°, R _e = 6.89a _o and D _e = 34.10 cm^?1 for the ground X²A′state. For the excited ⁴A′ state the minimum occurs at β _e = 104° and R _e = 5.90a _o with D _e = 75.42 cm^?1. The resulting IE of the excited ⁴A′′ state reveals two minima separated by a saddle point. The most stable configuration occurs at β _e = 132°, R _e = 6.71a _o and D _e = 40.03 cm^?1. The corresponding vertical excitation energies and corresponding shifts with respect to the isolated CO molecule are calculated as a guideline for future theoretical and experimental work. In order to investigate the use of less demanding correlation methods, test density functional theory calculations using the mPW1PW exchange–correlation functional are also presented for comparison.     

Weak H-bonds. Comparisons of CH···O to NH···O in proteins and PH···N to direct P···N interactions

Whereas CH···O H-bonds are usually weaker than interpeptide NH···O H-bonds, this is not necessarily the case within proteins. The nominally weaker CH···O are surprisingly strong, comparable to, and in some cases stronger than, the NH···O H-bonds in the context of the forces that hold together the adjacent strands in protein β-sheets. The peptide NH is greatly weakened as proton donor in certain conformations of the protein backbone, particularly extended structures, and forms correspondingly weaker H-bonds. The PH group is a weak proton donor, but will form PH···N H-bonds. However, there is a stronger interaction in which P can engage, in which the P atom, not the H, directly approaches the N electron donor to establish a direct P···N interaction. This approach is stabilized by the same sort of electron transfer from the N lone pair to the P-H σ* antibond that characterizes the PH···N H-bond.     

Intramolecularly coordinated azobenzene selenium derivatives: effect of strength of the Se···N intramolecular interaction on luminescence

A series of selenium derivatives (6-12) of 2-phenylazophenyl have been synthesized using o-lithiation route. The effect of the strength of the intramolecular Se···N interaction on the absorption spectra as well as emission spectra has been studied. The studies suggest that the secondary bonding Se···N interaction give rise to fluorescence, however, the strength of Se···N interaction cannot be directly correlated with the intensity of the fluorescence. TD-DFT calculations show that the main transition involved in the absorption spectra of the compound is the ligand based π-π* type.     

Direct measurements of electric fields in weak OH···π hydrogen bonds

Hydrogen bonds and aromatic interactions are of widespread importance in chemistry, biology, and materials science. Electrostatics play a fundamental role in these interactions, but the magnitude of the electric fields that support them has not been quantified experimentally. Phenol forms a weak hydrogen bond complex with the π-cloud of benzene, and we used this as a model system to study the role of electric fields in weak OH···π hydrogen bonds. The effects of complex formation on the vibrational frequency of the phenol OH or OD stretches were measured in a series of benzene-based aromatic solvents. Large shifts are observed and these can be converted into electric fields via the measured vibrational Stark effect. A comparison of the measured fields with quantum chemical calculations demonstrates that calculations performed in the gas phase are surprisingly effective at capturing the electrostatics observed in solution. The results provide quantitative measurements of the magnitude of electric fields and electrostatic binding energies in these interactions and suggest that electrostatics dominate them. The combination of vibrational Stark effect (VSE) measurements of electric fields and high-level quantum chemistry calculations is a general strategy for quantifying and characterizing the origins of intermolecular interactions.     

The infrared spectrum of NN···CO+ trapped in solid neon

Codeposition of a Ne:N(2):CO = 200:1:1 mixture at 4.3 K with a beam of very pure neon atoms excited to their energy levels between 16.6 and 16.85 eV leads to stabilization in the resulting solid of sufficient NNCO(+) for detection of its NN- and CO-stretching vibration fundamentals. Detailed isotopic substitution studies and density functional calculations for the various isotopologues support the identification of NNCO(+) and permit estimation of the positions of two of its low-frequency fundamentals. A sufficient concentration of NOCN is also stabilized in the neon matrix for detection of its NO-stretching vibrational fundamental.     

Can a C-H···O interaction be a determinant of conformation?

Whether nonconventional hydrogen bonds, such as the C-H···O interaction, are a consequence or a determinant of conformation is a long-running and unresolved issue. Here we outline a solid-state and quantum mechanical study designed to investigate whether a C-H···O interaction can override the significant trans-planar conformational preferences of α-fluoroamide substituents. A profound change in dihedral angle from trans-planar((OCCF)) to cis-planar((OCCF)) observed on introducing an acceptor group for a C-H···O hydrogen bond is consistent with this interaction functioning as a determinant of conformation in certain systems. This testifies to the potential influence of the C-H···O hydrogen bond and is consistent with the assignment of this interaction as a contributor to overall conformation in both model and natural systems.