Geometry and spectral properties of the protonated homodimer of pyridine in the liquid and solid states. A combined NMR, X-ray diffraction and inelastic neutron scattering study

Weak, Broken, but Working-Intramolecular Hydrogen Bond in 2,2'-bipyridine

From an academic and practical point of view, it is desirable to be able to assess the possibility of the proton exchange of a given molecular system just by knowing the positions of the proton acceptor and the proton donor. This study addresses the difference between intramolecular hydrogen bonds in 2,2'-bipyridinium and 1,10-phenanthrolinium. Solid-state ¹⁵N NMR and model calculations show that these hydrogen bonds are weak; their energies are 25 kJ/mol and 15 kJ/mol, respectively. Neither these hydrogen bonds nor N-H stretches can be responsible for the fast reversible proton transfer observed for 2,2'-bipyridinium in a polar solvent down to 115 K. This process must have been caused by an external force, which was a fluctuating electric field present in the solution. However, these hydrogen bonds are the grain that tips the scales precisely because they are an integral part of a large system of interactions, including both intramolecular interactions and environmental influence.

Modeling of the Response of Hydrogen Bond Properties on an External Electric Field: Geometry, NMR Chemical Shift, Spin-Spin Scalar Coupling

The response of the geometric and NMR properties of molecular systems to an external electric field has been studied theoretically in a wide field range. It has been shown that this adduct under field approach can be used to model the geometric and spectral changes experienced by molecular systems in polar media if the system in question has one and only one bond, the polarizability of which significantly exceeds the polarizability of other bonds. If this requirement is met, then it becomes possible to model even extreme cases, for example, proton dissociation in hydrogen halides. This requirement is fulfilled for many complexes with one hydrogen bond. For such complexes, this approach can be used to facilitate a detailed analysis of spectral changes associated with geometric changes in the hydrogen bond. For example, in hydrogen-bonded complexes of isocyanide C≡¹⁵N-¹H⋯X, ¹J(¹⁵N¹H) depends exclusively on the N-H distance, while δ(¹⁵N) is also slightly influenced by the nature of X.

NMR Properties of the Cyanide Anion, a Quasisymmetric Two-Faced Hydrogen Bonding Acceptor

The isotopically enriched cyanide anion, (13C≡15N)−, has a great potential as the NMR probe of non-covalent interactions. However, hydrogen cyanide is highly toxic and can decompose explosively. It is therefore desirable to be able to theoretically estimate any valuable results of certain experiments in advance in order to carry out experimental studies only for the most suitable molecular systems. We report the effect of hydrogen bonding on NMR properties of 15N≡13CH···X and 13C≡15NH···X hydrogen bonding complexes in solution, where X = 19F, 15N, and O=31P, calculated at the ωB97XD/def2tzvp and the polarizable continuum model (PCM) approximations. In many cases, the isotropic 13C and 15N chemical shieldings of the cyanide anion are not the most informative NMR properties of such complexes. Instead, the anisotropy of these chemical shieldings and the values of scalar coupling constants, including those across hydrogen bonds, can be used to characterize the geometry of such complexes in solids and solutions. 1J(15N13C) strongly correlates with the length of the N≡C bond.

Actual Symmetry of Symmetric Molecular Adducts in the Gas Phase, Solution and in the Solid State

This review discusses molecular adducts, whose composition allows a symmetric structure. Such adducts are popular model systems, as they are useful for analyzing the effect of structure on the property selected for study since they allow one to reduce the number of parameters. The main objectives of this discussion are to evaluate the influence of the surroundings on the symmetry of these adducts, steric hindrances within the adducts, competition between different noncovalent interactions responsible for stabilizing the adducts, and experimental methods that can be used to study the symmetry at different time scales. This review considers the following central binding units: hydrogen (proton), halogen (anion), metal (cation), water (hydrogen peroxide).

1,3,5-Triaza-7-Phosphaadamantane (PTA) as a 31P NMR Probe for Organometallic Transition Metal Complexes in Solution

Due to the rigid structure of 1,3,5-triaza-7-phosphaadamantane (PTA), its ³¹P chemical shift solely depends on non-covalent interactions in which the molecule is involved. The maximum range of change caused by the most common of these, hydrogen bonding, is only 6 ppm, because the active site is one of the PTA nitrogen atoms. In contrast, when the PTA phosphorus atom is coordinated to a metal, the range of change exceeds 100 ppm. This feature can be used to support or reject specific structural models of organometallic transition metal complexes in solution by comparing the experimental and Density Functional Theory (DFT) calculated values of this ³¹P chemical shift. This approach has been tested on a variety of the metals of groups 8-12 and molecular structures. General recommendations for appropriate basis sets are reported.

Modeling of Solute-Solvent Interactions Using an External Electric Field-From Tautomeric Equilibrium in Nonpolar Solvents to the Dissociation of Alkali Metal Halides

An implicit account of the solvent effect can be carried out using traditional static quantum chemistry calculations by applying an external electric field to the studied molecular system. This approach allows one to distinguish between the effects of the macroscopic reaction field of the solvent and specific solute-solvent interactions. In this study, we report on the dependence of the simulation results on the use of the polarizable continuum approximation and on the importance of the solvent effect in nonpolar solvents. The latter was demonstrated using experimental data on tautomeric equilibria between the pyridone and hydroxypyridine forms of 2,6-di-tert-butyl-4-hydroxy-pyridine in cyclohexane and chloroform.

Editorial to the Special Issue "Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions"

Noncovalent interactions allow our world to exist [...].

Electric field effect on 31P NMR magnetic shielding

Magnetic shielding depends on molecular structure and noncovalent interactions. This study shows that it is also measurably dependent on the electric field generated by surrounding molecules. This effect has been observed explicitly for ³¹P nucleus using the adduct under field approach. The results obtained indicate that the field strength experienced by molecules in crystals consisting of molecules with large dipole moments is similar to that in polar solvents. Therefore, magnetic shielding should explicitly depend on solvent polarity. It is important to note that this effect cannot be reproduced correctly within the polarizable continuum model approach.

NMR Study of Intercalates and Grafted Organic Derivatives of H2La2Ti3O10

The protonated perovskite-like titanate H2La2Ti3O10 has been used to produce organic-inorganic hybrids with simple organic molecules: methylamine, methanol, monoethanolamine, and n-butylamine. The optimal pathways for the preparation of such hybrids are summarized. Solid-state NMR, combined with thermal analysis, Raman, and IR spectroscopy, has been applied to determine the bonding type in the obtained organic-inorganic hybrids. It has been found that, in the methanolic hybrid, the organic residues are covalently bound to the inorganic matrix. In contrast, in the methylamine and n-butylamine hybrids, the organic molecules are intercalated into the inorganic matrix in cationic forms. The structure of the monoethanolamine hybrid is composite and includes both the covalently bound and intercalated organic species.

Inter- vs. Intramolecular Hydrogen Bond Patterns and Proton Dynamics in Nitrophthalic Acid Associates

Noncovalent interactions are among the main tools of molecular engineering. Rational molecular design requires knowledge about a result of interplay between given structural moieties within a given phase state. We herein report a study of intra- and intermolecular interactions of 3-nitrophthalic and 4-nitrophthalic acids in the gas, liquid, and solid phases. A combination of the Infrared, Raman, Nuclear Magnetic Resonance, and Incoherent Inelastic Neutron Scattering spectroscopies and the Car-Parrinello Molecular Dynamics and Density Functional Theory calculations was used. This integrated approach made it possible to assess the balance of repulsive and attractive intramolecular interactions between adjacent carboxyl groups as well as to study the dependence of this balance on steric confinement and the effect of this balance on intermolecular interactions of the carboxyl groups.

Hydrogen Bond and Other Lewis Acid-Lewis Base Interactions as Preliminary Stages of Chemical Reactions

Various Lewis acid-Lewis base interactions are discussed as initiating chemical reactions and processes. For example, the hydrogen bond is often a preliminary stage of the proton transfer process or the tetrel and pnicogen bonds lead sometimes to the SN2 reactions. There are numerous characteristics of interactions being first stages of reactions; one can observe a meaningful electron charge transfer from the Lewis base unit to the Lewis acid; such interactions possess at least partly covalent character, one can mention other features. The results of different methods and approaches that are applied in numerous studies to describe the character of interactions are presented here. These are, for example, the results of the Quantum Theory of Atoms in Molecules, of the decomposition of the energy of interaction or of the structure-correlation method.

For Whom a Puddle Is the Sea? Adsorption of Organic Guests on Hydrated MCM-41 Silica

Thermal and hydration effects on the mobility of compact and branched organic molecules and a bulky pharmaceutical substance loaded in submonolayer amounts onto mesoporous silica have been elucidated using ¹H and ³¹P solid-state NMR. In all cases, the ambient hydration has a stronger effect than an increase in temperature to 370 K for water-free silica. The effect of hydration depends on the guest and ranges from complete solvation to a silica-water-guest sandwich structure to a silica-guest/silica-water pattern. The mobility of the guests under different conditions has been described. The specific structure of the MCM-41 surface allows one to study very slow surface diffusion, a diffusivity of about 10^-15-10^-16 m²/s. The data reported are relevant to any nonfunctionalized silica, while the method used is applicable to any phosphor-containing guest on any host.

Symmetry of three-center, four-electron bonds

Three-center, four-electron bonds provide unusually strong interactions; however, their nature remains ununderstood. Investigations of the strength, symmetry and the covalent versus electrostatic character of three-center hydrogen bonds have vastly contributed to the understanding of chemical bonding, whereas the assessments of the analogous three-center halogen, chalcogen, tetrel and metallic Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> -type long bonding are still lagging behind. Herein, we disclose the X-ray crystallographic, NMR spectroscopic and computational investigation of three-center, four-electron [D–X–D]⁺ bonding for a variety of cations (X⁺ = H⁺, Li⁺, Na⁺, F⁺, Cl⁺, Br⁺, I⁺, Ag⁺ and Au⁺) using a benchmark bidentate model system. Formation of a three-center bond, [D–X–D]⁺ is accompanied by an at least 30% shortening of the D–X bonds. We introduce a numerical index that correlates symmetry to the ionic size and the electron affinity of the central cation, X⁺. Providing an improved understanding of the fundamental factors determining bond symmetry on a comprehensive level is expected to facilitate future developments and applications of secondary bonding and hypervalent chemistry.

The factors determining the symmetry and the fundamental nature of the three-center, four-electron bonds are assessed.

Adduct under Field-A Qualitative Approach to Account for Solvent Effect on Hydrogen Bonding

The location of a mobile proton in acid-base complexes in aprotic solvents can be predicted using a simplified Adduct under Field (AuF) approach, where solute–solvent effects on the geometry of hydrogen bond are simulated using a fictitious external electric field. The parameters of the field have been estimated using experimental data on acid-base complexes in CDF₃/CDClF₂. With some limitations, they can be applied to the chemically similar CHCl₃ and CH₂Cl₂. The obtained data indicate that the solute–solvent effects are critically important regardless of the type of complexes. The temperature dependences of the strength and fluctuation rate of the field explain the behavior of experimentally measured parameters.

The Partner Does Matter: The Structure of Heteroaggregates of Acridine Orange in Water

Self-assembly of organic molecules in aqueous solutions is governed by a delicate entropy/enthalpy balance. Even small changes in their intermolecular interactions can cause critical changes in the structure of the aggregates and their spectral properties. The experimental results reported here demonstrate that protonated cations of acridine orange, acridine, and acridin-9-amine form stable J-heteroaggregates when in water. The structures of these aggregates are justified by the homonuclear ¹H cross-relaxation nuclear magnetic resonance (NMR). The absorption and fluorescence of these aggregates deviate characteristically from the known H-homoaggregates of the protonated cations of acridine orange. The latter makes acridine orange a handy optical sensor for soft matter studies.

Correlations of NHN hydrogen bond energy with geometry and 1H NMR chemical shift difference of NH protons for aniline complexes

In this computational work, we propose to use the NMR chemical shift difference of NH₂ protons for 1:1 complexes formed by aniline and nitrogen-containing proton acceptors for the estimation of the hydrogen bond energy and geometry (N⋯H and N⋯N distances). The proposed correlations could be applied to other aromatic amines as well, in a gas phase, a solution, or a solid state, for both inter- and intramolecular hydrogen bonds. We considered a set of 21 complexes with the NHN hydrogen bond without proton transfer, including hydrogen bonds from weak to medium strong ones (2-21 kcal/mol), with neutral or anionic bases and with sp³ and sp² hybridized nitrogen proton acceptors. For each complex apart from direct hydrogen bond energy calculation, we have tested several other ways to estimate the energy: (a) using a correlation between NH stretching band intensity and hydrogen bond energy and (b) using correlations between electron density properties at (3, -1) bond critical point (quantum theory of atoms in molecules analysis) and hydrogen bond energy. Besides for the studied type of complexes, we obtained refined linear correlations linking the local electron kinetic (G) and potential (V) energy densities with the hydrogen bond energy.

Bismuth as a versatile cation for luminescence in coordination polymers from BiX3/4,4'-bipy: understanding of photophysics by quantum chemical calculations and structural parallels to lanthanides

Coordination polymers (CPs) with bismuth(iii) as a connectivity centre have been prepared from BiX3 (X = Cl-I) and 4,4'-bipyridine (bipy) in order to implement Bi-based luminescence. The products were obtained via different synthetic routes such as solution chemistry, melt syntheses or mechanochemical reactions. Five neutral and anionic 1D-CPs are presented that show a chemical parallel to trivalent lanthanides forming isostructural or closely related 1D-CPs, of which five additional compounds are described. Bi3+ proves to be a versatile cation for luminescence resulting from energy transfer processes between a metal and a ligand in the presented CPs. Quantum chemical calculations were carried out to investigate Bi3+-participation in the luminescence processes. The calculated results allow an assignment of the bright transitions composed of mainly metal-to-ligand-charge transfer (MLCT) character. These results show that Bi3+ can form strongly luminescent coordination compounds with N-donor ligands.

Applying neutron diffraction with isotopic substitution to the structure and proton-transport pathways in protic imidazolium bis{(trifluoromethyl)sulfonyl}imide ionic liquids

Neutron diffraction with isotopic substitution has been applied to examine the potential for complex-ion formation in protic imidazolium bis{(trifluoromethyl)sulfonyl}imide ionic liquids.

NMR Study of Solvation Effect on the Geometry of Proton-Bound Homodimers of Increasing Size

Hydrogen bond geometries in the proton-bound homodimers of quinoline and acridine derivatives in an aprotic polar solution have been experimentally studied using ¹H NMR at 120 K. The reported results show that an increase of the dielectric permittivity of the medium results in contraction of the N···N distance. The degree of contraction depends on the homodimer's size and its substituent-specific solvation features. Neither of these effects can be reproduced using conventional implicit solvent models employed in computational studies. In general, the N···N distance in the homodimers of pyridine, quinoline, and acridine derivatives decreases in the sequence gas phase > solid state > polar solvent.

Dynamics of proton transfer in imidazole hydrogen-bond chains

Potential energy curve of H-bond (2) in G4-[1]^(ω1=−92) is nearly identical to H-bond (1) in G2-[1]^(ω1=−94), the protonated H-bond (2) becomes a new precursor for the next transfer and confirms the Eigen–Zundel–Eigen mechanism.

Counterion influence on the N-I-N halogen bond

A detailed investigation of the influence of counterions on the [N-I-N]+ halogen bond in solution, in the solid state and in silico is presented. Translational diffusion coefficients indicate close attachment of counterions to the cationic, three-center halogen bond in dichloromethane solution. Isotopic perturbation of equilibrium NMR studies performed on isotopologue mixtures of regioselectively deuterated and nondeuterated analogues of the model system showed that the counterion is incapable of altering the symmetry of the [N-I-N]+ halogen bond. This symmetry remains even in the presence of an unfavorable geometric restraint. A high preference for the symmetric geometry was found also in the solid state by single crystal X-ray crystallography. Molecular systems encompassing weakly coordinating counterions behave similarly to the corresponding silver(i) centered coordination complexes. In contrast, systems possessing moderately or strongly coordinating anions show a distinctly different behavior. Such silver(i) complexes are converted into multi-coordinate geometries with strong Ag-O bonds, whereas the iodine centered systems remain linear and lack direct charge transfer interaction with the counterion, as verified by 15N NMR and DFT computation. This suggests that the [N-I-N]+ halogen bond may not be satisfactorily described in terms of a pure coordination bond typical of transition metal complexes, but as a secondary bond with a substantial charge-transfer character.

NMR studies of active-site properties of human carbonic anhydrase II by using (15) N-labeled 4-methylimidazole as a local probe and histidine hydrogen-bond correlations

By using a combination of liquid and solid-state NMR spectroscopy, (15) N-labeled 4-methylimidazole (4-MI) as a local probe of the environment has been studied: 1) in the polar, wet Freon CDF3 /CDF2 Cl down to 130 K, 2) in water at pH 12, and 3) in solid samples of the mutant H64A of human carbonic anhydrase II (HCA II). In the latter, the active-site His64 residue is replaced by alanine; the catalytic activity is, however, rescued by the presence of 4-MI. For the Freon solution, it is demonstrated that addition of water molecules not only catalyzes proton tautomerism but also lifts its quasidegeneracy. The possible hydrogen-bond clusters formed and the mechanism of the tautomerism are discussed. Information about the imidazole hydrogen-bond geometries is obtained by establishing a correlation between published (1) H and (15) N chemical shifts of the imidazole rings of histidines in proteins. This correlation is useful to distinguish histidines embedded in the interior of proteins and those at the surface, embedded in water. Moreover, evidence is obtained that the hydrogen-bond geometries of His64 in the active site of HCA II and of 4-MI in H64A HCA II are similar. Finally, the degeneracy of the rapid tautomerism of the neutral imidazole ring His64 reported by Shimahara et al. (J. Biol. Chem.- 2007, 282, 9646) can be explained with a wet, polar, nonaqueous active-site conformation in the inward conformation, similar to the properties of 4-MI in the Freon solution. The biological implications for the enzyme mechanism are discussed.

How short is the strongest hydrogen bond in the proton-bound homodimers of pyridine derivatives?

Hydrogen bond geometries in the proton-bound homodimers of ortho-unsubstituted and ortho-methylsubstituted pyridine derivatives in aprotic polar solution were estimated using experimental NMR data. Within the series of homodimers studied the hydrogen bond lengths depend on the proton affinity of pyridines and--at least for the ortho-methylsubstituted pyridines--on the pKa of the conjugate acids in an approximately quadratic manner. The shortest possible hydrogen bond in the homodimers of ortho-unsubstituted pyridines is characterized by the N···N distance of 2.613 Å. Steric repulsion between the methyl groups of the ortho-methylsubstituted pyridines becomes operative at an N···N distance of ∼2.7 Å and limits the closest approach to 2.665 Å.

Variable-temperature study of hydrogen-bond symmetry in cyclohexene-1,2-dicarboxylate monoanion in chloroform-d

The symmetry of the hydrogen bond in hydrogen cyclohexene-1,2-dicarboxylate monoanion was determined in chloroform using the NMR method of isotopic perturbation. As the temperature decreases, the (18)O-induced (13)C chemical-shift separations increase not only at carboxyl carbons but also at ipso (alkene) carbons. The magnitude of the ipso increase is consistent with an (18)O isotope effect on carboxylic acid acidity. Therefore it is concluded that this monoanion is a mixture of tautomers in rapid equilibrium, rather than a single symmetric structure in which a chemical-shift separation arises from coupling between a desymmetrizing vibration and anharmonic isotope-dependent vibrations, which is expected to show the opposite temperature dependence.

Energy Analysis of Competing Non-Covalent Interaction in 1:1 and 1:2 Adducts of Collidine with Benzoic Acids by Means of X-Ray Diffraction

The hydrogen bond pattern and the types of non-covalent interactions in the crystals of the 1:1 and 1:2 adducts of 2,4,6-trimethylpyridine and benzoic acids are studied using high-resolution X-ray diffraction. The geometries of the hydrogen bonds are estimated using a combined XRD/DFT approach that provides the geometrical parameters within the margin of error of neutron diffraction studies. The energies of the non-covalent interactions are estimated on the base of the experimental electron density distribution function. It is shown that the structures of the adducts are governed by the NOH and OHO hydrogen bonds. In turn, C-H...O contacts and stacking interactions define the packing of the adducts in the crystal. On the other hand, it is important to note that the latter interactions affect the competition of the former hydrogen bonds in some 1:2 adducts.

Acridine – a Promising Fluorescence Probe of Non-Covalent Molecular Interactions

Fluorescence and absorption spectral parameters of acridine have been studied in solution at room temperature in the presence of different proton donors aiming to inspect whether or not acridine can be used as a spectroscopic probe suitable to measure the geometry of hydrogen bonds under different conditions. It has been shown that the most appropriate spectral parameter is the position of fluorescence maximum that changes heavily upon a contraction of the N···H distance. Presumably, also the intensity of the maximum strongly depends on the hydrogen bond geometry. These two parameters can be used to establish two independent, mutually complementary correlations connecting the spectral manifestations and the geometry of hydrogen bond.