Towards an unified hydrogen-bond theory

Physical origin of chemical phenomena: Interpretation of acidity, basicity, and hydride affinity by trichotomy paradigm

Some of the most important aspects of modeling in chemistry are discussed in detail. It is argued that the interpretive side of (quantum) chemistry is indispensable, since it gives sense to a myriad of experimental and computational results. The usefulness of some physical modeling is illustrated by the trichotomy approach in rationalizing acidity, basicity, and hydride affinities of neutral organic compounds. According to trichotomy paradigm, the simple chemical reaction of protonation and H- attachment can be decomposed into three separate sequential steps, which in turn mirror the initial-, intermediate-, and final-state effects. Ample evidence is given, which convincingly shows that the trichotomy approach has some distinct advantages in interpreting aforementioned properties that belong to the most important ones in chemistry and biochemistry.

Correlated proton motion in hydrogen bonded systems: tuning proton affinities

The theorem of matching proton affinities (PA) has been widely used in the analysis of hydrogen bonds. However, most experimental and theoretical investigations have to cope with the problem that the variation of the PA of one partner in the hydrogen bond severely affects the properties of the interface between both molecules. The B3LYP/d95+(d,p) analysis of two hydrogen bonds coupled by a 5-methyl-1H-imidazole molecule showed that it is possible to change the PA of one partner of the hydrogen bond while maintaining the properties of the interface. This technique allowed us to correlate various properties of the hydrogen bond directly with the difference in the PAs between both partners: it is possible to tune the potential energy surface of the bonding hydrogen atom from that of an ordinary hydrogen bond (localized hydrogen atom) to that of a low barrier hydrogen bond (LBHB, delocalized hydrogen atom) just by varying the proton affinity of one partner. This correlation shows clearly that matching PAs are of lesser importance for the formation of a LBHB than the relative energy difference between the two tautomers of the hydrogen bond.

Short Strong Hydrogen Bonds in 2-Acetyl-1,8-dihydroxy-3,6-dimethylnaphthalene: An Outlier to Current Hydrogen Bonding Theory?

The environmental influence on the electronic character of two O-H...O hydrogen bonds in a beta-diketone, 2-acetyl-1,8-dihydroxy-3,6-dimethylnaphthalene, is studied by low-temperature synchrotron X-ray diffraction and high-level density functional theory (DFT) calculations. It is revealed that one of the hydrogen bonds is very strong, yet partial localization is found. This result is analyzed by atoms in molecules (AIM) theory and applying the source function. Model compounds, with less steric strain, reveal that the strong hydrogen bond is not merely a result of steric compression.

Hydrogen bonding and dynamic behaviour in crystals and polymorphs of dicarboxylic-diamine adducts: a comparison between NMR parameters and X-ray diffraction studies

Fumaric, malonic, maleic, and hydromuconic (HOOCCH2(CH)2CH2COOH) acids were used to prepare a series of hydrogen-bonded adducts or salts, depending on whether acid-base proton transfer takes place, with the dibase [N(muCH2CH2)3N] in various stoichiometric ratios. The resulting compounds have been investigated by using the 1H MAS, 15N, and 13C cross polarisation magic-angle spinning (CPMAS) methods and discussed in relation to X-ray diffraction studies to ascertain the nature of the O-HO, NH-O, and N+-HO- hydrogen bonds between the various species. In addition, two polymorphic forms of the malonic compound and a hydrate in the maleic case were examined. We also present the correlations between the chemical shifts of the hydrogen-bonded protons and those from the proton transfer reaction (acid-to-base) with the heavy atom distances. The dynamic behaviour in the solid-state of the [N(muCH2CH2)3N] adducts with fumaric 2:1, maleic 1:1 hydrate, and hydromuconic acids, and a malonate 2:1 polymorph adduct have been investigated by using variable-temperature 1H spin-lattice relaxation times. A substantial agreement between the activation energies obtained from fitting the T1 data and the results of potential energy barrier calculations demonstrates that the facile reorientation of the [N(muCH2CH2)3N] molecule occurs in several of the adducts.

Intramolecular H-Bonds: DFT and QTAIM Studies on 3-(Aminomethylene)pyran-2,4-dione and Its Derivatives

Intramolecular N-H...O hydrogen bonds in 3-(aminomethylene)pyran-2,4-dione and its simple derivatives (F, Li, and BeH substituents) were analyzed theoretically. The systems were optimized at the B3LYP/6-311++G(d,p) level of approximation. For some fluorine derivatives the corresponding tautomers with O-H...N intramolecular H-bonds were investigated, and for such pairs of tautomers, the calculations on transition states of the N-H...O <--> N...H-O proton-transfer reaction were carried out. The geometrical and energetic parameters for these species were characterized. The topological parameters derived from Bader theory were also analyzed; these are characteristics of H-bond critical points and also of ring critical points. Besides N-H...O and O-H...N intramolecular hydrogen bonds, there are the other intramolecular interactions, mostly ionic such as Be(+delta)...(-delta)O, Li(+delta)...(-delta)O, and Li(+delta)...(-delta)F. The F...O interactions also exist for some of species investigated. They may be classified as energetically stabilizing ones since the corresponding bond paths and critical points exist. The numerous correlations and dependencies between geometrical, topological, and energetic parameters were detected and described.

Structure of the Boronic Acid Dimer and the Relative Stabilities of Its Conformers

Despite the widespread use of boronic acids in materials science and as pharmaceutical agents, many aspects of their structure and reactivity are not well understood. In this research the boronic acid dimer, [HB(OH)(2)](2), was studied by second-order Møller-Plesset (MP2) perturbation theory and coupled cluster methodology with single and double excitations (CCSD). Pople split-valence 6-31+G*, 6-311G**, and 6-311++G** and Dunning-Woon correlation-consistent cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ basis sets were employed for the calculations. A doubly hydrogen-bonded conformer (1) of the dimer was consistently found to be lowest in energy; the structure of 1 was planar (C(2h)) at most computational levels employed but was significantly nonplanar (C(2)) at the MP2/6-311++G** and CCSD/6-311++G** levels, the result of an intrinsic problem with Pople-type sp-diffuse basis functions on heavy atoms. The dimerization energy, enthalpy, and free energy for the formation of (1) from the exo-endo conformer of the monomer were -10.8, -9.2, and +1.2 kcal/mol, respectively, at the MP2/aug-cc-pVTZ level. Several other hydrogen-bonded conformers of the dimer were local minima on the potential energy surface (PES) and ranged from 2 to 5 kcal/mol higher in energy than 1. Nine doubly OH-bridged conformers, in which the boron atoms were tetracoordinated, were also local minima on the PES, but they were all greater than 13 kcal/mol higher in energy than 1; doubly H-bridged structures proved to be transition states. MP2 and CCSD results were compared to those from the BLYP, B3LYP, OLYP, O3LYP, PBE1PBE, and TPSS functionals with the 6-311++G** and aug-cc-pVTZ basis sets; the PBE1PBE functional performed best relative to the MP2 and CCSD results. Self-consistent reaction field (SCRF) calculations predict that boronic acid dimerization is less favorable in solution than in vacuo.

Molecular recognition in organic crystals: directed intermolecular bonds or nonlocalized bonding?

Molecules are held together mainly by forces acting between individual atoms. Does the same apply to molecular clusters? Does intermolecular cohesion depend on weak bonds between individual atoms in different molecules or on less localized, more diffuse interactions between molecules? We discuss these questions from several viewpoints and in particular compare interpretations based on the extension of Bader's atoms in molecules (AIM) theory to cover closed-shell intermolecular interactions with interpretations based on the new pixel method for the calculation of coulombic, polarization, dispersion, and repulsion energies from the electron density of molecular clusters.

Effect of methylation on the coordination of copper by small azacryptands; the role of geometrically constrained hydrogen bonding in stabilizing terminally coordinated oxygen species

Treatment of N-methyl substituted aminocryptand hosts with copper(II) generates monocopper(II) cryptates where copper(II) coordinates an oxygen-centered species, formally H3O+, which is also strongly hydrogen bonded to three aminocryptand N-methyl atoms via bonds which may best be viewed as NH(delta+)...O(delta-) in consequence of charge transfer. The strength of this hydrogen bonding precludes successful competition of another copper ion for the second coordination site thus suppressing formation of any Cu-Cu bonded average-valent system.

Recognition forces in ligand-protein complexes: blending information from different sources

A variety of ligands interact with proteins in many biological processes; shape complementarity, electrostatic forces and hydrophobicity are the main factors governing these interactions. Although this is accepted by the scientific community, confusion about the significance of certain terms (e.g. hydrophobicity, salt bridge) and the difficulty of discussing the balance of acting forces rather than their single contributions, are two of the main problems encountered by researchers working in the field. These difficulties are sometimes enhanced by the unskilled use of informatics tools, which give great help in understanding the topic (especially from the visual standpoint), but only if used critically. After explaining some general chemical concepts, the commentary discusses the main forces governing ligand-protein interactions, focusing on those generating confusion among scientists with different backgrounds. Three examples of ligand-protein interactions are then discussed to illustrate the advantages and drawbacks of some in silico tools, highlighting the main interactions responsible for complex formation. The same examples are used to point out the limits in separating forces that are mandatory for occurrence of a given interaction and additional forces.

Chemical Bonds without “Chemical Bonding”? A Combined Experimental and Theoretical Charge Density Study on an Iron Trimethylenemethane Complex

High-resolution X-ray diffraction data, in conjunction with DFT(B3LYP) quantum calculations, have been used in a QTAIM analysis of the charge density in the trimethylenemethane (TMM) complex Fe(eta(4)-C[CH(2)](3))(CO)(3). The agreement between the theoretical and experimental topological properties is excellent. Only one bond path is observed between the TMM ligand and the Fe atom, from the central C(alpha) atom. However, much evidence, including from the delocalization indices and the source function, suggests that there is a strong chemical interaction between the Fe and C(beta) atoms, despite the formal lack of chemical bonding according to QTAIM.

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

The H(2)CO...(HF)(n) (n = 1, ..., 9) complexes were investigated using the MP2 method and the following basis sets: 6-311++G(d,p), aug-cc-pVDZ and aug-cc-pVTZ. It was found that the cooperativity effect enhances significantly the F-H...O hydrogen bond; in some of cases one can detect the covalent nature of hydrogen bonding. To deepen the nature of the interactions investigated, the scheme of decomposition of the interaction energy was applied; for stronger H-bonds where the cooperativity is more important, the delocalization energy term increases. The ratio of delocalization energy to electrostatic energy increases for stronger hydrogen bonds where the proton...acceptor distance is shorter. The Bader theory was also applied, and it was found that for stronger H-bonds the electronic energy density at the proton...acceptor bond critical point is negative and may be attributed to the partly covalent interaction.

Interpretation of Hydrogen Bonding in the Weak and Strong Regions Using Conceptual DFT Descriptors

Hydrogen bonding is among the most fundamental interactions in biology and chemistry, providing an extra stabilization of 1-40 kcal/mol to the molecular systems involved. This wide range of stabilization energy underlines the need for a general and comprehensive theory that will explain the formation of hydrogen bonds. While a simple electrostatic model is adequate to describe the bonding patterns in the weak and moderate hydrogen bond regimes, strong hydrogen bonds, on the other hand, require a more complete theory due to the appearance of covalent interactions. In this study, conceptual DFT tools such as local hardness, eta(r) and local softness, s(r), have been used in order to get an alternative view on solving this hydrogen-bonding puzzle as described by Gilli et al. [J. Mol. Struct. 2000, 552, 1]. A series of both homonuclear and heteronuclear resonance-assisted hydrogen bonds of the types O-H...N, N-H...O, N-H...N, and O-H...O with strength varying from weak to very strong have been studied. First of all, DeltaPA and DeltapK(a) values were calculated and correlated to the hydrogen bond energy. Then the electrostatic effects were examined as hard-hard interactions accessible through molecular electrostatic potential, natural population analysis (NPA) charge, and local hardness calculations. Finally, secondary soft-soft interaction effects were entered into the picture described by the local softness values, providing insight into the covalent character of the strong hydrogen bonds.

Heteronuclear Intermolecular Resonance-Assisted Hydrogen Bonds. The Structure of Pyrrole-2-Carboxamide (PyCa)

The crystal and molecular structure of pyrrole-2-carboxamide (PyCa) determined by single crystal X-ray diffraction is presented. Molecular conformations of PyCa are also analyzed by FT-IR and NMR techniques. Additionally DFT calculations at the B3LYP/6-311++G(d,p) level of approximation are performed for dimers of PyCa and for related species. The existence of two tautomeric forms for the analyzed dimers differing in H-bond motifs, N-H...O or O-H...N, is studied. The geometrical and energetic features of such H-bonds show that these interactions may be classified as intermolecular resonance-assisted hydrogen bonds. Additionally the Bader theory is applied to determine and to analyze bond critical points.

How resonance assists hydrogen bonding interactions: An energy decomposition analysis

Block-localized wave function (BLW) method, which is a variant of the ab initio valence bond (VB) theory, was employed to explore the nature of resonance-assisted hydrogen bonds (RAHBs) and to investigate the mechanism of synergistic interplay between pi delocalization and hydrogen-bonding interactions. We examined the dimers of formic acid, formamide, 4-pyrimidinone, 2-pyridinone, 2-hydroxpyridine, and 2-hydroxycyclopenta-2,4-dien-1-one. In addition, we studied the interactions in beta-diketone enols with a simplified model, namely the hydrogen bonds of 3-hydroxypropenal with both ethenol and formaldehyde. The intermolecular interaction energies, either with or without the involvement of pi resonance, were decomposed into the Hitler-London energy (DeltaEHL), polarization energy (DeltaEpol), charge transfer energy (DeltaECT), and electron correlation energy (DeltaEcor) terms. This allows for the examination of the character of hydrogen bonds and the impact of pi conjugation on hydrogen bonding interactions. Although it has been proposed that resonance-assisted hydrogen bonds are accompanied with an increasing of covalency character, our analyses showed that the enhanced interactions mostly originate from the classical dipole-dipole (i.e., electrostatic) attraction, as resonance redistributes the electron density and increases the dipole moments in monomers. The covalency of hydrogen bonds, however, changes very little. This disputes the belief that RAHB is primarily covalent in nature. Accordingly, we recommend the term "resonance-assisted binding (RAB)" instead of "resonance-assisted hydrogen bonding (RHAB)" to highlight the electrostatic, which is a long-range effect, rather than the electron transfer nature of the enhanced stabilization in RAHBs.

The Electron Density of Bridging Hydrides Observed via Experimental and Theoretical Investigations on [Cr2(μ2-H)(Co)10]-

The accurate experimental electron density distribution of [Cr2(mu2-H)(CO)10]- has been determined through X-ray diffraction at T = 28 K and gas phase theoretical calculations. The nature of the Cr-H-Cr bond has been investigated by means of the quantum theory of atoms in molecules, including the analysis of the Fermi hole distribution and the delocalization indicators from the pair density distribution. We were able to clarify not only the delocalization mechanism inside the three-center system but also the unexpected role of the equatorial carbonyls. In addition, the comparative study of a few Cr-H-X three center interactions has provided more insight into the nature of the M-H-M bond itself and has shed light on its peculiar stereochemical flexibility.

Dimers of Formic Acid, Acetic Acid, Formamide and Pyrrole-2-carboxylic Acid: an Ab Initio Study

The intermolecular hydrogen bonds in dimers of formic acid, acetic acid, and formamide were investigated. Additionally, three configurations of the pyrrole-2-carboxylic acid (PCA) dimer were studied to analyze how the pyrrole pi-electron system influences the carboxylic groups connected by double O-H...O hydrogen bonds. The ab initio calculations for the systems investigated were performed at MP2/6-311++G(d,p), MP2/aug-cc-pVDZ, and MP2/aug-cc-pVTZ//MP2/aug-cc-pVDZ levels of theory. The "atoms in molecules" theory of Bader was used and the analysis of the critical points was performed to study the nature of hydrogen bonds. The decomposition of the total interaction energy applied here reveals that the delocalization energy term is a particularly important attractive contribution in these systems, more important in the case of systems forming homonuclear O-H...O double hydrogen bonds than in the case of those connected through heteronuclear N-H...O bonds. Because the systems analyzed may be formally classified as the resonance-assisted hydrogen bonds (RAHBs), it seems that the dominant contribution from the delocalization interaction energy term is a distinguished feature of such interactions.

How Short Can the H···H Intermolecular Contact Be? New Findings that Reveal the Covalent Nature of Extremely Strong Interactions

Ab initio calculations at the MP2/6-311++G(d,p) and MP2/aug-cc-pVDZ//MP2/aug-cc-pVTZ levels have been performed for the following complexes: H2OH+...HBeH, H2OH+...HBeBeH, H2OH+...HBeF, HClOH+...HBeH, Cl2OH+...HBeH, and Cl2OH+...HBeF. For all dimers considered, extremely short H...H intermolecular contacts (1.0-1.3 A) were obtained. These are the shortest intermolecular distances which have ever been reported, with binding energies within the range of 13.7-24.3 kcal/mol (MP2/aug-cc-pVDZ//MP2/aug-cc-pVTZ level). The interaction energies of the complexes analyzed were also extrapolated to the complete basis set (CBS) limit. To explain the nature of such strong interactions, the Bader theory was applied, and the characteristics of the bond critical points (BCPs) were analyzed. It was pointed out that for the major part of the H...H contacts considered here the Laplacian of the electron density at H...H BCP is negative indicating the partly covalent nature of such a connection. The term "covalent character of the hydrogen bond" used sometimes in recent studies is discussed. An analysis of the interaction energy components for dihydrogen bonded systems considered indicates that in contrast to conventional hydrogen bonded systems the attractive electrostatic term is outweighed by the repulsive exchange energy term and that the higher order delocalization energy term is the most important attractive term.

Variable-Temperature X-ray Crystallographic and DFT Computational Study of the NH···O/N···HO Tautomeric Competition in 1-(Arylazo)-2-naphthols. Outline of a Transiton-State Hydrogen-Bond Theory

Phenyl-substituted 1-arylazo-2-naphthols (AAN) display ...HN-N=C-C=O... <==>...N=N-C=C-OH... ketohydrazone-azoenol tautomerism and can form intramolecular resonance-assisted H-bonds from pure N-H...O to pure N...H-O through tautomeric and dynamically disordered N-H...O <==>N...H-O bonds according to the electronic properties of their substituents. Three compounds of this series (m-OCH(3)-AAN = mOM; p-Cl-AAN = pCl; and p-NMe(2)-AAN = pNM2) have been studied by X-ray crystallography at four temperatures (100-295 K), showing that the remarkably short H-bonds formed (2.53 < or = d(N...O) < or = 2.55 A) are a pure N-H...O in mOM, a dynamically disordered mixture in pCl (N-H...O:N...H-O = 69:31 at 100 K), and a statically disordered mixture in pNM2 (N-H...O:N...H-O = 21:79 at 100 K). These compounds, integrated by the p-H-, p-NO(2)-, p-F-, and p-O(-)-substituted derivatives, have been emulated by DFT methods (B3LYP/6-31+G(d,p) level) with full geometry optimization of the stationary points along the proton-transfer (PT) pathway: N-H...O and N...H-O ground states and N...H...O transition state. Analysis of DFT-calculated energies and geometries by the methods of the rate-equilibrium Marcus theory shows that all H-bond features (stability and tautomerism, as well as position and height of the PT barrier) can be coherently interpreted in the frame of the transition-state (or activated-complex) theory by considering the bond as a chemical reaction N-H...O <==> N...H...O <==> N...H-O which is bimolecular in both directions and proceeds via the N...H...O PT transition state (the activated complex).

Dinuclear complexes of a pseudocalixarene macrocycle: structural consequences of intramolecular hydrogen bonding

A series of dinuclear complexes of a pseudocalixarene macrocycle H6L containing two 2,2'-methylenediphenol groups have been synthesised and structurally characterised. Using divalent metal ions, complexes containing a common hyperbolic paraboloid (saddle) M2(H4L)2+ core are formed. The structure is controlled by two strong O-H-O interactions resulting from metal ion-promoted monodeprotonation of the methylenediphenol units. The metal ions are located in a cleft within which neutral or anionic guests can bind. Use of trivalent metal ions leads to complete deprotonation of the phenol groups and loss of the saddle conformation.

Novel organometallic building blocks for molecular crystal engineering. Part 4. Synthesis and characterization of mono- and bis-amido derivatives of [CoIII(η5-C5H4COOH)2]+ and their utilization as ligands

The synthesis and structural characterization of the hexafluorophosphate salts of the substituted bis-amido molecular complexes [Co(III)(eta5-C5H4CONHC4H3N2)2]+ (1), [Co(III)(eta5-C5H4CONHCH2C5H4N)2]+ (2), [Co(III)(eta5-C5H4CON(C5H4N)2)2]+ (3), and of the amido-carboxyl complexes [Co(III)(eta5-C5H4CON(C5H4N)2)(eta5-C5H4COOH)]+ (4), and [Co(III)(eta5-C5H4CONHC2N3(C5H4N)2)(eta5-C5H4COOH)]+ (5) are reported. The pyridyl and pyrazine substituted amido ligands on the sandwich cores have been chosen because they allow both coordination to metal centres and participation in hydrogen bonding. The hydrogen bonding interactions established by the family of complexes in the solid state has been investigated. The utilization of complex 5 for the preparation of the complex of complexes[Cd(NO3)2{Co(III)(eta5-C5H4CONHC2N3(C5H4N)(C5H4NH))(eta5-C5H4COOH)}2]6+ (6) is reported as a first example of the potential of the substituted mono-and bis-amides as ligands. The isolation and structural characterization of the carbonyl chloride cation [Co(III)(eta5-C5H4COCl)2]+ (7) as its tetrachloro cobaltate anion salt is also described.

Covalent versus electrostatic nature of the strong hydrogen bond: discrimination among single, double, and asymmetric single-well hydrogen bonds by variable-temperature X-ray crystallographic methods in beta-diketone enol RAHB systems

Beta-diketone enols are known to form intramolecular...O=C-C=C-OH... resonance-assisted hydrogen bonds (RAHBs) with O...O distances as short as 2.39-2.44 A. However, even the most accurate diffraction studies have not been able to assess with certainty whether these very strong hydrogen bonds (H-bonds) are to be described as proton-centered O...H...O bonds in a single-well (SW) potential or as the dynamic or static mixing of two O-H...O <= => O...H-O tautomers in a double-well (DW) one. This contribution reexamines the problem and shows that diffraction methods are fairly able to assess the SW or DW nature of the H-bond formed and, in the second case, its dynamic or static nature, provided a Bayesian approach is used which associates a number of experimental techniques (X-ray crystallography at variable temperature, difference Fourier maps, least-squares refinement of proton populations, Hirshfeld's rigid-bond test) with a reasonable prior, that is the full set of possible proton-transfer (PT) pathways for the O-H...O system derived from theoretical calculations. The method is first applied to three beta-diketone enols, whose crystal structures were determined in the interval of temperatures 100-295 K and then generalized to the interpretation of a much wider set of beta-diketone enol structures derived from the literature, making it possible to establish a general relationship between chemical structure (symmetric or dissymmetric substitution, steric compression or stretching, increased pi-bond delocalizability), H-bond strength, and the shape of the PT-barrier. Final results are interpreted in terms of simplified VB theory and state-correlation (or avoided-crossing) diagrams.

Structure of a 4-Nitroso-5-aminopyrazole and Its Salts: Tautomerism, Protonation, and E/Z Isomerism

The structures of 1-benzyl-4-nitroso-5-aminopyrazole (1) and its hydrochloride (1H+) have been determined in the solid state and in solution in DMSO, methanol, and ethanol. The free base exists in solution as a mixture of amino/nitroso tautomers 2a and 2b rather than in the imino/oxime tautomers 3. The conjugated cation 1H+ results from the protonation of the nitroso group. X-ray crystallography showed that both amino hydrogen atoms of 2a form NH...O=N hydrogen bonds: one is intramolecular, the other links adjacent molecules in an infinite chain.