On differences between hydrogen bonding and improper blue-shifting hydrogen bonding.

Twenty two hydrogen-bonded and improper blue-shifting hydrogen-bonded complexes were studied by means of the HF, MP2 and B3LYP methods using the 6-31G(d,p) and 6--311 ++G(d,p) basis sets. In contrast to the standard H bonding, the origin of the improper blue-shifting H bonding is still not fully understood. Contrary to a frequently presented idea, the electric field of the proton acceptor cannot solely explain the different behavior of the H-bonded and improper blue-shifting H-bonded complexes. Compression of the hydrogen bond due to different attractive forces-dispersion or electrostatics--makes an important contribution as well. The symmetry-adapted perturbation theory (SAPT) has been utilized to decompose the total interaction energy into physically meaningful contributions. In the red-shifting complexes, the induction energy is mostly larger than the dispersion energy while, in the case of blue-shifting complexes, the situation is opposite. Dispersion as an attractive force increases the blue shift in the blue-shifting complexes as it compresses the H bond and, therefore, it increases the Pauli repulsion. On the other hand, dispersion in the red-shifting complexes increases their red shift.     

Contra-thermodynamic behavior in intermolecular hydrogen transfer of alkylperoxy radicals.

Quantum chemical investigation of bimolecular hydrogen transfer involving alkylperoxy radicals, a key reaction family in the free-radical oxidation of hydrocarbons, was performed to establish structure-reactivity relationships. Eight different reactions were investigated featuring four different alkane substrates (methane, ethane, propane and isobutane) and two different alkylperoxy radicals (methylperoxy and iso-propylperoxy). Including forward and reverse pairs, sixteen different activation energies and enthalpies of reaction were used to formulate structure-reactivity relationships to describe this chemistry. We observed that the enthalpy of formation of loosely bound intermediate states has a strong inverse correlation with the overall heat of reaction and that this results in unique contra-thermodynamic behavior such that more exothermic reactions have higher activation barriers. A new structure-reactivity relationship was proposed that fits the calculated data extremely well: E(A)=E(o)+alphaDeltaH(rxn) where alpha=-0.10 for DeltaH(rxn)<0, and alpha=1.10 for DeltaH(rxn)>0 and E(o)=3.05 kcal mol(-1).     

Hydrogen-hydrogen bonding: a stabilizing interaction in molecules and crystals

Bond paths linking two bonded hydrogen atoms that bear identical or similar charges are found between the ortho-hydrogen atoms in planar biphenyl, between the hydrogen atoms bonded to the C1-C4 carbon atoms in phenanthrene and other angular polybenzenoids, and between the methyl hydrogen atoms in the cyclobutadiene, tetrahedrane and indacene molecules corseted with tertiary-tetra-butyl groups. It is shown that each such H-H interaction, rather than denoting the presence of "nonbonded steric repulsions", makes a stabilizing contribution of up to 10 kcal mol(-1) to the energy of the molecule in which it occurs. The quantum theory of atoms in molecules-the physics of an open system-demonstrates that while the approach of two bonded hydrogen atoms to a separation less than the sum of their van der Waals radii does result in an increase in the repulsive contributions to their energies, these changes are dominated by an increase in the magnitude of the attractive interaction of the protons with the electron density distribution, and the net result is a stabilizing change in the energy. The surface virial that determines the contribution to the total energy decrease resulting from the formation of the H-H interatomic surface is shown to account for the resulting stability. It is pointed out that H-H interactions must be ubiquitous, their stabilization energies contributing to the sublimation energies of hydrocarbon molecular crystals, as well as solid hydrogen. H-H bonding is shown to be distinct from "dihydrogen bonding", a form of hydrogen bonding with a hydridic hydrogen in the role of the base atom.     

Determining the geometry of hydrogen bonds in solids with picometer accuracy by quantum-chemical calculations and NMR spectroscopy.

The structure of multiply hydrogen-bonded systems is determined with picometer accuracy by a combined solid-state NMR and quantum-chemical approach. On the experimental side, advanced 1H-15N dipolar recoupling NMR techniques are capable of providing proton-nitrogen distances of up to about 250 pm with an accuracy level of +/-1 pm for short distances (i.e., around 100 pm) and +/-5 pm for longer ones (i.e., 180 to 250 pm). The experiments were performed under fast magic-angle spinning, which ensures sufficient dipolar decoupling and spectral resolution of the 1H resonance lines. On the quantum-chemical side, the structures of the hydrogen-bonded systems were computationally optimised, yielding complete sets of nitrogen-proton and proton-proton distances, which are essential for correctly interpreting the experimental NMR data. In this way, nitrogen-proton distances were determined with picometer accuracy, so that vibrational averaging effects on dipole-dipole couplings need to be considered. The obtained structures were finally confirmed by the complete agreement of computed and experimental 'H and '5N chemical shifts. This demonstrates that solid-state NMR and quantum-chemical methods ideally complement each other and, in a combined manner, represent a powerful approach for reliable, high-precision structure determination whenever scattering techniques are inapplicable.     

Telomere structure and stability: covalency in hydrogen bonds, not resonance assistance, causes cooperativity in guanine quartets

We show that the cooperative reinforcement between hydrogen bonds in guanine quartets is not caused by resonance-assisted hydrogen bonding (RAHB). This follows from extensive computational analyses of guanine quartets (G(4)) and xanthine quartets (X(4)) based on dispersion-corrected density functional theory (DFT-D). Our investigations cover the situation of quartets in the gas phase, in aqueous solution as well as in telomere-like stacks. A new mechanism for cooperativity between hydrogen bonds in guanine quartets emerges from our quantitative Kohn-Sham molecular orbital (MO) and corresponding energy decomposition analyses (EDA). Our analyses reveal that the intriguing cooperativity originates from the charge separation that goes with donor-acceptor orbital interactions in the σ-electron system, and not from the strengthening caused by resonance in the π-electron system. The cooperativity mechanism proposed here is argued to apply, beyond the present model systems, also to other hydrogen bonds that show cooperativity effects.     

Asymmetry induction by cooperative intermolecular hydrogen bonds in surface-anchored layers of achiral molecules.

The mesoscale induction of two-dimensional supramolecular chirality (formation of 2D organic domains with a single handedness) was achieved by self-assembly of 1,2,4-benzenetricarboxylic (trimellitic) acid on a Cu(100) surface at elevated temperatures. The combination of spectroscopic [X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS)], real-space-probe [scanning tunneling microscopy (STM)], and computational [density functional theory (DFT)] methods allows a comprehensive characterization of the obtained organic adlayers, where details of molecular adsorption geometry, intermolecular coupling, and surface chemical bonding are elucidated. The trimellitic acid species, comprising three functional carboxylic groups, form distinct stable mirror-symmetric hydrogen-bonded domains. The chiral ordering is associated with conformational restriction in the domains: molecules anchor to the substrate with an ortho carboxylate group, providing two para carboxylic acid moieties for collective lateral interweaving through H bonding, which induces a specific tilt of the molecular plane. The ease of molecular symmetry switching in domain formation makes homochiral-signature propagation solely limited by the terrace width. The molecular layer modifies the morphology of the underlying copper substrate and induces mum-sized strictly homochiral terraces.     

Iridium Catalyzed Carbocyclizations: Efficient (5+2) Cycloadditions of Vinylcyclopropanes and Alkynes

Third‐row transition metal catalysts remain a largely untapped resource in cycloaddition reactions for the formation of medium‐sized rings. Herein, we report the first examples of iridium‐catalyzed inter‐ and intramolecular vinylcyclopropane (VCP)–alkyne (5+2) cycloadditions. DFT modeling suggests that catalysis by iridium(I) proceeds through a mechanism similar to that previously reported for rhodium(I)‐catalyzed VCP–alkyne cycloadditions, but a smaller free energy span for iridium enables substantially faster catalysis under favorable conditions. The system is characterized by up to quantitative yields and is amenable to an array of disubstituted alkynes and vinylcyclopropanes.     

Neutral and ionic hydrogen bonding in Schiff bases

Low-temperature, high-resolution X-ray studies of charge distributions in the three Schiff bases, the dianil of 2-hydroxy-5-methylisophthaldehyde, 3,5-dinitro-N-salicylidenoethylamine and 3-nitro-N-salicylidenocyclohexylamine, have been carried out. These structures exhibit interesting weak interactions, including two extreme cases of intramolecular hydrogen bonds that are ionic N(+)-H...O- and neutral O-H...N in nature. These two types of hydrogen bond reflect differences in geometrical parameters and electron density distribution. At the level of geometry, the neutral O-H...N hydrogen bond is accompanied by an increase in the length of the C(1)-O(1) bond, opening of the ipso-C(1) angle, elongation of the aromatic C-C bonds, shortening of the C(7)-N(2) bond and increased length of the C(1)-C(7) bond, relative to the ionic hydrogen bond type. According to the geometrical and critical point parameters, the neutral O-H...N hydrogen bond seems to be stronger than the ionic ones. There are also differences between charge density parameters of the aromatic rings consistent with the neutral hydrogen bond being stronger than the ionic ones, with a concomitant reduction in the aromaticity of the ring. Compounds with the ionic hydrogen bonds show a larger double-bond character in the C-O bond than appears in the compound containing a neutral hydrogen bond; this suggests that the electronic structure of the former pair of compounds includes a contribution from a zwitterionic canonical form. Furthermore, in the case of ionic hydrogen bonds, the corresponding interaction lines appear to be curved in the vicinity of the hydrogen atoms. In the 3-nitro-N-salicylidenocyclohexylamine crystal there exists, in addition to the intramolecular hydrogen bond, a pair of intermolecular O...H interactions in a centrosymmetric dimer unit.     

Controlling the conformation of arylamides: computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers

The role of an ortho-alkylthioether group in controlling the conformation around the ring-N bonds of meta-connected arylamide oligomers is studied. Density functional theory (DFT) geometries of model compounds, including acetanilide, an ether acetanilide, and a thioether acetanilide, and their corresponding diamides, show that for either monoamide or diamide the alkyl side chain of the thioether should be perpendicular to the aryl plane, whereas for the ether monoamide, the alkyl side chain is in the aryl plane. DFT ring-N torsional potentials and constrained geometries of the model compounds demonstrate that carbonyl-S repulsion leads to a high torsional barrier and that intramolecular N-H...S and C-H...O hydrogen bonds and ring-amide conjugation lead to N-H having a preferred orientation in the benzene plane pointing towards S. The N-H bond lengthens and the ortho-ring C-H bond shortens in a regular pattern in the approach to the preferred orientation. Calculated IR frequencies for the N-H stretch show a clear red shift between model compounds without and with the thioether side chain.     

Determining the strengths of hydrogen bonds in solid-state ammonia and urea: insight from periodic DFT calculations

Plane-wave density functional theory has been applied to determine the strengths of hydrogen bonds in the phase I crystal structures of ammonia and urea. For ammonia, each component of the trifurcated hydrogen bond has been found to be almost as strong as a standard N-H.N interaction, and for urea the strengths of the two different N-H.O interactions have been determined by a quantum mechanical technique for the first time.     

Partition potential for hydrogen bonding in formic acid dimers

The ground-state energy and density of 4 low-energy conformations of the formic acid dimer were calculated via partition density functional theory (PDFT). The differences between isolated and PDFT monomer densities display similar deformation patterns for primary and secondary hydrogen bonds (HBs) among all 4 dimers. In contrast, the partition potential shows no transferable features in the bonding regions. These observations highlight the global character of the partition potential and the cooperative effect that occurs when a dimer is bound via more than 1 HB. We also provide numerical confirmation of the intuitive (but unproven) observation that fragment deformation energies are larger for systems with larger binding energies.     

Hydrogen bonding in mimics of Watson-Crick base pairs involving C-H proton donor and F proton acceptor groups: a theoretical study.

We have theoretically analyzed mimics of Watson-Crick adenine-thymine (AT) and guanine-cytosine (GC) base pairs in which N-H...O and N...H-N hydrogen bonds are replaced by N-H...F and N...H-C, respectively, by using the generalized gradient approximation of density functional theory at BP86/TZ2P. The general effect of the above substitutions is an elongation and weakening of the hydrogen bonds that hold together the base pairs. However, the precise effects depend on how many and, in particular, on which hydrogen bonds are substituted in AT and GC. Another purpose of this work is to clarify the relative importance of electrostatic attraction versus orbital interaction in the weak hydrogen bonds involved in the mimics, by using a quantitative bond-energy decomposition scheme. At variance with widespread believe, the orbital interaction component in these weak hydrogen bonds is found to contribute 34-42% of the attractive interactions and is thus of the same order of magnitude as the electrostatic component, which provides the remaining attraction component.