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 M?ller-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.     

Spectroscopic and computational studies of the intramolecular hydrogen bonding of 2-indanol

2-Indanol in its most stable form is stabilized by internal hydrogen bonding, which exists between the hydroxyl hydrogen atom and the pi-cloud of the benzene ring. A comprehensive ab initio calculation using the MP2/cc-pVTZ level of theory showed that 2-indanol can exist in four possible conformations, which can interchange through the ring-puckering vibration and the internal rotation of the OH group on the five-membered ring. A potential energy surface in terms of these two vibrational coordinates was calculated. Density functional theory calculations were used to predict the vibrational frequencies and to help in normal mode assignments. Fluorescence excitation spectra of 2-indanol confirm the presence of the four conformers in the electronic ground and excited states. The spectral intensities indicate that, at 90 degrees C, 82% of the molecules exist in its most stable form with the intramolecular hydrogen bonding. The other isomers are present at approximately 11, 5, and 3%. The MP2/6-311++G(d,p) calculation predicts a distribution of 70, 13, 9, and 8% at 90 degrees C, the experimental sample temperature.     

Theoretical study of hydrogen bonding in homodimers and heterodimers of amide, boronic acid, and carboxylic acid, free and in encapsulation complexes

The homodimers and the heterodimers of two amides, two boronic acids, and two carboxylic acids have been calculated in the gas phase and in N,N-dimethylformamide (DMF) and CCl(4) solvents using the DFT (M06-2X and M06-L) and the MP2 methods in conjunction with the 6-31G(d,p) and 6-311+G(d,p) basis sets. Furthermore, their pairwise coencapsulation was studied to examine its effect on the calculated properties of the hydrogen bonds at the ONIOM[M06-2X/6-31G(d,p);PM6], ONIOM[MP2/6-31G(d,p); PM6], and M06-2X/6-31G(d,p) levels of theory. The present work is directed toward the theoretical rationalization and interpretation of recent experimental results on hydrogen bonding in encaptulation complexes [D. Ajami et al. J. Am. Chem. Soc. 2011, 133, 9689-9691]. The calculated dimerization energy (ΔE) values range from 0.74 to 0.35 eV for the different dimers in the gas phase, with the ordering carboxylic homodimers > amide-carboxylic dimers > amide homodimers > boronic-carboxylic dimers > amide-boronic dimers > boronic homodimers. In solvents, generally smaller ΔE values are calculated with only small variations in the ordering. In the capsule, the ΔE values range between 0.67 and 0.33 eV with practically the same ordering as in the gas phase. The calculated % distributions of the encapsulated dimers, taking into account statistical factors, are in agreement with the experimental distribution, where the occurrence of boronic homodimer dominates, even though it is calculated to have the smallest ΔE.     

Molecular tectonics. Use of the hydrogen bonding of boronic acids to direct supramolecular construction

Tetraboronic acids 1 and 2 have four -B(OH)(2) groups oriented tetrahedrally by cores derived from tetraphenylmethane and tetraphenylsilane. Crystallization produces isostructural diamondoid networks held together by hydrogen bonding of the -B(OH)(2) groups, in accord with the tendency of simple arylboronic acids to form cyclic hydrogen-bonded dimers in the solid state. Five-fold interpenetration of the networks is observed, but 60% and 64% of the volumes of crystals of tetraboronic acids 1 and 2, respectively, remain available for the inclusion of disordered guests. Guests occupy two types of interconnected channels aligned with the a and b axes; those in crystals of tetraphenylmethane 1 measure approximately 5.9 x 5.9 A(2) and 5.2 x 8.6 A(2) in cross section at the narrowest points, whereas those in crystals of tetraphenylsilane 2 are approximately 6.4 x 6.4 A(2) and 6.4 x 9.0 A(2). These channels provide access to the interior and permit guests to be exchanged quantitatively without loss of crystallinity. Because the Si-C bonds at the core of tetraboronic acid 2 are longer (1.889(3) A) than the C-C bonds at the core of tetraboronic acid 1 (1.519(6) A), the resulting network is expanded rationally. By associating to form robust isostructural networks with predictable architectures and properties of porosity, compounds 1 and 2 underscore the usefulness of molecular tectonics as a strategy for making ordered materials.     

The hydrogen bonding properties of cytosine: a computational study of cytosine complexed with hydrogen fluoride, water, and ammonia

Density functional theory is used to study the hydrogen bonding pattern in cytosine, which does not contain alternating proton donor and acceptor sites and therefore is unique compared with the other pyrimidines. Complexes between various small molecules (HF, H(2)O, and NH(3)) and four main binding sites in (neutral and (N1) anionic) cytosine are considered. Two complexes (O2(N1) and N3(N4)) involve neighboring cytosine proton acceptor and donor sites, which leads to cooperative interactions and bidendate hydrogen bonds. The third (less stable) complex (N4) involves a single cytosine donor. The final (O2-N3) complex involves two cytosine proton acceptors, which leads to an anticooperative hydrogen bonding pattern for H(2)O and NH(3). On the neutral surface, the anticooperative O2-N3 complex is less stable than those involving bidentate hydrogen bonds, and the H(2)O complex cannot be characterized when diffuse functions are included in the (6-31G(d,p)) basis set. On the contrary, the anionic O2-N3 structure is the most stable complex, while the HF and H(2)O N3(N4) complexes cannot be characterized with diffuse functions. B3LYP and MP2 potential energy surface scans are used to consider the relationship between the water N3(N4) and O2-N3 complexes. These calculations reveal that diffuse functions reduce the conversion barrier between the two complexes on both the neutral and anionic surfaces, where the reduction leads to a (O2-N3) energy plateau on the neutral surface and complete (N3(N4)) complex destabilization on the anionic surface. From these complexes, the effects of hydrogen bonds on the (N1) acidity of cytosine are determined, and it is found that the trends in the effects of hydrogen bonds on the (N1) acidity are similar for all pyrimidines.     

C-H...O hydrogen bonding in 4-phenyl-benzaldehyde: a comprehensive crystallographic, spectroscopic and computational study

The crystal structure of 4-phenyl-benzaldehyde reveals the presence of a dimer linked by the C=O and C9-H groups of adjacent molecules. In the liquid phase, the presence of C-H...O bonded forms is revealed by both vibrational and NMR spectroscopy. A DeltaH value of -8.2 +/- 0.5 kJ mol(-1) for the dimerisation equilibrium is established from the temperature-dependent intensities of the bands assigned to the carbonyl-stretching modes. The NMR data suggest the preferential engagement of the C(2,6)-H and C(10/12)/C(11)-H groups as hydrogen bond donors, instead of the C(9)-H group. While ab initio calculations for the isolated dimers are unable to corroborate these NMR results, the radial distribution functions obtained from molecular dynamics simulations show a preference for C(2,6)-H and C(10/12)/C(11)-H...O contacts relative to the C(9)-H...O ones.     

Violuric acid monohydrate: a second polymorph with more extensive hydrogen bonding

Crystals of a second polymorph of violuric acid monohydrate [systematic name: pyrimidine‐2,4,5,6(1H,3H)‐tetrone monohydrate], C₄H₃N₃O₄·H₂O, have higher density and a more extensive hydrogen‐bonding arrangement than the previously reported polymorph. Violuric acid and water molecules form essentially planar hydrogen‐bonded sheets, which are stacked in an offset …ABCABC… repeat pattern involving no ring‐stacking interactions.     

Relative importance of hydrogen bonding and coordinating groups in modulating the zinc-water acidity

The presence of second-sphere -NH(2) groups in the proximity of a zinc(ii)-bound water molecule enhances its acidity by ca. 2 pK(a) units.     

Fluoroolefins as peptide mimetics: a computational study of structure, charge distribution, hydration, and hydrogen bonding

The design of peptide mimetic compounds is greatly facilitated by the identification of functionalities that can act as peptide replacements. The fluoroalkene moiety has recently been employed for that purpose. The purpose of this work is to characterize prototypical fluoroalkenes (fluoroethylene and 2-fluoro-2-butene) with respect to key properties of peptides (amides) including structure, charge distribution, hydration, and hydrogen bonding. The results are compared to those obtained for model peptides (formamide, N-methylacetamide). Calculations have been carried out at the MP2 and B3LYP levels of theory with the 6-311++G(2d,p) and 6-311++G(2d,2p) basis sets. The results suggest that the fluoroalkene is similar in steric requirements to a peptide bond but that there is less charge separation. Calculations of the hydration free energies with the PCM bulk continuum solvent model indicate that the fluoroalkene has much smaller hydration free energies than an amide but that the difference in solvation free energy for cis and trans isomers is comparable. In studies of complexes with water molecules, the fluoroalkene is found to engage in interactions that are analogous to backbone hydrogen-bonding interactions that govern many properties of natural peptides and proteins but with smaller interaction energies. In addition, key structural differences are noted when the fluoroalkene is playing the role of hydrogen-bond acceptor which may have implications in binding, aggregation, and conformational preferences in fluoroalkene peptidomimetics. The issue of cooperativity in hydrogen-bonding interactions in complexes with multiple waters has also been investigated. The fluoroalkene is found to exhibit cooperative effects that mirror those of the peptide but are smaller in magnitude. Thus, pairwise addivitity of interactions appears to more adequately describe the fluoroalkenes than the peptides they are intended to mimic.     

Origins of the diastereoselectivity in hydrogen bonding directed Diels-Alder reactions of chiral dienes with achiral dienophiles: a computational study

In this study, the origins of diastereoselectivity in the hydrogen bonding assisted Diels-Alder reactions of chiral dienes with achiral dienophiles have been investigated with density functional methods. The distortion/interaction model has been applied to shed light on the origins of selectivity. C9-Substituted chiral anthracene templates (R = (CH(3))(OCH(3))(H), R = (CH(3))(OH)(H), R = (CH(3))(CH(2)CH(3))(H) and R = (-CH(2)-C(CH(3))(OCH(3))(H)) are used to rationalize the role of a stereogenic center and H-bonding on the product distribution ratio. Even though hydrogen bonding increases the reactivity of the diene, the stereoselectivity is reduced because of the hydrogen bonding capacity of both diastereomeric transition states. The interaction energies of the studied anthracene templates with N-methyl maleimide at the transition state correlate linearly with an increase in reactivity. The selectivity is determined by both favorable distortion and interaction energies. The π-facial selectivity induced by the presence of a chiral auxiliary in 1-substituted 1,3-pentadienes (R1 = (CH(3))(OCH(3))(H) and R1 = (CH(3))(OH)(H)) has also been modeled in order to rationalize the role of the stereogenic center and H-bonding on the stereoselectivity of an aliphatic diene. In both parts, the product distribution ratios calculated from Boltzmann distributions based on Gibbs free energies are in reasonable agreement with the experimental results. Finally the role of OH-substituted five-membered pyrrolidine on C9 of anthracene is investigated since the successful usage of the conformationally rigid pyrrolidines in asymmetric synthesis is well known. Overall, both in the acyclic system and in anthracene, the facilitation due to H-bonding is reflected in the interaction energies: the higher the difference in interaction energies in the transition structures of the two diastereomers, the more selective the H-bonding assisted Diels-Alder reaction is.     

Studies in hydrogen bonding: Association within mixed dimers of water,methanol, ammonia,and methylamine using the empirical potential EPEN

An empirical potential EPEN has been used to find the stable geometries and approximate hydrogenbond energies of the mixed dimers formed between molecules of water, methanol, ammonia, and methylamine. These results are compared with results in the literature obtained using ab initio methods.     

Structure,hydrogen bonding and vibrational spectra of pyruvic acid

The complete vibrational spectra of liquid pyruvic acid and the infrared spectrum of crystalline pyruvic acid at about 20 K have been recorded and analyzed. A vibrational assignment is proposed based on these spectra and comparison with spectra of derivatives of pyruvic acid.The spectra of pyruvic acid can best be interpreted in terms of a cyclic hydrogen-bonded dimer structure in which the two carbonyl groups are in a trans configuration in the pure liquid phase. A similar structure has been reported for crystalline pyruvic acid by X-ray diffraction. In dilute solution the structure appears to be monomeric with an internal hydrogen bond, in essential agreement with the structures of the monomer reported from microwave spectroscopic measurements.     

Studies on hydrogen bonding of adrenaline/acetone and adrenaline/methanol complexes: computational and experimental approach

Structural Chemistry - In this investigation, we elucidate the potential interaction of volatile organic solvents such as acetone and ethanol with adrenaline hormone through hydrogen bonding. There...     

Thermodynamics and kinetics of imidazole formation from glyoxal, methylamine, and formaldehyde: a computational study

Density functional theory calculations, including Poisson-Boltzmann implicit solvent and free energy corrections, are applied to study the mechanism of experimentally observed imidazole formation from the reaction of glyoxal and methylamine in solution. Our calculations suggest that a diimine species is an important intermediate in the reaction. Under acidic conditions, we find that the diimine acts as a nucleophile in attacking the carbonyl group of either formaldehyde or glyoxal to first generate an acyclic enol intermediate, which then goes on to close the ring and form imidazoles. Our results confirm that formaldehyde and, by extension, other small aldehydes are likely to be incorporated into imidazole ions in the presence of glyoxal and primary amines in clouds and aqueous aerosol. This is a new mechanism of aerosol formation by formaldehyde, the most abundant aldehyde in the atmosphere. The amount of aerosol formed will depend on the amounts of glyoxal and amines present.