Bifurcate hydrogen bonds. Interaction of intramolecularly H-bonded systems with Lewis bases

The structure and the hydrogen bonding in the systems formed by the intramolecularly H-bonded systems, namely, maltol (3-hydroxy-2-methyl-4-pyrone), 5, 2,4,6-trinitrophenol, 6, acetylacetone enol, 7, with Lewis bases, phosgene, 8, dioxane, 9, and DMSO, 10, have been studied by density functional theory (B3LYP) and MP2 using the 6-311G* basis set. The continuum solvent effect was simulated by IEF-PCM model. The hydrogen bond analysis using the atoms in molecules (AIM) method was applied by using the MP2(full)/6-311++G** electron density to establish the nature of the bifurcate hydrogen bond (BHB) in these systems as well as contributory factors for its stabilization. The nature of interaction in the intermolecular H-complexes formed by compounds 5- 7 with the Lewis bases 8- 10 was shown to depend on the strength of the intramolecular hydrogen bond O...H and the strength of the base. The critical values of the CO...H and NO...H angles for which the formation of BHB is possible, have been determined.     

The nature and energy characteristics of intramolecular hydrogen bonds in crystals

The review concerns the results of systematic X-ray diffraction studies of the electron density distribution in the crystals of compounds with strong intramolecular hydrogen bonds N-H...O, O-H...O, O-H...N, and N-H...S. The advantages of the topological analysis of the electron density distribution function in the analysis of the nature and estimation of the H-bond energies directly from experimental data are discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 1–14, January, 2006.     

MNDO calculations of systems containing hydrogen bonds

A modified MNDO method, which can be used in the studies on structures with hydrogen bonds X-H-X, X, X = N, O, is described. Results for a wide range of molecular complexes are reported. Energies of hydrogen bonds are reproduced with useful accuracy. The modified MNDO seems to give more reliable values of hydrogen bond energies and barrier heights of proton transfers than 4-31G ab initio model.     

The possible covalent nature of N-H...O hydrogen bonds in formamide dimer and related systems: an ab initio study

The N-H...O hydrogen bonds are analyzed for formamide dimer and its simple fluorine derivatives representing a wide spectrum of more or less covalent interactions. The calculations were performed at the MP2/6-311++G(d,p) level of approximation. To explain the nature of such interactions, the Bader theory was also applied, and the characteristics of the bond critical points (BCPs) were analyzed: the electron density at BCP and its Laplacian, the electron energy density at BCP and its components, the potential electron energy density, and the kinetic electron energy density. These parameters are used to justify the statement that some of the interactions analyzed are partly covalent in nature. An analysis of the interaction energy components for the systems considered indicates that the covalent character of the hydrogen bond is manifested by a markedly increased contribution of the delocalization term relative to the electrostatic interaction energy. Moreover, the ratio of stabilizing the delocalization/electrostatic contributions grows linearly with the decreasing lengths of the hydrogen bond.     

MNDO calculations of systems with hydrogen bonds S-H

The MNDO method has been modified for the calculation of the properties of complexes with hydrogen bonds S-H-X, X = N, O, F, S. The results obtained are in good agreement with the experimental data.     

Probing the nature of three-centered hydrogen bonds in minor-groove ligand-DNA interactions: the contribution of fluorine hydrogen bonds to complex stability

Double-stranded DNA sequences have been prepared in which single atoms (the O2-carbonyls of selected thymines) have been replaced by fluorine or methyl. To maintain normal Watson-Crick hydrogen bonding with the complementary purines, these analogue derivatives have been prepared as C-nucleosides. The O2-carbonyls of interest for this study are those involved in a bifurcated (or three-centered) hydrogen bond with the minor groove binding ligand 4',6-diamidino-2-phenylindole (DAPI). TM studies of the duplexes illustrate that the DNA duplexes are destabilized when fluorine or methyl replaces one or both of the minor groove O2-carbonyls, which can in part be explained by changes in minor groove hydration. In the presence of DAPI, most of the duplexes exhibit an increased TM due to the presence of DAPI bound in the minor groove. The extent of helix overstabilization negatively correlates with the presence of one or both methyl groups in the minor groove, suggesting that ligand binding is weakened in the presence of the non-carbonyl functional groups. The presence of single fluorine appears to promote helix stabilization, and native-like stabilization occurs when both fluorines are present. KD values quantitate binding effects between DAPI and the native and analogue sequences. Sequences with one or both methyl groups exhibit very poor binding with DAPI, while those containing a single fluorine behave essentially like native carbonyl-containing sequences. With both fluorines present, KD values were observed to increase by a moderate 3-fold at 100 mM NaCl and somewhat more at 200 mM NaCl. Binding affinities with both methyl groups present were 500-1000-fold weaker than native. The results suggest that organofluorines can function as hydrogen-bond acceptors, at least in the bifurcated interaction that contributes to minor groove binding by DAPI.     

Pion study of hydrogen bonds of water in chemical systems

The use of the pion capture method in structural chemistry is demonstrated by experiments performed in Dubna on various hydrogen-bonded chemical systems: pure water and ammonia in solid, liquid, and gaseous phases; aquacompiexes; and solutions of acids and salts. The experimental information, the capture probability of stopped ^– mesons by protons, is related to the electron density near the proton in the molecule.     

Hydrogen bonds, improper hydrogen bonds and dihydrogen bonds

The structures, interaction energies and vibrational spectra of a large number of molecular complexes, formed by binary combination of the covalent hydrides of some of the elements of the first two rows of the periodic table, have been determined by means of ab initio molecular orbital theory at the MP2 level, using the 6-311++G(d,p) basis set. The results are discussed in terms of a variety of different types of interaction experienced by the monomer species as they undergo association, namely conventional hydrogen bonding, improper hydrogen bonding, dihydrogen bonding and electron donor–acceptor interaction.     

The degree of rotation independence of conjugation of S-N bonds

The electron delocalization in pi-electron systems is frequently described qualitatively by the concept of conjugation between formal double bonds separated by a formal single bond. In carbon compounds the optimum conjugation usually requires a rather strict, geometrical condition: the exact or near coplanarity of the participating carbon atoms. However, the geometrical conditions are much less strict for third-row atoms if the bonding involves valence-shell d orbitals. In some sulfur compounds, such as N-sulfonylsulfilimines, the conjugation is almost unaffected within large ranges of bond-rotation angles, which amounts to rotation-independent conjugation. On the basis of the indications of earlier, limited studies using only minimal basis set and no geometry optimization, in the more extensive present study Density Functional Theory B3LYP calculations using 6-31G basis set provide more reliable evidence for such flexible conjugation in some sulfur compounds and give an explanation for the experimentally observed interconversion of chiral conformers of N-sulfonylsulfilimines.     

The proton potential in short hydrogen bonds

The state of knowledge of the proton potential in systems for which double minimum and symmetrical, single minimum type curves have been envisaged is critically reviewed. In particular, the proposed model potentials for carboxylic acids, for KDP type ferroelectrics and for the shortest hydrogen bonds are confronted with experimental data, particularly from vibrational spectra. The early attempts at explaining the complex features in the AH stretching region by level splitting in one-dimensional double minimum potentials have not been successful. The interest in the profile of the potential surface is shifted from this aspect to its role in anharmonic interaction based general band-shaping mechanisms.     

Role of hydrogen bonds in controlling the morphology of self-assembling carbamate systems

With a view to understand the role of hydrogen bonding in controlling the morphology of self-assembling carbamate systems, N-octadecylcarbamate dodecyl ester was blended individually with a low molecular weight polyethylene and two commercial clarifiers, namely Kemamide S and Kemamide E 180. The effect of blending on the morphology of this long chain carbamate was investigated using optical microscopy, differential scanning calorimetry, and X-ray diffraction. The crystal structure of the carbamate was not affected by the addition of polyethylene or Kemamide S. The heterogeneous nucleation of the carbamate by the polyethylene or Kemamide S resulted in the reduction of the spherulite size of the carbamate, but it did not improve the transparency of the sample due to phase separation. On the other hand, significant improvement of transparency was achieved when the carbamate was blended with Kemamide E 180. Blending reduced the crystallite and spherulite size, heat of fusion, and crystallinity. An exchange of hydrogen bonds between the carbamate and Kemamide E is indicated in the IR spectra, and this affects the packing of the alkyl chains of the carbamates. This heterogeneous blending shows similar effects on the morphology as was achieved by blending two homologous carbamates in our previous study (J. Phys. Chem. B 2003, 107, 8416).     

The role of hydrogen bonds in Baeyer-Villiger reactions

Various Baeyer-Villiger (B-V) oxidation reactions were examined by density functional theory calculations. Proton movements in transition states (TSs) of the two key steps, the nucleophilic addition of a peroxyacid molecule to a ketone (TS1) and the migration-cleavage of O-O (TS3), were discussed. A new TS of a hydrogen-bond rearrangement in the Criegee intermediate (TS2) was found. The hydrogen-bond directionality requires a trimer of the peroxyacid molecules at the nucleophilic addition of a peroxyacid molecule to a ketone TS (TS1). At the migration-cleavage of O-O TS (TS3), also three peroxyacid molecules are needed. Elementary processes of the B-V reaction were determined by the use of the (acetone and (H-CO-OOH)n, n=3) system. The geometries of the nucleophilic addition of a peroxyacid molecule to a ketone TS (TS1) and the migration-cleavage of O-O TS (TS3) in the trimer (n=3) participating are nearly insensitive to the substituent on the peroxyacid. The directionality is satisfied in those geometries. The migration-cleavage of O-O TS (TS3) was found to be rate-determining in reactions, [Me2C=O+(H-CO-OOH)3], [Me2C=O+(F3C-CO-OOH)3], and [Me2C=O+(MCPBA)3]. In contrast, the nucleophilic addition of a peroxyacid molecule to a ketone (TS1) is rate-determining in the reaction, [Ph(Me)C=O+(H-CO-OOH)3].     

Ionic hydrogen bonds controlling two-dimensional supramolecular systems at a metal surface

Hydrogen-bond formation between ionic adsorbates on an Ag(111) surface under ultrahigh vacuum was studied by scanning tunneling microscopy/spectroscopy (STM/STS), X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS), and molecular dynamics calculations. The adsorbate, 1,3,5-benzenetricarboxylic acid (trimesic acid, TMA), self-assembles at low temperatures (250-300 K) into the known open honeycomb motif through neutral hydrogen bonds formed between carboxyl groups, whereas annealing at 420 K leads to a densely packed quartet structure consisting of flat-lying molecules with one deprotonated carboxyl group per molecule. The resulting charged carboxylate groups form intermolecular ionic hydrogen bonds with enhanced strength compared to the neutral hydrogen bonds; this represents an alternative supramolecular bonding motif in 2D supramolecular organization.     

The role of weak hydrogen bonds in chiral recognition

Chiral recognition has been studied in neutral or ionic weakly bound complexes isolated in the gas phase by combining laser spectroscopy and quantum chemical calculations. Neutral complexes of the two enantiomers of lactic ester derivatives with chiral chromophores have been formed in a supersonic expansion. Their structure has been elucidated by means of IR-UV double resonance spectroscopy in the 3 μm region. In both systems described here, the main interaction ensuring the cohesion of the complex is a strong hydrogen bond between the chromophore and methyl-lactate. However, an additional hydrogen bond of much weaker strength plays a discriminative role between the two enantiomers. For example, the 1:1 heterochiral complex between R-(+)-2-naphthyl-ethanol and S-(+) methyl-lactate is observed, in contrast with the 1:1 homochiral complex which lacks this additional hydrogen bond. On the other hand, the same kind of insertion structures is formed for the complex between S-(±)-cis-1-amino-indan-2-ol and the two enantiomers of methyl-lactate, but an additional addition complex is formed for R-methyl-lactate only. This selectivity rests on the formation of a weak CHπ interaction which is not possible for the other enantiomer. The protonated dimers of Cinchona alkaloids, namely quinine, quinidine, cinchonine and cinchonidine, have been isolated in an ion trap and studied by IRMPD spectroscopy in the region of the ν(OH) and ν(NH) stretch modes. The protonation site is located on the alkaloid nitrogen which acts as a strong hydrogen bond donor in all the dimers studied. While the nature of the intermolecular hydrogen bond is similar in the homochiral and heterochiral complexes, the heterochiral complex displays an additional weak CHO hydrogen bond located on its neutral part, which results in slightly different spectroscopic fingerprints in the ν(OH) stretch region. This first spectroscopic evidence of chiral recognition in protonated dimers opens the way to the study of the complexes of Cinchona alkaloids involved in enantioselective catalysis. These examples show how secondary hydrogen bonds controlled by stereochemical factors govern molecular recognition processes.     

Counterpoise-corrected potential energy surfaces of simple H-bonded systems

Geometries and stabilization energies of various simple H-bonded complexes (water dimer, hydrogen fluoride dimer, formamide dimer, formic acid dimer) have been determined by a gradient optimization that eliminates the basis set superposition error (BSSE) by the counterpoise (CP) method in each gradient cycle as well as by the standard gradient optimization. Both optimization methods lead to different potential energy surfaces (PES). The difference depends on the theoretical level used and is larger if correlation energy is considered. Intermolecular distances from the CP-corrected PES are consistently longer, and this difference might be significant (∼0.1 ?); also angular characteristics determined from both surfaces differ significantly. Different geometries were obtained even when passing to larger basis sets (aug-cc-pVDZ). The standard optimization procedure can result in a completely wrong structure. For example, the “quasi-linear” structure of the (HF)₂ (global minimum) does not exist at the standard MP2/ 6-31G** PES (where only cyclic structure was detected) and is found only at the CP-corrected PES. Stabilization energies obtained from the CP-corrected PES are always larger than these from the standard PES where the BSSE is added only a posteriori for the final optimized structure; both energies converge only when passing to a larger basis set (aug-cc-pVDZ). Received: 11 March 1998 / Accepted: 19 June 1998 / Published online: 4 September 1998 RID=" ID=" <E6>Acknowledgements.</E6> The project was supported by the Grant Agency of the Czech Republic (Grant No. 203/98/1166). RID=" ID=" <E5>Correspondence to</E5>: P. Hobza