The basicity of unsaturated hydrocarbons as probed by hydrogen-bond-acceptor ability: bifurcated N-H+ ...pi hydrogen bonding

The competitive substitution of the anion (A(-)) in contact ion pairs of the type [Oct3NH+]B(C6F5)4 (-) by unsaturated hydrocarbons (L) in accordance with the equilibrium Oct3NH+...A(-) + nL right arrow over left arrow [Oct3NH+...Ln]A(-) has been studied in CCl4. On the basis of equilibrium constants, K, and shifts of nuNH to low frequency, it has been established that complexed Oct3NH...+Ln cations with n=1 and 2 are formed and have unidentate and bifurcated N--H+...pi hydrogen bonds, respectively. Bifurcated hydrogen bonds to unsaturated hydrocarbons have not been observed previously. The unsaturated hydrocarbons studied include benzene and methylbenzenes, fused-ring aromatics, alkenes, conjugated dienes, and alkynes. From the magnitude of the redshifts in the N--H stretching frequencies, Delta nuNH, a new scale for ranking the pi basicity of unsaturated hydrocarbons is proposed: fused-ring aromatics相似文献   

Microwave spectrum of 3-butyne-1-thiol: evidence for intramolecular S-H...pi hydrogen bonding

The microwave spectrum of 3-butyne-1-thiol has been studied by means of Stark-modulation microwave spectroscopy and quantum-chemical calculations employing the B3LYP/6-311++G(3df,2pd), MP2/aug-cc-pVTZ, MP2/6-311++G(3df,2pd), and G3 methods. Rotational transitions attributable to two conformers of this molecule were assigned. One of these conformers possesses an antiperiplanar arrangement of the atoms S-C1-C2-C3, while the other is synclinal and stabilized by the formation of an intramolecular hydrogen bond between the H-atom of the thiol group and the pi-electrons of the C[triple bond]C triple bond. The energy difference between these conformers was estimated to be 1.7(4) kJ mol(-1) by relative intensity measurements, with the hydrogen-bonded conformer being lower in energy. The spectra of five vibrationally excited states of the synclinal conformer were observed, and an assignment of these states to particular vibrational modes was made with the aid of a density functional theory (DFT) calculation of the vibrational frequencies at the B3LYP/6-311++G(3df,2pd) level of theory.     

Conformations of protonated gas-phase bradykinin ions: evidence for intramolecular hydrogen bonding

The post-source decay of bradykinin, Lys1-bradykinin, des-Arg1-bradykinin, des-Arg9-bradykinin and [D-Phe7]-bradykinin [M + H]+ ions was examined in order to assertain the influence of secondary structure on peptide ion dissociation. Fragment ions corresponding to the elimination of H2O and HN=C=NH are observed in the product ion mass spectra of Lys1-bradykinin and des-Arg1-bradykinin but not in the spectra of bradykinin or des-Arg9-bradykinin. Cleavage reactions at the Phe-Ser and/or Ser-Pro bonds are observed for all peptide [M + H]+ ions with the exception of des-Arg9-bradykinin. The product ions arising from the processes described above are rationalized in terms of the intramolecular solvation of the protonated guanidino groups of the arginines. The strongest intramolecular interaction appears to be a proton bridge between the guanidino groups of the N- and C-terminal arginines in bradykinin. In addition, increased abundances of fragment ions in the vicinity of Ser-Pro may be attributed to intramolecular solvation of the protonated C-terminal guanidino group by the Ser-Pro portion of the molecule. This self-solvation of the ionizing proton leads to a gas-phase peptide conformation that is supported by solution-phase NMR studies at elevated temperatures and in non-polar solvents but which is different from the conformation in polar solvents.     

The orientation of N-H...O=C and N-H...N hydrogen bonds in biological systems: How good is a point charge as a model for a hydrogen bonding atom?

In order to design new ligands for protein-binding sites of unknownstructure, it would be useful to predict the likely sites of hydrogenbonding of an unknown protein fragment to a known molecule. The positions ofmaxima and minima in the electrostatic potential at appropriate distancesfrom the van der Waals surface were calculated for various small molecules,nucleic acid bases, peptide units and amino acid side chains containinggroups which can form the biologically important N-H...O=C andN-H...N hydrogen bonds. Their ability to predict the positions of H andO/N in hydrogen bonded complexes, as predicted by optimising theelectrostatic interactions of pairs of such molecules constrained by themolecular shapes, was assessed. It is shown that extrema in theelectrostatic potential around the isolated molecules give worthwhilepredictions for the locations of hydrogen bonding partners. For moleculesbound by a single N-H...O=C hydrogen bond, the electrostatic maximumassociated with the H is usually less than 1 Å from an acceptor atom,while a C=O electrostatic minimum is generally less than 1.5 Å fromthe hydrogen bond proton. However, a significant number of hydrogen bondsform to the opposite lone pair from the electrostatic minimum, in which casethe separation is up to 3.3 Å. This reflects the broad electrostaticpotential well around a carbonyl oxygen between the lone pair directions.The model predicts when neighbouring atoms drastically change the hydrogenbonding characteristics of an N-H or C=O group. Although the geometries ofhydrogen bonded complexes are influenced by the other van der Waals contactsbetween the molecules, particularly multiple hydrogen bonds, theseinfluences are constant when considering hydrogen bonding to a specificuncharacterised binding site. Hence, the consideration of stericallyaccessible electrostatic extrema will be useful in the design of newligands.     

N-H...S hydrogen bonds in a ferredoxin model

The Fe4S4 complex {(CH3)3NCH2CONH2}2[Fe4S4((tBuS)4] (1) was synthesized to replicate the ferredoxin active site with a subset of its N-H...S hydrogen bonds. The two cationic counterions mimic the polypeptide backbone of ferredoxin (Fd) as amide hydrogen-bond donors to sulfur atoms of the iron-sulfur cluster. X-ray crystallographic data show that the organic sulfur (Sgamma) of one tert-butylthiolate ligand and one inorganic sulfur of the cluster core serve as N-H...S hydrogen-bond acceptors. The cluster core of complex 1 is tetragonally elongated in contrast to that of Fd, which is tetragonally compressed. This is the first observation of an elongated [Fe4S4]2+ cluster core. Additionally, this is the first synthetic Fd model in which N-H...S hydrogen bonding to a cluster has been achieved.     

Antioxidant activity of o-bisphenols: the role of intramolecular hydrogen bonding

A kinetic and thermodynamic investigation on the antioxidant activity of 2,2'-methylenebis(6-tert-butyl-4-methylphenol) (2), 2,2'-ethylidenebis(4,6-di-tert-butylphenol) (3), and 4,4'-methylenebis(2,6-di-tert-butylphenol) (4) are reported. EPR studies of the equilibration between 3 or 4 and a reference phenol, and the corresponding phenoxyl radicals, allowed us to determine the O-H bond dissociation enthalpy (BDE) of the O-H bond as 81.2 and 81.1 kcal/mol in 3 and 4, respectively. Despite this similarity, the absolute rate constants for the reaction with peroxyl radicals, determined by autoxidation studies under controlled conditions, indicate that the o-bisphenols 2 and 3 behave as excellent antioxidants while the p-bisphenol 4 is less effective by a factor of 64 and 22, respectively. FT-IR spectroscopy and product studies suggest that the very good antioxidant activity of the o-bisphenols largely arises from both the reduced steric crowding about the hydroxyl group and the stabilization of the aroxyl radical due to the formation of an intramolecular hydrogen bond between the residual OH and the oxygen radical center.     

N-H...pi interactions in pyrroles: systematic trends from the vibrational spectroscopy of clusters

Pyrrole and some of its methylated derivatives are aggregated in a controlled way in pulsed supersonic jet expansions. The cluster N-H stretching dynamics is studied using FTIR and Raman spectroscopy. Dimers, trimers and tetramers can be differentiated. Systematic trends in the dimer N-H...pi interaction as a function of methyl substitution are identified and explored for predictions. Overtone jet absorption spectroscopy is used to extract anharmonicities for the N-H bond in different environments. The N-H anharmonicity constant increases by 10% upon dimerization. Bulk matrix shifts can be emulated by the formation of Ar-decorated clusters. The experimental results are expected to serve as benchmarks for an accurate ab initio characterization of the N-H...pi hydrogen bond.     

Theoretical study of hydrogen bonding interaction in nitroxyl (HNO) dimer: interrelationship of the two N-H...O blue-shifting hydrogen bonds

The hydrogen bonding interactions of the HNO dimer have been investigated using ab initio molecular orbital and density functional theory (DFT) with the 6-311++G(2d,2p) basis set. The natural bond orbital (NBO) analysis and atom in molecules (AIM) theory were applied to understand the nature of the interactions. The interrelationship between one N-H...O hydrogen bond and the other N-H...O hydrogen bond has been established by performing partial optimizations. The dimer is stabilized by the N-H...O hydrogen bonding interactions, which lead to the contractions of N-H bonds as well as the characteristic blue-shifts of the stretching vibrational frequencies nu(N-H). The NBO analysis shows that both rehybridization and electron density redistribution contribute to the large blue-shifts of the N-H stretching frequencies. A quantitative correlations of the intermolecular distance H...O (r(H...O)) with the parameters: rho at bond critical points (BCPs), s-characters of N atoms in N-H bonds, electron densities in the sigma*(N-H), the blue-shift degrees of nu(N-H) are presented. The relationship between the difference of rho (|Deltarho|) for the one hydrogen bond compared with the other one and the difference of interaction energy (DeltaE) are also illustrated. It indicates that for r(H...O) ranging from 2.05 to 2.3528 A, with increasing r(H...O), there is the descending tendency for one rho(H...O) and the ascending tendency for the other rho(H...O). r(H...O) ranging from 2.3528 to 2.85 A, there are descending tendencies for the two rho(H...O) with increasing r(H...O). On the potential energy surface of the dimer, the smaller the difference between one rho(H...O) and the other rho(H...O) is, the more stable the structure is. As r(H...O) increases, the blue-shift degrees of nu(N-H) decrease. The cooperative descending tendencies in s-characters of two N atoms with increasing r(H...O) contribute to the decreases in blue-shift degrees of nu(N-H). Ranging from 2.05 to 2.55 A, the increase of the electron density in one sigma*(N-H) with elongating r(H...O) weakens the blue-shift degrees of nu(N-H), simultaneously, the decrease of the electron density in the other sigma*(N-H) with elongating r(H...O) strengthens the blue-shift degrees of nu(N-H). Ranging from 2.55 to 2.85 A, the cooperative ascending tendencies of the electron densities in two sigma*(N-H) with increasing r(H...O) contribute to the decreases in blue-shift degrees of nu(N-H).     

Preorganization-enhanced halogen bonding via intramolecular hydrogen bonding: a theoretical study

Structural Chemistry - Cationic and neutral halogen bonding (XB) donors use two types (I and II) of intramolecular hydrogen bonding (HB) to preorganize structures and increase the efficiency of...     

Halogen bonding and pi...pi stacking control reactivity in the solid state

The halogen bonding and the pi...pi stacking interactions induce the noncovalent self-assembly of modules into photoreactive supramolecular architecture. The pi...pi interaction pre-organizes the template, and the halogen bonding aligns the olefins to conform to the topochemical principle for photoreaction. The UV irradiation of the crystal resulted in a cyclization product with quantitative yield and stereospecificity.     

N-methylformamide-benzene complex as a prototypical peptide N-H...pi hydrogen-bonded system: density functional theory and MP2 studies

Although the existence of peptide N-H...pi hydrogen bonds recently has been reported in protein structures, little is known about their strength and binding nature and, therefore, the relative importance of the interaction. To shed light on this binding, the N-methylformamide-benzene complex, as a model of the peptide N-H...pi hydrogen bonding, was studied by using density functional theory and M?ller-Plesset second-order perturbation (MP2) methods. The geometry of the complex was fully optimized at the B3LYP/6-31G(d,p) and MP2/6-31G(d,p) levels. The optimized interaction distances are about 3.6 and 3.2 A, respectively, at the two levels. The binding energy corrected by basis set superposition error with the MP2/cc-pVTZ method based on the MP2/6-31G geometry is -4.37 kcal/mol, which is as strong as the conventional hydrogen bonding. The calculated results suggest that the peptide N-H...pi hydrogen bonding is of sufficient strength to play an important role in the stabilization of protein structures. These results are helpful to better understand the characteristics and nature of the peptide N-H...pi interaction as well as to modify current force fields to better represent this special interaction.     

The role of hydrogen bonding in excited state intramolecular charge transfer

Intramolecular charge transfer (ICT) that occurs upon photoexcitation of molecules is a vital process in nature and it has ample applications in chemistry and biology. The ICT process of the excited molecules is affected by several environmental factors including polarity, viscosity and hydrogen bonding. The effect of polarity and viscosity on the ICT processes is well understood. But, despite the fact that hydrogen bonding significantly influences the ICT process, the specific role of hydrogen bonding in the formation and stabilization of the ICT state is not unambiguously established. Some literature reports predicted that the hydrogen bonding of the solvent with a donor promotes the formation of a twisted intramolecular charge transfer (TICT) state. Some other reports stated that it inhibits the formation of the TICT state. Alternatively, it was proposed that the hydrogen bonding of the solvent with an acceptor favors the TICT state. It is also observed that a dynamic equilibrium is established between the free and the hydrogen bonded ICT states. This perspective focuses on the specific role played by hydrogen bonding of the solvent with the donor and the acceptor, and by proton transfer in the ICT process. The utility of such influence in molecular recognition and anion sensing is discussed with a few recent literature examples in the end.     

Nanosecond time-resolved IR emission from molecules excited in a supersonic jet: intramolecular dynamics of NO2 near dissociation

IR emission from NO2 cooled in a supersonic jet and excited to a single, B 2B1 state rovibronic level at 22 994.92 cm(-1) above the ground-state zero point was detected with 10(-8)-s time resolution. The IR emission together with the laser-induced fluorescence decay measurement allows the deduction of the relaxation dynamics near the dissociation of NO2. Following the excitation this single rovibronic B 2B1 level decays on 1.0-s time scale primarily through electronic radiation. Collisions induce internal conversion with a rate constant of 3.0 x 10(7) Torr(-1) s(-1) to the mixed AX states. Collisions further induce internal conversion of the AX mixed states into highly vibrationally excited levels in the X states with a rate constant at least one order of magnitude slower. This mechanism results in the observation of a double-exponential decay in the laser-induced fluorescence and a rise in the IR emission intensity corresponding to the fast decay in the fluorescence intensity. The IR emission rate of the highly vibrationally excited X-state levels is estimated to be about one order of magnitude larger than the isoenergetic AX mixed states and much larger than the B 2B1 level, both with much less vibrational excitation.     

Study of geometrical parameters in N-H...N type of hydrogen bonds

Geometrical parameters associated with N-H ... N types of hydrogen bonds have been analysed using crystal structure data on nucleic acids, amino acids and related compounds. Histograms depicting the frequency distribution of N-H ... N length (l) and H-N ... N angle (θ) have been drawn and conclusions on the favoured geometry of such bonds have been arrived at. The distribution ofl shows a pronounced maximum in the range between 2.9? and 3.0? with an overall average of 2.98 ?. The θ distribution shows a pronounced maximum for the hydrogen bond angle in the range 0°-10°, with a rapid fall-off in frequency for nonlinear hydrogen bonds. The frequency shows a cos⁶θ dependence as compared to cos²θ dependence term used earlier to predict the angular dependence of hydrogen bond potential energy in proteins and polypeptides.     

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.     

The molecular structure of the tris(2-mercapto-1-tolylimidazolyl)hydroborato zinc(2-mercapto-1-tolylimidazole) complex, [[Tm(p-Tol)]Zn(mim(p-Tol))][ClO4]: intermolecular N-H...OClO3versus intramolecular N-H...S hydrogen bonding interactions of the mercaptoimidazole ligand

The molecular structure of the tris(2-mercapto-1-tolylimidazolyl)hydroborato complex [[Tm(p-Tol)]Zn(mim(p-Tol))][ClO(4)].3MeCN has been determined by X-ray diffraction, thereby demonstrating that the mim(p-Tol) ligand exhibits a N-H...O hydrogen bond with the [ClO(4)](-) counterion, [[Tm(p-Tol)]Zn(mim(p-Tol))...(OClO(3))], rather than hydrogen bond with a sulfur of the [Tm(p-Tol)] ligand. DFT calculations on a series of related complexes, namely [[Tm(Me)]Zn(mim(Me))](+), [[Tm(Me)]Zn(mim(Me))]...(OClO(3))], [[Tm(Me)]Zn(mim(Me))]...[O(H)Me]](+), and [[Tm(Me)]Zn(mim(Me))]...(NCMe)](+) demonstrate that an intramolecular N-H...S hydrogen bond within [[Tm(Me)]Zn(mim(Me))](+) is also less favored than the corresponding hydrogen bonding interactions with MeCN, MeOH, and [ClO(4)](-). The inability of the sulfur atoms of [Tm(R)] ligand to act as an effective hydrogen bond acceptor is in marked contrast to the ability of sulfur atoms in thiolate ligands to participate in the formation of N-H...S hydrogen bonds, an observation that reflects the "thione"versus"thiolate" nature of the [Tm(R)] ligand.     

Insights into DNA binding of ruthenium arene complexes: role of hydrogen bonding and pi stacking

Density functional theory (DFT) methods are used to investigate the binding of ruthenium arene complexes, proposed as promising anticancer drugs, to isolated nucleobases. This shows a clear preference for binding at guanine over any other base and an approximately 100 kJ mol (-1) difference in binding between guanine and adenine in the gas phase, while binding to cytosine and inosine are intermediate in energy between these extremes. Solvation reduces binding energies and the discrimination between bases but maintains the overall pattern of binding. DFT and ab initio data on arene-base interactions in the absence of ruthenium show that stacking and hydrogen-bonding interactions play a significant role but cannot account for all of the energy difference between bases observed. Atoms-in-molecules analysis allows further decomposition of binding energies into contributions from covalent-binding, hydrogen-bonding, and pi-stacking interactions. Larger arenes undergo stabilizing stacking interactions, whereas N-H...X hydrogen bonding is independent of arene. Pairing of guanine to cytosine is affected by ruthenium complexation, with individual hydrogen-bonding energies being altered but the overall pairing energy remaining almost constant.     

Oxa-bicyclocalixarenes: a new cage for anions via C-H...anion hydrogen bonds and anion...pi interactions

Density functional theory calculations indicate that the cage molecule 4 can trap F- in the gas phase (-80.5 kcal/mol) as well as in CH2Cl2 (-14.7 kcal/mol) via strong C-H...F- hydrogen bonds and pi...F- interaction.