Characterization of highly unusual NH+-O hydrogen bonding to ester ether oxygen atoms through spectroscopic and computational studies

We characterize a highly unusual, charged NH-O hydrogen bond formed within esters of 8-(dimethylamino)naphthalen-1-ol in which an ammonium ion serves as an intramolecular hydrogen bond donor to spatially proximate ester ether oxygen atoms. Infrared spectroscopic analysis of the ester carbonyl frequencies demonstrates significant blue-shifting when ether hydrogen bonding is possible, in stark contrast to the more commonly observed red shift that occurs upon hydrogen bonding to the ester carbonyl oxygen. The intrinsic behavior of the linkage (i.e., in which counterions and solvent effects are eliminated) is provided by vibrational predissociation spectroscopy of the isolated gas-phase cations complexed with weakly bound D(2) molecules.     

Structure of 7-azaindole···2-fluoropyridine dimer in a supersonic jet: competition between N-H···N and N-H···F interactions

In the present work, we have investigated the structure of 7-azaindole···2-fluoropyridine dimer in a supersonic jet by employing resonant two photon ionization (R2PI), IR-UV, and UV-UV double resonance spectroscopic techniques combined with quantum chemistry calculations. The R2PI spectrum of the dimer is recorded by electronic excitation of the 7-azaindole moiety, and a few low frequency intermolecular vibrations of the dimer are clearly observed in the spectrum. The electronic origin band of the dimer is red-shifted by 1278 cm(-1) from the S(1) ← S(0) origin band of 7-azaindole monomer. The presence of a single conformer of the dimer is confirmed by IR-UV and UV-UV hole-burning spectroscopic techniques. RIDIR (Resonant ion dip infrared) spectrum of the dimer shows a red-shift of 265 cm(-1) in the N-H stretching frequency with respect to that of the 7-azaindole monomer. Two planar double hydrogen bonded cyclic structures of the dimer have been predicted from DFT calculations. Comparison of experimental and theoretical N-H stretching frequencies confirms that the observed dimer is stabilized by N-H···N and C-H···N hydrogen bonding interactions. The less stable conformer with N-H···F and C-H···N interactions are not observed in the experiment. The competition between N-H···N and N-H···F interactions in the two dimeric structures are discussed from natural bond orbital (NBO) analysis. The current results demonstrate that fluorine makes a hydrogen bond of intermediate strength through cooperative interaction of another hydrogen bond (C-H···N) present in the dimer, although fluorine is believed to be very weak hydrogen bond acceptor.     

The gold-ammonia bonding patterns of neutral and charged complexes Au m 0+/-1-(NH3)n. I. Bonding and charge alternation

The gold-ammonia bonding patterns of the complexes which are formed between the ammonia clusters (NH(3))(1< or =n< or =3) and gold clusters of different sizes that range from one gold atom to the tri-, tetra-, and 20-nanogold clusters are governed by two basic and fundamentally different ingredients: the anchoring Au-N bond and the nonconventional N-H...Au hydrogen bond. The latter resembles, by all features, a conventional hydrogen bond and is formed between a typical conventional proton donor N-H group and the gold cluster that behaves as a nonconventional proton acceptor. We provide strong computational evidence that the gold-ammonia bonding patterns exhibit distinct characteristics as the Z charge state of the gold cluster varies within Z=0,+/-1. The analysis of these bonding patterns and their effects on the N-H...N H-bonded ammonia clusters are the subject of this paper.     

Dependence of amide vibrations on hydrogen bonding

The effect of hydrogen bonding on the amide group vibrational spectra has traditionally been rationalized by invoking a resonance model where hydrogen bonding impacts the amide functional group by stabilizing its [(-)O-C=NH (+)] structure over the [O=C-NH] structure. However, Triggs and Valentini's UV-Raman study of solvation and hydrogen bonding effects on epsilon-caprolactum, N, N-dimethylacetamide (DMA), and N-methylacetamide (NMA) ( Triggs, N. E.; Valentini, J. J. J. Phys. Chem. 1992, 96, 6922-6931) casts doubt on the validity of this model by demonstrating that, contrary to the resonance model prediction, carbonyl hydrogen bonding does not impact the AmII' frequency of DMA. In this study, we utilize density functional theory (DFT) calculations to examine the impact of hydrogen bonding on the C=O and N-H functional groups of NMA, which is typically used as a simple model of the peptide bond. Our calculations indicate that, as expected, the hydrogen bonding frequency dependence of the AmI vibration predominantly derives from the C=O group, whereas the hydrogen bonding frequency dependence of the AmII vibration primarily derives from N-H hydrogen bonding. In contrast, the hydrogen bonding dependence of the conformation-sensitive AmIII band derives equally from both C=O and N-H groups and thus, is equally responsive to hydrogen bonding at the C=O or N-H site. Our work shows that a clear understanding of the normal mode composition of the amide vibrations is crucial for an accurate interpretation of the hydrogen bonding dependence of amide vibrational frequencies.     

Vibrational dynamics of N-H, C-D, and C=O modes in formamide

By means of heterodyned two-dimensional IR photon echo experiments on liquid formamide and isotopomers the vibrational frequency dynamics of the N-H stretch mode, the C-D mode, and the C=O mode were obtained. In each case the vibrational frequency correlation function is fitted to three exponentials representing ultrafast (few femtoseconds), intermediate (hundreds of femtoseconds), and slow (many picoseconds) correlation times. In the case of N-H there is a significant underdamped contribution to the correlation decay that was not seen in previous experiments and is attributed to hydrogen-bond librational modes. This underdamped motion is not seen in the C-D or C=O correlation functions. The motions probed by the C-D bond are generally faster than those seen by N-H and C=O, indicating that the environment of C-D interchanges more rapidly, consistent with a weaker C-D...O=C bond. The correlation decays of N-H and C=O are similar, consistent with both being involved in strong H bonding.     

NH-S hydrogen bonding in zinc enzyme model complex with S2N2 binding set studied by normal coordinate analysis of vibrational spectra

In order to provide theoretical evidence for the existence and effect of NH-S hydrogen bonding in the zinc enzyme model complex [Zn(S-2-C6H4NHCOC6H5)2(1-MeIm)2] (1-MeIm = 1-methylimidazole) in addition to the spectroscopic and crystallographic investigations, normal coordinate analysis (NCA) was carried out using a modified Urey-Bradley force field. The vibrational frequencies of the complex with and without the NH-S hydrogen bonding as well as the corresponding internal coordinates were obtained. The good agreement found between the calculated and observed frequencies in the presence of the NH-S hydrogen bond, supports the reliability of the analysis. The stretching force constant of the NH-S hydrogen bond obtained from the calculation is 0.18 mdyne per A. The calculation shows that the N-H bond is weakened by formation of the NH-S hydrogen bond. The results are indicative of the existence of the NH-S hydrogen bond in the complex.     

Probing C-H...X hydrogen bonds in amide-functionalized imidazolium salts under high pressure

We have probed under high pressure the C-H hydrogen bonds formed by N,N(')-disubstituted imidazolium ions having PF(6) (-) and Br(-) counterions. High-pressure infrared spectral profiles, x-ray crystallographic analysis, and ab initio calculations allow us to make a vibrational assignment of these compounds. The appearance of a signal for the free-NH unit (or weakly bonded N-H...F unit) in the infrared spectrum of the PF(6) (-) salt indicates that conventional N-H...O and N-H...N hydrogen bonds do not fully dominate the packing. It is likely that the charge-enhanced C(2)-H...F interactions, combined with other weak hydrogen bonds, disturb the formation of N-H hydrogen bonds in the PF(6) (-) salt. This finding is consistent with the pressure-dependent results, which reveal that the C(2)-H...F interaction is enhanced upon increasing the pressure. In contrast to the PF(6) (-) salt, the imidazolium C-H bonds of the Br(-) salt have low sensitivity to high pressure. This finding suggests that the hydrogen bonding patterns are determined by the relative hydrogen bond acceptor strengths of the Br(-) and PF(6) (-) ions.     

Photochemical electron transfer mediated addition of naphthylamine derivatives to electron-deficient alkenes

Using photochemical electron transfer, N,N-dimethylnaphthylamine derivatives are added to α,β-unsaturated carboxylates. The addition takes place exclusively in the α-position of electron-deficient alkenes and mainly in the 4-position of N,N-dimethylnaphthalen-1-amine. A minor regioisomer results from the addition in the 5-position of this naphthylamine. A physicochemical study reveals that the fluorescence quenching of N,N-dimethylnaphthalen-1-amine is diffusion-controlled and that the back electron transfer is highly efficient. Therefore no transformation is observed at lower concentrations. To overcome this limitation and to induce an efficient transformation, minor amounts of water or another proton donor as well as an excess of the naphthylamine derivative are necessary. A mechanism involving a contact radical ion pair is discussed. Isotopic labeling experiments reveal that no hydrogen is directly transferred between the substrates. The hydrogen transfer to the furanone moiety observed in the overall reaction therefore results from an exchange with the reaction medium. An electrophilic oxoallyl radical generated from the furanone reacts with the naphthylamine used in excess. Concerning some mechanistic details, the reaction is compared with radical and electrophilic aromatic substitutions. The transformation was carried out with a variety of electron-deficient alkenes. Sterically hindered furanone derivatives are less reactive under standard conditions. In a first experiment, such a compound was transformed using heterogeneous electron transfer photocatalysis with TiO(2).     

The empirical correlation between hydrogen bonding strength and excited-state intramolecular proton transfer in 2-pyridyl pyrazoles

A series of 2-pyridyl pyrazoles 1a and 1-5 with various functional groups attached to either pyrazole or pyridyl moieties have been strategically designed and synthesized in an aim to probe the hydrogen bonding strength in the ground state versus dynamics of excited-state intramolecular proton transfer (ESIPT) reaction. The title compounds all possess a five-membered-ring (pyrazole)N-H···N(pyridine) intramolecular hydrogen bond, in which both the N-H bond and the electron density distribution of the pyridyl nitrogen lone-pair electrons are rather directional, so that the hydrogen bonding strength is relatively weak, which is sensitive to the perturbation of subtle chemical substitution and consequently reflected from the associated ESIPT dynamics. Various approaches such as (1)H NMR (N-H proton) to probe the hydrogen bonding strength and absorption titration to assess the acidity-basicity property were made for all the title analogues. The results, together with supplementary support provided by a computational approach, affirm that the increase of acidity (basicity) on the hydrogen bonding donor (acceptor) sites leads to an increase of hydrogen-bonding strength among the title 2-pyridyl pyrazoles. Luminescence results and the associated ESIPT dynamics further reveal an empirical correlation in that the increase of the hydrogen bonding strength leads to an increase of the rate of ESIPT for the title 2-pyridyl pyrazoles, demonstrating an interesting relationship among N-H acidity, hydrogen bonding strength, and the associated ESIPT rate.     

Systematic ab initio study of 15N-15N and 15N-1H spin-spin coupling constants across N-H+-N hydrogen bonds: predicting N-N and N-H coupling constants and relating them to hydrogen bond type

A systematic ab initio EOM-CCSD study of 15N-15N and 15N-1H spin-spin coupling constants has been carried out for a series of complexes formed from 11 nitrogen bases with experimentally measured proton affinities. When these complexes are arranged in order of increasing proton affinity of the proton-acceptor base and, for each proton acceptor, increasing order of proton affinity of the protonated N-H donor, trends in distances and signs of coupling constants are evident that are indicative of the nature of the hydrogen bond. All two-bond spin-spin coupling constants (2hJ(N-N)) are positive and decrease as the N-N distance increases. All one-bond N-H coupling constants (1J(N-H)) are negative (1K(N-H) are positive). 1J(N-H) is related to the N-H distance and the hybridization of the donor N atom. One-bond H...N coupling constants (1hJ(H-N)) are positive (1hK(H-N) are negative) for traditional hydrogen bonds, but 1hJ(H-N) becomes negative when the hydrogen bond acquires sufficient proton-shared character. The N-N and H...N distances at which 1hJ(H-N) changes sign are approximately 2.71 and 1.62 A, respectively. Predictions are made of the values of 2hJ(N-N) and 1J(N-H), and the signs of 1hJ(H-N), for those complexes that are too large for EOM-CCSD calculations.     

Infrared depletion spectra of 2-aminopyridine2-pyridone, a Watson-Crick mimic of adenine.uracil

The 2-aminopyridine2-pyridone (2AP2PY) dimer is linked by N-H...O=C and N-H...N hydrogen bonds, providing a model for the Watson-Crick hydrogen bond configuration of the adenine.thymine and adenine.uracil nucleobase pairs. Mass-specific infrared spectra of 2AP2PY and its seven N-H deuterated isotopomers have been measured between 2550 and 3650 cm(-1) by IR laser depletion combined with UV two-color resonant two-photon ionization. The 2PY amide N-H stretch is a very intense band spread over the range 2700-3000 cm(-1) due to large anharmonic couplings. It is shifted to lower frequency by 710 cm(-1) or approximately 20% upon H bonding to 2AP. On the 2AP moiety, the "bound" amino N-H stretch gives rise to a sharp band at 3140 cm(-1), which is downshifted by 354 cm(-1) or approximately 10% upon H bonding to 2PY. The amino group "free" N-H stretch and the H-N-H bend overtone are sharp bands at approximately 3530 cm(-1) and 3320 cm(-1). Ab initio structures and harmonic vibrations were calculated at the Hartree-Fock level and with the PW91 and B3LYP density functionals. The PW91/6-311++G(d,p) method provides excellent predictions for the frequencies and IR intensities of all the isotopomers.     

Comparative analysis of hydrogen bonding with participation of the nitrogen, oxygen and sulfur atoms in the 2(2'-heteroaryl)pyrroles and their trifluoroacetyl derivatives based on the 1H, 13C, 15N spectroscopy and DFT calculations

The N-H...X (X = N,O,S) intramolecular hydrogen bond in the series of 2(2'-heteroaryl)pyrroles and their trifluoroacetyl derivatives is examined by the (1)H, (13)C, (15)N spectroscopy and density functional theory (DFT) calculations. The influence of the hydrogen bond on coupling and shielding constants is considered. It is shown that the N-H...N intramolecular hydrogen bond causes a larger increase in the absolute size of the (1)J(N,H) coupling constant and a larger deshielding of the bridge proton than the N-H...O hydrogen bond. The effect of the N-H...S interaction on the (1)J(N,H) coupling constant and the shielding of the bridge proton is small. The NMR parameter changes in the series of the 2(2'-heteroaryl)pyrroles due to N-H...X hydrogen bond and the series of the 1-vinyl-2-(2'-heteroaryl)-pyrroles due to C-H...X hydrogen bond have the same order. The proximity of the nitrogen, oxygen or sulfur lone pair to the F...H hydrogen bridge quenches the trans-hydrogen bond spin-spin couplings (1h)J(F,H-1) and (2h)J(F,N).     

Neutralization-Reionization of alkenylammonium cations: An experimental and ab initio study of intramolecular N-H … C=C interactions in cations and hypervalent ammonium radicals

A series of isomeric hexenylammonium and hexenyldimethylammonium cations were neutralized by collisional electron transfer in the gas phase in an attempt to generate hypervalent ammonium radicals. The radicals dissociated completely on the 4.8–5.4 µs time scale. Radicals in which the hexene double bond was in the 3-, 4-, and 5-positions dissociated by competitive N-H and N=C bond cleavages. Allylic 2-hexen-1-ylammonium and 2-hexen-1-yldimethylammonium radicals underwent predominant cleavages of allylic N-C bonds. Deuterium labeling experiments revealed no intramolecular hydrogen transfer from the hypervalent ammonium group to the hexene double bond. Ab initio and density functional theory calculations showed that alkenylammonium and alkenylmethyloxonium ions preferred hydrogen bonded structures in the gas phase. The stabilization through intramolecular H bonding in 3-buten-1-ylammonium and 3-buten-1-yl methyloxonium ions was calculated by B3LYP/6-311G(2d,p) at 26 and 18 kJ mol^?1, respectively. No intramolecular hydrogen bonding was found for the allylammonium ion. The hypervalent 3-buten-1-yl-methyloxonium radical was calculated to be unbound and predicted to dissociate exothermically by O-H bond cleavage. This dissociation may provide kinetic energy for the hydrogen atom to overcome a small energy barrier for exothermic addition to the double bond. The 3-butten-1-ylammonium and allylammonium radicals were found to be bound and preferred gauche conformations without intramolecular hydrogen bonding. Vertical neutralization of alkenylammonium ions was accompanied by small Franck-Condon effects. The failure to detect stable or metastable hypervalent alkenylammonium radicals was ascribed to the low activation barriers to exothermic dissociations by N-H and N-C bond cleavages.     

A theoretical study on structural, spectroscopic and energetic properties of acetamide clusters [CH3CONH2] (n=1-15)

Insights into the formation of hydrogen bonded clusters are of outstanding importance and quantum chemical calculations play a pivotal role in achieving this understanding. Structure and energetic comparison of linear, circular and standard forms of (acetamide)(n) clusters (n = 1-15) at the B3LYP/D95** level of theory including empirical dispersion correction reveals significant cooperativity of hydrogen bonding and size dependent structural preference. A substantial amount of impact of BSSE is observed in these calculations as the cluster size increases irrespective of the kind of arrangement. The interaction energy per monomer increases from dimer to 15mer by 90% in the case of the circular arrangement, by 76% in the case of the linear arrangement and by 34% in the case of the standard arrangement respectively. The cooperativity in hydrogen bonding is also manifested by a regular decrease in average OH and C-N bond distances, while average C=O and N-H bond lengths increase with increasing cluster size. Atoms-In-Molecules (AIM) analysis is used to characterize the nature of hydrogen bonding between the acetamide molecules in the cluster on the basis of electron density (ρ) values obtained at the bond critical point. An analysis of N-H bond stretching frequencies as a function of the cluster size shows a marked red shift as the cluster size increases from 1 to 15.     

Molecular structure, vibrational spectra and nonlinear optical properties of l-Valine Hydrobromide: DFT study

FT-IR and Raman spectra of the nonlinear optical material l-Valine Hydrobromide crystal have been recorded and analyzed. The equilibrium geometry, bonding features and the harmonic vibrational wavenumbers of LVB have been calculated with the help of density functional theory (DFT) calculation. The lowering of NH stretching wavenumber indicates the formation of NH?Br hydrogen bonding. The calculated First order hyperpolarizability value shows that LVB is the potential candidate for the NLO applications. The electronic effects and the hydrogen bonding were explained using natural bond orbital analysis.     

Crystal growth, structural and spectroscopic analysis of hypoxanthinium chloride monohydrate

Protonated form of hypoxanthinium chloride monohydrate single crystal has been grown from dilute hydrochloric acid. Single crystal X-ray analysis was carried out and the titled crystal belong to the monoclinic P2(1)/c space group. Hypoxanthine is protonated at N(1) with the hypoxanthine cations, linked to chlorine anion via weak bifurcated N-H...Cl hydrogen bonds and interconnected by hydrogen bonding contacts of the type N-H...O. Infrared, Raman and UV spectroscopic tools were applied to characterize hypoxanthinium chloride monohydrate. By applying group theoretical methods the internal and external modes of vibrations of the title crystal have been identified and discussed.     

Synthesis and Structural Studies of 6-（2,5-Dimethyl-1H-pyrrol-1-yl）pyridin-2-amine

6-(2,5-Dimethyl-1H-pyrrol-1-yl)pyridin-2-amine (1) was synthesized and characte-rized by elemental analyses,1H-NMR and 13C-NMR,FTIR,Uv-Vis,mass spectral studies and single-crystal X-ray diffraction.All data obtained from spectral studies support the structural properties of 1.Intermolecular N-H…N hydrogen bonds produce an R22(8) ring.An extensive three-dimensional network formed by C-H…π and N-H…π-facial hydrogen bonds is responsible for the crystal stabilization.The combination of C-H…π interactions produces R33(12),R43(19) and R44(20) rings.     

Natural bond orbital analysis, electronic structure, non-linear properties and vibrational spectral analysis of L-histidinium bromide monohydrate: a density functional theory

The spectroscopic properties of the crystallized nonlinear optical molecule L-histidinium bromide monohydrate (abbreviated as L-HBr-mh) have been recorded and analyzed by FT-IR, FT-Raman and UV techniques. The equilibrium geometry, vibrational wavenumbers and the first order hyperpolarizability of the crystal were calculated with the help of density functional theory computations. The optimized geometric bond lengths and bond angles obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The natural bond orbital (NBO) analysis confirms the occurrence of strong intra and intermolecular N-H?O hydrogen bonding.     

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.     

Hydrogen bonding and covalent effects in binding of cisplatin to purine bases: ab initio and atoms in molecules studies

Ab initio and density functional calculations are employed to investigate the role of hydrogen bonding in the binding of cisplatin to the purine bases guanine and adenine. Through the use of the theory of atoms in molecules (AIM), it is shown that hydrogen bonds are ubiquitous in such systems, with N-H...N and N-H...Cl interactions present in addition to the expected N-H...O. This in turn means that the known stability of cisplatin-guanine complexes cannot be ascribed solely to hydrogen bonding and allows decomposition of total binding energy into contributions from covalent and hydrogen bonds. To do so, a new method for predicting hydrogen bond energies from bond critical point properties is proposed, employing partial least-squares analysis to remove the family dependence of simple models. Still more hydrogen bond motifs are found in bifunctional complexes of the general type purine-[Pt(NH(3))(2)](2+)-purine, including purine...purine contacts, though again the energetics of these are insufficient to explain the observed trends in stability. Finally, the effect of platination on the pairing of guanine with cytosine is studied in a similar manner, revealing large redistributions of hydrogen bonding but surprisingly small overall changes in pairing energy.