Characterization and Photofragmentation Studies of the Benzimidazole Homodimer: Evidence for Excited-State Charge-Coupled Proton Transfer.

The spectroscopic characterization of the benzimidazole (BIM) homodimer was carried out in a molecular beam in the ground state as well as in the cationic state using the R2PI and RIDIR methods. Primarily, interest in the dimer was due to the observation of a proton-transferred BIM fragment at energies well below its thermodynamic threshold (i.e.

O-H stretching frequency red shifts do not correlate with the dissociation energies in the dimethylether and dimethylsulfide complexes of phenol derivatives.

In this perspective, we present a comprehensive report on the spectroscopic and computational investigations of the hydrogen bonded (H-bonded) complexes of Me2O and Me2S with seven para-substituted H-bond donor phenols. The salient finding was that although the dissociation energies, D0, of the Me2O complexes were consistently higher than those of the analogous Me2S complexes, the red-shifts in phenolic O-H frequencies, Δν(O-H), showed the exactly opposite trend. This is in contravention of the general perception that the red shift in the X-H stretching frequency in the X-HY hydrogen bonded complexes is a reliable indicator of H-bond strength (D0), a concept popularly known as the Badger-Bauer rule.

Exploration of the theobromine-water dimer: comparison with DNA microhydration.

Understanding the molecular basis of the appearance of life on Earth is an exciting research field. Many factors may have influenced the election of the molecules used by living beings and evolution may have modified those original compounds. In an attempt to understand the role played by intermolecular interactions in the election of CGAT as the alphabet of life, we present here a thorough experimental and computational study on the interaction of theobromine with water.

C-HS interaction exhibits all the characteristics of conventional hydrogen bonds.

This is a tale of a pair of a hydrogen bond donor and acceptor, namely the CH donor and sulphur acceptor, neither of which is a conventional hydrogen bond participant. Sulfur (S), being less electronegative (2.58) compared to its first row analogue oxygen (3.

Revisiting the spectroscopy of xanthine derivatives: theobromine and theophylline.

We explore the influence of the relative position of the methyl substituent on the photophysics of theophylline and theobromine, two molecules that are structurally related to the DNA bases. Using a combination of spectroscopic techniques and quantum mechanical calculations, we show that moving the methyl group from N1 in theophylline to N7 in theobromine causes significant differences in their excited state properties, i.e.

Electronic and Infrared Spectroscopy of Benzene-(HS) ( = 1 and 2): The Prototype of the SH-π Interaction.

Benzene-(HS) ( = 1 and 2) clusters are the simplest prototype exemplifying the SH-π interaction. Electronic and infrared spectroscopies were applied to the benzene-(HS) clusters under the molecular beam condition. The S-S electronic spectrum was observed by one-color resonant two-photon ionization combined with mass spectrometry.

C-H···O Hydrogen Bond Anchored Water Bridge in 1,2,4,5-Tetracyanobenzene-Water Clusters.

The hydrogen-bonded chain of water molecules is known to play a very important role in proton/H transfer in chemistry and biology. This kind of water chain mainly starts from a conventional hydrogen bond (HB) donor/acceptor site. Here, we report the experimental evidence of water chain formation on an unconventional C-H HB donor site in 1,2,4,5-tetracyanobenzene (TCNB).

N-H···S Interaction Continues To Be an Enigma: Experimental and Computational Investigations of Hydrogen-Bonded Complexes of Benzimidazole with Thioethers.

The N-H···S hydrogen bond, even though classified as an unconventional hydrogen bond, is found to bear important structural implications on protein structure and folding. In this article, we report a gas-phase study of the N-H···S hydrogen bond between the model compounds of histidine (benzimidazole, denoted BIM) and methionine (dimethyl sulfide, diethyl sulfide, and tetrahydrothiophene, denoted MeS, EtS, and THT, respectively). A combination of laser spectroscopic methods such as laser-induced fluorescence (LIF), two-color resonant two-photon ionization (2cR2PI), and fluorescence depletion by infrared spectroscopy (FDIR) is used in conjunction with DFT and ab initio calculations to characterize the nature of this prevalent H-bonding interaction in simple bimolecular complexes.

Nature and Hierarchy of Noncovalent Interactions in Gas-Phase Binary Complexes of Indole and Benzimidazole with Ethers.

Hierarchy among the weak noncovalent interactions such as van der Waals, electrostatic, hydrogen bonding, etc. dictates the secondary and tertiary structures of proteins as well as their interactions with various ligands. In this work, we investigate the competition between conventional (N-H···O) hydrogen bonds, unconventional (C-H···O) hydrogen bonds, and the van der Waals interaction in the model compounds of the chromophores of the amino acids, tryptophan, and histidine.

Conformational Heterogeneity and the Role of the C(2)-H Donor in Mono- and Dihydrated Clusters of Benzoxazole.

The significance of the heteroatom in influencing the acidity and binding affinity of the C(2)-H donor in five-membered heterocyclic rings is explored. The water clusters of benzoxazole (BOX) are studied in a supersonic jet by IR-UV double resonance spectroscopy and compared with those of benzimidazole (BIM) and its N-methyl derivative (MBIM). Two conformers are identified for the monohydrated cluster, both of which are O-H···N bound and differ in their orientation with respect to the intermolecular hydrogen bond.

Role of the C(2)-H Hydrogen Bond Donor in Gas-Phase Microsolvation of Imidazole Derivatives with ROH (R = CH, CH).

Although the hydrogen-bonding properties of the protic solvents are comparable, a comparison of the gas-phase structures of water with those of the alcohols reveals certain similarities as well as differences. In this work we report the microsolvated clusters of imidazole derivatives, Benzimidazole (BIM) and N-methylbenzimidazole (MBIM) by methanol (M) and ethanol (E) in supersonic jet using electronic and vibrational spectroscopy and compare them with their hydrated clusters. The cluster sizes up to 1:2 of BIM/MBIM with methanol and ethanol, and up to 1:3 in the case of MBIM-methanol were observed.

Water bridges anchored by a C-HO hydrogen bond: the role of weak interactions in molecular solvation.

The imidazole group, characterized by an activated C(2)-H bond sandwiched between two N atoms, occurs in several biomolecules including alkaloids, amino acids, and nucleobases. The speculated role of this potential hydrogen bond donor in shaping the solvation shell around the neutral imidazole moiety, however, remains unidentified. In contrast, hydrogen bonding and electrostatic interactions are commonly observed in the imidazolium cation where the acidity of the C(2)-H bond is markedly enhanced.

Acid-Base Formalism Extended to Excited State for O-H···S Hydrogen Bonding Interaction.

Hydrogen bond can be regarded as an interaction between a base and a proton covalently bound to another base. In this context the strength of hydrogen bond scales with the proton affinity of the acceptor base and the pKa of the donor, i.e.

Dissociation Energies of Sulfur-Centered Hydrogen-Bonded Complexes.

In this work we have determined dissociation energies of O-H···S hydrogen bond in the H2S complexes of various phenol derivatives using 2-color-2-photon photofragmentation spectroscopy in combination with zero kinetic energy photoelectron (ZEKE-PE) spectroscopy. This is the first report of direct determination of dissociation energy of O-H···S hydrogen bond. The ZEKE-PE spectra of the complexes revealed a long progression in the intermolecular stretching mode with significant anharmonicity.

Conformational preferences of monohydrated clusters of imidazole derivatives revisited.

We present the IR spectroscopic investigations of benzimidazole (BIM), N-methylbenzimidazole (MBIM), and their monohydrates (W1) carried out in a supersonic jet in the region of N-H, C-H, and O-H stretching fundamentals. The C-H stretching modes in the monomers were studied with the aim of identifying the C(2)H mode (the C atom between the two N atoms in the imidazole moiety) which is known to play an important role as a H-bond donor in enzymes and ionic liquids. The assignment was aided by quantum chemical calculations as well as the literature data for FTIR measurements in the matrix.

Acid-base formalism in dispersion-stabilized S-H···Y (Y═O, S) hydrogen-bonding interactions.

The role of sulfhydryl (S-H) group as hydrogen bond donor is not as well studied as that of hydroxyl (O-H). In this work we report on the hydrogen-bonding properties of S-H donor in 1:1 complexes of H2S with diethyl ether (Et2O), dibutyl ether (Bu2O), and 1,4-dioxane (DO). The complexes were prepared in supersonic jet and investigated using infrared predissociation spectroscopy based on VUV photoionization detection.

ZEKE photoelectron spectroscopy of p-fluorophenol···H2S/H2O complexes and dissociation energy measurement using the Birge-Sponer extrapolation method.

In this work we have shown that the Birge-Sponer extrapolation method can be successfully used to determine the dissociation energies (D0) of noncovalently bound complexes. The O-H···S hydrogen-bonding interaction in the cationic state of the p-fluorophenol···H2S complex was characterized using zero kinetic energy (ZEKE) photoelectron spectroscopy. This is the first ZEKE report on the O-H···S hydrogen-bonding interaction.

C-H···N hydrogen-bonding interaction in 7-azaindole:CHX3 (X=F, Cl) complexes.

The C-H···Y (Y=hydrogen-bond acceptor) interactions are somewhat unconventional in the context of hydrogen-bonding interactions. Typical C-H stretching frequency shifts in the hydrogen-bond donor C-H group are not only small, that is, of the order of a few tens of cm(-1) , but also bidirectional, that is, they can be red or blue shifted depending on the hydrogen-bond acceptor. In this work we examine the C-H···N interaction in complexes of 7-azaindole with CHCl3 and CHF3 that are prepared in the gas phase through supersonic jet expansion using the fluorescence depletion by infra-red (FDIR) method.

Molecular-level understanding of ground- and excited-state O-H...O hydrogen bonding involving the tyrosine side chain: a combined high-resolution laser spectroscopy and quantum chemistry study.

The present study combines both laser spectroscopy and ab initio calculations to investigate the intermolecular OH⋅⋅⋅O hydrogen bonding of complexes of the tyrosine side chain model chromophore compounds phenol (PH) and para-cresol (pCR) with H2 O, MeOH, PH and pCR in the ground (S0 ) state as well as in the electronic excited (S1 ) state. All the experimental and computational findings suggest that the H-bond strength increases in the S1 state and irrespective of the hydrogen bond acceptor used, the dispersion energy contribution to the total interaction energy is about 10-15 % higher in the S1 state compared to that in the S0 state. The alkyl-substituted (methyl; +I effect) H-bond acceptor forms a significantly stronger H bond both in the S0 and the S1 state compared to H2 O, whereas the aryl-substituted (phenyl; -R effect) H-bond donor shows a minute change in energy compared to H2 O.

O-H···S hydrogen bonds conform to the acid-base formalism.

Hydrogen bonding interaction between the ROH hydrogen bond donor and sulfur atom as an acceptor has not been as well characterized as the O-H···O interaction. The strength of O-H···O interactions for a given donor has been well documented to scale linearly with the proton affinity (PA) of the H-bond acceptor. In this regard, O-H···O interactions conform to the acid-base formalism.

The Intermolecular S−H⋅⋅⋅Y (Y=S,O) hydrogen bond in the H2S dimer and the H2 S-MeOH complex.

The nature of the S−H⋅⋅⋅S hydrogen-bonding interaction in the H2 S dimer and its structure has been the focus of several theoretical studies. This is partly due to its structural similarity and close relationship with the well-studied water dimer and partly because it represents the simplest prototypical example of hydrogen bonding involving a sulfur atom. Although there is some IR data on the H2 S dimer and higher homomers from cold matrix experiments, there are no IR spectroscopic reports on S−H⋅⋅⋅S hydrogen bonding in the gas phase to-date.

C-H···Y hydrogen bonds in the complexes of p-cresol and p-cyanophenol with fluoroform and chloroform.

In this work, we present spectroscopic investigations of hydrogen bonded complexes of CHF3 and CHCl3 with p-cresol and p-cyanophenol. The systems were chosen as the potential candidates bound by C-H···Y type hydrogen bonds that are known to exhibit unconventional blue shifts in the C-H stretching frequency. The two phenol derivatives chosen offer multiple hydrogen bonding acceptor sites.

OH···X (X = O, S) hydrogen bonding in thetrahydrofuran and tetrahydrothiophene.

In this article, hydrogen bonding interaction between p-cresol (p-CR) and cyclic ether, tetrahydrofuran (THF) and thioether, tetrahydrothiophene (THT) has been investigated. Two-color resonantly enhanced two-photon ionization in conjunction with the fluorescence detected IR (FDIR) spectroscopy was used to record the changes in the OH stretching frequency in these complexes. The FDIR spectra showed existence of a single conformer of the p-CR·THF and two conformers of the p-CR·THT complex.

Structure of the indole-benzene dimer revisited.

The structure of the indole-benzene dimer has been investigated using experimental techniques, namely, UV spectroscopy and infrared-ultraviolet (IR/UV) double resonance spectroscopy, combined with quantum chemical calculations such as MP2 and dispersion corrected DFT methods. The red shift of the indole N-H stretch frequency in the dimer provides direct evidence that the experimentally observed indole-benzene dimer is an N-H···π bound hydrogen bonded complex. Theoretical investigations suggest that the potential energy surface (PES) of the complex is rather flat along the coordinate describing the tilt angle between the molecular planes of indole and benzene, with several minima of similar energies, namely, parallel displaced (PD), right-angle T-shaped (T), and other intermediate structures which can be categorized as tilted T-shaped (T') and tilted parallel displaced (PD') structures.

O-H...O versus O-H...S hydrogen bonding. 2. Alcohols and thiols as hydrogen bond acceptors.

In this paper, the effect of alkyl substitution at the hydrogen bond acceptor and its chain length on the strength and nature of hydrogen bonding is presented. In the present study we combine both experimental and computational methods to investigate the characteristics of O-H..