Aloke Das

Conformations of indan and 2-indanol: A combined study by UV laser spectroscopy and quantum chemistry calculation

Three conformational isomers of 2-indanol are identified by use of resonance enhanced two-photon ionization (R2PI) and single vibronic level dispersed fluorescence spectroscopy in a supersonic jet expansion. By combining the experimental results with the predictions of the ab initio quantum chemistry calculations at the MP2/6-311++G(d,p) level of theory, the major species is identified as a conformational isomer in which the hydroxyl hydrogen is involved in an intramolecular hydrogen bonding with the π-electrons of the aromatic ring. The theoretical estimate of the hydrogen bond energy is ∼6.5 kJ/mol. A comparative investigation with indan reveals that this weak hydrogen bonding in the former significantly affects the puckering potential of the five-member side ring. The dispersed fluorescence data indicate for a much higher ring-puckering barrier in the ground state than what has been suggested recently by measuring rotational spectra of the unsubstituted indan.

Competition between hydrogen bonding and dispersion interactions in the indole···pyridine dimer and (indole)2···pyridine trimer studied in a supersonic jet.

Structures of the indole···pyridine dimer and (indole)2···pyridine trimer have been investigated in a supersonic jet using resonant two-photon ionization (R2PI) and IR-UV double resonance spectroscopic techniques combined with quantum chemistry calculations. R2PI spectra of the dimer and the trimer recorded by electronic excitation of the indole moiety show that the red-shift in the band origin of the dimer with respect to the 0(0)(0) band of the monomer is larger compared to that of the trimer. The presence of only one conformer in the case of both the dimer and the trimer has been confirmed from IR-UV hole-burning spectroscopy. The structures of the dimer and the trimer have been determined from resonant ion dip infrared (RIDIR) spectra combined with ab initio as well as DFT/M05-2X and DFT/M06-2X calculations. It has been found that the dimer, observed in the experiment, has a V-shaped geometry stabilized by N–H···N and C–H···N hydrogen bonding interactions, as well as C–H···π and π···π dispersion interactions. The geometry of the trimer has been found to be a cyclic one stabilized by N–H···N, N–H···π, C–H···π, and C–H···N interactions. The most important finding of this current study is the observation of the mixed dimer and trimer, which are stabilized by hydrogen bonding as well as dispersion interactions.

Hydrogen atom dislocation in the excited state of anthranilic acid: probing the carbonyl stretch fundamental and the effects of water complexation

This paper describes further efforts to understand the excited state hydrogen atom dislocation of anthranilic acid. Resonant ion-dip infrared spectroscopy was used to probe the carbonyl stretch fundamental in both the ground and excited states in an effort to observe the excited state behavior of the heavy atoms surrounding the displaced hydrogen. A small peak in the excited state infrared spectrum was tentatively assigned to the carbonyl stretch fundamental, shifted 80 cm−1 to the red of its position in the ground state, indicative of a significant weakening of the CO bond. CASSCF calculations on a prototypical system, 3-amino-2-propenoic acid, were carried out to aid interpretation of vibrational frequencies and intensities. The effects of water complexation on the excited state hydrogen atom dislocation were also investigated. The vibronic spectrum, acquired by resonant two-photon ionization, displayed similar features as the monomer spectrum, as well as a progression in a low frequency intermolecular vibration. The infrared spectrum of the water complex, supported by density functional theory calculations, established that the water binds between the carbonyl oxygen and the acid hydrogen. The NH stretch fundamentals of the water complex in the ground and excited state were quite similar to those of the monomer, indicating complexation to water has little effect on the hydrogen atom dislocation

Observation of exciplex emission from the mixed dimer of naphthalene and 2-methoxynaphthalene: A laser-induced fluorescence study in supersonic jet

Exciplex formation in the van der Waals mixed dimer of naphthalene and 2-methoxynaphthalene has been investigated by using laser-induced fluorescence spectroscopy in supersonic jet. In contrast to the barrierless excimer formation in the S1 state of naphthalene homodimer, the exciplex formation in the mixed dimer occurs with a vibrational energy barrier of 466 cm−1. The energy gap between the S1 states of two molecules in the mixed dimer is 1000 cm−1. Therefore, the contribution of the exciton resonance interaction to the stability of the exciplex state is considered to be insignificant. Charge transfer interaction and the mixing of the charge transfer state with the locally excited state due to orbital overlap between two molecules at suitable geometry are proposed to be the decisive factors in formation of the exciplex.

Observation of exclusively π-stacked heterodimer of indole and hexafluorobenzene in the gas phase.

In this study, the structure of the indole···hexafluorobenzene dimer has been investigated in the gas phase by using resonant two photon ionzation (R2PI) and IR-UV double resonance spectroscopy combined with quantum chemistry calculations. We have confirmed the presence of exclusively π-stacked structure of the dimer from both experimental and theoretical IR spectra in the N-H stretching region. Observation of a single stable structure of the dimer has also been verified through 3D potential energy surface scan of the π-stacked dimer by varying the parallel displacement of the hexafluorobenzene unit simultaneously along the major and minor axes of the indole moiety. π-stacking interaction is present very often between the tryptophan and phenylalanine residues in proteins. But this interaction has not been observed earlier in the gas phase experiment by studying indole···benzene dimer because the N-H group of indole predominately directs towards the N-H···π hydrogen bonded T-shaped structure. The chosen molecular systems in this study not only rule out the possibility of the formation of the N-H···π bound T-shaped dimer but also enable the determination of the structure by probing the N-H group. The π-stacked indole···hexafluorobenzene dimer has a unique structure where the center of the hexafluorobenznene ring is aligned with the center of the shared bond of the indole ring. Our work provides useful insight in designing unnatural proteins having strong π-stacking interaction between the tryptophan and phenylalanine residues.

Structure of indole···imidazole heterodimer in a supersonic jet: a gas phase study on the interaction between the aromatic side chains of tryptophan and histidine residues in proteins.

In this study, we have investigated the binding motifs between the aromatic side chains of tryptophan and histidine residues in proteins by studying the indole···imidazole heterodimer in a supersonic jet. Different spectroscopic techniques including resonant two-photon ionization (R2PI), UV-UV hole-burning, and resonant ion dip infrared (RIDIR) spectroscopy merged with quantum chemistry calculations have been used for this work. UV-UV hole-burning spectroscopy has been used to confirm the presence of only one structure of the dimer in the experiment. From the comparison of the RIDIR spectrum of the observed dimer with the theoretical IR spectra of different structures of the dimer, it is found that the dimer present in the experiment has a V-shaped structure held by N-H···N hydrogen bond, C-H···π, and weakly present π···π stacking interactions. The most important finding of the present study is that the noncovalent interactions present in the observed dimer have a close resemblance with those present between tryptophan and histidine residues in a nonfluorescent flavoprotein. The present spectroscopic investigation on the indole···imidazole dimer has also immense pharmaceutical significance as this imparts molecular level understanding about the binding motifs of the imidazole drugs with the indole chromophore present in proteins.

Direct Spectroscopic Evidence for an n→π* Interaction

The n→π* interaction is an extremely weak but very important noncovalent interaction. Although this interaction is widely present in biomolecules and materials, its existence is counterintuitive and so has been debated extensively. Herein, we have reported direct spectroscopic evidence for an n→π* interaction for the first time by probing the carbonyl stretching frequency in phenyl formate using isolated gas-phase IR spectroscopy. This result also demonstrates that the conformational preference for the cis conformer of phenyl formate compared to the trans conformer arises due to the presence of the n→π* interaction in the former. The direct proof reported herein for this controversial but important noncovalent interaction should stimulate further experimental and theoretical investigation on this intriguing research topic.

Effect of acceptor heteroatoms on π-hydrogen bonding interactions: A study of indole⋅⋅⋅thiophene heterodimer in a supersonic jet

Resonant two photon ionization (R2PI), IR-UV, and UV-UV double resonance spectroscopic techniques combined with quantum chemistry calculations have been used to determine the structure of indole···thiophene dimer observed in a supersonic jet. With the help of combined experimental and theoretical IR spectra it has been found that the observed dimer has a N-H···π hydrogen bonded slanted T-shaped structure. The present study demonstrates the effect of heteroatoms present in the acceptors on the strength of the π-hydrogen bonding interactions. It was concluded by Sherrill and co-workers from their theoretical study of benzene···pyridine dimer that aromatic rings containing heteroatoms are poorest π-hydrogen bond acceptors [E. G. Hohenstein and C. D. Sherrill, J. Phys. Chem. A 113, 878 (2009)]. But the current spectroscopic investigation exhibits that five membered aromatic heterocycles are favorable π-hydrogen bond acceptors. In this study, it has also been shown that thiophene is a better π-hydrogen bond acceptor than furan. The present work has immense biological significance as indole is the chromophore of tryptophan residue in the proteins and thiophene derivatives have potential therapeutic applications. Thus, understanding the binding motif between indole and thiophene in the heterodimer studied in this work may help in designing efficient drugs.

Mimicking trimeric interactions in the aromatic side chains of the proteins: A gas phase study of indole…(pyrrole)2 heterotrimer

Aromatic trimeric interactions are extremely significant in the stabilization of the specific structures of the proteins as well as protein-protein, and protein-ligand interactions. Here we have reported a direct evidence of the observation of a cyclic asymmetric structure of indole...(pyrrole)(2) trimer bound by three N-H...π hydrogen bonding interactions in a supersonic jet. The experiment has been performed by using resonant two-photon ionization (R2PI), IR-UV, and UV-UV double resonance spectroscopic techniques. Density functional theory (DFT) calculations nicely corroborate the experimental results showing one weakly allowed IR-active band due to symmetric stretch of the N-H bonds and two strongly allowed IR-active bands due to two types of asymmetric stretches of the N-H bonds in the trimer. The present spectroscopic investigation demonstrates that the strength of the three N-H...π bound intermolecular interactions in the cyclic asymmetric trimer is quite different unlike the corresponding interactions of similar strength in a cyclic symmetric trimer.

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.