The Hydrogen-Bonded 2-Pyridone Dimer Model System. 2. Femtosecond Mid-Infrared Pump−Probe Study

Effect of the weak intermolecular C-H···O=C hydrogen bonding, solvent polarity and concentration on the frequency of the C=O stretch mode of 2-thiophenecarboxaldehyde

The vibrational frequency shift in the C=O stretch mode of 2-thiophenecarboxaldehyde (2TC) in the condensed phase is still not fully understood. In this paper, the vibrational spectra of 2TC were investigated using the FT-Raman, FT-IR and resonance Raman spectroscopies in conjunction with the density functional theory calculation. The pure compound (in the neat liquid) exhibits three vibrational bands 1658, 1672 and 1687 cm^-1 in the ν_C=O spectral region. It differs from the band pair 1672 and 1682 cm^-1 for 2-cyclohexene-1-one (CHO) and the single band 1700 cm^-1 for benzaldehyde. The relative intensities of observed bands vary with the polarity of aprotic solvents and the compound's concentration. In a diluted solution, the strongest band in the resonance Raman spectra of 2TC appears the C=O stretch mode at 1690 cm^-1 in cyclohexane and 1674/1675 cm^-1 in acetonitrile. The imparting factors that shift the C=O stretch mode frequency in the neat liquid and solvents with different polarities were examined. The spectral sources of the vibrational bands at 1658 and 1672 cm^-1 in the neat liquid and a dilute solution were determined, and the resonance Raman spectra were assigned. It is concluded that tetramers and monomer are the major sources of the bands at 1658 and 1672 cm^-1 in the neat liquid, respectively, while the monomer is the main source of the bands at 1674/1675 cm^-1 in acetonitrile and the band at 1690 cm^-1 in cyclohexane with a dilute concentration. The band's source at 1662/1663 cm^-1 in acetonitrile (a dilute concentration) can be either the dimers or 2TC-CH₃CN clusters. The C=O bond's electronic charge density is the main factor that shifts the vibrational frequency of the C=O stretch mode of 2TC monomer when an aprotic solvent is used. The larger the polarity of an aprotic solvent, the more negative the electronic charge-density of the C=O bond for the monomer, the lower the frequency of the C=O stretch mode.

A combined experimental and density functional theory investigation of the hydrogen bonding of 2-cyclohexen-1-one and 3-methyl- 2-cyclohexen-1-one in solvents

Hydrogen bonding is a weak chemical interaction widely existed in the variety of organic and biological molecules. As an important structural motif of pyrimidine bases, the solvent effect of the hydrogen bonding of 2-cyclohexen-1-one (CHO) and 3-methyl- 2-cyclohexen-1-one (3MCHO) and its effect on the frequency shift of the CO stretching mode were investigated by using the FT-Raman and UV absorption spectra and density functional theory calculations. The electronic transitions associated with the UV absorptions in different solvents were calculated at B3LYP-TD/6-31++G(d,p) level of theory and employing SCIPCM solvent model. The vibrational spectra of CHO and 3MCHO were assigned on the basis of the FT-Raman spectra in neat liquid and different solvents, the calculated vibrational spectra of monomer and CHO dimers, and the concentration dependent experiments of the band pair intensities. Hydrogen bonding energies of CHO-(H₂O)_n (n = 1,2) clusters were predicted. The results reveal that the CHO-(H₂O)₂ cluster and CHO monomer are respectively the major source of spectral observation in water and cyclohexane, while CHO dimmer and CHO monomer coexist in acetonitrile. The difference in the frequency of the ν_C=O stretching mode between 3MCHO monomer and CHO monomer in cyclohexane were explored.

Biomolecule Analogues 2-Hydroxypyridine and 2-Pyridone Base Pairing on Ice Nanoparticles

Ice nanoparticles (H2O)N, N ≈ 450 generated in a molecular beam experiment pick up individual gas phase molecules of 2-hydroxypyridine and 2-pyridone (HP) evaporated in a pickup cell at temperatures between 298 and 343 K. The mass spectra of the doped nanoparticles show evidence for generation of clusters of adsorbed molecules (HP)n up to n = 8. The clusters are ionized either by 70 eV electrons or by two photons at 315 nm (3.94 eV). The two ionization methods yield different spectra, and their comparison provides an insight into the neutral cluster composition, ionization and intracluster ion-molecule reactions, and cluster fragmentation. Quite a few molecules were reported not to coagulate on ice nanoparticles previously. The (HP)n cluster generation on ice nanoparticles represents the first evidence for coagulating of molecules and cluster formation on free ice nanoparticles. For comparison, we investigate the coagulation of HP molecules picked up on large clusters ArN, N ≈ 205, and also (HP)n clusters generated in supersonic expansions with Ar buffer gas. This comparison points to a propensity for the (HP)2 dimer generation on ice nanoparticles. This shows the feasibility of base pairing for model of biological molecules on free ice nanoparticles. This result is important for hypotheses of the biomolecule synthesis on ice grains in the space. We support our findings by theoretical calculations that show, among others, the HP dimer structures on water clusters.

Structural analysis of neutral tetracycline using anharmonicity of delocalized vibrations

While tetracyclines are in active medical use, their bioactive atomic compositions are still questionable. Here, we investigate the structural properties of neutral tetracycline in dimethyl sulfoxide - the environment used often to mimic the environment in vivo. We compare the measured linear and nonlinear infrared spectra to those calculated for a collection of stable and energetically plausible tautomers, and describe the structurally sensitive off-diagonal peaks using anharmonicities of the normal modes. The comparison of experimental and theoretical 2DIR spectra is consistent with the numerical predictions of statistical thermodynamics on the relative weights of possible tautomers. In result, we provide the systematic account of the structural realizations of neutral tetracycline in DMSO.

Sub-four-cycle laser pulses directly from a high-repetition-rate optical parametric chirped-pulse amplifier at 3.4 μm

We generate sub-four-cycle pulses (41.6 fs) with 12 μJ of pulse energy in the mid-infrared spectral range (center wavelength 3.4 μm) from a high-repetition-rate, collinear three-stage optical parametric chirped-pulse amplifier (OPCPA) operating at 50 kHz. Apodized aperiodically poled MgO:LiNbO3 crystals with a negative chirp rate are employed as gain media to achieve ultrabroadband phase-matching while minimizing optical parametric generation. The seed pulses are obtained via a 1.56 μm femtosecond fiber laser, which is spectrally broadened in a dispersion-shifted telecom fiber to support 1000 nm bandwidth idler pulses in the mid-infrared.

N-H stretching excitations in adenosine-thymidine base pairs in solution: pair geometries, infrared line shapes, and ultrafast vibrational dynamics

We explore the N-H stretching vibrations of adenosine-thymidine base pairs in chloroform solution with linear and nonlinear infrared spectroscopy. Based on estimates from NMR measurements and ab initio calculations, we conclude that adenosine and thymidine form hydrogen bonded base pairs in Watson-Crick, reverse Watson-Crick, Hoogsteen, and reverse Hoogsteen configurations with similar probability. Steady-state concentration and temperature dependent linear FT-IR studies, including H/D exchange experiments, reveal that these hydrogen-bonded base pairs have complex N-H/N-D stretching spectra with a multitude of spectral components. Nonlinear 2D-IR spectroscopic results, together with IR-pump-IR-probe measurements, as also corroborated by ab initio calculations, reveal that the number of N-H stretching transitions is larger than the total number of N-H stretching modes. This is explained by couplings to other modes, such as an underdamped low-frequency hydrogen-bond mode, and a Fermi resonance with NH(2) bending overtone levels of the adenosine amino-group. Our results demonstrate that modeling based on local N-H stretching vibrations only is not sufficient and call for further refinement of the description of the N-H stretching manifolds of nucleic acid base pairs of adenosine and thymidine, incorporating a multitude of couplings with fingerprint and low-frequency modes.