Unraveling the structure of hydrogen bond stretching mode infrared absorption bands: An anharmonic density functional theory study on 7-azaindole dimers

Spectroscopic Manifestations of Indirect Vibrational State Mixing: Novel Anharmonic Effects on a Prereactive H Atom Transfer Surface

The NH stretch region of the IR spectrum of methyl anthranilate is modeled in the S₁ state to understand the connection between the absence of this fundamental in the fluorescence-dip infrared spectra of Blodgett et al. [Phys. Chem. Chem. Phys. 2020, 22, 14077] and its relevance to the H atom dislocation that occurs upon electronic excitation. A set of coordinates are chosen that highlight the role of certain low-frequency modes. A Hamiltonian is developed in which a large-amplitude two-dimensional surface describing the H-bonded H atom is linearly and quadratically coupled to the remaining degrees of freedom which are treated at the harmonic level. The surface is calculated within the time-dependent density functional theory framework by using the B3LYP/6-311++(d, p) level of theory with dispersion. Our spectral results show that indirect couplings lead to massive intensity sharing over hundreds of wavenumbers. This sharing is predicted to be dramatically reduced upon deuteration. The spectral broadening mechanism is found to involve off-resonant doorway states that are themselves strongly coupled to states nearly degenerate with the NH stretch fundamental and represents a complementary mechanism to previous explanations based on Fermi resonance or the presence of Franck-Condon like combination bands with low-frequency motions. Consistent with the spectra predictions, time-dependent calculations show that if the NH stretch fundamental were excited with an ultrafast laser, it would decay within 40 fs. The competition between H atom dislocation and vibrational relaxation is discussed.

Shifting formic acid dimers into perspective: vibrational scrutiny in helium nanodroplets

A metastable dimer of formic acid has been prepared inside superfluid helium nanodroplets and examined using IR spectroscopy and quantum chemical calculations.

Intra-cavity proton bonding and anharmonicity in the anionophore cyclen

Proton bonding drives the supramolecular chemistry of a broad range of materials with polar moieties. Proton delocalization and electronic charge redistribution have a profound impact on the structure of proton-bound molecular frameworks, and pose fundamental challenges to quantum chemical modelling. This study provides insights into the structural and spectral signatures of the intramolecular proton bond formed in a benchmark polyazamacrocycle anionophore (cyclen, 1,4,7,10-tetraazacyclododecane). Infrared action spectroscopy is employed to characterize the macrocycle, isolated in protonated form. In its most stable configuration, protonated cyclen adopts an open arrangement of Cs symmetry with a particularly strong NHδ+N bond across the cavity. The quantum chemical analysis of the infrared spectrum reveals intrinsic difficulties for the accurate description of the vibrational modes of the system. The reconciliation of the computational predictions with experiment demands a careful anharmonic treatment of the proton motion, which exposes the limitations of current methods. Best results are obtained with the incorporation of anharmonicity only to the fundamental modes directly related to motions of the proton. However, the full anharmonic treatment of the system fails to describe correctly the vibrations related to the macrocycle backbone. The results should serve as motivation for new developments in the modelling of proton bonded systems.

Interpreting Quasi-Thermal Effects in Ultrafast Spectroscopy of Hydrogen-Bonded Systems

Vibrational excitation of molecules in the condensed phase relaxes through vibrational modes of decreasing energy to ultimately generate an equilibrium state in which the energy is distributed among low-frequency modes. In ultrafast vibrational spectroscopy, changes in the vibrational features of hydrogen-bonded NH and OH stretch modes are typically observed to persist long after these high-frequency vibrations have relaxed. Due to the resemblance to the spectral changes caused by heating the sample, these features are typically described as arising from a hot ground state. However, these spectral features appear on ultrafast time scales that are much too fast to result from a true thermal state, and significant differences between the thermal difference spectrum and the induced quasi-thermal changes in ultrafast spectroscopy are often observed. Here, we examine and directly compare the thermal and quasi-thermal responses of the hydrogen-bonded homodimer of 7-azaindole with temperature-dependent FTIR spectroscopy and ultrafast mid-IR continuum spectroscopy. We find that the thermal difference spectra contain contributions from both dissociation of the hydrogen bonds and from frequency shifts due to changes in the thermal population of low-frequency modes. The transient spectra in ultrafast vibrational spectroscopy are also found to contain two contributions: initial frequency shifts over 2.3 ± 0.11 ps associated with equilibration of the initial excitation, and frequency shifts associated with the excitation of several fingerprint modes, which decay over 21.8 ± 0.11 ps, giving rise to a quasi-thermal response caused by a distribution of fingerprint modes being excited within the sample ensemble. This resembles the thermal frequency shifts due to population changes of low-frequency modes, but not the overall thermal spectrum, which is dominated by features caused by dimer dissociation. These findings provide insight into the changes in the vibrational spectrum from different origins and are important for assigning, analyzing, and comparing features in thermal and ultrafast vibrational spectroscopy of hydrogen-bonded complexes.

Selectively Probing the Structures and Dynamics of β-Peptide Aggregates Using the Amide-A Vibrational Marker

The N-H stretching vibration in a β-peptide model compound, N-ethylpropionamide (NEPA), was characterized by one-dimensional infrared (1D IR) and two-dimensional (2D) IR experiments and ab initio anharmonic frequency computations. A narrowband pump-broadband probe 2D IR method was applied to selectively probe a subensemble of the N-H stretching vibrations from a mixture of different NEPA molecular aggregates that were formed via an intermolecular hydrogen bond. Vibrational lifetime and anharmonicity were found to be sensitive to the aggregation ensembles. In particular, diagonal anharmonicities were observed experimentally and confirmed computationally to be smaller for NEPA trimer than for dimer, which was explained by the presence of non-negligible off-diagonal anharmonicities in coupled N-H stretching modes.

Structural dynamics of N-ethylpropionamide clusters examined by nonlinear infrared spectroscopy

In this work, the structural dynamics of N-ethylpropionamide (NEPA), a model molecule of β-peptides, in four typical solvents (DMSO, CH3CN, CHCl3, and CCl4), were examined using the N-H stretching vibration (or the amide-A mode) as a structural probe. Steady-state and transient infrared spectroscopic methods in combination with quantum chemical computations and molecular dynamics simulations were used. It was found that in these solvents, NEPA exists in different aggregation forms, including monomer, dimer, and oligomers. Hydrogen-bonding interaction and local-solvent environment both affect the amide-A absorption profile and its vibrational relaxation dynamics and also affect the structural dynamics of NEPA. In particular, a correlation between the red-shifted frequency for the NEPA monomer from nonpolar to polar solvent and the vibrational excitation relaxation rate of the N-H stretching mode was observed.

X-ray crystal structure, vibrational spectra and DFT calculations of 3-chloro-7-azaindole: a case of dual N-H⋯N hydrogen bonds in dimers

3-Chloro-7-azaindole (3Cl7AI) is the carrier ligand in a new anticancer platinum(II) agent cis-[PtCl2(3Cl7AI)2]. In this work 3Cl7AI has been studied by a single crystal X-ray diffraction, infrared and Raman spectroscopy and density functional calculations. The compound crystallizes in the monoclinic system, space group P21/n, with a=12.3438(3), b=3.85964(11), c=14.4698(4)Å, β=100.739(2)°, V=677.31(3)Å(3) and Z=4. In the crystal, a pair of 3Cl7AI molecules forms a centrosymmetric dimer linked by the moderately strong dual N-H⋯N hydrogen bonds. The nitrogen atom in the pyrrole ring acts as the proton donor, while the nitrogen atom in the pyridine ring is the proton acceptor. The FT-IR and FT-Raman spectra (3500-60 cm(-1)) have been recorded. The theoretical studies on the molecular structures and vibrational spectra of the monomeric and dimeric forms of 3Cl7AI and its N-deuterated derivative were performed using the B3LYP method with 6-311++G(d,p) basis set. The theoretically predicted Raman spectrum for the dimer shows very good agreement with experiment. Detailed vibrational assignments for the two isotopomers have been made on the basis of the calculated potential energy distributions (PEDs). The dual N-H⋯N hydrogen bonds in 3Cl7AI dimer are characterized by a very broad and complicated structure of the absorption band between 3300 and 2500 cm(-1), which is caused by multiple Fermi resonances between the N-H stretching vibration and various combinations bands.

Strong intermolecular vibrational coupling through cyclic hydrogen-bonded structures revealed by ultrafast continuum mid-IR spectroscopy

Cyclic hydrogen-bonded structures are common motifs in biological systems, providing structural stability and mediating proton transfer for redox reactions. The mechanism of proton transfer across hydrogen-bonded interfaces depends on the strength of the intermolecular coupling between bridging OH/NH vibrational modes. Here we present a novel ultrafast continuum mid-IR spectroscopy experiment to study the vibrational dynamics of the 7-azaindole-acetic acid (7AI-Ac) heterodimer as a model system for asymmetric cyclic hydrogen-bonded structures. In addition to spreading of the excitation across the whole OH band within the time resolution of the experiment, excitation of a 300 cm(-1) region of the ∼1000 cm(-1) broad OH stretching mode of the acetic acid monomer leads to a frequency shift in the NH stretching mode of the 7AI monomer. This indicates that the NH and OH stretching modes located on the two monomers are strongly coupled despite being separated by 750 cm(-1). The strong coupling further causes the OH and NH bands to decay with a common decay time of ∼2.5 ps. This intermolecular coupling is mediated through the hydrogen-bonded structure of the 7AI-Ac heterodimer and is likely a general property of cyclic hydrogen-bonded structures. Characterizing the vibrational dynamics of and the coupling between the high-frequency OH/NH modes will be important for understanding proton transfer across such molecular interfaces.

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.

Ultrafast vibrational frequency shifts induced by electronic excitations: naphthols in low dielectric media

We study the solvent-induced frequency shifts of the OH-stretching mode of 1-naphthol and 2-naphthol in nonpolar/weakly polar solvents, subject to electronic excitation, with ultrafast UV/mid-infrared pump-probe spectroscopy and theoretical modeling based on Pullin's perturbative treatment of vibrational solvatochromic effects. The model is parametrized at the density functional theory (DFT) level, including the B3LYP/TZVP and TD-B3LYP/TZVP descriptions, for the naphthol chromophores in the S(0)- and (1)L(b)-states and accounts for both the static and the optical dielectric response of the solvent on time scales comparable to that of the OH-stretching vibrational motions. The favorable comparison between experimental and theoretical values of the solvent-induced vibrational frequency shifts suggests that the ultrafast dielectric response of the solvent contributes predominantly to the solvatochromic shifts in solvents of moderate polarity where specific solute-solvent interactions are absent.

Estimating the hydrogen bond energy

First, different approaches to detect hydrogen bonds and to evaluate their energies are introduced newly or are extended. Supermolecular interaction energies of 256 dimers, each containing one single hydrogen bond, were correlated to various descriptors by a fit function depending both on the donor and acceptor atoms of the hydrogen bond. On the one hand, descriptors were orbital-based parameters as the two-center or three-center shared electron number, products of ionization potentials and shared electron numbers, and the natural bond orbital interaction energy. On the other hand, integral descriptors examined were the acceptor-proton distance, the hydrogen bond angle, and the IR frequency shift of the donor-proton stretching vibration. Whereas an interaction energy dependence on 1/r(3.8) was established, no correlation was found for the angle. Second, the fit functions are applied to hydrogen bonds in polypeptides, amino acid dimers, and water cluster, thus their reliability is demonstrated. Employing the fit functions to assign intramolecular hydrogen bond energies in polypeptides, several side chain CH...O and CH...N hydrogen bonds were detected on the fly. Also, the fit functions describe rather well intermolecular hydrogen bonds in amino acid dimers and the cooperativity of hydrogen bond energies in water clusters.

Theoretical modeling of infrared spectra of the hydrogen and deuterium bond in aspirin crystal

An extended quantum theoretical approach of the nu(X-H) IR lineshape of cyclic dimers of weakly H-bonded species is proposed. We have extended a previous approach [M.E.-A. Benmalti, P. Blaise, H.T. Flakus, O. Henri-Rousseau, Chem. Phys. 320 (2006) 267] by accounting for the anharmonicity of the slow mode which is described by a "Morse" potential in order to reproduce the polarized infrared spectra of the hydrogen and deuterium bond in acetylsalicylic acid (aspirin) crystals. From comparison of polarized IR spectra of isotopically neat and isotopically diluted aspirin crystals it resulted that centrosymmetric aspirin dimer was the bearer of the crystal main spectral properties. In this approach, the adiabatic approximation is performed for each separate H-bond bridge of the dimer and a strong non-adiabatic correction is introduced into the model via the resonant exchange between the fast mode excited states of the two moieties. Within the strong anharmonic coupling theory, according to which the X-H...Y high-frequency mode is anharmonically coupled to the H-bond bridge, this model incorporated the Davydov coupling between the excited states of the two moieties, the quantum direct and indirect dampings and the anharmonicity for the H-bond bridge. The spectral density is obtained within the linear response theory by Fourier transform of the damped autocorrelation functions. The evaluated spectra are in fairly good agreement with the experimental ones by using a minimum number of independent parameters. The effect of deuteration has been well reproduced by reducing simply the angular frequency of the fast mode and the anharmonic coupling parameter.

Theoretical study of the nuO-H IR spectra for the hydrogen bond dimers from the polarized spectra of glutaric and 1-naphthoic acid crystals: Fermi resonances effects

A full quantum theoretical model is proposed to study the nu(O-H) experimental IR line shapes of polarized crystalline glutaric and 1-naphthoic acid dimer crystals at room and liquid nitrogen temperatures. This work is an application of a previous model [M. E-A. Benmalti, D. Chamma, P. Blaise, and O. Henri-Rousseau, J. Mol. Struct. 785 (2006) 27-31] by accounting for Fermi resonances. The approach is dealing with the strong anharmonic coupling, Davydov coupling, multiple Fermi resonances between the first harmonics of some bending modes and the first excited state of the symmetric combination of the two nu(O-H) modes and the quantum direct and indirect relaxation. Numerical results show that mixing of all these effects allows to reproduce satisfactorily the main features of the experimental IR line shapes of crystalline hydrogenated and deuterated glutaric and 1-naphthoic acid crystals and are expected to provide efficient of Fermi resonances effects.

Ultrafast N-H vibrational dynamics of cyclic doubly hydrogen-bonded homo- and heterodimers

Hydrogen-bonded interfaces are essential structural elements in biology. Furthermore, they can mediate electron transport by coupling the electron to proton transfer within the interface. The specific hydrogen-bonding configuration and strength have a large impact on the proton transfer, which exchanges the hydrogen-bonded donor and acceptor species (i.e., NH...O --> N...HO). Modulations of the hydrogen-bonding environment, such as the hydrogen-bond stretch and twist modes, affect the proton-transfer dynamics. Here, we present transient grating and echo peak shift measurements of the NH stretch vibrations of four doubly hydrogen-bonded cyclic dimers in their electronic ground state. The equilibrium vibrational dynamics exhibit strong coherent modulations that we attribute to coupling of the high-frequency NH vibration to the low-frequency interdimer stretch and twist modes and not to interference between multiple Fermi resonances that dominate the substructure of the linear spectra.