Franck–Condon-like Progressions in Infrared Spectra of Biological Molecules

Regularities and Anomalies in Neon Matrix Shifts of Hydrogen-Bonded O-H Stretching Fundamentals

O-H bond stretching vibrations in hydrogen-bonded complexes embedded into cryogenic neon matrices are subtly downshifted from cold gas phase reference wavenumbers. To the extent that this shift is systematic, it enables neon matrices as more universally applicable spectroscopic benchmark environments for quantum chemical predictions. Outliers are indicative of either an assignment problem in one of the two cryogenic experiments or they reveal interesting dynamics or structural effects on the complexes as a function of the environment. We compile 6 literature-known pairs of experimental data in jet and neon matrix expansions and realize a 6-fold expansion of that number through targeted matrix isolation and/or slit jet expansion spectroscopy presented in this work. In many cases, the neon matrix shift is less than the uncertainty of the currently best-performing blind quantum chemical predictions for the gas phase, but in specific cases, it may exceed the currently achievable theoretical accuracy. Some evidence for a positive correlation of the matrix shift with the hydrogen bond shift is found, similar to observations for helium nanodroplets. Outliers in particular for water acting as a donor are discussed, and in a few cases they call for a future reinvestigation. Substantial improvement in the correlation of the matrix shift with the hydrogen bond shift is achieved for ketone monohydrates by removing a vibrational resonance. New insights into nitrile hydration isomerism are obtained, and the linear OH stretching spectrum of the jet-cooled ammonia-water complex is presented for the first time. Vibrational spectroscopy in weakly perturbing solid rare gas quantum matrices for the benchmarking of gas phase theory and future explicit theoretical treatments of the quantum matrix environment to better understand the outliers are both encouraged.

Two-Dimensional Infrared Spectroscopy of Isolated Molecular Ions

Two-dimensional infrared (2D IR) spectroscopy of mass-selected, cryogenically cooled molecular ions is presented. Nonlinear response pathways, encoded in the time-domain photodissociation action response of weakly bound N2 messenger tags, were isolated using pulse shaping techniques following excitation with four collinear ultrafast IR pulses. 2D IR spectra of Re(CO)3(CH3CN)3+ ions capture off-diagonal cross-peak bleach signals between the asymmetric and symmetric carbonyl stretching transitions. These cross peaks display intensity variations as a function of pump-probe delay time due to coherent coupling between the vibrational modes. Well-resolved 2D IR features in the congested fingerprint region of protonated caffeine (C8H10N4O2H+) are also reported. Importantly, intense cross-peak signals were observed at 3 ps waiting time, indicating that tag-loss dynamics are not competing with the measured nonlinear signals. These demonstrations pave the way for more precise studies of molecular interactions and dynamics that are not easily obtainable with current condensed-phase methodologies.

Vibrational Dynamics of the Intramolecular H-Bond in Acetylacetone Investigated with Transient and 2D IR Spectroscopy

Acetylacetone (AcAc) has proven to be a fruitful but highly challenging model system for the experimental and computational interrogation of strong intramolecular hydrogen bonds. Key questions remain, however, regarding the identity of the minimum-energy structure of AcAc and the dynamics of intramolecular proton transfer. Here, we investigate the OH/OD stretch and bend regions of the enol tautomer of AcAc and its deuterated isotopologue with transient absorption and 2D IR spectroscopy. The OH bend region reveals a single dominant diagonal transition near 1625 cm^-1 with intense cross peaks to lower-frequency modes, demonstrating highly mixed fingerprint transitions that contain OH bend character. The anharmonic coupling of the OH bend results in a highly elongated OH bend excited-state absorption transition that indicates a large manifold of OH bend overtone/combination bands in the OH stretch region that leads to strong bend-stretch Fermi resonance interactions. The OH and OD stretch regions consist of broad ground-state bleach signals, but there is no clear evidence of ω₂₁ excited-state absorptions due to rapid population relaxation arising from strong intramolecular coupling to bending, fingerprint, and low-frequency H-bond modes. Orientational relaxation dynamics persist for timescales longer than the vibrational lifetimes, with polarization anisotropy components decaying within approximately 2 and 10 periods of the O-O oscillation for the OH and OD stretch, respectively. The significant isotopic dependence of the orientational dynamics is discussed in the context of intramolecular mode coupling, diffusional processes, and contributions from proton/deuteron transfer dynamics.

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.

Structure and Vibrational Spectra of ArnH+ (n = 2-3)

The structure and vibrational spectra of protonated Ar clusters Ar_nH⁺ (n = 2-3) are studied using potential energy surfaces at the CCSD(T)/aug-cc-pVTZ level and basis set. Ar binding energies, as well as position isomerism in Ar₃H⁺, were investigated. In our previous work, the spectra of Ar₂H⁺ reveal a strong progression of combination bands, which involves the asymmetric Ar-H⁺ stretch with multiple quanta of the symmetric Ar-H⁺ stretch. In this work, insights on the origin of such progression were examined using an adiabatic model. In addition, contributions from mechanical and electrical anharmonicity on the progressions' intensities were also examined. Comparison of the calculated spectrum for the bare and Ar-tagged ions reveals that the reduction of the symmetry group, from D_∞h to either C_∞v or C_2v, results in a richer vibrational structure in the 500-1700 cm^-1 region. When compared with previously reported action spectra (D. C. McDonald III, D. T. Mauney, D. Leicht, J. H. Marks, J. A. Tan, J.-L. Kuo, and M. A. Duncan, J. Chem. Phys., 2016, 145, 231,101), it appears that the position isomers, because of the binding of the weakly bound Ar messenger, are needed to account for the additional bands in the infrared photodissociation spectrum for Ar₃H⁺. These findings demonstrate the active role of the messenger atom in relaxing some of the selection rules for the bare ion's vibrational transitions - resulting in an augmentation of the bands in the action spectrum.

An effective Hamiltonian analysis of a Franck-Condon-like pattern in the IR spectra of phenol-alkylsilane dihydrogen-bonded clusters in the S1 state

Infrared (IR) spectra in a region of the OH stretch band of phenol (PhOH)-ethyldimethylsilane (EDMS), phenol (PhOH)-triethylsilane (TES), and phenol (PhOH)-t-butyldimethylsilane (BDMS) dihydrogen-bonded clusters in the S₁ state were observed. All of the species exhibited unconventional band patterns in which many combination bands appeared with comparable intensities to those of allowed bands. Such a behavior is sometimes called a Franck-Condon-like pattern. In the case of the PhOH-BDMS, one intermolecular vibrational mode is involved in this behavior. The observed IR spectra were well reproduced based on the concept of the Franck-Condon-like behavior. As an alternative treatment, we analyzed the band patterns on the concept of intensity borrowing due to the vibrational anharmonic interaction. The analysis was based on an effective Hamiltonian involving an anharmonic interaction between the OH stretch and intermolecular vibrational modes. Two treatments provided the same results. Thus, it was confirmed that the Franck-Condon-like behavior originates from vibrational anharmonic interactions. In the cases of the PhOH-EDMS and PhOH-TES, we carried out a two-dimensional Franck-Condon and an effective Hamiltonian analysis to interpret the Franck-Condon-like patterns. We examined vibrational wave functions obtained by the latter analysis. Shapes of the wave functions suggest that a recombination of the intermolecular vibrational modes occurs during the excitation of OH stretch mode in these clusters, which is a similar behavior to the Duschinsky effect in the electronic transition.

On the turn-inducing properties of asparagine: the structuring role of the amide side chain, from isolated model peptides to crystallized proteins

The anchoring properties of an asparagine (Asn) residue to its local backbone environment in turn model peptides is characterized using gas phase laser spectroscopy and compared to crystallized protein structures.