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Combining two-color infared pump-probe spectroscopy and anharmonic force field calculations we characterize the anharmonic coupling patterns between fingerprint modes and the hydrogen-bonded symmetric NH$_2$ stretching vibration in adenine-thymine dA$_{20}$-dT$_{20}$ DNA oligomers. Specifically, it is shown that the anharmonic coupling between the NH$_2$ bending and the CO stretching vibration, both absorbing around 1665 cm-1, can be used to assign the NH$_2$ fundamental transition at 3215 cm-1 despite the broad background absorption of water.
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We develop a fully quantum mechanical methodology to describe the static properties and the dynamics of a single anharmonic vibrational mode interacting with a quantized infrared cavity field in the strong and ultrastrong coupling regimes. By comparing multiconfiguration time-dependent Hartree (MCTDH) simulations for a Morse oscillator in a cavity, with an equivalent formulation of the problem in Hilbert space, we describe for the first time the essential role of permanent dipole moments in the femtosecond dynamics of vibrational polariton wavepackets. We show that depending on the shape of the electric dipole function $d_e(q)$ along the vibrational mode coordinate $q$, molecules can be classified into three general families. For molecules that are polar and have a positive slope of the dipole function at equilibrium, we show that an initial diabatic light-matter product state without vibrational or cavity excitations can evolve into a polariton wavepacket with a large number of intracavity photons, for interaction strengths at the onset of ultrastrong coupling. This build up of intracavity photon amplitude is accompanied by an effective $lengthening$ of the vibrational mode of nearly $10%$, comparable with a laser-induced vibrational excitation in free space. In contrast, molecules that are also polar at equilibrium but have a negative slope of the dipole function, experience an effective mode $shortening$ under equivalent coupling conditions. Our model predictions are numerically validated using realistic $ab$-$initio$ potentials and dipole functions for HF and CO$_2$ molecules in their ground electronic states. We finally propose a non-adiabatic state preparation scheme to generate vibrational polaritons using nanoscale infrared antennas and UV-vis photochemistry or electron tunneling, to enable the far-field detection of spontaneously generated infrared quantum light.
While powerful techniques exist to accurately account for anharmonicity in vibrational molecular spectroscopy, they are computationally very expensive and cannot be routinely employed for large species and/or at non- zero vibrational temperatures. Motivated by the study of Polycyclic Aromatic Hydrocarbon (PAH) emission in space, we developed a new code, which takes into account all modes and can describe all IR transitions including bands becoming active due to resonances as well as overtones, combination and difference bands. In this article, we describe the methodology that was implemented and discuss how the main difficulties were overcome, so as to keep the problem tractable. Benchmarking with high-level calculations was performed on a small molecule. We carried out specific convergence tests on two prototypical PAHs, pyrene (C$_{16}$H$_{10}$) and coronene (C$_{24}$H$_{12}$), aiming at optimising tunable parameters to achieve both acceptable accuracy and computational costs for this class of molecules. We then report the results obtained at 0 K for pyrene and coronene, comparing the calculated spectra with available experimental data. The theoretical band positions were found to be significantly improved compared to harmonic Density Functional Theory (DFT) calculations. The band intensities are in reasonable agreement with experiments, the main limitation being the accuracy of the underlying calculations of the quartic force field. This is a first step towards calculating moderately high-temperature spectra of PAHs and other similarly rigid molecules using Monte Carlo sampling.
We propose a cavity QED approach to describe light-matter interaction between an individual anharmonic molecular vibration and an infrared cavity field. Starting from a generic Morse oscillator with quantized nuclear motion, we derive a multi-level quantum Rabi model to study vibrational polaritons beyond the rotating-wave approximation. We analyze the spectrum of vibrational polaritons in detail and compare with available experiments. For high excitation energies, the spectrum exhibits a dense manifold of true and avoided level crossings as the light-matter coupling strength and cavity frequency are tuned. These crossings are governed by a pseudo parity selection rule imposed by the cavity field. We also analyze polariton eigenstates in nuclear coordinate space. We show that the bond length of a vibrational polariton at a given energy is never greater than the bond length of a bare Morse oscillator with the same energy. This type of bond hardening of vibrational polaritons occurs at the expense of the creation of virtual infrared cavity photons, and may have implications in chemical reactivity.
We present a vibrational dynamical mean-field theory (VDMFT) of the dynamics of atoms in solids with anharmonic interactions. Like other flavors of DMFT, VDMFT maps the dynamics of a periodic anharmonic lattice of atoms onto those of a self-consistently defined impurity problem with local anharmonicity and coupling to a bath of harmonic oscillators. VDMFT is exact in the harmonic and molecular limits, nonperturbative, systematically improvable through its clusters extensions, and usable with classical or quantum impurity solvers, depending on the importance of nuclear quantum effects. When tested on models of anharmonic optical and acoustic phonons, we find that classical VDMFT gives good agreement with classical molecular dynamics, including the temperature dependence of phonon frequencies and lifetimes. Using a quantum impurity solver, signatures of nuclear quantum effects are observed at low temperatures.
Helices are a key folding motif in protein structure. The question which factors determine helix stability for a given polypeptide or protein is an ongoing challenge. Here we use van der Waals corrected density-functional theory to address a part of this question in a bottom-up approach. We show how intrinsic helical structure is stabilized with length and temperature for a series of experimentally well studied unsolvated alanine based polypeptides, Ac-Alan-LysH+. By exploring extensively the conformational space of these molecules, we find that helices emerge as the preferred structure in the length range n=4-8 not just due to enthalpic factors (hydrogen bonds and their cooperativity, van der Waals dispersion interactions, electrostatics), but importantly also by a vibrational entropic stabilization over competing conformers at room temperature. The stabilization is shown to be due to softer low-frequency vibrational modes in helical conformers than in more compact ones. This observation is corroborated by including anharmonic effects explicitly through emph{ab initio} molecular dynamics, and generalized by testing different terminations and considering larger helical peptide models.
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