Two-Dimensional Spectroscopy of Extended Molecular Systems: Applications to Energy Transport and Relaxation in an α-Helix

A simulation study of the coupled dynamics of amide I and amide II vibrations in an α-helix dissolved in water shows that two-dimensional (2D) infrared spectroscopy may be used to disentangle the energy transport along the helix through each of these modes from the energy relaxation between them. Time scales for both types of processes are obtained. Using polarization-dependent 2D spectroscopy is an important ingredient in the method we propose. The method may also be applied to other two-band systems, both in the infrared (collective vibrations) and the visible (excitons) parts of the spectrum.

Vibrational Spectra of a Mechanosensitive Channel

We report the simulated vibrational spectra of a mechanosensitive membrane channel in different gating states. Our results show that while linear absorption is insensitive to structural differences, linear dichroism and sum-frequency generation spectroscopies are sensitive to the orientation of the transmembrane helices, which is changing during the opening process. Linear dichroism cannot distinguish an intermediate structure from the closed structure, but sum-frequency generation can. In addition, we find that two-dimensional infrared spectroscopy can be used to distinguish all three investigated gating states of the mechanosensitive membrane channel.

Revealing Hidden Vibration Polariton Interactions by 2D IR Spectroscopy

We report the first experimental two-dimensional infrared (2D IR) spectra of novel molecular photonic excitations - vibrational-polaritons. The application of advanced 2D IR spectroscopy onto novel vibrational-polariton challenges and advances our understanding in both fields. From spectroscopy aspect, 2D IR spectra of polaritons differ drastically from free uncoupled molecules; from vibrational-polariton aspects, 2D IR uniquely resolves hybrid light-matter polariton excitations and unexpected dark states in a state-selective manner and revealed hidden interactions between them. Moreover, 2D IR signals highlight the role of vibrational anharmonicities in generating non-linear signals. To further advance our knowledge on 2D IR of vibrational polaritons, we develop a new quantum-mechanical model incorporating the effects of both nuclear and electrical anharmonicities on vibrational-polaritons and their 2D IR signals. This work reveals polariton physics that is difficult or impossible to probe with traditional linear spectroscopy and lays the foundation for investigating new non-linear optics and chemistry of molecular vibrational-polaritons

Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy

We propose a new method to determine the proton transfer (PT) rate in channel proteins by two-dimensional infrared (2DIR) spectroscopy. Proton transport processes in biological systems, such as proton channels, trigger numerous fundamental biochemical reactions. Due to the limitation in both spatial and time resolution of the traditional experimental approaches, describing the whole proton transport process and identifying the rate limiting steps at the molecular level is challenging. In the present paper, we focus on proton transport through the Gramicidin A channel. Using a kinetic PT model derived from all-atom molecular dynamics simulations, we model the amide I region of the 2DIR spectrum of the channel protein to examine its sensitivity to the proton transport process. We demonstrate that the 2DIR spectrum of the isotope-labeled channel contain information on the PT rate, which may be extracted by analyzing the antidiagonal linewidth of the spectral feature related to the labeled site. Such experiments in combination with detailed numerical simulations should allow the extraction of site dependent PT rates, providing a method for identifying possible rate limiting steps for proton channel transfer.

Signatures of β-sheet secondary structures in linear and two-dimensional infrared spectroscopy

Using idealized models for parallel and antiparallel β sheets, we calculate the linear and two-dimensional infrared spectra of the amide I vibration as a function of size and secondary structure. The model assumes transition–dipole coupling between the amide I oscillators in the sheet and accounts for the anharmonic nature of these oscillators. Using analytical and numerical methods, we show that the nature of the one-quantum vibrational eigenstates, which govern the linear spectrum, is, to a large extent, determined by the symmetry of the system and the relative magnitude of interstrand interactions. We also find that the eigenstates, in particular their trends with system size, depend sensitively on the secondary structure of the sheet. While in practice these differences may be difficult to distinguish in congested linear spectra, we demonstrate that they give rise to promising markers for secondary structure in the two-dimensional spectra. In particular, distinct differences occur between the spectra of parallel and antiparallel bsheets and between β hairpins and extended β sheets.

Weyl semimetal from spontaneous inversion symmetry breaking in pyrochlore oxides

We study the electronic properties of strongly spin-orbit coupled electrons on the elastic pyrochlore lattice. Akin to the Peierls transition in one-dimensional systems, the coupling of the lattice to the electronic degrees of freedom can stabilize a spontaneous deformation of the crystal. This deformation corresponds to a breathing mode, which breaks the inversion symmetry. We find that for intermediate values of the staggered strain, the inversion-symmetry broken phase realizes a topological Weyl semimetal. In the temperature-elasticity phase diagram, the Weyl semimetal shows a reentrant phase behavior: it can be reached from a symmetric phase realized both at higher and at lower temperatures. The symmetric phase is a Dirac semimetal, which is protected by the non-symmorphic space group of the pyrochlore lattice. Beyond a critical value of the staggered strain, the symmetry-broken phase is a fully gapped trivial insulator. The surface states of the Weyl semimetal form open Fermi arcs and we observe that their connectivity depends on the termination of the crystal. In particular, for the $\{111\}$ films, the semiclassical closed electronic orbits of the surface states in a magnetic field cross the bulk either twice, four, six or twelve times. We demonstrate how one can tune the number of bulk crossings through a Lifshitz-like transition of the Fermi arcs, which we call Weyl-Lifshitz transition, by applying a surface potential. Our results offer a route to a topological Weyl semimetal in nonmagnetic materials and might be relevant for pyrochlore oxides with heavy transition-metal ions such as alloys of iridates.Comment: 18 pages, 11 figure