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Semiclassical (SC) vibrational spectroscopy is a technique capable of reproducing quantum effects (such as zero-point energies, quantum resonances, and anharmonic overtones) from classical dynamics runs even in the case of very large dimensional systems. In a previous study [Conte et al. J. Chem. Phys. 151, 214107 (2019)], a preliminary sampling based on adiabatic switching has been shown to be able to improve the precision and accuracy of semiclassical results for challenging model potentials and small molecular systems. In this paper, we investigate the possibility to extend the technique to larger (bio)molecular systems whose dynamics must be integrated by means of ab initio "on-the-fly" calculations. After some preliminary tests on small molecules, we obtain the vibrational frequencies of glycine improving on pre-existing SC calculations. Finally, the new approach is applied to 17-atom proline, an amino acid characterized by a strong intramolecular hydrogen bond.

Incorporation of fluorescent proteins into biochemical systems has revolutionized the field of bioimaging. In a bottom-up approach, understanding the photophysics of fluorescent proteins requires detailed investigations of the light-absorbing chromophore, which can be achieved by studying the chromophore in isolation. This paper reports a photodissociation action spectroscopy study on the deprotonated anion of the red Kaede fluorescent protein chromophore, demonstrating that at least three isomers-assigned to deprotomers-are generated in the gas phase. Deprotomer-selected action spectra are recorded over the S 1 ← S 0 band using an instrument with differential mobility spectrometry coupled with photodissociation spectroscopy. The spectrum for the principal phenoxide deprotomer spans the 480-660 nm range with a maximum response at ≈610 nm. The imidazolate deprotomer has a blue-shifted action spectrum with a maximum response at ≈545 nm. The action spectra are consistent with excited state coupled-cluster calculations of excitation wavelengths for the deprotomers. A third gas-phase species with a distinct action spectrum is tentatively assigned to an imidazole tautomer of the principal phenoxide deprotomer. This study highlights the need for isomer-selective methods when studying the photophysics of biochromophores possessing several deprotonation sites.

Changes in the electronic structure of pigments in protein environments and of polar molecules in solution inevitably induce a re-adaption of molecular nuclear structure. Both changes of electronic and vibrational energies can be probed with visible or infrared lasers, such as two-dimensional electronic spectroscopy or vibrational spectroscopy. The extent to which the two changes are correlated remains elusive. The recent demonstration of two-dimensional electronic-vibrational (2DEV) spectroscopy potentially enables a direct measurement of this correlation experimentally. However, it has hitherto been unclear how to characterize the correlation from the spectra. In this paper, we present a theoretical formalism to demonstrate the slope of the nodal line between the excited state absorption and ground state bleach peaks in the spectra as a characterization of the correlation between electronic and vibrational transition energies. We also show the dynamics of the nodal line slope is correlated to the vibrational spectral dynamics. Additionally, we demonstrate the fundamental 2DEV spectral line-shape of a monomer with newly developed response functions.

Non-Markovian Quantum State Diffusion (NMQSD) has turned out to be an efficient method to calculate excitonic properties of aggregates composed of organic chromophores, taking into account the coupling of electronic transitions to vibrational modes of the chromophores. NMQSD is an open quantum system approach that incorporates environmental degrees of freedom (the vibrations in our case) in a stochastic way. We show in this paper that for linear optical spectra (absorption, circular dichroism), no stochastics is needed, even for finite temperatures. Thus, the spectra can be obtained by propagating a single trajectory. To this end, we map a finite temperature environment to the zero temperature case using the so-called thermofield method. The resulting equations can then be solved efficiently by standard integrators.

Understanding the structure of water near cell membranes is crucial for characterizing water-mediated events such as molecular transport. To obtain structural information of water near a membrane, it is useful to have a surface-selective technique that can probe only interfacial water molecules. One such technique is vibrational sum-frequency generation (VSFG) spectroscopy. As model systems for studying membrane headgroup/water interactions, in this paper we consider lipid and surfactant monolayers on water. We adopt a theoretical approach combining molecular dynamics simulations and phase-sensitive VSFG to investigate water structure near these interfaces. Our simulated spectra are in qualitative agreement with experiments and reveal orientational ordering of interfacial water molecules near cationic, anionic, and zwitterionic interfaces. OH bonds of water molecules point toward an anionic interface leading to a positive VSFG peak, whereas the water hydrogen atoms point away from a cationic interface leading to a negative VSFG peak. Coexistence of these two interfacial water species is observed near interfaces between water and mixtures of cationic and anionic lipids, as indicated by the presence of both negative and positive peaks in their VSFG spectra. In the case of a zwitterionic interface, OH orientation is toward the interface on the average, resulting in a positive VSFG peak.

Sum frequency generation (SFG) is a surface-selective spectroscopy that provides a wealth of molecular-level information on the structure and dynamics at surfaces and interfaces. This paper addresses the general issue of spectral resolution and sensitivity of the broad-band (BB) SFG that involves a spectrally narrow nonresonant (usually visible) and a BB resonant (usually infrared) laser pulses. We examine how the spectral width and temporal shape of the two pulses, and the time delay between them, relate to the spectroscopic line shape and signal level in the BB-SFG measurement. By combining experimental and model calculations, we show that the best spectral resolution and highest signal level are simultaneously achieved when the nonresonant narrow-band upconversion pulse arrives with a nonzero time delay after the resonant BB pulse. The nonzero time delay partially avoids the linear trade-off of improving spectral resolution at the expense of decreasing signal intensity, which is common in BB-SFG schemes utilizing spectral filtering to produce narrow-band visible pulses.

An analytical expression is found for the accurate ab initio potential energy curve of the fluorine molecule that has been determined in the preceding two papers. With it, the vibrational and rotational energy levels of F(2) are calculated using the discrete variable representation. The comparison of this theoretical spectrum with the experimental spectrum, which had been measured earlier using high-resolution electronic spectroscopy, yields a mean absolute deviation of about 5 cm(-1) over the 22 levels. The dissociation energy with respect to the lowest vibrational energy is calculated within 30 cm(-1) of the experimental value of 12 953+/-8 cm(-1). The reported agreement of the theoretical spectrum and dissociation energy with experiment is contingent upon the inclusion of the effects of core-generated electron correlation, spin-orbit coupling, and scalar relativity. The Dunham analysis [Phys. Rev. 41, 721 (1932)] of the spectrum is found to be very accurate. New values are given for the spectroscopic constants.

Real-space grids for electronic structure calculations are efficient because the potential is diagonal while the second derivative in the kinetic energy may be sparsely evaluated with finite differences or finite elements. In applications to vibrational problems in chemical physics a family of methods known as spectral differences has improved finite differences by several orders of magnitude. In this paper the use of spectral differences for electronic structure is studied. Spectral differences are implemented in two electronic structure programs PARSEC and HARES which currently employ finite differences. Applications to silicon clusters and lattices indicate that spectral differences achieve the same accuracy as finite differences with less computational work., ((c) 2004 American Institute of Physics)