Introduction 4546 2. General Information on the Structure of Photosynthetic Complexes and StructureÀFunction Relationships 4548 2.1. Photosystem I (PSI) and Photosystem II (PSII) 4548 2.2. Basic Aspects of Bacterial Photosynthesis 4549 3. Interpigment Interactions, Excitation Energy Transfer (EET), and Charge Separation (CS) Rates-General Considerations 4550 4. Fundamentals of Spectral Hole-Burning (SHB) and Fluorescence Line-Narrowing Spectroscopy (FLNS) and Single Photosynthetic Complex Spectroscopy (SPCS) 4552 4.1. Zero-Phonon Lines, Homogeneous and Inhomogeneous Broadening 4553 4.1.1. ZPLs and Phonon Sidebands (PSBs) 4554 4.1.2. ElectronÀPhonon Coupling and Homogeneous Line Shapes 4555 4.2. Nonphotochemical, Photochemical, and Transient SHB Spectroscopy 4557 4.3. Mechanism of Nonphotochemical Hole-Burning (NPHB) 4558 4.4. Kinetics of NPHB 4559 4.5. Zero-Phonon Action (ZPA) Spectroscopy: Site Distribution Function (SDF) 4560 4.6. Hole Shapes and FLN Line Shapes-Electron Phonon Coupling and ΔFLNS 4561 4.7. Ground and Excited State Vibrational Frequencies 4567 4.8. SHB in Excitonically Coupled Systems 4567 4.9. Basic Principles of SPCS 4568 4.10. Basic Principles of Two-Dimensional Electronic Spectroscopy (2D ES) 4569 5. Examples of Applications of NPHB, FLNS, SPCS, and 2D ES to Photosynthesis 4570 5.1. Light-Harvesting and EET in Antenna Complexes 4570 5.1.1. Peripheral Antenna Systems of Photosystem II (

Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and inter-protein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an allencompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semi-empirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository website (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-theart multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.

We report low temperature (T) optical spectra of the isolated CP47 antenna complex from Photosystem II (PSII) with a low-T fluorescence emission maximum near 695 nm and not, as previously reported, at 690-693 nm. The latter emission is suggested to result from three distinct bands: a lowest-state emission band near 695 nm (labeled F1) originating from the lowest-energy excitonic state A1 of intact complexes (located near 693 nm and characterized by very weak oscillator strength) as well as emission peaks near 691 nm (FT1) and 685 nm (FT2) originating from subpopulations of partly destabilized complexes. The observation of the F1 emission is in excellent agreement with the 695 nm emission observed in intact PSII cores and thylakoid membranes. We argue that the band near 684 nm previously observed in singlet-minus-triplet spectra originates from a subpopulation of partially destabilized complexes with lowest-energy traps located near 684 nm in absorption (referred to as AT2) giving rise to FT2 emission. It is demonstrated that varying contributions from the F1, FT1, and FT2 emission bands led to different maxima of fluorescence spectra reported in the literature. The fluorescence spectra are consistent with the zero-phonon hole action spectra obtained in absorption mode, the profiles of the nonresonantly burned holes as a function of fluence, as well as the fluorescence line-narrowed spectra obtained for the Q(y) band. The lowest Q(y) state in absorption band (A1) is characterized by an electron-phonon coupling with the Huang-Rhys factor S of approximately 1 and an inhomogeneous width of approximately 180 cm(-1). The mean phonon frequency of the A1 band is 20 cm(-1). In contrast to previous observations, intact isolated CP47 reveals negligible contribution from the triplet-bottleneck hole, i.e., the AT2 trap. It has been shown that Chls in intact CP47 are connected via efficient excitation energy transfer to the A1 trap near 693 nm and that the position of the fluorescence maximum depends on the burn fluence. That is, the 695 nm fluorescence maximum shifts blue with increasing fluence, in agreement with nonresonant hole burned spectra. The above findings provide important constraints and parameters for future excitonic calculations, which in turn should offer new insight into the excitonic structure and composition of low-energy absorption traps.