We provide a new and definitive spectral assignment for the absorption, emission, high-resolution fluorescence excitation, linear dichroism, and/or magnetic circular dichroism spectra of 32 chlorophyllides in various environments. This encompases all data used to justify previous assignments and provides a simple interpretation of unexplained complex decoherence phenomena associated with Qx → Qy relaxation. Whilst most chlorophylls conform to the Gouterman model and display two independent transitions Qx (S2) and Qy (S1), strong vibronic coupling inseparably mixes these states in chlorophyll-a. This spreads x-polarized absorption intensity over the entire Q-band system to influence all exciton-transport, relaxation and coherence properties of chlorophyll-based photosystems. The fraction of the total absorption intensity attributed to Qx ranges between 7% and 33%, depending on chlorophyllide and coordination, and is between 10% and 25% for chlorophyll-a. CAM-B3LYP density-functional-theory calculations of the band origins, relative intensities, vibrational Huang-Rhys factors, and vibronic coupling strengths fully support this new assignment.
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http://dx.doi.org/10.1038/srep02761 | DOI Listing |
J Am Chem Soc
January 2025
Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States.
Ribonucleotide reductase (RNR) is essential for DNA synthesis and repair in all living organisms. The mechanism of RNR requires long-range radical transport through a proton-coupled electron transfer (PCET) pathway spanning two different protein subunits. Herein, the direct PCET reaction between the interfacial tyrosine residues, Y356 and Y731, is investigated with a vibronically nonadiabatic theory that treats the transferring proton and all electrons quantum mechanically.
View Article and Find Full Text PDFPhotochem Photobiol
January 2025
Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences (IPAC RAS), Chernogolovka, Russia.
Recently (Photochem Photobiol. 2023;100:1277-1289. doi:10.
View Article and Find Full Text PDFJ Phys Chem A
January 2025
Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy.
We here simulate in the gas phase the population dynamics of guanine/cytosine (GC) and cytosine/guanine (CG) stacked dimers in B-DNA and A-DNA arrangement, following excitation in the lowest-energy band, and considering the four lowest-energy ππ* bright excited states, the three lowest-energy π* states, and the G → C charge-transfer (CT) state. We resort to a generalized Linear Vibronic Coupling (LVC) model parametrized with time-dependent density functional theory (TD-DFT) computations, exploiting a fragment-based diabatization and we run nonadiabatic quantum dynamical simulations with the multilayer version of the Multiconfigurational Time-Dependent Hartree (ML-MCTDH) approach. G → C CT results in a major decay process for GC in B-DNA but less in A-DNA arrangement, where also the population transfer to the lowest-energy excited state localized on C is an important intermonomer process.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Department of Chemistry, The University of Manchester, Manchester M13 9PL, U.K.
The linear vibronic coupling (LVC) model is an approach for approximating how a molecular Hamiltonian changes in response to small changes in molecular geometry. The LVC framework thus has the ability to approximate molecular Hamiltonians at low computational expense but with quality approaching multiconfigurational calculations, when the change in geometry compared to the reference calculation used to parametrize it is small. Here, we show how the LVC approach can be used to project approximate spin Hamiltonians of a solvated lanthanide complex along a room-temperature molecular dynamics trajectory.
View Article and Find Full Text PDFJ Phys Chem A
January 2025
Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States.
The cyano-cyclopentadiene molecule (CN-CH) has attracted significant interest since its detection in the interstellar medium, but the radical (CN-CH) and anionic (CN-CH) forms of cyano-cyclopentadiene have not been studied. The cyano-cyclopentadienyl radical (CN-Cp) has a strong dipole moment, rendering it an ideal system for vibrational and rotational spectroscopy. We report an investigation of the cryogenically cooled cyano-cyclopentadienide anion (CN-Cp) using high-resolution photoelectron imaging, photodetachment spectroscopy, and resonant photoelectron imaging.
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