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      Quantum–Classical Approach for Calculations of Absorption and Fluorescence: Principles and Applications

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          Abstract

          Absorption and fluorescence spectroscopy techniques provide a wealth of information on molecular systems. The simulations of such experiments remain challenging, however, despite the efforts put into developing the underlying theory. An attractive method of simulating the behavior of molecular systems is provided by the quantum–classical theory—it enables one to keep track of the state of the bath explicitly, which is needed for accurate calculations of fluorescence spectra. Unfortunately, until now there have been relatively few works that apply quantum–classical methods for modeling spectroscopic data. In this work, we seek to provide a framework for the calculations of absorption and fluorescence lineshapes of molecular systems using the methods based on the quantum–classical Liouville equation, namely, the forward–backward trajectory solution (FBTS) and the non-Hamiltonian variant of the Poisson bracket mapping equation (PBME-nH). We perform calculations on a molecular dimer and the photosynthetic Fenna–Matthews–Olson complex. We find that in the case of absorption, the FBTS outperforms PBME-nH, consistently yielding highly accurate results. We next demonstrate that for fluorescence calculations, the method of choice is a hybrid approach, which we call PBME-nH-Jeff, that utilizes the effective coupling theory [ ;J. Chem. Phys.2020, 152, 051103[ PubMed]] to estimate the excited state equilibrium density operator. Thus, we find that FBTS and PBME-nH-Jeff are excellent candidates for simulating, respectively, absorption and fluorescence spectra of real molecular systems.

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          UCSF Chimera--a visualization system for exploratory research and analysis.

          The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. Copyright 2004 Wiley Periodicals, Inc.
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            Semiclassical Description of Nonadiabatic Quantum Dynamics

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              The structural basis for the difference in absorbance spectra for the FMO antenna protein from various green sulfur bacteria.

              The absorbance spectrum of the Fenna-Matthews-Olson protein--a component of the antenna system of Green Sulfur Bacteria--is always one of two types, depending on the species of the source organism. The FMO from Prosthecochloris aestuarii 2K has a spectrum of type 1 while that from Chlorobaculum tepidum is of type 2. The previously reported crystal structures for these two proteins did not disclose any rationale that would explain their spectral differences. We have collected a 1.3 A X-ray diffraction dataset of the FMO from Prosthecochloris aestuarii 2K, which has allowed us to identify an additional Bacteriochlorophyll-a molecule with chemical attachments to both sides of the central magnesium atom. A new analysis of the previously published X-ray data for the Chlorobaculum tepidum FMO shows the presence of a Bacteriochlorophyll-a molecule in an equivalent location but with a chemical attachment from only one side. This difference in binding is shown to be predictive of the spectral type of the FMO.
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                Author and article information

                Journal
                J Chem Theory Comput
                J Chem Theory Comput
                ct
                jctcce
                Journal of Chemical Theory and Computation
                American Chemical Society
                1549-9618
                1549-9626
                07 October 2021
                09 November 2021
                : 17
                : 11
                : 7157-7168
                Affiliations
                []Institute of Chemical Physics, Faculty of Physics, Vilnius University , Saulėtekio Avenue 9-III, LT-10222 Vilnius, Lithuania
                []Department of Molecular Compound Physics, Center for Physical Sciences and Technology , Saulėtekio Avenue 3, LT-10257 Vilnius, Lithuania
                Author notes
                Author information
                https://orcid.org/0000-0002-7598-2569
                https://orcid.org/0000-0002-1356-8477
                https://orcid.org/0000-0001-5902-0506
                Article
                10.1021/acs.jctc.1c00777
                8719324
                34618457
                f206853e-d59a-418c-b1be-a2979e7e2ca0
                © 2021 American Chemical Society

                Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained ( https://creativecommons.org/licenses/by/4.0/).

                History
                : 03 August 2021
                Funding
                Funded by: Lietuvos Mokslo Taryba, doi 10.13039/501100004504;
                Award ID: S-MIP-20-44
                Funded by: European Social Fund, doi 10.13039/501100004895;
                Award ID: 09.3.3.-LMT-K-712
                Categories
                Article
                Custom metadata
                ct1c00777
                ct1c00777

                Computational chemistry & Modeling
                Computational chemistry & Modeling

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