The use of flavins and flavoproteins in photocatalytic, sensing, and biotechnological applications has led to a growing interest in computationally modeling the excited-state electronic structure and photophysics of flavin. However, there is limited consensus regarding which computational methods are appropriate for modeling flavin's photophysics. We compare the energies of low-lying excited states of flavin computed with time-dependent density functional theory (TD-DFT), equation-of-motion coupled cluster (EOM-EE-CCSD), scaled opposite-spin configuration interaction [SOS-CIS(D)], multiconfiguration pair-density functional theory (MC-PDFT), and several multireference perturbation theory (MR-PT2) methods. In the first part, we focus on excitation energies of the first singlet excited state (S) of five different redox and protonation states of flavin, with the goal of finding a suitable active space for MR-PT2 calculations. In the second part, we construct two sets of one-dimensional potential energy surfaces connecting the S and S equilibrium geometries (S-S path) and the S (π,π*) and S (,π*) equilibrium geometries (S-S path). The first path therefore follows a Franck-Condon active mode of flavin while the second path maps crossings points between low-lying singlet and triplet states in flavin. We discuss the similarities and differences in the TD-DFT, EOM-EE-CCSD, SOS-CIS(D), MC-PDFT and MR-PT2 energy profiles along these paths. We find that (TD-)DFT methods are suitable for applications such as simulating the spectra of flavins but are inconsistent with several other methods when used for some geometry optimizations and when describing the energetics of dark (,π*) states. MR-PT2 methods show promise for the simulation of flavin's low-lying excited states, but the selection of orbitals for the active space and the number of roots used for state averaging must be done carefully to avoid artifacts. Some properties, such as the intersystem crossing geometry and energy between the S (π,π*) and T (,π*) states, may require additional benchmarking before they can be determined quantitatively.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11317985 | PMC |
http://dx.doi.org/10.1021/acs.jpcb.4c03748 | DOI Listing |
Nat Commun
January 2025
Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
Glucose deprivation, a hallmark of the tumor microenvironment, compels tumor cells to seek alternative energy sources for survival and growth. Here, we show that glucose deprivation upregulates the expression of mitochondrial-cytochrome c oxidase II (MT-CO2), a subunit essential for the respiratory chain complex IV, in facilitating glutaminolysis and sustaining tumor cell survival. Mechanistically, glucose deprivation activates Ras signaling to enhance MT-CO2 transcription and inhibits IGF2BP3, an RNA-binding protein, to stabilize MT-CO2 mRNA.
View Article and Find Full Text PDFCancer Res
January 2025
University of California, San Diego, La Jolla, CA, United States.
Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest solid cancers; thus, identifying more effective therapies is a major unmet need. In this study, we characterized the super enhancer (SE) landscape of human PDAC to identify drivers of the disease that might be targetable. This analysis revealed MICAL2 as a super enhancer-associated gene in human PDAC, which encodes the flavin monooxygenase MICAL2 that induces actin depolymerization and indirectly promotes SRF transcription by modulating the availability of serum response factor coactivators myocardin-related transcription factors (MRTF-A and MRTF-B).
View Article and Find Full Text PDFJ Maine Med Cent
January 2024
Department of Medicine, MaineHealth, Portland, Maine.
Introduction: Average length of stay (ALOS) has increased in many US hospitals in the post-COVID-19-pandemic world. We undertook a process improvement initiative to reduce the ALOS in our community hospital.
Methods: Three core tactics were developed with a goal of reducing our ALOS by 10%.
Photochem Photobiol Sci
December 2024
Biophysical Chemistry and Diagnostics, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany.
Flavin-dependent halogenases (FDHs) are promising candidates for the sustainable production of halogenated organic molecules by biocatalysis. FDHs require only oxygen, halide and a fully reduced flavin adenine dinucleotide (FADH) cofactor to generate the reactive HOX that diffuses 10 Å to the substrate binding pocket and enables regioselective oxidative halogenation. A key challenge for the application of FDHs is the regeneration of the FADH.
View Article and Find Full Text PDFNat Commun
December 2024
Living Systems Institute, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, UK.
The radical pair mechanism accounts for the magnetic field sensitivity of a large class of chemical reactions and is hypothesised to underpin numerous magnetosensitive traits in biology, including the avian compass. Traditionally, magnetic field sensitivity in this mechanism is attributed to radical pairs with weakly interacting, well-separated electrons; closely bound pairs were considered unresponsive to weak fields due to arrested spin dynamics. In this study, we challenge this view by examining the FAD-superoxide radical pair within cryptochrome, a protein hypothesised to function as a biological magnetosensor.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!