Article
Chemistry, Inorganic & Nuclear
Angela A. Shiau, Heui Beom Lee, Paul H. Oyala, Theodor Agapie
Summary: This article reports the synthesis and characterization of a stable (Mn4O4)-O-IV cuboidal complex supported by a disiloxide ligand. The substitution of an anionic acetate or amidate ligand with a dianionic disiloxide ligand improves the stability and shifts the reduction potential of the complex.
INORGANIC CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Maria Drosou, Gerard Comas-Vila, Frank Neese, Pedro Salvador, Dimitrios A. . Pantazis
Summary: Recent advancements in serial femtosecond crystallography have provided geometric models of distinct intermediates in the catalytic S-state cycle of the oxygen-evolving complex (OEC). However, the interpretation of these models is controversial due to discrepancies in the Mn4CaO5 cluster of the OEC.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Masahiro Saito, Keisuke Saito, Hiroshi Ishikita
Summary: Despite the abundance of iron on earth, manganese serves as the catalytic center for water splitting in photosystem II. In order to understand why nature employs manganese instead of iron, a study investigated the Fe4CaO5 cluster in the PSII protein environment using a QM/MM approach. It was found that substituting manganese with iron resulted in protonation of mu-oxo bridges, highlighting the relevance of manganese in natural water splitting.
Article
Chemistry, Physical
Kizashi Yamaguchi, Koichi Miyagawa, Mitsuo Shoji, Hiroshi Isobe, Takashi Kawakami
Summary: A multiple S-3 intermediates model for water oxidation in the oxygen evolving complex of photosystem II is examined based on key intermediates elucidated by calculations. The results suggest that the Mn-Hydroxide configuration plays a major role in the S3 state, while Mn-Oxyl has only a partial contribution. The oxyl-radical character is significantly reduced by the coordination of the Ca ion.
CHEMICAL PHYSICS LETTERS
(2022)
Article
Chemistry, Physical
Hiroshi Isobe, Mitsuo Shoji, Takayoshi Suzuki, Jian-Ren Shen, Kizashi Yamaguchi
Summary: In photosystem II, water is oxidized to dioxygen through a Mn4CaO5 cluster, with two competing reaction routes, stepwise and concerted, affecting the formation of the final stable closed structure.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Henrique S. Fernandes, Sergio F. Sousa, Nuno M. F. S. A. Cerqueira
Summary: This study utilized advanced computational methods to investigate the catalytic mechanism of SARS-CoV-2 M-pro, providing insights for the design of new antiviral drugs.
MOLECULAR DIVERSITY
(2022)
Review
Chemistry, Inorganic & Nuclear
Kizashi Yamaguchi, Mitsuo Shoji, Hiroshi Isobe, Takashi Kawakami, Koichi Miyagawa, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen
Summary: This review elucidates the geometric and electronic structures of the catalytic CaMn4Ox (x = 5, 6) cluster in the water oxidation process in PSII, using high-resolution X-ray diffraction and serial femtosecond crystallography experiments, as well as theoretical computations. The interplay between experimental and theoretical methods effectively reveals the coordination structures and spin states of the cluster, and implications of these findings for artificial catalyst development are discussed.
COORDINATION CHEMISTRY REVIEWS
(2022)
Article
Chemistry, Physical
Jose Luis Velazquez-Libera, Julio Caballero, Jans Alzate-Morales, J. Javier Ruiz-Pernia, Inaki Tunon
Summary: We conducted a computational study on the reaction mechanism of USP7 with Ubiquitin-Rhodamine 110-G substrate using a robust methodology. Our findings provide insights into the dynamic nature of USP7 enzyme-substrate complexes and describe the conformational changes observed in our simulations. The protein-protein interactions and geometric states identified in this study could be utilized for designing potent and selective inhibitors for USP7's activity.
Article
Plant Sciences
Keisuke Saito, Shu Nakao, Hiroshi Ishikita
Summary: The Mn4CaO5 cluster in photosystem II forms hydrogen bonds with D1-His337 and a water molecule. The hydrogen bond distances differ between the two monomer units and can be attributed to protonation and overreduction states.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Chemistry, Physical
Niko Prasetyo, Alberto Krishna Ksatria Winning Kusuma, La Ode Muhammad Iqbal
Summary: The spin component scale MP2/molecular mechanics molecular dynamics simulation was used to investigate the formation of hydration shell and dynamics of hydrated Cd2+ in a water environment. The first hydration shell consisted of six water molecules with an average distance of 2.27 Å between water and Cd2+. The dynamics were analyzed by calculating the mean residence time (MRT) of water molecules in the first and second hydration shells, which were determined to be 31.8 and 1.92 ps, respectively, indicating the strong influence of Cd2+ in the first shell. Despite the strong interaction between Cd2+ and water molecules in the first shell, the influence of ions in the second hydration shell remained weak.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2023)
Article
Chemistry, Physical
J. A. Ocadiz-Flores, A. E. Gheribi, J. Vlieland, K. Dardenne, J. Rothe, R. J. M. Konings, A. L. Smith
Summary: This study investigates the phase diagram equilibria in the LiF-UF4 system, proposing a CALPHAD-type assessment that links structural and thermodynamic properties with a rigorous physical description of the melt.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Cell Biology
Vasily V. Terentyev, Anna K. Shukshina, Angelina A. Chetverkina
Summary: Chlamydomonas reinhardtii is commonly used in studies on green algae to investigate photosynthesis and biotechnological approaches. The study found that using low concentrations of 2,6-dichloro-1,4-benzoquinone (DCBQ) paired with potassium ferricyanide (FeCy) is necessary to achieve the maximum rate of O-2 evolution. Higher concentrations of DCBQ can strongly suppress O-2 evolution. The concentration of DCBQ required depends on the presence of a cell wall, with 0.1 mM for cells with a cell wall and 0.2-0.4 mM for cells without a cell wall.
Article
Chemistry, Physical
Ann Varghese, Shobhit S. Chaturvedi, Bella DiCastri, Emerald Mehler, Gregg B. Fields, Tatyana G. Karabencheva-Christova
Summary: Matrix metalloproteinase-1 (MMP-1) is an enzyme involved in collagen degradation. This study used computational analysis to characterize the structure and geometry of the catalytic zinc ion in MMP-1 and explored the effects of substrate removal and cobalt substitution on the protein's structure and geometry. The results were consistent with experimental data and provided insights into the catalytic mechanism of MMP-1.
Article
Chemistry, Physical
Hai-Yang Sun, Zi-Yue Yu, Ai-Ping Zhou, Shu-Li Wei, Qiang Chang, Tian Zhang, Yu-Ping Sun
Summary: The luminescent mechanism of two novel TADF emitters with aggregation-induced emission (AIE) features, PPZTPI and PPZPPI, are theoretically studied in this article using first-principles calculations. Both PPZTPI and PPZPPI exhibit excellent TADF and AIE properties with similar luminescence mechanisms. In the solid state, the delayed fluorescence of the molecules mainly depends on the reverse intersystem crossing process, and the aggregation enhances the molecular radiation rates by 1-2 orders of magnitude. The solid-state environment has a greater influence on PPZTPI's molecular properties due to the substitution of tert-butyl groups and their steric hindrance effects.
Article
Chemistry, Multidisciplinary
Wenyuan Zhang, Eric A. C. Bushnell
Summary: In this study, the QM/MM approach was used to investigate the impact of the second environmental shell of the active site on the catalytic conversion of acetylene to acetaldehyde by acetylene hydratase (AH). Results indicated that the presence of the second shell environment significantly affected the reaction, and substitutions of sulfur atoms with selenium atoms had a notable impact on the Gibbs energy for acetylene binding. The study suggested that substituting key W-coordinating sulfur atoms with selenium atoms may enhance the catalytic mechanism of AH.
CANADIAN JOURNAL OF CHEMISTRY
(2021)
Article
Cardiac & Cardiovascular Systems
Jan R. Kraehling, Zhengrong Hao, Monica Y. Lee, David J. Vinyard, Heino Velazquez, Xinran Liu, Radu V. Stan, Gary W. Brudvig, William C. Sessa
CIRCULATION RESEARCH
(2016)
Article
Plant Sciences
David J. Vinyard, Jennifer S. Sun, Javier Gimpel, Gennady M. Ananyev, Stephen P. Mayfield, G. Charles Dismukes
PHOTOSYNTHESIS RESEARCH
(2016)
Article
Biochemistry & Molecular Biology
David J. Vinyard, Mikhail Askerka, Richard J. Debus, Victor S. Batista, Gary W. Brudvig
Article
Chemistry, Inorganic & Nuclear
Dania L. Huang, David J. Vinyard, James D. Blakemore, Sara M. Hashmi, Robert H. Crabtree
Article
Chemistry, Physical
David J. Vinyard, Sahr Khan, Mikhail Askerka, Victor S. Batista, Gary W. Brudvig
JOURNAL OF PHYSICAL CHEMISTRY B
(2017)
Article
Chemistry, Multidisciplinary
Jennifer L. Peper, David J. Vinyard, Gary W. Brudvig, James M. Mayer
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2017)
Article
Chemistry, Multidisciplinary
Megan Mohadjer Beromi, Ainara Nova, David Balcells, Ann M. Brasacchio, Gary W. Brudvig, Louise M. Guard, Nilay Hazari, David J. Vinyard
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2017)
Article
Chemistry, Multidisciplinary
Dimitar Y. Shopov, Benjamin Rudshteyn, Jesus Campos, David J. Vinyard, Victor S. Batista, Gary W. Brudvig, Robert H. Crabtree
Article
Hematology
Monica Y. Lee, Ana Gamez-Mendez, Jiasheng Zhang, Zhenwu Zhuang, David J. Vinyard, Jan Kraehling, Heino Velazquez, Gary W. Brudvig, Themis R. Kyriakides, Michael Simons, William C. Sessa
ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY
(2018)
Article
Multidisciplinary Sciences
Ananya Mukherjee, Chun Sing Lau, Charlotte E. Walker, Ashwani K. Rai, Camille I. Prejean, Gary Yates, Thomas Emrich-Mills, Spencer G. Lemoine, David J. Vinyard, Luke C. M. Mackinder, James V. Moroney
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Multidisciplinary Sciences
David J. Vinyard, Syed Lal Badshah, M. Rita Riggio, Divya Kaur, Annaliesa R. Fanguy, M. R. Gunner
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Multidisciplinary Sciences
Drew M. Hood, Ryan A. Johnson, Alex E. Carpenter, Jarod M. Younker, David J. Vinyard, George G. Stanley
Article
Biochemistry & Molecular Biology
Christopher J. Gisriel, Gaozhong Shen, Ming-Yang Ho, Vasily Kurashov, David A. Flesher, Jimin Wang, William H. Armstrong, John H. Golbeck, Marilyn R. Gunner, David J. Vinyard, Richard J. Debus, Gary W. Brudvig, Donald A. Bryant
Summary: Far-red light photoacclimation expands the range of photosynthetically active radiation for terrestrial cyanobacteria, providing a growth advantage. This process modifies the structure of photosystem II and lowers the energy required for water oxidation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Plant Sciences
Brandon P. Russell, David J. Vinyard
Summary: The study found that the first Mn2+ oxidation event in the assembly of the oxygen-evolving complex in Photosystem II requires chloride-facilitated deprotonation. This process is dependent on the presence of calcium at physiologically relevant pH values.
PHOTOSYNTHESIS RESEARCH
(2022)
Article
Plant Sciences
David J. Vinyard
Summary: Unlike laboratory conditions, real environments have dynamic light intensity. Researchers have developed a simple and affordable system that uses a commercial dimmable LED panel to simulate a sinusoidal function representing daylight hours and includes stochastic shading events. The system closely replicates light intensity measurements on Earth's surface during partly cloudy days or in lower levels of plant canopies. This tool may be valuable for researchers studying photosynthetic acclimation responses.
PHOTOSYNTHESIS RESEARCH
(2023)