| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Li, Xichen, et al.
(författare)
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A comparison between artificial and natural water oxidation
- 2011
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Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 40:42, s. 11296-11307
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Tidskriftsartikel (refereegranskat)abstract
- Two artificial water oxidation catalysts, the blue dimer and the Llobet catalyst, have been studied using hybrid DFT methods. The results are compared to those for water oxidation in the natural photosystem II enzyme. Studies on the latter system have now reached a high level of understanding, at present much higher than the one for the artificial systems. A recent high resolution X-ray structural investigation of PSII has confirmed the main features of the structure of the oxygen evolving complex (OEC) suggested by previous DFT cluster studies. The O-O bond formation mechanism suggested is of direct coupling (DC) type between an oxygen radical and a bridging oxo ligand. A similar DC mechanism is found for the Llobet catalyst, while an acid-base (AB) mechanism is preferred for the blue dimer. All of them require at least one oxygen radical. Full energy diagrams, including both redox and chemical steps, have been constructed illustrating similarities and differences to the natural system. Unlike previous DFT studies, the results of the present study suggest that the blue dimer is rate-limited by the initial redox steps, and the Llobet catalyst by O(2) release. The results could be useful for further improvement of the artificial systems.
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| 3. |
- Li, Xichen, et al.
(författare)
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Alternative mechanisms for O-2 release and O-O bond formation in the oxygen evolving complex of photosystem II
- 2015
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Owner Societies 2015. - 1463-9076 .- 1463-9084. ; 17:18, s. 12168-12174
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Tidskriftsartikel (refereegranskat)abstract
- In a previous detailed study of all the steps of water oxidation in photosystem II, it was surprisingly found that O-2 release is as critical for the rate as O-O bond formation. A new mechanism for O-2 release has now been found, which can be described as an opening followed by a closing of the interior of the oxygen evolving complex. A transition state for peroxide rotation forming a superoxide radical, missed in the previous study, and a structural change around the outside manganese are two key steps in the new mechanism. However, O-2 release may still remain rate-limiting. Additionally, for the step forming the O-O bond, an alternative, experimentally suggested, mechanism was investigated. The new model calculations can rule out the precise use of that mechanism. However, a variant with a rotation of the ligands around the outer manganese by about 301 will give a low barrier, competitive with the old DFT mechanism. Both these mechanisms use an oxyl-oxo mechanism for O-O bond formation involving the same two manganese atoms and the central oxo group (O5).
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| 4. |
- Li, Xichen, et al.
(författare)
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Simulation of the isotropic EXAFS spectra for the S-2 and S-3 structures of the oxygen evolving complex in photosystem II
- 2015
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 112:13, s. 3979-3984
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Tidskriftsartikel (refereegranskat)abstract
- Most of the main features of water oxidation in photosystem II are now well understood, including the mechanism for O-O bond formation. For the intermediate S-2 and S-3 structures there is also nearly complete agreement between quantum chemical modeling and experiments. Given the present high degree of consensus for these structures, it is of high interest to go back to previous suggestions concerning what happens in the S-2-S-3 transition. Analyses of extended X-ray adsorption fine structure (EXAFS) experiments have indicated relatively large structural changes in this transition, with changes of distances sometimes larger than 0.3 angstrom and a change of topology. In contrast, our previous density functional theory (DFT)(B3LYP) calculations on a cluster model showed very small changes, less than 0.1 angstrom. It is here found that the DFT structures are also consistent with the EXAFS spectra for the S2 and S3 states within normal errors of DFT. The analysis suggests that there are severe problems in interpreting EXAFS spectra for these complicated systems.
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| 5. |
- Li, Xichen, et al.
(författare)
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Theoretical EXAFS studies of a model of the oxygen-evolving complex of photosystem II obtained with the quantum cluster approach
- 2013
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 113:4, s. 474-478
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Tidskriftsartikel (refereegranskat)abstract
- The oxygen-evolving complex (OEC) of photosystem II is the only natural system that can form O2 from water and sunlight and it consists of a Mn4Ca cluster. In a series of publications, Siegbahn has developed a model of the OEC with the quantum mechanical (QM) cluster approach that is compatible with available crystal structures, able to form O2 with a reasonable energetic barrier, and has a significantly lower energy than alternative models. In this investigation, we present a method to restrain a QM geometry optimization toward experimental polarized extended X-ray absorption fine structure (EXAFS) data. With this method, we show that the cluster model is compatible with the EXAFS data and we obtain a refined cluster model that is an optimum compromise between QM and polarized EXAFS data.
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| 6. |
- Li, Xichen, et al.
(författare)
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Water Oxidation for Simplified Models of the Oxygen-Evolving Complex in Photosystem II
- 2015
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Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 21:51, s. 18821-18827
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Tidskriftsartikel (refereegranskat)abstract
- For the main parts of the mechanism for water oxidation in photosystem II there has recently been very strong experimental support for the mechanism suggested by theoretical model studies. The question addressed in the present study is to what extent this knowledge can be used for the design of artificial catalysts. A major requirement for a useful artificial catalyst is that it is small enough to be synthesized. Small catalysts also have the big advantage that they could improve the catalysis per surface area. To make the mechanism found for PSII useful in this context, it needs to be analyzed in detail. A small model system was therefore used and the ligands were replaced one by one by water-derived ligands. Only the main chemical step of O-O bond formation was investigated in this initial study. The energetics for this small model and the larger one previously used for PSII are remarkably similar, which is the most important result of the present study. This shows that small model complexes have a potential for being very good water oxidation catalysts. It was furthermore found that there is a clear correlation between the barrier height for O-O bond formation and the type of optimal structure for the S-3 state. The analysis shows that a flexible central part of the complex is the key for efficient water oxidation.
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| 7. |
- Li, Xichen, et al.
(författare)
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Water Oxidation Mechanism for Synthetic Co-Oxides with Small Nuclearity
- 2013
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 135:37, s. 13804-13813
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Tidskriftsartikel (refereegranskat)abstract
- Hybrid DFT model calculations have been performed for some cobalt complexes capable of oxidizing water. Since a very plausible mechanism for the oxygen-evolving complex involving the cuboidal Mn4Ca structure in photosystem II (PSII) has recently been established, the most important part of the present study concerns a detailed comparison between cobalt and manganese as water oxidation catalysts. One similarity found is that a M(IV)-O-center dot state is the key precursor for O-O bond formation in both cases. This means that simply getting a M(IV) state is not enough; a formal M(V)=O state is required, with two oxidations on one center from M(III). For cobalt, not even that is enough. A singlet coupled state is required at this oxidation level, which is not the ground state. It is shown that there are also more fundamental differences between catalysts based on these metals. The favorable low-barrier direct coupling mechanism found for PSII is not possible for the corresponding cobalt complexes. The origin of this difference is explained. For the only oxygen-evolving cubic Co4O4 complex with a defined structure, described by Dismukes et al., the calculated results are in good agreement with experiments. For the Co-4 models of the amorphous cobalt-oxo catalyst found by Nocera et al., higher barriers are found than the one obtained experimentally. The reasons for this are discussed.
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| 8. |
- Siegbahn, Per E. M., et al.
(författare)
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Cluster size convergence for the energetics of the oxygen evolving complex in PSII
- 2017
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 38:25, s. 2157-2160
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Tidskriftsartikel (refereegranskat)abstract
- Density functional theory calculations have been made to investigate the stability of the energetics for the oxygen evolving complex of photosystem II. Results published elsewhere have given excellent agreement with experiments for both energetics and structures, where many of the experimental results were obtained several years after the calculations were done. The computational results were obtained after a careful extension from small models to a size of about 200 atoms, where stability of the results was demonstrated. However, recently results were published by Isobe et al., suggesting that very different results could be obtained if the model was extended from 200 to 340 atoms. The present study aims at understanding where this difference comes from.
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