| 1. |
- Botan, Alexandru, et al.
(författare)
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Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions
- 2015
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 119:49, s. 15075-15088
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Tidskriftsartikel (refereegranskat)abstract
- Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR. experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files (https://zenodo.org/collection/user-nmrlipids) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers.
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| 2. |
- Boulanger, Nicolas, et al.
(författare)
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Enhanced Sorption of Radionuclides by Defect-Rich Graphene Oxide
- 2020
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Ingår i: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 12:40, s. 45122-45135
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Tidskriftsartikel (refereegranskat)abstract
- Extremely defect graphene oxide (dGO) is proposed as an advanced sorbent for treatment of radioactive waste and contaminated natural waters. dGO prepared using a modified Hummers oxidation procedure, starting from reduced graphene oxide (rGO) as a precursor, shows significantly higher sorption of U(VI), Am(III), and Eu(III) than standard graphene oxides (GOs). Earlier studies revealed the mechanism of radionuclide sorption related to defects in GO sheets. Therefore, explosive thermal exfoliation of graphite oxide was used to prepare rGO with a large number of defects and holes. Defects and holes are additionally introduced by Hummers oxidation of rGO, thus providing an extremely defect-rich material. Analysis of characterization by XPS, TGA, and FTIR shows that dGO oxygen functionalization is predominantly related to defects, such as flake edges and edge atoms of holes, whereas standard GO exhibits oxygen functional groups mostly on the planar surface. The high abundance of defects in dGO results in a 15-fold increase in sorption capacity of U(VI) compared to that in standard Hummers GO. The improved sorption capacity of dGO is related to abundant carboxylic group attached hole edge atoms of GO flakes as revealed by synchrotron-based extended X-ray absorption fine structure (EXAFS) and high-energy resolution fluorescence detected X-ray absorption near edge structure (HERFD-XANES) spectroscopy.
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| 3. |
- Canton, Sophie E., et al.
(författare)
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Ultrafast Jahn-Teller Photoswitching in Cobalt Single-Ion Magnets
- 2023
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Ingår i: Advanced Science. - 2198-3844. ; 10:21
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Tidskriftsartikel (refereegranskat)abstract
- Single-ion magnets (SIMs) constitute the ultimate size limit in the quest for miniaturizing magnetic materials. Several bottlenecks currently hindering breakthroughs in quantum information and communication technologies could be alleviated by new generations of SIMs displaying multifunctionality. Here, ultrafast optical absorption spectroscopy and X-ray emission spectroscopy are employed to track the photoinduced spin-state switching of the prototypical complex [Co(terpy)2]2+ (terpy = 2,2′:6′,2″-terpyridine) in solution phase. The combined measurements and their analysis supported by density functional theory (DFT), time-dependent-DFT (TD-DFT) and multireference quantum chemistry calculations reveal that the complex undergoes a spin-state transition from a tetragonally elongated doublet state to a tetragonally compressed quartet state on the femtosecond timescale, i.e., it sustains ultrafast Jahn-Teller (JT) photoswitching between two different spin multiplicities. Adding new Co-based complexes as possible contenders in the search for JT photoswitching SIMs will greatly widen the possibilities for implementing magnetic multifunctionality and eventually controlling ultrafast magnetization with optical photons.
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| 4. |
- de Groot, Frank M. F., et al.
(författare)
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2p x-ray absorption spectroscopy of 3d transition metal systems
- 2021
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Ingår i: Journal of Electron Spectroscopy and Related Phenomena. - : Elsevier BV. - 0368-2048 .- 1873-2526. ; 249
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Tidskriftsartikel (refereegranskat)abstract
- This review provides an overview of the different methods and computer codes that are used to interpret 2p x-ray absorption spectra of 3d transition metal ions. We first introduce the basic parameters and give an overview of the methods used. We start with the semi-empirical multiplet codes and compare the different codes that are available. A special chapter is devoted to the user friendly interfaces that have been written on the basis of these codes. Next we discuss the first principle codes based on band structure, including a chapter on Density Functional theory based approaches. We also give an overview of the first-principle multiplet codes that start from a cluster calculation and we discuss the wavefunction based methods, including multi-reference methods. We end the review with a discussion of the link between theory and experiment and discuss the open issues in the spectral analysis.
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| 5. |
- Krewald, Vera, et al.
(författare)
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Metal oxidation states in biological water splitting
- 2015
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Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 6:3, s. 1676-1695
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Tidskriftsartikel (refereegranskat)abstract
- A central question in biological water splitting concerns the oxidation states of the manganese ions that comprise the oxygen-evolving complex of photosystem II. Understanding the nature and order of oxidation events that occur during the catalytic cycle of five Si states (i = 0-4) is of fundamental importance both for the natural system and for artificial water oxidation catalysts. Despite the widespread adoption of the so-called "high-valent scheme"-where, for example, the Mn oxidation states in the S-2 state are assigned as III, IV, IV, IV-the competing "low-valent scheme" that differs by a total of two metal unpaired electrons (i.e. III, III, III, IV in the S-2 state) is favored by several recent studies for the biological catalyst. The question of the correct oxidation state assignment is addressed here by a detailed computational comparison of the two schemes using a common structural platform and theoretical approach. Models based on crystallographic constraints were constructed for all conceivable oxidation state assignments in the four (semi) stable S states of the oxygen evolving complex, sampling various protonation levels and patterns to ensure comprehensive coverage. The models are evaluated with respect to their geometric, energetic, electronic, and spectroscopic properties against available experimental EXAFS, XFEL-XRD, EPR, ENDOR and Mn K pre-edge XANES data. New 2.5 K Mn-55 ENDOR data of the S-2 state are also reported. Our results conclusively show that the entire S state phenomenology can only be accommodated within the high-valent scheme by adopting a single motif and protonation pattern that progresses smoothly from S-0 (III, III, III, IV) to S-3 (IV, IV, IV, IV), satisfying all experimental constraints and reproducing all observables. By contrast, it was impossible to construct a consistent cycle based on the low-valent scheme for all S states. Instead, the low-valent models developed here may provide new insight into the over-reduced S states and the states involved in the assembly of the catalytically active water oxidizing cluster.
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| 6. |
- Naumova, Maria A., et al.
(författare)
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Nonadiabatic Charge Transfer within Photoexcited Nickel Porphyrins
- 2024
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Ingår i: Journal of Physical Chemistry Letters. - 1948-7185. ; 15:13, s. 3627-3638
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Tidskriftsartikel (refereegranskat)abstract
- Metalloporphyrins with open d-shell ions can drive biochemical energy cycles. However, their utilization in photoconversion is hampered by rapid deactivation. Mapping the relaxation pathways is essential for elaborating strategies that can favorably alter the charge dynamics through chemical design and photoexcitation conditions. Here, we combine transient optical absorption spectroscopy and transient X-ray emission spectroscopy with femtosecond resolution to probe directly the coupled electronic and spin dynamics within a photoexcited nickel porphyrin in solution. Measurements and calculations reveal that a state with charge-transfer character mediates the formation of the thermalized excited state, thereby advancing the description of the photocycle for this important representative molecule. More generally, establishing that intramolecular charge-transfer steps play a role in the photoinduced dynamics of metalloporphyrins with open d-shell sets a conceptual ground for their development as building blocks capable of boosting nonadiabatic photoconversion in functional architectures through “hot” charge transfer down to the attosecond time scale.
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| 7. |
- Retegan, Marius, et al.
(författare)
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A five-coordinate Mn(IV) intermediate in biological water oxidation : spectroscopic signature and a pivot mechanism for water binding
- 2016
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Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 7:1, s. 72-84
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Tidskriftsartikel (refereegranskat)abstract
- Among the four photo-driven transitions of the water-oxidizing tetramanganese-calcium cofactor of biological photosynthesis, the second-last step of the catalytic cycle, that is the S-2 to S-3 state transition, is the crucial step that poises the catalyst for the final O-O bond formation. This transition, whose intermediates are not yet fully understood, is a multi-step process that involves the redox-active tyrosine residue and includes oxidation and deprotonation of the catalytic cluster, as well as the binding of a water molecule. Spectroscopic data has the potential to shed light on the sequence of events that comprise this catalytic step, which still lacks a structural interpretation. In this work the S-2-S-3 state transition is studied and a key intermediate species is characterized: it contains a Mn3O4Ca cubane subunit linked to a five-coordinate Mn(IV) ion that adopts an approximately trigonal bipyramidal ligand field. It is shown using high-level density functional and multireference wave function calculations that this species accounts for the near-infrared absorption and electron paramagnetic resonance observations on metastable S-2-S-3 intermediates. The results confirm that deprotonation and Mn oxidation of the cofactor must precede the coordination of a water molecule, and lead to identification of a novel low-energy water binding mode that has important implications for the identity of the substrates in the mechanism of biological water oxidation.
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