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We present a linear-scaling method based on the use of density-functional theory (DFT) for the system-wide optimization of x-ray structural coordinates and apply it to optimize the 150 000 atoms of the photosystem-I (PS-I) trimer. The method is based on repetitive applications of a multilevel ONIOM procedure using the PW91/6-31G(d) DFT calculations for the high level and PM3 for the lower level; this method treats all atoms in the structure equivalently, a structure in which the majority of the atoms can be considered as part of some internal "active site." To obtain a realistic single structure, some changes to the original protein model were necessary but these are kept to a minimum in order that the optimized structure most closely resembles the original x-ray one. Optimization has profound effects on the perceived electronic properties of the cofactors, with, e.g., optimization lowering the internal energy of the chlorophylls by on average 53 kcal mol-1 and eliminates the enormous 115 kcal -1 energy spread depicted by the original x-ray heavy-atom coordinates. A highly precise structure for PS-I results that is suitable for analysis of device function. Significant qualitative features of the structure are also improved such as correction of an error in the stereochemistry of one of the chlorophylls in the "special pair" of the reaction center, as well as the replacement of a water molecule with a metal cation in a critical region on the C3 axis. The method also reveals other unusual features of the structure, leading both to suggestions concerning device functionality and possible mutations between gene sequencing and x-ray structure determination. The optimization scheme is thus shown to augment the molecular modeling schemes that are currently used to add medium-resolution structural information to the raw scattering data in order to obtain atomically resolved structures. System-wide optimization is now a feasible process and its use within protein x-ray data refinement should be considered. [ABSTRACT FROM AUTHOR]

The [Q.sub.y] absorption of photosystem-I from Thermosynecochoccus elongatus is measured by using the CAM-B3LYP density functional and INDO methods. The results are shown to be a realistic first-principles prediction of the absorption band that has identified the nature of the red-shifted chlorophylls as well as the energies of the reaction-center chlorophylls and the exciton couplings acting between them.

The main objective of the AtmoFlow experiment is the investigation of convective flows in thespherical gap geometry. Gaining fundamental knowledge on the origin and behavior of flowphenomena such as global cells and planetary waves is interesting not only from ameteorological perspective. Understanding the interaction between atmosphericcirculation and a planet’s climate, be it Earth, Mars, Jupiter, or a distant exoplanet,contributes to various fields of research such as astrophysics, geophysics, fluidphysics, and climatology. The main feature of AtmoFlow is its spherical geometry andaims to observe flows in a thin gap that are subjected to a central force field. Sucha condition, obviously impossible to reach on ground, is achieved by simulatingbuoyancy driven convection through a central dielectrophoretic field in micro-gravityconditions e.g. on the ISS. Without losing its overall view on the complex physics,circulation in planetary atmospheres can be reduced to a simple model of the in- andoutgoing energy (e.g. radiation) and rotational effects. Both input parameters aredetermined by the boundaries of the system. This strongly simplified assumptionmakes it possible to break some generic cases down to test models which can beinvestigated by laboratory experiments and numerical simulations. Varying differentialrotation rates and temperature boundary conditions represent different types ofplanets. This is a very basic approach, but various open questions regarding localpattern formation or global planetary cells can be investigated with that setup. Aconcept has been defined for developing a payload that could be installed and utilizedon-board the International Space Station. This concept is based on the micro-gravityexperiment GeoFlow, which has been conducted successfully between 2008 and 2016 onthe ISS. We present the scientific goals, the experimental setup, the concept forimplementation of the AtmoFlow experiment on the ISS and first numerical results. [ABSTRACT FROM AUTHOR]

The term "polytopal rearrangement" describes any shape changing process operating on a coordination "polyhedron"-the solid figure defined by the positions of the ligand atoms directly attached to the central atom of a coordination entity. Developed in the latter third of the last century, the polytopal rearrangement model of stereoisomerization is a general mathematical approach for analyzing and accommodating the complexity of such processes for any coordination number. The motivation for the model was principally to deal with the complexity, such as Berry pseudorotation in pentavalent phosphorus species, arising from rearrangements in inorganic coordination complexes of higher coordination numbers. The model is also applicable to lower coordination centers, for example, thermal "inversion" at nitrogen in NH 3 and amines. We present the history of the model focusing on its essential features, and review some of the more subtle aspects addressed in recent literature. We then introduce a more detailed and rigorous modern approach for describing such processes using an assembly of existing concepts, with the addition of formally described terminology and representations. In our outlook, we contend that the rigorous and exhaustive application of the principles of the polytopal rearrangement model, when combined with torsional isomerism, will provide a basis for a mathematically complete, general, and systematic classification for all stereoisomerism and stereoisomerization. This is essential for comprehensively mapping chemical structure and reaction spaces., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)

The Qy absorption spectrum of Photosystem-I from Thermosynecochoccus elongatus (formerly Synecochoccus elongatus) is calculated using the CAM-B3LYP density functional and INDO schemes based on a quantum-mechanically refined structure for the entire photosystem obtained using the PW91 density functional. These methods present a priori predictions of the absorption and linear dichroism spectra and include protein electrostatic effects, short range inductive effects, long-range and short-range exciton couplings, and superexchange effects involving aromatic residues and carotenes. CAM-B3LYP is used as it is the only known density functional that correctly describes the Q bands of chlorophylls, all other methods contaminating them with erroneous charge-transfer excitations. A critical feature is found to be the use of fully optimized heavy-atom coordinates, with those obtained from just X-ray crystallography providing a poor description of the electronic properties of the chromophores. The result is a realistic first-principles prediction of the observed absorption band that identifies the nature of the red-shifted chlorophylls as well as the energies of the reaction-center chlorophylls and the exciton couplings acting between them. The "special pair" appears more like a dimer of dimers than a self-contained functional unit, with the exciton couplings between its members and the accessory chlorophylls exceeding the internal coupling.