The developments of the open-source chemistry software environment since spring 2020 are described,
with a focus on novel functionalities accessible in the stable branch
of the package or via interfaces with other packages. These developments
span a wide range of topics in computational chemistry and are presented
in thematic sections: electronic structure theory, electronic spectroscopy
simulations, analytic gradients and molecular structure optimizations,
ab initio molecular dynamics, and other new features. This report
offers an overview of the chemical phenomena and processes can address, while showing that is an attractive platform for state-of-the-art
atomistic computer simulations.
Proteorhodopsin (PR) is a photoactive proton pump found in marine bacteria. There are two phenotypes of PR exhibiting an environmental adaptation to the ocean's depth which tunes their maximum absorption: blue-absorbing proteorhodopsin (BPR) and green-absorbing proteorhodopsin (GPR). This blue/green color-shift is controlled by a glutamine to leucine substitution at position 105 which accounts for a 20 nm shift. Typically, spectral tuning in rhodopsins is rationalized by the external point charge model but the Q105L mutation is charge neutral. To study this tuning mechanism, we employed the hybrid QM/MM method with sampling from molecular dynamics. Our results reveal that the positive partial charge of glutamine near the C 14 À C 15 bond of retinal shortens the effective conjugation length of the chromophore compared to the leucine residue. The derived mechanism can be applied to explain the color regulation in other retinal proteins and can serve as a guideline for rational design of spectral shifts.
This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.
ClC transport proteins show a distinct "broken-helix" architecture, in which certain α-helices are oriented with their N-terminal ends pointed toward the binding sites where the chloride ions are held extensively by the backbone amide nitrogen atoms from the helices. To understand the effectiveness of such binding structures, we carried out natural bond orbital analysis and energy decomposition analysis employing truncated active-site model systems for the bound chloride ions along the translocation pore of the EcClC proteins. Our results indicated that the chloride ions are stabilized in such a binding environment by electrostatic, polarization, and charge-transfer interactions with the backbone and a few side chains. Up to ~25% of the formal charges of the chloride ions were found smeared out to the surroundings primarily via charge transfer from the chloride's lone pair n(Cl) orbitals to the protein's antibonding σ*(N-H) or σ*(O-H) orbitals; those σ* orbitals are localized at the polar N-H and O-H bonds in the chloride's first solvation shells formed by the backbone amide groups and the side chains of residues Ser107, Arg147, Glu148, and Tyr445. Polarizations by the chloride ions were dominated by the redistribution of charge densities among the π orbitals and lone pair orbitals of the protein atoms, in particular the atoms of the backbone peptide links and of the side chains of Arg147, Glu148, and Tyr445. The substantial amounts of electron density involved in charge transfer and in polarization were consistent with the large energetic contributions by the two processes revealed by the energy decomposition analysis. The significant polarization and charge-transfer effects may have impacts on the mechanisms and dynamics of the chloride transport by the ClC proteins.
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