Constraint methods for determining pathways and free energy of activated processes

Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and rate-determining barrier regions are not sufficiently sampled by usual simulation techniques. Constraints on a reaction coordinate r have turned out to be a suitable means to explore difficult pathways without changing potential function, energy or temperature. For a dense sequence of values of r, the corresponding sequence of simulations provides a pathway for the process. As only one coordinate among thousands is fixed during each simulation, the pathway essentially reflects the system's internal dynamics. From mean forces the free energy profile can be calculated to obtain reaction rates and insight in the reaction mechanism. In the last decade, theoretical tools and computing capacity have been developed to a degree where simulations give impressive qualitative insight in the processes at quantitative agreement with experiments. Here, we give an introduction to reaction pathways and coordinates, and develop the theory of free energy as the potential of mean force. We clarify the connection between mean force and constraint force which is the central quantity evaluated, and discuss the mass metric tensor correction. Well-behaved coordinates without tensor correction are considered. We discuss the theoretical background and practical implementation on the example of the reaction coordinate of targeted molecular dynamics simulation. Finally, we compare applications of constraint methods and other techniques developed for the same purpose, and discuss the limits of the approach

Strain-induced strengthening of the weakest link : the importance of intermediate geometry for the outcome of mechanochemical reactions

Mechanochemically facilitated retro [2 + 2] cycloaddition of four-membered ketene dimer rings was investigated using density functional theory and ultrasound induced scission experiments. The results reveal that, in contrast to many other mechanochemical processes, the activation energy for mechanochemical ring-opening of cyclobutane-1,3-diones increases in the presence of an external force. Thus, a strengthening of bonds in the four-membered ring is observed under the influence of an extensional force on cis-substituents. A force on trans-substituents weakens the bonds, but to a smaller extent than initially stronger bonds outside the ring. Mechanochemical scission experiments of ketene dimers incorporated in the main chain of a polymer using ultrasound confirmed that scission of the chains does not occur via retro [2 + 2] cycloaddition, but elsewhere in the chain

The ecology and control of fireweed (Senecio madagascariensis Poir)

The improvement of molecular electronic devices such as organic light-emitting diodes requires fundamental knowledge about the structural and electronic properties of the employed molecules as well as their interactions with neighboring molecules or interfaces. We show that highly resolved scanning tunneling microscopy (STM) and spectroscopy (STS) are powerful tools to correlate the electronic properties of phosphorescent complexes (i.e., triplet emitters) with their molecular structure as well as the local environment around a single molecule. We used spectroscopic mapping to visualize several occupied and unoccupied molecular frontier orbitals of Pt(II) complexes adsorbed on Au(111). The analysis showed that the molecules exhibit a peculiar localized strong hybridization that leads to partial depopulation of a dz² orbital, while the ligand orbitals are almost unchanged. We further found that substitution of functional groups at well-defined positions can alter specific molecular orbitals without influencing the others. The results open a path toward the tailored design of electronic and optical properties of triplet emitters by smart ligand substitution, which may improve the performance of future OLED devices

Scanning-Tunneling-Spectroscopy-Directed Design of Tailored Deep-Blue Emitters

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Colour-tunable asymmetric cyclometalated Pt(II) complexes and STM-assisted stability assessment of ancillary ligands for OLEDs

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Mixed Si-Ge nanoparticle quantum dots: a density functional theory study

73.22.-f Electronic structure of nanoscale materials: clusters, nanoparticles, nanotubes, and nanocrystals, 78.67.Bf Nanocrystals and nanoparticles,