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Myriapods (e. g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.
Quantum chemical approach to atomic manipulation of chlorobenzene on the Si(111)-7 x 7 surface
(2017)
We present a cluster model to describe the localization of hot charge carriers on the Si(111)-7 x 7 surface, which leads to (nonlocal) desorption of chlorobenzene molecules in scanning tunneling microscope (STM) manipulation experiments. The localized charge carriers are modeled by a small cluster. By means of quantum chemical calculations, this cluster model explains many experimental findings from STM manipulation. We show that the negative charge is mainly localized in the surface, while the positive one also resides on the molecule. Both resonances boost desorption: In the negative resonance the adatom is elevated; in the positive one the chemisorption bond between the silicon surface adatom and chlorobenzene is broken. We find normal modes promoting desorption matching experimental low-temperature activation energies for electron-and hole-induced desorption.
We use quantum chemical cluster models together with constrained density STM Ph CI functional theory (DFT) and ab initio molecular dynamics (AIMD) for open system to simulate tip and rationalize nonlocal scanning tunneling microscope (STM) manipulation experiments for Philh ci chlorobenzene (PhCl) on a Si(111)-7 X 7 surface. We consider three different processes, namely, the electron-induced dissociation of the carbon-chlorine bond for physisorbed PhCl molecules at low temperatures and the electron- or hole-induced desorption of chemisorbed PhCl at 300 K. All processes can be induced nonlocally, i.e., up to several nanometers (nm) away from the injection site, in STM experiments. We rationalize and explain the experimental findings regarding the STM-induced dissociation using constrained DFT. The coupling of STM-induced ion resonances to nuclear degrees of freedom is simulated with AIMD using the Gadzuk averaging approach for open systems. From this data, we predict a 4 fs lifetime for the cationic resonance. For the anion model, desorption could not be observed. In addition, the same cluster models are used for transition-state theory calculations, which are compared to and validated against time-lapse STM experiments.
Motivated by recent atomic manipulation experiments, we report quantum chemical calculations for chemi- and physisorption minima of chlorobenzene on the Si(111)-7x7 surface. A density functional theory cluster approach is applied, using the B3LYP hybrid functional alongside Grimme's empirical dispersion corrections (D3). We were able to identify chemisorption sites of binding energies of 1.6 eV and physisorption energies of 0.6 eV, both in encouraging agreement with the trend of experimental data. The cluster approach opens up the possibility of a first-principles based dynamical description of STM manipulation experiments on this system, the interpretation of which involves both the chemi- and physisorbed states. However, we found that special care has to be taken regarding the choice of clusters, basis sets, and the evaluation of the dispersion corrections.