High gene space divergence contrasts with frozen vegetative architecture in the moss family Funariaceae.

A new paradigm has slowly emerged regarding the diversification of bryophytes, with inferences from molecular data highlighting a dynamic evolution of their genome. However, comparative studies of expressed genes among closely related taxa is so far missing. Here we contrast the dimensions of the vegetative transcriptome of Funaria hygrometrica and Physcomitrium pyriforme against the genome of their relative, Physcomitrium (Physcomitrella) patens. These three species of Funariaceae share highly conserved vegetative bodies, and are partially sympatric, growing on mineral soil in mostly temperate regions. We analyzed the vegetative gametophytic transcriptome of F. hygrometrica and P. pyriforme and mapped short reads, transcripts, and proteins to the genome and gene space of P. patens. Only about half of the transcripts of F. hygrometrica map to their ortholog in P. patens, whereas at least 90% of those of P. pyriforme align to loci in P. patens. Such divergence is unexpected given the high morphological similarity of the gametophyte but reflects the estimated times of divergence of F. hygrometrica and P. pyriforme from P. patens, namely 55 and 20 mya, respectively. The newly sampled transcriptomes bear signatures of at least one, rather ancient, whole genome duplication (WGD), which may be shared with one reported for P. patens. The transcriptomes of F. hygrometrica and P. pyriforme reveal significant contractions or expansions of different gene families. While transcriptomes offer only an incomplete estimate of the gene space, the high number of transcripts obtained suggest a significant divergence in gene sequences, and gene number among the three species, indicative of a rather strong, dynamic genome evolution, shaped in part by whole, partial or localized genome duplication. The gene ontology of their specific and rapidly-evolving protein families, suggests that the evolution of the Funariaceae may have been driven by the diversification of metabolic genes that may optimize the adaptations to environmental conditions, a hypothesis well in line with ecological patterns in the genetic diversity and structure in seed plants.

Interplay of charge state, lability, and magnetism in the molecule-like Au25(SR)18 cluster.

Au25(SR)18 (R = -CH2-CH2-Ph) is a molecule-like nanocluster displaying distinct electrochemical and optical features. Although it is often taken as an example of a particularly well-understood cluster, very recent literature has provided a quite unclear or even a controversial description of its properties. We prepared monodisperse Au25(SR)18(0) and studied by cyclic voltammetry, under particularly controlled conditions, the kinetics of its reduction or oxidation to a series of charge states, -2, -1, +1, +2, and +3. For each electrode process, we determined the standard heterogeneous electron-transfer (ET) rate constants and the reorganization energies. The latter points to a relatively large inner reorganization. Reduction to form Au25(SR)18(2-) and oxidation to form Au25(SR)18(2+) and Au25(SR)18(3+) are chemically irreversible. The corresponding decay rate constants and lifetimes are incompatible with interpretations of very recent literature reports. The problem of how ET affects the Au25 magnetism was addressed by comparing the continuous-wave electron paramagnetic resonance (cw-EPR) behaviors of radical Au25(SR)18(0) and its oxidation product, Au25(SR)18(+). As opposed to recent experimental and computational results, our study provides compelling evidence that the latter is a diamagnetic species. The DFT-computed optical absorption spectra and density of states of the -1, 0, and +1 charge states nicely reproduced the experimentally estimated dependence of the HOMO-LUMO energy gap on the actual charge carried by the cluster. The conclusions about the magnetism of the 0 and +1 charge states were also reproduced, stressing that the three HOMOs are not virtually degenerate as routinely assumed: In particular, the splitting of the HOMO manifold in the cation species is severe, suggesting that the usefulness of the superatom interpretation is limited. The electrochemical, EPR, and computational results thus provide a self-consistent picture of the properties of Au25(SR)18 as a function of its charge state and may furnish a methodology blueprint for understanding the redox and magnetic behaviors of similar molecule-like gold nanoclusters.

Effect of the charge state (z = -1, 0, +1) on the nuclear magnetic resonance of monodisperse Au25[S(CH2)2Ph]18(z) clusters.

Monodisperse Au(25)L(18)(0) (L = S(CH(2))(2)Ph) and [n-Oct(4)N(+)][Au(25)L(18)(-)] clusters were synthesized in tetrahydrofuran. An original strategy was then devised to oxidize them: in the presence of bis(pentafluorobenzoyl) peroxide, the neutral or the negatively charged clusters react as efficient electron donors in a dissociative electron-transfer (ET) process, in the former case yielding [Au(25)L(18)(+)][C(6)F(5)CO(2)(-)]. As opposed to other reported redox methods, this dissociative ET approach is irreversible, easily controllable, and clean, particularly for NMR purposes, as no hydrogen atoms are introduced. By using this approach, the -1, 0, and +1 charge states of Au(25)L(18) could be fully characterized by (1)H and (13)C NMR spectroscopy, using one- and two-dimensional techniques, in various solvents, and as a function of temperature. For all charge states, the NMR results and analysis nicely match recent structural findings about the presence of two different ligand populations in the capping monolayer, each resonance of the two ligand families displaying distinct NMR patterns. The radical nature of Au(25)L(18)(0) is particularly evident in the (1)H and (13)C NMR patterns of the inner ligands. The NMR behavior of radical Au(25)L(18)(0) was also simulated by DFT calculations, and the interplay between theory and experiments revealed a fundamental paramagnetic contribution coming from Fermi contact shifts. Interestingly, the NMR patterns of Au(25)L(18)(-) and Au(25)L(18)(+) were found to be quite similar, pointing to the latter cluster form as a diamagnetic species.

Au25(SEt)18, a nearly naked thiolate-protected Au25 cluster: structural analysis by single crystal X-ray crystallography and electron nuclear double resonance.

X-ray crystallography has been fundamental in discovering fine structural features of ultrasmall gold clusters capped by thiolated ligands. For still unknown structures, however, new tools capable of providing relevant structural information are sought. We prepared a 25-gold atom nanocluster protected by the smallest ligand ever used, ethanethiol. This cluster displays the electrochemistry, mass spectrometry, and UV-vis absorption spectroscopy features of similar Au25 clusters protected by 18 thiolated ligands. The anionic and the neutral form of Au25(SEt)18 were fully characterized by (1)H and (13)C NMR spectroscopy, which confirmed the monolayer's properties and the paramagnetism of neutral Au25(SEt)18(0). X-ray crystallography analysis of the latter provided the first known structure of a gold cluster protected by a simple, linear alkanethiolate. Here, we also report the direct observation by electron nuclear double resonance (ENDOR) of hyperfine interactions between a surface-delocalized unpaired electron and the gold atoms of a nanocluster. The advantages of knowing the exact molecular structure and having used such a small ligand allowed us to compare the experimental values of hyperfine couplings with DFT calculations unaffected by structure's approximations or omissions.