Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fast-tree-computing-large-minimum-evolution-trees-with-4grq0gwfpy.pdf

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

2.3. [4 + 4] Cycloadditions 1058 2.4. Photocycloadditions of Aromatic Compounds 1058 2.4.1. Benzene Derivatives 1058 2.4.2. Condensed Aromatic Compounds 1060 3. Photochemical Rearrangements 1061 4. Cyclizations 1064 4.1. Pericyclizations 1064 4.2. Norrish−Yang Reaction 1066 5. Photochemical Extrusion of Small Molecules 1067 6. Photochemical Electron Transfer 1068 6.1. Photochemical Electron-Transfer Reactions with a Catalytic Sensitizer 1068

Photochemical Reactions as Key Steps in Organic Synthesis

We introduce a measure of the local density of chirality of the electromagnetic field. This optical chirality determines the asymmetry in the rates of excitation between a small chiral molecule and its mirror image, and applies to molecules in electromagnetic fields with arbitrary spatial dependence. A continuity equation for optical chirality in the presence of material currents describes the flow of chirality, in a manner analogous to the Poynting theorem for electromagnetic energy. ``Superchiral'' solutions to Maxwell's equations show larger chiral asymmetry, in some regions of space, than is found in circularly polarized plane waves.

/pdf/optical-chirality-and-its-interaction-with-matter-4w9nb3y2se.pdf

Optical chirality and its interaction with matter.

Various present and future specialized applications of magnets require monodisperse, small magnetic particles, and the discovery of molecules that can function as nanoscale magnets was an important development in this regard. These molecules act as single-domain magnetic particles that, below their blocking temperature, exhibit magnetization hysteresis, a classical property of macroscopic magnets. Such 'single-molecule magnets' (SMMs) straddle the interface between classical and quantum mechanical behaviour because they also display quantum tunnelling of magnetization and quantum phase interference. Quantum tunnelling of magnetization can be advantageous for some potential applications of SMMs, for example, in providing the quantum superposition of states required for quantum computing. However, it is a disadvantage in other applications, such as information storage, where it would lead to information loss. Thus it is important to both understand and control the quantum properties of SMMs. Here we report a supramolecular SMM dimer in which antiferromagnetic coupling between the two components results in quantum behaviour different from that of the individual SMMs. Our experimental observations and theoretical analysis suggest a means of tuning the quantum tunnelling of magnetization in SMMs. This system may also prove useful for studying quantum tunnelling of relevance to mesoscopic antiferromagnets.

Exchange-biased quantum tunnelling in a supramolecular dimer of single-molecule magnets

We present 2.5-30 mum spectra from the Short-Wavelength Spectrometer of the Infrared Space Observatory for a total of 23 sources. The sources include embedded young stellar objects spanning a wide range of mass and luminosity, together with field stars sampling quiescent dark clouds and the diffuse interstellar medium. Expanding on results of previous studies, we use these spectra to investigate ice composition as a function of environment. The spectra reveal an extremely rich set of absorption features attributed to simple molecules in the ices. We discuss the observed properties of these absorption features and review their assignments. Among the species securely identified are H2O, CO, CO2, CH3OH, and CH4. Likely identified species include OCS, H2CO, and HCOOH. There is also evidence for NH3 and OCN- ice features, but these identifications are more controversial. Features that continue to defy identification include the 3.3-3.7 mum "ice band wing'' and the bulk of the 6.8 mum feature. In addition, we find evidence for excess absorption at 6.0 mum that cannot be attributed to H2O ice. We examine the degree of intercorrelation of the 6.8 mum, 4.62 mum ("XCN'') and 6.0 mum (excess) features. Our results are consistent with the interpretation of the 6.8 and 4.62 mum features as due to NH4+ and OCN- ions, respectively, though alternative explanations cannot currently be ruled out. We find that the optical depth correlations are dependent on the profile of the 6.8 mum feature but not on the mass of the YSO nor the ice temperature along the line of sight. We discuss the implications for our current understanding of ice processing. We briefly discuss the composition, origin, and evolution of interstellar ices.

/pdf/interstellar-ice-the-infrared-space-observatory-legacy-1fsfio7fnf.pdf

Interstellar Ice: The Infrared Space Observatory Legacy

The cometary Rosetta mission visited the nucleus of Comet 67P/Churyumov-Gerasimenko by placing the Philae Lander on its surface. Philae was equipped with a time-of-flight mass spectrometer that analyzed, for the first time, cometary surface material in situ. Uwe J. Meierhenrich and co-workers describe in their Research Article (DOI: 10.1002/anie.202201925) the characterization of this mass spectrum through non-negative least square fitting and Monte Carlo analysis revealing the chemical composition of cometary ices. 

Back Cover: ESA's Cometary Mission Rosetta—Re‐Characterization of the COSAC Mass Spectrometry Results (Angew. Chem. Int. Ed. 29/2022)

One of the most interesting phenomena on Earth is the chirality of biomolecules, the origin of which remains unknown. A challenge arising from this phenomenon is the selective, atom-economic synthesis of enantiomerically pure target molecules from nonchiral starting materials. Herein, new developments in the field of asymmetric photochemistry and photochirogenesis are described with special emphasis on absolute asymmetric synthesis. In this context, the elucidation of the ultimate cause of homochirality phenomena on earth and the possible correlation with physicochemical parameters are also presented.

Asymmetric Photochemistry and Photochirogenesis.

Es wird davon ausgegangen, dass das älteste weitgehend unveränderte Material aus der Frühphase des Sonnensystems in Form von Eis und Staub in Kometen vorliegt. Die ESA-Mission Rosetta trug daher mit Philae eine Landeeinheit, die die Zusammensetzung des Nukleus von Komet 67P/Churyumov-Gerassimenko in situ untersuchen sollte. Fünfundzwanzig Minuten nach dem ersten Bodenkontakt Philaes im November 2014 nahm das COSAC Flugzeit-Massenspektrometer ein Spektrum der Gasphase des Kometen auf. Eine erneute Analyse dieses Spektrums mittels non-negative least-squares Fitting und einer Monte-Carlo Simulation ergibt neue Erkenntnisse über die chemische Zusammensetzung des Kometen 67P. Insgesamt 12 organische Moleküle, von denen 9 bereits in der ersten Analyse der Daten identifiziert wurden, zeigen eine hohe statistische Wahrscheinlichkeit für eine Präsenz im Eis des Kometen. Diese flüchtigen organischen Verbindungen mit zum Teil hoher Konzentration stellen die ersten molekularen Ingredienzien des frühen Sonnensystems dar. 

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ange.202201925

ESAs Kometen‐Mission Rosetta – Neu‐Analyse der Daten des COSAC Massenspektrometers

Im Sommer dieses Jahres fand die 10. ISSOL-Konferenz zusammen mit der 13. Internationalen Konferenz uber den Ursprung des Lebens in Oaxaca, Mexiko, statt. 274 Teilnehmer der Konferenz befassten sich mit Entwicklungen aus zentralen Gebieten der Chemischen Evolution.

Die 10. ISSOL-Konferenz in Oaxaca, Mexiko

The chemistry of life is purely stereospecific. The fundamental biopolymers - proteins and nucleic acids - are intrinsically chiral due to their molecular building blocks, namely L-amino acids and D-sugars. Hypotheses for the evolutionary origin of that strict stereochemical selection include the asymmetric photochemistry model by which circularly polarized (CP) photons induced an enantiomeric excess in chiral organic molecules via asymmetric photolysis. The transfer of a distinct chirality from chiral photons to organic molecules is assumed to have occurred in environments of interstellar molecular clouds. This model is strengthened by the observation of CP light in the star-forming region of Orion. Due to our laboratory experiments mimicking cometary ice evolution, we show that molecules of prebiotic interest such as amino and diamino acids are formed in inter/protostellar environments and might have been subjected to CP vacuum-UV radiation before and during their space journey to the early Earth.

/pdf/the-origin-of-biomolecular-asymmetry-insights-from-cometary-2klccnnyfh.pdf

Uwe J. Meierhenrich

Papers

Back Cover: ESA's Cometary Mission Rosetta—Re‐Characterization of the COSAC Mass Spectrometry Results (Angew. Chem. Int. Ed. 29/2022)

Asymmetric Photochemistry and Photochirogenesis.

ESAs Kometen‐Mission Rosetta – Neu‐Analyse der Daten des COSAC Massenspektrometers

Die 10. ISSOL-Konferenz in Oaxaca, Mexiko

The origin of biomolecular asymmetry - Insights from cometary and meteoritic matter