Surviving Mass Extinctions through Biomineralized DNA

Even in the worst of conditions, such as those which occurred during mass extinction events, life on Earth never totally stopped. Aggressive chemical and physical attacks able to sterilize or poison living organisms occurred repeatedly. Surprisingly, DNA was not degraded, denatured or modified to the point of losing the capability of transferring the genetic information to the next generations. After the events of mass extinction life was able to survive and thrive. DNA was passed on despite being an extremely fragile biomolecule. The potential implications of hydroxyapatite protection of DNA are discussed in this Concept article including how DNA acts as a template for hydroxyapatite (HAp) formation, how cell death can trigger biomineralization, and how DNA can be successfully released from HAp when the conditions are favorable for life.     

The Trifluoromethyl Anion

First evidence for the existence of free trifluoromethyl anion CF₃^? has been obtained. The 3D‐caged potassium cation in [K(crypt‐222)]⁺ is inaccessible to CF₃^?, thus rendering it uncoordinated (“naked”). Ionic [K(crypt‐222)]⁺ CF₃^? has been characterized by single‐crystal X‐ray diffraction, solution NMR spectroscopy, DFT calculations, and reactivity toward electrophiles.     

Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design

Conformationally restricted amino acids are promising candidates to serve as basic pieces in redesigned protein motifs which constitute the basic modules in synthetic nanoconstructs. Here we study the ability of constrained cyclic amino acid 1-aminocyclohexane-1-carboxylic acid (Ac6c) to stabilize highly regular beta-helical motifs excised from naturally occurring proteins. Calculations indicate that the conformational flexibility observed in both the ring and the main chain is significantly higher than that detected for other 1-aminocycloalkane-1-carboxylic acids (Acnc, where n refers to the size of the ring) with smaller cycles. Incorporation of Ac6c into the flexible loops of beta-helical motifs indicates that the stability of such excised building blocks as well as the nanoassemblies derived from them is significantly enhanced. Thus, the intrinsic Ac6c tendency to adopt folded conformations combined with the low structural strain of the cyclohexane ring confers the ability to both self-adapt to the beta-helix motif and to stabilize the overall structure by absorbing part of its conformational fluctuations. Comparison with other Acnc residues indicates that the ability to adapt to the targeted position improves considerably with the ring size, i.e., when the rigidity introduced by the strain of the ring decreases.     

Anion-pi-pi interactions in a dinuclear M2L2 metallocycle

The combination of the square-planar cis-protected [Pt(dppp)(O 3SCF 3) 2] (M) with the ditopic N, N'-bis(3,5-dimethyl-4-pyridinyl)-4-ethoxy-2,6-pyridinedicarboxamide ligand (L) leads both in solution and in the solid state to the quantitative self-assembly of a M 2L 2 metallocycle. We also report crystallographic evidence derived from the solid-state structure of the dinuclear metallocycle in support of the existence of anion-pi-pi interactions.     

QSAR models for biocides: The example of the prediction of Daphnia magna acute toxicity

ABSTRACT

Biocides are multi-component products used to control undesired and harmful organisms able to affect human or animal health or to damage natural and manufactured products. Because of their widespread use, aquatic and terrestrial ecosystems could be contaminated by biocides. The environmental impact of biocides is evaluated through eco-toxicological studies with model organisms of terrestrial and aquatic ecosystems. We focused on the development of in silico models for the evaluation of the acute toxicity (EC₅₀) of a set of biocides collected from different sources on the freshwater crustacean Daphnia magna, one of the most widely used model organisms in aquatic toxicology. Toxicological data specific for biocides are limited, so we developed three models for daphnid toxicity using different strategies (linear regression, random forest, Monte Carlo (CORAL)) to overcome this limitation. All models gave satisfactory results in our datasets: the random forest model showed the best results with a determination coefficient r² = 0.97 and 0.89, respectively, for the training (TS) and the validation sets (VS) while linear regression model and the CORAL model had similar but lower performance (r² = 0.83 and 0.75, respectively, for TS and VS in the linear regression model and r² = 0.74 and 0.75 for the CORAL model).     

Exploring the picosecond time domain of the solvation dynamics of coumarin 153 within beta-cyclodextrins

We report molecular dynamics simulation results of equilibrium and dynamical characteristics pertaining to the solvation of the dye coumarin 153 (C153) trapped within hydrophobic cavities of di- and trimethylated beta-cyclodextrins (CD) in aqueous solutions. We found that stable configurations of the encapsulated probe are characterized by a slanted docking, in which the plane of the C153 lies mostly parallel to one of the glucose units of the CD. "In and out" dynamical modes of the encapsulated probe present very small amplitudes. The rotational dynamics of the trapped coumarin can be cast in terms of a simple model that includes diffusive motions within a local restrictive environment coupled to the overall rotational motion of the CD. We have examined the early stages of the solvation response of the environment following a vertical excitation of the probe. Regardless of the degree of CD methylation, the water dynamical response seems to be completed within 2-3 ps and does not differ substantially from that observed for nonencapsulated probes. The CD response is characterized by a single, subpicosecond relaxation that involves intramolecular motions. We also explored dynamical modes that could account for the recently reported persistence of Stokes shifts in the nanosecond time domain. In all cases, the only sources of ultraslow dynamics that we detected were those associated with gauche-trans interconversions in primary hydroxyl chains of the CD, which do not seem to be directly connected to the electronic excitation of the probe.     

A novel [Cu II 4] cluster from the assembly of two [Cu II 2L]+ units by a central mu4-1,1,2,2 perchlorate ligand

A perchlorate ligand in the rare mu4-1,1,2,2 binding mode is seen for the first time as the sole support for the assembly of two cationic [Cu II 2L]+ fragments (H3L = a dinucleating ligand) in the formation of a magnetically-exchanged tetranuclear cluster.     

A Convenient Stereoselective Synthesis of (1R,2S,3R,4S)-3-(Neopentyloxy)isoborneol

A convenient preparation of (1R,2S,3R,4S)-3-(neopentyloxy)isoborneol (= (1R,2S,3R,4S)-3-(2,2-dimethyl-propoxy)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-ol; 1a ), a valuable chiral auxiliary, is described. The synthesis involves six steps starting from the readily available camphorquinone ( 5 ) and gives 1a in 48% overall yield. The key step is the chemoselective hydrolysis of the less hindered 1,3-dioxolane moiety in the camphorquinone di-acetal 4 .     

The missing link between the Hydration Force and interfacial water: Evidence from computer simulations

In this article I briefly review Molecular Dynamics Simulations studies relevant to the understanding of the physical origin of the controversial Hydration Force. The focus of the review is in simulations of realistic models of hydrophilic surfaces. The results reviewed here show a molecular perspective on how this repulsive, stabilizing force comes from interfacial water.     

Interaction of monovalent ions with hydrophobic and hydrophilic colloids: charge inversion and ionic specificity

Here we study experimentally and by simulations the interaction of monovalent organic and inorganic anions with hydrophobic and hydrophilic colloids. In the case of hydrophobic colloids, our experiments show that charge inversion is induced by chaotropic inorganic monovalent ions but it is not induced by kosmotropic inorganic anions. For organic anions, giant charge inversion is observed at very low electrolyte concentrations. In addition, charge inversion disappears for both organic and inorganic ions when turning to hydrophilic colloids. These results provide an experimental evidence for the hydrophobic effect as the driving force for both ion specific effects and charge inversion. In the case of organic anions, our molecular dynamics (MD) simulations with full atomic detail show explicitly how the large adsorption free energies found for hydrophobic colloids are transformed into large repulsive barriers for hydrophilic colloids. Simulations confirm that solvation free energy (and hence the hydrophobic effect) is responsible for the build up of a Stern layer of adsorbed ions and charge inversion in hydrophobic colloids and it is also the mechanism preventing charge inversion in hydrophilic colloids. Overall, our experimental and simulation results suggest that the interaction of monovalent ions with interfaces is dominated by solvation thermodynamics, that is, the chaotropic/kosmotropic character of ions and the hydrophobic/hydrophilic character of surfaces.