Diamond Quantum Devices in Biology

The currently available techniques for molecular imaging capable of reaching atomic resolution are limited to low temperatures, vacuum conditions, or large amounts of sample. Quantum sensors based on the spin‐dependent photoluminescence of nitrogen‐vacancy (NV) centers in diamond offer great potential to achieve single‐molecule detection with atomic resolution under ambient conditions. Diamond nanoparticles could also be prepared with implanted NV centers, thereby generating unique nanosensors that are able to traffic into living biological systems. Therefore, this technique might provide unprecedented access and insight into the structure and function of individual biomolecules under physiological conditions as well as observation of biological processes down to the quantum level with atomic resolution. The theory of diamond quantum sensors and the current developments from their preparation to sensing techniques have been critically discussed in this Minireview.     

Application of the Rodriguez-Pattenden photo-ring contraction: total synthesis and configurational reassignment of 11-gorgiacerol and 11-epigorgiacerol

A stereospecific photochemical ring contraction was used as the key step in the first total synthesis of the marine pseudopteranyl diterpene 11-gorgiacerol and its 11-epimer. The synthesis allowed the correction of the configurations that had been misassigned in the literature. In addition, some novel pseudopteranyl derivatives have been made.     

3-Fluoro-N-methyl-D-aspartic acid (3F-NMDA) stereoisomers as conformational probes for exploring agonist binding at NMDA receptors

N-Methyl-D-aspartate (NMDA) is the prototypical agonist of the NMDA receptor subtype of ionotropic glutamate receptors. Stereogenic placement of a C-F bond at the 3-position of (S)-NMDA generates either the (2S,3S)- or (2S,3R)- diastereoisomers of 3F-NMDA. The individual diastereoisomers were prepared by synthesis in enantiomerically pure forms and it was found that (2S,3S)-3F-NMDA is an agonist with a comparable potency to NMDA itself, whereas the (2S,3R)-diastereoisomer has negligible potency. The difference in potency of these stereoisomers is attributed to a preference of the C-F bond (2S,3S)-3F-NMDA to adopt a gauche conformation to the C-N(+) bond in the binding conformation, whereas the (2S,3R)-3F-NMDA forces these bonds anti, losing electrostatic stabilisation, to achieve the required binding conformation. These observations illustrate the utility of stereoselective fluorination in influencing the molecular conformation of β-fluorinated amino acids and thus probing the active conformations of bioactive compounds at receptors.     

TFD: Torsion Fingerprints as a new measure to compare small molecule conformations

Advantages like intuitive interpretation, objectivity, general applicability, and its easy, automated calculation make the rmsd (root-mean-squared deviation) the measure of choice for the investigation of the accuracy of conformational model generators. For comparing conformations of a single molecule this is a clearly superior method. Single molecule analysis is, however, a rare scenario. Typically, conformations are generated for huge corporate or external vendor databases of high diversity which are then further investigated with high-throughput computational methods like docking or pharmacophore searching, in virtual screening campaigns. Representative subsets for accuracy investigations of computational methods need to mimic this diversity. Averaged rmsd values over these data sets are frequently used to assess the accuracy of the methods. There are, however, significant weaknesses in rmsd comparisons for such kind of data sets. The interpretation is for example no longer intuitive because what can be expected in terms of good or bad rmsd values crucially depends on the data set composition like size or number of rotatable bonds of the underlying molecules. Further, rmsd lacks normalization which might result in very high averaged rmsd values for highly flexible molecules and thus might completely skew results. We have developed a novel measure to compare conformations of molecules called Torsion Fingerprint Deviation (TFD). It extracts, weights, and compares Torsion Fingerprints from a query molecule and generated conformations under consideration of acyclic bonds as well as ring systems. TFD is alignment-free and overcomes major limitations of rmsd while retaining its advantages.     

Template-directed synthesis in 3'- and 5'-direction with reversible termination

Extending both ways: A method for DNA-templated synthesis on solid support is described. Controlled, stepwise chain extension was demonstrated both in the direction favored by nature (3'-extension; see scheme) and in the direction typical for conventional DNA synthesizers (5'-extension).     

Hydrated-ion ordering in electrical double layers

In this work we revisit the surface forces measured between two atomically flat mica surfaces submerged in a reservoir of potassium nitrate (KNO(3)) solution. We consider a comprehensive range of concentrations from 0.08 mM to 2.6 M. The significantly improved resolution available from the extended surface force apparatus (eSFA) allows the distinction of hydration structures and hydrated-ion correlations. Above concentrations of 0.3 mM, hydrated-ion correlations give rise to multiple collective transitions (4 ± 1 ?) in the electrical double layers upon interpenetration. These features are interpreted as the result of hydrated-ion ordering (e.g. layering), in contrast to the traditional interpretation invoking water layering. The hydrated-ion layer adjacent to the surface (i.e. outer Helmholtz layer) is particularly well defined and plays a distinctive role. It can be either collectively expelled in a 5.8 ± 0.3 ? film-thickness transition or collectively forced to associate with the surface by external mechanical work. The latter is observed as a characteristic 2.9 ± 0.3 ? film-thickness transition along with an abrupt decrease of surface adhesion at concentrations above 1 mM. At concentrations as low as 20 mM, attractive surface forces are measured in deviation to the DLVO theory. The hydration number in the confined electrolyte seems to be significantly below that of the bulk. A 1-3 nm thick ionic layer solidifies at the surfaces at concentrations >100 mM, i.e. below bulk saturation.     

Resonant shattering of neutron star crusts

The resonant excitation of neutron star (NS) modes by tides is investigated as a source of short gamma-ray burst (SGRB) precursors. We find that the driving of a crust-core interface mode can lead to shattering of the NS crust, liberating ～10{46}-10{47} erg of energy seconds before the merger of a NS-NS or NS-black-hole binary. Such properties are consistent with Swift/BAT detections of SGRB precursors, and we use the timing of the observed precursors to place weak constraints on the crust equation of state. We describe how a larger sample of precursor detections could be used alongside coincident gravitational wave detections of the inspiral by Advanced LIGO class detectors to probe the NS structure. These two types of observations nicely complement one another, since the former constrains the equation of state and structure near the crust-core boundary, while the latter is more sensitive to the core equation of state.     

Low-energy electron scattering with the purine bases of DNA/RNA using the R-matrix method

R-matrix calculations on electron collisions with the purine bases found in DNA and RNA (i.e., adenine and guanine) are presented. Resonant anion states of these systems are identified by employing different approximation levels of ab initio theoretical methods, such as the static exchange, the static exchange plus polarization, and the close-coupling methods. The results are compared with other available calculations and experiments. All of these ab initio approximations, which we refer to as a scattering "model," give four shape resonances of (2)A' (π) symmetry within the energy range of 10 eV for both molecules. For adenine, the most sophisticated method, the close-coupling model, gives two very narrow (2)A' (σ) symmetry Feshbach-type resonances at energies above 5 eV. Quantitative results for the total elastic and electronic excitation cross sections are also presented.     

Different growth regimes on prepatterned surfaces: consistent evidence from simulations and experiments

Molecule deposition on a prepatterned substrate is a recently developed technique to generate desired structures of organic molecules on surfaces via self-organization. For the case of prepatterned stripes, the time-resolved process of structure formation is studied via lattice Monte Carlo simulations. By systematic variation of the interaction strength, three distinct growth regimes can be identified: localized growth, bulge formation, and cluster formation. All three growth regimes can be recovered in the experiment when choosing appropriate organic molecules. Some key microscopic observables, reflecting the properties of the structure formation, display a non-monotonous dependence on the interaction strength.