Density functional theory calculations of hydrogen-bond-mediated NMR J coupling in the solid state

A recently developed method for calculating NMR J coupling in solid-state systems is applied to calculate hydrogen-bond-mediated (2h) J NN couplings across intra- or intermolecular N-H...N hydrogen bonds in two 6-aminofulvene-1-aldimine derivatives and the ribbon structure formed by a deoxyguanosine derivative. Excellent quantitative agreement is observed between the calculated solid-state J couplings and those previously determined experimentally in two recent spin-echo magic-angle-spinning NMR studies ( Brown, S. P. ; et al. Chem. Commun. 2002, 1852-1853 and Pham, T. N. ; et al. Phys. Chem. Chem. Phys. 2007, 9, 3416-3423 ). For the 6-aminofulvene-1-aldimines, the differences in (2h) J NN couplings in pyrrole and triazole derivatives are reproduced, while for the guanosine ribbons, an increase in (2h) J NN is correlated with a decrease in the N-H...N hydrogen-bond distance. J couplings are additionally calculated for isolated molecules of the 6-aminofulevene-1-aldimines extracted from the crystal with and without further geometry optimization. Importantly, it is shown that experimentally observed differences between J couplings determined by solution- and solid-state NMR are not solely due to differences in geometry; long-range electrostatic effects of the crystal lattice are shown to be significant also. J couplings that are yet to be experimentally measured are calculated. Notably, (2h) J NO couplings across N-H...O hydrogen bonds are found to be of a similar magnitude to (2h) J NN couplings, suggesting that their utilization and quantitative determination should be experimentally feasible.     

Hierarchically Structured Allotropes of Phosphorus from Data‐Driven Exploration

The discovery of materials is increasingly guided by quantum‐mechanical crystal‐structure prediction, but the structural complexity in bulk and nanoscale materials remains a bottleneck. Here we demonstrate how data‐driven approaches can vastly accelerate the search for complex structures, combining a machine‐learning (ML) model for the potential‐energy surface with efficient, fragment‐based searching. We use the characteristic building units observed in Hittorf's and fibrous phosphorus to seed stochastic (“random”) structure searches over hundreds of thousands of runs. Our study identifies a family of hierarchically structured allotropes based on a P8 cage as principal building unit, including one‐dimensional (1D) single and double helix structures, nanowires, and two‐dimensional (2D) phosphorene allotropes with square‐lattice and kagome topologies. These findings yield new insight into the intriguingly diverse structural chemistry of phosphorus, and they provide an example for how ML methods may, in the long run, be expected to accelerate the discovery of hierarchical nanostructures.     

On the nature of pulsars

The paper contains a relatively non-technical summary of some recent work by the author and Jeremy Butterfield. The goal is to find a way of assigning meaningful truth values to propositions in quantum theory: something that is not possible in the normal, instrumentalist interpretation. The key mathematical tool is presheaf theory where multi-valued, contextual truth values arise naturally. We show how this can be applied to quantum theory, with the ‘contexts’ chosen to be Boolean subalgebras of the set of all projection operators.     

Absolute binding free energies for octa-acids and guests in SAMPL5

As part of the SAMPL5 blind prediction challenge, we calculate the absolute binding free energies of six guest molecules to an octa-acid (OAH) and to a methylated octa-acid (OAMe). We use the double decoupling method via thermodynamic integration (TI) or Hamiltonian replica exchange in connection with the Bennett acceptance ratio (HREM-BAR). We produce the binding poses either through manual docking or by using GalaxyDock-HG, a docking software developed specifically for this study. The root mean square deviations for our most accurate predictions are 1.4 kcal mol^?1 for OAH with TI and 1.9 kcal mol^?1 for OAMe with HREM-BAR. Our best results for OAMe were obtained for systems with ionic concentrations corresponding to the ionic strength of the experimental solution. The most problematic system contains a halogenated guest. Our attempt to model the σ-hole of the bromine using a constrained off-site point charge, does not improve results. We use results from molecular dynamics simulations to argue that the distinct binding affinities of this guest to OAH and OAMe are due to a difference in the flexibility of the host. We believe that the results of this extensive analysis of host-guest complexes will help improve the protocol used in predicting binding affinities for larger systems, such as protein-substrate compounds.     

Encapsulation and Polymerization of White Phosphorus Inside Single-Wall Carbon Nanotubes

Elemental phosphorus displays an impressive number of allotropes with highly diverse chemical and physical properties. White phosphorus has now been filled into single-wall carbon nanotubes (SWCNTs) from the liquid and thereby stabilized against the highly exothermic reaction with atmospheric oxygen. The encapsulated tetraphosphorus molecules were visualized with transmission electron microscopy, but found to convert readily into chain structures inside the SWCNT “nanoreactors”. The energies of the possible chain structures were determined computationally, highlighting a delicate balance between the extent of polymerization and the SWCNT diameter. Experimentally, a single-stranded zig-zag chain of phosphorus atoms was observed, which is the lowest energy structure at small confinement diameters. These one-dimensional chains provide a glimpse into the very first steps of the transformation from white to red phosphorus.     

Sauerstoffbestimmung in Eisen und Stahl

Ohne Zusammenfassung     

Comparison of model chemistry and density functional theory thermochemical predictions with experiment for formation of ionic clusters of the ammonium cation complexed with water and ammonia; atmospheric implications

The G2, G3, CBS-QB3, and CBS-APNO model chemistry methods and the B3LYP, B3P86, mPW1PW, and PBE1PBE density functional theory (DFT) methods have been used to calculate deltaH(o) and deltaG(o) values for ionic clusters of the ammonium ion complexed with water and ammonia. Results for the clusters NH4(+) (NH3)n and NH4(+) (H2O)n, where n = 1-4, are reported in this paper and compared against experimental values. Agreement with the experimental values for deltaH(o) and deltaG(o) for formation of NH4(+) (NH3)n clusters is excellent. Comparison between experiment and theory for formation of the NH4(+) (H2O)n clusters is quite good considering the uncertainty in the experimental values. The four DFT methods yield excellent agreement with experiment and the model chemistry methods when the aug-cc-pVTZ basis set is used for energetic calculations and the 6-31G* basis set is used for geometries and frequencies. On the basis of these results, we predict that all ions in the lower troposphere will be saturated with at least one complete first hydration shell of water molecules.