Visualising many-body electron dynamics using one-body densities and orbitals

As experimental techniques begin to probe electronic motions in increasing detail, the need is arising for compact and informative visualisations of simulations of such processes. The inherent challenge is that a full many-electron wavefunction is a high-dimensional object, representing the complicated correlations of strongly repulsive bodies in a small molecular volume. A general procedure is needed to distill this to a smaller amount of information that does not rely on any specific level of approximation. The result should allow for easy and intuitive interpretation while drawing out nontrivial aspects of the underlying many-body dynamics, such as the complex phase information inherent of a nonstationary state. Current visualisation schemes based on physical observables or the qualitative information contained in simple wavefunctions, such as time-dependent configuration-interaction-singles (TD-CIS) and time-dependent self-consistent-field (TD-SCF), are discussed. This information is compared to an analysis based on the one-body reduced density operator (1-RDO), which is well-defined for general wavefunctions. It is seen that the distinction between two paradigms of many-body dynamics, electron transport and energy transport, is reflected in the coherences of a difference-1-RDO, or lack thereof.     

Chiral Amine Synthesis Using ω‐Transaminases: An Amine Donor that Displaces Equilibria and Enables High‐Throughput Screening

The widespread application of ω‐transaminases as biocatalysts for chiral amine synthesis has been hampered by fundamental challenges, including unfavorable equilibrium positions and product inhibition. Herein, an efficient process that allows reactions to proceed in high conversion in the absence of by‐product removal using only one equivalent of a diamine donor (ortho‐xylylenediamine) is reported. This operationally simple method is compatible with the most widely used (R)‐ and (S)‐selective ω‐TAs and is particularly suitable for the conversion of substrates with unfavorable equilibrium positions (e.g., 1‐indanone). Significantly, spontaneous polymerization of the isoindole by‐product generates colored derivatives, providing a high‐throughput screening platform to identify desired ω‐TA activity.     

Purification of a 166mHo solution by successive high-performance liquid chromatography and gravitational chromatography for half-life determination

A methodology to purify a ^166mHo solution has been developed by a combination of activity and mass concentration measurements in order to further determine the ^166mHo half-life. The isobaric interference at m/q ? 166 requires Ho purification from non-natural Er with a high purification degree due to the large amount of Ho as opposed to Er. The Ho/Er separation was achieved using high-performance liquid chromatography on a semi-preparative column followed by purification on gravitational chromatography. The efficiency of the separation was evaluated after precise determination of the Er isotopic composition. The purification methodology enabled to separate Ho from Er.     

A Cucurbit[8]uril 2:2 Complex with a Negative pKa Shift

A viologen derivative carrying a benzimidazole group ( V-P-I ²⁺; viologen–phenylene–imidazole V-P-I ) can be dimerized in water using cucurbit[8]uril (CB[8]) in the form of a 2:2 complex resulting in a negative shift of the guest pK_a, by more than 1 pH unit, contrasting with the positive pK_a shift usually observed for CB-based complexes. Whereas 2:2 complex protonation is unclear by NMR, silver cations have been used for probing the accessibility of the imidazole groups of the 2:2 complexes. The protonation capacity of the buried imidazole groups is reduced, suggesting that CB[8] could trigger proton release upon 2:2 complex formation. The addition of CB[8] to a solution containing V-P- I ³⁺ indeed released protons as monitored by pH-metry and visualized by a coloured indicator. This property was used to induce a host/guest swapping, accompanied by a proton transfer, between V-P-I ³⁺ ⋅ CB[7] and a CB[8] complex of 1-methyl-4-(4-pyridyl)pyridinium. The origin of this negative pK_a shift is proposed to stand in an ideal charge state, and in the position of the two pH-responsive fragments inside the two CB[8] which, alike residues engulfed in proteins, favour the deprotonated form of the guest molecules. Such proton release triggered by a recognition event is reminiscent of several biological processes and may open new avenues toward bioinspired enzyme mimics catalyzing proton transfer or chemical reactions.     

Call for Papers: GRC, CADD, and statistics, and all that

Molecular modeling and the art of computer-aided drug discovery seldom make much use of statistics, despite being fields that can not calculate important properties with great reliability. The 2013 CADD Gordon conference intends to examine what prevents a more effective use of statistics in routine modeling and to raise consciousness as to what is possible. Practical methods will be discussed, deeper issues in applying standard approaches addressed and research on successes and failures in other disciplines presented by invited experts.