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1. Building molecular band-pass filters via molecular sequestration

   Yichi Zhang, Christian Cuba ( December 2022 , Proceedings of the IEEE conference on decision and control)

   Engineered genetic circuits with tailored functions that mimic how cells process information in changing environments (e.g. cell fate decision, chemotaxis, immune response) have great applications in biomedicine and synthetic biology. Although there is a lot of progress toward the design of gene circuits yielding desired steady states (e.g. logic-based networks), building synthetic circuits for dynamic signal processing (e.g. filters, frequency modulation, and controllers) is still challenging. Here, we provide a model-based approach to build gene networks that can operate as band-pass filters by taking advantage of molecular sequestration. By suitably approximating the dynamics of molecular sequestration, we analyze an Incoherent Feed-Forward Loop (IFFL) and a Negative Feedback (NF) circuit and illustrate how they can achieve band-pass filter behavior. Computational analysis shows that a circuit that incorporates both IFFL and NF motifs improves the filter performance. Our approach facilitates the design of sequestration-based filters, and may support the synthesis of molecular controllers with desired specifications. 

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2. Accessing Centnerszwer's quasiracemate – molecular shape controlled molecular recognition

   https://doi.org/10.1039/C6RA08131B  

   Spaniol, Jacqueline M. ; Wheeler, Kraig A. ( January 2016 , RSC Advances)

   M. Centnerszwer's seminal 1899 report investigated the stereochemical relationship between optical antipodes of different substances using melting-point behavior. One intriguing melting-point phase diagram produced from this early investigation combined (+)-2-chlorosuccinic acid [(+)- 1 ] and (−)-2-bromosuccinic acid [(−)- 2 ]. While Centnerszwer's data clearly indicates the formation of a quasiracemic phase – i.e. , materials constructed from pairs of isosteric molecules of opposite handedness – at the 1 : 1 component ratio, this material is energetically less favorable than the chiral counterparts. The consequence of this crystal instability is significant as evident by the absence of literature sited crystal structures for the quasiracemic phase (+)- 1 /(−)- 2 and racemates (±)- 1 and (±)- 2 . This study circumvented this challenge by generating multi-molecular assemblies using additional crystallizing agents capable of complementing the hydrogen-bond abilities of succinic acids 1 and 2 . Both imidazole (Im) and 4,4′-bipyridyl- N , N ′-dioxide (BPDO) served as tailor-made additives that effectively modified the crystal packing landscape of quasiracemate of (+)- 1 /(−)- 2 . Combining imidazole with the quasiracemate, racemate, and enantiopure forms of 1 and 2 resulted in crystal structures characterized as molecular salts with layered motifs formed from highly directional N + –H⋯carboxylate and carboxyl⋯carboxylate interactions. In contrast to the enantiopure [(+)- 1 ·Im and (−)- 2 ·Im] and racemic [(±)- 1 ·Im and (±)- 2 ·Im] systems, neighboring molecular layers observed in quasiracemate (+)- 1 /(−)- 2 ·Im are organized by approximate inversion symmetry. Assessment of the crystal packing efficiency for this series of molecular salts via crystal densities and packing coefficients ( C k ) indicates imidazole greatly alters the crystal landscape of the system in favor of racemic and quasiracemic crystal packing. A similar desymmetrized crystal environment was also realized for the ternary cocrystalline system of (+)- 1 /(−)- 2 ·BPDO where the components organize via N + –O − ⋯carboxyl contacts. This study underscores the importance of molecular shape to molecular recognition processes and the stabilizing effect of tailor-made additives for creating new crystalline phases of previously inaccessible crystalline materials. 

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3. Molecular Magnets

   https://doi.org/10.1036/1097-8542.YB150547  

   Holmes, S. M. ( October 2015 , McGraw-Hill yearbook of science and technology)
4. Control over Molecular Orbital Gating and Marcus Inverted Charge Transport in Molecular Junctions with Conjugated Molecular Wires

   https://doi.org/10.1002/aelm.202200637  

   Nijhuis, Christian A. ; Zhang, Ziyu ; Adoah, Francis ; Nickle, Cameron ; Karuppannan, Senthil Kumar ; Wang, Lejia ; Jiang, Li ; Tadich, Anton ; Cowie, Bruce ; Salim, Teddy ; et al ( January 2022 , Advanced Electronic Materials)
5. Characterization of Amino Acid Based Molecular Micelles with Molecular Modeling

   https://doi.org/10.4236/ojpc.2019.94014  

   Billiot, Alexander ; Fang, Yayin ; Morris, Kevin F. ( January 2019 , Open Journal of Physical Chemistry)