Roles of Metal Ions in Foldamers and Other Conformationally Flexible Supramolecular Systems

Anion Tuned Structural Modulation and Nonlinear Optical Effects of Metal-Ion Directed 310 -Helix Networks

Metals play an important role in the structure and functions of various proteins. The combination of metal ions and peptides have been emerging as an attractive field to create advanced structures and biomaterials. Here, we are reporting the anion-influenced, silver ion coordinated diverse networks of designed short tripeptide 310 -helices with terminal pyridyl groups. The short peptides adopted classical right-handed, left-handed and 310 EL -helical conformations in the presence of different silver salts. The peptides have displayed conformational flexibility to accommodate different sizes and interactions of anions to yield a variety of metal-coordinated networks. The complexes of metal ions and peptides have shown different porous networks, right- and left-handed helical polymers, transformation of helix into superhelix and 2 : 2 metal-peptide macrocycles. Further, the metal-peptide crystals with inherent dipoles of helical peptides gave striking second harmonic generation response. The optical energy upconversion from NIR to red and green light is demonstrated. Overall, we have shown the utilization of short 310 -helices for the construction of diverse metal-coordinated helical networks and notable non-linear optical effects.

Anion-Dependent Hydrogen-Bond Polarity Switching in Ethylene-bridged Urea Oligomers

The reversible coordination of anions to an N,N'-disubstituted 3,5-bis(trifluoromethyl)phenylurea located at a terminus of a linear chain of ethylene-bridged hydrogen-bonded ureas triggers a cascade of conformational changes. A series of hydrogen-bond polarity reversals propagates along the oligomer, leading to a global switch of its hydrogen-bond directionality. The induced polarity switch, transmitted through four reversible urea groups, results in a change in emission and excitation wavelengths of a fluorophore located at the opposite terminus of the oligomer. The molecule thus behaves as a chemical sensor with a relayed remote spectroscopic response to variations in anion concentration. The polarity switch induced by anion concentration constitutes an artificial communication mechanism for conveying information through oligomeric structures.

Stoichiometric Control of Guest Recognition of Self-Assembled Palladium(II)-Based Supramolecular Architectures

We report flexible [Pd(L)2 ]2+ complexes where there is self-recognition, driven by π-π interactions between electron-rich aromatic arms and the cationic regions they are tethered to. This self-recognition hampers the association of these molecules with aromatic molecular targets in solution. In one case, this complex can be reversibly converted to an 'open' [Pd2 (L)2 ]4+ macrocycle through introduction of more metal ion. This is accomplished by the ligand having two bidentate binding sites: a 2-pyridyl-1,2,3-triazole site, and a bis-1,2,3-triazole site. Due to favourable hydrogen bonding, the 2-pyridyl-1,2,3-triazole units reliably coordinate in the [Pd(L)2 ]2+ complex to control speciation: a second equivalent of Pd(II) is required to enforce coordination to bis-triazole sites and form the macrocycle. The macrocycle interacts with a molecular substrate with higher affinity. In this fashion we are able to use stoichiometry to reversibly switch between two different species and regulate guest binding.

Non-Covalent Interactions Enforce Conformation in Switchable and Water-Soluble Diketopiperazine-Pyridine Foldamers

To reach their potential as mimics of the dynamic molecules present in biological systems, foldamers must be designed to display stimulus-responsive behavior. Here we report such a foldamer architecture based on alternating pyridine-diketopiperazine linkers. Epimerization is conveniently prevented through a copper-catalyzed coupling protocol. The compounds' native unswitched conformation is first discovered in the solid and solution state. The foldamers can be solubilized in DMSO and pH 9.5 buffer, retaining conformational control to a large degree. Lastly, dynamic switching is demonstrated through treatment with acid, leading to behaviour we describe as stimulus-responsive sidechain reconfiguration.

Assessment of Density Functional Theory Methods for the Structural Prediction of Transition and Post-Transition Metal-Nucleic Acid Complexes

Understanding the structure of metal-nucleic acid systems is important for many applications such as the design of new pharmaceuticals, metal detection platforms, and nanomaterials. Herein, we explore the ability of 20 density functional theory (DFT) functionals to reproduce the crystal structure geometry of transition and post-transition metal-nucleic acid complexes identified in the Protein Data Bank and Cambridge Structural Database. The environmental extremes of the gas phase and implicit water were considered, and analysis focused on the global and inner coordination geometry, including the coordination distances. Although gas-phase calculations were unable to describe the structure of 12 out of the 53 complexes in our test set regardless of the DFT functional considered, accounting for the broader environment through implicit solvation or constraining the model truncation points to crystallographic coordinates generally afforded agreement with the experimental structure, suggesting that functional performance for these systems is likely due to the models rather than the methods. For the remaining 41 complexes, our results show that the reliability of functionals depends on the metal identity, with the magnitude of error varying across the periodic table. Furthermore, minimal changes in the geometries of these metal-nucleic acid complexes occur upon use of the Stuttgart-Dresden effective core potential and/or inclusion of an implicit water environment. The overall top three performing functionals are ωB97X-V, ωB97X-D3(BJ), and MN15, which reliably describe the structure of a broad range of metal-nucleic acid systems. Other suitable functionals include MN15-L, which is a cheaper alternative to MN15, and PBEh-3c, which is commonly used in QM/MM calculations of biomolecules. In fact, these five methods were the only functionals tested to reproduce the coordination sphere of Cu²⁺-containing complexes. For metal-nucleic acid systems that do not contain Cu²⁺, ωB97X and ωB97X-D are also suitable choices. These top-performing methods can be utilized in future investigations of diverse metal-nucleic acid complexes of relevance to biology and material science.

Exploring Helical Peptides and Foldamers for the Design of Metal Helix Frameworks: Current Trends and Future Perspectives

Flexible and biocompatible metal peptide frameworks (MPFs) derived from short and ultra-short peptides have been explored for the storage of greenhouse gases, molecular recognition, and chiral transformations. In addition to short flexible peptides, peptides with specifically folded conformations have recently been utilized to fabricate a variety of metal helix frameworks (MHFs). The secondary structures of the peptides govern the structure-assembly relationship and thereby control the formation of three-dimensional (3D)-MHFs. Particularly, the hierarchical structural organization of peptide-based MHFs has not yet been discussed in detail. Here, we describe the recent progress of metal-driven folded peptide assembly to construct 3D porous structures for use in future energy storage, chiral recognition, and biomedical applications, which could be envisioned as an alternative to the conventional metal-organic frameworks (MOFs).