Author Archive

Tryptophan, Featuring BN/CC Isosterism

Ever wanted to find a way to replace a carbon-carbon (CC) double bond with another bond that will change the physical and chemical properties of a molecule without significantly altering its sterics? Look no further than a boron-nitrogen bond! BN/CC isosterism involves substituting a CC double bond with a BN bond, which can substantially change the electronic properties of a molecule while keeping it the same size. This isosterism could be a powerful tool in biomedical studies of biologically relevant arene-containing organic molecules, which are plentiful. However, few studies report on the differences in functions cause by substituting a BN bond into an arene. Initial results suggest that the BN compounds can have similar or increased activity and availability when compared to the natural, all carbon molecules.

Figure 1. Image of naturally occuring tryptophan and the BN-tryptophan analogue.

Researchers in the United States synthesized a BN-analogue of tryptophan (Figure 1) for use as an unnatural amino acid (UAA) to study and intentionally alter the properties of proteins. Tryptophan, in addition to making Americans sleepy at Thanksgiving, is relatively rare, but participates in pi system interactions and is the primary source of native protein fluorescence. This makes it an important target for UAA research. The researchers synthesized the sodium salt of BN-tryptophan in a 6-step process, which can be modified to resolve the two enantiomers by chiral HPLC. The BN-tryptophan exhibits noticeably red-shifted absorbance and emission spectra, with the fluorescence maximum shifted by almost 40 nm in the BN compound.

In order to test whether the BN-tryptophan could be incorporated into proteins, researchers incorporated it into media without tryptophan and monitored whether E. coli cells that lacked the ability to produce tryptophan would grow. They found that the cells grew when in the presence of BN-tryptophan, but to a significantly lesser degree than with an equivalent quantity of natural tryptophan. However, cell growth increased when the media contained both BN-tryptophan and natural tryptophan. This suggests that cells will accept BN-tryptophan as a tryptophan analogue, but they don’t tolerate full replacement well.

Figure 2. Representation of the protein sequence, structures of other tryptophan analogues, and fluorescence plot for the studied substrates.

Further studies incorporated BN-tryptophan and three other previously utilized tryptophan analogues into a green fluorescent protein (GFP). For fluorescence to be detected, the analogue must be incorporated into the protein and then accurately read by cells. The BN-tryptophan performs as well or better than the established tryptophan analogues, proving its functionality (Figure 2). The proteins with BN-tryptophan also demonstrate several different properties than those containing natural tryptophan; their fluorescence is red shifted and they are more susceptible to oxidation by hydrogen peroxide. These alterations in activity could prove useful in future studies.

To find out more please read:

Synthesis and characterization of an unnatural boron and nitrogen-containing tryptophan analogue and its incorporation into proteins

Katherine Boknevitz, James S. Italia, Bo Li, Abhishek Chatterjee and Shih-Yuan Liu

Chem. Sci., 2019, 10, 4994–4998.

About the blogger:

Beth Mundy is a PhD candidate in chemistry in the Cossairt lab at the University of Washington in Seattle, Washington. Her research focuses on developing new and better ways to synthesize nanomaterials for energy applications. She is often spotted knitting in seminars or with her nose in a good book. You can find her on Twitter at @BethMundySci.

Digg This
Reddit This
Stumble Now!
Share on Facebook
Bookmark this on Delicious
Share on LinkedIn
Bookmark this on Technorati
Post on Twitter
Google Buzz (aka. Google Reader)

One-Pot MOFs

Metal-organic frameworks, commonly known as MOFs, are one to three-dimensional structures composed of metal ions coordinated to organic linkers. They’ve drawn substantial research interest given their highly porous nature, the extreme tunability of their properties, and, in the early days, relative ease of synthesis. As the field has matured, the syntheses of the organic linkers have increased in complexity. New linkers require substantial expertise in synthetic organic chemistry and can be time and cost intensive to produce. One strategy to avoid the linker-induced bottleneck in MOF development is to create one-pot procedures, generating both the linker and the MOF in a single vessel. While the idea is straightforward, in practice it involves carefully balancing conditions to crystalize the MOF without producing unwanted side reactions.

Figure 1. Reaction motifs utilized for in-situ ligand generation. a) nitro-compound reduction, b) diazo coupling of nitro compounds, c) condensation of boronic acids, and d) imidization of an anhydride and an amine.

Researchers in China recently examined several classes of organic reactions to test the viability of in-situ ligand and MOF synthesis. The basic procedure involves complex ligand generation, formation of small metal clusters, and finally crystallization of the final MOF structure. They chose reduction and diazo coupling of nitro compounds, condensation of boronic acids, and imidization between anhydrides and amines (Figure 1). A rigid, nitro-containing dicarboxylic acid proved the most robust for the reduction studies.  When combined with a hydrated metal salt (copper, zinc, and indium nitrates and manganese chloride), exposed to a protic solvent, and heated, a MOF formed in a single vessel without the addition of a purposeful reductant. This specific ligand didn’t have the proper geometry to produce MOFs via diazo couplings, but a similar motif was used to create a new ligand with greater distance separating the carboxylic acid groups. The researchers dissolved the ligand and various metal salts in DMF, then added proton source, and heated the mixture. The reactions with zirconium, zinc, cadmium, and indium all produced MOFs. The reaction conditions varied from metal to metal, producing different forms of the ligand in-situ that resulted in MOFs of a range of morphologies (Figure 2).

Figure 2. Structures of zirconium, zinc, cadmium, and indium-based MOFs synthesized by ligands generated via diazo coupling.

While these MOFs formed via strong, irreversible reactions, the covalent organic framework literature utilizes the plethora of reversible reactions to expand the scope of possible MOFs. This inspired the researchers to use boronic acid derivatives as a proof of concept. When a ligand with both boronic and carboxylic acid motifs reacted with zirconium or hafnium and formic acid, the researchers isolated a MOF with tetrahedral cages. This approach also proved successful when combining two ligands in a Schiff base synthesis to form a zirconium-based MOF. The reversible reactions required meticulous tuning of the acid source to effectively crystalize and assemble the MOFs. However, the ease of reaction set up allows more rapid screening of conditions than full-scale ligand synthesis.

This relatively simple and efficient strategy for producing new MOFs likely has broader applications than the few reactions currently explored. This will hopefully increase the speed of new MOF discovery with increasingly complex ligands.

To find out more please read:

Constructing new metal-organic frameworks with complicated ligands from “One-Pot” in situ reactions

Xiang-Jing Kong, Tao He, Yong-Zheng Zhang, Xue-Quian Wu, Si-Nan Wang, Ming-Ming Xu, Guang-Rui Si, and Jian-Rong Li

Chem. Sci., 2019, 10, 3949 – 3955.

About the blogger:

Beth Mundy is a PhD candidate in chemistry in the Cossairt lab at the University of Washington in Seattle, Washington. Her research focuses on developing new and better ways to synthesize nanomaterials for energy applications. She is often spotted knitting in seminars or with her nose in a good book. You can find her on Twitter at @BethMundySci.

Digg This
Reddit This
Stumble Now!
Share on Facebook
Bookmark this on Delicious
Share on LinkedIn
Bookmark this on Technorati
Post on Twitter
Google Buzz (aka. Google Reader)

Molecular Switching: from Blue Biradicals to Colorless Housanes

As chemists, we typically first encounter molecular switches, the general term for any molecule that exists in at least two stable or meta-stable states, as pH indicators in introductory chemistry classes. The external factor that causes the conversion can vary from a redox event to UV light. This makes molecular switches attractive sensors for a range of chemically relevant applications. The reversible and controllable bond-making and bond-breaking also provides a system within which to interrogate the nature of chemical bonding.

Figure 1. The biradical (left) and housane (right) in solution along with their simplified chemical structures.

Chemists at the University of Rostock in Germany explored light-driven molecular switching behavior in a class of heterocyclic molecules. These can exist as either biradicals or housanes (see Figure 1 for why the name makes sense) with a bond between the two phosphorus atoms. Understanding the mechanism by which the photo-isomerization occurs is important for future applications of the biradical system in small molecule activation. The in-depth studies used the 2,6-dimethylphenyl (2Dmp) derivative, since it was the most stable of the synthesized derivatives. The researchers monitored the conversion between species by examining their dramatically different 31P NMR spectra, with the housane resonances between -50 and -200 ppm and the biradical resonances between 200 and 300 ppm. An additional distinguishing feature between is color: the starting biradical is blue while the housane is colorless. The researchers found that biradical converts to the housane, which has a half-life of about 7 minutes at room temperature in solution, with an almost 25% quantum yield.

Figure 2. A single crystal of the biradical. Upon irradiation, the transition to the colorless housane can be observed, along with extensive cracking of the crystal.

This switching occurs not only in solution, but also in the solid state (Figure 2). The cracking evident in the images of a single crystal is attributed to the stress caused by changes to the crystal lattice by conversion of the biradical to the housane. Despite various efforts by the team, including crystallization attempts under constant irradiation, they were unable to obtain high enough quality crystals to acquire a crystal structure of the housane. The specific isomerization mechanism was computationally modeled and showed that the photoexcitation of the biradical led to a bonding interaction and distortion, allowing for housane formation. The reverse, thermally activated process, occurs due to the intersection of the ground and excited state energies near a transition state.

Given this enhanced understanding of the isomerization mechanism, the researchers manipulated the reactivity of the biradical by adding tert-butyl isocyanide (tBuNC). tBuNC catalyzed the thermal conversion of the housane back to the diradical. While the mechanism of the catalysis is unknown, it’s an exciting proof-of-concept for easily tuning molecular switching behavior.

To find out more please read:

A chemical reaction controlled by light-activatedmolecular switches based on hetero-cyclopentanediyls

Jonas Bresien, Thomas Kröger-Badge, Stefan Lochbrunner, Dirk Michalik, Henrik Müller, Axel Schultz, and Edgar Zander

Chem. Sci., 2019, 10, 3486-3493

About the blogger:

 

Beth Mundy is a PhD candidate in chemistry in the Cossairt lab at the University of Washington in Seattle, Washington. Her research focuses on developing new and better ways to synthesize nanomaterials for energy applications. She is often spotted knitting in seminars or with her nose in a good book. You can find her on Twitter at @BethMundySci.

Digg This
Reddit This
Stumble Now!
Share on Facebook
Bookmark this on Delicious
Share on LinkedIn
Bookmark this on Technorati
Post on Twitter
Google Buzz (aka. Google Reader)