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Studying Anticancer Agents with XFM

23 Jun 2020

It turns out that rhenium-based compounds have been showing some promising anticancer activity as they’re stable, allow for real time imaging, structurally diverse, and have low off-site toxicity. The most commonly studied complexes are based around a Re(I) tricarbonyl core with the other three binding sites occupied by ligands of varying complexity. Researchers in the US and Australia developed a tricarbonyl Re isonitrile polypyridyl complex fac-[Re(CO)3(dmphen)(para-tolyl-isonitrile)]+, where dmphen = 2,9-dimethyl-1,10-phenanthro-line, called TRIP for short. TRIP showed promising cytotoxicity and can be imaged using confocal fluorescence microscopy, taking advantage of the emissive metal to ligand charge transfer (MLCT) state. The persistence of the emission indicates that the ligands remain bound to the Re even within cells. The complex’s cytotoxicity stems from its inducement of cells to accumulate misfolded proteins, resulting in apoptosis from the unfolded protein response (UPR). UPR induced cell death is relatively uncommon and led the researchers to find a method to characterize the speciation of TRIP in vitro. They used synchrotron X-ray fluorescence microscopy (XFM) to probe the cellular uptake and distribution of TRIP and an iodo-derivative I-TRIP by looking at elemental signals.

Figure 1. Chemical structures of TRIP and I-TRIP

I-TRIP is particularly well-suited to this type of study, as the iodine provides an additional spectroscopic handle on the isonitrile ligand absent in TRIP. Of course, the researchers had to confirm that I-TRIP possessed similar cytotoxicity and working mechanism to TRIP. Various assays and biological studies showed evidence of comparable cytotoxicity and mechanism, demonstrating that altering the substitution of the isonitrile ligand doesn’t significantly impact the bioactivity of the complex. With that settled, the experiments could move to the synchrotron to probe elemental distributions.

Figure 2. XFM elemental distribution maps of HeLa cervical cancer cells treated with either DMSO (control), TRIP, or I-TRIP.

Cells treated with both TRIP and I-TRIP show a clear Re signal, confirming that they can enter and persist in cells. Critically, the colocalization of the Re and I maps for I-TRIP samples indicate that the isonitrile ligand remains bound as a part of the Re complex inside the cells. This strongly suggests that the Re complex is intact while it induces cell death, adding to the developing mechanistic understanding of their activity. This work shows the utility of XRM as a technique to study the distribution of organometallic complexes in living cells. Additionally, the tunability and stable bioactivity of the Re complexes shows that they’re amenable to study by a wide range of techniques that will allow for further mechanistic probing.

To find out more, please read:

X-Ray fluorescence microscopy reveals that rhenium(I) tricarbonyl isonitrile complexes remain intact in vitro

Chilaluck C. Konkankit, James Lovett, Hugh H. Harris and Justin J. Wilson

Chem. Commun., 2020, 56, 6515-6518

About the blogger:

Dr. Beth Mundy is a recent PhD in chemistry from the Cossairt lab at the University of Washington in Seattle, Washington. Her research focused 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.

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Generating Electricity from Urea Using NiCoMo/Graphene Catalysts

12 Jun 2020

Electro-oxidizing urea in water has the dual benefit of generating electricity and treating wastewater. In alkaline media, the sluggish kinetics of the urea oxidation reaction, CO(NH₂)₂ + 6OH^– → N₂↑ + CO₂↑ + 5H₂O + 6e^–, due to its transfer of six electrons demand efficient catalysts to speed up this process.

A research team led by Xiujuan Sun and Rui Ding, both at Xiangtan University, China, used a co-precipitation method to synthesize urea-oxidation catalysts. These catalysts comprised of graphene-anchored nanoparticles of metallic Ni, Co, and Mo, as well as their alloys and hydro/oxides (NCM/G) (Figure 1). NCM/G with the optimal composition displayed a mass activity of 140.9 mA cm^-2 mg_cat^-1 and an onset potential of 1.32 V vs. RHE (current density = 10 mA/cm²). Their results are published in Chemical Communications (DOI: 10.1039/D0CC02132F).

Figure 1. Representative (a) transmission electron microscopy image and (b-f) elemental mappings of the synthesized catalyst.

The catalysts exhibited different catalytic activities dependent on their chemical compositions, which were tunable by varying the moles of the Ni, Co, and Mo precursors. Cyclic voltammograms of various NCM/G all showed markedly increased current density at potentials beyond 0.3 V vs. Ag/AgCl in urea-containing aqueous solutions (Figure 2a), marking their catalytic activity for urea oxidation. Among all the tested catalysts, NCM/G with Ni:Co:Mo = 80:10:10 achieved the largest current density at 0.6 V vs. Ag/AgCl, indicating its highest catalytic activity. Additionally, chronoamperometry demonstrated that increasing the Mo content was beneficial for maintaining catalyst stability, as the current density of NCM/G with the lowest amount of Mo (the black curve in Figure 2b) decayed the fastest. Combining the results of cyclic voltammetry and chronoamperometry, the authors deduced that the optimal molar ratio of Ni:Co:Mo was 80:10:10.

Figure 2. (a) Cyclic voltammograms (scan rate: 1 mV/s) and (b) chronoamperometry (potential: 0.5 V vs. Ag/AgCl) profiles of NCM/G with different Ni, Co, and Mo contents. Electrolyte: 1.0 M KOH + 0.33 M urea in water. The molar ratios of Ni:Co:Mo of NCM/G 90505, 811, and 71515 are 90:5:5. 80:10:10, and 70:15:15, respectively.

The optimization of the chemical composition demonstrated in this work can rationalize the development of high-performance, metallic electrocatalysts for urea oxidation.

For expanded understanding, please read:

Trimetallic NiCoMo/Graphene Multifunctional Electrocatalysts with Moderate Structural/Electronic Effects for Highly Efficient Alkaline Urea Oxidation Reaction

Wei Shi, Xiujuan Sun, Rui Ding, Danfeng Ying, Yongfa Huang, Yuxi Huang, Caini Tan, Ziyang Jia, and Enhui Liu

Chem. Commun., 2020, DOI: 10.1039/D0CC02132F

Tianyu Liu acknowledges Zacary Croft at Virginia Tech, U.S., for his careful proofreading of this post.

About the blogger:

Tianyu Liu obtained his Ph.D. (2017) in Chemistry from the University of California, Santa Cruz, in the United States. He is passionate about the communication of scientific endeavors to both the general public and other scientists with diverse research expertise to introduce cutting-edge research to broad audiences. He is a blog writer for Chem. Comm. and Chem. Sci. More information about him can be found at http://liutianyuresearch.weebly.com/.

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Teachable micromotors

27 May 2020

Micromotors, for the uninitiated aka me, are a specific type of colloidal structure that harvests energy from their environment and turns it into motion. In order for them to be truly effective for possible applications though, they must be able to communicate and coordinate with one another. If you want to make microbots, they can’t just move about all willy-nilly with no regard for each other. Recently, scientists have created a mixed system where one structure sheds silver ions that cause other micromotors to accelerate, an approach that mimics natural systems like bee colonies.

Researchers in China developed a system where photochemically powered micromotors can spontaneously “teach” catalytic micromotors to oscillate without any external influence. The teachers are Janus-type microparticles composed of either polymethylmethacrylate (PMMA) or silicon dioxide particles half coated with silver. Under irradiation with KCl and H₂O₂, the silver can interconvert between Ag(0) and Ag(1), causing the oscillatory motion of the entire particle. In contrast, the two non-oscillatory micromotors, either polystyrene spheres half coated with platinum (PS-PT) or gold-rhodium microrods (Au-Rh), catalytically decompose H₂O₂ to move autonomously in standard Brownian motion. When the two types of micromotors are mixed under UV light, the motion of the non-oscillatory materials changes from random to clearly oscillating (Figure 1). The intensity of the motion change depends on the proximity of the learner to the teacher, with learners closer to the teacher displaying more intense oscillations.

Figure 1. Change in movement of non-oscillating micromotors when exposed to oscillating “teacher” structures.

In fact, the Au-Rh rods will demonstrate more intense oscillations than the PMMA-Ag particles. The researchers propose a mechanism where the PMMA-Ag particles release silver ions as they oscillate, which then deposit onto the Au-Rh rods. The silver increases the catalytic activity of the rods and then, given the operating conditions, undergoes the same redox process that causes oscillation in the PMMA-Ag system.

Figure 2. Proposed mechanism of silver release and adsorption onto Au-Rh rods.

This hypothesized mechanism is supported by the development of oscillatory behavior by the Au-Rh rods in under reaction conditions where the PMMA-Ag particles are replaced by silver ions in solution. The silver on the rod surface isn’t merely adsorbed – it forms into small silver nanoparticles which can be seen via electron microscopy, making a new trimetallic structure. These nanoparticles change the trajectories of the rods, causing them to move in circles. While this system isn’t perfect, the student structures have imperfect memories and cannot teach one another, it provides a strategy for working with groups of micromotors to move towards coordinated motion and further applications.

To find out more, please read:

Non-oscillatory micromotors ‘‘learn’’ to oscillate on-the-fly from oscillating Ag micromotors

Chao Zhou, Qizhang Wang, Xianglong Lv and Wei Wang

Chem. Commun., 2020, Advance Article

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Potassium-Ion Batteries Welcome A New Electrode from Iron Compounds

28 Apr 2020

A research team led by Jiang Zhou and Shuquan Liang of Central South University, China, recently identified iron oxyhydroxide (β-FeOOH) as a K-ion battery electrode material. It is reportedly the first iron-oxide-based compound to serve in K-ion batteries. The results have been published in Chemical Communications (DOI: 10.1039/d0cc01009j).

K-ion batteries are a new type of rechargeable battery emerging after Li-ion batteries, the charge-storage functionality of which is associated with the intercalation and de-intercalation of K⁺. Due to the relative abundance of K⁺ to Li⁺, K-ion batteries are poised as a promising alternative to Li-ion batteries.

The researchers made the electrode by a hydrothermal reaction. Specifically, they dispersed Super P® (SP), an electrically conductive additive, into FeCl₃ aqueous solutions. The mixture was then heated at 150 °C for 10 h. The resultant powder (FeOOH-SP), comprised of uniformly mixed, crystalline β-FeOOH nanorods and Super P particles (Fig. 1), was directly used as an electrode material.

Figure 1. Transmission electron microscopy images of (a, b) FeOOH-SP and (c) FeOOH. (d) Elemental mappings of C, Fe, and O in FeOOH-SP.

The authors investigated the electrochemical properties of FeOOH-SP in K-ion batteries. At a current density of 100 mA/g, FeOOH-SP exhibited a stable specific capacity of ~200 mAh/g, approximately double and quadruple that of SP and FeOOH alone, respectively (Fig. 2a). The specific capacity of FeOOH-SP was maintained at ~100 mAh/g when the current density increased to 2000 mA/g (Fig. 2b), showing its fast-charging capability. Additionally, the authors observed that the crystalline β-FeOOH nanorods amorphized upon K⁺ intercalation after being discharged (Fig. 2c). Their crystallinity was only partially restored when being re-charged (Fig. 2d). The loss of crystallinity, however, did not undermine the charge-storage capacity of FeOOH-SP.

Figure 2. (a) Specific capacities of FeOOH-SP, SP, and FeOOH at different charge-discharge cycles. Current density: 100 mA/g. (b) Rate capability of FeOOH-SP. (c, d) Transmission electron microscopy images of (c) discharged and (d) charged FeOOH-SP. Red dashed boxes highlight crystalline regions. The electrolyte was a mixture of ethylene carbonate and diethyl carbonate containing 1 M potassium bis(fluorosulfonyl)imide.

Considering the low-cost of iron oxyhydroxide, FeOOH-SP could reduce the manufacturing cost of K-ion batteries and increase the affordability of electrochemical charge storage devices.

For expanded understanding, please read:

β-FeOOH: A New Anode for Potassium-Ion Batteries

Xiaodong Shi, Liping Qin, Guofu Xu, Shan Guo, Shuci Ma, Yunxiang Zhao, Jiang Zhou, and Shuquan Liang

Chem. Commun., 2020, 56, 3713-3716.

Tianyu Liu acknowledges Zacary Croft at Virginia Tech, U.S., for his careful proofreading of this post.

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Upgrading Methanol Using Zinc-Indium-Sulfide and Solar Light

11 Feb 2020

Based on the chemical formulae, can you figure out how to convert methanol (CH₃OH) into ethylene glycol (HOCH₂CH₂OH)? If you have constantly practiced your organic chemistry, you might have already found the answer: combining two methanol molecules and eliminating one hydrogen molecule (H₂). Indeed, this methanol-coupling reaction is a promising, low-cost chemical route to upgrade methanol to chemicals with more carbon atoms. The feasibility of this route, however, is low under mild conditions without catalysts to drive the reaction.

A group of scientists led by Shunji Xie and Ye Wang, both at Xiamen University, China, has developed an environmentally friendly catalyst, Zn₂In₂S₅, for room-temperature methanol coupling to produce ethylene glycol using solar light. This work has been published in Chemical Communications (DOI: 10.1039/c9cc09205f).

The synthesized Zn₂In₂S₅ catalyst is comprised of 1-3 layers of nanosheets. Through a hydrothermal reaction, the researchers first synthesized multi-layer Zn₂In₂S₅ stacks in an aqueous solution (Fig. 1a). Subsequent ultrasonication exfoliated the stacks into few-layer Zn₂In₂S₅ nanosheets that were confirmed by transmission electron microscopy (Fig. 1b). Zn₂In₂S₅ is a semiconductor and its valence band (VB) resides below the redox potential of ethylene glycol/methanol (Fig. 1c). The band alignment enables Zn₂In₂S₅ to catalyze the oxidation of methanol to ethylene glycol.

Figure 1. (a) A scheme of the synthesis procedures of few-layer Zn_mIn₂S_m+3 (m=1-3) nanosheets. (b) Transmission electron microscopy images of few-layer Zn₂In₂S₅ nanosheets. (c) Positions of the valence bands (VBs) and conduction bands (CBs) of different metal-sulfide semiconductors.

Zn₂In₂S₅ and its composite exhibited high catalytic activity. Upon irradiation with visible light and solar light (AM 1.5), photo-induced electrons and holes generated in Zn₂In₂S₅ (Fig. 2a). The electrons reduced protons in electrolytes and liberated hydrogen gas, while the holes moved to the Zn₂In₂S₅ surface and split the C—H bond of methanol, forming ·CH₂OH radicals. These radicals then dimerized into ethylene glycol. Through depositing a hydrogen evolution co-catalyst, cobalt monophosphide (CoP), and illuminating using AM 1.5 solar light, the authors observed that the CoP/Zn₂In₂S₅ catalyst achieved a rapid formation rate (18.9 mmol g_cat^-1 h^-1) and high selectivity (~90%) of ethylene glycol (Fig. 2b). The yield of ethylene glycol after 12 h of reaction was 4.5%.

Figure 2. (a) A scheme of the formation mechanisms of ethylene (from methanol) and 2,3-butanediol (from ethanol) on Zn₂In₂S₅. EG: ethylene glycol. 2,3-BD: 2,3-butanediol. (b) Formation rates and ethylene glycol selectivity of Zn₂In₂S₅ and CoP/Zn₂In₂S₅ under two illumination conditions. AM 1.5: air mass 1.5 solar irradiance. HCHO is a byproduct.

Zn₂In₂S₅ was demonstrated to effectively catalyze C—H cleavages and C—C couplings of different alcohols, e.g., from ethanol to 2,3-butanediol.

To find out more, please read:

C–H Activations of Methanol and Ethanol and C–C Couplings into Diols by Zinc–Indium–Sulfide Under Visible Light

Haikun Zhang, Shunji Xie, Jinyuan Hu, Xuejiao Wu, Qinghong Zhang, Jun Cheng, and Ye Wang

Chem. Commun., 2020, DOI: 10.1039/c9cc09205f

The blogger acknowledges Zac Croft at Virginia Tech, U.S., for his careful proofreading of this post.

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What Does the New Carbon Allotrope Look Like, Theoretically?

13 Dec 2019

A long-lasting dispute regarding the most stable structure of cyclo[18]carbon, a new carbon allotrope, has been settled. Cyclo[18]carbon is an all-carbon ring comprised of eighteen interconnected carbon atoms. It is proposed to have two possible structures: the cumulenic structure with only carbon-carbon double bonds (Figure 1a), and the polyynic structure having alternating carbon-carbon triple and single bonds (Figure 1b). Recent experiments have confirmed that the polyynic structure is the stable form, but theorists were still puzzled: Why can’t the various computational methods reach an agreement on the molecular structure of cyclo[18]carbon?

Figure 1. The (a) cumulenic and (b) polyynic structures of cyclo[18]carbon.

Anton J. Stasyuk and coworkers from the University of Girona, Spain, offered an answer in ChemComm (DOI: 10.1039/C9CC08399E). They found that the simulated structure strongly depended on the type of functionals used in density functional theory (DFT), which is a computational tool to derive energy-minimum molecular structures. The functionals used for DFT calculations are mathematical terms that can tune the simulation accuracy.

The authors discovered that the weight of the exact exchange term (HF% exchange) in the DFT functionals determined the most stable simulated structure of cyclo[18]carbon. The researchers compared 13 functionals with various percentages of HF% exchanges. They found that functionals with the HF% exchange higher than 50% predicted the appreciably different lengths of the neighboring bonds (quantified as the bond length alternation, the vertical axis of Figure 2), corresponding to the polyynic structure (Figure 2, red zone). This structure was recently observed experimentally. Functionals with lower HF% exchange either obtained the cumulenic structure (Figure 2, green zone) or the mixed cumulenic-polyynic structure (Figure 2, gray zone).

Figure 2. Variation in the HF% exchange of the B3LYP functional changed the predicted molecular structure of cyclo[18]carbon. BLA: Bond length alternation.

With the correct functionals identified, the authors revealed the electronic properties of cyclo[18]carbon. Calculations showed that cyclo[18]carbon was a strong electron acceptor, making it the smallest all-carbon electron acceptor reported so far.

To find out more, please read:

Cyclo[18]Carbon: Smallest All-Carbon Electron Acceptor

Anton J. Stasyuk, Olga A. Stasyuk, Miquel Solà, and Alexander Voityuk

Chem. Commun., 2019, DOI: 10.1039/C9CC08399E

Tianyu Liu acknowledges Zac Croft at Virginia Tech, U.S., for his careful proofreading of this post.

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Tuning Zeolite Catalysis with Organic Molecules

11 Dec 2019

Zeolites, a class of porous alumina-silicate materials, are industrially critical adsorbents and catalysts. Their highly robust nature and wide range of structural types (over 200!) make them suited to a range of applications. In particular, the general zeolite topology and pore size are selected to match and stabilize the intermediates of a chemical reaction. However, the tunability of zeolites is limited when compared to molecular catalysts, making them more like a solvent than, say, an enzyme. An active field of research is bridging the gap between the robust, scalable zeolites and highly controllable homogenous catalysts. Recent work identified organic residues maintained with the zeolite pores as key in the transformation of methanol to hydrocarbons. Previous fundamental studies demonstrated that a wide range of carbonyl and carbonyl derivative compounds promote the dehydration of methanol to dimethyl ether (DME).

Researchers at BP used methyl mono- and di-carboxylate esters to dehydrate methanol to DME at low temperatures. The mild reaction conditions allowed for high selectivity for DME while eliminating convoluting side reactions. They added either methyl formate or methyl n-hexanoate to a series of zeolite with pores ranging from narrow to wide. At a 5 mol% concentration relative to methanol they saw significant increases in DME production, particularly for the medium and wide pores. Systematic testing of carboxylate chain length found that increasing chain length increased turnovers occurred until methyl n-hexanoate, after which no further benefits were observed as the n-methyl hexanoate had already saturated the catalyst (Figure 1). All proved highly selective for converting methanol to DME with no observed hydrocarbon formation.

Figure 1. Production of DME on a medium-pore zeolite with methyl carboxylate esters of varying chain lengths.

The experimental results were coupled with theoretical work modeling the energetics of the adsorption of the ester onto the zeolite. The calculations showed an increase in adsorption energy with increased chain length, attributed to van der Waals interactions.

Figure 2. Transition state predicted by molecular modeling with methanol attacking the organic promoter adsorbed on the zeolite catalyst.

They also gave even higher energies to molecules with two carboxylate esters, like dimethyl adipate. In fact, the strongly binding molecules produced increased catalysis at loadings as low as 0.001% with respect to methanol. The promoters can be easily switched by changing the input, demonstrating the reversibility of binding at the active site. Additional molecular modeling was used to study possible transition states to develop a catalytic cycle. A proposed transition state involves a direct reaction between the methanol and the organic promotor, however specific evidence has yet to be seen. Additional work examining the role of the water present as a co-adsorbate and its impacts on transition states has yet to be done. Overall, the use of various organic molecules as promotors for the dehydration of methanol to DME on various zeolite catalysts was explored. This represents exciting fundamental study of industrially-relevant chemistry with significant room for future work.

To find out more, please read:

Getting zeolite catalysts to play your tune: methyl carboxylate esters as switchable promoters for methanol dehydration to DME

Benjamin J. Dennis-Smither, Zhiqiang Yang, Corneliu Buda, Xuebin Liu, Neil Sainty, Xingzhi Tan and Glenn J. Sunley

Chem. Commun., 2019, 55, 13804-13807.

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.

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How does LiNO3 Make Lithium–Sulfur Batteries Long-Lasting?

28 Nov 2019

Lithium–sulfur (Li–S) batteries are rechargeable batteries with elemental sulfur and metallic lithium as the cathode and anode, respectively. These batteries are promising electrochemical energy storage devices because their energy densities are three to five times higher than those of Li-ion batteries. Unfortunately, the practicality of Li–S batteries is hindered by their short lifetimes due to two processes that occur on the Li anode surface: the growth of Li dendrites and the irreversible polysulfide reduction. Adding LiNO₃ into battery electrolytes has proven to be useful to prolong battery lifetimes, but the underlying mechanism is uncertain.

In Chemical Communications (doi: 10.1039/c9cc06504k), Sawangphruk and coworkers from Vidyasirimedhi Institute of Science and Technology, Thailand have offered valuable insights to settle the dispute over the effects of LiNO₃. The researchers performed theoretical reactive molecular dynamics simulations and elucidated two roles of LiNO₃ in Li–S batteries.

The first discovery was that LiNO₃ promoted the formation of smooth, double-layered solid electrolyte interfaces (SEIs) on the Li surface. SEIs are thin layers composed of electrolyte-decomposition products, including Li-containing organic compounds and inorganic salts. By simulating the charge distribution near a Li metal surface, the authors mapped the Li-Li radial pair distribution profiles in three phases (Fig. 1a). The similarity between the profiles of the dense phase (the Li metal) and the nest phase evidenced the presence of an amorphous, Li-containing layer atop the Li metal surface. Beyond this amorphous layer was a liquid-like film with Li element distributed homogenously. This double-layered SEI altered the kinetics of Li deposition onto the Li surface upon charging, resulting in smooth and dense SEIs (Figs. 1b and c) that avoided Li dendrite formation.

Figure 1. (a) Li-Li radial pair distribution functions of the dense phase (Li metal), nest phase (the layer atop Li), and disperse phase (the outermost layer). (b and c) Top-view scanning electron microscopy images of the Li metal surface in (b) LiNO₃-free and (c) LiNO₃-containing electrolytes. Both electrolytes had lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) as a solute, and 1,3-dioxolane (DOL) and 1,2-dimethoxyethane (DME) as solvents.

Another effect of LiNO₃ was to capture polysulfide compounds. Through their simulations, the authors deduced the reaction pathways involving the electrolyte molecules, LiNO₃ or LiClO₄ additives, and lithium polysulfide compounds (Fig. 2a). The concentration of Li_xNO_y, the reduction products of LiNO₃ when contacted Li metal, in the LiNO₃-containing electrolyte was much higher than those in the additive-free and LiClO₄-containing electrolytes. First-principle calculations proved that the highly electro-negative N and O atoms in Li_xNO_y could capture lithium polysulfides via dipole-dipole interactions. This process reduced the likelihood of polysulfide reduction on Li that passivated anodes.

Figure 2. (a) A scheme of the reaction pathways involving the electrolyte, additive, and polysulfide molecules. (b) Product distributions in electrolytes without additives and with LiNO₃ or LiClO₄.

LiNO₃ elongates the lifetimes of Li–S batteries by forming smooth SEIs to impede Li dendrite formation, while maintaining the reactivity of Li anodes by capturing lithium polysulfides.

To find out more, please read:

Insight into the Effect of Additives Widely Used in Lithium–Sulfur Batteries

Salatan Duangdangchote, Atiweena Krittayavathananon, Nutthaphon Phattharasupakun, Nattanon Joraleechanchai, and Montree Sawangphruk

Chem. Commun., 2019, 55, 13951-13954

Tianyu Liu acknowledges John Elliott of Virginia Tech, the U.S., for his careful proofreading of this post.

About the blogger:

Tianyu Liu obtained his Ph.D. (2017) in Chemistry from the University of California, Santa Cruz, in the United States. He is passionate about the communication of scientific endeavors to both the general public and other scientists with diverse research expertise to introduce cutting-edge research to broad audiences. He is a blog writer for Chem. Commun. and Chem. Sci. More information about him can be found at http://liutianyuresearch.weebly.com/.

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Designing Syntheses with Machine Learning

22 Nov 2019

I don’t know if you’ve looked at the structure of pharmaceuticals recently, but most novel drugs are rather complicated. Identifying promising new targets is just the start for synthetic chemists; they then need to figure out how to use a series of reactions to take simple (and commercially available) molecules and transform them into a new drug. They also must predict all possible side reactions and products given a set of reaction conditions, particularly when a range of functional groups are involved. Historic approaches involved manual curation of reaction rules, limited by personal experience and the state of the accessed chemical literature. Newer approaches seek to create templates directly from data but are defined by available data sets and cannot reliably extrapolate. The emergence of machine learning offers the opportunity to move beyond traditional templating and atom mapping of reactants to products. It also offers to take full advantage of novel technologies and address problems with dataset bias and ineffective modeling systems.

In a collaboration between academics in the UK and industrial scientists in the US, researchers used Molecular Transformer, an attention-based machine translation model, to perform both reaction prediction and retrosynthesis analysis after training on a publicly available dataset. Instead of atom mapping, which moves atoms from the reactants to the products, Molecular Transformer (MT) relies on SMILES text strings, which represent structures in a line format. A unique aspect of this work is the validation and training performed using proprietary data of drug targets from Pfizer. They used three datasets: the first a literature standard from the US Patent and Trade Office (USPTO), the second from internal medicinal chemistry projects in Pfizer, and the final a diverse range of 50,000 reactions from US patents (USPTO-R). Building on previous research from the authors, they trained the MT on both the Pfizer data and the initial USPTO data sets. They found that the Pfizer data provided the most accurate product predictions and that the MT could also return a confidence rating to determine the probability the prediction is correct.

Figure 1. Sample syntheses predicted by Molecular Transformer for various bioactive molecules of interest.

While synthesis predictions can easily be checked, it’s harder to confirm accuracy with retrosynthesis since there is not a single correct answer. The researchers used the broad USPTO-R to train MT, which consistently outperformed both a benchmark template-based program and another literature machine learning method also trained on USPTO-R. When tested on the Pfizer dataset, the MT performed best with 31.5% accuracy despite the datasets coming from different regions of chemical space (which increased to 91% when MT was trained on Pfizer data). Figure 1 shows several predicted routes for the synthesis of bioactive molecules as predicted by MT, which generally agree with established syntheses. These data suggest the highly generalizable nature of MT as a tool for developing novel pharmaceutically interesting molecules.

To find out more, please read:

Molecular Transformer unifies reaction prediction and retrosynthesis across pharma chemical space

Alpha A. Lee, Qingyi Yang, Vishnu Sresht, Peter Bolgar, Xinjun Hou, Jacquelyn L. Klug-McLeod and Christopher R. Butler

Chem. Commun., 2019, 55, 12152-12155.

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Strengthening Li+-Coordination Decelerates Li-Dendrite Growth in Li-Metal Batteries

14 Nov 2019

Lithium-metal batteries are a family of rechargeable batteries with higher charge-storage capacities than those of lithium-ion batteries. The boosted charge-storage performance of lithium-metal batteries is rooted in its anode material – Li metal, as it possesses an ultrahigh theoretical capacity (3860 mAh/g). However, the growth of dendrites on Li surfaces during charging could short-circuit batteries, cause combustion, and trigger explosions.

A research group led by Feng Li at the Institute of Metal Research, Chinese Academy of Sciences, recently devised a strategy to suppress the notorious Li dendrite growth in lithium-metal batteries. By tuning the composition of the electrolytes, the authors strengthened the coordination between Li⁺ and electrolyte solvents, which slowed the growth of Li dendrites. This work has been published in Chemical Communications (doi: 10.1039/C9CC07092C).

The researchers introduced an electrolyte additive, tetraethylene glycol dimethyl ether (TEGDME), as a coordination ligand to Li⁺. Compared to other components in the electrolyte, i.e., 1,2-dimethoxyethane (DME) and 1,3-dioxolane (DOL), TEGDME contains more oxygen atoms that can form multiple, robust coordination bonds with Li⁺. Specifically, density functional theory calculations showed that the binding energy between Li⁺ and electrolyte molecules increased by 0.31 eV after introducing TEGDME, reaching an absolute value of 4.93 eV. The enhanced binding force made the separation of Li⁺ from TEGDME (a prerequisite for Li-dendrite growth) energetically consuming and kinetically sluggish (Figure 1). These characteristics could decelerate Li-dendrite formation and elongate battery lifetimes.

Figure 1. Lithium-dendrite growth in different electrolytes: (a) weak coordination with Li+ promotes fast dendrite growth while (b) strong coordination with Li+ decelerates dendrite formation.

To confirm the above idea, the authors assembled lithium batteries with TEGDME+DME+DOL or DME+DOL electrolytes. Cycling stability tests demonstrated that the battery with the TEGDME-added electrolyte survived 60 charge-discharge cycles at a current density of 1C, whereas the capacity of the battery without TEGDME rapidly decayed beyond 30 cycles under identical testing conditions (Figure 2a). Scanning electron microscopy images revealed that the number of rod-shaped Li dendrites on the anode in the TEGDME-added electrolyte (Figure 2c) was less than that in the TEGDME-free electrolyte (Figure 2b), further confirming that the enhanced cycling stability resulted from the Li-dendrite suppressing effect of TEGDME.

Figure 2. (a) Cycling stability performance of lithium-metal batteries with two different electrolytes. The cathode material in both batteries was lithium iron phosphate (LFP). (b and c) SEM images of the Li anode surface after charging in (b) DME+DOL and (c) DME+DOL+TEGDME electrolytes.

This work highlights the importance of tailoring the electrolyte composition for preserving the stability and safety of lithium-metal batteries.

To find out more, please read:

Suppressing Lithium Dendrite Formation by Slowing Its Desolvation Kinetics

Huicong Yang, Lichang Yin, Huifa Shi, Kuang He, Hui-Ming Cheng, and Feng Li

Chem. Commun., 2019, doi: 10.1039/C9CC07092C

Tianyu Liu acknowledges Xiaozhou Yang of Virginia Tech, the U.S., for his careful proofreading of this post.

About the blogger:

Tianyu Liu obtained his Ph.D. (2017) in Chemistry from the University of California, Santa Cruz, in the United States. He is passionate about the communication of scientific endeavors to both the general public and other scientists with diverse research expertise as a way to introduce cutting-edge research to broad audiences. He is a blog writer for Chem. Commun. and Chem. Sci. More information about him can be found at http://liutianyuresearch.weebly.com/.

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