Microscopic Control of Nonequilibrium Systems: When Electrochemistry Meets Nanotechnology
- Chong Liu*Chong Liu*Email: [email protected]Department of Chemistry and Biochemistry, California Nanoscience Institute, University of California Los Angeles, Los Angeles, California 90095, United StatesMore by Chong Liu
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Over the past decades, electrochemistry has transformed our society. Batteries loaded with nanomaterials now allow us to drive cars without the humming of an internal combustion engine; chemical synthesis is being electrified with the benefits from nanomaterial-based catalysts with greener feedstocks and energy sources; and miniaturized electrochemical sensors sit in the center of gadgets that monitor the sugar level in your body. With such remarkable achievements from electrochemistry, one might ask the following: is there anything else that electrochemistry can help with? For researchers in the field of nanoscience and nanotechnology, one might ask more specifically this question: are there any other synergies by integrating electrochemistry and nanotechnology? This Viewpoint is meant to offer some pondering in this context from a junior faculty who is excited about both electrochemistry and nanoscience.
Electrochemistry, by its own very nature, offers a method of spatiotemporally controlling the concentration profiles of chemical species and hence their free energies μ and entropies S in solution (Figure 1). Electrochemical charge transfer at the material–liquid interface transduces electronic signal into concentration gradients away from the electrode’s surface. While such a mass transport limitation is often less desirable as it strains performances in some devices, fundamentally those electrochemically created concentration gradients lead to nonequilibrium chemical systems that will be temporally modulated by electrochemical signals. Under a given electrode geometry and electrochemical boundary conditions, well-defined differential equations that include reaction kinetics and mass transport allow quantitative control of the established nonequilibrium systems. (1,2) Steady-state or kinetic systems near equilibrium can be maintained, and complex time-dependent dissipative systems can be generated, too. Those features in electrochemistry contribute to the fact that the classic oscillatory Belousov–Zhabotinsky (BZ) reaction was first quantitatively monitored and modulated by electrochemistry. (3)
The gradient-generating nature of electrochemistry allows researchers to create and control nonequilibrium systems in chemistry and biology. We live in a world away from equilibrium, and spatiotemporal heterogeneity is ubiquitously critical to biological processes. Here, we just list a few examples: the heterogeneous local microenvironment of soil and root nodules dictates the microbiota composition in agriculture; (4) the temporally dynamic O2 and nutrient gradients radially and axially in the intestine offer the metabolic diversity of gut microbiomes; (5) and it is the interdependence among microbes in different microenvironments that leads to the difficulty of enriching and culturing the predominant majority of natural microorganisms. (6) By creating concentration gradients electrochemically, a digitally controlled electrochemical device has the potential of establishing and spatiotemporally modulating extracellular microenvironments at will. Such devices can mimic the natural microenvironment and offer a customizable perturbation for fundamental studies and applications noted above. Also, the spatiotemporal control of biochemical processes inspires researchers to design new chemical transformation pathways. For example, it is proposed that the O2 gradient within micrometer-sized aerobic diazotrophic bacteria enables microbial N2 fixation in air with O2-sensitive nitrogenase and O2 as the terminal electron acceptor; (7) can we establish new chemical transformations with similar seemingly incompatible steps? Since it is shown that local concentrations of reaction intermediates are paramount to the reaction rate in cascade tandem reactions, (8) can we leverage the local concentrations generated electrochemically and design faster cascades? Electrochemically generated chemical gradients will lead to the successful demonstrations of such new reaction cascades that we may never see in homogeneous solutions.
So, what can nanotechnology and nanoscience help with under the forgoing argument for electrochemically controlled nonequilibrium systems? Fundamentally, electrochemistry’s capability of controlling concentration gradients is determined and limited by the electrodes’ dimension and boundary conditions. It is challenging if not impossible to control a gradient of nanometer-scale resolution with a micrometer-sized electrode. The diffusion at nanoscale shortens the time to establish the desirable gradients and hence increases temporal resolution. As demonstrated in the porous-electrode model developed by Newman in the 1960s, (9) nanomaterial electrodes create exponential gradients for chemical species, which is different from the simple linear gradients from planar electrodes. Finally, the interfacial engineering at the nanoscale will yield selective electrochemical reactions that precisely modulate the gradients of targeted species but do not interfere with others, which is particularly important for biological applications when a myriad of chemicals are in the solution. Therefore, the introduction of nanomaterials and nanotechnology will allow electrochemistry to modulate gradients in chemistry and biology with higher spatiotemporal resolutions, more varied gradient shapes, and more selective control for the targeted species. Because it is the microscopic spatiotemporal gradients that govern the examples noted above, the benefits generated by nanotechnology are mission-critical for the control of those nonequilibrium scenarios.
Excited by such a prospect, the author’s research group has made a few advances synergistically combining electrochemistry and nanotechnology (see Figure 1). With the use of a nanowire array electrode, we created a CH4-to-CH3OH catalytic cycle of seemingly incompatible steps in which ambient CH4 activation by O2-sensitive RhII metalloradicals is followed by O2-driven hydroxylation that yields CH3OH. (10,11) We also mimicked the O2 gradient in root nodules and housed O2-sensitive symbiotic rhizobia for electricity-driven N2 fixation in air. (12) Finally, machine-learning-based algorithms have been developed to model the yielded concentration gradients from nanowire arrays. (13) The author contends that those demonstrated works will introduce more examples of nanoscopically controlled nonequilibrium systems in chemistry and biology. Taking such a road less traveled will yield a different yet beautiful scenery.
Figure 1
Figure 1. Combining electrochemistry and nanotechnology will lead to spatiotemporally controlled nonequilibrium systems at the nanoscale.
Author Information
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- Chong Liu, Department of Chemistry and Biochemistry, California Nanoscience Institute, University of California Los Angeles, Los Angeles, California 90095, United States,
https://orcid.org/0000-0001-5546-3852,
Acknowledgments
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C.L. thanks Prof. Long Luo for constructive inputs. C.L. acknowledges the financial support of the National Institute of Health (R35GM138241).
References
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This article references 13 other publications.
- 1Bard, A. J.; Faulkner, L. R. Electrochemical Methods: Fundamentals and Applications, 2nd ed.; John Wiley & Sons, Inc.: New York, 2001.Google ScholarThere is no corresponding record for this reference.
- 2Newman, J.; Thomas-Alyea, K. E. Electrochemical Systems, 3rd ed.; Wiley-Interscienc: Hoboken, NJ, 2004.Google ScholarThere is no corresponding record for this reference.
- 3Epstein, I. R.; Pojman, J. A. An introduction to Nonlinear Chemical Dynamics: Oscillations, Waves, Patterns, and Chaos; Oxford University Press; New York, 1998.Google ScholarThere is no corresponding record for this reference.
- 4Wilpiszeski, R. L.; Aufrecht, J. A.; Retterer, S. T.; Sullivan, M. B.; Graham, D. E.; Pierce, E. M.; Zablocki, O. D.; Palumbo, A. V.; Elias, D. A. Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales. Appl. Environ. Microbiol. 2019, 85, e00324– 00319, DOI: 10.1128/AEM.00324-19Google Scholar4https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhs1OksL7I&md5=b5f2c015aada50904976f93c8fd66cadSoil aggregate microbial communities: towards understanding microbiome interactions at biologically relevant scalesWilpiszeski, Regina L.; Aufrecht, Jayde A.; Retterer, Scott T.; Sullivan, Matthew B.; Graham, David E.; Pierce, Eric M.; Zablocki, Olivier D.; Palumbo, Anthony V.; Elias, Dwayne A.Applied and Environmental Microbiology (2019), 85 (14), e00324-19CODEN: AEMIDF; ISSN:1098-5336. (American Society for Microbiology)Soils contain a tangle of minerals, water, nutrients, gases, plant roots, decaying org. matter, and microorganisms which work together to cycle nutrients and support terrestrial plant growth. Most soil microorganisms live in periodically interconnected communities closely assocd. with soil aggregates, i.e., small (<2 mm), strongly bound clusters of minerals and org. carbon that persist through mech. disruptions and wetting events. Their spatial structure is important for biogeochem. cycling, and we cannot reliably predict soil biol. activities and variability by studying bulk soils alone. To fully understand the biogeochem. processes at work in soils, it is necessary to understand the micrometer-scale interactions that occur between soil particles and their microbial inhabitants. Here, we review the current state of knowledge regarding soil aggregate microbial communities and identify areas of opportunity to study soil ecosystems at a scale relevant to individual cells. We present a framework for understanding aggregate communities as "microbial villages" that are periodically connected through wetting events, allowing for the transfer of genetic material, metabolites, and viruses. We describe both top-down (whole community) and bottom-up (reductionist) strategies for studying these communities. Understanding this requires combining "model system" approaches (e.g., developing mock community artificial aggregates), field observations of natural communities, and broader study of community interactions to include understudied community members, like viruses. Initial studies suggest that aggregate-based approaches are a crit. next step for developing a predictive understanding of how geochem. and community interactions govern microbial community structure and nutrient cycling in soil.
- 5Albenberg, L. Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology 2014, 147, 1055– 1063, DOI: 10.1053/j.gastro.2014.07.020Google Scholar5https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2cbkt1yhtw%253D%253D&md5=d6e40de86e1b9376f1865eae3fd1e53bCorrelation between intraluminal oxygen gradient and radial partitioning of intestinal microbiotaAlbenberg Lindsey; Judge Colleen P; Baldassano Robert N; Esipova Tatiana V; Bittinger Kyle; Laughlin Alice; Grunberg Stephanie; Bushman Frederic D; Chen Jun; Li Hongzhe; Lewis James D; Thom Stephen R; Vinogradov Sergei A; Wu Gary DGastroenterology (2014), 147 (5), 1055-63.e8 ISSN:.BACKGROUND & AIMS: The gut microbiota is a complex and densely populated community in a dynamic environment determined by host physiology. We investigated how intestinal oxygen levels affect the composition of the fecal and mucosally adherent microbiota. METHODS: We used the phosphorescence quenching method and a specially designed intraluminal oxygen probe to dynamically quantify gut luminal oxygen levels in mice. 16S ribosomal RNA gene sequencing was used to characterize the microbiota in intestines of mice exposed to hyperbaric oxygen, human rectal biopsy and mucosal swab samples, and paired human stool samples. RESULTS: Average Po2 values in the lumen of the cecum were extremely low (<1 mm Hg). In altering oxygenation of mouse intestines, we observed that oxygen diffused from intestinal tissue and established a radial gradient that extended from the tissue interface into the lumen. Increasing tissue oxygenation with hyperbaric oxygen altered the composition of the gut microbiota in mice. In human beings, 16S ribosomal RNA gene analyses showed an increased proportion of oxygen-tolerant organisms of the Proteobacteria and Actinobacteria phyla associated with rectal mucosa, compared with feces. A consortium of asaccharolytic bacteria of the Firmicute and Bacteroidetes phyla, which primarily metabolize peptones and amino acids, was associated primarily with mucus. This could be owing to the presence of proteinaceous substrates provided by mucus and the shedding of the intestinal epithelium. CONCLUSIONS: In an analysis of intestinal microbiota of mice and human beings, we observed a radial gradient of microbes linked to the distribution of oxygen and nutrients provided by host tissue.
- 6Lewis, W. H.; Tahon, G.; Geesink, P.; Sousa, D. Z.; Ettema, T. J. G. Innovations to culturing the uncultured microbial majority. Nat. Rev. Microbiol. 2021, 19, 225– 240, DOI: 10.1038/s41579-020-00458-8Google Scholar6https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitFGqtb3N&md5=1fe9faa73c4f49c58cc809ad44fa7a47Innovations to culturing the uncultured microbial majorityLewis, William H.; Tahon, Guillaume; Geesink, Patricia; Sousa, Diana Z.; Ettema, Thijs J. G.Nature Reviews Microbiology (2021), 19 (4), 225-240CODEN: NRMACK; ISSN:1740-1526. (Nature Research)Abstr.: Despite the surge of microbial genome data, exptl. testing is important to confirm inferences about the cell biol., ecol. roles and evolution of microorganisms. As the majority of archaeal and bacterial diversity remains uncultured and poorly characterized, culturing is a priority. The growing interest in and need for efficient cultivation strategies has led to many rapid methodol. and technol. advances. In this Review, we discuss common barriers that can hamper the isolation and culturing of novel microorganisms and review emerging, innovative methods for targeted or high-throughput cultivation. We also highlight recent examples of successful cultivation of novel archaea and bacteria, and suggest key microorganisms for future cultivation attempts.
- 7Bergersen, F. J.; Turner, G. L.; Gibson, A. H.; Dudman, W. F. Nitrogenase activity and respiration of cultures of Rhizobium spp. with special reference to concentration of dissolved oxygen. Biochim. Biophys. Acta, Gen. Subj. 1976, 444, 164– 174, DOI: 10.1016/0304-4165(76)90233-6Google Scholar7https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaE28XltF2gu7k%253D&md5=d4731e0d87f54cb2b01a7ff653e53429Nitrogenase activity and respiration of cultures of Rhizobium spp. with special reference to concentration of dissolved oxygenBergersen, Fraser J.; Turner, Graham L.; Gibson, Alan H.; Dudman, William F.Biochimica et Biophysica Acta, General Subjects (1976), 444 (1), 164-74CODEN: BBGSB3; ISSN:0304-4165.Studies of nitrogenase in cultures of the cowpea rhizobia (Rhizobium species) strains 32H1 and CB756 are reported. Preliminary expts. established that, even when agar cultures were grown in air, suspensions of bacteria prepd. anaerobically from them were most active at low concns. of free dissolved O2. Consequently, assays for activity used low concns. of O2, stabilized by adding the nodule pigment leghemoglobin. In continuous, glutamine-limited cultures of 32H1, nitrogenase activity appeared only when the concn. of dissolved O2 in the cultures approached 1 μM. Lowering the glutamine concn. in the medium supplied to the culture from 2 to 1 mM halved the cell yield and nitrogenase activity was also diminished. Omitting succinate from the medium caused the concn. of dissolved O2 to rise and nitrogenase activity was lost. Upon restoration of the succinate supply, the O2 concn. immediately fell and nitrogenase was restored. The activity doubled in ∼8 hr, whereas the doubling time of this culture was 14 hr. Sonic exts. of 32H1 cells from continuous cultures with active nitrogenase contained components reacting with antiserum against nitrogenase Mo-Fe protein from soybean bacteroids. Continuous cultures grown at higher O2 concn., with only a trace of active nitrogenase, contained less of these antigens and they were not detected in highly aerobic cultures. Nitrogenase activity of a continuous culture was repressed by NH4+; the apparent half-life was ∼90 min. Cells of 32H1 from a continuous culture growing at between 30 and 100 μM dissolved O2 possessed a protective mechanism which permitted respiration to increase following exposure to a rapid increase in O2 concn. from low levels (O2 shock). This effect disappeared as the O2 concn. for growth was reduced towards 1 μM.
- 8Wheeldon, I.; Minteer, S. D.; Banta, S.; Barton, S. C.; Atanassov, P.; Sigman, M. Substrate channelling as an approach to cascade reactions. Nat. Chem. 2016, 8, 299– 309, DOI: 10.1038/nchem.2459Google Scholar8https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xks1Cru7Y%253D&md5=5056edbd76a5aa2266906be9e23c579bSubstrate channelling as an approach to cascade reactionsWheeldon, Ian; Minteer, Shelley D.; Banta, Scott; Barton, Scott Calabrese; Atanassov, Plamen; Sigman, MatthewNature Chemistry (2016), 8 (4), 299-309CODEN: NCAHBB; ISSN:1755-4330. (Nature Publishing Group)A review. Millions of years of evolution have produced biol. systems capable of efficient one-pot multi-step catalysis. The underlying mechanisms that facilitate these reaction processes are increasingly providing inspiration in synthetic chem. Substrate channeling, where intermediates between enzymic steps are not in equil. with the bulk soln., enables increased efficiencies and yields in reaction and diffusion processes. Here, we review different mechanisms of substrate channeling found in nature and provide an overview of the anal. methods used to quantify these effects. The incorporation of substrate channeling into synthetic cascades is a rapidly developing concept, and recent examples of the fabrication of cascades with controlled diffusion and flux of intermediates are presented.
- 9Newman, J. S.; Tobias, C. W. Theoretical Analysis of Current Distribution in Porous Electrodes. J. Electrochem. Soc. 1962, 109, 1183– 1191, DOI: 10.1149/1.2425269Google Scholar9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaF3sXht12qsw%253D%253D&md5=232a8e9cd6d89666940cf3ae8366ed73Theoretical analysis of current distribution in porous electrodesNewman, John S.; Tobias, Charles W.Journal of the Electrochemical Society (1962), 109 (), 1183-91CODEN: JESOAN; ISSN:0013-4651.General equations describing the behavior of porous electrodes were developed. These equations were used to det. the initial and the steady-state conditions in one-dimensional porous electrodes of uniform geometry and polarization parameters. In particular, it is shown that the current and reaction distributions in the depth of the electrode are strongly influenced by the type of activation polarization and by mass transport of the reacting ionic species, in addn. to the effective conds. of the two phases. A linear approxn. to a Tafel curve leads to an inadequate description of actual behavior when the reaction is distributed nonuniformly in the depth of the electrode.
- 10Natinsky, B. S.; Lu, S.; Copeland, E. D.; Quintana, J. C.; Liu, C. Solution Catalytic Cycle of Incompatible Steps for Ambient Air Oxidation of Methane to Methanol. ACS Cent. Sci. 2019, 5, 1584– 1590, DOI: 10.1021/acscentsci.9b00625Google Scholar10https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhsVOrtr3I&md5=13dda8a7ed154f03a6d26bab45d1e1d0Solution Catalytic Cycle of Incompatible Steps for Ambient Air Oxidation of Methane to MethanolNatinsky, Benjamin S.; Lu, Shengtao; Copeland, Emma D.; Quintana, Jason C.; Liu, ChongACS Central Science (2019), 5 (9), 1584-1590CODEN: ACSCII; ISSN:2374-7951. (American Chemical Society)Direct chem. synthesis from methane and air under ambient conditions is attractive yet challenging. Low-valent organometallic compds. are known to activate methane, but their electron-rich nature seems incompatible with O2 and prevents catalytic air oxidn. We report selective oxidn. of methane to methanol with an O2-sensitive metalloradical as the catalyst and air as the oxidant at room temp. and ambient pressure. The incompatibility between C-H activation and O2 oxidn. is reconciled by electrochem. and nanomaterials, with which a concn. gradient of O2 within the nanowire array spatially segregated incompatible steps in the catalytic cycle. An unexpected 220 000-fold increase of the apparent reaction rate consts. within the nanowire array leads to a turnover no. up to 52 000 within 24 h. The synergy between nanomaterials and organometallic chem. warrants a new catalytic route for CH4 functionalization.
- 11Natinsky, B. S.; Jolly, B. J.; Dumas, D. M.; Liu, C. Efficacy analysis of compartmentalization for ambient CH4 activation mediated by a RhII metalloradical in a nanowire array electrode. Chem. Sci. 2021, 12, 1818– 1825, DOI: 10.1039/D0SC05700BGoogle Scholar11https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXisFWrt7nK&md5=32d84aebfe327b8d13ae912582329ceeEfficacy analysis of compartmentalization for ambient CH4 activation mediated by a RhII metalloradical in a nanowire array electrodeNatinsky, Benjamin S.; Jolly, Brandon J.; Dumas, David M.; Liu, ChongChemical Science (2021), 12 (5), 1818-1825CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)Compartmentalization is a viable approach for ensuring the turnover of a soln. cascade reaction with ephemeral intermediates, which may otherwise deactivate in the bulk soln. In biochem. or enzyme-relevant cascade reactions, extensive models have been constructed to quant. analyze the efficacy of compartmentalization. Nonetheless, the application of compartmentalization and its quant. anal. in non-biochem. reactions is seldom performed, leaving much uncertainty about whether compartmentalization remains effective for non-biochem. reactions, such as organometallic, cascade reactions. Here, we report our exemplary efficacy anal. of compartmentalization in our previously reported cascade reaction for ambient CH4-to-CH3OH conversion, mediated by an O2-deactivated RhII metalloradical with O2 as the terminal oxidant in a Si nanowire array electrode. We exptl. identified and quantified the key reaction intermediates, including the RhII metalloradical and reactive oxygen species (ROS) from O2. Based on such findings, we exptl. detd. that the nanowire array enables about 81% of the generated ephemeral intermediate RhII metalloradical in air, to be utilized towards CH3OH formation, which is 0% in a homogeneous soln. Such an exptl. detd. value was satisfactorily consistent with the results from our semi-quant. kinetic model. The consistency suggests that the reported CH4-to-CH3OH conversion surprisingly possesses minimal unforeseen side reactions, and is favorably efficient as a compartmentalized cascade reaction. Our quant. evaluation of the reaction efficacy offers design insights and caveats into application of nanomaterials to achieve spatially controlled organometallic cascade reactions.
- 12Lu, S.; Guan, X.; Liu, C. Electricity-Powered Artificial Root Nodule. Nat. Commun. 2020, 11, 1505, DOI: 10.1038/s41467-020-15314-9Google Scholar12https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXlvFCqu7k%253D&md5=45cec18c23215af32d310bd978ba5792Electricity-powered artificial root noduleLu, Shengtao; Guan, Xun; Liu, ChongNature Communications (2020), 11 (1), 1505CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)Abstr.: Root nodules are agricultural-important symbiotic plant-microbe composites in which microorganisms receive energy from plants and reduce dinitrogen (N2) into fertilizers. Mimicking root nodules using artificial devices can enable renewable energy-driven fertilizer prodn. This task is challenging due to the necessity of a microscopic dioxygen (O2) concn. gradient, which reconciles anaerobic N2 fixation with O2-rich atm. Here we report our designed electricity-powered biol.|inorg. hybrid system that possesses the function of root nodules. We construct silicon-based microwire array electrodes and replicate the O2 gradient of root nodules in the array. The wire array compatibly accommodates N2-fixing symbiotic bacteria, which receive energy and reducing equiv. from inorg. catalysts on microwires, and fix N2 in the air into biomass and free ammonia. A N2 redn. rate up to 6.5 mg N2 per g dry biomass per h is obsd. in the device, about two orders of magnitude higher than the natural counterparts.
- 13Hoar, B. B.; Lu, S.; Liu, C. Machine-Learning-Enabled Exploration of Morphology Influence on Wire-Array Electrodes for Electrochemical Nitrogen Fixation. J. Phys. Chem. Lett. 2020, 11, 4625– 4630, DOI: 10.1021/acs.jpclett.0c01128Google Scholar13https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhtVaqsrvN&md5=043d93ee292a194439d2dcd46968b500Machine-Learning-Enabled Exploration of Morphology Influence on Wire-Array Electrodes for Electrochemical Nitrogen FixationHoar, Benjamin B.; Lu, Shengtao; Liu, ChongJournal of Physical Chemistry Letters (2020), 11 (12), 4625-4630CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)Neural networks, trained on data generated by a microkinetic model and finite-element simulations, expand explorable parameter space by significantly accelerating the predictions of electrocatalytic performance. In addn. to modeling electrode reactivity, the authors use micro/nanowire arrays as a well-defined, easily tuned, and exptl. relevant exemplary morphol. for electrochem. N fixation. This model system provides the data necessary for training neural networks which are subsequently exploited for electrocatalytic material morphol. optimizations and explorations into the influence of geometry on N fixation electrodes, feats untenable without large-scale simulations, on both a global and a local basis.
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Figure 1
Figure 1. Combining electrochemistry and nanotechnology will lead to spatiotemporally controlled nonequilibrium systems at the nanoscale.
References
ARTICLE SECTIONSThis article references 13 other publications.
- 1Bard, A. J.; Faulkner, L. R. Electrochemical Methods: Fundamentals and Applications, 2nd ed.; John Wiley & Sons, Inc.: New York, 2001.Google ScholarThere is no corresponding record for this reference.
- 2Newman, J.; Thomas-Alyea, K. E. Electrochemical Systems, 3rd ed.; Wiley-Interscienc: Hoboken, NJ, 2004.Google ScholarThere is no corresponding record for this reference.
- 3Epstein, I. R.; Pojman, J. A. An introduction to Nonlinear Chemical Dynamics: Oscillations, Waves, Patterns, and Chaos; Oxford University Press; New York, 1998.Google ScholarThere is no corresponding record for this reference.
- 4Wilpiszeski, R. L.; Aufrecht, J. A.; Retterer, S. T.; Sullivan, M. B.; Graham, D. E.; Pierce, E. M.; Zablocki, O. D.; Palumbo, A. V.; Elias, D. A. Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales. Appl. Environ. Microbiol. 2019, 85, e00324– 00319, DOI: 10.1128/AEM.00324-19Google Scholar4https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhs1OksL7I&md5=b5f2c015aada50904976f93c8fd66cadSoil aggregate microbial communities: towards understanding microbiome interactions at biologically relevant scalesWilpiszeski, Regina L.; Aufrecht, Jayde A.; Retterer, Scott T.; Sullivan, Matthew B.; Graham, David E.; Pierce, Eric M.; Zablocki, Olivier D.; Palumbo, Anthony V.; Elias, Dwayne A.Applied and Environmental Microbiology (2019), 85 (14), e00324-19CODEN: AEMIDF; ISSN:1098-5336. (American Society for Microbiology)Soils contain a tangle of minerals, water, nutrients, gases, plant roots, decaying org. matter, and microorganisms which work together to cycle nutrients and support terrestrial plant growth. Most soil microorganisms live in periodically interconnected communities closely assocd. with soil aggregates, i.e., small (<2 mm), strongly bound clusters of minerals and org. carbon that persist through mech. disruptions and wetting events. Their spatial structure is important for biogeochem. cycling, and we cannot reliably predict soil biol. activities and variability by studying bulk soils alone. To fully understand the biogeochem. processes at work in soils, it is necessary to understand the micrometer-scale interactions that occur between soil particles and their microbial inhabitants. Here, we review the current state of knowledge regarding soil aggregate microbial communities and identify areas of opportunity to study soil ecosystems at a scale relevant to individual cells. We present a framework for understanding aggregate communities as "microbial villages" that are periodically connected through wetting events, allowing for the transfer of genetic material, metabolites, and viruses. We describe both top-down (whole community) and bottom-up (reductionist) strategies for studying these communities. Understanding this requires combining "model system" approaches (e.g., developing mock community artificial aggregates), field observations of natural communities, and broader study of community interactions to include understudied community members, like viruses. Initial studies suggest that aggregate-based approaches are a crit. next step for developing a predictive understanding of how geochem. and community interactions govern microbial community structure and nutrient cycling in soil.
- 5Albenberg, L. Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology 2014, 147, 1055– 1063, DOI: 10.1053/j.gastro.2014.07.020Google Scholar5https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2cbkt1yhtw%253D%253D&md5=d6e40de86e1b9376f1865eae3fd1e53bCorrelation between intraluminal oxygen gradient and radial partitioning of intestinal microbiotaAlbenberg Lindsey; Judge Colleen P; Baldassano Robert N; Esipova Tatiana V; Bittinger Kyle; Laughlin Alice; Grunberg Stephanie; Bushman Frederic D; Chen Jun; Li Hongzhe; Lewis James D; Thom Stephen R; Vinogradov Sergei A; Wu Gary DGastroenterology (2014), 147 (5), 1055-63.e8 ISSN:.BACKGROUND & AIMS: The gut microbiota is a complex and densely populated community in a dynamic environment determined by host physiology. We investigated how intestinal oxygen levels affect the composition of the fecal and mucosally adherent microbiota. METHODS: We used the phosphorescence quenching method and a specially designed intraluminal oxygen probe to dynamically quantify gut luminal oxygen levels in mice. 16S ribosomal RNA gene sequencing was used to characterize the microbiota in intestines of mice exposed to hyperbaric oxygen, human rectal biopsy and mucosal swab samples, and paired human stool samples. RESULTS: Average Po2 values in the lumen of the cecum were extremely low (<1 mm Hg). In altering oxygenation of mouse intestines, we observed that oxygen diffused from intestinal tissue and established a radial gradient that extended from the tissue interface into the lumen. Increasing tissue oxygenation with hyperbaric oxygen altered the composition of the gut microbiota in mice. In human beings, 16S ribosomal RNA gene analyses showed an increased proportion of oxygen-tolerant organisms of the Proteobacteria and Actinobacteria phyla associated with rectal mucosa, compared with feces. A consortium of asaccharolytic bacteria of the Firmicute and Bacteroidetes phyla, which primarily metabolize peptones and amino acids, was associated primarily with mucus. This could be owing to the presence of proteinaceous substrates provided by mucus and the shedding of the intestinal epithelium. CONCLUSIONS: In an analysis of intestinal microbiota of mice and human beings, we observed a radial gradient of microbes linked to the distribution of oxygen and nutrients provided by host tissue.
- 6Lewis, W. H.; Tahon, G.; Geesink, P.; Sousa, D. Z.; Ettema, T. J. G. Innovations to culturing the uncultured microbial majority. Nat. Rev. Microbiol. 2021, 19, 225– 240, DOI: 10.1038/s41579-020-00458-8Google Scholar6https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitFGqtb3N&md5=1fe9faa73c4f49c58cc809ad44fa7a47Innovations to culturing the uncultured microbial majorityLewis, William H.; Tahon, Guillaume; Geesink, Patricia; Sousa, Diana Z.; Ettema, Thijs J. G.Nature Reviews Microbiology (2021), 19 (4), 225-240CODEN: NRMACK; ISSN:1740-1526. (Nature Research)Abstr.: Despite the surge of microbial genome data, exptl. testing is important to confirm inferences about the cell biol., ecol. roles and evolution of microorganisms. As the majority of archaeal and bacterial diversity remains uncultured and poorly characterized, culturing is a priority. The growing interest in and need for efficient cultivation strategies has led to many rapid methodol. and technol. advances. In this Review, we discuss common barriers that can hamper the isolation and culturing of novel microorganisms and review emerging, innovative methods for targeted or high-throughput cultivation. We also highlight recent examples of successful cultivation of novel archaea and bacteria, and suggest key microorganisms for future cultivation attempts.
- 7Bergersen, F. J.; Turner, G. L.; Gibson, A. H.; Dudman, W. F. Nitrogenase activity and respiration of cultures of Rhizobium spp. with special reference to concentration of dissolved oxygen. Biochim. Biophys. Acta, Gen. Subj. 1976, 444, 164– 174, DOI: 10.1016/0304-4165(76)90233-6Google Scholar7https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaE28XltF2gu7k%253D&md5=d4731e0d87f54cb2b01a7ff653e53429Nitrogenase activity and respiration of cultures of Rhizobium spp. with special reference to concentration of dissolved oxygenBergersen, Fraser J.; Turner, Graham L.; Gibson, Alan H.; Dudman, William F.Biochimica et Biophysica Acta, General Subjects (1976), 444 (1), 164-74CODEN: BBGSB3; ISSN:0304-4165.Studies of nitrogenase in cultures of the cowpea rhizobia (Rhizobium species) strains 32H1 and CB756 are reported. Preliminary expts. established that, even when agar cultures were grown in air, suspensions of bacteria prepd. anaerobically from them were most active at low concns. of free dissolved O2. Consequently, assays for activity used low concns. of O2, stabilized by adding the nodule pigment leghemoglobin. In continuous, glutamine-limited cultures of 32H1, nitrogenase activity appeared only when the concn. of dissolved O2 in the cultures approached 1 μM. Lowering the glutamine concn. in the medium supplied to the culture from 2 to 1 mM halved the cell yield and nitrogenase activity was also diminished. Omitting succinate from the medium caused the concn. of dissolved O2 to rise and nitrogenase activity was lost. Upon restoration of the succinate supply, the O2 concn. immediately fell and nitrogenase was restored. The activity doubled in ∼8 hr, whereas the doubling time of this culture was 14 hr. Sonic exts. of 32H1 cells from continuous cultures with active nitrogenase contained components reacting with antiserum against nitrogenase Mo-Fe protein from soybean bacteroids. Continuous cultures grown at higher O2 concn., with only a trace of active nitrogenase, contained less of these antigens and they were not detected in highly aerobic cultures. Nitrogenase activity of a continuous culture was repressed by NH4+; the apparent half-life was ∼90 min. Cells of 32H1 from a continuous culture growing at between 30 and 100 μM dissolved O2 possessed a protective mechanism which permitted respiration to increase following exposure to a rapid increase in O2 concn. from low levels (O2 shock). This effect disappeared as the O2 concn. for growth was reduced towards 1 μM.
- 8Wheeldon, I.; Minteer, S. D.; Banta, S.; Barton, S. C.; Atanassov, P.; Sigman, M. Substrate channelling as an approach to cascade reactions. Nat. Chem. 2016, 8, 299– 309, DOI: 10.1038/nchem.2459Google Scholar8https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xks1Cru7Y%253D&md5=5056edbd76a5aa2266906be9e23c579bSubstrate channelling as an approach to cascade reactionsWheeldon, Ian; Minteer, Shelley D.; Banta, Scott; Barton, Scott Calabrese; Atanassov, Plamen; Sigman, MatthewNature Chemistry (2016), 8 (4), 299-309CODEN: NCAHBB; ISSN:1755-4330. (Nature Publishing Group)A review. Millions of years of evolution have produced biol. systems capable of efficient one-pot multi-step catalysis. The underlying mechanisms that facilitate these reaction processes are increasingly providing inspiration in synthetic chem. Substrate channeling, where intermediates between enzymic steps are not in equil. with the bulk soln., enables increased efficiencies and yields in reaction and diffusion processes. Here, we review different mechanisms of substrate channeling found in nature and provide an overview of the anal. methods used to quantify these effects. The incorporation of substrate channeling into synthetic cascades is a rapidly developing concept, and recent examples of the fabrication of cascades with controlled diffusion and flux of intermediates are presented.
- 9Newman, J. S.; Tobias, C. W. Theoretical Analysis of Current Distribution in Porous Electrodes. J. Electrochem. Soc. 1962, 109, 1183– 1191, DOI: 10.1149/1.2425269Google Scholar9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaF3sXht12qsw%253D%253D&md5=232a8e9cd6d89666940cf3ae8366ed73Theoretical analysis of current distribution in porous electrodesNewman, John S.; Tobias, Charles W.Journal of the Electrochemical Society (1962), 109 (), 1183-91CODEN: JESOAN; ISSN:0013-4651.General equations describing the behavior of porous electrodes were developed. These equations were used to det. the initial and the steady-state conditions in one-dimensional porous electrodes of uniform geometry and polarization parameters. In particular, it is shown that the current and reaction distributions in the depth of the electrode are strongly influenced by the type of activation polarization and by mass transport of the reacting ionic species, in addn. to the effective conds. of the two phases. A linear approxn. to a Tafel curve leads to an inadequate description of actual behavior when the reaction is distributed nonuniformly in the depth of the electrode.
- 10Natinsky, B. S.; Lu, S.; Copeland, E. D.; Quintana, J. C.; Liu, C. Solution Catalytic Cycle of Incompatible Steps for Ambient Air Oxidation of Methane to Methanol. ACS Cent. Sci. 2019, 5, 1584– 1590, DOI: 10.1021/acscentsci.9b00625Google Scholar10https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhsVOrtr3I&md5=13dda8a7ed154f03a6d26bab45d1e1d0Solution Catalytic Cycle of Incompatible Steps for Ambient Air Oxidation of Methane to MethanolNatinsky, Benjamin S.; Lu, Shengtao; Copeland, Emma D.; Quintana, Jason C.; Liu, ChongACS Central Science (2019), 5 (9), 1584-1590CODEN: ACSCII; ISSN:2374-7951. (American Chemical Society)Direct chem. synthesis from methane and air under ambient conditions is attractive yet challenging. Low-valent organometallic compds. are known to activate methane, but their electron-rich nature seems incompatible with O2 and prevents catalytic air oxidn. We report selective oxidn. of methane to methanol with an O2-sensitive metalloradical as the catalyst and air as the oxidant at room temp. and ambient pressure. The incompatibility between C-H activation and O2 oxidn. is reconciled by electrochem. and nanomaterials, with which a concn. gradient of O2 within the nanowire array spatially segregated incompatible steps in the catalytic cycle. An unexpected 220 000-fold increase of the apparent reaction rate consts. within the nanowire array leads to a turnover no. up to 52 000 within 24 h. The synergy between nanomaterials and organometallic chem. warrants a new catalytic route for CH4 functionalization.
- 11Natinsky, B. S.; Jolly, B. J.; Dumas, D. M.; Liu, C. Efficacy analysis of compartmentalization for ambient CH4 activation mediated by a RhII metalloradical in a nanowire array electrode. Chem. Sci. 2021, 12, 1818– 1825, DOI: 10.1039/D0SC05700BGoogle Scholar11https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXisFWrt7nK&md5=32d84aebfe327b8d13ae912582329ceeEfficacy analysis of compartmentalization for ambient CH4 activation mediated by a RhII metalloradical in a nanowire array electrodeNatinsky, Benjamin S.; Jolly, Brandon J.; Dumas, David M.; Liu, ChongChemical Science (2021), 12 (5), 1818-1825CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)Compartmentalization is a viable approach for ensuring the turnover of a soln. cascade reaction with ephemeral intermediates, which may otherwise deactivate in the bulk soln. In biochem. or enzyme-relevant cascade reactions, extensive models have been constructed to quant. analyze the efficacy of compartmentalization. Nonetheless, the application of compartmentalization and its quant. anal. in non-biochem. reactions is seldom performed, leaving much uncertainty about whether compartmentalization remains effective for non-biochem. reactions, such as organometallic, cascade reactions. Here, we report our exemplary efficacy anal. of compartmentalization in our previously reported cascade reaction for ambient CH4-to-CH3OH conversion, mediated by an O2-deactivated RhII metalloradical with O2 as the terminal oxidant in a Si nanowire array electrode. We exptl. identified and quantified the key reaction intermediates, including the RhII metalloradical and reactive oxygen species (ROS) from O2. Based on such findings, we exptl. detd. that the nanowire array enables about 81% of the generated ephemeral intermediate RhII metalloradical in air, to be utilized towards CH3OH formation, which is 0% in a homogeneous soln. Such an exptl. detd. value was satisfactorily consistent with the results from our semi-quant. kinetic model. The consistency suggests that the reported CH4-to-CH3OH conversion surprisingly possesses minimal unforeseen side reactions, and is favorably efficient as a compartmentalized cascade reaction. Our quant. evaluation of the reaction efficacy offers design insights and caveats into application of nanomaterials to achieve spatially controlled organometallic cascade reactions.
- 12Lu, S.; Guan, X.; Liu, C. Electricity-Powered Artificial Root Nodule. Nat. Commun. 2020, 11, 1505, DOI: 10.1038/s41467-020-15314-9Google Scholar12https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXlvFCqu7k%253D&md5=45cec18c23215af32d310bd978ba5792Electricity-powered artificial root noduleLu, Shengtao; Guan, Xun; Liu, ChongNature Communications (2020), 11 (1), 1505CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)Abstr.: Root nodules are agricultural-important symbiotic plant-microbe composites in which microorganisms receive energy from plants and reduce dinitrogen (N2) into fertilizers. Mimicking root nodules using artificial devices can enable renewable energy-driven fertilizer prodn. This task is challenging due to the necessity of a microscopic dioxygen (O2) concn. gradient, which reconciles anaerobic N2 fixation with O2-rich atm. Here we report our designed electricity-powered biol.|inorg. hybrid system that possesses the function of root nodules. We construct silicon-based microwire array electrodes and replicate the O2 gradient of root nodules in the array. The wire array compatibly accommodates N2-fixing symbiotic bacteria, which receive energy and reducing equiv. from inorg. catalysts on microwires, and fix N2 in the air into biomass and free ammonia. A N2 redn. rate up to 6.5 mg N2 per g dry biomass per h is obsd. in the device, about two orders of magnitude higher than the natural counterparts.
- 13Hoar, B. B.; Lu, S.; Liu, C. Machine-Learning-Enabled Exploration of Morphology Influence on Wire-Array Electrodes for Electrochemical Nitrogen Fixation. J. Phys. Chem. Lett. 2020, 11, 4625– 4630, DOI: 10.1021/acs.jpclett.0c01128Google Scholar13https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhtVaqsrvN&md5=043d93ee292a194439d2dcd46968b500Machine-Learning-Enabled Exploration of Morphology Influence on Wire-Array Electrodes for Electrochemical Nitrogen FixationHoar, Benjamin B.; Lu, Shengtao; Liu, ChongJournal of Physical Chemistry Letters (2020), 11 (12), 4625-4630CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)Neural networks, trained on data generated by a microkinetic model and finite-element simulations, expand explorable parameter space by significantly accelerating the predictions of electrocatalytic performance. In addn. to modeling electrode reactivity, the authors use micro/nanowire arrays as a well-defined, easily tuned, and exptl. relevant exemplary morphol. for electrochem. N fixation. This model system provides the data necessary for training neural networks which are subsequently exploited for electrocatalytic material morphol. optimizations and explorations into the influence of geometry on N fixation electrodes, feats untenable without large-scale simulations, on both a global and a local basis.