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Sathyan A, Archontakis E, Spiering AJH, Albertazzi L, Palmans ARA. Effect of Particle Heterogeneity in Catalytic Copper-Containing Single-Chain Polymeric Nanoparticles Revealed by Single-Particle Kinetics. Molecules 2024; 29:1850. [PMID: 38675670 PMCID: PMC11054931 DOI: 10.3390/molecules29081850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Single-chain polymeric nanoparticles (SCPNs) have been extensively explored as a synthetic alternative to enzymes for catalytic applications. However, the inherent structural heterogeneity of SCPNs, arising from the dispersity of the polymer backbone and stochastic incorporation of different monomers as well as catalytic moieties, is expected to lead to variations in catalytic activity between individual particles. To understand the effect of structural heterogeneities on the catalytic performance of SCPNs, techniques are required that permit researchers to directly monitor SCPN activity at the single-polymer level. In this study, we introduce the use of single-molecule fluorescence microscopy to study the kinetics of Cu(I)-containing SCPNs towards depropargylation reactions. We developed Cu(I)-containing SCPNs that exhibit fast kinetics towards depropargylation and Cu-catalyzed azide-alkyne click reactions, making them suitable for single-particle kinetic studies. SCPNs were then immobilized on the surface of glass coverslips and the catalytic reactions were monitored at a single-particle level using total internal reflection fluorescence (TIRF) microscopy. Our studies revealed the interparticle turnover dispersity for Cu(I)-catalyzed depropargylations. In the future, our approach can be extended to different polymer designs which can give insights into the intrinsic heterogeneity of SCPN catalysis and can further aid in the rational development of SCPN-based catalysts.
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Affiliation(s)
- Anjana Sathyan
- Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands; (A.S.); (A.J.H.S.)
| | - Emmanouil Archontakis
- Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands; (E.A.); (L.A.)
| | - A. J. H. Spiering
- Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands; (A.S.); (A.J.H.S.)
| | - Lorenzo Albertazzi
- Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands; (E.A.); (L.A.)
| | - Anja R. A. Palmans
- Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands; (A.S.); (A.J.H.S.)
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2
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White D, Smith MA, Chanda B, Goldsmith RH. Strategies for Overcoming the Single-Molecule Concentration Barrier. ACS MEASUREMENT SCIENCE AU 2023; 3:239-257. [PMID: 37600457 PMCID: PMC10436376 DOI: 10.1021/acsmeasuresciau.3c00002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 08/22/2023]
Abstract
Fluorescence-based single-molecule approaches have helped revolutionize our understanding of chemical and biological mechanisms. Unfortunately, these methods are only suitable at low concentrations of fluorescent molecules so that single fluorescent species of interest can be successfully resolved beyond background signal. The application of these techniques has therefore been limited to high-affinity interactions despite most biological and chemical processes occurring at much higher reactant concentrations. Fortunately, recent methodological advances have demonstrated that this concentration barrier can indeed be broken, with techniques reaching concentrations as high as 1 mM. The goal of this Review is to discuss the challenges in performing single-molecule fluorescence techniques at high-concentration, offer applications in both biology and chemistry, and highlight the major milestones that shatter the concentration barrier. We also hope to inspire the widespread use of these techniques so we can begin exploring the new physical phenomena lying beyond this barrier.
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Affiliation(s)
- David
S. White
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Mackinsey A. Smith
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Baron Chanda
- Center
for
Investigation of Membrane Excitability Diseases, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Randall H. Goldsmith
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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3
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Das M, Ray DS. Critical and scaling behavior of delayed bifurcations in nonlinear systems with dynamic disorder. J CHEM SCI 2023. [DOI: 10.1007/s12039-023-02148-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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4
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Zuo L, Ren K, Guo X, Pokhrel P, Pokhrel B, Hossain MA, Chen ZX, Mao H, Shen H. Amalgamation of DNAzymes and Nanozymes in a Coronazyme. J Am Chem Soc 2023; 145:5750-5758. [PMID: 36795472 PMCID: PMC10325850 DOI: 10.1021/jacs.2c12367] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Artificial enzymes such as nanozymes and DNAzymes are economical and stable alternatives to natural enzymes. By coating Au nanoparticles (AuNPs) with a DNA corona (AuNP@DNA), we amalgamated nanozymes and DNAzymes into a new artificial enzyme with catalytic efficiency 5 times higher than AuNP nanozymes, 10 times higher than other nanozymes, and significantly greater than most of the DNAzymes on the same oxidation reaction. The AuNP@DNA demonstrates excellent specificity as its reactivity on a reduction reaction does not change with respect to pristine AuNP. Single-molecule fluorescence and force spectroscopies and density functional theory (DFT) simulations indicate a long-range oxidation reaction initiated by radical production on the AuNP surface, followed by radical transport to the DNA corona, where the binding and turnover of substrates take place. The AuNP@DNA is named coronazyme because of its natural enzyme mimicking capability through the well-orchestrated structures and synergetic functions. By incorporating different nanocores and corona materials beyond DNAs, we anticipate that the coronazymes represent generic enzyme mimics to carry out versatile reactions in harsh environments.
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Affiliation(s)
- Li Zuo
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Kehao Ren
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | - Xianming Guo
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Pravin Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | - Bishal Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | | | - Zhao-Xu Chen
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | - Hao Shen
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
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5
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An S, Patel P, Liu C, Skodje RT. Computational Aspects of Single-Molecule Kinetics for Coupled Catalytic Cycles: A Spectral Analysis. J Phys Chem A 2022; 126:3783-3796. [PMID: 35658508 DOI: 10.1021/acs.jpca.2c02153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Catalysis from single active sites is analyzed using methods developed from single-molecule kinetics. Using a stochastic Markov-state description, the observable properties of general catalytic networks of reactions are expressed using an eigenvalue decomposition of the transition matrix for the Markov process. By the use of a sensitivity analysis, the necessary eigenvalues and eigenvectors are related to the energies of controlling barriers and wells located along the reaction routes. A generalization of the energetic span theory allows the eigenvalues to be computed from several activation energies corresponding to distinct barrier-well pairings. The formalism is demonstrated for model problems and for a physically realistic mechanism for an alkene hydrogenation reaction on a single-atom catalyst. The spectral analysis permits a hierarchy of timescales to be identified from the single-molecule signal, which correspond to specific relaxation modes in the network.
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Affiliation(s)
- Suming An
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Prajay Patel
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60639, United States
| | - Cong Liu
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60639, United States
| | - Rex T Skodje
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
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6
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Microscopic mechanisms of cooperative communications within single nanocatalysts. Proc Natl Acad Sci U S A 2022; 119:2115135119. [PMID: 35022239 PMCID: PMC8784103 DOI: 10.1073/pnas.2115135119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 01/30/2023] Open
Abstract
Catalysis is an experimental approach to accelerate chemical reactions. It plays a critical role in modern industries. Recent experimental studies uncovered striking observations of cooperative communications for reactions on nanocatalysts. In these experiments, it was shown that the chemical reactions observed at specific active sites might effectively stimulate the same reactions at the neighboring sites. We developed a theoretical model to investigate the microscopic mechanisms of these phenomena. Our idea is that the catalytic communication is the result of the complex dynamics of charged holes. Explicit calculations are able to quantitatively explain all experimental observations, clarifying the molecular origin of cooperative communications. The presented theoretical framework might be utilized for developing efficient catalytic systems with better control over chemical reactions. Catalysis is a method of accelerating chemical reactions that is critically important for fundamental research as well as for industrial applications. It has been recently discovered that catalytic reactions on metal nanoparticles exhibit cooperative effects. The mechanism of these observations, however, remains not well understood. In this work, we present a theoretical investigation on possible microscopic origin of cooperative communications in nanocatalysts. In our approach, the main role is played by positively charged holes on metal surfaces. A corresponding discrete-state stochastic model for the dynamics of holes is developed and explicitly solved. It is shown that the observed spatial correlation lengths are given by the average distances migrated by the holes before they disappear, while the temporal memory is determined by their lifetimes. Our theoretical approach is able to explain the universality of cooperative communications as well as the effect of external electric fields. Theoretical predictions are in agreement with experimental observations. The proposed theoretical framework quantitatively clarifies some important aspects of the microscopic mechanisms of heterogeneous catalysis.
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7
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Punia B, Chaudhury S, Kolomeisky AB. Understanding the Reaction Dynamics on Heterogeneous Catalysts Using a Simple Stochastic Approach. J Phys Chem Lett 2021; 12:11802-11810. [PMID: 34860518 DOI: 10.1021/acs.jpclett.1c03557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Recent experimental advances on investigating nanoparticle catalysts with multiple active sites provided a large amount of quantitative information on catalytic processes. These observations stimulated significant theoretical efforts, but the underlying molecular mechanisms are still not well-understood. We introduce a simple theoretical method to analyze the reaction dynamics on catalysts with multiple active sites based on a discrete-state stochastic description and obtain a comprehensive description of the dynamics of chemical reactions on such catalysts. We explicitly determine how the dynamics of catalyzed chemical reactions depend on the number of active sites, on the number of intermediate chemical transitions, and on the topology of underlying chemical reactions. It is argued that the theory provides quantitative bounds for realistic dynamic properties of catalytic processes that can be directly applied to analyze the experimental observations. In addition, this theoretical approach clarifies several important aspects of the molecular mechanisms of chemical reactions on catalysts.
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Affiliation(s)
- Bhawakshi Punia
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - A B Kolomeisky
- Department of Chemistry and Center for Theoretical Biological Physics, Department of Chemical and Biomolecular Engineering, Department of Physics and Astronomy, Rice University, Houston, Texas 77005-1892, United States
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8
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Lin YC, Roa R, Dzubiella J. Electrostatic Reaction Inhibition in Nanoparticle Catalysis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:6800-6810. [PMID: 34032431 DOI: 10.1021/acs.langmuir.1c00903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Electrostatic reaction inhibition in heterogeneous catalysis emerges if charged reactants and products with similar charges are adsorbed on the catalyst and thus repel the approaching reactants. In this work, we study the effects of electrostatic inhibition on the reaction rate of unimolecular reactions catalyzed on the surface of a spherical model nanoparticle using particle-based reaction-diffusion simulations. Moreover, we derive closed rate equations based on an approximate Debye-Smoluchowski rate theory, valid for diffusion-controlled reactions, and a modified Langmuir adsorption isotherm, relevant for reaction-controlled reactions, to account for electrostatic inhibition in the Debye-Hückel limit. We study the kinetics of reactions ranging from low to high adsorptions on the nanoparticle surface and from the surface- to diffusion-controlled limits for charge valencies 1 and 2. In the diffusion-controlled limit, electrostatic inhibition drastically slows down the reactions for strong adsorption and low ionic concentration, which is well described by our theory. In particular, the rate decreases with adsorption affinity because, in this case, the inhibiting products are generated at a high rate. In the (slow) reaction-controlled limit, the effect of electrostatic inhibition is much weaker, as semiquantitatively reproduced by our electrostatic-modified Langmuir theory. We finally propose and verify a simple interpolation formula that describes electrostatic inhibition for all reaction speeds ("diffusion-influenced" reactions) in general.
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Affiliation(s)
- Yi-Chen Lin
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
| | - Rafael Roa
- Departamento de Física Aplicada I, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos S/N, E-29071 Málaga, Spain
| | - Joachim Dzubiella
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
- Research Group for Simulations of Energy Materials, Helmholtz-Zentrum Berlin, D-14109 Berlin, Germany
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9
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Patel P, Wells RH, Kaphan DM, Delferro M, Skodje RT, Liu C. Computational Investigation of the Role of Active Site Heterogeneity for a Supported Organovanadium(III) Hydrogenation Catalyst. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00688] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Prajay Patel
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439-4801, United States
| | - Robert H. Wells
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309-0215, United States
| | - David M. Kaphan
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439-4801, United States
| | - Massimiliano Delferro
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439-4801, United States
| | - Rex T. Skodje
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309-0215, United States
| | - Cong Liu
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439-4801, United States
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10
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Lin M, Zhou Y, Bu L, Bai C, Tariq M, Wang H, Han J, Huang X, Zhou X. Single-Nanoparticle Coulometry Method with High Sensitivity and High Throughput to Study the Electrochemical Activity and Oscillation of Single Nanocatalysts. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2007302. [PMID: 33719172 DOI: 10.1002/smll.202007302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/16/2021] [Indexed: 06/12/2023]
Abstract
To explore nanocatalysts with high electro-catalytic performance and less loading of precious metals, efforts have been made to develop electrochemical methods with high spatial resolution at the single nanoparticle level. Herein, a highly sensitive single-nanoparticle coulometry method is successfully developed to study the electrochemical activity and oscillation of single PtTe nanocatalysts. Based on microbattery reactions involving the formic acid electro-oxidation and the deposition of Ag on the single PtTe nanocatalyst surface, this method enables the transition from the undetectable sub-fA electric signal of the formic acid electro-oxidation into strong localized surface plasmon resonance scattering signal of Ag detected by dark-field microscopy. The lowest limiting current for a single nanocatalyst is found to be as low as 25.8 aA. Different trends of activity versus the formic acid concentration and types of activity of the single nanocatalyst have been discovered. Unveiled frequency-amplitude graph shows that the two electrochemical oscillation modes of low frequency with high amplitude and vice versa coexist in a single PtTe nanocatalyst, indicating the abundantly smooth surfaces and defects of nanocatalysts. This conducted study will open up the new avenue for further behavioral and mechanistic investigation of more types of nanocatalysts in the electrochemistry community.
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Affiliation(s)
- Mohan Lin
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Suzhou, 215123, China
- Division of Advanced Nanomaterials, Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Yingke Zhou
- Division of Advanced Nanomaterials, Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, 215123, China
- School of Materials Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Lingzheng Bu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Chuang Bai
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Suzhou, 215123, China
- Division of Advanced Nanomaterials, Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Muhammad Tariq
- Division of Advanced Nanomaterials, Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Huihui Wang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Suzhou, 215123, China
- Division of Advanced Nanomaterials, Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Jinli Han
- Division of Advanced Nanomaterials, Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, 215123, China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaoqing Huang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Xiaochun Zhou
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Suzhou, 215123, China
- Division of Advanced Nanomaterials, Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, 215123, China
- Key Laboratory of Nanodevices and Applications, Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, 215123, China
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11
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Kang J, Park SJ, Kim JH, Chen P, Sung J. Stochastic Kinetics of Nanocatalytic Systems. PHYSICAL REVIEW LETTERS 2021; 126:126001. [PMID: 33834800 DOI: 10.1103/physrevlett.126.126001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/18/2020] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
Catalytic reaction events occurring on the surface of a nanoparticle constitute a complex stochastic process. Although advances in modern single-molecule experiments enable direct measurements of individual catalytic turnover events occurring on a segment of a single nanoparticle, we do not yet know how to measure the number of catalytic sites in each segment or how the catalytic turnover counting statistics and the catalytic turnover time distribution are related to the microscopic dynamics of catalytic reactions. Here, we address these issues by presenting a stochastic kinetics for nanoparticle catalytic systems. We propose a new experimental measure of the number of catalytic sites in terms of the mean and variance of the catalytic event count. By considering three types of nanocatalytic systems, we investigate how the mean, the variance, and the distribution of the catalytic turnover time depend on the catalytic reaction dynamics, the heterogeneity of catalytic activity, and communication among catalytic sites. This work enables accurate quantitative analyses of single-molecule experiments for nanocatalytic systems and enzymes with multiple catalytic sites.
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Affiliation(s)
- Jingyu Kang
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
| | - Seong Jun Park
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
| | - Ji-Hyun Kim
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Jaeyoung Sung
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
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12
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Gehlen MH, Foltran LS, Kienle DF, Schwartz DK. Single-Molecule Observations Provide Mechanistic Insights into Bimolecular Knoevenagel Amino Catalysis. J Phys Chem Lett 2020; 11:9714-9724. [PMID: 33136415 DOI: 10.1021/acs.jpclett.0c03030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
While single-molecule (SM) methods have provided new insights to various catalytic processes, bimolecular reactions have been particularly challenging to study. Here, the fluorogenic Knoevenagel condensation of an aromatic aldehyde with methyl cyanoacetate promoted by surface-immobilized piperazine is quantitatively characterized using super-resolution fluorescence imaging and stochastic analysis using hidden Markov modeling (HMM). Notably, the SM results suggest that the reaction follows the iminium intermediate pathway before the formation of a fluorescent product with intramolecular charge-transfer character. Moreover, the overall process is limited by the turnover rate of the catalyst, which is involved in multiple steps along the reaction coordinate.
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Affiliation(s)
- Marcelo H Gehlen
- Department of Physical Chemistry, Institute of Chemistry of São Carlos, University of São Paulo, 13566-590 São Carlos, SP, Brazil
| | - Larissa S Foltran
- Department of Physical Chemistry, Institute of Chemistry of São Carlos, University of São Paulo, 13566-590 São Carlos, SP, Brazil
| | - Daniel F Kienle
- Department of Chemistry and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Daniel K Schwartz
- Department of Chemistry and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
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13
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Chen X, Schwartz SD. Multiple Reaction Pathways in the Morphinone Reductase-Catalyzed Hydride Transfer Reaction. ACS OMEGA 2020; 5:23468-23480. [PMID: 32954200 PMCID: PMC7496013 DOI: 10.1021/acsomega.0c03472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
Morphinone reductase (MR) is an important model system for studying the contribution of protein motions to H-transfer reactions. In this research, we used quantum mechanical/molecular mechanics (QM/MM) simulation together with transition path sampling (TPS) simulation to study two important topics of current research on MR: the existence of multiple catalytic reaction pathways and the involvement of fast protein motions in the catalytic process. We have discovered two reaction pathways for the wild type and three reaction pathways for the N189A mutant. With the committor distribution analysis method, we found reaction coordinates for all five reaction pathways. Only one wild-type reaction pathway has a rate-promoting vibration from His186, while all of the other four pathways do not involve any protein motions in their catalytic process through the transition state. The rate-promoting vibration in the wild-type MR, which comes from a direction perpendicular to the donor-acceptor axis, functions to decrease the donor-acceptor distance by causing a subtle "out-of-plane" motion of a donor atom. By comparing reaction pathways between the two enzymes, we concluded that the major effect of the N189A point mutation is to increase the active site volume by altering the active site backbone and eliminating the Asn189 side chain. This effect causes a different NADH geometry at the reactant state, which very well explains the different reaction mechanisms between the two enzymes, as well as the disappearance of the His186 rate-promoting vibrations in the N189A mutant. The unfavorable geometry of the NADH pyridine ring induced by the N189A point mutation is the potential cause of multiple reaction pathways in N189A mutants.
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14
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Mahdavi-Shakib A, Sempel J, Babb L, Oza A, Hoffman M, Whittaker TN, Chandler BD, Austin RN. Combining Benzyl Alcohol Oxidation Saturation Kinetics and Hammett Studies as Mechanistic Tools for Examining Supported Metal Catalysts. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02212] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Akbar Mahdavi-Shakib
- Department of Chemistry, Barnard College of Columbia University, 3009 Broadway, New York, New York 10027, United States
- Department of Chemistry, Trinity University, San Antonio, Texas 78212-7200, United States
| | - Janine Sempel
- Department of Chemistry, Barnard College of Columbia University, 3009 Broadway, New York, New York 10027, United States
| | - Lauren Babb
- Department of Chemistry, Barnard College of Columbia University, 3009 Broadway, New York, New York 10027, United States
| | - Aisha Oza
- Department of Chemistry, Barnard College of Columbia University, 3009 Broadway, New York, New York 10027, United States
| | - Maya Hoffman
- Department of Chemistry, Barnard College of Columbia University, 3009 Broadway, New York, New York 10027, United States
| | - Todd N. Whittaker
- Department of Chemistry, Trinity University, San Antonio, Texas 78212-7200, United States
| | - Bert D. Chandler
- Department of Chemistry, Trinity University, San Antonio, Texas 78212-7200, United States
| | - Rachel Narehood Austin
- Department of Chemistry, Barnard College of Columbia University, 3009 Broadway, New York, New York 10027, United States
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15
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Gao P, Feng Y, Wang M, Jiang N, Qi W, Su R, He Z. Ferrocene-Modified Metal–Organic Frameworks as a Peroxidase-Mimicking Catalyst. Catal Letters 2020. [DOI: 10.1007/s10562-020-03314-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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16
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Dogantzis NP, Hodgson GK, Impellizzeri S. Optical writing and single molecule reading of photoactivatable and silver nanoparticle-enhanced fluorescence. NANOSCALE ADVANCES 2020; 2:1956-1966. [PMID: 36132516 PMCID: PMC9418025 DOI: 10.1039/d0na00049c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 02/28/2020] [Indexed: 05/27/2023]
Abstract
We designed a hybrid nanoparticle-molecular system composed of silver nanostructures (AgNP) and a fluorogenic boron dipyrromethene (BODIPY) that can be selectively activated by UVA or UVC light in the presence of an appropriate photoacid generator (PAG). Light irradiation of the PAG encourages the release of p-toluenesulfonic, triflic or hydrobromic acid, any of which facilitate optical 'writing' by promoting the formation of a fluorescent species. Metal-enhanced fluorescence (MEF) by AgNP was achieved through rational design of the nano-molecular system in accordance with the principles of radiative decay engineering. In addition to increasing signal to noise, AgNP permitted shorter reaction times and low irradiance - all of which have important implications for applications of fluorescence activation in portable fluorescence patterning, bioimaging and super-resolution microscopy. Single molecule fluorescence microscopy provided unique insights into the MEF mechanism which were hidden by ensemble-averaged measurements, demonstrating that single molecule 'reading' is a valuable tool for characterizing particle-molecule interactions such as those responsible for the relative contributions of increased excitation and plasmophoric emission toward overall MEF. This work represents a step forward in the contemporary design of synergistic nano-molecular systems, and showcases the advantage of fusion between classic spectroscopic techniques and single molecule methods in terms of improved quantitative understanding of fluorophore-nanoparticle interactions, and how these interactions can be exploited to the fullest extent possible.
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Affiliation(s)
- Nicholas P Dogantzis
- Laboratory for Nanomaterials and Molecular Plasmonics, Department of Chemistry and Biology, Ryerson University 350 Victoria St. Toronto ON M5B 2K3 Canada
| | - Gregory K Hodgson
- Laboratory for Nanomaterials and Molecular Plasmonics, Department of Chemistry and Biology, Ryerson University 350 Victoria St. Toronto ON M5B 2K3 Canada
| | - Stefania Impellizzeri
- Laboratory for Nanomaterials and Molecular Plasmonics, Department of Chemistry and Biology, Ryerson University 350 Victoria St. Toronto ON M5B 2K3 Canada
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Menges JA, Grandjean A, Clasen A, Jung G. Kinetics of Palladium(0)‐Allyl Interactions in the Tsuji‐Trost Reaction, derived from Single‐Molecule Fluorescence Microscopy. ChemCatChem 2020. [DOI: 10.1002/cctc.202000032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Johannes A. Menges
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
| | - Alexander Grandjean
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
| | - Anne Clasen
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
| | - Gregor Jung
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
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Zhdanov VP. Kinetics of Reaction on a Single Catalytic Particle in a Fluidic Nanochannel. Catal Letters 2019. [DOI: 10.1007/s10562-019-03082-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
One of the frontiers in heterogeneous catalysis is focused on reactions occurring on single catalytic nanoparticles. In this context, a reaction taking place on a single nanoparticle in a fluidic nanochannel is herein described by using the equation similar to that employed for a plug-flow reactor with dispersion. In the literature, one can find various boundary conditions for this equation. In the practically interesting case of a relatively long channel, the Dirichlet boundary conditions are shown to be valid. The corresponding analytical and numerical results illustrate the specifics of the profiles of the reactant concentration along the channel and the dependence of the reaction rate on the parameters. For comparison, the Danckwerts boundary conditions were used as well.
Graphic Abstract
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