1
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Khalilian MH, DiLabio GA. Non-Aufbau electronic structure in radical enzymes and control of the highly reactive intermediates. Chem Sci 2024; 15:11865-11874. [PMID: 39092113 PMCID: PMC11290419 DOI: 10.1039/d4sc01785d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 06/07/2024] [Indexed: 08/04/2024] Open
Abstract
Radicals are highly reactive, short-lived chemical species that normally react indiscriminately with biological materials, and yet, nature has evolved thousands of enzymes that employ radicals to catalyze thermodynamically challenging chemistry. How these enzymes harness highly reactive radical intermediates to steer the catalysis to the correct outcome is a topic of intense investigation. Here, the results of detailed QM/MM calculations on archetype radical B12-enzymes are presented that provide new insights into how these enzymes control the reactivity of radicals within their active sites. The catalytic cycle in B12-enzymes is initiated through the formation of the 5'-deoxyadenosyl (Ado˙) moiety, a primary carbon-centred radical, which must migrate up to 8 Å to reach the target substrate to engage in the next step of the catalytic process, a hydrogen atom abstraction. Our calculations reveal that Ado˙ within the protein environment exhibits an unusual non-Aufbau electronic structure in which the singly occupied molecular orbital is lower in energy than the doubly occupied orbitals, an uncommon phenomenon known as SOMO-HOMO inversion (SHI). We find that the magnitude of SHI in the initially formed Ado˙ is larger compared to when the Ado˙ is near the intended substrate, leading to the former being relatively less reactive. The modulation of the SHI originates from Coulombic interactions of a quantum nature between a negative charge on a conserved glutamate residue and the spin on the Ado˙. Our findings support a novel hypothesis that these enzymes utilize this quantum Coulombic effect as a means of maintaining exquisite control over the chemistry of highly reactive radical intermediates in enzyme active sites.
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Affiliation(s)
- M Hossein Khalilian
- Department of Chemistry, The University of British Columbia 3247 University Way Kelowna British Columbia V1V 1V7 Canada +1-250-807-6617
| | - Gino A DiLabio
- Department of Chemistry, The University of British Columbia 3247 University Way Kelowna British Columbia V1V 1V7 Canada +1-250-807-6617
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2
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Xia Y, Xu J, Li J, Chen B, Dai Y, Zare RN. Visualization of the Charging of Water Droplets Sprayed into Air. J Phys Chem A 2024; 128:5684-5690. [PMID: 38968601 DOI: 10.1021/acs.jpca.4c02981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2024]
Abstract
Water droplets are spraying into air using air as a nebulizing gas, and the droplets pass between two parallel metal plates with opposite charges. A high-speed camera records droplet trajectories in the uniform electric field, providing visual evidence for the Lenard effect, that is, smaller droplets are negatively charged whereas larger droplets are positively charged. By analyzing the velocities of the droplets between the metal plates, the charges on the droplets can be estimated. Some key observations include: (1) localized electric fields with intensities on the order of 109 V/m are generated, and charges are expected to jump (micro-lightening) between a positively charged larger droplet and the negatively charged smaller droplet as they separate; (2) the strength of the electric field is sufficiently powerful to ionize gases surrounding the droplets; and (3) observations in an open-air mass spectrometer reveal the presence of ions such as N2+, O2+, NO+, and NO2+. These findings provide new insight into the origins of some atmospheric ions and have implications for understanding ionization processes in the atmosphere and chemical transformations in water droplets, advancing knowledge in the field of aerosol science and water microdroplet chemistry.
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Affiliation(s)
- Yu Xia
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, P. R. China
| | - Jinheng Xu
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Juan Li
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, P. R. China
| | - Bolei Chen
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, P. R. China
| | - Yifan Dai
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - Richard N Zare
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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3
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Shaik S. My Vision of Electric-Field-Aided Chemistry in 2050. ACS PHYSICAL CHEMISTRY AU 2024; 4:191-201. [PMID: 38800723 PMCID: PMC11117677 DOI: 10.1021/acsphyschemau.3c00064] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/06/2024] [Accepted: 01/09/2024] [Indexed: 05/29/2024]
Abstract
This manuscript outlines my outlook on the development of electric-field (EF)-mediated-chemistry and the vision of its state by 2050. I discuss applications of oriented-external electric-fields (OEEFs) on chemical reactions and proceed with relevant experimental verifications. Subsequently, the Perspective outlines other ways of generating EFs, e.g., by use of pH-switchable charges, ionic additives, water droplets, and so on. A special section summarizes conceptual principles for understanding and predicting OEEF effects, e.g., the "reaction-axis rule", the capability of OEEFs to act as tweezers that orient reactants and accelerate their reaction, etc. Finally, I discuss applications of OEEFs in continuous-flow setups, which may, in principle, scale-up to molar concentrations. The Perspective ends with the vision that by 2050, OEEF usage will change chemical education, if not also the art of making new molecules.
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Affiliation(s)
- Sason Shaik
- Institute of Chemistry, The
Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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4
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Meyer KAE, Garand E. The impact of solvation on the structure and electric field strength in Li +GlyGly complexes. Phys Chem Chem Phys 2024; 26:12406-12421. [PMID: 38623633 DOI: 10.1039/d3cp06264c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
To scrutinise the impact of electric fields on the structure and vibrations of biomolecules in the presence of water, we study the sequential solvation of lithium diglycine up to three water molecules with cryogenic infrared action spectroscopy. Conformer-specific IR-IR spectroscopy and H2O/D2O isotopic substitution experiments provide most of the information required to decipher the structure of the observed conformers. Additional confirmation is provided by scaled harmonic vibrational frequency calculations using MP2 and DFT. The first water molecule is shown to bind to the Li+ ion, which weakens the electric field experienced by the peptide and as a consequence, also the strength of an internal NH⋯NH2 hydrogen bond in the diglycine backbone. The strength of this hydrogen bond decreases approximately linearly with the number of water molecules as a result of the decreasing electric field strength and coincides with an increase in the number of conformers observed in our spectra. The addition of two water molecules is already sufficient to change the preferred conformation of the peptide backbone, allowing for Li+ coordination to the lone pair of the terminal amine group.
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Affiliation(s)
- Katharina A E Meyer
- University of Wisconsin-Madison, Department of Chemistry, 1101 University Ave, Madison, WI 53706, USA.
| | - Etienne Garand
- University of Wisconsin-Madison, Department of Chemistry, 1101 University Ave, Madison, WI 53706, USA.
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5
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Song Z, Zhu C, Gong K, Wang R, Zhang J, Zhao S, Li Z, Zhang X, Xie J. Deciphering the Microdroplet Acceleration Factors of Aza-Michael Addition Reactions. J Am Chem Soc 2024; 146:10963-10972. [PMID: 38567839 DOI: 10.1021/jacs.4c02312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Microdroplet chemistry is emerging as a great tool for accelerating reactions by several orders of magnitude. Several unique properties such as extreme pHs, interfacial electric fields (IEFs), and partial solvation have been reported to be responsible for the acceleration; however, which factor plays the key role remains elusive. Here, we performed quantum chemical calculations to explore the underlying mechanisms of an aza-Michael addition reaction between methylamine and acrylamide. We showed that the acceleration in methanol microdroplets results from the cumulative effects of several factors. The acidic surface of the microdroplet plays a dominating role, leading to a decrease of ∼9 kcal/mol in the activation barrier. We speculated that the dissociation of both methanol and trace water contributes to the surface acidity. An IEF of 0.1 V/Å can further decrease the barrier by ∼2 kcal/mol. Partial solvation has a negligible effect on lowering the activation barrier in microdroplets but can increase the collision frequency between reactants. With acidity revealed to be the major accelerating factor for methanol droplets, reactions on water microdroplets should have even higher rates because water is more acidic. Both theoretically and experimentally, we confirmed that water microdroplets significantly accelerate the aza-Michael reaction, achieving an acceleration factor that exceeds 107. This work elucidates the multifactorial influences on the microdroplet acceleration mechanism, and with such detailed mechanistic investigations, we anticipate that microdroplet chemistry will be an avenue rich in opportunities in the realm of green synthesis.
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Affiliation(s)
- Zhexuan Song
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Chenghui Zhu
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Ke Gong
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Ruijing Wang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Jianze Zhang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Supin Zhao
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Zesheng Li
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Xinxing Zhang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Jing Xie
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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6
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Ruiz-Pernía JJ, Świderek K, Bertran J, Moliner V, Tuñón I. Electrostatics as a Guiding Principle in Understanding and Designing Enzymes. J Chem Theory Comput 2024; 20:1783-1795. [PMID: 38410913 PMCID: PMC10938506 DOI: 10.1021/acs.jctc.3c01395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/28/2024]
Abstract
Enzyme design faces challenges related to the implementation of the basic principles that govern the catalytic activity in natural enzymes. In this work, we revisit basic electrostatic concepts that have been shown to explain the origin of enzymatic efficiency like preorganization and reorganization. Using magnitudes such as the electrostatic potential and the electric field generated by the protein, we explain how these concepts work in different enzymes and how they can be used to rationalize the consequences of point mutations. We also discuss examples of protein design in which electrostatic effects have been implemented. For the near future, molecular simulations, coupled with the use of machine learning methods, can be used to implement electrostatics as a guiding principle for enzyme designs.
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Affiliation(s)
| | - Katarzyna Świderek
- Biocomp
group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón Spain
| | - Joan Bertran
- Departament
de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra, Spain
| | - Vicent Moliner
- Biocomp
group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón Spain
| | - Iñaki Tuñón
- Departament
de Química Física, Universitat
de València, 46100 Burjassot, Spain
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7
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Wang B, Wang M, Fan Z, Ma C, Xi S, Chang LY, Zhang M, Ling N, Mi Z, Chen S, Leow WR, Zhang J, Wang D, Lum Y. Nanocurvature-induced field effects enable control over the activity of single-atom electrocatalysts. Nat Commun 2024; 15:1719. [PMID: 38409205 PMCID: PMC10897157 DOI: 10.1038/s41467-024-46175-1] [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: 08/04/2023] [Accepted: 02/16/2024] [Indexed: 02/28/2024] Open
Abstract
Tuning interfacial electric fields provides a powerful means to control electrocatalyst activity. Importantly, electric fields can modify adsorbate binding energies based on their polarizability and dipole moment, and hence operate independently of scaling relations that fundamentally limit performance. However, implementation of such a strategy remains challenging because typical methods modify the electric field non-uniformly and affects only a minority of active sites. Here we discover that uniformly tunable electric field modulation can be achieved using a model system of single-atom catalysts (SACs). These consist of M-N4 active sites hosted on a series of spherical carbon supports with varying degrees of nanocurvature. Using in-situ Raman spectroscopy with a Stark shift reporter, we demonstrate that a larger nanocurvature induces a stronger electric field. We show that this strategy is effective over a broad range of SAC systems and electrocatalytic reactions. For instance, Ni SACs with optimized nanocurvature achieved a high CO partial current density of ~400 mA cm-2 at >99% Faradaic efficiency for CO2 reduction in acidic media.
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Affiliation(s)
- Bingqing Wang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore
| | - Meng Wang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Ziting Fan
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore
| | - Chao Ma
- Department of Chemistry, Tsinghua University, Tsinghua, China
| | - Shibo Xi
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Singapore, 627833, Republic of Singapore
| | - Lo-Yueh Chang
- National Synchrotron Radiation Research Centre, Hsinchu, Taiwan
| | - Mingsheng Zhang
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Ning Ling
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore
| | - Ziyu Mi
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Singapore, 627833, Republic of Singapore
| | - Shenghua Chen
- Department of Chemistry, Tsinghua University, Tsinghua, China
| | - Wan Ru Leow
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Singapore, 627833, Republic of Singapore
| | - Jia Zhang
- Institute of High Performance Computing (IHPC), Agency for Science, Technology, and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Republic of Singapore
| | - Dingsheng Wang
- Department of Chemistry, Tsinghua University, Tsinghua, China
| | - Yanwei Lum
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore.
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore.
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8
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Yang F, Urban RD, Lorenz J, Griebel J, Koohbor N, Rohdenburg M, Knorke H, Fuhrmann D, Charvat A, Abel B, Azov VA, Warneke J. Control of Intermediates and Products by Combining Droplet Reactions and Ion Soft-Landing. Angew Chem Int Ed Engl 2024; 63:e202314784. [PMID: 37917653 DOI: 10.1002/anie.202314784] [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: 10/02/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/04/2023]
Abstract
Despite being recognized primarily as an analytical technique, mass spectrometry also has a large potential as a synthetic tool, enabling access to advanced synthetic routes by reactions in charged microdroplets or ionic thin layers. Such reactions are special and proceed primarily at surfaces of droplets and thin layers. Partial solvation of the reactants is usually considered to play an important role for reducing the activation barrier, but many mechanistic details still need to be clarified. In our study, we showcase the synergy between two sequentially applied "preparative mass spectrometry" methods: initiating accelerated reactions within microdroplets during electrospray ionization to generate gaseous ionic intermediates in high abundance, which are subsequently mass-selected and soft-landed to react with a provided reagent on a substrate. This allows the generation of products at a nanomolar scale, amenable to further characterization. In this proof-of-concept study, the contrasting reaction pathways between intrinsically neutral and pre-charged reagents, respectively, both in microdroplets and in layers generated by ion soft-landing are investigated. This provides new insights into the role of partially solvated reagents at microdroplet surfaces for increased reaction rates. Additionally, further insights into reactions of ions of the same polarity under various conditions is obtained.
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Affiliation(s)
- Fangshun Yang
- Leibniz Institute of Surface Engineering (IOM), Permoserstrasse 15, 04318, Leipzig, Germany
| | - Raphael D Urban
- Leibniz Institute of Surface Engineering (IOM), Permoserstrasse 15, 04318, Leipzig, Germany
| | - Jonas Lorenz
- Leibniz Institute of Surface Engineering (IOM), Permoserstrasse 15, 04318, Leipzig, Germany
| | - Jan Griebel
- Leibniz Institute of Surface Engineering (IOM), Permoserstrasse 15, 04318, Leipzig, Germany
| | - Nima Koohbor
- Leibniz Institute of Surface Engineering (IOM), Permoserstrasse 15, 04318, Leipzig, Germany
| | - Markus Rohdenburg
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, University Leipzig, Linnéstrasse 2, 04103, Leipzig, Germany
| | - Harald Knorke
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, University Leipzig, Linnéstrasse 2, 04103, Leipzig, Germany
| | - Daniel Fuhrmann
- Institute for Inorganic Chemistry, University Leipzig, Johannisallee 29, 04103, Leipzig, Germany
| | - Ales Charvat
- Leibniz Institute of Surface Engineering (IOM), Permoserstrasse 15, 04318, Leipzig, Germany
- Institute of Chemical Technology, University Leipzig, 04103, Leipzig, Germany
| | - Bernd Abel
- Leibniz Institute of Surface Engineering (IOM), Permoserstrasse 15, 04318, Leipzig, Germany
- Institute of Chemical Technology, University Leipzig, 04103, Leipzig, Germany
| | - Vladimir A Azov
- Department of Chemistry, University of the Free State, 9300, Bloemfontein, South Africa
| | - Jonas Warneke
- Leibniz Institute of Surface Engineering (IOM), Permoserstrasse 15, 04318, Leipzig, Germany
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, University Leipzig, Linnéstrasse 2, 04103, Leipzig, Germany
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9
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Siddiqui SA, Stuyver T, Shaik S, Dubey KD. Designed Local Electric Fields-Promising Tools for Enzyme Engineering. JACS AU 2023; 3:3259-3269. [PMID: 38155642 PMCID: PMC10752214 DOI: 10.1021/jacsau.3c00536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 12/30/2023]
Abstract
Designing efficient catalysts is one of the ultimate goals of chemists. In this Perspective, we discuss how local electric fields (LEFs) can be exploited to improve the catalytic performance of supramolecular catalysts, such as enzymes. More specifically, this Perspective starts by laying out the fundamentals of how local electric fields affect chemical reactivity and review the computational tools available to study electric fields in various settings. Subsequently, the advances made so far in optimizing enzymatic electric fields through targeted mutations are discussed critically and concisely. The Perspective ends with an outlook on some anticipated evolutions of the field in the near future. Among others, we offer some pointers on how the recent data science/machine learning revolution, engulfing all science disciplines, could potentially provide robust and principled tools to facilitate rapid inference of electric field effects, as well as the translation between optimal electrostatic environments and corresponding chemical modifications.
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Affiliation(s)
- Shakir Ali Siddiqui
- Molecular Simulation Lab, Department of Chemistry,
School of Natural Sciences, Shiv Nadar Institution of Eminence,
Delhi NCR, India 201314
| | - Thijs Stuyver
- Ecole Nationale Supérieure de
Chimie de Paris, Université PSL, CNRS, Institute of Chemistry for Life and Health
Sciences, 75 005 Paris, France
| | - Sason Shaik
- Institute of Chemistry, Edmond J Safra Campus,
The Hebrew University of Jerusalem, Givat Ram, Jerusalem,
9190400, Israel
| | - Kshatresh Dutta Dubey
- Molecular Simulation Lab, Department of Chemistry,
School of Natural Sciences, Shiv Nadar Institution of Eminence,
Delhi NCR, India 201314
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10
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Song Z, Liang C, Gong K, Zhao S, Yuan X, Zhang X, Xie J. Harnessing the High Interfacial Electric Fields on Water Microdroplets to Accelerate Menshutkin Reactions. J Am Chem Soc 2023; 145:26003-26008. [PMID: 38011046 DOI: 10.1021/jacs.3c11650] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Even though it is still an emerging field, the application of a high external electric field (EEF) as a green and efficient catalyst in synthetic chemistry has recently received significant attention for the ability to deliver remarkable control of reaction selectivity and acceleration of reaction rates. Here, we extend the application of the EEF to Menshutkin reactions by taking advantage of the spontaneous high electric field at the air-water interfaces of sprayed water microdroplets. Experimentally, a series of Menshutkin reactions were accelerated by 7 orders of magnitude. Theoretically, both density functional theory calculations and ab initio molecular dynamics simulations predict that the reaction barrier decreases significantly in the presence of oriented external electric fields, thereby supporting the notion that the electric fields in the water droplets are responsible for the catalysis. In addition, the ordered solvent and reactant molecules oriented by the electric field alleviate the steric effect of solvents and increase the successful collision rates, thus facilitating faster nucleophilic attack. The success of Menshutkin reactions in this study showcases the great potential of microdroplet chemistry for green synthesis.
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Affiliation(s)
- Zhexuan Song
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Chiyu Liang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin 300071, China
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, China
| | - Ke Gong
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Supin Zhao
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Xu Yuan
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin 300071, China
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, China
| | - Xinxing Zhang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin 300071, China
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, China
| | - Jing Xie
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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11
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Zheng C, Ji Z, Mathews II, Boxer SG. Enhanced active-site electric field accelerates enzyme catalysis. Nat Chem 2023; 15:1715-1721. [PMID: 37563323 PMCID: PMC10906027 DOI: 10.1038/s41557-023-01287-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/29/2023] [Indexed: 08/12/2023]
Abstract
The design and improvement of enzymes based on physical principles remain challenging. Here we demonstrate that the principle of electrostatic catalysis can be leveraged to substantially improve a natural enzyme's activity. We enhanced the active-site electric field in horse liver alcohol dehydrogenase by replacing the serine hydrogen-bond donor with threonine and replacing the catalytic Zn2+ with Co2+. Based on the electric field enhancement, we make a quantitative prediction of rate acceleration-50-fold faster than the wild-type enzyme-which was in close agreement with experimental measurements. The effects of the hydrogen bonding and metal coordination, two distinct chemical forces, are described by a unified physical quantity-electric field, which is quantitative, and shown here to be additive and predictive. These results suggest a new design paradigm for both biological and non-biological catalysts.
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Affiliation(s)
- Chu Zheng
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Zhe Ji
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA, USA.
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12
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Vaissier Welborn V. Understanding Cysteine Reactivity in Protein Environments with Electric Fields. J Phys Chem B 2023; 127:9936-9942. [PMID: 37962274 DOI: 10.1021/acs.jpcb.3c05749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The role cysteine residues play in proteins is mediated by their protonation state, whereby the thiolate form of the side chain is highly reactive while the thiol form is more inert. However, the pKa of cysteine residues is hard to predict as it can differ widely from its reference value in solution, an effect that is accentuated by local effects in the heterogeneous protein environment. Here, we present a new approach to the prediction of cysteine reactivity based on electric field calculations at the thiol/thiolate group. We validated our approach by predicting the protonation state of cysteine residues in different protein environments (in the active site, at the protein surface, and buried within the protein interior), including Cys-25 in papaya protease omega, which was proven problematic for the more traditional constant pH molecular dynamics (MD) technique. We predict pKa shifts consistent with experimental observations, and the decomposition of the electric fields into contributions from molecular fragments provides a direct handle to rationalize local pH and pKa effects in proteins without introducing parameters other than those of the force field used for MD simulations.
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Affiliation(s)
- Valerie Vaissier Welborn
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
- Macromolecules Innovation Institute (MII),Virginia Tech, Blacksburg, Virginia 24060, United States
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13
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Piskorz TK, Martí-Centelles V, Spicer RL, Duarte F, Lusby PJ. Picking the lock of coordination cage catalysis. Chem Sci 2023; 14:11300-11331. [PMID: 37886081 PMCID: PMC10599471 DOI: 10.1039/d3sc02586a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/29/2023] [Indexed: 10/28/2023] Open
Abstract
The design principles of metallo-organic assembly reactions have facilitated access to hundreds of coordination cages of varying size and shape. Many of these assemblies possess a well-defined cavity capable of hosting a guest, pictorially mimicking the action of a substrate binding to the active site of an enzyme. While there are now a growing collection of coordination cages that show highly proficient catalysis, exhibiting both excellent activity and efficient turnover, this number is still small compared to the vast library of metal-organic structures that are known. In this review, we will attempt to unpick and discuss the key features that make an effective coordination cage catalyst, linking structure to activity (and selectivity) using lessons learnt from both experimental and computational analysis of the most notable exemplars. We will also provide an outlook for this area, reasoning why coordination cages have the potential to become the gold-standard in (synthetic) non-covalent catalysis.
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Affiliation(s)
- Tomasz K Piskorz
- Chemistry Research Laboratory, University of Oxford Oxford OX1 3TA UK
| | - Vicente Martí-Centelles
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València Camino de Vera, s/n 46022 Valencia Spain
| | - Rebecca L Spicer
- Department of Chemistry, Lancaster University Lancaster LA14YB UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, University of Oxford Oxford OX1 3TA UK
| | - Paul J Lusby
- EaStCHEM School of Chemistry, University of Edinburgh Edinburgh Scotland EH9 3FJ UK
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14
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Diao W, Farrell JD, Wang B, Ye F, Wang Z. Preorganized Internal Electric Field Promotes a Double-Displacement Mechanism for the Adenine Excision Reaction by Adenine DNA Glycosylase. J Phys Chem B 2023; 127:8551-8564. [PMID: 37782825 DOI: 10.1021/acs.jpcb.3c04928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Adenine DNA glycosylase (MutY) is a monofunctional glycosylase, removing adenines (A) misinserted opposite 8-oxo-7,8-dihydroguanine (OG), a common product of oxidative damage to DNA. Through multiscale calculations, we decipher a detailed adenine excision mechanism of MutY that is consistent with all available experimental data, involving an initial protonation step and two nucleophilic displacement steps. During the first displacement step, N-glycosidic bond cleavage is accompanied by the attack of the carboxylate group of residue Asp144 at the anomeric carbon (C1'), forming a covalent glycosyl-enzyme intermediate to stabilize the fleeting oxocarbenium ion. After departure of the excised base, water nucleophiles can be recruited to displace Asp144, completing the catalytic cycle with retention of stereochemistry at the C1' position. The two displacement reactions are found to mostly involve the movement of the oxocarbenium ion, occurring with large charge reorganization and thus sensitive to the internal electric field (IEF) exerted by the polar protein environment. Intriguingly, we find that the negatively charged carboxylate group is a good nucleophile for the oxocarbenium ion, yet an unactivated water molecule is not, and that the electric field catalysis strategy is used by the enzyme to enable its unique double-displacement reaction mechanism. A strong IEF, pointing toward 5' direction of the substrate sugar ring, greatly facilitates the second displacement reaction at the expense of elevating the barrier of the first one, thereby allowing both reactions to occur. These findings not only increase our understanding of the strategies used by DNA glycosylases to repair DNA lesions, but also have important implications for how internal/external electric field can be applied to modulate chemical reactions.
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Affiliation(s)
- Wenwen Diao
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - James D Farrell
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Fangfu Ye
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang 325000, China
| | - Zhanfeng Wang
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
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15
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Zhu C, Pham LN, Yuan X, Ouyang H, Coote ML, Zhang X. High Electric Fields on Water Microdroplets Catalyze Spontaneous and Fast Reactions in Halogen-Bond Complexes. J Am Chem Soc 2023; 145:21207-21212. [PMID: 37724917 DOI: 10.1021/jacs.3c08818] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
The use of external electric fields as green and efficient catalysts in synthetic chemistry has recently received significant attention for their ability to deliver remarkable control of reaction selectivity and acceleration of reaction rates. Technically, methods of generating high electric fields in the range of 1-10 V/nm are limited, as in-vacuo techniques have obvious scalability issues. The spontaneous high fields at various interfaces promise to solve this problem. In this study, we take advantage of the spontaneous high electric field at the air-water interface of sprayed water microdroplets in the reactions of several halogen bond systems: Nu:--X-X, where Nu: is pyridine or quinuclidine and X is bromine or iodine. The field facilitates ultrafast electron transfer from Nu:, yielding a Nu-X covalent bond and causing the X-X bond to cleave. This reaction occurs in microseconds in microdroplets but takes days to weeks in bulk solution. Density functional theory calculations predict that the reaction becomes barrier-free in the presence of oriented external electric fields, supporting the notion that the electric fields in the water droplets are responsible for the catalysis. We anticipate that microdroplet chemistry will be an avenue rich in opportunities in the reactions facilitated by high electric fields and provides an alternative way to tackle the scalability problem.
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Affiliation(s)
- Chenghui Zhu
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin, 300071, China
- Beijing National Laboratory for Molecular Sciences, Beijing, 100190, China
| | - Le Nhan Pham
- Institute for Nanoscale Science & Technology, Flinders University, Adelaide, South Australia 5042, Australia
| | - Xu Yuan
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin, 300071, China
- Beijing National Laboratory for Molecular Sciences, Beijing, 100190, China
| | - Haoran Ouyang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin, 300071, China
- Beijing National Laboratory for Molecular Sciences, Beijing, 100190, China
| | - Michelle L Coote
- Institute for Nanoscale Science & Technology, Flinders University, Adelaide, South Australia 5042, Australia
| | - Xinxing Zhang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin, 300071, China
- Beijing National Laboratory for Molecular Sciences, Beijing, 100190, China
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16
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Bofill JM, Severi M, Quapp W, Ribas-Ariño J, Moreira IDPR, Albareda G. An algorithm to find the optimal oriented external electrostatic field for annihilating a reaction barrier in a polarizable molecular system. J Chem Phys 2023; 159:114112. [PMID: 37724726 DOI: 10.1063/5.0167749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023] Open
Abstract
The use of oriented external electric fields (OEEFs) to promote and control chemical reactivity has motivated many theoretical and computational studies in the last decade to model the action of OEEFs on a molecular system and its effects on chemical processes. Given a reaction, a central goal in this research area is to predict the optimal OEEF (oOEEF) required to annihilate the reaction energy barrier with the smallest possible field strength. Here, we present a model rooted in catastrophe and optimum control theories that allows us to find the oOEEF for a given reaction valley in the potential energy surface (PES). In this model, the effective (or perturbed) PES of a polarizable molecular system is constructed by adding to the original, non-perturbed, PES a term accounting for the interaction of the OEEF with the intrinsic electric dipole and polarizability of the molecular system, so called the polarizable molecular electric dipole (PMED) model. We demonstrate that the oOEEF can be established by locating a point in the original PES with unique topological properties: the optimal barrier breakdown or bond-breaking point (oBBP). The essential feature of the oBBP structure is the fact that this point maintains its topological properties for all the applied OEEFs, also for the unperturbed PES, thus becoming much more relevant than the commonly used minima and transition state structures. The PMED model proposed here has been implemented in an open access package and is shown to successfully predict the oOEEF for two processes: an isomerization reaction of a cumulene derivative and the Huisgen cycloaddition reaction.
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Affiliation(s)
- Josep Maria Bofill
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institut de Química Teòrica i Computacional, (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Marco Severi
- Department of Chemistry G. Ciamician, University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Wolfgang Quapp
- Mathematisches Institut, Universität Leipzig, PF 100920, D-04009 Leipzig, Germany
| | - Jordi Ribas-Ariño
- Institut de Química Teòrica i Computacional, (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Departament de Ciència de Materials i Química Física, Secció de Química Física, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Ibério de P R Moreira
- Institut de Química Teòrica i Computacional, (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Departament de Ciència de Materials i Química Física, Secció de Química Física, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Guillermo Albareda
- Ideaded, Carrer de la Tecnologia, 35, 08840 Viladecans, Barcelona, Spain
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17
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Langer N, LeGrand M, Kedem O. Cationic Polymer Coating Increases the Catalytic Activity of Gold Nanoparticles toward Anionic Substrates. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37289992 DOI: 10.1021/acsami.3c04087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Organic coatings on catalytic metal nanoparticles (NPs) typically hinder their activity due to the blocking of active sites. Therefore, considerable effort is made to remove organic ligands when preparing supported NP catalytic materials. Here, cationic polyelectrolyte coatings are shown to increase the catalytic activity of partially embedded gold nanoislands (Au NIs) toward transfer hydrogenation and oxidation reactions with anionic substrates compared to the activity of identical but uncoated Au NIs. Any potential steric hindrance caused by the coating is countered by a decrease in the activation energy of the reaction by half, resulting in overall enhancement. The direct comparison to identical but uncoated NPs isolates the role of the coating and provides conclusive evidence of enhancement. Our findings show that engineering the microenvironment of heterogeneous catalysts, creating hybrid materials that cooperatively interact with the reactants involved, is a viable and exciting path to improving their performance.
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Affiliation(s)
- Nicholas Langer
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Mason LeGrand
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Ofer Kedem
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
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18
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Yan S, Ji X, Peng W, Wang B. Evaluating the Transition State Stabilization/Destabilization Effects of the Electric Fields from Scaffold Residues by a QM/MM Approach. J Phys Chem B 2023; 127:4245-4253. [PMID: 37155960 DOI: 10.1021/acs.jpcb.3c01054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The protein scaffolds of enzymes not only provide structural support for the catalytic center but also exert preorganized electric fields for electrostatic catalysis. In recent years, uniform oriented external electric fields (OEEFs) have been widely applied to enzymatic reactions to mimic the electrostatic effects of the environment. However, the electric fields exerted by individual residues in proteins may be quite heterogeneous across the active site, with varying directions and strengths at different positions of the active site. Here, we propose a QM/MM-based approach to evaluate the effects of the electric fields exerted by individual residues in the protein scaffold. In particular, the heterogeneity of the residue electric fields and the effect of the native protein environment can be properly accounted for by this QM/MM approach. A case study of the O-O heterolysis reaction in the catalytic cycle of TyrH shows that (1) for scaffold residues that are relatively far from the active site, the heterogeneity of the residue electric field in the active site is not very significant and the electrostatic stabilization/destabilization due to each residue can be well approximated with the interaction energy between a uniform electric field and the QM region dipole; (2) for scaffold residues near the active site, the residue electric fields can be highly heterogeneous along the breaking O-O bond. In such a case, approximating the residue electric fields as uniform fields may misrepresent the overall electrostatic effect of the residue. The present QM/MM approach can be applied to evaluate the residues' electrostatic impact on enzymatic reactions, which also can be useful in computational optimization of electric fields to boost the enzyme catalysis.
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Affiliation(s)
- Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Xinwei Ji
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Wei Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
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19
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Liang Q, Zhu C, Yang J. Water Charge Transfer Accelerates Criegee Intermediate Reaction with H 2O - Radical Anion at the Aqueous Interface. J Am Chem Soc 2023; 145:10159-10166. [PMID: 37011411 DOI: 10.1021/jacs.3c00734] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Criegee intermediates (CIs) are important carbonyl oxides that may react with atmospheric trace chemicals and impact the global climate. The CI reaction with water has been widely studied and is a main channel for trapping CIs in the troposphere. Previous experimental and computational reports have largely focused on reaction kinetic processes in various CI-water reactions. The molecular-level origin of CI's interfacial reactivity at the water microdroplet surface (e.g., as found in aerosols and clouds) is unclear. In this study, by employing the quantum mechanical/molecular mechanical (QM/MM) Born-Oppenheimer molecular dynamics with the local second-order Møller-Plesset perturbation theory, our computational results reveal a substantial water charge transfer up to ∼20% per water, which creates the surface H2O+/H2O- radical pairs to enhance the CH2OO and anti-CH3CHOO reactivity with water: the resulting strong CI-H2O- electrostatic attraction at the microdroplet surface facilitates the nucleophilic attack to the CI carbonyl by water, which may counteract the apolar hindrance of the substituent to accelerate the CI-water reaction. Our statistical analysis of the molecular dynamics trajectories further resolves a relatively long-lived bound CI(H2O-) intermediate state at the air/water interface, which has not been observed in gaseous CI reactions. This work provides insights into what may alter the oxidizing power of the troposphere by the next larger CIs than simple CH2OO and implicates a new perspective on the role of interfacial water charge transfer in accelerating molecular reactions at aqueous interfaces.
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Affiliation(s)
- Qiujiang Liang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Chongqin Zhu
- College of Chemistry, Key Laboratory of Theoretical & Computational Photochemistry of Ministry of Education, Beijing Normal University, Beijing 100190, People's Republic of China
| | - Jun Yang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, People's Republic of China
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20
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Amer GE, Razak FIA, Sapari S, Nur H, Setu SA. Elucidating the alkene hydrogenation reaction based on cotton textile reduced graphene oxide under the influence of external electric field: Illustration of new noble method. Heliyon 2023; 9:e14888. [PMID: 37025917 PMCID: PMC10070902 DOI: 10.1016/j.heliyon.2023.e14888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/07/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
The hydrogenation reaction of alkene is one of the most used industrial chemical process for various materials of daily life and energy consumption. This is a heterogeneous reaction and traditionally carried out by metallic catalysis. However, these conventional catalytic hydrogenations of alkene suffer from various setbacks such as catalyst poisoning, less recyclability and are environmentally unfriendly. Therefore, in recent years, researchers have been trying to develop the alternatives to metal catalysis hydrogenation of alkene. Heterogeneous catalysis under the external electric field is considered the future of green catalysis. In this paper, we report a comprehensive investigation dealing with the theoretical basis for simulating the phenomenon of heterogeneous catalysis, on a molecular level, under an external electric field. The illustration of the prospect as well as the effects of the mostly used catalytic systems, reduced graphene oxide, under the influence of external electric fields is provided. Moreover, a noble method of alkene hydrogenation reaction based on cotton textile reduced graphene oxide (CT-RGO) under the influence of an external electric field is introduced. The corresponding theoretical investigation was carried out within the framework of the density functional theory (DFT) method using first-principles calculations. The study has been carried out by elucidating DFT calculations for three different proposed catalytic systems, namely without electricity, with electricity and with an external electric field of 2 milli-Atomic unit. The obtained results indicate that adsorption energy of H2 on the CT-RGO surface is significantly higher when the electric field is applied along the bond axis, suggesting thereby that hydrogenation of alkene can be induced with CT-RGO catalyst support under external electric fields. The obtained results shed light on the effect of the external electricity field on the graphene-hydrogen complex, the activation energy of graphene radicals to achieve the transition states as well as the adsorption of the hydrogen atoms over the graphene surface. Altogether, the theoretical results presented herein suggested that the proposed catalytic system holds promise for facilitating the alkene hydrogenation under external electric fields.
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21
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A catastrophe theory-based model for optimal control of chemical reactions by means of oriented electric fields. Theor Chem Acc 2023. [DOI: 10.1007/s00214-023-02959-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
AbstractThe effect of oriented external electric fields (OEEF) on chemical reactivity has been studied theoretically and computationally in the last decades. A central goal in this research area is to predict the orientation and the smallest amplitude electric field that renders a barrierless chemical process with the smallest possible strength. Recently, a model to find the optimal electric field has been proposed and described (Bofill JM et al., J. Chem. Theory Comput. 18:935, 2022). We here proof that this model is based on catastrophe and optimum control theories. Based on both theories a technical treatment of the model is given and applied to a two-dimensional generic example that provides insight into its nature and capability. Finally, the model is applied to determine the optimal OEEF for the trans-to-cis isomerization of a [3]cumulene derivative.
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22
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Neves RP, Ramos MJ, Fernandes PA. Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis. J Chem Inf Model 2023; 63:20-26. [PMID: 36534708 PMCID: PMC9832474 DOI: 10.1021/acs.jcim.2c01337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We describe an approach to identify enzyme mutants with increased turnover using the enzyme DszC as a case study. Our approach is based on recalculating the barriers of alanine mutants through single-point energy calculations at the hybrid QM/MM level in the wild-type reactant and transition state geometries. We analyze the difference in the electron density between the reactant and transition state to identify sites/residues where electrostatic interactions stabilize the transition state over the reactants. We also assess the insertion of a unit probe charge to identify positions in which the introduction of charged residues lowers the barrier.
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23
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Brunner syndrome caused by point mutation explained by multiscale simulation of enzyme reaction. Sci Rep 2022; 12:21889. [PMID: 36536002 PMCID: PMC9763434 DOI: 10.1038/s41598-022-26296-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Brunner syndrome is a disorder characterized by intellectual disability and impulsive, aggressive behavior associated with deficient function of the monoamine oxidase A (MAO-A) enzyme. These symptoms (along with particularly high serotonin levels) have been reported in patients with two missense variants in MAO-A (p.R45W and p.E446K). Herein, we report molecular simulations of the rate-limiting step of MAO-A-catalyzed serotonin degradation for these variants. We found that the R45W mutation causes a 6000-fold slowdown of enzymatic function, whereas the E446K mutation causes a 450-fold reduction of serotonin degradation rate, both of which are practically equivalent to a gene knockout. In addition, we thoroughly compared the influence of enzyme electrostatics on the catalytic function of both the wild type MAO-A and the p.R45W variant relative to the wild type enzyme, revealing that the mutation represents a significant electrostatic perturbation that contributes to the barrier increase. Understanding genetic disorders is closely linked to understanding the associated chemical mechanisms, and our research represents a novel attempt to bridge the gap between clinical genetics and the underlying chemical physics.
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24
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Vaissier Welborn V, Archer WR, Schulz MD. Characterizing Ion-Polymer Interactions in Aqueous Environment with Electric Fields. J Chem Inf Model 2022; 63:2030-2036. [PMID: 36533730 DOI: 10.1021/acs.jcim.2c01048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Polymers make the basis of highly tunable materials that could be designed and optimized for metal recovery from aqueous environments. While experimental studies show that this approach has potential, it suffers from a limited knowledge of the detailed molecular interaction between polymers and target metal ions. Here, we propose to calculate intrinsic electric fields from polarizable force field molecular dynamics simulations to characterize the driving force behind Eu3+ motion in the presence of poly(ethylenimine methylenephosphonate), a specifically designed metal chelating polymer. Focusing on the metal chelation initiation step (i.e., before binding), we can rationalize the role of each molecule on ion dynamics by projecting these electric fields along the direction of ion motion. We find that the polymer functional groups act indirectly, and the polymer-metal ion interaction is actually mediated by water. This result is consistent with the experimental observation that metal sequestration by these polymers is entropically driven. This study suggests that electric field calculations can help the design of metal chelating polymers, for example, by seeking to optimize polymer-solvent interactions rather than polymer-ion interactions.
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Affiliation(s)
- Valerie Vaissier Welborn
- Department of Chemistry, Macromolecules Innovation Institute (MII), Virginia Tech, Blacksburg, Virginia24060, United States
| | - William R. Archer
- Department of Chemistry, Macromolecules Innovation Institute (MII), Virginia Tech, Blacksburg, Virginia24060, United States
| | - Michael D. Schulz
- Department of Chemistry, Macromolecules Innovation Institute (MII), Virginia Tech, Blacksburg, Virginia24060, United States
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25
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Ji Z, Boxer SG. β-Lactamases Evolve against Antibiotics by Acquiring Large Active-Site Electric Fields. J Am Chem Soc 2022; 144:22289-22294. [PMID: 36399691 PMCID: PMC10075085 DOI: 10.1021/jacs.2c10791] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A compound bound covalently to an enzyme active site can act either as a substrate if the covalent linkage is readily broken up by the enzyme or as an inhibitor if the bond dissociates slowly. We tracked the reactivity of such bonds associated with the rise of the resistance to penicillin G (PenG) in protein evolution from penicillin-binding proteins (PBPs) to TEM β-lactamases and with the development of avibactam (Avb) to overcome the resistance. We found that the ester linkage in PBP-PenG is resistant to hydrolysis mainly due to the small electric fields present in the protein active site. Conversely, the same linkage in the descendant TEM-PenG experiences large electric fields that stabilize the more charge-separated transition state and thus lower the free energy barrier to hydrolysis. Specifically, the electric fields were improved from -59 to -140 MV/cm in an ancient evolution dating back billions of years, contributing 5 orders of magnitude rate acceleration. This trend continues today in the nullification of newly developed antibiotic drugs. The fast linkage hydrolysis acquired from evolution is counteracted by the upgrade of PenG to Avb whose linkage escapes from the hydrolysis by returning to a low-field environment. Using the framework of electrostatic catalysis, the electric field, an observable from vibrational spectroscopy, provides a unifying physical metric to understand protein evolution and to guide the design of covalent drugs.
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Affiliation(s)
- Zhe Ji
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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26
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Jiang Y, Stull SL, Shao Q, Yang ZJ. Convergence in determining enzyme functional descriptors across Kemp eliminase variants. ELECTRONIC STRUCTURE (BRISTOL, ENGLAND) 2022; 4:044007. [PMID: 37425623 PMCID: PMC10327861 DOI: 10.1088/2516-1075/acad51] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Molecular simulations have been extensively employed to accelerate biocatalytic discoveries. Enzyme functional descriptors derived from molecular simulations have been leveraged to guide the search for beneficial enzyme mutants. However, the ideal active-site region size for computing the descriptors over multiple enzyme variants remains untested. Here, we conducted convergence tests for dynamics-derived and electrostatic descriptors on 18 Kemp eliminase variants across six active-site regions with various boundary distances to the substrate. The tested descriptors include the root-mean-square deviation of the active-site region, the solvent accessible surface area ratio between the substrate and active site, and the projection of the electric field (EF) on the breaking C-H bond. All descriptors were evaluated using molecular mechanics methods. To understand the effects of electronic structure, the EF was also evaluated using quantum mechanics/molecular mechanics methods. The descriptor values were computed for 18 Kemp eliminase variants. Spearman correlation matrices were used to determine the region size condition under which further expansion of the region boundary does not substantially change the ranking of descriptor values. We observed that protein dynamics-derived descriptors, including RMSDactive_site and SASAratio, converge at a distance cutoff of 5 Å from the substrate. The electrostatic descriptor, EFC-H, converges at 6 Å using molecular mechanics methods with truncated enzyme models and 4 Å using quantum mechanics/molecular mechanics methods with whole enzyme model. This study serves as a future reference to determine descriptors for predictive modeling of enzyme engineering.
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Affiliation(s)
- Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Sebastian L Stull
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Zhongyue J Yang
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, United States of America
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States of America
- Data Science Institute, Vanderbilt University, Nashville, TN 37235, United States of America
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, United States of America
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27
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Meyer KAE, Nickson KA, Garand E. The impact of the electric field of metal ions on the vibrations and internal hydrogen bond strength in alkali metal ion di- and triglycine complexes. J Chem Phys 2022; 157:174301. [DOI: 10.1063/5.0117311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Using infrared predissociation spectroscopy of cryogenic ions, we revisit the vibrational spectra of alkali metal ion (Li+, Na+, K+) di- and triglycine complexes. We assign their most stable conformation, which involves metal ion coordination to all C=O groups and an internal NH⋯NH2 hydrogen bond in the peptide backbone. An analysis of the spectral shifts of the OH and C=O stretching vibrations across the different metal ions and peptide chain lengths shows that these are largely caused by the electric field of the metal ion, which varies in strength as a function of the square of the distance. The metal ion–peptide interaction also remotely modulates the strength of internal hydrogen bonding in the peptide backbone via the weakening of the amide C=O bond, resulting in a decrease in internal hydrogen bond strength from Li+ > Na+ > K+.
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Affiliation(s)
- Katharina A. E. Meyer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, USA
| | - Kathleen A. Nickson
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, USA
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, USA
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28
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Peng W, Yan S, Zhang X, Liao L, Zhang J, Shaik S, Wang B. How Do Preorganized Electric Fields Function in Catalytic Cycles? The Case of the Enzyme Tyrosine Hydroxylase. J Am Chem Soc 2022; 144:20484-20494. [DOI: 10.1021/jacs.2c09263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, People Republic of China
| | - Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, People Republic of China
| | - Xuan Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, People Republic of China
| | - Langxing Liao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, People Republic of China
| | - Jinyan Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, People Republic of China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407 Jerusalem, Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, People Republic of China
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29
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Hao H, Ruiz Pestana L, Qian J, Liu M, Xu Q, Head‐Gordon T. Chemical transformations and transport phenomena at interfaces. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hongxia Hao
- Kenneth S. Pitzer Theory Center and Department of Chemistry University of California Berkeley California USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
| | - Luis Ruiz Pestana
- Department of Civil and Architectural Engineering University of Miami Coral Gables Florida USA
| | - Jin Qian
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
| | - Meili Liu
- Department of Civil and Architectural Engineering University of Miami Coral Gables Florida USA
| | - Qiang Xu
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
| | - Teresa Head‐Gordon
- Kenneth S. Pitzer Theory Center and Department of Chemistry University of California Berkeley California USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
- Department of Bioengineering and Chemical and Biomolecular Engineering University of California Berkeley California USA
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30
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Wang Z, Xiao F, Shen X, Zhang D, Chu W, Zhao H, Zhao G. Electronic Control of Traditional Iron-Carbon Electrodes to Regulate the Oxygen Reduction Route to Scale Up Water Purification. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13740-13750. [PMID: 36130282 DOI: 10.1021/acs.est.2c03673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Shifting four-electron (4e-) oxygen reduction in fuel cell technology to a two-electron (2e-) pathway with traditional iron-carbon electrodes is a critical step for hydroxyl radical (HO•) generation. Here, we fabricated iron-carbon aerogels with desired dimensions (e.g., 40 cm × 40 cm) as working electrodes containing atomic Fe sites and Fe3C subnanoclusters. Electron-donating Fe3C provides electrons to FeN4 through long-range activation for achieving the ideal electronic configuration, thereby optimizing the binding energy of the *OOH intermediate. With an iron-carbon aerogel benefiting from finely tuned electronic density, the selectivity of 2e- oxygen reduction increased from 10 to 90%. The resultant electrode exhibited unexpectedly efficient HO• production and fast elimination of organics. Notably, the kinetic constant kM for sulfamethoxazole (SMX) removal is 60 times higher than that in a traditional iron-carbon electrode. A flow-through pilot device with the iron-carbon aerogel (SA-Fe0.4NCA) was built to scale up micropolluted water decontamination. The initial total organic carbon (TOC) value of micropolluted water was 4.02 mg L-1, and it declined and maintained at 2.14 mg L-1, meeting the standards for drinking water quality in China. Meanwhile, the generation of emerging aromatic nitrogenous disinfection byproducts (chlorophenylacetonitriles) declined by 99.2%, satisfying the public safety of domestic water. This work provides guidance for developing electrochemical technologies to satisfy the flexible and economic demand for water purification, especially in water-scarce areas.
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Affiliation(s)
- Zining Wang
- Shanghai Key Laboratory of Chemical Assessment and Sustainability, Key Laboratory of Yangtze River Water Environment, School of Chemical Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Fan Xiao
- Shanghai Key Laboratory of Chemical Assessment and Sustainability, Key Laboratory of Yangtze River Water Environment, School of Chemical Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xuqian Shen
- Shanghai Key Laboratory of Chemical Assessment and Sustainability, Key Laboratory of Yangtze River Water Environment, School of Chemical Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Di Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Wenhai Chu
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Hongying Zhao
- Shanghai Key Laboratory of Chemical Assessment and Sustainability, Key Laboratory of Yangtze River Water Environment, School of Chemical Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Guohua Zhao
- Shanghai Key Laboratory of Chemical Assessment and Sustainability, Key Laboratory of Yangtze River Water Environment, School of Chemical Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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31
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Diao W, Yan S, Farrell JD, Wang B, Ye F, Wang Z. Preorganized Internal Electric Field Powers Catalysis in the Active Site of Uracil-DNA Glycosylase. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wenwen Diao
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - James D. Farrell
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Fangfu Ye
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang 325001, China
| | - Zhanfeng Wang
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
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32
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Freindorf M, Delgado AAA, Kraka E. CO bonding in hexa‐ and pentacoordinate carboxy‐neuroglobin: A quantum mechanics/molecular mechanics and local vibrational mode study. J Comput Chem 2022. [DOI: 10.1002/jcc.26973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marek Freindorf
- Department of Chemistry Southern Methodist University Dallas Texas USA
| | | | - Elfi Kraka
- Department of Chemistry Southern Methodist University Dallas Texas USA
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33
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Hoffmann NM, Wang X, Berkelbach TC. Linear Free Energy Relationships in Electrostatic Catalysis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Norah M. Hoffmann
- Department of Chemistry, Columbia University, New York, New York 10027 United States
| | - Xiao Wang
- Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010 United States
| | - Timothy C. Berkelbach
- Department of Chemistry, Columbia University, New York, New York 10027 United States
- Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010 United States
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34
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Zhang S, Zhang J, Luo W, Wang P, Zhu Y. A preorganization oriented computational method for de novo design of Kemp elimination enzymes. Enzyme Microb Technol 2022; 160:110093. [DOI: 10.1016/j.enzmictec.2022.110093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/13/2022] [Accepted: 06/30/2022] [Indexed: 11/26/2022]
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35
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Wan M, Yue H, Notarangelo J, Liu H, Che F. Deep Learning-Assisted Investigation of Electric Field-Dipole Effects on Catalytic Ammonia Synthesis. JACS AU 2022; 2:1338-1349. [PMID: 35783174 PMCID: PMC9241008 DOI: 10.1021/jacsau.2c00003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 05/21/2023]
Abstract
External electric fields can modify binding energies of reactive surface species and enhance catalytic performance of heterogeneously catalyzed reactions. In this work, we used density functional theory (DFT) calculations-assisted and accelerated by a deep learning algorithm-to investigate the extent to which ruthenium-catalyzed ammonia synthesis would benefit from application of such external electric fields. This strategy allows us to determine which electronic properties control a molecule's degree of interaction with external electric fields. Our results show that (1) field-dependent adsorption/reaction energies are closely correlated to the dipole moments of intermediates over the surface, (2) a positive field promotes ammonia synthesis by lowering the overall energetics and decreasing the activation barriers of the potential rate-limiting steps (e.g., NH2 hydrogenation) over Ru, (3) a positive field (>0.6 V/Å) favors the reaction mechanism by avoiding kinetically unfavorable N≡N bond dissociation over Ru(1013), and (4) local adsorption environments (i.e., dipole moments of the intermediates in the gas phase, surface defects, and surface coverage of intermediates) influence the resulting surface adsorbates' dipole moments and further modify field-dependent reaction energetics. The deep learning algorithm developed here accelerates field-dependent energy predictions with acceptable accuracies by five orders of magnitudes compared to DFT alone and has the capacity of transferability, which can predict field-dependent energetics of other catalytic surfaces with high-quality performance using little training data.
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Affiliation(s)
- Mingyu Wan
- Department
of Chemical Engineering, University of Massachusetts
Lowell, Lowell 01854, United States
| | - Han Yue
- Michtom
School of Computer Science, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Jaime Notarangelo
- Department
of Chemical Engineering, University of Massachusetts
Lowell, Lowell 01854, United States
| | - Hongfu Liu
- Michtom
School of Computer Science, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Fanglin Che
- Department
of Chemical Engineering, University of Massachusetts
Lowell, Lowell 01854, United States
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36
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Geoffroy-Neveux A, Labet V, Alikhani ME. Influence of an Oriented External Electric Field on the Mechanism of Double Proton Transfer between Pyrazole and Guanidine: from an Asynchronous Plateau Transition State to a Synchronous or Stepwise Mechanism. J Phys Chem A 2022; 126:3057-3071. [PMID: 35544749 DOI: 10.1021/acs.jpca.1c10553] [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
The double proton transfer (DPT) reaction between pyrazole and guanidine, a concerted reaction but strongly asynchronous and presenting a "plateau transition region", has been theoretically reinvestigated in the presence of an external uniform electric field. First, we computed the reaction path by DFT and proposed a very detailed description of the constitutive electronic events, based on the ELF topology and the bond evolution theory. Then, we studied the effect of an oriented external electric field (OEEF) on the reaction mechanism, for an OEEF oriented along the proton transfer axis. We observe that in one direction, the DPT reaction can be transformed into a stepwise reaction, going through a stabilized single proton transferred intermediate. Contrarily, the two proton transfers occur simultaneously when the electric field is applied in the opposite direction. In the latter case, the order in which the two protons are transferred in the same elementary step can even be reversed if the OEEF is intense enough. Finally, it has been shown that the evolution of the double proton transfer reaction in the presence of an electric field could be quantitatively anticipated by analyzing the ELF value at the bifurcation point between V(A, H) proton donor and V(B) proton acceptor of the double hydrogen bonded complex in the entrance channel.
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Affiliation(s)
| | - Vanessa Labet
- MONARIS UMR 8233 CNRS, Sorbonne Université, 4 place Jussieu, 75252 Paris Cedex 05, France
| | - M Esmail Alikhani
- MONARIS UMR 8233 CNRS, Sorbonne Université, 4 place Jussieu, 75252 Paris Cedex 05, France
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37
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A two-directional vibrational probe reveals different electric field orientations in solution and an enzyme active site. Nat Chem 2022; 14:891-897. [PMID: 35513508 PMCID: PMC10082611 DOI: 10.1038/s41557-022-00937-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/25/2022] [Indexed: 12/26/2022]
Abstract
The catalytic power of an electric field depends on its magnitude and orientation with respect to the reactive chemical species. Understanding and designing new catalysts for electrostatic catalysis thus requires methods to measure the electric field orientation and magnitude at the molecular scale. We demonstrate that electric field orientations can be extracted using a two-directional vibrational probe by exploiting the vibrational Stark effect of both the C=O and C-D stretches of a deuterated aldehyde. Combining spectroscopy with molecular dynamics and electronic structure partitioning methods, we demonstrate that, despite distinct polarities, solvents act similarly in their preference for electrostatically stabilizing large bond dipoles at the expense of destabilizing small ones. In contrast, we find that for an active-site aldehyde inhibitor of liver alcohol dehydrogenase, the electric field orientation deviates markedly from that found in solvents, which provides direct evidence for the fundamental difference between the electrostatic environment of solvents and that of a preorganized enzyme active site.
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38
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Kelty ML, McNeece AJ, Kurutz JW, Filatov AS, Anderson JS. Electrostatic vs. inductive effects in phosphine ligand donor properties and reactivity. Chem Sci 2022; 13:4377-4387. [PMID: 35509471 PMCID: PMC9007067 DOI: 10.1039/d1sc04277g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 03/15/2022] [Indexed: 11/21/2022] Open
Abstract
Enhanced rates and selectivity in enzymes are enabled in part by precisely tuned electric fields within active sites. Analogously, the use of charged groups to leverage electrostatics in molecular systems is a promising strategy to tune reactivity. However, separation of the through space and through bond effects of charged functional groups is a long standing challenge that limits the rational application of electric fields in molecular systems. To address this challenge we developed a method using the phosphorus selenium coupling value (J P-Se) of anionic phosphine selenides to quantify the electrostatic contribution of the borate moiety to donor strength. In this analysis we report the synthesis of a novel anionic phosphine, PPh2CH2BF3K, the corresponding tetraphenyl phosphonium and tetraethyl ammonium selenides [PPh4][SePPh2CH2BF3] and [TEA][SePPh2CH2BF3], and the Rh carbonyl complex [PPh4][Rh(acac)(CO)(PPh2(CH2BF3))]. Solvent-dependent changes in J P-Se were fit using Coulomb's law and support up to an 80% electrostatic contribution to the increase in donor strength of [PPh4][SePPh2CH2BF3] relative to SePPh2Et, while controls with [TEA][SePPh2CH2BF3] exclude convoluting ion pairing effects. Calculations using explicit solvation or point charges effectively replicate the experimental data. This J P-Se method was extended to [PPh4][SePPh2(2-BF3Ph)] and likewise estimates up to a 70% electrostatic contribution to the increase in donor strength relative to SePPh3. The use of PPh2CH2BF3K also accelerates C-F oxidative addition reactivity with Ni(COD)2 by an order of magnitude in comparison to the comparatively donating neutral phosphines PEt3 and PCy3. This enhanced reactivity prompted the investigation of catalytic fluoroarene C-F borylation, with improved yields observed for less fluorinated arenes. These results demonstrate that covalently bound charged functionalities can exert a significant electrostatic influence under common solution phase reaction conditions and experimentally validate theoretical predictions regarding electrostatic effects in reactivity.
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Affiliation(s)
- Margaret L Kelty
- Department of Chemistry, University of Chicago 929 E 57th St Chicago IL 60637 USA
| | - Andrew J McNeece
- Department of Chemistry, University of Chicago 929 E 57th St Chicago IL 60637 USA
| | - Josh W Kurutz
- Department of Chemistry, University of Chicago 929 E 57th St Chicago IL 60637 USA
| | - Alexander S Filatov
- Department of Chemistry, University of Chicago 929 E 57th St Chicago IL 60637 USA
| | - John S Anderson
- Department of Chemistry, University of Chicago 929 E 57th St Chicago IL 60637 USA
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39
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Jiang Y, Yan B, Chen Y, Juarez RJ, Yang ZJ. Molecular Dynamics-Derived Descriptor Informs the Impact of Mutation on the Catalytic Turnover Number in Lactonase Across Substrates. J Phys Chem B 2022; 126:2486-2495. [PMID: 35324218 DOI: 10.1021/acs.jpcb.2c00142] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics simulations have been extensively employed to reveal the roles of protein dynamics in mediating enzyme catalysis. However, simulation-derived predictive descriptors that inform the impacts of mutations on catalytic turnover numbers remain largely unexplored. In this work, we report the identification of molecular modeling-derived descriptors to predict mutation effect on the turnover number of lactonase SsoPox with both native and non-native substrates. The study consists of 10 enzyme-substrate complexes resulting from a combination of five enzyme variants with two substrates. For each complex, we derived 15 descriptors from molecular dynamics simulations and applied principal component analysis to rank the predictive capability of the descriptors. A top-ranked descriptor was identified, which is the solvent-accessible surface area (SASA) ratio of the substrate to the active site pocket. A uniform volcano-shaped plot was observed in the distribution of experimental activation free energy against the SASA ratio. To achieve efficient lactonase hydrolysis, a non-native substrate-bound enzyme variant needs to involve a similar range of the SASA ratio to the native substrate-bound wild-type enzyme. The descriptor reflects how well the enzyme active site pocket accommodates a substrate for reaction, which has the potential of guiding optimization of enzyme reaction turnover for non-native chemical transformations.
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Affiliation(s)
- Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Bailu Yan
- Department of Biostatistics, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Yu Chen
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Reecan J Juarez
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Zhongyue J Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States.,Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
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40
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Lawal MM, Vaissier Welborn V. Structural dynamics support electrostatic interactions in the active site of Adenylate Kinase. Chembiochem 2022; 23:e202200097. [PMID: 35303385 DOI: 10.1002/cbic.202200097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Indexed: 11/12/2022]
Abstract
Electrostatic preorganization as well as structural and dynamic heterogeneity are often used to rationalize the remarkable catalytic efficiency of enzymes. However, they are often presented as incompatible because the generation of permanent electrostatic effects implies that the protein structure remains rigid. Here, we use a metric, electric fields, that can treat electrostatic contributions and dynamics effects on equal footing, for a unique perspective on enzymatic catalysis. We find that the residues that contribute the most to electrostatic interactions with the substrate in the active site of Adenylate Kinase (our working example) are also the most flexible residues. Further, entropy-tuning mutations raise flexibility at the picosecond timescale where more conformations can be visited on short time periods, thereby softening the sharp heterogeneity normally visible at the microsecond timescale.
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Affiliation(s)
| | - Valerie Vaissier Welborn
- Virginia Polytechnic Institute and State University, Chemistry, Davidson 421A, 1040 Drillfield Drive, 24073, Blacksburg, UNITED STATES
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41
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Tarzia A, Jelfs KE. Unlocking the computational design of metal-organic cages. Chem Commun (Camb) 2022; 58:3717-3730. [PMID: 35229861 PMCID: PMC8932387 DOI: 10.1039/d2cc00532h] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/22/2022] [Indexed: 12/11/2022]
Abstract
Metal-organic cages are macrocyclic structures that can possess an intrinsic void that can hold molecules for encapsulation, adsorption, sensing, and catalysis applications. As metal-organic cages may be comprised from nearly any combination of organic and metal-containing components, cages can form with diverse shapes and sizes, allowing for tuning toward targeted properties. Therefore, their near-infinite design space is almost impossible to explore through experimentation alone and computational design can play a crucial role in exploring new systems. Although high-throughput computational design and screening workflows have long been known as powerful tools in drug and materials discovery, their application in exploring metal-organic cages is more recent. We show examples of structure prediction and host-guest/catalytic property evaluation of metal-organic cages. These examples are facilitated by advances in methods that handle metal-containing systems with improved accuracy and are the beginning of the development of automated cage design workflows. We finally outline a scope for how high-throughput computational methods can assist and drive experimental decisions as the field pushes toward functional and complex metal-organic cages. In particular, we highlight the importance of considering realistic, flexible systems.
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Affiliation(s)
- Andrew Tarzia
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, London, W12 0BZ, UK.
| | - Kim E Jelfs
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, London, W12 0BZ, UK.
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42
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Li WL, Hao H, Head-Gordon T. Optimizing the Solvent Reorganization Free Energy by Metal Substitution for Nanocage Catalysis. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05980] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Wan-Lu Li
- Kenneth S. Pitzer Center for Theoretical Chemistry, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hongxia Hao
- Kenneth S. Pitzer Center for Theoretical Chemistry, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
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43
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Léonard NG, Chantarojsiri T, Ziller JW, Yang JY. Cationic Effects on the Net Hydrogen Atom Bond Dissociation Free Energy of High-Valent Manganese Imido Complexes. J Am Chem Soc 2022; 144:1503-1508. [PMID: 35041788 PMCID: PMC9118977 DOI: 10.1021/jacs.1c09583] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Local electric fields can alter energy landscapes to impart enhanced reactivity in enzymes and at surfaces. Similar fields can be generated in molecular systems using charged functionalities. Manganese(V) salen nitrido complexes (salen = N,N'-ethylenebis(salicylideneaminato)) appended with a crown ether unit containing Na+ (1-Na), K+, (1-K), Ba2+ (1-Ba), Sr2+ (1-Sr), La3+ (1-La), or Eu3+ (1-Eu) cation were investigated to determine the effect of charge on pKa, E1/2, and the net bond dissociation free energy (BDFE) of N-H bonds. The series, which includes the manganese(V) salen nitrido without an appended crown, spans 4 units of charge. Bounds for the pKa values of the transient imido complexes were used with the Mn(VI/V) reduction potentials to calculate the N-H BDFEs of the imidos in acetonitrile. Despite a span of >700 mV and >9 pKa units across the series, the hydrogen atom BDFE only spans ∼6 kcal/mol (between 73 and 79 kcal/mol). These results suggest that the incorporation of cationic functionalities is an effective strategy for accessing wide ranges of reduction potentials and pKa values while minimally affecting the BDFE, which is essential to modulating electron, proton, or hydrogen atom transfer pathways.
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Affiliation(s)
- Nadia G Léonard
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Teera Chantarojsiri
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Joseph W Ziller
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Jenny Y Yang
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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44
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Hennefarth MR, Alexandrova AN. Advances in optimizing enzyme electrostatic preorganization. Curr Opin Struct Biol 2022; 72:1-8. [PMID: 34280872 PMCID: PMC8761209 DOI: 10.1016/j.sbi.2021.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/28/2021] [Accepted: 06/05/2021] [Indexed: 12/19/2022]
Abstract
Utilizing electric fields to catalyze chemical reactions is not a new idea, but in enzymology it undergoes a renaissance, inspired by Warhsel's concept of electrostatic preorganization. According to this concept, the source of the immense catalytic efficiency of enzymes is the intramolecular electric field that permanently favors the reaction transition state over the reactants. Within enzyme design, computational efforts have fallen short in designing enzymes with natural-like efficacy. The outcome could improve if long-range electrostatics (often omitted in current protocols) would be optimized. Here, we highlight the major developments in methods for analyzing and designing electric fields generated by the protein scaffolds, in order to both better understand how natural enzymes function, and aid artificial enzyme design.
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Affiliation(s)
- Matthew R Hennefarth
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA; California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, CA 90095-1569, USA.
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45
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Bofill JM, Quapp W, Albareda G, Moreira IDPR, Ribas-Ariño J. Controlling Chemical Reactivity with Optimally Oriented Electric Fields: A Generalization of the Newton Trajectory Method. J Chem Theory Comput 2022; 18:935-952. [PMID: 35044173 DOI: 10.1021/acs.jctc.1c00943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of oriented external electric fields (OEEF) as a tool to accelerate chemical reactions has recently attracted much interest. A new model to calculate the optimal OEEF of the least intensity to induce a barrierless chemical reaction path is presented. A suitable ansatz is provided by defining an effective potential energy surface (PES), which considers the unperturbed or original PES of the molecular reactive system and the action of a constant OEEF on the overall dipole moment of system. Based on a generalization of the Newton Trajectories (NT) method, it is demonstrated that the optimal OEEF can be determined upon locating a special point of the potential energy surface (PES), the so-called "optimal bond-breaking point" (optimal BBP), for which two different algorithms are proposed. At this point, the gradient of the original or unperturbed PES is an eigenvector of zero eigenvalue of the Hessian matrix of the effective PES. A thorough discussion of the geometrical aspects of the optimal BBP and the optimal OEEF is provided using a two-dimensional model, and numerical calculations of the optimal OEEF for a SN2 reaction and the 1,3-dipolar retrocycloaddition of isoxazole to fulminic acid plus acetylene reaction serve as a proof of concept. The knowledge of the orientation of optimal OEEF provides a practical way to reduce the effective barrier of a given chemical process.
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Affiliation(s)
- Josep Maria Bofill
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.,Institut de Química Teòrica i Computacional, (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Wolfgang Quapp
- Mathematisches Institut, Universität Leipzig, PF 100920, D-04009 Leipzig, Germany
| | - Guillermo Albareda
- Institut de Química Teòrica i Computacional, (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.,Max Planck Institute for the Structure and Dynamics of Matter and Center for Free Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Ibério de P R Moreira
- Institut de Química Teòrica i Computacional, (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.,Departament de Ciència de Materials i Química Física, Secció de Química Física, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Jordi Ribas-Ariño
- Institut de Química Teòrica i Computacional, (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.,Departament de Ciència de Materials i Química Física, Secció de Química Física, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
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46
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Hao H, Leven I, Head-Gordon T. Can electric fields drive chemistry for an aqueous microdroplet? Nat Commun 2022; 13:280. [PMID: 35022410 PMCID: PMC8755715 DOI: 10.1038/s41467-021-27941-x] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 12/14/2021] [Indexed: 11/20/2022] Open
Abstract
Reaction rates of common organic reactions have been reported to increase by one to six orders of magnitude in aqueous microdroplets compared to bulk solution, but the reasons for the rate acceleration are poorly understood. Using a coarse-grained electron model that describes structural organization and electron densities for water droplets without the expense of ab initio methods, we investigate the electric field distributions at the air-water interface to understand the origin of surface reactivity. We find that electric field alignments along free O-H bonds at the surface are ~16 MV/cm larger on average than that found for O-H bonds in the interior of the water droplet. Furthermore, electric field distributions can be an order of magnitude larger than the average due to non-linear coupling of intramolecular solvent polarization with intermolecular solvent modes which may contribute to even greater surface reactivity for weakening or breaking chemical bonds at the droplet surface.
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Affiliation(s)
- Hongxia Hao
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, 94720, USA
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, CA, 94720, USA
- Departments of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Itai Leven
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, 94720, USA
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, CA, 94720, USA
- Departments of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Teresa Head-Gordon
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, 94720, USA.
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, CA, 94720, USA.
- Departments of Chemistry, University of California, Berkeley, CA, 94720, USA.
- Departments of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- Departments of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.
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47
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Chen K, Li WL, Head-Gordon T. Linear Combination of Atomic Dipoles to Calculate the Bond and Molecular Dipole Moments of Molecules and Molecular Liquids. J Phys Chem Lett 2021; 12:12360-12369. [PMID: 34936765 DOI: 10.1021/acs.jpclett.1c03476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We report a linear combination of atomic dipole (LCAD) method for calculating the bond dipole moments of molecules. We show that the LCAD method reproduces the known molecular dipole moments of small to large molecules with a small error with respect to experimental and benchmark ab initio calculations, and molecular dipole distributions of bulk water that agree with maximally localized Wannier functions. The bond dipole moments derived from LCAD are also chemically interpretable in terms of the trend in bond ionicity in going from neutral to charged molecules. Moreover, the LCAD method accurately captures the influence of electric fields, supported by the correct trend in the change of the dipole moment under a uniform external electric field. The better grounding of bond dipole calculations indicates that it should also serve as a useful approach to bond dipole-field models used in catalysis or to reconstruct the small dipole of a H-terminated graphene flake.
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Affiliation(s)
- Kaixuan Chen
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, California 94720, United States
- Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Wan-Lu Li
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, California 94720, United States
- Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, California 94720, United States
- Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
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48
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Besalú-Sala P, Solà M, Luis JM, Torrent-Sucarrat M. Fast and Simple Evaluation of the Catalysis and Selectivity Induced by External Electric Fields. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Pau Besalú-Sala
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, 17003 Girona, Catalonia, Spain
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, 17003 Girona, Catalonia, Spain
| | - Josep M. Luis
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, 17003 Girona, Catalonia, Spain
| | - Miquel Torrent-Sucarrat
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO-CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Euskadi, Spain
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Euskadi, Spain
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49
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Hu D, Gu X, Lyu L, Pei J, Cui B. Investigating the aging mechanism of asphaltene and its dependence on environmental factors through AIMD simulations and DFT calculations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 795:148897. [PMID: 34328939 DOI: 10.1016/j.scitotenv.2021.148897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/01/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
To understand the complex aging mechanism of asphalt and its dependence on environmental factors, the chemical reactivity of asphaltene during aging under different environmental conditions was studied through first-principles molecular simulations and density functional theory calculations. The aging of asphaltene was demonstrated to involve a series of subreactions along different pathways on the asphaltene molecules, including hydrogen abstraction from carbon, formation of polar groups, aromatization of cycloalkanes, and homolysis of side chains. These subreactions occurred with different free-energy barriers and, therefore, had different kinetic rates. Asphaltene aging was found to be slightly accelerated in the presence of water owing to the improved electron transfer ability of the asphaltene molecule in an aqueous solvent. Under ultraviolet radiation, the asphaltene molecule transitioned to an excited state with an excitation energy of 348.7 kJ/mol, significantly increasing its aging rate. This work bridges the gap between electronic-scale modeling and diversified experimental observations related to asphalt aging and is expected to provide theoretical guidance for strategies to prevent or delay the aging-induced failure of asphalt pavements.
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Affiliation(s)
- Dongliang Hu
- School of Transportation, Southeast University, Nanjing, Jiangsu 211189, China
| | - Xingyu Gu
- School of Transportation, Southeast University, Nanjing, Jiangsu 211189, China; College of Engineering, Tibet University, Lhasa, Tibet 850000, China.
| | - Lei Lyu
- School of Highway, Chang'an University, Xi'an, Shaanxi 710064, China
| | - Jianzhong Pei
- School of Highway, Chang'an University, Xi'an, Shaanxi 710064, China
| | - Bingyan Cui
- School of Transportation, Southeast University, Nanjing, Jiangsu 211189, China
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50
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Xu X, Yan S, Hou X, Song W, Wang L, Wu T, Qi M, Wu J, Rao Y, Wang B, Liu L. Local Electric Field Modulated Reactivity of Pseudomonas aeruginosa Acid Phosphatase for Enhancing Phosphorylation of l-Ascorbic Acid. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xin Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 360015, P. R. China
| | - Xiaodong Hou
- State Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Wei Song
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, P. R. China
| | - Lei Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Tianfu Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Mengya Qi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Jing Wu
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, P. R. China
| | - Yijian Rao
- State Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 360015, P. R. China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
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