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Tantillo DJ. Quantum Chemical Interrogation of Reactions Promoted by Dirhodium Tetracarboxylate Catalysts─Mechanism, Selectivity, and Nonstatistical Dynamic Effects. Acc Chem Res 2024; 57:1931-1940. [PMID: 38920276 DOI: 10.1021/acs.accounts.4c00214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
ConspectusRh2L4 catalysts have risen in popularity in the world of organic synthesis, being used to accomplish a variety of reactions, including C-H insertion and cyclopropanation, and often doing so with high levels of stereocontrol. While the mechanisms and origins of selectivity for such reactions have been examined with computational quantum chemistry for decades, only recently have detailed pictures of the dynamic behavior of reacting Rh2L4-complexed molecules become accessible. Our computational studies on Rh2L4 catalyzed reactions are described here, with a focus on C-H insertion reactions of Rh2L4-carbenes. Several issues complicate the modeling of these reactions, each providing an opportunity for greater understanding and each revealing issues that should be incorporated into future rational design efforts. First, the fundamental mechanism of C-H insertion is discussed. While early quantum chemical studies pointed to transition structures with 3-center [C-H-C] substructures and asynchronous hydride transfer/C-C bond formation, recent examples of reactions with particularly flat potential energy surfaces and even discrete zwitterionic intermediates have been found. These reactions are associated with systems bearing π-donating groups at the site of hydride transfer, allowing for an intermediate with a carbocation substructure at that site to be selectively stabilized. Second, the possible importance of solvent coordination at the Rh atom distal to the carbene is discussed. While effects on reactivity and selectivity were found to be small, they turn out not to be negligible in some cases. Third, it is shown that, in contrast to many other transition metal promoted reactions, many Rh2L4 catalyzed reactions likely involve dissociation of the Rh2L4 catalyst before key chemical steps leading to products. When to expect dissociation is associated with specific features of substrates and the product-forming reactions in question. Often, dissociation precedes transition structures for pericyclic reactions that involve electrons that would otherwise bind to Rh2L4. Finally, the importance of nonstatistical dynamic effects, characterized through ab initio molecular dynamics studies, in some Rh2L4 catalyzed reactions is discussed. These are reactions where transition structures are shown to be followed by flat regions, very shallow minima, and/or pathways that bifurcate, all allowing for trajectories from a single transition state to form multiple different products. The likelihood of encountering such a situation is shown to be associated again with the likelihood of formation of zwitterionic structures along reaction paths, but ones for which pathways to multiple products are expected to be associated with very low or no barriers. The connection between these features and reduced yields of desired products are highlighted, as are the means by which some Rh2L4 catalysts modulate dynamic behavior to produce particular products in high yield.
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Affiliation(s)
- Dean J Tantillo
- Department of Chemistry, University of California─Davis, 1 Shields Avenue, Davis, California 95616, United States
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2
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Wheeler JI, Schaefer AJ, Ess DH. Trajectory-Based Time-Resolved Mechanism for Benzene Reductive Elimination from Cyclopentadienyl Mo/W Phenyl Hydride Complexes. J Phys Chem A 2024; 128:4775-4786. [PMID: 38836889 DOI: 10.1021/acs.jpca.4c01788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Calculated potential energy structures and landscapes are very often used to define the sequence of reaction steps in an organometallic reaction mechanism and interpret kinetic isotope effect (KIE) measurements. Underlying most of this structure-to-mechanism translation is the use of statistical rate theories without consideration of atomic/molecular motion. Here we report direct dynamics simulations for an organometallic benzene reductive elimination reaction, where nonstatistical intermediates and dynamic-controlled pathways were identified. Specifically, we report single spin state as well as mixed spin state quasiclassical direct dynamics trajectories in the gas phase and explicit solvent for benzene reductive elimination from Mo and W bridged cyclopentadienyl phenyl hydride complexes ([Me2Si(C5Me4)2]M(H)(Ph), M = Mo and W). Different from the energy landscape mechanistic sequence, the dynamics trajectories revealed that after the benzene C-H bond forming transition state (often called reductive coupling), σ-coordination and π-coordination intermediates are either skipped or circumvented and that there is a direct pathway to forming a spin flipped solvent caged intermediate, which occurs in just a few hundred femtoseconds. Classical molecular dynamics simulations were then used to estimate the lifetime of the caged intermediate, which is between 200 and 400 picoseconds. This indicates that when the η2-π-coordination intermediate is formed, it occurs only after the first formation of the solvent-caged intermediate. This dynamic mechanism intriguingly suggests the possibility that the solvent-caged intermediate rather than a coordination intermediate is responsible (or partially responsible) for the inverse KIE value experimentally measured for W. Additionally, this dynamic mechanism prompted us to calculate the kH/kD KIE value for the C-H bonding forming transition states of Mo and W. Surprisingly, Mo gave a normal value, while W gave an inverse value, albeit small, due to a much later transition state position.
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Affiliation(s)
- Joshua I Wheeler
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604, United States
| | - Anthony J Schaefer
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604, United States
| | - Daniel H Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604, United States
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3
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Bogetti A, Zwier MC, Chong LT. Revisiting Textbook Azide-Clock Reactions: A "Propeller-Crawling" Mechanism Explains Differences in Rates. J Am Chem Soc 2024; 146:12828-12835. [PMID: 38687173 PMCID: PMC11078601 DOI: 10.1021/jacs.4c03360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
An ongoing challenge to chemists is the analysis of pathways and kinetics for chemical reactions in solution, including transient structures between the reactants and products that are difficult to resolve using laboratory experiments. Here, we enabled direct molecular dynamics simulations of a textbook series of chemical reactions on the hundreds of ns to μs time scale using the weighted ensemble (WE) path sampling strategy with hybrid quantum mechanical/molecular mechanical (QM/MM) models. We focused on azide-clock reactions involving addition of an azide anion to each of three long-lived trityl cations in an acetonitrile-water solvent mixture. Results reveal a two-step mechanism: (1) diffusional collision of reactants to form an ion-pair intermediate; (2) "activation" or rearrangement of the intermediate to the product. Our simulations yield not only reaction rates that are within error of experiment but also rates for individual steps, indicating the activation step as rate-limiting for all three cations. Further, the trend in reaction rates is due to dynamical effects, i.e., differing extents of the azide anion "crawling" along the cation's phenyl-ring "propellers" during the activation step. Our study demonstrates the power of analyzing pathways and kinetics to gain insights on reaction mechanisms, underscoring the value of including WE and other related path sampling strategies in the modern toolbox for chemists.
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Affiliation(s)
- Anthony
T. Bogetti
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Matthew C. Zwier
- Department
of Chemistry, Drake University, Des Moines, Iowa 50311, United States
| | - Lillian T. Chong
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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4
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Schaefer AJ, Ess DH. Vibrational synchronization and its reaction pathway influence from an entropic intermediate in a dirhodium catalyzed allylic C-H activation/Cope rearrangement reaction. Phys Chem Chem Phys 2024; 26:11386-11394. [PMID: 38586933 DOI: 10.1039/d4cp00657g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
In reactions with consecutive transition states without an intermediate, and an energy surface bifurcation, atomic motion generally determines product selectivity. Understanding this dynamic-based selectivity can be straightforward if there is extremely fast descent from the first transition state to a product. However, in cases where a nonstatistical roaming/entropic intermediate occurs prior to product formation the motion that influences selectivity can be difficult to identify. Here we report quasiclassical direct dynamics trajectories for the dirhodium catalyzed reaction between styryldiazoacetate and 1,4-cyclohexadiene and prior experiments by Davies showed competitive allylic C-H insertion and Cope products. Trajectories confirmed the proposed energy surface bifurcation and revealed that dirhodium vinylcarbenoid when reacting with 1,4-cyclohexadiene can induce either a dynamically concerted pathway or a dynamically stepwise pathway with a nonstatistical entropic tight ion-pair intermediate. In the dynamically stepwise reaction pathway C-H insertion versus Cope selectivity is highly influenced by whether or not vibrational synchronization occurs in the nonstatistical entropic intermediate. This vibrational synchronization highlights the possible need for an entropic intermediate to have organized transition state-like motion to proceed to a product.
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Affiliation(s)
- Anthony J Schaefer
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604, USA.
| | - Daniel H Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604, USA.
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5
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Figueira Nunes JP, Ibele LM, Pathak S, Attar AR, Bhattacharyya S, Boll R, Borne K, Centurion M, Erk B, Lin MF, Forbes RJG, Goff N, Hansen CS, Hoffmann M, Holland DMP, Ingle RA, Luo D, Muvva SB, Reid AH, Rouzée A, Rudenko A, Saha SK, Shen X, Venkatachalam AS, Wang X, Ware MR, Weathersby SP, Wilkin K, Wolf TJA, Xiong Y, Yang J, Ashfold MNR, Rolles D, Curchod BFE. Monitoring the Evolution of Relative Product Populations at Early Times during a Photochemical Reaction. J Am Chem Soc 2024; 146:4134-4143. [PMID: 38317439 PMCID: PMC10870701 DOI: 10.1021/jacs.3c13046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 02/07/2024]
Abstract
Identifying multiple rival reaction products and transient species formed during ultrafast photochemical reactions and determining their time-evolving relative populations are key steps toward understanding and predicting photochemical outcomes. Yet, most contemporary ultrafast studies struggle with clearly identifying and quantifying competing molecular structures/species among the emerging reaction products. Here, we show that mega-electronvolt ultrafast electron diffraction in combination with ab initio molecular dynamics calculations offer a powerful route to determining time-resolved populations of the various isomeric products formed after UV (266 nm) excitation of the five-membered heterocyclic molecule 2(5H)-thiophenone. This strategy provides experimental validation of the predicted high (∼50%) yield of an episulfide isomer containing a strained three-membered ring within ∼1 ps of photoexcitation and highlights the rapidity of interconversion between the rival highly vibrationally excited photoproducts in their ground electronic state.
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Affiliation(s)
| | - Lea Maria Ibele
- CNRS,
Institut de Chimie Physique UMR8000, Université
Paris-Saclay, Orsay, 9140, France
| | - Shashank Pathak
- J.R.
Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, Kansas 66506, United States
| | - Andrew R. Attar
- SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Surjendu Bhattacharyya
- J.R.
Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, Kansas 66506, United States
| | | | - Kurtis Borne
- J.R.
Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, Kansas 66506, United States
| | - Martin Centurion
- University
of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Benjamin Erk
- Deutsches
Elektronen Synchrotron DESY, Hamburg, 22607, Germany
| | - Ming-Fu Lin
- SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Ruaridh J. G. Forbes
- SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Nathan Goff
- Brown University, Providence, Rhode Island 02912, United States
| | | | - Matthias Hoffmann
- SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | | | - Rebecca A. Ingle
- Department
of Chemistry, University College London, London, WC1H 0AJ, U.K.
| | - Duan Luo
- SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Sri Bhavya Muvva
- University
of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Alexander H. Reid
- SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | | | - Artem Rudenko
- J.R.
Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, Kansas 66506, United States
| | - Sajib Kumar Saha
- University
of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Xiaozhe Shen
- SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Anbu Selvam Venkatachalam
- J.R.
Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, Kansas 66506, United States
| | - Xijie Wang
- SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Matt R. Ware
- SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | | | - Kyle Wilkin
- University
of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Thomas J. A. Wolf
- SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
- Stanford
PULSE Institute, SLAC National Accelerator
Laboratory, Menlo
Park, California 94025, United States
| | - Yanwei Xiong
- University
of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Jie Yang
- SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | | | - Daniel Rolles
- J.R.
Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, Kansas 66506, United States
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6
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Joy J, Schaefer AJ, Teynor MS, Ess DH. Dynamical Origin of Rebound versus Dissociation Selectivity during Fe-Oxo-Mediated C-H Functionalization Reactions. J Am Chem Soc 2024; 146:2452-2464. [PMID: 38241715 DOI: 10.1021/jacs.3c09891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
The mechanism of catalytic C-H functionalization of alkanes by Fe-oxo complexes is often suggested to involve a hydrogen atom transfer (HAT) step with the formation of a radical-pair intermediate followed by diverging pathways for radical rebound, dissociation, or desaturation. Recently, we showed that in some Fe-oxo reactions, the radical pair is a nonstatistical-type intermediate and dynamic effects control rebound versus dissociation pathway selectivity. However, the effect of the solvent cage on the stability and lifetime of the radical-pair intermediate has never been analyzed. Moreover, because of the extreme complexity of motion that occurs during dynamics trajectories, the underlying physical origin of pathway selectivity has not yet been determined. For the reaction between [(TQA_Cl)FeIVO]+ and cyclohexane, here, we report explicit solvent trajectories and machine learning analysis on transition-state sampled features (e.g., vibrational, velocity, and geometric) that identified the transferring hydrogen atom kinetic energy as the most important factor controlling rebound versus nonrebound dynamics trajectories, which provides an explanation for our previously proposed dynamic matching effect in fast rebound trajectories that bypass the radical-pair intermediate. Manual control of the reaction trajectories confirmed the importance of this feature and provides a mechanism to enhance or diminish selectivity for the rebound pathway. This led to a general catalyst design principle and proof-of-principle catalyst design that showcases how to control rebound versus dissociation reaction pathway selectivity.
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Affiliation(s)
- Jyothish Joy
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604, United States
| | - Anthony J Schaefer
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604, United States
| | - Matthew S Teynor
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604, United States
| | - Daniel H Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604, United States
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7
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Pu M, Nielsen CDT, Senol E, Sperger T, Schoenebeck F. Post-Transition-State Dynamic Effects in the Transmetalation of Pd(II)-F to Pd(II)-CF 3. JACS AU 2024; 4:263-275. [PMID: 38274253 PMCID: PMC10806791 DOI: 10.1021/jacsau.3c00724] [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: 11/17/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024]
Abstract
The observation of post-transition-state dynamic effects in the context of metal-based transformation is rare. To date, there has been no reported case of a dynamic effect for the widely employed class of palladium-mediated coupling reactions. We performed an experimental and computational study of the trifluoromethylation of Pd(II)F, which is a key step in the Pd(0)/Pd(II)-catalyzed trifluoromethylation of aryl halides or acid fluorides. Our experiments show that the cis/trans speciation of the formed Pd(II)CF3 is highly solvent- and transmetalation reagent-dependent. We employed GFN2-xTB- and B3LYP-D3-based molecular dynamics trajectory calculations (with and without explicit solvation) along with high-level QM calculations and found that depending on the medium, different transmetalation mechanisms appear to be operative. A statistically representative number of Born-Oppenheimer molecular dynamics (MD) simulations suggest that in benzene, a difluorocarbene is generated in the transmetalation with R3SiCF3, which subsequently recombines with the Pd via two distinct pathways, leading to either the cis- or trans-Pd(II)CF3. Conversely, GFN2-xTB simulations in MeCN suggest that in polar/coordinating solvents an ion-pair mechanism is dominant. A CF3 anion is initially liberated and then rebinds with the Pd(II) cation to give a cis- or trans-Pd(II). In both scenarios, a single transmetalation transition state gives rise to both cis- and trans-species directly, owing to bifurcation after the transition state. The potential subsequent cis- to trans isomerization of the Pd(II)CF3 was also studied and found to be strongly inhibited by free phosphine, which in turn was experimentally identified to be liberated through displacement by a polar/coordinating solvent from the cis-Pd(II)CF3 complex. The simulations also revealed how the variation of the Pd-coordination sphere results in divergent product selectivities.
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Affiliation(s)
- Maoping Pu
- Institute of Organic Chemistry,
RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| | | | - Erdem Senol
- Institute of Organic Chemistry,
RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| | - Theresa Sperger
- Institute of Organic Chemistry,
RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| | - Franziska Schoenebeck
- Institute of Organic Chemistry,
RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
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8
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Zhou Q, Kukier G, Gordiy I, Hoffmann R, Seeman JI, Houk KN. A 21st Century View of Allowed and Forbidden Electrocyclic Reactions. J Org Chem 2024; 89:1018-1034. [PMID: 38153322 PMCID: PMC10804416 DOI: 10.1021/acs.joc.3c02103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/29/2023]
Abstract
In 1965, Woodward and Hoffmann proposed a theory to predict the stereochemistry of electrocyclic reactions, which, after expansion and generalization, became known as the Woodward-Hoffmann Rules. Subsequently, Longuet-Higgins and Abrahamson used correlation diagrams to propose that the stereoselectivity of electrocyclizations could be explained by the correlation of reactant and product orbitals with the same symmetry. Immediately thereafter, Hoffmann and Woodward applied correlation diagrams to explain the mechanism of cycloadditions. We describe these discoveries and their evolution. We now report an investigation of various electrocyclic reactions using DFT and CASSCF. We track the frontier molecular orbitals along the intrinsic reaction coordinate and modeled trajectories and examine the correlation between HOMO and LUMO for thermally forbidden systems. We also investigate the electrocyclizations of several highly polarized systems for which the Houk group had predicted that donor-acceptor substitution can induce zwitterionic character, thereby providing low-energy pathways for formally forbidden reactions. We conclude with perspectives on the field of pericyclic reactions, including a refinement as the meaning of Woodward and Hoffmann's "Violations. There are none!" Lastly, we comment on the burgeoning influence of computations on all fields of chemistry.
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Affiliation(s)
- Qingyang Zhou
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California90095, United States
| | - Garrett Kukier
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California90095, United States
| | - Igor Gordiy
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California90095, United States
| | - Roald Hoffmann
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York14850, United States
| | - Jeffrey I. Seeman
- Department
of Chemistry, University of Richmond, Richmond, Virginia 23173United States
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California90095-1569. United States
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9
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Robinson MS, Küpper J. Unraveling the ultrafast dynamics of thermal-energy chemical reactions. Phys Chem Chem Phys 2024; 26:1587-1601. [PMID: 38131437 DOI: 10.1039/d3cp03954d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
In this perspective, we discuss how one can initiate, image, and disentangle the ultrafast elementary steps of thermal-energy chemical dynamics, building upon advances in technology and scientific insight. We propose that combinations of ultrashort mid-infrared laser pulses, controlled molecular species in the gas phase, and forefront imaging techniques allow to unravel the elementary steps of general-chemistry reaction processes in real time. We detail, for prototypical first reaction systems, experimental methods enabling these investigations, how to sufficiently prepare and promote gas-phase samples to thermal-energy reactive states with contemporary ultrashort mid-infrared laser systems, and how to image the initiated ultrafast chemical dynamics. The results of such experiments will clearly further our understanding of general-chemistry reaction dynamics.
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Affiliation(s)
- Matthew S Robinson
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
- Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Jochen Küpper
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
- Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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10
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Davenport MT, Kirkland JK, Ess DH. Dynamic-dependent selectivity in a bisphosphine iron spin crossover C-H insertion/π-coordination reaction. Chem Sci 2023; 14:9400-9408. [PMID: 37712027 PMCID: PMC10498510 DOI: 10.1039/d3sc02078a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 08/13/2023] [Indexed: 09/16/2023] Open
Abstract
Reaction pathway selectivity is generally controlled by competitive transition states. Organometallic reactions are complicated by the possibility that electronic spin state changes rather than transition states can control the relative rates of pathways, which can be modeled as minimum energy crossing points (MECPs). Here we show that in the reaction between bisphosphine Fe and ethylene involving spin state crossover (singlet and triplet spin states) that neither transition states nor MECPs model pathway selectivity consistent with experiment. Instead, single spin state and mixed spin state quasiclassical trajectories demonstrate nonstatistical intermediates and that C-H insertion versus π-coordination pathway selectivity is determined by the dynamic motion during reactive collisions. This example of dynamic-dependent product outcome provides a new selectivity model for organometallic reactions with spin crossover.
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Affiliation(s)
- Michael T Davenport
- Department of Chemistry and Biochemistry, Brigham Young University Provo Utah USA 84604
| | - Justin K Kirkland
- Department of Chemistry and Biochemistry, Brigham Young University Provo Utah USA 84604
| | - Daniel H Ess
- Department of Chemistry and Biochemistry, Brigham Young University Provo Utah USA 84604
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11
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Xu R, Meisner J, Chang AM, Thompson KC, Martínez TJ. First principles reaction discovery: from the Schrodinger equation to experimental prediction for methane pyrolysis. Chem Sci 2023; 14:7447-7464. [PMID: 37449065 PMCID: PMC10337770 DOI: 10.1039/d3sc01202f] [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: 03/06/2023] [Accepted: 06/02/2023] [Indexed: 07/18/2023] Open
Abstract
Our recent success in exploiting graphical processing units (GPUs) to accelerate quantum chemistry computations led to the development of the ab initio nanoreactor, a computational framework for automatic reaction discovery and kinetic model construction. In this work, we apply the ab initio nanoreactor to methane pyrolysis, from automatic reaction discovery to path refinement and kinetic modeling. Elementary reactions occurring during methane pyrolysis are revealed using GPU-accelerated ab initio molecular dynamics simulations. Subsequently, these reaction paths are refined at a higher level of theory with optimized reactant, product, and transition state geometries. Reaction rate coefficients are calculated by transition state theory based on the optimized reaction paths. The discovered reactions lead to a kinetic model with 53 species and 134 reactions, which is validated against experimental data and simulations using literature kinetic models. We highlight the advantage of leveraging local brute force and Monte Carlo sensitivity analysis approaches for efficient identification of important reactions. Both sensitivity approaches can further improve the accuracy of the methane pyrolysis kinetic model. The results in this work demonstrate the power of the ab initio nanoreactor framework for computationally affordable systematic reaction discovery and accurate kinetic modeling.
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Affiliation(s)
- Rui Xu
- Department of Chemistry, The PULSE Institute, Stanford University Stanford CA 94305 USA
- SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
| | - Jan Meisner
- Department of Chemistry, The PULSE Institute, Stanford University Stanford CA 94305 USA
- SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
| | - Alexander M Chang
- Department of Chemistry, The PULSE Institute, Stanford University Stanford CA 94305 USA
- SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
| | - Keiran C Thompson
- Department of Chemistry, The PULSE Institute, Stanford University Stanford CA 94305 USA
- SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
| | - Todd J Martínez
- Department of Chemistry, The PULSE Institute, Stanford University Stanford CA 94305 USA
- SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
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12
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Murakami T, Ibuki S, Hashimoto Y, Kikuma Y, Takayanagi T. Dynamics study of the post-transition-state-bifurcation process of the (HCOOH)H + → CO + H 3O +/HCO + + H 2O dissociation: application of machine-learning techniques. Phys Chem Chem Phys 2023; 25:14016-14027. [PMID: 37161528 DOI: 10.1039/d3cp00252g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The process of protonated formic acid dissociating from the transition state was studied using ring-polymer molecular dynamics (RPMD), classical MD, and quasi-classical trajectory (QCT) simulations. Temperature had a strong influence on the branching fractions for the HCO+ + H2O and CO + H3O+ dissociation channels. The RPMD and classical MD simulations showed similar behavior, but the QCT dynamics were significantly different owing to the excess energies in the quasi-classical trajectories. Machine-learning analysis identified several key features in the phase information of the vibrational motions at the transition state. We found that the initial configuration and momentum of a hydrogen atom connected to a carbon atom and the shrinking coordinate of the CO bond at the transition state play a role in the dynamics of HCO+ + H2O production.
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Affiliation(s)
- Tatsuhiro Murakami
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan.
- Department of Materials & Life Sciences, Faculty of Science & Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Shunichi Ibuki
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan.
| | - Yu Hashimoto
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan.
| | - Yuya Kikuma
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan.
| | - Toshiyuki Takayanagi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan.
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13
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Joy J, Ess DH. Direct Dynamics Trajectories Demonstrate Dynamic Matching and Nonstatistical Radical Pair Intermediates during Fe-Oxo-Mediated C-H Functionalization Reactions. J Am Chem Soc 2023; 145:7628-7637. [PMID: 36952628 DOI: 10.1021/jacs.3c01196] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The generally proposed mechanism for the reaction between non-heme Fe-oxo complexes and alkane C-H bonds involves a hydrogen atom transfer (HAT) reaction step with a radical pair intermediate that then has competitive radical rebound, dissociation, or desaturation pathways. Here, we report density functional theory-based quasiclassical direct dynamics trajectories that examine post-HAT reaction dynamics. Trajectories revealed that the radical pair intermediate can be a nonstatistical type intermediate without complete internal vibrational redistribution and post-HAT selectivity is generally determined by dynamic effects. Fast rebound trajectories occur through dynamic matching between the rotational motion of the newly formed Fe-OH bond and collision with the alkane radical, and all of this occurs through a nonsynchronous dynamically concerted process that circumvents the radical pair intermediate structure. For radical pair dissociation, trajectories proceeded to the radical pair intermediate for a very brief time, followed by complete dissociation. These trajectories provide a new viewpoint and model to understand the inherent reaction pathway selectivity for non-heme Fe-oxo-mediated C-H functionalization reactions.
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Affiliation(s)
- Jyothish Joy
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Daniel H Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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14
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Rashmi R, Yadav PK, Seal A, Paranjothy M, Lourderaj U. E-Z Isomerization in Guanidine: Second-order Saddle Dynamics, Non-statisticality, and Time-frequency Analysis. Chemphyschem 2023; 24:e202200640. [PMID: 36205532 DOI: 10.1002/cphc.202200640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/06/2022] [Indexed: 01/20/2023]
Abstract
Our recent work on the E-Z isomerization reaction of guanidine using ab initio chemical dynamics simulations [Rashmi et al., Regul. Chaotic Dyn. 2021, 26, 119] emphasized the role of second-order saddle (SOS) in the isomerization reaction; however, we could not unequivocally establish the non-statistical nature of the dynamics followed in the reaction. In the present study, we performed thousands of on-the-fly trajectories using forces computed at the MNDO level to investigate the influence of second-order saddle in the E-Z isomerization reaction of guanidine and the role of intramolecular vibrational energy redistribution (IVR) on the reaction dynamics. The simulations reveal that while majority of the trajectories follow the traditional transition state pathways, 15 % of the trajectories follow the SOS path. The dynamics was found to be highly non-statistical with the survival probabilities of the reactants showing large deviations from those obtained within the RRKM assumptions. In addition, a detailed analysis of the dynamics using time-dependent frequencies and the frequency ratio spaces reveal the existence of multiple resonance junctions that indicate the existence of regular dynamics and long-lived quasi-periodic trajectories in the phase space associated with non-RRKM behavior.
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Affiliation(s)
- Richa Rashmi
- National Insitute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute P. O. Jatni, Khurdha, Odisha, 752050, India
| | - Pankaj Kumar Yadav
- National Insitute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute P. O. Jatni, Khurdha, Odisha, 752050, India
| | - Aniruddha Seal
- National Insitute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute P. O. Jatni, Khurdha, Odisha, 752050, India
| | - Manikandan Paranjothy
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
| | - Upakarasamy Lourderaj
- National Insitute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute P. O. Jatni, Khurdha, Odisha, 752050, India
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15
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Carpenter BK. Prediction of Kinetic Product Ratios: Investigation of a Dynamically Controlled Case. J Phys Chem A 2023; 127:224-239. [PMID: 36594780 PMCID: PMC9841574 DOI: 10.1021/acs.jpca.2c08301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Of the various factors influencing kinetically controlled product ratios, the role of nonstatistical dynamics is arguably the least well understood. In this paper, reactions were chosen in which dynamics played a dominant role in product selection, by design. Specifically, the reactions studied were the ring openings of cyclopropylidene to allene and tetramethylcyclopropylidene to tetramethylallene (2,4-dimethylpenta-2,3-diene). Both reactions have intrinsic reaction coordinates that bifurcate symmetrically, leading to products that are enantiomeric once the atoms are uniquely labeled. The question addressed in the study was whether the outcomes─that is, which product well on the potential energy surface was selected─could be predicted from their initial conditions for individual trajectories in quasiclassical dynamics simulations. Hybrid potentials were developed based on cooperative interaction between molecular mechanics and artificial neural networks, trained against data from electronic structure calculations. These potentials allowed simulations of both gas-phase and condensed-phase reactions. The outcome was that, for both reactions, prediction of initial selection of product wells could be made with >95% success from initial conditions of the trajectories in the gas phase. However, when trajectories were run for longer, looking for "final" products for each trajectory, the predictability dropped off dramatically. In the gas-phase simulations, this drop off was caused by trajectories hopping between product wells on the potential energy surface. That behavior could be suppressed in condensed phases, but then new uncertainty was introduced because the intermolecular interactions between solute and bath, necessary to permit intermolecular energy transfer and cooling of the hot initial products, often led to perturbations of the initial directions of trajectories on the potential energy surface. It would consequently appear that a general ability to predict outcomes for reactions in which nonstatistical dynamics dominate remains a challenge even in the age of sophisticated machine-learning capabilities.
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16
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Lei YK, Zhang Z, Han X, Yang YI, Zhang J, Gao YQ. Locating Transition Zone in Phase Space. J Chem Theory Comput 2022; 18:6124-6133. [PMID: 36135927 DOI: 10.1021/acs.jctc.2c00385] [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
Understanding the reaction mechanism is required for better control of chemical reactions and is usually achieved by locating transition states (TSs) along a proper one-dimensional coordinate called reaction coordinate (RC). The identification of RC can be very difficult for high-dimensional realistic systems. A number of methods have been proposed to tackle this problem. A machine learning method is developed here to incorporate the influence of velocity on the reaction process. The method is also free of the unbalanced label problem resulting from the rather low fraction of configurations near the TS and can be easily extended to large systems. It locates the transition zone in the phase space and defines the dividing surface with a high transmission coefficient. Moreover, considering that the reaction environment can not only change the reaction path but also activate the reactive mode through energy transfer, we devise two measures to quantify the influence of these two factors on the reaction process and find that solvents can assist the reaction by directly doing work along the reactive mode. Not surprisingly, there is a positive correlation between the efficiency of energy transfer into the reactive mode and the reaction rate.
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Affiliation(s)
- Yao-Kun Lei
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China
| | - Zhen Zhang
- School of Physics and Technology, Tangshan Normal University, 063000 Tangshan, China
| | - Xu Han
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China
| | - Yi Isaac Yang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China
| | - Jun Zhang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, 100871 Beijing, China
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17
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Abstract
Differences in entropies of competing transition states can direct kinetic selectivity. Understanding and modeling such entropy differences at the molecular level is complicated by the fact that entropy is statistical in nature; i.e., it depends on multiple vibrational states of transition structures, the existence of multiple dynamically accessible pathways past these transition structures, and contributions from multiple transition structures differing in conformation/configuration. The difficulties associated with modeling each of these contributors are discussed here, along with possible solutions, all with an eye toward the development of portable qualitative models of use to experimentalists aiming to design reactions that make use of entropy to control kinetic selectivity.
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Affiliation(s)
- Dean J Tantillo
- Department of Chemistry, University of California-Davis, 1 Shields Ave, Davis, California 95616, United States
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18
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Pandey P, Keshavamurthy S. Dynamic matching ‐ revisiting the Carpenter model. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Priyanka Pandey
- Department of Chemistry Indian Institute of Technology Kanpur Uttar Pradesh India
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19
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Melville J, Hargis C, Davenport MT, Hamilton RS, Ess DH. Machine Learning Analysis of Dynamic‐Dependent Bond Formation in Trajectories with Consecutive Transition States. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4405] [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)
- Jesse Melville
- Department of Chemistry and Biochemistry Brigham Young University Provo Utah USA
| | - Cal Hargis
- Department of Chemistry and Biochemistry Brigham Young University Provo Utah USA
| | - Michael T. Davenport
- Department of Chemistry and Biochemistry Brigham Young University Provo Utah USA
| | - R. Spencer Hamilton
- Department of Chemistry and Biochemistry Brigham Young University Provo Utah USA
| | - Daniel H. Ess
- Department of Chemistry and Biochemistry Brigham Young University Provo Utah USA
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20
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Saluga SJ, Dibble DJ, Blum SA. Superresolved Motions of Single Molecular Catalysts during Polymerization Show Wide Distributions. J Am Chem Soc 2022; 144:10591-10598. [PMID: 35670469 DOI: 10.1021/jacs.2c03566] [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 motion of single molecular ruthenium catalysts during and after single turnover events of ring-opening metathesis polymerization is imaged through single-molecule superresolution tracking with a positional accuracy of ±32 nm. This tracking is achieved through the real-time incorporation of spectrally tagged monomer units into active polymer chain ends during living polymerization; thus, by design, only active-catalyst motion is detected and imaged, without convolution by inactive catalysts. The catalysts show diverse individualistic diffusive behaviors with respect to time that persist for up to 20 s. Catalysts occupy three mobility populations: quasi-stationary (23%), intermediate (53%, 65 nm), and large (24%, 145 nm) step sizes. Differences in catalyst mobility populations also exist between individual aggregates (p < 0.001). Such differential motion indicates widely different local catalyst microenvironments during the catalytic turnover. These mobility differences are uniquely observable through single-catalyst microscopy and are not measurable through traditional ensemble analytical techniques for characterizing the behavior of molecular catalysts, such as nuclear magnetic resonance spectroscopy. The measured distributions of active molecular catalyst motions would not be readily predictable through modeling or first-principles, and the range likely impacts individual catalyst turnover rate and selectivity. This range plausibly contributes to property distributions observable in bulk polymers, such as molecular weight polydispersity (e.g., 1.9 in this system), leading to a revised understanding of the mechanistic, microscale origins of macroscale polymer properties.
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Affiliation(s)
- Shannon J Saluga
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - David Josh Dibble
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Suzanne A Blum
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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21
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Rush LA, Gallo KF, Stumetz KS, Rodríguez‐Pérez IA, Cremeens ME. Non‐statistical Dynamics for the Allene Oxide to Cyclopropanone Conversion. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lydia A. Rush
- Department of Chemistry and Biochemistry Gonzaga University Spokane Washington United States
| | - Kara F. Gallo
- Department of Chemistry and Biochemistry Gonzaga University Spokane Washington United States
| | - Kyle S. Stumetz
- Department of Chemistry and Biochemistry Gonzaga University Spokane Washington United States
| | | | - Matthew E. Cremeens
- Department of Chemistry and Biochemistry Gonzaga University Spokane Washington United States
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22
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Seeman JI. My First and My Latest Publication
†. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Deal AM, Frandsen BN, Vaida V. Lactic acid photochemistry following excitation of S
0
to S
1
at 220 to 250 nm. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alexandra M. Deal
- Department of Chemistry and Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder Boulder CO USA
| | - Benjamin N. Frandsen
- Department of Chemistry and Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder Boulder CO USA
| | - Veronica Vaida
- Department of Chemistry and Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder Boulder CO USA
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24
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Zou Y, Houk KN. Mechanisms and Dynamics of Synthetic and Biosynthetic Formation of Delitschiapyrones: Solvent Control of Ambimodal Periselectivity. J Am Chem Soc 2021; 143:11734-11740. [PMID: 34297552 PMCID: PMC9307257 DOI: 10.1021/jacs.1c05293] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The mechanism and dynamics for the formation of the delitschiapyrone family of natural products are studied by density functional theory (DFT) calculations and quasiclassical molecular dynamics simulations with DFT and xTB. In the uncatalyzed reaction, delitschiapyrones A and B are formed by Diels-Alder reactions through a single transition state and a post-transition state bifurcation that favors formation of delitschiapyrone B. In water and most likely in the enzyme, the acidic hydroxyquinone ionizes, and the resulting conjugate base undergoes cycloaddition preferentially to delitschiapyrone A. We demonstrate a new type of biosynthetic transformation and variable selectivity from a (4 + 2)/(4 + 3) ambimodal transition state.
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Affiliation(s)
- Yike Zou
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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25
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Teynor MS, Scott W, Ess DH. Catalysis with a Skip: Dynamically Coupled Addition, Proton Transfer, and Elimination during Au- and Pd-Catalyzed Diol Cyclizations. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Matthew S. Teynor
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Windsor Scott
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Daniel H. Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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26
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Yang B, Schouten A, Ess DH. Direct Dynamics Trajectories Reveal Nonstatistical Coordination Intermediates and Demonstrate that σ and π-Coordination Are Not Required for Rhenium(I)-Mediated Ethylene C-H Activation. J Am Chem Soc 2021; 143:8367-8374. [PMID: 34037393 DOI: 10.1021/jacs.1c01709] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The C-H activation reaction between Cp(PMe3)2Re and ethylene results in kinetic selectivity for the Re-vinyl hydride I over the thermodynamically more stable Cp(PMe3)2Re(η2-ethylene) π-complex II. While transition-state and variational transition-state structures were located for individual pathways leading to I and II, DFT and CCSD(T) energies predict a large kinetic selectivity of 102-104, which is incompatible with the experimental 10:1 ratio. DFT direct quasiclassical trajectories revealed that the transition states do not provide a qualitatively correct reaction mechanism or a quantitatively correct selectivity due to a nonstatistical σ-CH coordination intermediate that precedes the transition states for C-H activation and π coordination. Using metadynamics and quasiclassical direct dynamics, we show that trajectories for the reaction between Cp(PMe3)2Re and ethylene result in direct formation of either the Re-vinyl hydride I or the π-complex II. Trajectories leading to the Re-vinyl hydride skip σ-coordination and do not require π-coordination. Consistent with experiments, trajectory selectivity provides a relatively small kinetic selectivity for the Re-vinyl hydride.
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Affiliation(s)
- Bo Yang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Anna Schouten
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Daniel H Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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27
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Maley SM, Melville J, Yu S, Teynor MS, Carlsen R, Hargis C, Hamilton RS, Grant BO, Ess DH. Machine learning classification of disrotatory IRC and conrotatory non-IRC trajectory motion for cyclopropyl radical ring opening. Phys Chem Chem Phys 2021; 23:12309-12320. [PMID: 34018524 DOI: 10.1039/d1cp00612f] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quasiclassical trajectory analysis is now a standard tool to analyze non-minimum energy pathway motion of organic reactions. However, due to the large amount of information associated with trajectories, quantitative analysis of the dynamic origin of reaction selectivity is complex. For the electrocyclic ring opening of cyclopropyl radical, more than 4000 trajectories were run showing that allyl radicals are formed through a mixture of disrotatory intrinsic reaction coordinate (IRC) motion as well as conrotatory non-IRC motion. Geometric, vibrational mode, and atomic velocity transition-state features from these trajectories were used for supervised machine learning analysis with classification algorithms. Accuracy >80% with a random forest model enabled quantitative and qualitative assessment of transition-state trajectory features controlling disrotatory IRC versus conrotatory non-IRC motion. This analysis revealed that there are two key vibrational modes where their directional combination provides prediction of IRC versus non-IRC motion.
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Affiliation(s)
- Steven M Maley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - Jesse Melville
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - Spencer Yu
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - Matthew S Teynor
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - Ryan Carlsen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - Cal Hargis
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - R Spencer Hamilton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - Benjamin O Grant
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - Daniel H Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
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28
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Carlsen R, Maley SM, Ess DH. Timing and Structures of σ-Bond Metathesis C–H Activation Reactions from Quasiclassical Direct Dynamics Simulations. Organometallics 2021. [DOI: 10.1021/acs.organomet.1c00102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryan Carlsen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo 84602, Utah, United States
| | - Steven M. Maley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo 84602, Utah, United States
| | - Daniel H. Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo 84602, Utah, United States
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29
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Zhang H, Novak AJE, Jamieson CS, Xue XS, Chen S, Trauner D, Houk KN. Computational Exploration of the Mechanism of Critical Steps in the Biomimetic Synthesis of Preuisolactone A, and Discovery of New Ambimodal (5 + 2)/(4 + 2) Cycloadditions. J Am Chem Soc 2021; 143:6601-6608. [PMID: 33887906 PMCID: PMC11321821 DOI: 10.1021/jacs.1c01856] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Computational studies with ωB97X-D density functional theory of the mechanisms of the steps in Trauner's biomimetic synthesis of preuisolactone A have elaborated and refined mechanisms of several unique processes. An ambimodal transition state has been identified for the cycloaddition between an o-quinone and a hydroxy-o-quinone; this leads to both (5 + 2) (with H shift) and (4 + 2) cycloaddition products, which can in principle interconvert via α-ketol rearrangements. The origins of periselectivity of this ambimodal cycloaddition have been investigated computationally with molecular dynamics simulations and tested further by an experimental study. In the presence of bicarbonate ions, the deprotonated hydroxy-o-quinone leads to only the (5 + 2) cycloaddition adduct. A new mechanism for a benzilic acid rearrangement resulting in ring contraction is proposed.
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Affiliation(s)
- Hong Zhang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Alexander J E Novak
- Department of Chemistry, New York University, Silver Center, 100 Washington Square East, Room 712, New York, New York 10002, United States
| | - Cooper S Jamieson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Xiao-Song Xue
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Shuming Chen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Dirk Trauner
- Department of Chemistry, New York University, Silver Center, 100 Washington Square East, Room 712, New York, New York 10002, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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30
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Tantillo DJ. Dynamic effects on organic reactivity—Pathways to (and from) discomfort. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Dean J. Tantillo
- Department of Chemistry University of California, Davis Davis California USA
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31
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Feng Z, Tantillo DJ. Dynamic Effects on Migratory Aptitudes in Carbocation Reactions. J Am Chem Soc 2021; 143:1088-1097. [PMID: 33400509 DOI: 10.1021/jacs.0c11850] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Carbocation rearrangement reactions are of great significance to synthetic and biosynthetic chemistry. In pursuit of a scale of inherent migratory aptitude that takes into account dynamic effects, both uphill and downhill ab initio molecular dynamics (AIMD) simulations were used to examine competing migration events in a model system designed to remove steric and electronic biases. The results of these simulations were combined with detailed investigations of potential energy surface topography and variational transition state theory calculations to reveal the importance of nonstatistical dynamic effects on migratory aptitude.
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Affiliation(s)
- Zhitao Feng
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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32
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Liu Y, Li J. Quantitative Dynamics of the N 2O + C 2H 2 → Oxadiazole Reaction: A Model for 1,3-Dipolar Cycloadditions. ACS OMEGA 2020; 5:23343-23350. [PMID: 32954185 PMCID: PMC7496009 DOI: 10.1021/acsomega.0c03210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/24/2020] [Indexed: 06/11/2023]
Abstract
The reaction N2O + C2H2 → oxadiazole has been considered as a prototype for 1,3-dipolar cycloadditions. Here, we report a comprehensive dynamical study of this important reaction on a full-dimensional potential energy surface, which is fitted to about 64 000 high-level ab initio data by a machine learning approach. Comprehensive dynamical simulations are carried out to provide quantitative chemical insight into its reaction dynamics. In addition to confirming the enhancement effect of the N2O bending mode on the reactivity, intricate mode specificity effects of other vibrational modes in reactants are revealed for the first time. The asymmetric stretching mode of N2O and the C-C-H bending mode of C2H2 show no effect. All remaining modes can enhance the reactivity. In particular, the vibrational excitation of the N2O symmetric stretching mode shows similar enhancement effect on the title reaction, compared to its bending mode excitation. Detailed analysis reveals that the concerted mechanism dominates with the reactants propelled sufficiently close to each other to yield product. This study advances our understanding of the chemical dynamics of the title reaction.
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33
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Bai M, Feng Z, Li J, Tantillo DJ. Bouncing off walls - widths of exit channels from shallow minima can dominate selectivity control. Chem Sci 2020; 11:9937-9944. [PMID: 34094255 PMCID: PMC8162169 DOI: 10.1039/d0sc04036c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A selectivity model based on the widths of pathways to competing products, rather than barrier heights, is formulated for the butadiene + allyl cation reaction. This model was arrived at via analysis of stationary points, intrinsic reaction coordinates, potential energy surface shapes and direct dynamics trajectories, all determined using quantum chemical methods.
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Affiliation(s)
- Mengna Bai
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University No. 55 Daxuecheng South Rd., Shapingba Chongqing 401331 China.,Department of Chemistry, University of California Davis One Shields Avenue Davis CA 95616 USA
| | - Zhitao Feng
- Department of Chemistry, University of California Davis One Shields Avenue Davis CA 95616 USA
| | - Jun Li
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University No. 55 Daxuecheng South Rd., Shapingba Chongqing 401331 China
| | - Dean J Tantillo
- Department of Chemistry, University of California Davis One Shields Avenue Davis CA 95616 USA
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34
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Tang E, Ju H, Baum GL, Roalf DR, Satterthwaite TD, Pasqualetti F, Bassett DS. Control of brain network dynamics across diverse scales of space and time. Phys Rev E 2020; 101:062301. [PMID: 32688528 PMCID: PMC8728948 DOI: 10.1103/physreve.101.062301] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/12/2020] [Indexed: 12/30/2022]
Abstract
The human brain is composed of distinct regions that are each associated with particular functions and distinct propensities for the control of neural dynamics. However, the relation between these functions and control profiles is poorly understood, as is the variation in this relation across diverse scales of space and time. Here we probe the relation between control and dynamics in brain networks constructed from diffusion tensor imaging data in a large community sample of young adults. Specifically, we probe the control properties of each brain region and investigate their relationship with dynamics across various spatial scales using the Laplacian eigenspectrum. In addition, through analysis of regional modal controllability and partitioning of modes, we determine whether the associated dynamics are fast or slow, as well as whether they are alternating or monotone. We find that brain regions that facilitate the control of energetically easy transitions are associated with activity on short length scales and slow timescales. Conversely, brain regions that facilitate control of difficult transitions are associated with activity on long length scales and fast timescales. Built on linear dynamical models, our results offer parsimonious explanations for the activity propagation and network control profiles supported by regions of differing neuroanatomical structure.
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Affiliation(s)
- Evelyn Tang
- Department of Bioengineering, School of Engineering & Applied Science, University of Pennsylvania, Pennsylvania 19104, USA
- Max Planck Institute for Dynamics and Self-Organization, Göttingen 37079, Germany
| | - Harang Ju
- Department of Bioengineering, School of Engineering & Applied Science, University of Pennsylvania, Pennsylvania 19104, USA
- Neuroscience Graduate Program, Perelman School of Medicine, University of Pennsylvania, Pennsylvania 19104, USA
| | - Graham L Baum
- Department of Bioengineering, School of Engineering & Applied Science, University of Pennsylvania, Pennsylvania 19104, USA
- Neuroscience Graduate Program, Perelman School of Medicine, University of Pennsylvania, Pennsylvania 19104, USA
| | - David R Roalf
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Pennsylvania 19104, USA
| | - Theodore D Satterthwaite
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Pennsylvania 19104, USA
| | - Fabio Pasqualetti
- Department of Mechanical Engineering, University of California, Riverside, Riverside, California 92521, USA
| | - Danielle S Bassett
- Department of Bioengineering, School of Engineering & Applied Science, University of Pennsylvania, Pennsylvania 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Pennsylvania 19104, USA
- Department of Physics & Astronomy, College of Arts & Sciences, University of Pennsylvania, Pennsylvania 19104, USA
- Department of Electrical & Systems Engineering, School of Engineering & Applied Science, University of Pennsylvania, Pennsylvania 19104, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Pennsylvania 19104, USA
- Santa Fe Institute, Santa Fe, New Mexico 87501, USA
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35
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Tantillo DJ. Interrogating chemical mechanisms in natural products biosynthesis using quantum chemical calculations. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dean J. Tantillo
- Department of Chemistry University of California–Davis Davis California
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36
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Abstract
Nonstatistical dynamics is important for many chemical reactions. The Rice-Ramsperger-Kassel-Marcus (RRKM) theory of unimolecular kinetics assumes a reactant molecule maintains a statistical microcanonical ensemble of vibrational states during its dissociation so that its unimolecular dynamics are time independent. Such dynamics results when the reactant's atomic motion is chaotic or irregular. Intrinsic non-RRKM dynamics occurs when part of the reactant's phase space consists of quasiperiodic/regular motion and a bottleneck exists, so that the unimolecular rate constant is time dependent. Nonrandom excitation of a molecule may result in short-time apparent non-RRKM dynamics. For rotational activation, the 2J + 1 K levels for a particular J may be highly mixed, making K an active degree of freedom, or K may be a good quantum number and an adiabatic degree of freedom. Nonstatistical dynamics is often important for bimolecular reactions and their intermediates and for product-energy partitioning of bimolecular and unimolecular reactions. Post–transition state dynamics is often highly complex and nonstatistical.
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Affiliation(s)
- Bhumika Jayee
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
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37
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Teynor MS, Carlsen R, Ess DH. Relationship Between Energy Landscape Shape and Dynamics Trajectory Outcomes for Methane C–H Activation by Cationic Cp*(PMe3)Ir/Rh/Co(CH3). Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00108] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Matthew S. Teynor
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Ryan Carlsen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Daniel H. Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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38
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Laconsay CJ, Tsui KY, Tantillo DJ. Tipping the balance: theoretical interrogation of divergent extended heterolytic fragmentations. Chem Sci 2020; 11:2231-2242. [PMID: 32190279 PMCID: PMC7059201 DOI: 10.1039/c9sc05161a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/08/2020] [Indexed: 01/24/2023] Open
Abstract
Herein we interrogate a type of heterolytic fragmentation reaction called a 'divergent fragmentation' using density functional theory (DFT), natural bond orbital (NBO) analysis, ab initio molecular dynamics (AIMD), and external electric field (EEF) calculations. We demonstrate that substituents, electrostatic environment and non-statistical dynamic effects all influence product selectivity in reactions that involve divergent fragmentation pathways. Direct dynamics simulations reveal an unexpected post-transition state bifurcation (PTSB), and EEF calculations suggest that some transition states for divergent pathways can, in principle, be selectively stabilized if an electric field of the correct magnitude is oriented appropriately.
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Affiliation(s)
- Croix J Laconsay
- Department of Chemistry , University of California , Davis , CA 95616 , USA .
| | - Ka Yi Tsui
- Department of Chemistry , University of California , Davis , CA 95616 , USA .
| | - Dean J Tantillo
- Department of Chemistry , University of California , Davis , CA 95616 , USA .
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39
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The cascade unzipping of ladderane reveals dynamic effects in mechanochemistry. Nat Chem 2020; 12:302-309. [DOI: 10.1038/s41557-019-0396-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 11/15/2019] [Indexed: 11/08/2022]
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40
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Wheeler JI, Carlsen R, Ess DH. Mechanistic molecular motion of transition-metal mediated β-hydrogen transfer: quasiclassical trajectories reveal dynamically ballistic, dynamically unrelaxed, two step, and concerted mechanisms. Dalton Trans 2020; 49:7747-7757. [DOI: 10.1039/d0dt01687j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Quasiclassical direct dynamics reveal new dynamical mechanisms for metal-alkyl to ethylene β-hydrogen transfer.
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Affiliation(s)
- Josh I. Wheeler
- Department of Chemistry and Biochemistry
- Brigham Young University
- Provo
- USA
| | - Ryan Carlsen
- Department of Chemistry and Biochemistry
- Brigham Young University
- Provo
- USA
| | - Daniel H. Ess
- Department of Chemistry and Biochemistry
- Brigham Young University
- Provo
- USA
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41
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Ito T, Harabuchi Y, Maeda S. AFIR explorations of transition states of extended unsaturated systems: automatic location of ambimodal transition states. Phys Chem Chem Phys 2020; 22:13942-13950. [DOI: 10.1039/d0cp02379e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on the artificial force induced reaction (AFIR) method, we proposed a procedure to systematically explore ambimodal transition states (TSs) that cause the dynamical bifurcation.
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Affiliation(s)
- Takuma Ito
- Graduate School of Chemical Sciences and Engineering
- Hokkaido University
- Sapporo 060-8628
- Japan
| | - Yu Harabuchi
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
| | - Satoshi Maeda
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
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42
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Sangolkar AA, Pawar R. Prediction of the [4 + 2]- and [5 + 4]-cycloaddition reactions in zig-zag carbon nanotubes via an ambimodal transition state: density functional theory calculations. RSC Adv 2020; 10:11111-11120. [PMID: 35495313 PMCID: PMC9050518 DOI: 10.1039/c9ra10252c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/26/2020] [Indexed: 11/21/2022] Open
Abstract
A unique type of chemical reaction known as an ambimodal reaction has drawn tremendous attention owing to its intriguing feature of forming multiple (two or more) products from the same (single) transition state. In contrast to conventional reactions, bifurcation of the potential energy surface takes place in ambimodal reactions. Density functional theory (DFT) based calculations were performed to probe the Diels–Alder (DA) cycloaddition reactions of various carbon nanotubes (CNTs) with 1,3-butadiene. The present investigation reveals the possibility of ambimodal transition state formation on a potential energy surface (PES) corresponding to an unusual [5 + 4]-cycloadduct along with the conventional [4 + 2]-cycloadduct. The ground state of the [5 + 4]-cycloadduct obtained from butadiene and the H-terminated CNTs is a triplet (3T) state, but on the other hand the [4 + 2]-cycloadduct is a singlet (1S) state. The [5 + 4]-adduct is energetically more stable in comparison with the [4 + 2]-adduct. The possibility of the formation of the [5 + 4]-adduct is validated using frontier molecular orbitals. The length of the nanotube significantly influences the overall kinetics and thermodynamics of the reaction. A DFT study has been performed to unveil the ambimodal reaction in H-terminated CNTs.![]()
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Affiliation(s)
| | - Ravinder Pawar
- Department of Chemistry
- National Institute of Technology (NIT) Warangal
- India
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43
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Castiñeira Reis M, López CS, Nieto Faza O, Tantillo DJ. Pushing the limits of concertedness. A waltz of wandering carbocations. Chem Sci 2019; 10:2159-2170. [PMID: 30881640 PMCID: PMC6385557 DOI: 10.1039/c8sc03567a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/10/2018] [Indexed: 12/21/2022] Open
Abstract
Among the array of complex terpene-forming carbocation cyclization/rearrangement reactions, the so-called "triple shift" reactions are among the most unexpected. Such reactions involve the asynchronous combination of three 1,n-shifts into a concerted process, e.g., a 1,2-alkyl shift followed by a 1,3-hydride shift followed by a second 1,2-alkyl shift. This type of reaction so far has been proposed to occur during the biosynthesis of diterpenes and the sidechains of sterols. Here we describe efforts to push the limits of concertedness in this type of carbocation reaction by designing, and characterizing with quantum chemical computations, systems that could couple additional 1,n-shift events to a triple shift leading, in principle to quadruple, pentuple, etc. shifts. While our designs did not lead to clear-cut examples of quadruple, etc. shifts, they did lead to reactions with surprisingly flat energy surfaces where more than five chemical events connect reactants and plausible products. Ab initio molecular dynamics simulations demonstrate that the formal minima on these surfaces interchange on short timescales, both with each other and with additional unexpected structures, allowing us a glimpse into a very complex manifold that allows ready access to great structural diversity.
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Affiliation(s)
- Marta Castiñeira Reis
- Departamento de Química Orgánica , Universidade de Vigo , Lagoas-Marcosende , 36310 , Vigo , Spain
| | - Carlos Silva López
- Departamento de Química Orgánica , Universidade de Vigo , Lagoas-Marcosende , 36310 , Vigo , Spain
| | - Olalla Nieto Faza
- Departamento de Química Orgánica , Universidade de Vigo , As Lagoas , 32004 , Ourense , Spain .
| | - Dean J Tantillo
- Department of Chemistry , University of California , One Shields Ave , Davis , CA 95616 , USA .
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44
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Lee YM, Kim S, Ohkubo K, Kim KH, Nam W, Fukuzumi S. Unified Mechanism of Oxygen Atom Transfer and Hydrogen Atom Transfer Reactions with a Triflic Acid-Bound Nonheme Manganese(IV)-Oxo Complex via Outer-Sphere Electron Transfer. J Am Chem Soc 2019; 141:2614-2622. [PMID: 30646680 DOI: 10.1021/jacs.8b12935] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Outer-sphere electron transfer from styrene, thioanisole, and toluene derivatives to a triflic acid (HOTf)-bound nonheme Mn(IV)-oxo complex, [(N4Py)MnIV(O)]2+-(HOTf)2 (N4Py = N, N-bis(2-pyridylmethyl)- N-bis(2-pyridyl)methylamine), has been shown to be the rate-determining step of different types of redox reactions such as epoxidation, sulfoxidation, and hydroxylation of styrene, thioanisole, and toluene derivatives, respectively, by [(N4Py)MnIV(O)]2+-(HOTf)2. The rate constants of HOTf-promoted epoxidation of all styrene derivatives with [(N4Py)MnIV(O)]2+ and electron transfer from electron donors to [(N4Py)MnV(O)]2+ exhibit a remarkably unified correlation with the driving force of outer-sphere electron transfer in light of the Marcus theory of electron transfer. The same electron-transfer driving force dependence is observed in the oxygen atom transfer from [(N4Py)MnIV(O)]2+-(HOTf)2 to thioanisole derivatives as well as in the hydrogen atom transfer from toluene derivatives to [(N4Py)MnIV(O)]2+-(HOTf)2. Thus, mechanisms of oxygen atom transfer (epoxidation and sulfoxidation) reactions of styrene and thioanisole derivatives and hydrogen atom transfer (hydroxylation) reactions of toluene derivatives by [(N4Py)MnIV(O)]2+-(HOTf)2 have been unified for the first time as the same reaction pathway via outer-sphere electron transfer, followed by the fast bond-forming step, which exhibits the singly unified electron-transfer driving force dependence of the rate constants as outer-sphere electron-transfer reactions. In the case of the epoxidation of cis-stilbene by [(N4Py)MnIV(O)]2+-(HOTf)2, the isomerization of cis-stilbene radical cation to trans-stilbene radical cation occurs after outer-sphere electron transfer from cis-stilbene to [(N4Py)MnIV(O)]2+-(HOTf)2 to yield trans-stilbene oxide selectively, which is also taken as evidence for the occurrence of electron transfer in the acid-catalyzed epoxidation.
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Affiliation(s)
- Yong-Min Lee
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea
| | - Surin Kim
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea
| | - Kei Ohkubo
- Institute for Advanced Co-Creation Studies, Open and Transdisciplinary Research Initiatives , Osaka University , Suita , Osaka 565-0871 , Japan
| | - Kyung-Ha Kim
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea.,State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences , Lanzhou 730000 , China
| | - Shunichi Fukuzumi
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea.,Faculty of Science and Engineering , Meijo University , SENTAN, Japan Science and Technology Agency (JST), Nagoya , Aichi 468-0073 , Japan
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45
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Monte Carlo stochastic simulation of the master equation for unimolecular reaction systems. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/b978-0-444-64207-3.00007-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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46
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Chen S, Yu P, Houk KN. Ambimodal Dipolar/Diels–Alder Cycloaddition Transition States Involving Proton Transfers. J Am Chem Soc 2018; 140:18124-18131. [DOI: 10.1021/jacs.8b11080] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Shuming Chen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Peiyuan Yu
- Energy Storage and Distributed Resources Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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47
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Yu Y, Yang Z, Houk KN. Molecular dynamics of the intramolecular 1, 3-dipolar ene reaction of a nitrile oxide and an alkene: non-statistical behavior of a reaction involving a diradical intermediate. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1549338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Yanmin Yu
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, Beijing University of Technology, Beijing, People’s Republic of China
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Zhongyue Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
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48
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Lermyte F, Valkenborg D, Loo JA, Sobott F. Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure. MASS SPECTROMETRY REVIEWS 2018; 37:750-771. [PMID: 29425406 PMCID: PMC6131092 DOI: 10.1002/mas.21560] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 05/11/2023]
Abstract
In recent years, electron capture (ECD) and electron transfer dissociation (ETD) have emerged as two of the most useful methods in mass spectrometry-based protein analysis, evidenced by a considerable and growing body of literature. In large part, the interest in these methods is due to their ability to induce backbone fragmentation with very little disruption of noncovalent interactions which allows inference of information regarding higher order structure from the observed fragmentation behavior. Here, we review the evolution of electron-based dissociation methods, and pay particular attention to their application in "native" mass spectrometry, their mechanism, determinants of fragmentation behavior, and recent developments in available instrumentation. Although we focus on the two most widely used methods-ECD and ETD-we also discuss the use of other ion/electron, ion/ion, and ion/neutral fragmentation methods, useful for interrogation of a range of classes of biomolecules in positive- and negative-ion mode, and speculate about how this exciting field might evolve in the coming years.
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Affiliation(s)
- Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - Dirk Valkenborg
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Agoralaan, Diepenbeek, Belgium
- Applied Bio and Molecular Systems, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California
- UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, California
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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49
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McCulley CH, Tantillo DJ. Secondary Carbocations in the Biosynthesis of Pupukeanane Sesquiterpenes. J Phys Chem A 2018; 122:8058-8061. [PMID: 30209949 DOI: 10.1021/acs.jpca.8b07961] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The results of quantum chemical calculations on putative biosynthetic carbocation cyclization/rearrangements leading to pupukeanane and related sesquiterpenes indicate that a secondary carbocation proposed as an intermediate is not a minimum on the potential energy surface and instead resides in a region of the potential energy surface associated with a plateau containing multiple exit channels.
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Affiliation(s)
- Christina H McCulley
- Department of Chemistry , University of California-Davis , Davis , California 95616 , United States
| | - Dean J Tantillo
- Department of Chemistry , University of California-Davis , Davis , California 95616 , United States
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50
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Geng C, Li J, Weiske T, Schwarz H. Thermal O–H Bond Activation of Water As Mediated by Heteronuclear [Al2Mg2O5]•+: Evidence for Oxygen-Atom Scrambling. J Am Chem Soc 2018; 140:9275-9281. [DOI: 10.1021/jacs.8b05618] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Caiyun Geng
- Institut für Chemie, Technische Universität Berlin, Straße des 17 Juni 115, Berlin 10623, Germany
| | - Jilai Li
- Institut für Chemie, Technische Universität Berlin, Straße des 17 Juni 115, Berlin 10623, Germany
- Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Thomas Weiske
- Institut für Chemie, Technische Universität Berlin, Straße des 17 Juni 115, Berlin 10623, Germany
| | - Helmut Schwarz
- Institut für Chemie, Technische Universität Berlin, Straße des 17 Juni 115, Berlin 10623, Germany
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