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Sun Q, Lu X, Tantillo DJ. Dynamic Effects in Intramolecular Schmidt Reactions: Entropy, Electrostatic Drag, and Selectivity Prediction. Chemphyschem 2021; 22:649-656. [PMID: 33567140 DOI: 10.1002/cphc.202100033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/16/2022]
Abstract
Electrostatic drag in the intramolecular Schmidt reactions of azidopropylcyclohexanones is characterized using density functional theory (DFT) calculations and direct dynamics simulations. Despite resulting from enthalpically favorable interactions, electrostatic drag slows down N2 loss during formation of bridged lactam products, an effect with implications for controlling product selectivity.
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Affiliation(s)
- Qing Sun
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang, 330063, China
| | - Xin Lu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, CA 95616, USA
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2
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Jiang H, Tao X, Kammler M, Ding F, Wodtke AM, Kandratsenka A, Miller TF, Bünermann O. Small Nuclear Quantum Effects in Scattering of H and D from Graphene. J Phys Chem Lett 2021; 12:1991-1996. [PMID: 33596383 DOI: 10.1021/acs.jpclett.0c02933] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We study nuclear quantum effects in H/D sticking to graphene, comparing scattering experiments at near-zero coverage with classical, quantized, and transition-state calculations. The experiment shows H/D sticking probabilities that are indistinguishable from one another and markedly smaller than those expected from a consideration of zero-point energy shifts of the chemisorption transition state. Inclusion of dynamical effects and vibrational anharmonicity via ring-polymer molecular dynamics (RPMD) yields results that are in good agreement with the experimental results. RPMD also reveals that nuclear quantum effects, while modest, arise primarily from carbon and not from H/D motion, confirming the importance of a C atom rehybridization mechanism associated with H/D sticking on graphene.
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Affiliation(s)
- Hongyan Jiang
- Department of Dynamics at Surfaces, Max-Planck-Institute for Biophysical Chemistry, Am Faßerg 11, 37077 Göttingen, Germany
| | - Xuecheng Tao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Marvin Kammler
- Department of Dynamics at Surfaces, Max-Planck-Institute for Biophysical Chemistry, Am Faßerg 11, 37077 Göttingen, Germany
| | - Feizhi Ding
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Alec M Wodtke
- Department of Dynamics at Surfaces, Max-Planck-Institute for Biophysical Chemistry, Am Faßerg 11, 37077 Göttingen, Germany
- Institut für Physikalische Chemie, Georg-Georg-August-Universität Göttingen, Tammanstraße 6, 37077 Göttingen, Germany
- International Center for Advanced Studies of Energy Conversion, Georg-August University of Göttingen, Tammanstraße 6, 37077 Göttingen, Germany
| | - Alexander Kandratsenka
- Department of Dynamics at Surfaces, Max-Planck-Institute for Biophysical Chemistry, Am Faßerg 11, 37077 Göttingen, Germany
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Oliver Bünermann
- Department of Dynamics at Surfaces, Max-Planck-Institute for Biophysical Chemistry, Am Faßerg 11, 37077 Göttingen, Germany
- Institut für Physikalische Chemie, Georg-Georg-August-Universität Göttingen, Tammanstraße 6, 37077 Göttingen, Germany
- International Center for Advanced Studies of Energy Conversion, Georg-August University of Göttingen, Tammanstraße 6, 37077 Göttingen, Germany
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Burns JM, Boittier ED. Pathway Bifurcation in the (4 + 3)/(5 + 2)-Cycloaddition of Butadiene and Oxidopyrylium Ylides: The Significance of Molecular Orbital Isosymmetry. J Org Chem 2019; 84:5997-6005. [DOI: 10.1021/acs.joc.8b03236] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jed M. Burns
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4067 Queensland, Australia
| | - Eric D. Boittier
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4067 Queensland, Australia
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Hare SR, Li A, Tantillo DJ. Post-transition state bifurcations induce dynamical detours in Pummerer-like reactions. Chem Sci 2018; 9:8937-8945. [PMID: 30627409 PMCID: PMC6296359 DOI: 10.1039/c8sc02653j] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 09/25/2018] [Indexed: 12/28/2022] Open
Abstract
A post-transition state bifurcation (PTSB) involved in a Pummerer-type rearrangement is characterized using density functional theory (DFT) calculations on potential energy stationary points and direct dynamics simulations. A sensitivity of the ratio of products produced via this PTSB to solvent dielectric constant is revealed and implications of such a dependence for selectivity control of organic reactions are discussed.
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Affiliation(s)
| | - Ang Li
- Shanghai Institute of Organic Chemistry , China
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5
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Blümel M, Nagasawa S, Blackford K, Hare SR, Tantillo DJ, Sarpong R. Rearrangement of Hydroxylated Pinene Derivatives to Fenchone-Type Frameworks: Computational Evidence for Dynamically-Controlled Selectivity. J Am Chem Soc 2018; 140:9291-9298. [DOI: 10.1021/jacs.8b05804] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Marcus Blümel
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Shota Nagasawa
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Katherine Blackford
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Stephanie R. Hare
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Dean J. Tantillo
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Richmond Sarpong
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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Mandal N, Datta A. Dynamical Effects along the Bifurcation Pathway Control Semibullvalene Formation in Deazetization Reactions. J Phys Chem B 2018; 122:1239-1244. [PMID: 29316395 DOI: 10.1021/acs.jpcb.7b09533] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Post-transition-state dynamics during the deazetization of 3 resulting in two degenerate semibullvalenes (4 and 5) have been investigated with density functional theory (DFT) and quasi-classical trajectory (QCT) calculations. Removal of N2 from 3 occurs through a synchronous and concerted pathway through an ambimodal transition-state (TS1). In addition to TS2, the exclusively anticipated product from minimum energy pathway (MEP) calculations, trajectories initiated from TS1 produce 4, TS2, and 5 in 1:1:1 ratio. Isotopic substitutions (12C(13C/14C)-H(D) at 1-2 positions) result in purely Newtonian kinetic isotope effects (4:5 ≈ 1.4 for 13C1-13C2), an unequivocal evidence for dynamics controlled product formation.
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Affiliation(s)
- Nilangshu Mandal
- Department of Spectroscopy, Indian Association for the Cultivation of Science , 2A and 2B Raja S.C. Mallick Road, Kolkata 700032, India
| | - Ayan Datta
- Department of Spectroscopy, Indian Association for the Cultivation of Science , 2A and 2B Raja S.C. Mallick Road, Kolkata 700032, India
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7
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Hare SR, Tantillo DJ. Post-transition state bifurcations gain momentum – current state of the field. PURE APPL CHEM 2017. [DOI: 10.1515/pac-2017-0104] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe existence of post-transition state bifurcations on potential energy surfaces for organic and biological reaction mechanisms has been known for decades, but recently, new reports of bifurcations have been occurring at a much higher rate. Beyond simply discovering bifurcations, computational chemists are developing techniques to understand what aspects of molecular structure and vibrations control the product selectivity in systems containing bifurcations. For example, the distribution of products seen in simulations has been found to be extremely sensitive to the local environment of the reacting system (i.e. the presence of a catalyst, enzyme, or explicit solvent molecules). The outlook for the future of this field is discussed, with an eye towards the application of the principles discussed here by experimental chemists to design a reaction setup to efficiently generate desired products.
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Affiliation(s)
- Stephanie R. Hare
- University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Dean J. Tantillo
- University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
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Doubleday C, Boguslav M, Howell C, Korotkin SD, Shaked D. Trajectory Calculations for Bergman Cyclization Predict H/D Kinetic Isotope Effects Due to Nonstatistical Dynamics in the Product. J Am Chem Soc 2016; 138:7476-9. [PMID: 27281683 DOI: 10.1021/jacs.6b03466] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An unusual H/D kinetic isotope effect (KIE) is described, in which isotopic selectivity arises primarily from nonstatistical dynamics in the product. In DFT-based quasiclassical trajectories of Bergman cyclization of (Z)-3-hexen-1,5-diyne (1) at 470 K, the new CC bond retains its energy, and 28% of nascent p-benzyne recrosses back to the enediyne on a vibrational time scale. The competing process of intramolecular vibrational redistribution (IVR) in p-benzyne is too slow to prevent this. Deuteration increases the rate of IVR, which decreases the fraction of recrossing and increases the yield of statistical (trapable) p-benzyne, 2. Trapable yields for three isotopomers of 2 range from 72% to 86%. The resulting KIEs for Bergman cyclization differ substantially from KIEs predicted by transition state theory, which suggests that IVR in this reaction can be studied by conventional KIEs. Leakage of vibrational zero point energy (ZPE) into the reaction coordinate was probed by trajectories in which initial ZPE in the CH/CD stretching modes was reduced by 25%. This did not change the predicted KIEs.
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Affiliation(s)
- Charles Doubleday
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
| | - Mayla Boguslav
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
| | - Caronae Howell
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
| | - Scott D Korotkin
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
| | - David Shaked
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
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10
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Kramer ZC, Carpenter BK, Ezra GS, Wiggins S. Reaction Path Bifurcation in an Electrocyclic Reaction: Ring-Opening of the Cyclopropyl Radical. J Phys Chem A 2015; 119:6611-30. [DOI: 10.1021/acs.jpca.5b02834] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zeb C. Kramer
- Department
of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, New York 14853 United States
| | - Barry K. Carpenter
- School
of Chemistry, University of Cardiff, Cardiff CF10 3AT, United Kingdom
| | - Gregory S. Ezra
- Department
of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, New York 14853 United States
| | - Stephen Wiggins
- School
of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
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11
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Alabugin IV, Bresch S, dos Passos Gomes G. Orbital hybridization: a key electronic factor in control of structure and reactivity. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3382] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Igor V. Alabugin
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL 32306-4390 USA
| | - Stefan Bresch
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL 32306-4390 USA
| | - Gabriel dos Passos Gomes
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL 32306-4390 USA
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12
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Samanta D, Rana A, Schmittel M. Nonstatistical dynamics in the thermal Garratt-Braverman/[1,5]-H shift of one ene-diallene: an experimental and computational study. J Org Chem 2014; 79:8435-9. [PMID: 25189090 DOI: 10.1021/jo501324w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A mechanistic study of the thermal Garratt-Braverman/[1,5]-H shift of ene-diallene 6 leading to alkenes (E)-8 and (Z)-8 is reported. The product ratio was found to be temperature-independent and does not agree with the computed energy barriers (i.e., TS2E(⧧) and TS2Z(⧧)). On the basis of experimental and DFT computational results, we propose a mechanism that is strongly controlled by nonstatistical dynamic effects.
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Affiliation(s)
- Debabrata Samanta
- Department of Chemistry and Biology, Universität Siegen , Adolf-Reichwein-Strasse, D-57068 Siegen, Germany
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13
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Alabugin IV, Bresch S, Manoharan M. Hybridization trends for main group elements and expanding the Bent's rule beyond carbon: more than electronegativity. J Phys Chem A 2014; 118:3663-77. [PMID: 24773162 DOI: 10.1021/jp502472u] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Trends in hybridization were systematically analyzed through the combination of DFT calculations with NBO analysis for the five elements X (X = B, C, N, O, and F) in 75 HnX-YHm compounds, where Y spans the groups 13-17 of the periods 2-4. This set of substrates probes the flexibility of the hybridization at five atoms X through variations in electronegativity, polarizability, and orbital size of Y. The results illustrate the scope and limitations of the Bent's rule, the classic correlation between electronegativity and hybridization, commonly used in analyzing structural effects in carbon compounds. The rehybridization effects are larger for fluorine- and oxygen-bonds than they are in the similar bonds to carbon. For bonds with the larger elements Y of the lower periods, trends in orbital hybridization depend strongly on both electronegativity and orbital size. For charged species, the effects of substituent orbital size in the more polarizable bonds to heavier elements show a particularly strong response to the charge introduction at the central atom. In the final section, we provide an example of the interplay between hybridization effects with molecular structure and reactivity. In particular, the ability to change hybridization without changes in polarization provides an alternative way to control structure and reactivity, as illustrated by the strong correlation of strain in monosubstituted cyclopropanes with hybridization in the bond to the substituent.
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Affiliation(s)
- Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306-4390, United States
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Samanta D, Rana A, Schmittel M. Quantification of Nonstatistical Dynamics in an Intramolecular Diels–Alder Cyclization without Trajectory Computation. J Org Chem 2014; 79:2368-76. [DOI: 10.1021/jo500035b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Debabrata Samanta
- Department of Chemistry and
Biology, Universität Siegen, Adolf-Reichwein-Strasse, D-57068 Siegen, Germany
| | - Anup Rana
- Department of Chemistry and
Biology, Universität Siegen, Adolf-Reichwein-Strasse, D-57068 Siegen, Germany
| | - Michael Schmittel
- Department of Chemistry and
Biology, Universität Siegen, Adolf-Reichwein-Strasse, D-57068 Siegen, Germany
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