1
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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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2
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Yue X, Zhou Q, Houk KN. Computational Exploration of the Thermal Rearrangement of Basketene: One Forbidden versus Two Allowed Pericyclic Reactions. J Org Chem 2023; 88:14303-14307. [PMID: 37768874 DOI: 10.1021/acs.joc.3c00993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
The thermal rearrangement of basketene to Nenitzescu's hydrocarbon has been explored using density functional theory (M06-2X and ωB97X-D) and DLPNO-CCSD(T) quantum mechanics. Both the sequential thermally allowed retro Diels-Alder followed by Cope rearrangement and the thermally forbidden retro-[2 + 2] cycloaddition were studied. The controlling role of orbital symmetry rather than reaction thermodynamics is demonstrated.
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Affiliation(s)
- Xiaolin Yue
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- College of Chemistry, Nankai University, Tianjin 300071, China
| | - Qingyang Zhou
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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3
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Peluzo BMTC, Makoś MZ, Moura RT, Freindorf M, Kraka E. Linear versus Bent Uranium(II) Metallocenes─A Local Vibrational Mode Study. Inorg Chem 2023. [PMID: 37478353 DOI: 10.1021/acs.inorgchem.3c01761] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Uranium metallocenes have recently attracted attention driven by their use as catalysts in organometallic synthesis. In addition to bent U(IV) and U(III), an U(II) metallocene [(η5-C5i Pr5)2U] was synthesized with an unusual linear Cp-U-Cp angle. In this work, we investigated 22 U(II) metallocenes, (i) assessing the intrinsic strength of the U-ring interactions in these complexes with a novel bond strength measure based on our local vibrational mode analysis and (ii) systematically exploring what makes these U(II) metallocenes bent. We included relativistic effects through the NESCau Hamiltonian and complemented the local mode analysis with natural bonding orbital (NBO) and quantum theory of atoms in molecules (QTAIM) data. Our study led to the following results: (i) reduction of bulky U-ring ligand substituents does not lead to bent complexes for alkyl substituents (iPr and iBu) in contrast to SiMe3 ring substituents, which are all bent. (ii) The most bent complexes are [(η5-C5H4SiMe3)2U] (130°) and [η5-P5H5)2U] (143°). (iii) Linear complexes showed one hybridized NBO with s/d character, while bent structures were characterized by s/d/f mixing. (iv) We did not observe a correlation between the strength of the U-ring interaction and the amount of the ring-U-ring bend; the strongest interaction was found for [η5-Cp)2U] and the weakest for [η5-P5H5)2U]. In conclusion, our results provide a foundation for the design of U(II) metallocenes with specific physicochemical properties and increased reactivity.
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Affiliation(s)
- Bárbara M T C Peluzo
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Małgorzata Z Makoś
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Renaldo T Moura
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
- Department of Chemistry and Physics, Center of Agrarian Sciences, Federal University of Paraíba, Areia 58397-000, Paraíba, Brazil
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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4
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Kraka E, Antonio JJ, Freindorf M. Reaction mechanism - explored with the unified reaction valley approach. Chem Commun (Camb) 2023; 59:7151-7165. [PMID: 37233449 DOI: 10.1039/d3cc01576a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
One of the ultimate goals of chemistry is to understand and manipulate chemical reactions, which implies the ability to monitor the reaction and its underlying mechanism at an atomic scale. In this article, we introduce the Unified Reaction Valley Approach (URVA) as a tool for elucidating reaction mechanisms, complementing existing computational procedures. URVA combines the concept of the potential energy surface with vibrational spectroscopy and describes a chemical reaction via the reaction path and the surrounding reaction valley traced out by the reacting species on the potential energy surface on their way from the entrance to the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting species is registered by a change in the normal vibrational modes spanning the reaction valley and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction, with curvature minima reflecting minimal change and curvature maxima indicating the location of important chemical events such as bond breaking/formation, charge polarization and transfer, rehybridization, etc. A decomposition of the path curvature into internal coordinate components or other coordinates of relevance for the reaction under consideration, provides comprehensive insight into the origin of the chemical changes taking place. After giving an overview of current experimental and computational efforts to gain insight into the mechanism of a chemical reaction and presenting the theoretical background of URVA, we illustrate how URVA works for three diverse processes, (i) [1,3] hydrogen transfer reactions; (ii) α-keto-amino inhibitor for SARS-CoV-2 Mpro; (iii) Rh-catalyzed cyanation. We hope that this article will inspire our computational colleagues to add URVA to their repertoire and will serve as an incubator for new reaction mechanisms to be studied in collaboration with our experimental experts in the field.
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Affiliation(s)
- Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX 75275-0314, USA.
| | - Juliana J Antonio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX 75275-0314, USA.
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX 75275-0314, USA.
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5
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Zhang X, Tian X, Li J, Li M, Gao T, Zou S, Chen J, Xu X, Gou Q, Grabow JU. Insights into the Diels-Alder Reaction of Furan with Maleic Anhydride from Its Prereactive Intermediate. J Phys Chem Lett 2023; 14:604-608. [PMID: 36633594 DOI: 10.1021/acs.jpclett.2c03560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The prereactive intermediate in the furan-maleic anhydride cycloaddition, a classical Diels-Alder reaction, has been captured and characterized in pulsed jets by Fourier transform microwave spectroscopy for the first time. The observed species is stabilized by the π-π* interaction between the two moieties, which connects to the endo channel of the cycloaddition. The secondary interactions between the C=C and C=O in the observed isomer are accountable for its lower energy with respect to the one with the exo channel. The present study tries to fill the significant void of the experimental information on prereactive intermediates as the first stage of Diels-Alder cycloadditions, by outlining the stability of the prereactive intermediate and its accurate molecular structure and by emphasizing the role of the π-π* interaction in governing the stereochemical outcome of the reaction.
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Affiliation(s)
- Xinyue Zhang
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Xiao Tian
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Jiayi Li
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Meng Li
- Institut für Physikalische Chemie & Elektrochemie, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - Tianyue Gao
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Siyu Zou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Junhua Chen
- School of Pharmacy, Guizhou Medical University, Guiyang 550025, Guizhou, China
| | - Xuefang Xu
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Qian Gou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie & Elektrochemie, Leibniz Universität Hannover, 30167 Hannover, Germany
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6
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Georgieva MK, Santos AG. Theoretical Study on Chiral Boron Complex‐Promoted Asymmetric Diels‐Alder Cycloadditions. European J Org Chem 2022. [DOI: 10.1002/ejoc.202201082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Miglena K. Georgieva
- LAQV-REQUIMTE, Department of Chemistry NOVA School of Science and Technology Universidade Nova de Lisboa 2829-516 Caparica Portugal
| | - A. Gil Santos
- LAQV-REQUIMTE, Department of Chemistry NOVA School of Science and Technology Universidade Nova de Lisboa 2829-516 Caparica Portugal
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7
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Seeman JI. Fifty Years of a Dispute. A Triptych: Why Woodward?**. CHEM REC 2022; 22:e202200150. [DOI: 10.1002/tcr.202200150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Jeffrey I. Seeman
- Department of Chemistry University of Richmond Richmond VA 23173 USA
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8
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Mechanistic Details of the Sharpless Epoxidation of Allylic Alcohols—A Combined URVA and Local Mode Study. Catalysts 2022. [DOI: 10.3390/catal12070789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In this work, we investigated the catalytic effects of a Sharpless dimeric titanium (IV)–tartrate–diester catalyst on the epoxidation of allylalcohol with methyl–hydroperoxide considering four different orientations of the reacting species coordinated at the titanium atom (reactions R1–R4) as well as a model for the non-catalyzed reaction (reaction R0). As major analysis tools, we applied the URVA (Unified Reaction Valley Approach) and LMA (Local Mode Analysis), both being based on vibrational spectroscopy and complemented by a QTAIM analysis of the electron density calculated at the DFT level of theory. The energetics of each reaction were recalculated at the DLPNO-CCSD(T) level of theory. The URVA curvature profiles identified the important chemical events of all five reactions as peroxide OO bond cleavage taking place before the TS (i.e., accounting for the energy barrier) and epoxide CO bond formation together with rehybridization of the carbon atoms of the targeted CC double bond after the TS. The energy decomposition into reaction phase contribution phases showed that the major effect of the catalyst is the weakening of the OO bond to be broken and replacement of OH bond breakage in the non-catalyzed reaction by an energetically more favorable TiO bond breakage. LMA performed at all stationary points rounded up the investigation (i) quantifying OO bond weakening of the oxidizing peroxide upon coordination at the metal atom, (ii) showing that a more synchronous formation of the new CO epoxide bonds correlates with smaller bond strength differences between these bonds, and (iii) elucidating the different roles of the three TiO bonds formed between catalyst and reactants and their interplay as orchestrated by the Sharpless catalyst. We hope that this article will inspire the computational community to use URVA complemented with LMA in the future as an efficient mechanistic tool for the optimization and fine-tuning of current Sharpless catalysts and for the design new of catalysts for epoxidation reactions.
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9
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Han X, Zhang J, Yang YI, Zhang Z, Yang L, Gao YQ. Enhanced Sampling Simulation Reveals How Solvent Influences Chirogenesis of the Intra-Molecular Diels-Alder Reaction. J Chem Theory Comput 2022; 18:4318-4326. [PMID: 35666128 DOI: 10.1021/acs.jctc.2c00233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The timescale involved in chemical reactions is quite often beyond that of normal molecular dynamics simulations. Here, we combine metadynamics with selective integrated tempering sampling to simulate an intra-molecular Diels-Alder reaction in explicit solvents. Based on a one-dimensional collective variable obtained from harmonic linear discriminant analysis, four chiral isomers of products were observed in the simulation. Analyses of reactive trajectories showed that this reaction follows a concerted mechanism in all four solvents. In addition, the hydrogen bond between the reactant and water solvent plays an important role in the water-accelerated reaction mechanism. The dynamics of chirality formation varies significantly with solvents. The chirality of products forms significantly before the transition state, especially in ionic liquid.
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Affiliation(s)
- Xu Han
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jun Zhang
- Changping Laboratory, Beijing 102206, China
| | - Yi Isaac Yang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, China
| | - Zhen Zhang
- School of Physics and Technology, Tangshan Normal University, Tangshan 063000, China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, China
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10
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BF3–Catalyzed Diels–Alder Reaction between Butadiene and Methyl Acrylate in Aqueous Solution—An URVA and Local Vibrational Mode Study. Catalysts 2022. [DOI: 10.3390/catal12040415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In this study we investigate the Diels–Alder reaction between methyl acrylate and butadiene, which is catalyzed by BF3 Lewis acid in explicit water solution, using URVA and Local Mode Analysis as major tools complemented with NBO, electron density and ring puckering analyses. We considered four different starting orientations of methyl acrylate and butadiene, which led to 16 DA reactions in total. In order to isolate the catalytic effects of the BF3 catalyst and those of the water environment and exploring how these effects are synchronized, we systematically compared the non-catalyzed reaction in gas phase and aqueous solution with the catalyzed reaction in gas phase and aqueous solution. Gas phase studies were performed at the B3LYP/6-311+G(2d,p) level of theory and studies in aqueous solution were performed utilizing a QM/MM approach at the B3LYP/6-311+G(2d,p)/AMBER level of theory. The URVA results revealed reaction path curvature profiles with an overall similar pattern for all 16 reactions showing the same sequence of CC single bond formation for all of them. In contrast to the parent DA reaction with symmetric substrates causing a synchronous bond formation process, here, first the new CC single bond on the CH2 side of methyl acrylate is formed followed by the CC bond at the ester side. As for the parent DA reaction, both bond formation events occur after the TS, i.e., they do not contribute to the energy barrier. What determines the barrier is the preparation process for CC bond formation, including the approach diene and dienophile, CC bond length changes and, in particular, rehybridization of the carbon atoms involved in the formation of the cyclohexene ring. This process is modified by both the BF3 catalyst and the water environment, where both work in a hand-in-hand fashion leading to the lowest energy barrier of 9.06 kcal/mol found for the catalyzed reaction R1 in aqueous solution compared to the highest energy barrier of 20.68 kcal/mol found for the non-catalyzed reaction R1 in the gas phase. The major effect of the BF3 catalyst is the increased mutual polarization and the increased charge transfer between methyl acrylate and butadiene, facilitating the approach of diene and dienophile and the pyramidalization of the CC atoms involved in the ring formation, which leads to a lowering of the activation energy. The catalytic effect of water solution is threefold. The polar environment leads also to increased polarization and charge transfer between the reacting species, similar as in the case of the BF3 catalyst, although to a smaller extend. More important is the formation of hydrogen bonds with the reaction complex, which are stronger for the TS than for the reactant, thus stabilizing the TS which leads to a further reduction of the activation energy. As shown by the ring puckering analysis, the third effect of water is space confinement of the reacting partners, conserving the boat form of the six-member ring from the entrance to the exit reaction channel. In summary, URVA combined with LMA has led to a clearer picture on how both BF3 catalyst and aqueous environment in a synchronized effort lower the reaction barrier. These new insights will serve to further fine-tune the DA reaction of methyl acrylate and butadiene and DA reactions in general.
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11
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Kilaj A, Wang J, Straňák P, Schwilk M, Rivero U, Xu L, von Lilienfeld OA, Küpper J, Willitsch S. Conformer-specific polar cycloaddition of dibromobutadiene with trapped propene ions. Nat Commun 2021; 12:6047. [PMID: 34663806 PMCID: PMC8523519 DOI: 10.1038/s41467-021-26309-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Diels–Alder cycloadditions are efficient routes for the synthesis of cyclic organic compounds. There has been a long-standing discussion whether these reactions proceed via stepwise or concerted mechanisms. Here, we adopt an experimental approach to explore the mechanism of the model polar cycloaddition of 2,3-dibromo-1,3-butadiene with propene ions by probing its conformational specificities in the entrance channel under single-collision conditions in the gas phase. Combining a conformationally controlled molecular beam with trapped ions, we find that both conformers of the diene, gauche and s-trans, are reactive with capture-limited reaction rates. Aided by quantum-chemical and quantum-capture calculations, this finding is rationalised by a simultaneous competition of concerted and stepwise reaction pathways, revealing an interesting mechanistic borderline case. Identifying a concerted or stepwise mechanism in Diels–Alder reactions is experimentally challenging. Here the authors demonstrate the coexistence of both mechanisms in the reaction of 2,3-dibromobuta-1,3-diene with propene ions, using a conformationally controlled molecular beam reacting with trapped ions and ab initio computations
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Affiliation(s)
- Ardita Kilaj
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland
| | - Jia Wang
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Patrik Straňák
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland
| | - Max Schwilk
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland.,Faculty of Physics, University of Vienna, 1090, Vienna, Austria
| | - Uxía Rivero
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland
| | - Lei Xu
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland
| | - O Anatole von Lilienfeld
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland.,Faculty of Physics, University of Vienna, 1090, Vienna, Austria
| | - Jochen Küpper
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany. .,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany. .,Department of Chemistry, Universität Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany. .,Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
| | - Stefan Willitsch
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland.
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12
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Freindorf M, Beiranvand N, Delgado AAA, Tao Y, Kraka E. On the formation of CN bonds in Titan's atmosphere-a unified reaction valley approach study. J Mol Model 2021; 27:320. [PMID: 34633543 DOI: 10.1007/s00894-021-04917-8] [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: 07/01/2021] [Accepted: 09/15/2021] [Indexed: 08/30/2023]
Abstract
In this work, we investigated the formation of protonated hydrogen cyanide HCNH+ and methylene amine cation CH[Formula: see text] (both identified in Titan's upper atmosphere) from three different pathways which stem from the interaction between CH4 and N+(3P). As a mechanistic tool, we used the Unified Reaction Valley Approach (URVA) complemented with the Local Mode Analysis (LMA) assessing the strength of the CN bonds formed in these reactions. Our URVA studies could provide a comprehensive overview on bond formation/cleavage processes relevant to the specific mechanism of eight reactions R1- R8 that occur across the three pathways. In addition, we could explain the formation of CH[Formula: see text] and the appearance of HCNH+ and CHNH[Formula: see text] along these paths. Although only smaller molecules are involved in these reactions including isomerization, hydrogen atom abstraction, and hydrogen molecule capture, we found a number of interesting features, such as roaming in reaction R3 or the primary interaction of H2 with the carbon atom in HCNH+ in reaction R8 followed by migration of one of the H2 hydrogen atoms to the nitrogen which is more cost effective than breaking the HH bond first; a feature often found in catalysis. In all cases, charge transfer between carbon and nitrogen could be identified as a driving force for the CN bond formation. As revealed by LMA, the CN bonds formed in reactions R1-R8 cover a broad bond strength range from very weak to very strong, with the CN bond in protonated hydrogen cyanide HCNH+ identified as the strongest of all molecules investigated in this work. Our study demonstrates the large potential of both URVA and LMA to shed new light into these extraterrestrial reactions to help better understand prebiotic processes as well as develop guidelines for future investigations involving areas of complex interstellar chemistry. In particular, the formation of CN bonds as a precursor to the extraterrestrial formation of amino acids will be the focus of future investigations. Formation of CN bonds in Titan's atmosphere visualized via the reaction path curvature.
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Affiliation(s)
- Marek Freindorf
- Chemistry Department, SMU, Fondren Science Building, Dallas, 75275-0314, TX, USA
| | - Nassim Beiranvand
- Chemistry Department, SMU, Fondren Science Building, Dallas, 75275-0314, TX, USA
| | - Alexis A A Delgado
- Chemistry Department, SMU, Fondren Science Building, Dallas, 75275-0314, TX, USA
| | - Yunwen Tao
- Chemistry Department, SMU, Fondren Science Building, Dallas, 75275-0314, TX, USA
| | - Elfi Kraka
- Chemistry Department, SMU, Fondren Science Building, Dallas, 75275-0314, TX, USA.
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13
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Makoś MZ, Freindorf M, Tao Y, Kraka E. Theoretical Insights into [NHC]Au(I) Catalyzed Hydroalkoxylation of Allenes: A Unified Reaction Valley Approach Study. J Org Chem 2021; 86:5714-5726. [PMID: 33780251 DOI: 10.1021/acs.joc.1c00208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hydroxylation is an effective approach for the synthesis of carbon-oxygen bonds and allylic ethers. The [NHC]Au(I) catalyzed intermolecular hydroalkoxylation of allene was studied at the DFT and Coupled Cluster level of theory. Using the Unified Reaction Valley Approach (URVA), we carry out a comprehensive mechanistic analysis of [NHC]Au(I)-catalyzed and noncatalyzed reactions. The URVA study of several possible reaction pathways reveal that the [NHC]Au(I) catalyst enables the hydroalkoxylation reaction to occur via a two step mechanism based upon the Au ability to switch between π- and σ-complexation. The first step of the mechanism involves the formation of a CO bond after the transition state with no energy penalty. Following the CO bond breakage, the OH bond breaks and CH bond forms during the second step of the mechanism, as the catalyst transforms into the more stable π-Au complex. The URVA results were complemented with local vibrational mode analysis to provide measures of intrinsic bond strength for Au(I)-allene interactions of all stationary points, and NBO analysis was applied in order to observe charge transfer events along the reaction pathway. Overall, the π-Au C═C interactions of the products are stronger than those of the reactants adding to their exothermicity. Our work on the hydroxylation of allene provides new insights for the design of effective reaction pathways to produce allylic ethers and also unravels new strategies to form C-O bonds by activation of C═C bonds.
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Affiliation(s)
- Małgorzata Z Makoś
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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14
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Houk KN, Liu F, Yang Z, Seeman JI. Die Evolution des Diels‐Alder‐Reaktionsmechanismus seit den 1930er Jahren: Woodward, Houk zusammen mit Woodward und der Einfluss der Computerchemie auf das Verständnis von Cycloadditionen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202001654] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Kendall N. Houk
- Department of Chemistry and Biochemistry University of California Los Angeles California 90005 USA
| | - Fang Liu
- Department of Chemistry and Biochemistry University of California Los Angeles California 90005 USA
- College of Sciences Nanjing Agricultural University Nanjing 210095 China
| | - Zhongyue Yang
- Department of Chemistry and Biochemistry University of California Los Angeles California 90005 USA
| | - Jeffrey I. Seeman
- Department of Chemistry University of Richmond Richmond Virginia 23173 USA
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15
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Houk KN, Liu F, Yang Z, Seeman JI. Evolution of the Diels–Alder Reaction Mechanism since the 1930s: Woodward, Houk with Woodward, and the Influence of Computational Chemistry on Understanding Cycloadditions. Angew Chem Int Ed Engl 2021; 60:12660-12681. [DOI: 10.1002/anie.202001654] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 06/30/2020] [Indexed: 01/16/2023]
Affiliation(s)
- Kendall N. Houk
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90005 USA
| | - Fang Liu
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90005 USA
- College of Sciences Nanjing Agricultural University Nanjing 210095 China
| | - Zhongyue Yang
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90005 USA
| | - Jeffrey I. Seeman
- Department of Chemistry University of Richmond Richmond VA 23173 USA
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16
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Nanayakkara S, Freindorf M, Tao Y, Kraka E. Modeling Hydrogen Release from Water with Borane and Alane Catalysts: A Unified Reaction Valley Approach. J Phys Chem A 2020; 124:8978-8993. [PMID: 33064477 DOI: 10.1021/acs.jpca.0c07244] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The unified reaction valley approach combined with the local vibrational mode and ring puckering analysis is applied to investigate the hydrogen evolution from water in the presence of small hydrides such as BH3, metal hydrides as AlH3, and their derivatives. We studied a series of reactions involving BH3, AlH3, B2H6, Al2H6, and AlH3BH3 with one- and two-water molecules, considering multiple reaction paths. In addition, the influence of the aqueous medium was examined. A general reaction mechanism was identified for most of the reactions. Those that deviate could be associated with unusually high reaction barriers with no hydrogen release. The charge transfer along the reaction path suggests that a viable hydrogen release is achieved when the catalyst adopts the role of a charge donor during the chemical processes. The puckering analysis showed that twistboat and boat forms are the predominant configurations in the case of an intermediate six-membered ring formation, which influences the activation barrier. The local mode analysis was used as a tool to detect the H-H bond formation as well as to probe catalyst regenerability. Based on the correlation between the activation energy and the change in the charge separation for cleaving O-H and B(Al)-H bonds, two promising subsets of reactions could be identified along with prescriptions for lowering the reaction barrier individually with electron-donating/withdrawing substituents.
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Affiliation(s)
- Sadisha Nanayakkara
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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17
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Exploring the Mechanism of Catalysis with the Unified Reaction Valley Approach (URVA)—A Review. Catalysts 2020. [DOI: 10.3390/catal10060691] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The unified reaction valley approach (URVA) differs from mainstream mechanistic studies, as it describes a chemical reaction via the reaction path and the surrounding reaction valley on the potential energy surface from the van der Waals region to the transition state and far out into the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting molecules is registered by a change in their normal vibrational modes and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction with curvature minima reflecting minimal change and curvature maxima, the location of important chemical events such as bond breaking/forming, charge polarization and transfer, rehybridization, etc. A unique decomposition of the path curvature into internal coordinate components provides comprehensive insights into the origins of the chemical changes taking place. After presenting the theoretical background of URVA, we discuss its application to four diverse catalytic processes: (i) the Rh catalyzed methanol carbonylation—the Monsanto process; (ii) the Sharpless epoxidation of allylic alcohols—transition to heterogenous catalysis; (iii) Au(I) assisted [3,3]-sigmatropic rearrangement of allyl acetate; and (iv) the Bacillus subtilis chorismate mutase catalyzed Claisen rearrangement—and show how URVA leads to a new protocol for fine-tuning of existing catalysts and the design of new efficient and eco-friendly catalysts. At the end of this article the pURVA software is introduced. The overall goal of this article is to introduce to the chemical community a new protocol for fine-tuning existing catalytic reactions while aiding in the design of modern and environmentally friendly catalysts.
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18
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Casals‐Sainz JL, Francisco E, Martín Pendás Á. The Activation Strain Model in the Light of Real Space Energy Partitions. Z Anorg Allg Chem 2020. [DOI: 10.1002/zaac.202000038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- José Luis Casals‐Sainz
- Departamento de Química Física y Analítica Facultad de Química Universidad de Oviedo 33006 Oviedo Spain
| | - Evelio Francisco
- Departamento de Química Física y Analítica Facultad de Química Universidad de Oviedo 33006 Oviedo Spain
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica Facultad de Química Universidad de Oviedo 33006 Oviedo Spain
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19
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Ordon P, Zaklika J, Jędrzejewski M, Komorowski L. Bond Softening Indices Studied by the Fragility Spectra for Proton Migration in Formamide and Related Structures. J Phys Chem A 2020; 124:328-338. [PMID: 31815477 DOI: 10.1021/acs.jpca.9b09426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computational scheme to obtain bond softening index λ, defined within the conceptual DFT, has been obtained with the use of the reaction fragility (RF) concept. Numerical results were obtained with the RF spectra for the proton transfer reaction in formamide molecule (H2NCHO) and the water assisted proton migration in H2NCHO·H2O complex. Double proton transfer reaction in the formamide dimer, (H2NCHO)2, and its analogues, (H2NCHS)2 and (H2NCHO)·(H2NCHS), have also been studied. The atomic and bond RF spectra clearly describe the density reorganization in the backbone of each molecule, resulting from proton displacement in the systems. The obtained softening indices have been calculated for hydrogen atoms in the reactant state (RS) and product state (PS) configuration. These indices provide fine characteristics for the local sensitivity of the reacting system to a disturbance of the position of a chosen atom.
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Affiliation(s)
- Piotr Ordon
- Department of Physics and Biophysics , Wrocław University of Environmental and Life Sciences , ul. Norwida 25 , 50-373 Wrocław , Poland
| | - Jarosław Zaklika
- Department of Physical and Quantum Chemistry , Wrocław University of Science and Technology , Wyb. Wyspiańskiego 27 , 50-370 Wrocław , Poland
| | - Mateusz Jędrzejewski
- Department of Physical and Quantum Chemistry , Wrocław University of Science and Technology , Wyb. Wyspiańskiego 27 , 50-370 Wrocław , Poland
| | - Ludwik Komorowski
- Department of Physical and Quantum Chemistry , Wrocław University of Science and Technology , Wyb. Wyspiańskiego 27 , 50-370 Wrocław , Poland
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20
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Abstract
In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.
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21
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Nanayakkara S, Kraka E. A new way of studying chemical reactions: a hand-in-hand URVA and QTAIM approach. Phys Chem Chem Phys 2019; 21:15007-15018. [PMID: 31241084 DOI: 10.1039/c9cp01933b] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bond formation and bond cleavage processes are central to a chemical reaction. They can be investigated by monitoring changes in the potential energy surface (PES) or changes in the electron density (ED) distribution ρ(r) taking place during the reaction. However, it is not yet clear how the corresponding changes in the PES and ED are related, although the connection between energy and density has been postulated in the famous Hohenberg-Kohn theorem. Our unified reaction valley approach (URVA) identifies the locations of bond formation/cleavage events along the reaction path via the reaction path curvature peaks and their decomposition into the internal coordinate components associated with the bond to be formed or cleaved. One can also investigate bond formation/cleavage events using the quantum theory of atoms-in-molecule (QTAIM) analysis by monitoring changes in the topological properties of ρ(r) and the associated Laplacian ∇2ρ(r). By a systematic comparison of these two approaches for a series of ten representative chemical reactions ranging from hydrogen migration to cycloaddition reactions and gold(i) catalysis, we could for the first time unravel the PES-ED relationship. In the case of a bond formation, all changes in the ED occur shortly before or at the corresponding curvature peak, and in a bond cleavage, the ED changes occur at or shortly after the curvature peak. In any case, the ED changes always occurred in the vicinity of the curvature peak in accordance with the Hohenberg-Kohn theorem. Our findings provide a comprehensive view on bond formation/cleavage processes seen through the eyes of both the PES and ED and offer valuable guidelines on where to search for significant ED changes associated with bond formation or cleavage events.
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Affiliation(s)
- Sadisha Nanayakkara
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA.
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA.
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22
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Freindorf M, Tao Y, Sethio D, Cremer D, Kraka E. New mechanistic insights into the Claisen rearrangement of chorismate – a Unified Reaction Valley Approach study. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1530464] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Daniel Sethio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
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23
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Braden DA, Matta CF. On the Unusual Synclinal Conformations of Hexafluorobutadiene and Structurally Similar Molecules. J Phys Chem A 2018; 122:4538-4548. [PMID: 29694045 DOI: 10.1021/acs.jpca.8b02157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An explanation is presented for the unusual conformations of some molecules that contain the C═C-C═C core, namely, butadienes, biphenyls, and styrenes. Small substituents often induce a synclinal conformation, which brings the substituents into close proximity, and sometimes, there is no anticlinal minimum at all. This would not be predicted from steric repulsion arguments nor would it be expected that atoms that are nonbonded in a Lewis structure would approach closer than the sum of their van der Waals radii. Atomic energies calculated according to the quantum theory of atoms in molecules (QTAIM) do not show a consistent pattern for these structurally similar molecules, nor are intersubstituent bond paths consistently found, nor favorable diatomic interaction energies calculated using the interacting quantum atoms (IQA) scheme. Instead, the synclinal conformations are found to be driven by the attraction energy of the electron distribution of the carbon atoms and the nuclei of the molecule.
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Affiliation(s)
- Dale A Braden
- 19460 Wilderness Drive , West Linn , Oregon 97068 , United States
| | - Chérif F Matta
- Department of Chemistry and Physics , Mount Saint Vincent University , Halifax , Nova Scotia B3M 2J6 , Canada
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24
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Baraban JH, Martin‐Drumel M, Changala PB, Eibenberger S, Nava M, Patterson D, Stanton JF, Ellison GB, McCarthy MC. The Molecular Structure of
gauche
‐1,3‐Butadiene: Experimental Establishment of Non‐planarity. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201709966] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Joshua H. Baraban
- Department of Chemistry and Biochemistry University of Colorado Boulder CO 80309 USA
- Current address: Dept. of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Marie‐Aline Martin‐Drumel
- Harvard-Smithsonian Center for Astrophysics and School of Engineering & Applied Sciences Harvard University Cambridge Massachusetts 02138 USA
- Current address: Institut des Sciences Moléculaires d'Orsay, CNRS Univ. Paris-Sud, Université Paris-Saclay Orsay France
| | - P. Bryan Changala
- JILA, National Institute of Standards and Technology and Department of Physics University of Colorado Boulder CO 80309 USA
| | | | - Matthew Nava
- Department of Chemistry Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA
- Current address: Department of Chemistry Harvard University Cambridge MA 02138 USA
| | - David Patterson
- Department of Physics Harvard University Cambridge MA 02138 USA
- Current address: Department of Physics University of California Santa Barbara CA 93106 USA
| | - John F. Stanton
- Quantum Theory Project Depts. of Chemistry and Physics Univ. of Florida Gainesville FL 32611 USA
| | - G. Barney Ellison
- Department of Chemistry and Biochemistry University of Colorado Boulder CO 80309 USA
| | - Michael C. McCarthy
- Harvard-Smithsonian Center for Astrophysics and School of Engineering & Applied Sciences Harvard University Cambridge Massachusetts 02138 USA
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25
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Baraban JH, Martin‐Drumel M, Changala PB, Eibenberger S, Nava M, Patterson D, Stanton JF, Ellison GB, McCarthy MC. The Molecular Structure of
gauche
‐1,3‐Butadiene: Experimental Establishment of Non‐planarity. Angew Chem Int Ed Engl 2018; 57:1821-1825. [DOI: 10.1002/anie.201709966] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Joshua H. Baraban
- Department of Chemistry and Biochemistry University of Colorado Boulder CO 80309 USA
- Current address: Dept. of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Marie‐Aline Martin‐Drumel
- Harvard-Smithsonian Center for Astrophysics and School of Engineering & Applied Sciences Harvard University Cambridge Massachusetts 02138 USA
- Current address: Institut des Sciences Moléculaires d'Orsay, CNRS Univ. Paris-Sud, Université Paris-Saclay Orsay France
| | - P. Bryan Changala
- JILA, National Institute of Standards and Technology and Department of Physics University of Colorado Boulder CO 80309 USA
| | | | - Matthew Nava
- Department of Chemistry Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA
- Current address: Department of Chemistry Harvard University Cambridge MA 02138 USA
| | - David Patterson
- Department of Physics Harvard University Cambridge MA 02138 USA
- Current address: Department of Physics University of California Santa Barbara CA 93106 USA
| | - John F. Stanton
- Quantum Theory Project Depts. of Chemistry and Physics Univ. of Florida Gainesville FL 32611 USA
| | - G. Barney Ellison
- Department of Chemistry and Biochemistry University of Colorado Boulder CO 80309 USA
| | - Michael C. McCarthy
- Harvard-Smithsonian Center for Astrophysics and School of Engineering & Applied Sciences Harvard University Cambridge Massachusetts 02138 USA
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26
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Freindorf M, Cremer D, Kraka E. Gold(I)-assisted catalysis – a comprehensive view on the [3,3]-sigmatropic rearrangement of allyl acetate. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1382735] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
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27
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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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28
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Chakraborty D, Das R, Chattaraj PK. Does Confinement Always Lead to Thermodynamically and/or Kinetically Favorable Reactions? A Case Study using Diels-Alder Reactions within ExBox+4
and CB[7]. Chemphyschem 2017; 18:2162-2170. [PMID: 28557293 DOI: 10.1002/cphc.201700308] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/29/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Debdutta Chakraborty
- Department of Chemistry and Centre for Theoretical Studies; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - Ranjita Das
- Department of Chemistry and Centre for Theoretical Studies; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - Pratim Kumar Chattaraj
- Department of Chemistry and Centre for Theoretical Studies; Indian Institute of Technology; Kharagpur 721302 West Bengal India
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29
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Sexton TM, Freindorf M, Kraka E, Cremer D. A Reaction Valley Investigation of the Cycloaddition of 1,3-Dipoles with the Dipolarophiles Ethene and Acetylene: Solution of a Mechanistic Puzzle. J Phys Chem A 2016; 120:8400-8418. [DOI: 10.1021/acs.jpca.6b07975] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
| | | | - Elfi Kraka
- Computational
and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
| | - Dieter Cremer
- Computational
and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
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30
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Castiñeira Reis M, López CS, Kraka E, Cremer D, Faza ON. Rational Design in Catalysis: A Mechanistic Study of β-Hydride Eliminations in Gold(I) and Gold(III) Complexes Based on Features of the Reaction Valley. Inorg Chem 2016; 55:8636-45. [DOI: 10.1021/acs.inorgchem.6b01188] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Carlos Silva López
- Departamento de Química Orgánica, Campus Lagoas-Marcosende, 36310 Vigo, Spain
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University (SMU), 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University (SMU), 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Olalla Nieto Faza
- Departamento de Química Orgánica, Universidade de Vigo, Campus As Lagoas, 32004 Ourense, Spain
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