1
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Li R. London Dispersion Effects on the Structure and Properties of Nonlinear Optical BiB 3O 6 Crystal. Chemphyschem 2024; 25:e202400142. [PMID: 38655698 DOI: 10.1002/cphc.202400142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 04/26/2024]
Abstract
α-BiB3O6 (BiBO) is an important nonlinear optical (NLO) material with high efficiency for applications in harmonic generations and quantum technology. Owing to its low symmetry and cooperative Bi3+ lone pair arrangement, it has also exceptional large piezoelectric and electro-optic coefficients and strong anisotropies on other material characteristics. Previous theoretical calculations on its physical (mainly optical) properties often gave confusing results. It is found here that London dispersion (LD) tends to stabilize structures with closer pack entities like lone pair heavy ion Bi3+ with large polarizabilities, which is ignored in most previous density functional theory (DFT) calculations. Present study shows that without considering the LD effect, the structure of α-BiB3O6 (BiBO) was predicted with an over-estimated (by over 10 %) unique b-axis while underestimates a and overestimates c in a less amount. Consequently it is not possible to use the calculated structure to obtain meaningful properties of this important material. By applying a modified post-DFT LD correction based on linear combination of atomic orbitals (LCAO) and B3LYP functional, the experimental structure is well reproduced with the theoretical optimized one. Many important material property tensors of BiBO crystal are calculated in unprecedented precisions, including: dielectric constants (static and in THz range), elastic and elasto-optic constants, piezoelectric constants, refractive indices, NLO and electro-optic (EO) coefficients. Among them, theoretical calculation of the refractive indices in the THz range by diagonalizing the clamped-ion dielectric constants was firstly achieved at least for BiBO crystal. The calculation also confirms that BiBO has an exceptional large piezoelectric constant d22=40 pC/N and largest free EO coefficientsγ 12 T ${{\gamma }_{12}^{T}}$ ,γ 22 T ${{\gamma }_{22}^{T}}$ ,γ 32 T ${{\gamma }_{32}^{T}}$ on the order of 10 pm/V among borate crystals. The calculation also reveals that the large free EO coefficients are largely originated from the piezoelectric induced photo-elastic effect and for practical high speed applications only the clamped-ion EO coefficients take effect. The clamped ion EO coefficient ofγ 53 S ${{\gamma }_{53}^{S}}$ =-4.17 pm/V,γ b 1 S ${{\gamma }_{{\rm b}1}^{S}}$ =-2.61 pm/V are obtained for the first time and may be consulted if one seeks to design BiBO crystal as a high-speed EO modulator. Furthermore, full tensor matrix of the elasto-optic constants was obtained on the first time. Together with the calculated elastic constants, it can help to design acoustic optic modulating devices with preferable figure of merits 10 times that of traditional quartz crystal.
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Affiliation(s)
- Rukang Li
- Beijing Centre for Crystal Research and Development, Key Laboratory of Functional Crystals and Laser Technology, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190
- China and Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
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2
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Li F, Lan J, Li X, Chung LW. A Synergistic Bimetallic Ti/Co-Catalyzed Isomerization of Epoxides to Allylic Alcohols Enabled by Two-State Reactivity. Inorg Chem 2024; 63:6285-6295. [PMID: 38517250 DOI: 10.1021/acs.inorgchem.4c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Isomerization of epoxides into versatile allylic alcohols is an atom-economical synthetic method to afford vicinal bifunctional groups. Comprehensive density functional theory (DFT) calculations were carried out to elucidate the complex mechanism of a bimetallic Ti/Co-catalyzed selective isomerization of epoxides to allyl alcohols by examining several possible pathways. Our results suggest a possible mechanism involving (1) radical-type epoxide ring opening catalyzed by Cp2Ti(III)Cl leading to a Ti(IV)-bound β-alkyl radical, (2) hydrogen-atom transfer (HAT) catalyzed by the Co(II) catalyst to form the Ti(IV)-enolate and Co(III)-H intermediate, (3) protonation to give the alcohols, and (4) proton abstraction to form the Co(I) species followed by electron transfer to regenerate the active Co(II) and Ti(III) species. Moreover, bimetallic catalysis and two-state reactivity enable the key rate-determining HAT step. Furthermore, a subtle balance between dispersion-driven bimetallic processes and entropy-driven monometallic processes determines the most favorable pathway, among which the monometallic process is energetically more favorable in all steps except the vital hydrogen-atom transfer step. Our study should provide an in-depth mechanistic understanding of bimetallic catalysis.
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Affiliation(s)
- Fangfang Li
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jialing Lan
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xin Li
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Lung Wa Chung
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
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3
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Schneider HJ. Distinction and Quantification of Noncovalent Dispersive and Hydrophobic Effects. Molecules 2024; 29:1591. [PMID: 38611870 PMCID: PMC11013637 DOI: 10.3390/molecules29071591] [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: 03/06/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
The possibilities of comparing computational results of noncovalent interactions with experimental data are discussed, first with respect to intramolecular interactions. For these a variety of experimental data such as heats of formation, crystal sublimation heats, comparison with energy minimized structures, and spectroscopic data are available, but until now largely have not found widespread application. Early force field and QM/MP2 calculations have already shown that the sublimation heats of hydrocarbons can be predicted with an accuracy of ±1%. Intermolecular interactions in solution or the gas phase are always accompanied by difficult to compute entropic contributions, like all associations between molecules. Experimentally observed T∆S values contribute 10% to 80% of the total ∆G, depending on interaction mechanisms within the complexes, such as, e.g., hydrogen bonding and ion pairing. Free energies ∆G derived from equilibrium measurements in solution allow us to define binding increments ∆∆G, which are additive and transferable to a variety of supramolecular complexes. Data from more than 90 equilibrium measurements of porphyrin receptors in water indicate that small alkanes do not bind to the hydrophobic flat surfaces within a measuring limit of ∆G = ±0.5 kJ/mol, and that 20 functions bearing heteroatoms show associations by dispersive interactions with up to ∆G = 8 kJ/mol, roughly as a function of their polarizability. Aromatic systems display size-dependent affinities ∆G as a linear function of the number of π-electrons.
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Affiliation(s)
- Hans-Jörg Schneider
- FR Organische Chemie, Universität des Saarlandes, D 66123 Saarbrücken, Germany
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4
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Rummel L, Schreiner PR. Advances and Prospects in Understanding London Dispersion Interactions in Molecular Chemistry. Angew Chem Int Ed Engl 2024; 63:e202316364. [PMID: 38051426 DOI: 10.1002/anie.202316364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023]
Abstract
London dispersion (LD) interactions are the main contribution of the attractive part of the van der Waals potential. Even though LD effects are the driving force for molecular aggregation and recognition, the role of these omnipresent interactions in structure and reactivity had been largely underappreciated over decades. However, in the recent years considerable efforts have been made to thoroughly study LD interactions and their potential as a chemical design element for structures and catalysis. This was made possible through a fruitful interplay of theory and experiment. This review highlights recent results and advances in utilizing LD interactions as a structural motif to understand and utilize intra- and intermolecularly LD-stabilized systems. Additionally, we focus on the quantification of LD interactions and their fundamental role in chemical reactions.
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Affiliation(s)
- Lars Rummel
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
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5
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Fokin AA. Long but Strong C-C Single Bonds: Challenges for Theory. CHEM REC 2024; 24:e202300170. [PMID: 37358335 DOI: 10.1002/tcr.202300170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/02/2023] [Indexed: 06/27/2023]
Abstract
Theoretical challenges in describing molecules with anomalously long single C-C bonds are analyzed in terms of the relative contributions of stabilizing and destabilizing intramolecular interactions. Diamondoid dimers that are stable despite the presence of C-C bonds up to 1.7 Å long, as well as other bulky molecules stabilized due to intramolecular noncovalent interactions (London dispersions) are discussed. The unexpected stability of highly crowded molecules, such as diamondoid dimers and tert-butyl-substituted hexaphenylethanes, calls for reconsideration of the "steric effect" traditionally thought to destabilize the molecule. Alternatively, "steric attraction" helps to understand bonding in sterically overloaded molecules, whose structural and energetic analysis requires a proper theoretical description of noncovalent interactions.
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Affiliation(s)
- Andrey A Fokin
- Department of Organic Chemistry, Igor Sikorsky Kyiv Polytechnic Institute, Beresteiskyi Ave 37, Kyiv, Ukraine
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6
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Wei X, Cui L, Liu C, Shen K, Xu J, Dilworth J, Xiao T, Cao F. The Calculation of Both Electrostatic and Van der Waals Effects to Probe the Efficiency of Solvent Extraction of Heterocyclic Aromatics from Heavy Oil. Chemistry 2023; 29:e202301954. [PMID: 37665039 DOI: 10.1002/chem.202301954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/05/2023]
Abstract
Due to the complex composition and similar structure, the extraction denitrification of aromatic rich oil is faced with the contradiction problem of denitrification efficiency and aromatic loss which cannot be efficiently solved by experiments. However, the complex interactions involved can be analyzed from the perspective of calculation, and the prediction criteria and methods are proposed. Based on rigorous density functional theory calculation data, Simple models based on electrostatic potential (ESP) and Van der Waals potential (VdWP)-based calculations were established and validated. The twofold model provided the best prediction for interactions between extractants and nitrogen compounds and between extractants and aromatics, which determines denitrification efficiency and aromatic loss, respectively, due to the most complete description of both electrostatic and VdW force. This provides a powerful tool for evaluating the non-covalent interactions and thence tuning the efficiency of the separation process. Thus, high denitrification efficiency (43.2~66.3 %) and moderate aromatic loss (1.7~4.4 %) were obtained using screened deep eutectic solvents (DESs). This ideal observation provided the potential for mild hydrodesulfurization and manufacture of high-grade carbon materials.
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Affiliation(s)
- Xingguo Wei
- School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Lingrui Cui
- School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Cao Liu
- School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Kaili Shen
- School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Jun Xu
- School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Jon Dilworth
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QR, UK
| | - Tiancun Xiao
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QR, UK
| | - Fahai Cao
- School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
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7
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Lu Q, Bian W. The Decay of Dispersion Interaction and Its Remarkable Effects on the Kinetics of Activation Reactions Involving Alkyl Chains. J Phys Chem Lett 2023; 14:10642-10647. [PMID: 38031665 DOI: 10.1021/acs.jpclett.3c02925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
The importance of dispersion interactions in many chemical processes is well recognized. It is known that the dispersion strength would decay with the increasing separation between the interacting groups; however, its effects on chemical reactivity have not been well understood. Here we reveal the decay law of dispersion interactions along the n-alkyl chain, its effective interaction ranges for common functional groups, and their remarkable effects on the kinetics of activation reactions involving alkyl chains. This is achieved by DLPNO-CCSD(T) calculations and the local energy decomposition analysis and is supported by experimental findings. In particular, our calculations indicate that the lifetime of alkyl-substituted cis-azobenzenes increases with the alkyl chain length but reaches a steady value when alkyl chains are longer than butyl groups, which is in satisfactory accordance with experimental measurements. We also propose a concise expression to describe the dispersion decay, which shows excellent agreement with our computed results.
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Affiliation(s)
- Qing Lu
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 100190 Beijing, China
| | - Wensheng Bian
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 100190 Beijing, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
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8
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Radiush EA, Wang H, Chulanova EA, Ponomareva YA, Li B, Wei QY, Salnikov GE, Petrakova SY, Semenov NA, Zibarev AV. Halide Complexes of 5,6-Dicyano-2,1,3-Benzoselenadiazole with 1 : 4 Stoichiometry: Cooperativity between Chalcogen and Hydrogen Bonding. Chempluschem 2023; 88:e202300523. [PMID: 37750466 DOI: 10.1002/cplu.202300523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 09/27/2023]
Abstract
The [M4 -Hal]- (M=the title compound; Hal=Cl, Br, and I) complexes were isolated in the form of salts of [Et4 N]+ cation and characterized by XRD, NMR, UV-Vis, DFT, QTAIM, EDD, and EDA. Their stoichiometry is caused by a cooperative interplay of σ-hole-driven chalcogen (ChB) and hydrogen (HB) bondings. In the crystal, [M4 -Hal]- are connected by the π-hole-driven ChB; overall, each [Hal]- is six-coordinated. In the ChB, the electrostatic interaction dominates over orbital and dispersion interactions. In UV-Vis spectra of the M+[Hal]- solutions, ChB-typical and [Hal]- -dependent charge-transfer bands are present; they reflect orbital interactions and allow identification of the individual [Hal]- . However, the structural situation in the solutions is not entirely clear. Particularly, the UV-Vis spectra of the solutions are different from the solid-state spectra of the [Et4 N]+ [M4 -Hal]- ; very tentatively, species in the solutions are assigned [M-Hal]- . It is supposed that the formation of the [M4 -Hal]- proceeds during the crystallization of the [Et4 N]+ [M4 -Hal]- . Overall, M can be considered as a chromogenic receptor and prototype sensor of [Hal]- . The findings are also useful for crystal engineering and supramolecular chemistry.
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Affiliation(s)
- Ekaterina A Radiush
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Hui Wang
- School of Physical Science and Technology, Southwest Jiaotong University, 610031, Chengdu, P. R. China
| | - Elena A Chulanova
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Current address: Institute for Applied Physics, University of Tübingen, 72076, Tübingen, Germany
| | - Yana A Ponomareva
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Department of Natural Sciences, National Research University - Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Bin Li
- School of Physical Science and Technology, Southwest Jiaotong University, 610031, Chengdu, P. R. China
| | - Qiao Yu Wei
- School of Physical Science and Technology, Southwest Jiaotong University, 610031, Chengdu, P. R. China
| | - Georgy E Salnikov
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Svetlana Yu Petrakova
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Nikolay A Semenov
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Andrey V Zibarev
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
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9
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Schümann JM, Ochmann L, Becker J, Altun A, Harden I, Bistoni G, Schreiner PR. Exploring the Limits of Intramolecular London Dispersion Stabilization with Bulky Dispersion Energy Donors in Alkane Solution. J Am Chem Soc 2023; 145:2093-2097. [PMID: 36688409 DOI: 10.1021/jacs.2c13301] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We present an experimental study of a cyclooctatetraene-based molecular balance disubstituted with increasingly bulky tert-butyl (tBu), adamantyl (Ad), and diamantyl (Dia) substituents in the 1,4-/1,6-positions for which we determined the valence-bond shift equilibrium in n-hexane (hex), n-octane (oct), and n-dodecane (dod). Computations including implicit and explicit solvation support our temperature-dependent NMR equilibrium measurements indicating that the more sterically crowded 1,6-isomer is always favored, irrespective of solvent, and that the free energy is quite insensitive to substituent size.
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Affiliation(s)
- Jan M Schümann
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Lukas Ochmann
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Jonathan Becker
- Institute of Analytical and Inorganic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Ahmet Altun
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Ingolf Harden
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.,Dipartmento di Chimica, Biologia e Biotechnologie, Università Degli Studi Di Perugia, Via Elce di sotto, 8, 06123 Perugia, Italy
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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10
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Guo R, Adak S, Bellotti P, Gao X, Smith WW, Le SN, Ma J, Houk KN, Glorius F, Chen S, Brown MK. Photochemical Dearomative Cycloadditions of Quinolines and Alkenes: Scope and Mechanism Studies. J Am Chem Soc 2022; 144:17680-17691. [PMID: 36106902 PMCID: PMC9840784 DOI: 10.1021/jacs.2c07726] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Photochemical dearomative cycloaddition has emerged as a useful strategy to rapidly generate molecular complexity. Within this context, stereo- and regiocontrolled intermolecular para-cycloadditions are rare. Herein, a method to achieve photochemical cycloaddition of quinolines and alkenes is shown. Emphasis is placed on generating sterically congested products and reaction of highly substituted alkenes and allenes. In addition, the mechanistic details of the process are studied, which revealed a reversible radical addition and a selectivity-determining radical recombination. The regio- and stereochemical outcome of the reaction is also rationalized.
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Affiliation(s)
- Renyu Guo
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana47405, United States
| | - Souvik Adak
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana47405, United States
| | - Peter Bellotti
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149Münster, Germany
| | - Xinfeng Gao
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana47405, United States
| | - W Walker Smith
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana47405, United States
| | - Sam Ngan Le
- Department of Chemistry and Biochemistry, Oberlin College, 119 Woodland Street, Oberlin, Ohio44074, United States
| | - Jiajia Ma
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149Münster, Germany
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California90095, United States
| | - Frank Glorius
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149Münster, Germany
| | - Shuming Chen
- Department of Chemistry and Biochemistry, Oberlin College, 119 Woodland Street, Oberlin, Ohio44074, United States
| | - M Kevin Brown
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana47405, United States
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11
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Roberts NJ, Johnson ER, Chitnis SS. Dispersion Stabilizes Metal–Metal Bonds in the 1,8-Bis(silylamido)naphthalene Ligand Environment. Organometallics 2022. [DOI: 10.1021/acs.organomet.2c00268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicholas J. Roberts
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
| | - Saurabh S. Chitnis
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
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12
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Lewis‐Atwell T, Townsend PA, Grayson MN. Machine learning activation energies of chemical reactions. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1593] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Toby Lewis‐Atwell
- Department of Computer Science, Faculty of Science University of Bath Bath UK
| | - Piers A. Townsend
- Department of Chemistry, Faculty of Science University of Bath Bath UK
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13
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Bedard J, Roberts NJ, Shayan M, Bamford KL, Werner-Zwanziger U, Marczenko KM, Chitnis SS. (PNSiMe 3 ) 4 (NMe) 6 : A Robust Tetravalent Phosphaza-adamantane Scaffold for Molecular and Macromolecular Construction. Angew Chem Int Ed Engl 2022; 61:e202204851. [PMID: 35384216 DOI: 10.1002/anie.202204851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Indexed: 01/03/2023]
Abstract
Tetraarylmethanes and adamantanes are important rigid covalent connectors that play a four-way scaffolding role in molecular and materials chemistry. We report the synthesis of a new tetravalent phosphaza-adamantane cage, (PNSiMe3 )4 (NMe)6 (2), that shows high thermal, air, and redox stability due to its geometry. It nevertheless participates in covalent four-fold functionalization reactions along its periphery. The combination of a robust core and reactive corona makes 2 a convenient inorganic scaffold upon which tetrahedral molecular and macromolecular chemistry can be constructed. This potential is demonstrated by the synthesis of a tetrakis(bis(phosphine)iminium) ion (in compound 3) and the first all P/N poly(phosphazene) network (5).
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Affiliation(s)
- Joseph Bedard
- Chemistry Department, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Nicholas J Roberts
- Chemistry Department, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Mohsen Shayan
- Chemistry Department, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Karlee L Bamford
- Chemistry Department, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Ulrike Werner-Zwanziger
- Chemistry Department, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia, B3H 4R2, Canada
| | | | - Saurabh S Chitnis
- Chemistry Department, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia, B3H 4R2, Canada
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14
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Bedard J, Roberts N, Shayan M, Bamford KL, Werner-Zwanziger U, Marczenko KM, Chitnis SS. (PNSiMe3)4(NMe)6: A Robust Tetravalent Phosphaza‐adamantane Scaffold for Molecular and Macromolecular Construction. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204851] [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)
| | | | | | | | | | | | - Saurabh S. Chitnis
- Dalhousie University Department of Chemistry Chemistry Building, 6274 Coburg Road B3H 4R2 Halifax CANADA
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15
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Kowalski PH, Krzemińska A, Pernal K, Pastorczak E. Dispersion Interactions between Molecules in and out of Equilibrium Geometry: Visualization and Analysis. J Phys Chem A 2022; 126:1312-1319. [PMID: 35166552 PMCID: PMC8883464 DOI: 10.1021/acs.jpca.2c00004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The London dispersion interactions between systems undergoing bond breaking, twisting, or compression are not well studied due to the scarcity and the high computational cost of methods being able to describe both the dynamic correlation and the multireference character of the system. Recently developed methods based on the Generalized Valence Bond wave function, such as EERPA-GVB and SAPT(GVB) (SAPT = symmetry-adapted perturbation theory), allow one to accurately compute and analyze noncovalent interactions between multireference systems. Here, we augment this analysis by introducing a local indicator for dispersion interactions inspired by Mata and Wuttke's Dispersion Interaction Density [ J. Comput. Chem. 2017, 38, 15-23] applied on top of an EERPA-GVB computation. Using a few model systems, we show what insights into the nature and evolution of the dispersion interaction during bond breaking and twisting such an approach is able to offer. The new indicator can be used at a minimal cost additional to an EERPA-GVB computation and can be complemented by an energy decomposition employing the SAPT(GVB) method. We explain the physics behind the initial increase, followed by a decrease in the interaction of linear molecules upon bond stretching. Namely, the elongation of covalent bonds leads to the enhancement of attractive dispersion interactions. For even larger bond lengths, this effect is canceled by the increase of the repulsive exchange forces resulting in a suppression of the interaction and finally leading to repulsion between monomers.
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Affiliation(s)
- Piotr H Kowalski
- Institute of Physics, Lodz University of Technology, ul. Wolczanska 217/221, 93-005 Lodz, Poland
| | - Agnieszka Krzemińska
- Institute of Physics, Lodz University of Technology, ul. Wolczanska 217/221, 93-005 Lodz, Poland
| | - Katarzyna Pernal
- Institute of Physics, Lodz University of Technology, ul. Wolczanska 217/221, 93-005 Lodz, Poland
| | - Ewa Pastorczak
- Institute of Physics, Lodz University of Technology, ul. Wolczanska 217/221, 93-005 Lodz, Poland
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16
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Paenurk E, Gershoni-Poranne R. Simple and efficient visualization of aromaticity: bond currents calculated from NICS values. Phys Chem Chem Phys 2022; 24:8631-8644. [PMID: 35132428 DOI: 10.1039/d1cp05757j] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Aromaticity is a fundamental concept in chemistry, underpinning the properties and reactivity of many organic compounds and materials. The ability to easily and accurately discern aromatic behavior is key to leveraging it as a design element, yet most aromaticity metrics struggle to combine accurate quantitative evaluation, intuitive interpretability, and user-friendliness. We introduce a new method, NICS2BC, which uses simple and inexpensive NICS calculations to generate information-rich and easily-interpreted bond-current graphs. We test the quantitative and qualitative characterizations afforded by NICS2BC for a selection of molecules of varying structural and electronic complexity, to demonstrate its accuracy and ease of analysis. Moreover, we show that NICS2BC successfully identifies ring-current patterns in molecules known to be difficult cases to interpret with NICS and enables deeper understanding of local aromaticity trends, demonstrating that our method adds additional insight.
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Affiliation(s)
- Eno Paenurk
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Renana Gershoni-Poranne
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.,Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel.
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17
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Solel E, Ruth M, Schreiner PR. London Dispersion Helps Refine Steric A-Values: Dispersion Energy Donor Scales. J Am Chem Soc 2021; 143:20837-20848. [PMID: 34846890 DOI: 10.1021/jacs.1c09222] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We suggest a scale of dispersion energy donors (DEDs) that allows for direct comparisons with steric effects. This scale is based on the classic A-values and allows groups to reorient to minimize strain, thereby providing an advantage over raw group polarizabilities. The A-value can no longer be considered purely a steric factor. Even for groups that do not participate in charge transfer or electrostatic interactions, the A-value includes Pauli repulsion (steric hindrance) and attractive London dispersion (LD) interactions. Although the common assumption is that, at the distances found in monosubstituted cyclohexanes, steric demands are the key factors influencing conformer preferences, we show in this computational study that there is a non-negligible LD part. We use this system to build a DED scale and a complementary steric scale. These scales are quantitatively comparable, as they are based on the same system, and allow for comparison of the two competing interactions in experimentally relevant settings. In addition, we show that LD interactions can be used to explain puzzling data regarding relative group sizes.
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Affiliation(s)
- Ephrath Solel
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Marcel Ruth
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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18
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Ikawa T, Yamamoto Y, Heguri A, Fukumoto Y, Murakami T, Takagi A, Masuda Y, Yahata K, Aoyama H, Shigeta Y, Tokiwa H, Akai S. Could London Dispersion Force Control Regioselective (2 + 2) Cyclodimerizations of Benzynes? YES: Application to the Synthesis of Helical Biphenylenes. J Am Chem Soc 2021; 143:10853-10859. [PMID: 34197100 DOI: 10.1021/jacs.1c05434] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In recent years, London dispersion interactions, which are the attractive component of the van der Waals potential, have been found to play an important role in controlling the regio- and/or stereoselectivity of various reactions. Particularly, the dispersion interactions between substrates and catalysts (or ligands) are dominant in various selective catalyzes. In contrast, repulsive steric interactions, rather than the attractive dispersion interactions, between bulky substituents are predominant in most of the noncatalytic reactions. Herein, we demonstrate the first example of London dispersion-controlled noncatalytic (2 + 2) cyclodimerization of substituted benzynes to selectively afford proximal biphenylenes in high yields and regioselectivities, depending on the extent of dispersion interactions in the substituents. This method can be applied for the synthesis of novel helical biphenylenes, which would be fascinating for chemists as these compounds are potential skeletons for ligands, catalysts, and medicines.
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Affiliation(s)
- Takashi Ikawa
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University, Daigaku-Nishi, Gifu 501-1196, Japan
| | - Yuta Yamamoto
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan
| | - Akito Heguri
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yutaka Fukumoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomonari Murakami
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Akira Takagi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuto Masuda
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kenzo Yahata
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan
| | - Shuji Akai
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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19
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Distinct roles of Ag(I) and Cu(II) as cocatalysts in the intramolecular cyclization of N-methyl-N-phenylanthranilic acid: A theoretical investigation. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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20
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Eschmann C, Song L, Schreiner PR. London Dispersion Interactions Rather than Steric Hindrance Determine the Enantioselectivity of the Corey-Bakshi-Shibata Reduction. Angew Chem Int Ed Engl 2021; 60:4823-4832. [PMID: 33205853 PMCID: PMC7986100 DOI: 10.1002/anie.202012760] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/22/2020] [Indexed: 12/11/2022]
Abstract
The well-known Corey-Bakshi-Shibata (CBS) reduction is a powerful method for the asymmetric synthesis of alcohols from prochiral ketones, often featuring high yields and excellent selectivities. While steric repulsion has been regarded as the key director of the observed high enantioselectivity for many years, we show that London dispersion (LD) interactions are at least as important for enantiodiscrimination. We exemplify this through a combination of detailed computational and experimental studies for a series of modified CBS catalysts equipped with dispersion energy donors (DEDs) in the catalysts and the substrates. Our results demonstrate that attractive LD interactions between the catalyst and the substrate, rather than steric repulsion, determine the selectivity. As a key outcome of our study, we were able to improve the catalyst design for some challenging CBS reductions.
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Affiliation(s)
- Christian Eschmann
- Institute of Organic Chemistry, Justus Liebig University, 35392, Giessen, Germany
| | - Lijuan Song
- Institute of Organic Chemistry, Justus Liebig University, 35392, Giessen, Germany.,Current address: Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, 35392, Giessen, Germany
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21
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Eschmann C, Song L, Schreiner PR. London Dispersion Interactions Rather than Steric Hindrance Determine the Enantioselectivity of the Corey–Bakshi–Shibata Reduction. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012760] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Christian Eschmann
- Institute of Organic Chemistry Justus Liebig University 35392 Giessen Germany
| | - Lijuan Song
- Institute of Organic Chemistry Justus Liebig University 35392 Giessen Germany
- Current address: Shenzhen Bay Laboratory Shenzhen 518055 China
| | - Peter R. Schreiner
- Institute of Organic Chemistry Justus Liebig University 35392 Giessen Germany
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22
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Wan Q, Yang J, To WP, Che CM. Strong metal-metal Pauli repulsion leads to repulsive metallophilicity in closed-shell d 8 and d 10 organometallic complexes. Proc Natl Acad Sci U S A 2021; 118:e2019265118. [PMID: 33372160 PMCID: PMC7817198 DOI: 10.1073/pnas.2019265118] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metallophilicity is defined as the interaction among closed-shell metal centers, the origin of which remains controversial, particularly for the roles of spd orbital hybridization (mixing of the spd atomic orbitals of the metal atom in the molecular orbitals of metal complex) and the relativistic effect. Our studies reveal that at close M-M' distances in the X-ray crystal structures of d8 and d10 organometallic complexes, M-M' closed-shell interactions are repulsive in nature due to strong M-M' Pauli repulsion. The relativistic effect facilitates (n + 1)s-nd and (n + 1)p-nd orbital hybridization of the metal atom, where (n + 1)s-nd hybridization induces strong M-M' Pauli repulsion and repulsive M-M' orbital interaction, and (n + 1)p-nd hybridization suppresses M-M' Pauli repulsion. This model is validated by both DFT (density functional theory) and high-level coupled-cluster singles and doubles with perturbative triples computations and is used to account for the fact that the intermolecular or intramolecular Ag-Ag' distance is shorter than the Au-Au' distance, where a weaker Ag-Ag' Pauli repulsion plays an important role. The experimental studies verify the importance of ligands in intermolecular interactions. Although the M-M' interaction is repulsive in nature, the linear coordination geometry of the d10 metal complex suppresses the L-L' (ligand-ligand) Pauli repulsion while retaining the strength of the attractive L-L' dispersion, leading to a close unsupported M-M' distance that is shorter than the sum of the van der Waals radius (rvdw) of the metal atoms.
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Affiliation(s)
- Qingyun Wan
- State Key Laboratory of Synthetic Chemistry, Department of Chemistry, The University of Hong Kong, Hong Kong SAR 999077, China;
| | - Jun Yang
- State Key Laboratory of Synthetic Chemistry, Department of Chemistry, The University of Hong Kong, Hong Kong SAR 999077, China;
| | - Wai-Pong To
- State Key Laboratory of Synthetic Chemistry, Department of Chemistry, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Chi-Ming Che
- State Key Laboratory of Synthetic Chemistry, Department of Chemistry, The University of Hong Kong, Hong Kong SAR 999077, China;
- Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen 518053, China
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23
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Elmi A, Cockroft SL. Quantifying Interactions and Solvent Effects Using Molecular Balances and Model Complexes. Acc Chem Res 2021; 54:92-103. [PMID: 33315374 DOI: 10.1021/acs.accounts.0c00545] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Where the basic units of molecular chemistry are the bonds within molecules, supramolecular chemistry is based on the interactions that occur between molecules. Understanding the "how" and "why" of the processes that govern molecular self-assembly remains an open challenge to the supramolecular community. While many interactions are readily examined in silico through electronic structure calculations, such insights may not be directly applicable to experimentalists. The practical limitations of computationally accounting for solvation is perhaps the largest bottleneck in this regard, with implicit solvation models failing to comprehensively account for the specific nature of solvent effects and explicit models incurring a prohibitively high computational cost. Since molecular recognition processes usually occur in solution, insight into the nature and effect of solvation is imperative not only for understanding these phenomena but also for the rational design of systems that exploit them.Molecular balances and supramolecular complexes have emerged as useful tools for the experimental dissection of the physicochemical basis of various noncovalent interactions, but they have historically been underexploited as a platform for the evaluation of solvent effects. Contrasting with large biological complexes, smaller synthetic model systems enable combined experimental and computational analyses, often facilitating theoretical analyses that can work in concert with experiment.Our research has focused on the development of supramolecular systems to evaluate the role of solvents in molecular recognition, and further characterize the underlying mechanisms by which molecules associate. In particular, the use of molecular balances has provided a framework to measure the magnitude of solvent effects and to examine the accuracy of solvent models. Such approaches have revealed how solvation can modulate the electronic landscape of a molecule and how competitive solvation and solvent cohesion can provide thermodynamic driving forces for association. Moreover, the use of simple model systems facilitates the interrogation and further dissection of the physicochemical origins of molecular recognition. This tandem experimental/computational approach has married less common computational techniques, like symmetry adapted perturbation theory (SAPT) and natural bonding orbital (NBO) analysis, with experimental observations to elucidate the influence of effects that are difficult to resolve experimentally (e.g., London dispersion and electron delocalization).
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Affiliation(s)
- Alex Elmi
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
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24
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Jorner K, Brinck T, Norrby PO, Buttar D. Machine learning meets mechanistic modelling for accurate prediction of experimental activation energies. Chem Sci 2021; 12:1163-1175. [PMID: 36299676 PMCID: PMC9528810 DOI: 10.1039/d0sc04896h] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/02/2020] [Indexed: 12/19/2022] Open
Abstract
Accurate prediction of chemical reactions in solution is challenging for current state-of-the-art approaches based on transition state modelling with density functional theory. Models based on machine learning have emerged as a promising alternative to address these problems, but these models currently lack the precision to give crucial information on the magnitude of barrier heights, influence of solvents and catalysts and extent of regio- and chemoselectivity. Here, we construct hybrid models which combine the traditional transition state modelling and machine learning to accurately predict reaction barriers. We train a Gaussian Process Regression model to reproduce high-quality experimental kinetic data for the nucleophilic aromatic substitution reaction and use it to predict barriers with a mean absolute error of 0.77 kcal mol−1 for an external test set. The model was further validated on regio- and chemoselectivity prediction on patent reaction data and achieved a competitive top-1 accuracy of 86%, despite not being trained explicitly for this task. Importantly, the model gives error bars for its predictions that can be used for risk assessment by the end user. Hybrid models emerge as the preferred alternative for accurate reaction prediction in the very common low-data situation where only 100–150 rate constants are available for a reaction class. With recent advances in deep learning for quickly predicting barriers and transition state geometries from density functional theory, we envision that hybrid models will soon become a standard alternative to complement current machine learning approaches based on ground-state physical organic descriptors or structural information such as molecular graphs or fingerprints. Hybrid reactivity models, combining mechanistic calculations and machine learning with descriptors, are used to predict barriers for nucleophilic aromatic substitution.![]()
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Affiliation(s)
- Kjell Jorner
- Early Chemical Development
- Pharmaceutical Sciences
- R&D
- AstraZeneca
- Macclesfield
| | - Tore Brinck
- Applied Physical Chemistry
- Department of Chemistry
- CBH
- KTH Royal Institute of Technology
- Stockholm
| | - Per-Ola Norrby
- Data Science & Modelling
- Pharmaceutical Sciences
- R&D
- AstraZeneca
- Gothenburg
| | - David Buttar
- Early Chemical Development
- Pharmaceutical Sciences
- R&D
- AstraZeneca
- Macclesfield
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25
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Otten R, Pádua RAP, Bunzel HA, Nguyen V, Pitsawong W, Patterson M, Sui S, Perry SL, Cohen AE, Hilvert D, Kern D. How directed evolution reshapes the energy landscape in an enzyme to boost catalysis. Science 2020; 370:1442-1446. [PMID: 33214289 PMCID: PMC9616100 DOI: 10.1126/science.abd3623] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/02/2020] [Indexed: 12/16/2022]
Abstract
The advent of biocatalysts designed computationally and optimized by laboratory evolution provides an opportunity to explore molecular strategies for augmenting catalytic function. Applying a suite of nuclear magnetic resonance, crystallography, and stopped-flow techniques to an enzyme designed for an elementary proton transfer reaction, we show how directed evolution gradually altered the conformational ensemble of the protein scaffold to populate a narrow, highly active conformational ensemble and accelerate this transformation by nearly nine orders of magnitude. Mutations acquired during optimization enabled global conformational changes, including high-energy backbone rearrangements, that cooperatively organized the catalytic base and oxyanion stabilizer, thus perfecting transition-state stabilization. The development of protein catalysts for many chemical transformations could be facilitated by explicitly sampling conformational substates during design and specifically stabilizing productive substates over all unproductive conformations.
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Affiliation(s)
- Renee Otten
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Ricardo A P Pádua
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - H Adrian Bunzel
- Laboratory of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Vy Nguyen
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Warintra Pitsawong
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - MacKenzie Patterson
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Shuo Sui
- Department of Chemical Engineering, Institute of Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Sarah L Perry
- Department of Chemical Engineering, Institute of Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland.
| | - Dorothee Kern
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA.
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26
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Bot M, Gorbachev V, Tsybizova A, Chen P. Bond Dissociation Energies in the Gas Phase for Large Molecular Ions by Threshold Collision-Induced Dissociation Experiments: Stretching the Limits. J Phys Chem A 2020; 124:8692-8707. [PMID: 32955888 DOI: 10.1021/acs.jpca.0c05712] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate bond dissociation energies for large molecules are difficult to obtain by either experimental or computational methods. The former methods are hampered by a range of physical and practical limitations in gas-phase measurement techniques, while the latter require incorporation of multiple approximations whose impact on accuracy may not always be clear. When internal benchmarks are not available, one hopes that experiment and theory can mutually support each other. A recent report found, however, a large discrepancy between gas-phase bond dissociation energies, measured mass spectrometrically, and the corresponding quantities computed using density functional theory (DFT)-D3 and DLPNO-CCSD(T) methods. With the widespread application of these computational methods to large molecular systems, the discrepancy needs to be resolved. We report a series of experimental studies that validate the mass spectrometric methods from small to large ions and find that bond dissociation energies extracted from threshold collision-induced dissociation experiments on large ions do indeed behave correctly. The implications for the computational studies are discussed.
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Affiliation(s)
- Marek Bot
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Vladimir Gorbachev
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Alexandra Tsybizova
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Peter Chen
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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27
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Laplaza R, Peccati F, A. Boto R, Quan C, Carbone A, Piquemal J, Maday Y, Contreras‐García J. NCIPLOT
and the analysis of noncovalent interactions using the reduced density gradient. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1497] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rubén Laplaza
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Departamento de Química Física Universidad de Zaragoza Zaragoza Spain
| | - Francesca Peccati
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Institut des Sciences du Calcul et des Données, ISCD, Sorbonne Université Paris France
| | - Roberto A. Boto
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Centro de Física de Materiales CFM‐MPC (CSIC‐UPV/EHU) Donostia Spain
| | - Chaoyu Quan
- Institut des Sciences du Calcul et des Données, ISCD, Sorbonne Université Paris France
- SUSTech International Center for Mathematics, and Department of Mathematics Southern University of Science and Technology Shenzhen China
| | - Alessandra Carbone
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB) Sorbonne Université Paris France
- Institut Universitaire de France Paris France
| | - Jean‐Philip Piquemal
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Institut Universitaire de France Paris France
| | - Yvon Maday
- SUSTech International Center for Mathematics, and Department of Mathematics Southern University of Science and Technology Shenzhen China
- Institut Universitaire de France Paris France
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28
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Joyce JP, Shores MP, Rappè AK. Protobranching as repulsion-induced attraction: a prototype for geminal stabilization. Phys Chem Chem Phys 2020; 22:16998-17006. [PMID: 32676632 DOI: 10.1039/d0cp02193h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Noncovalent interactions are traditionally defined within the context of their attractive components, such as electrostatics and dispersion. Sources of molecular strain are derived through the destabilization of Coulombic and exchange repulsion. Due to this binary designation, the underlying origin of geminal stability with respect to alkanes (referred to as protobranching) has been an active subject for debate between these competing perspectives. We recast this stabilization as a complementary (Gestalt) interaction between dispersion and exchange repulsion, each impacting the other. We use triplet hydrogen and argon dimer as foundational van der Waals adducts to develop a procedure for the visualization and quantification of both exchange repulsion, ΔρSCF, and medium-range correlation, ΔΔρ, as perturbations in electron density. We use the framework of the DFT-D3 correction to reproduce the shape of the dispersion potential at medium range and successfully model the trend in stability for the eighteen isomers of octane with a diverse series of functionals: BLYP, B3LYP, BP86, PBE, and PBE0. Collectively, our findings show that protobranching is a manifestation of steric repulsion-reduction in vibrational enthalpy and medium-range electron correlation.
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Affiliation(s)
- Justin P Joyce
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA.
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29
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Abstract
Thermally-robust bismuthanylstibanes are prepared in a one-step, high yield reaction, providing the first examples of neutral Bi-Sb σ-bonds in the solid state. DFT calculations indicate that the bis(silylamino)naphthalene scaffold is well-suited for supporting otherwise labile bonds. The reaction chemistry of the Bi-Sb bond is debuted by showing fission using NH3BH3 and insertion of a sulfur atom, the latter providing the first example of a Bi-S-Sb motif.
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Affiliation(s)
- Katherine M Marczenko
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada.
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30
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Miró J, Gensch T, Ellwart M, Han SJ, Lin HH, Sigman MS, Toste FD. Enantioselective Allenoate-Claisen Rearrangement Using Chiral Phosphate Catalysts. J Am Chem Soc 2020; 142:6390-6399. [PMID: 32182422 DOI: 10.1021/jacs.0c01637] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Herein we report the first highly enantioselective allenoate-Claisen rearrangement using doubly axially chiral phosphate sodium salts as catalysts. This synthetic method provides access to β-amino acid derivatives with vicinal stereocenters in up to 95% ee. We also investigated the mechanism of enantioinduction by transition state (TS) computations with DFT as well as statistical modeling of the relationship between selectivity and the molecular features of both the catalyst and substrate. The mutual interactions of charge-separated regions in both the zwitterionic intermediate generated by reaction of an amine to the allenoate and the Na+-salt of the chiral phosphate leads to an orientation of the TS in the catalytic pocket that maximizes favorable noncovalent interactions. Crucial arene-arene interactions at the periphery of the catalyst lead to a differentiation of the TS diastereomers. These interactions were interrogated using DFT calculations and validated through statistical modeling of parameters describing noncovalent interactions.
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Affiliation(s)
- Javier Miró
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Tobias Gensch
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Mario Ellwart
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Seo-Jung Han
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Kinomics Research Center and Division of Bio-Medical Science & Technology, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Hsin-Hui Lin
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Matthew S Sigman
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - F Dean Toste
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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31
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Rahman FU, Tzeli D, Petsalakis ID, Theodorakopoulos G, Ballester P, Rebek J, Yu Y. Chalcogen Bonding and Hydrophobic Effects Force Molecules into Small Spaces. J Am Chem Soc 2020; 142:5876-5883. [PMID: 32125842 DOI: 10.1021/jacs.0c01290] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Supramolecular capsules are desirable containers for the study of molecular behavior in small spaces and offer applications in transport, catalysis, and material science. We report here the use of chalcogen bonding to form container assemblies that are stable in water. Cavitands 1-3 functionalized with 2,1,3-benzoselenadiazole walls were synthesized in good yield from resorcin[4]arenes. The solid-state single-crystal X-ray structure of 3 showed a dimeric assembly cemented together through multiple Se···N chalcogen bonds. Binding of hydrophobic and amphiphilic guests in D2O was investigated by 1H NMR methods and revealed host-guest assemblies of 1:1, 2:1, and 2:2 stoichiometries. Small guests such as n-hexane or cyclohexane assembled as 2:2 capsular complexes, larger guests like cyclohexane carboxylic acid or cyclodecane formed 1:1 cavitand complexes, and longer linear guests like n-dodecane, cyclohexane carboxylic acid anhydride, and amides created 2:1 capsular complexes. The 2:1 complex of the capsule with cyclohexane carboxylic acid anhydride was stable over 2 weeks, showing that the seam of chalcogen bonds is "waterproof". Selective uptake of cyclohexane over benzene and methyl cyclohexane over toluene was observed in aqueous solution with the capsule. Hydrophobic forces and hydrogen-bonding attractions between guest molecules such as 3-methylbutanoic acid stabilized the assemblies in the presence of the competing effects of water. The high polarizability and modest electronegativity of Se provide a capsule lining complementary to guest C-H bonds. The 2,1,3-benzoselenadiazole walls impart an unusually high magnetic anisotropy to the capsule environment, which is supported by density functional theory calculations.
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Affiliation(s)
- Faiz-Ur Rahman
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China
| | - Demeter Tzeli
- Theoretical and Physical Chemistry Institute, The National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece.,Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens 157 71, Greece
| | - Ioannis D Petsalakis
- Theoretical and Physical Chemistry Institute, The National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece
| | - Giannoula Theodorakopoulos
- Theoretical and Physical Chemistry Institute, The National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece
| | - Pablo Ballester
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Julius Rebek
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China.,Skaggs Institute for Chemical Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yang Yu
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China
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32
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Tsybizova A, Fritsche L, Gorbachev V, Miloglyadova L, Chen P. Cryogenic ion vibrational predissociation (CIVP) spectroscopy of a gas-phase molecular torsion balance to probe London dispersion forces in large molecules. J Chem Phys 2019; 151:234304. [DOI: 10.1063/1.5124227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
| | - Lukas Fritsche
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | | | | | - Peter Chen
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
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33
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Zheng Q, Borsley S, Nichol GS, Duarte F, Cockroft SL. The Energetic Significance of Metallophilic Interactions. Angew Chem Int Ed Engl 2019; 58:12617-12623. [DOI: 10.1002/anie.201904207] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Qingshu Zheng
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Stefan Borsley
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Gary S. Nichol
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Fernanda Duarte
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
- Chemistry Research LaboratoryUniversity of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Scott L. Cockroft
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
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34
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Zheng Q, Borsley S, Nichol GS, Duarte F, Cockroft SL. The Energetic Significance of Metallophilic Interactions. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904207] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Qingshu Zheng
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Stefan Borsley
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Gary S. Nichol
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Fernanda Duarte
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
- Chemistry Research LaboratoryUniversity of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Scott L. Cockroft
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
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