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Peng Y, Yu W, Feng X, Xu T, Früchtl H, van Mourik T, Kirk SR, Jenkins S. The Cis-Effect Explained Using Next-Generation QTAIM. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27186099. [PMID: 36144830 PMCID: PMC9506152 DOI: 10.3390/molecules27186099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/05/2022] [Accepted: 09/14/2022] [Indexed: 11/22/2022]
Abstract
We used next-generation QTAIM (NG-QTAIM) to explain the cis-effect for two families of molecules: C2X2 (X = H, F, Cl) and N2X2 (X = H, F, Cl). We explained why the cis-effect is the exception rather than the rule. This was undertaken by tracking the motion of the bond critical point (BCP) of the stress tensor trajectories Tσ(s) used to sample the Uσ-space cis- and trans-characteristics. The Tσ(s) were constructed by subjecting the C1-C2 BCP and N1-N2 BCP to torsions ± θ and summing all possible Tσ(s) from the bonding environment. During this process, care was taken to fully account for multi-reference effects. We associated bond-bending and bond-twisting components of the Tσ(s) with cis- and trans-characteristics, respectively, based on the relative ease of motion of the electronic charge density ρ(rb). Qualitative agreement is found with existing experimental data and predictions are made where experimental data is not available.
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Affiliation(s)
- Yuting Peng
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Wenjing Yu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Xinxin Feng
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Tianlv Xu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Herbert Früchtl
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland, UK
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland, UK
| | - Steven R. Kirk
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
- Correspondence: (S.R.K.); (S.J.)
| | - Samantha Jenkins
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
- Correspondence: (S.R.K.); (S.J.)
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Mixed chiral and achiral character in substituted ethane: A next generation QTAIM perspective. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Xu T, Nie X, Li S, Yang Y, Früchtl H, van Mourik T, Kirk SR, Paterson MJ, Shigeta Y, Jenkins S. Chirality without Stereoisomers: Insight from the Helical Response of Bond Electrons. Chemphyschem 2021; 22:1989-1995. [PMID: 34269504 DOI: 10.1002/cphc.202100397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/14/2021] [Indexed: 11/05/2022]
Abstract
The association between molecular chirality and helical characteristics known as the chirality-helicity equivalence is determined for the first time by quantifying a chirality-helicity measure consistent with photoexcitation circular dichroism experiments. This is demonstrated using a formally achiral SN 2 reaction and a chiral SN 2 reaction. Both the achiral and chiral SN 2 reactions possess significant values of the chirality-helicity measure and display a Walden inversion, i. e. an inversion of the chirality between the reactant and product. We also track the chirality-helicity measure along the reaction path and discover the presence of chirality at the transition state and two intermediate structures for both reactions. We demonstrate the need for the chirality-helicity measure to differentiate between steric effects due to eclipsed conformations and chiral behaviors in formally achiral species. We explain the significance of this work for asymmetric synthetic reactions including the intermediate structures where the Cahn-Ingold-Prelog (CIP) rules cannot be used.
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Affiliation(s)
- Tianlv Xu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource, National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Xing Nie
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource, National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Shuman Li
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource, National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Yong Yang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource, National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Herbert Früchtl
- EaStCHEM School of Chemistry, University of Saint Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, United Kingdom
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of Saint Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, United Kingdom
| | - Steven R Kirk
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource, National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Martin J Paterson
- Institute of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, 305-8577, Japan
| | - Samantha Jenkins
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource, National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China
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Mahara B, Azizi A, Yang Y, Filatov M, Kirk SR, Jenkins S. Bond-path-rigidity and bond-path-flexibility of the ground state and first excited state of fulvene. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Wang L, Azizi A, Xu T, Filatov M, Kirk SR, Paterson MJ, Jenkins S. The role of the natural transition orbital density in the S0 → S1 and S0 → S2 transitions of fulvene with next generation QTAIM. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Xu T, Kirk SR, Jenkins S. A comparison of QTAIM and the stress tensor for Chirality-Helicity equivalence in S and R stereoisomers. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2019.136907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Tian T, Xu T, Kirk SR, Rongde IT, Tan YB, Manzhos S, Shigeta Y, Jenkins S. Intramolecular mode coupling of the isotopomers of water: a non-scalar charge density-derived perspective. Phys Chem Chem Phys 2020; 22:2509-2520. [DOI: 10.1039/c9cp05879f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Left: The BCP trajectories T(s) for H2O for the bending (Q1) mode, the axes labels of the trajectory T(s). The green spheres correspond to the bond critical point (BCPs). Right: The corresponding T(s) for H2O for the symmetric-stretch (Q2) mode.
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Affiliation(s)
- Tian Tian
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources
- College of Chemistry and Chemical Engineering
- Hunan Normal University
- Changsha
- China
| | - Tianlv Xu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources
- College of Chemistry and Chemical Engineering
- Hunan Normal University
- Changsha
- China
| | - Steven R. Kirk
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources
- College of Chemistry and Chemical Engineering
- Hunan Normal University
- Changsha
- China
| | - Ian Tay Rongde
- Department of Mechanical Engineering
- National University of Singapore
- Singapore
| | - Yong Boon Tan
- Department of Mechanical Engineering
- National University of Singapore
- Singapore
| | - Sergei Manzhos
- Centre Énergie Matériaux Télécommunications
- Institut National de la Recherche Scientifique
- 1650 boulevard Lionel-Boulet
- Varennes QC J3X1S2
- Canada
| | - Yasuteru Shigeta
- Center for Computational Sciences
- University of Tsukuba
- Tsukuba 305-8577
- Japan
| | - Samantha Jenkins
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources
- College of Chemistry and Chemical Engineering
- Hunan Normal University
- Changsha
- China
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Basha SJ, Chamundeeswari SV, Muthu S, Raajaraman BR. Quantum computational, spectroscopic investigations on 6-aminobenzimidazole by DFT/TD-DFT with different solvents and molecular docking studies. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111787] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Malcomson T, Azizi A, Momen R, Xu T, Kirk SR, Paterson MJ, Jenkins S. Stress Tensor Eigenvector Following with Next-Generation Quantum Theory of Atoms in Molecules: Excited State Photochemical Reaction Path from Benzene to Benzvalene. J Phys Chem A 2019; 123:8254-8264. [PMID: 31487180 DOI: 10.1021/acs.jpca.9b07519] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this investigation, we considered both the scalar and 3-D vector-based measures of bonding using next generation quantum theory of atoms in molecules (QTAIM), constructed from the preferred direction of electronic charge density accumulation, to better understand the photochemical reaction associated with of the formation of benzvalene from benzene. The formation of benzvalene from benzene resulted in two additional C-C bonds forming compared with the benzene. The creation of the additional C-C bonds was explained in terms of an increasing the favorability of the reaction process by maximizing the bonding density. The topological instability of the benzvalene structure was determined using the scalar and vector-based measures to explain the short chemical half-life of benzvalene in terms of the competition between the formation of unstable new C-C bonding that also destabilizes nearest neighbor C-C bonds. The explosive character of benzvalene is indicated by the unusual tendency of the C-C bonds to rupture as easily as weak bonding. The topological instability of the short strong C-C bonds was explained by the existence of measures from conventional and next generation QTAIM that previously have only been observed in weak interactions; such measures included twisted 3-D bonding descriptors.
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Affiliation(s)
- Thomas Malcomson
- Institute of Chemical Sciences, School of Engineering and Physical Sciences , Heriot-Watt University , Edinburgh , EH14 4AS , U.K
| | - Alireza Azizi
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha , Hunan 410081 , China
| | - Roya Momen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha , Hunan 410081 , China
| | - Tianlv Xu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha , Hunan 410081 , China
| | - Steven R Kirk
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha , Hunan 410081 , China
| | - Martin J Paterson
- Institute of Chemical Sciences, School of Engineering and Physical Sciences , Heriot-Watt University , Edinburgh , EH14 4AS , U.K
| | - Samantha Jenkins
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha , Hunan 410081 , China
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Xu T, Li JH, Momen R, Huang WJ, Kirk SR, Shigeta Y, Jenkins S. Chirality–Helicity Equivalence in the S and R Stereoisomers: A Theoretical Insight. J Am Chem Soc 2019; 141:5497-5503. [DOI: 10.1021/jacs.9b00823] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Tianlv Xu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource, National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
| | - Jia Hui Li
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource, National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
| | - Roya Momen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource, National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
| | - Wei Jie Huang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource, National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
| | - Steven Robert Kirk
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource, National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Samantha Jenkins
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource, National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
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