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Kirk SR, Jenkins S. Tools for overcoming reliance on energy-based measures in chemistry: a tutorial review. Chem Soc Rev 2023; 52:5861-5874. [PMID: 37564018 DOI: 10.1039/d3cs00350g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
The vast majority of literature in the chemical sciences describes fundamental chemical and physical phenomena using scalar measures, such as the energy, even though many phenomena are beyond the scope of scalar-based considerations. This problem exists no matter how accurately the associated energies are calculated. The solution that is explained in this work is to remove the reliance on scalar quantum chemical measures and instead utilize the vector-based and full symmetry-breaking nature of next generation quantum theory of atoms in molecules (NG-QTAIM). The connection with experiment on neutral chiral molecules is explained. A selection of non-energy-based explanations are provided: the functioning of molecular devices, why the cis-effect is the exception rather than the rule, stereochemical phenomena including chiral discrimination, quantifying chiral character of formally achiral molecules, mixed S and R stereoisomer character and the effect of an applied electric field. Current and future developments along with suggestions for future avenues of investigation are discussed. This tutorial review provides the practical details required to implement NG-QTAIM for a range of phenomena that are not accessible with energy-based measures. Step-by-step worked examples are included with data sets and instructions for use of commercial and open-source software along with examples of how to interpret the results.
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Affiliation(s)
- 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.
| | - 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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2
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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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Badala Viswanatha C, Stöckl J, Arnoldi B, Becker S, Aeschlimann M, Stadtmüller B. Vectorial Electron Spin Filtering by an All-Chiral Metal-Molecule Heterostructure. J Phys Chem Lett 2022; 13:6244-6249. [PMID: 35771050 PMCID: PMC9272820 DOI: 10.1021/acs.jpclett.2c00983] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The discovery of the electrons' chiral induced spin selective transmission (CISS) through chiral molecules has opened the pathway for manipulating spin transport in nonmagnetic structures on the nanoscale. CISS has predominantly been explored in structurally helical molecules on surfaces, where the spin selectivity affects only the spin polarization of the electrons along their direction of propagation. Here, we demonstrate a spin selective electron transmission for the point-chiral molecule 3-methylcyclohexanone (3-MCHO) adsorbed on the chiral Cu(643)R surface. Using spin- and momentum-resolved photoelectron spectroscopy, we detect a spin-dependent electron transmission through a single layer of 3-MCHO molecules that depends on all three components of the electrons' spin. Crucially, exchanging the enantiomers alters the electrons' spin component oriented parallel to the terraces of the Cu(643)R surface. The findings are attributed to the enantiomer-specific adsorption configuration on the surface. This opens the intriguing opportunity to selectively tune CISS by the enantiospecific molecule-surface interaction in all-chiral heterostructures.
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Affiliation(s)
- Chetana Badala Viswanatha
- Department
of Physics and Research Center OPTIMAS, University of Kaiserslautern, Erwin-Schrödinger-Straße 46, 67663 Kaiserslautern, Germany
| | - Johannes Stöckl
- Department
of Physics and Research Center OPTIMAS, University of Kaiserslautern, Erwin-Schrödinger-Straße 46, 67663 Kaiserslautern, Germany
| | - Benito Arnoldi
- Department
of Physics and Research Center OPTIMAS, University of Kaiserslautern, Erwin-Schrödinger-Straße 46, 67663 Kaiserslautern, Germany
| | - Sebastian Becker
- Department
of Physics and Research Center OPTIMAS, University of Kaiserslautern, Erwin-Schrödinger-Straße 46, 67663 Kaiserslautern, Germany
- Department
of Chemistry, University of Kaiserslautern, Erwin-Schrödinger-Straße
52, 67663 Kaiserslautern, Germany
| | - Martin Aeschlimann
- Department
of Physics and Research Center OPTIMAS, University of Kaiserslautern, Erwin-Schrödinger-Straße 46, 67663 Kaiserslautern, Germany
| | - Benjamin Stadtmüller
- Department
of Physics and Research Center OPTIMAS, University of Kaiserslautern, Erwin-Schrödinger-Straße 46, 67663 Kaiserslautern, Germany
- Institute
of Physics, Johannes Gutenberg University
Mainz, Staudingerweg
7, 55128 Mainz, Germany
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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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Garner MH, Corminboeuf C. Helical electronic transitions of spiroconjugated molecules. Chem Commun (Camb) 2021; 57:6408-6411. [DOI: 10.1039/d1cc01904j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The π–π* transitions of disubstituted spiropentadiene become helical due to mixing of its two perpendicular π-systems. The helicity is symmetry-protected and gives rise to experimentally observable effects, such as optical activity.
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Affiliation(s)
- Marc H. Garner
- Laboratory for Computational Molecular Design
- Institute of Chemical Sciences and Engineering
- Ecole Polytechnique Federale de Lausanne (EPFL)
- Lausanne 1015
- Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design
- Institute of Chemical Sciences and Engineering
- Ecole Polytechnique Federale de Lausanne (EPFL)
- Lausanne 1015
- Switzerland
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Azizi A, Momen R, Früchtl H, van Mourik T, Kirk SR, Jenkins S. Next-generation QTAIM for scoring molecular wires in E-fields for molecular electronic devices. J Comput Chem 2020; 41:913-921. [PMID: 31880358 DOI: 10.1002/jcc.26137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 12/11/2019] [Indexed: 11/08/2022]
Abstract
The effect of a varying, directional E x , E y , and E z electric field on the ethene molecule was investigated using next-generation quantum theory of atoms in molecules (QTAIM). Despite using low E-field strengths that are within the realm of experiment and do not measurably alter the molecular geometry, significant changes to the QTAIM properties were observed. Using conventional QTAIM, the shifting of the C─C and C─H bond critical points (BCPs) demonstrates polarization through an interchange in the size of the atoms involved in a bond, since a BCP is located on the boundary between a pair of bonded atoms. Next-generation QTAIM, however, demonstrates the polarization effect more directly with a change in morphology of the 3-D envelope around the BCP. Modest increases of ≈ 2% in the ellipticity ε of the BCP were uncovered when the C─C bond was aligned parallel or anti-parallel to the applied E x -field. Significant asymmetries were found in the response of the next-generation QTAIM 3-D paths of the C─H bonds to the applied E-field. When the E-field coincided with the C─C bond, the BCP moved in response and was accompanied by the envelope constructed from 3-D next-generation paths. The response displayed a polarization effect that increased with increasing magnitude of the E x -field parallel and anti-parallel to the C─C bond. Our analysis demonstrates that next-generation QTAIM is a useful tool for understanding the response of molecules to E-fields, for example, for the screening of molecular wires for the design of molecular electronic devices. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- 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, 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, China
| | - Herbert Früchtl
- EaStCHEM School of Chemistry, University of Saint Andrews, St Andrews, Fife, UK
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of Saint Andrews, St Andrews, Fife, 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, Hunan, China
| | - 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, China
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Huang Y, Fu Y, Li M, Jiang D, Kutyreff CJ, Engle JW, Lan X, Cai W, Chen T. Chirality-Driven Transportation and Oxidation Prevention by Chiral Selenium Nanoparticles. Angew Chem Int Ed Engl 2020; 59:4406-4414. [PMID: 31876049 PMCID: PMC7123465 DOI: 10.1002/anie.201910615] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/22/2019] [Indexed: 12/20/2022]
Abstract
The chirality of nanoparticles directly influences their transport and biological effects under physiological conditions, but the details of this phenomenon have rarely been explored. Herein, chiral GSH-anchored selenium nanoparticles (G@SeNPs) are fabricated to investigate the effect of their chirality on their transport and antioxidant activity. G@SeNPs modified with different enantiomers show opposite handedness with a tunable circular dichroism signal. Noninvasive positron emission tomography imaging clearly reveals that 64 Cu-labeled l-G@SeNPs experience distinctly different transport among the major organs from that of their d-and dl-counterparts, demonstrating that the chirality of the G@SeNPs influences the biodistribution and kinetics. Taking advantage of the strong homologous cell adhesion and uptake, l-G@SeNPs have been shown here to effectively prevent oxidation damage caused by palmitic acid in insulinoma cells.
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Affiliation(s)
- Yanyu Huang
- Department of Chemistry, Jinan University, Room 643, Department of Chemistry, Jinan University, Guangzhou, 510632, China
- Department of Radiology, Department of Medical Physics, University of Wisconsin- Madison, Room 7137, 1111 Highland Avenue, Madison, WI 53705-2275, U.S
| | - Yuanting Fu
- Department of Chemistry, Jinan University, Room 643, Department of Chemistry, Jinan University, Guangzhou, 510632, China
| | - Mengting Li
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022, China
| | - Dawei Jiang
- Department of Radiology, Department of Medical Physics, University of Wisconsin- Madison, Room 7137, 1111 Highland Avenue, Madison, WI 53705-2275, U.S
| | - Christopher J. Kutyreff
- Department of Radiology, Department of Medical Physics, University of Wisconsin- Madison, Room 7137, 1111 Highland Avenue, Madison, WI 53705-2275, U.S
| | - Jonathan W. Engle
- Department of Radiology, Department of Medical Physics, University of Wisconsin- Madison, Room 7137, 1111 Highland Avenue, Madison, WI 53705-2275, U.S
| | - Xiaoli Lan
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022, China
| | - Weibo Cai
- Department of Radiology, Department of Medical Physics, University of Wisconsin- Madison, Room 7137, 1111 Highland Avenue, Madison, WI 53705-2275, U.S
| | - Tianfeng Chen
- Department of Chemistry, Jinan University, Room 643, Department of Chemistry, Jinan University, Guangzhou, 510632, China
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Huang Y, Fu Y, Li M, Jiang D, Kutyreff CJ, Engle JW, Lan X, Cai W, Chen T. Chirality‐Driven Transportation and Oxidation Prevention by Chiral Selenium Nanoparticles. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201910615] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yanyu Huang
- Department of ChemistryJinan University Guangzhou 510632 China
- Department of RadiologyDepartment of Medical PhysicsUniversity of Wisconsin-Madison 1111 Highland Avenue Madison WI 53705-2275 USA
| | - Yuanting Fu
- Department of ChemistryJinan University Guangzhou 510632 China
| | - Mengting Li
- Department of Nuclear MedicineUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyHubei Province Key Laboratory of Molecular Imaging Wuhan 430022 China
| | - Dawei Jiang
- Department of RadiologyDepartment of Medical PhysicsUniversity of Wisconsin-Madison 1111 Highland Avenue Madison WI 53705-2275 USA
| | - Christopher J. Kutyreff
- Department of RadiologyDepartment of Medical PhysicsUniversity of Wisconsin-Madison 1111 Highland Avenue Madison WI 53705-2275 USA
| | - Jonathan W. Engle
- Department of RadiologyDepartment of Medical PhysicsUniversity of Wisconsin-Madison 1111 Highland Avenue Madison WI 53705-2275 USA
| | - Xiaoli Lan
- Department of Nuclear MedicineUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyHubei Province Key Laboratory of Molecular Imaging Wuhan 430022 China
| | - Weibo Cai
- Department of RadiologyDepartment of Medical PhysicsUniversity of Wisconsin-Madison 1111 Highland Avenue Madison WI 53705-2275 USA
| | - Tianfeng Chen
- Department of ChemistryJinan University Guangzhou 510632 China
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10
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Azizi A, Momen R, Kirk SR, Jenkins S. 3-D bond-paths of QTAIM and the stress tensor in neutral lithium clusters, Li m (m = 2-5), presented on the Ehrenfest force molecular graph. Phys Chem Chem Phys 2020; 22:864-877. [PMID: 31844863 DOI: 10.1039/c9cp05066c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this investigation we set out to understand the origins of non-nuclear attractors (NNAs) found for neutral lithium clusters Lim (m = 2-5) on the QTAIM molecular graph but not on the Ehrenfest force F(r) molecular graph. Therefore, we pursued the stress tensor σ(r) without using the dependency on the QTAIM partitioning, since previously σ(r) was only calculated within the QTAIM partitioning, to see if any indication of NNA character can be determined. Because the stress tensor σ(r) lacks an associated scalar- or vector-field as is the case for QTAIM and the Ehrenfest F(r) partitioning schemes respectively, a stress tensor σ(r) partitioning scheme cannot be constructed. Therefore, to overcome this difficulty we use next generation QTAIM, constructed from the most preferred directions of electronic charge density accumulation, to calculate the stress tensor σ(r) 3-D bond-paths on the Ehrenfest force F(r) molecular graph. Using next generation 3-D bond-paths within the Ehrenfest force F(r) partitioning, we can classify the degree of NNA character in the absence of NNAs. A much higher degree of NNA character is found to be present for the stress tensor σ(r) 3-D bond-paths than for the corresponding QTAIM or Ehrenfest force F(r) 3-D bond-paths. The stabilizing effect of the NNA is demonstrated by undertaking Li2 bond-path compression and stretching distortions sufficient to cause the annihilation of the NNA. The compression and stretching distortions also lead to a large increase in the 3-D bond-path asymmetry and persistent bond-path torsion respectively.
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Affiliation(s)
- 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.
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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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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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Li S, Xu T, van Mourik T, Früchtl H, Kirk SR, Jenkins S. Halogen and Hydrogen Bonding in Halogenabenzene/NH 3 Complexes Compared Using Next-Generation QTAIM. Molecules 2019; 24:E2875. [PMID: 31398800 PMCID: PMC6720212 DOI: 10.3390/molecules24162875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 11/17/2022] Open
Abstract
Next-generation quantum theory of atoms in molecules (QTAIM) was used to investigate the competition between hydrogen bonding and halogen bonding for the recently proposed (Y = Br, I, At)/halogenabenzene/NH3 complex. Differences between using the SR-ZORA Hamiltonian and effective core potentials (ECPs) to account for relativistic effects with increased atomic mass demonstrated that next-generation QTAIM is a much more responsive tool than conventional QTAIM. Subtle details of the competition between halogen bonding and hydrogen bonding were observed, indicating a mixed chemical character shown in the 3-D paths constructed from the bond-path framework set B. In addition, the use of SR-ZORA reduced or entirely removed spurious features of B on the site of the halogen atoms.
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Affiliation(s)
- 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, Changsha 410081, Hunan, 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, Changsha 410081, Hunan, China
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland, UK.
| | - Herbert Früchtl
- 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, Changsha 410081, Hunan, China.
| | - 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, Changsha 410081, Hunan, China.
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Xu T, Momen R, Azizi A, van Mourik T, Früchtl H, Kirk SR, Jenkins S. The destabilization of hydrogen bonds in an external E-field for improved switch performance. J Comput Chem 2019; 40:1881-1891. [PMID: 30980547 DOI: 10.1002/jcc.25843] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 03/26/2019] [Accepted: 03/31/2019] [Indexed: 01/03/2023]
Abstract
The effect of an electric field on a recently proposed molecular switch based on a quinone analogue was investigated using next-generation quantum theory of atoms in molecules (QTAIM) methodology. The reversal of a homogenous external electric field was demonstrated to improve the "OFF" functioning of the switch. This was achieved by destabilization of the H atom participating in the tautomerization process along the hydrogen bond that defines the switch. The "ON" functioning of the switch, from the position of the tautomerization barrier, is also improved by the reversal of the homogenous external electric field: this result was previously inaccessible. The "ON" and "OFF" functioning of the switch was visualized in terms of the response of the most preferred directions of motion of the electronic charge density to the applied external field. All measures from QTAIM and the stress tensor provide consistent results for the factors affecting the "ON" and "OFF" switch performance. Our analysis therefore demonstrates use for future design of molecular electronic devices. © 2019 Wiley Periodicals, Inc.
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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
| | - 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
| | - 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
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| | - Herbert Früchtl
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, 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
| | - 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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