1
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Zhou Q, Kukier G, Gordiy I, Hoffmann R, Seeman JI, Houk KN. A 21st Century View of Allowed and Forbidden Electrocyclic Reactions. J Org Chem 2024; 89:1018-1034. [PMID: 38153322 PMCID: PMC10804416 DOI: 10.1021/acs.joc.3c02103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/29/2023]
Abstract
In 1965, Woodward and Hoffmann proposed a theory to predict the stereochemistry of electrocyclic reactions, which, after expansion and generalization, became known as the Woodward-Hoffmann Rules. Subsequently, Longuet-Higgins and Abrahamson used correlation diagrams to propose that the stereoselectivity of electrocyclizations could be explained by the correlation of reactant and product orbitals with the same symmetry. Immediately thereafter, Hoffmann and Woodward applied correlation diagrams to explain the mechanism of cycloadditions. We describe these discoveries and their evolution. We now report an investigation of various electrocyclic reactions using DFT and CASSCF. We track the frontier molecular orbitals along the intrinsic reaction coordinate and modeled trajectories and examine the correlation between HOMO and LUMO for thermally forbidden systems. We also investigate the electrocyclizations of several highly polarized systems for which the Houk group had predicted that donor-acceptor substitution can induce zwitterionic character, thereby providing low-energy pathways for formally forbidden reactions. We conclude with perspectives on the field of pericyclic reactions, including a refinement as the meaning of Woodward and Hoffmann's "Violations. There are none!" Lastly, we comment on the burgeoning influence of computations on all fields of chemistry.
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Affiliation(s)
- Qingyang Zhou
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California90095, United States
| | - Garrett Kukier
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California90095, United States
| | - Igor Gordiy
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California90095, United States
| | - Roald Hoffmann
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York14850, United States
| | - Jeffrey I. Seeman
- Department
of Chemistry, University of Richmond, Richmond, Virginia 23173United States
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California90095-1569. United States
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3
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Akiyoshi M, Ikemoto K, Isobe H. Tier-grown Expansion of Design-of-Experiments Parameter Spaces for Synthesis of a Nanometer-scale Macrocycle. Chem Asian J 2023; 18:e202201141. [PMID: 36424827 DOI: 10.1002/asia.202201141] [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: 11/10/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 11/26/2022]
Abstract
A method to find optimum synthetic conditions was devised by combining a data-driven empirical model with a traditional mechanistic model. In this method, an experimental parameter space was empirically obtained by Design-of-Experiments optimizations with machine-learning supplements and was strategically expanded by examination of the mechanistic model of the reaction paths. An extra tier grown on the original 3×3×3 parameter space succeeded in allocating an optimum reaction condition in the expanded 3×3×4 parameter space. The method was specifically devised for the synthesis of a macrocycle, [n]cyclo-meta-phenylenes ([n]CMP), and the largest congener with n=12 was synthesized and fully characterized for the first time. Crystallographic and photophysical analyses revealed favorable features of [12]CMP for the material applications.
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Affiliation(s)
- Misato Akiyoshi
- Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koki Ikemoto
- Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hioyuki Isobe
- Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
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4
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Krenn M, Pollice R, Guo SY, Aldeghi M, Cervera-Lierta A, Friederich P, dos Passos Gomes G, Häse F, Jinich A, Nigam A, Yao Z, Aspuru-Guzik A. On scientific understanding with artificial intelligence. NATURE REVIEWS. PHYSICS 2022; 4:761-769. [PMID: 36247217 PMCID: PMC9552145 DOI: 10.1038/s42254-022-00518-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/30/2022] [Indexed: 05/27/2023]
Abstract
An oracle that correctly predicts the outcome of every particle physics experiment, the products of every possible chemical reaction or the function of every protein would revolutionize science and technology. However, scientists would not be entirely satisfied because they would want to comprehend how the oracle made these predictions. This is scientific understanding, one of the main aims of science. With the increase in the available computational power and advances in artificial intelligence, a natural question arises: how can advanced computational systems, and specifically artificial intelligence, contribute to new scientific understanding or gain it autonomously? Trying to answer this question, we adopted a definition of 'scientific understanding' from the philosophy of science that enabled us to overview the scattered literature on the topic and, combined with dozens of anecdotes from scientists, map out three dimensions of computer-assisted scientific understanding. For each dimension, we review the existing state of the art and discuss future developments. We hope that this Perspective will inspire and focus research directions in this multidisciplinary emerging field.
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Affiliation(s)
- Mario Krenn
- Max Planck Institute for the Science of Light (MPL), Erlangen, Germany
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario Canada
| | - Robert Pollice
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario Canada
| | - Si Yue Guo
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario Canada
| | - Matteo Aldeghi
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario Canada
| | - Alba Cervera-Lierta
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario Canada
| | - Pascal Friederich
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario Canada
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Gabriel dos Passos Gomes
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario Canada
| | - Florian Häse
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario Canada
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA USA
| | - Adrian Jinich
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, USA
| | - AkshatKumar Nigam
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario Canada
| | - Zhenpeng Yao
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario Canada
- Center of Hydrogen Science, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Innovation Center for Future Materials, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China
| | - Alán Aspuru-Guzik
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario Canada
- Canadian Institute for Advanced Research (CIFAR) Lebovic Fellow, Toronto, Ontario Canada
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5
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Quack M, Seyfang G, Wichmann G. Perspectives on parity violation in chiral molecules: theory, spectroscopic experiment and biomolecular homochirality. Chem Sci 2022; 13:10598-10643. [PMID: 36320700 PMCID: PMC9491092 DOI: 10.1039/d2sc01323a] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/26/2022] [Indexed: 11/21/2022] Open
Abstract
The reflection (or ‘mirror’) symmetry of space is among the fundamental symmetries of physics. It is connected to the conservation law for the quantum number parity and a fundamental ‘non-observable’ property of space (as defined by an absolute ‘left-handed’ or ‘right-handed’ coordinate system). The discovery of the violation of this symmetry – the non-conservation of parity or ‘parity violation’ – in 1956/1957 had an important influence on the further development of physics. In chemistry the mirror symmetry of space is connected to the existence of enantiomers as isomers of chiral (‘handed’) molecules. These isomers would relate to each other as idealized left or right hand or as image and mirror image and would be energetically exactly equivalent with perfect space inversion symmetry. Parity violation results in an extremely small ‘parity violating’ energy difference between the ground states of the enantiomers which can be theoretically calculated to be about 100 aeV to 1 feV (equivalent to 10−11 to 10−10 J mol−1), depending on the molecule, but which has not yet been detected experimentally. Its detection remains one of the great challenges of current physical–chemical stereochemistry, with implications also for fundamental problems in physics. In biochemistry and molecular biology one finds a related fundamental question unanswered for more than 100 years: the evolution of ‘homochirality’, which is the practically exclusive preference of one chiral, enantiomeric form as building blocks in the biopolymers of all known forms of life (the l-amino acids in proteins and d-sugars in DNA, not the reverse d-amino acids or l-sugars). In astrobiology the spectroscopic detection of homochirality could be used as strong evidence for the existence of extraterrestrial life, if any. After a brief conceptual and historical introduction we review the development, current status, and progress along these three lines of research: theory, spectroscopic experiment and the outlook towards an understanding of the evolution of biomolecular homochirality. The reflection (or ‘mirror’) symmetry of space is among the fundamental symmetries of physics. It is connected to the conservation law for the quantum number purity and its violation and has a fundamental relation to stereochemistry and molecular chirality.![]()
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Affiliation(s)
- Martin Quack
- Physical Chemistry, ETH Zürich, CH-8093 Zurich, Switzerland
| | - Georg Seyfang
- Physical Chemistry, ETH Zürich, CH-8093 Zurich, Switzerland
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6
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Aon MA. Computational Systems Biology and Artificial Intelligence. Methods Mol Biol 2022; 2399:1-6. [PMID: 35604550 DOI: 10.1007/978-1-0716-1831-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Aware of the rapid evolution of computational systems biology (CSB), which is the focus of this book, we address the emergence of artificial intelligence (AI). Consequently, one of the main purposes of this Introduction is to assess where the relationship between CSB and AI stands today, and to venture a vision for CSB.
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Affiliation(s)
- Miguel A Aon
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
- Laboratory of Cardiovascular Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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7
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Abstract
Chemical compound space (CCS), the set of all theoretically conceivable combinations of chemical elements and (meta-)stable geometries that make up matter, is colossal. The first-principles based virtual sampling of this space, for example, in search of novel molecules or materials which exhibit desirable properties, is therefore prohibitive for all but the smallest subsets and simplest properties. We review studies aimed at tackling this challenge using modern machine learning techniques based on (i) synthetic data, typically generated using quantum mechanics based methods, and (ii) model architectures inspired by quantum mechanics. Such Quantum mechanics based Machine Learning (QML) approaches combine the numerical efficiency of statistical surrogate models with an ab initio view on matter. They rigorously reflect the underlying physics in order to reach universality and transferability across CCS. While state-of-the-art approximations to quantum problems impose severe computational bottlenecks, recent QML based developments indicate the possibility of substantial acceleration without sacrificing the predictive power of quantum mechanics.
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Affiliation(s)
- Bing Huang
- Faculty
of Physics, University of Vienna, 1090 Vienna, Austria
| | - O. Anatole von Lilienfeld
- Faculty
of Physics, University of Vienna, 1090 Vienna, Austria
- Institute
of Physical Chemistry and National Center for Computational Design
and Discovery of Novel Materials (MARVEL), Department of Chemistry, University of Basel, 4056 Basel, Switzerland
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11
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Bahlke MP, Mogos N, Proppe J, Herrmann C. Exchange Spin Coupling from Gaussian Process Regression. J Phys Chem A 2020; 124:8708-8723. [DOI: 10.1021/acs.jpca.0c05983] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Marc Philipp Bahlke
- Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Natnael Mogos
- Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Jonny Proppe
- Institute of Physical Chemistry, Georg-August University, Tammannstr. 6, 37077 Göttingen, Germany
| | - Carmen Herrmann
- Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
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12
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Laikov DN. Optimization of atomic density-fitting basis functions for molecular two-electron integral approximations. J Chem Phys 2020; 153:114121. [PMID: 32962362 DOI: 10.1063/5.0014639] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A general procedure for the optimization of atomic density-fitting basis functions is designed with the balance between accuracy and numerical stability in mind. Given one-electron wavefunctions and energies, weights are assigned to the product densities, modeling their contribution to the exchange and second-order correlation energy, and a simple weighted error measure is minimized. Generally contracted Gaussian auxiliary basis sets are optimized to match the wavefunction basis sets [D. N. Laikov, Theor. Chem. Acc. 138, 40 (2019)] for all 102 elements in a scalar-relativistic approximation [D. N. Laikov, J. Chem. Phys. 150, 061103 (2019)].
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Affiliation(s)
- Dimitri N Laikov
- Chemistry Department, Moscow State University, 119991 Moscow, Russia
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