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Sidorov P, Tsuji N. A Primer on 2D Descriptors in Selectivity Modeling for Asymmetric Catalysis. Chemistry 2024; 30:e202302837. [PMID: 38010242 DOI: 10.1002/chem.202302837] [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: 08/31/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 11/29/2023]
Abstract
Machine learning has permeated all fields of research, including chemistry, and is now an integral part of the design of novel compounds with desired properties. In the field of asymmetric catalysis, the preference still lies with models based on a physical understanding of the catalysis phenomenon and the electronic and steric properties of catalysts. However, such models require quantum chemical calculations and are thus limited by their computational cost. Here, we highlight the recent advances in modeling catalyst selectivity by using the 2D structures of catalysts and substrates. While these have a less explicit mechanistic connection to the modeled property, 2D descriptors, such as topological indices, molecular fingerprints, and fragments, offer the tremendous advantages of low cost and high speed of calculations. This makes them optimal for the in-silico screening of large amounts of data. We provide an overview of common quantitative structure-property relationship workflow, model building and validation techniques, applications of these methodologies in asymmetric catalysis design, and an outlook on improving the understanding of 2D-based models.
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Affiliation(s)
- Pavel Sidorov
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Nobuya Tsuji
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
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2
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Wang X, Huang Y, Xie X, Liu Y, Huo Z, Lin M, Xin H, Tong R. Bayesian-optimization-assisted discovery of stereoselective aluminum complexes for ring-opening polymerization of racemic lactide. Nat Commun 2023; 14:3647. [PMID: 37339991 DOI: 10.1038/s41467-023-39405-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 06/12/2023] [Indexed: 06/22/2023] Open
Abstract
Stereoselective ring-opening polymerization catalysts are used to produce degradable stereoregular poly(lactic acids) with thermal and mechanical properties that are superior to those of atactic polymers. However, the process of discovering highly stereoselective catalysts is still largely empirical. We aim to develop an integrated computational and experimental framework for efficient, predictive catalyst selection and optimization. As a proof of principle, we have developed a Bayesian optimization workflow on a subset of literature results for stereoselective lactide ring-opening polymerization, and using the algorithm, we identify multiple new Al complexes that catalyze either isoselective or heteroselective polymerization. In addition, feature attribution analysis uncovers mechanistically meaningful ligand descriptors, such as percent buried volume (%Vbur) and the highest occupied molecular orbital energy (EHOMO), that can access quantitative and predictive models for catalyst development.
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Affiliation(s)
- Xiaoqian Wang
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, 635 Prices Fork Road, Blacksburg, VA, 24061, USA
| | - Yang Huang
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, 635 Prices Fork Road, Blacksburg, VA, 24061, USA
| | - Xiaoyu Xie
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, 635 Prices Fork Road, Blacksburg, VA, 24061, USA
| | - Yan Liu
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, 635 Prices Fork Road, Blacksburg, VA, 24061, USA
| | - Ziyu Huo
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, 635 Prices Fork Road, Blacksburg, VA, 24061, USA
| | - Maverick Lin
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, 635 Prices Fork Road, Blacksburg, VA, 24061, USA
| | - Hongliang Xin
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, 635 Prices Fork Road, Blacksburg, VA, 24061, USA.
| | - Rong Tong
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, 635 Prices Fork Road, Blacksburg, VA, 24061, USA.
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3
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Tsuji N, Sidorov P, Zhu C, Nagata Y, Gimadiev T, Varnek A, List B. Predicting Highly Enantioselective Catalysts Using Tunable Fragment Descriptors. Angew Chem Int Ed Engl 2023; 62:e202218659. [PMID: 36688354 DOI: 10.1002/anie.202218659] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023]
Abstract
Catalyst optimization processes typically rely on inductive and qualitative assumptions of chemists based on screening data. While machine learning models using molecular properties or calculated 3D structures enable quantitative data evaluation, costly quantum chemical calculations are often required. In contrast, readily available binary fingerprint descriptors are time- and cost-efficient, but their predictive performance remains insufficient. Here, we describe a machine learning model based on fragment descriptors, which are fine-tuned for asymmetric catalysis and represent cyclic or polyaromatic hydrocarbons, enabling robust and efficient virtual screening. Using training data with only moderate selectivities, we designed theoretically and validated experimentally new catalysts showing higher selectivities in a challenging asymmetric tetrahydropyran synthesis.
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Affiliation(s)
- Nobuya Tsuji
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Pavel Sidorov
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Chendan Zhu
- Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany
| | - Yuuya Nagata
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Timur Gimadiev
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Alexandre Varnek
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan.,Laboratory of Chemoinformatics, UMR 7140, CNRS, University of Strasbourg, 67081, Strasbourg, France
| | - Benjamin List
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan.,Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany
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4
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Duan C, Nandy A, Kulik HJ. Machine Learning for the Discovery, Design, and Engineering of Materials. Annu Rev Chem Biomol Eng 2022; 13:405-429. [PMID: 35320698 DOI: 10.1146/annurev-chembioeng-092320-120230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Machine learning (ML) has become a part of the fabric of high-throughput screening and computational discovery of materials. Despite its increasingly central role, challenges remain in fully realizing the promise of ML. This is especially true for the practical acceleration of the engineering of robust materials and the development of design strategies that surpass trial and error or high-throughput screening alone. Depending on the quantity being predicted and the experimental data available, ML can either outperform physics-based modes, be used to accelerate such models, or be integrated with them to improve their performance. We cover recent advances in algorithms and in their application that are starting to make inroads toward (a) the discovery of new materials through large-scale enumerative screening, (b) the design of materials through identification of rules and principles that govern materials properties, and (c) the engineering of practical materials by satisfying multiple objectives. We conclude with opportunities for further advancement to realize ML as a widespread tool for practical computational materials design. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Chenru Duan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; , , .,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; , , .,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; , ,
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5
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6
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Nandy A, Duan C, Taylor MG, Liu F, Steeves AH, Kulik HJ. Computational Discovery of Transition-metal Complexes: From High-throughput Screening to Machine Learning. Chem Rev 2021; 121:9927-10000. [PMID: 34260198 DOI: 10.1021/acs.chemrev.1c00347] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transition-metal complexes are attractive targets for the design of catalysts and functional materials. The behavior of the metal-organic bond, while very tunable for achieving target properties, is challenging to predict and necessitates searching a wide and complex space to identify needles in haystacks for target applications. This review will focus on the techniques that make high-throughput search of transition-metal chemical space feasible for the discovery of complexes with desirable properties. The review will cover the development, promise, and limitations of "traditional" computational chemistry (i.e., force field, semiempirical, and density functional theory methods) as it pertains to data generation for inorganic molecular discovery. The review will also discuss the opportunities and limitations in leveraging experimental data sources. We will focus on how advances in statistical modeling, artificial intelligence, multiobjective optimization, and automation accelerate discovery of lead compounds and design rules. The overall objective of this review is to showcase how bringing together advances from diverse areas of computational chemistry and computer science have enabled the rapid uncovering of structure-property relationships in transition-metal chemistry. We aim to highlight how unique considerations in motifs of metal-organic bonding (e.g., variable spin and oxidation state, and bonding strength/nature) set them and their discovery apart from more commonly considered organic molecules. We will also highlight how uncertainty and relative data scarcity in transition-metal chemistry motivate specific developments in machine learning representations, model training, and in computational chemistry. Finally, we will conclude with an outlook of areas of opportunity for the accelerated discovery of transition-metal complexes.
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Affiliation(s)
- Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chenru Duan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael G Taylor
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Fang Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Adam H Steeves
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Abstract
Computational methods have emerged as a powerful tool to augment traditional experimental molecular catalyst design by providing useful predictions of catalyst performance and decreasing the time needed for catalyst screening. In this perspective, we discuss three approaches for computational molecular catalyst design: (i) the reaction mechanism-based approach that calculates all relevant elementary steps, finds the rate and selectivity determining steps, and ultimately makes predictions on catalyst performance based on kinetic analysis, (ii) the descriptor-based approach where physical/chemical considerations are used to find molecular properties as predictors of catalyst performance, and (iii) the data-driven approach where statistical analysis as well as machine learning (ML) methods are used to obtain relationships between available data/features and catalyst performance. Following an introduction to these approaches, we cover their strengths and weaknesses and highlight some recent key applications. Furthermore, we present an outlook on how the currently applied approaches may evolve in the near future by addressing how recent developments in building automated computational workflows and implementing advanced ML models hold promise for reducing human workload, eliminating human bias, and speeding up computational catalyst design at the same time. Finally, we provide our viewpoint on how some of the challenges associated with the up-and-coming approaches driven by automation and ML may be resolved.
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Affiliation(s)
- Ademola Soyemi
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL 35487, USA.
| | - Tibor Szilvási
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL 35487, USA.
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8
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Zhang Y, Liu J, Wu X, Yang S, Li Y, Liu S, Zhu S, Cao X, Xie Z, Lei X, Huang H, Peng J. Anti-chronic myeloid leukemia activity and quantitative structure-activity relationship of novel thiazole aminobenzamide derivatives. Bioorg Med Chem Lett 2021; 44:128116. [PMID: 34015503 DOI: 10.1016/j.bmcl.2021.128116] [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: 02/04/2021] [Revised: 05/11/2021] [Accepted: 05/16/2021] [Indexed: 10/21/2022]
Abstract
The anti-chronic myeloid leukemia activity of thiazole aminobenzamide derivatives in vitro was tested by a methanethiosulfonate (MTS)-based viability assay method, and the result showed that some compounds exhibited good inhibitory activities against human chronic myeloid leukemia cell line K562, imatinib-resistant strain K562/R and T135I mutant cell line BaF3-ABL-BCR-T315I. Comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) methods were used to analyze the relationship between the structure of thiazole aminobenzamide derivatives and the inhibition of K562/R cell activity. In CoMFA, Q2 was 0.899 and R2 was 0.963; in CoMSIA, Q2 and R2 were 0.840 and 0.903, respectively. These data indicated that the selected test set showed suitable external predictive ability. Combined with the contour map results, we further analyzed the three-dimensional quantitative structure (3D-QSAR) model. The results demonstrated that in the backbone of the thiazole aminobenzamide derivative, the substitution of a small group at R1 position, or the introduction of a hydrophilic group at R2 position, or the introduction of a large-volume amino acid at R3 position may be beneficial to improve the anti-CML activity of the compound.
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Affiliation(s)
- Yuan Zhang
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, PR China; Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang City, Hunan Province 421001, PR China
| | - Juan Liu
- Department of Pharmacy, Yiyang Central Hospital, Hunan Province 413000, PR China
| | - Xin Wu
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, PR China
| | - Suming Yang
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, PR China
| | - Yao Li
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, PR China
| | - Songbin Liu
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, PR China
| | - Saifei Zhu
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, PR China
| | - Xuan Cao
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, PR China
| | - Zhizhong Xie
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, PR China
| | - Xiaoyong Lei
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, PR China
| | - Honglin Huang
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, PR China; Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang City, Hunan Province 421001, PR China.
| | - Junmei Peng
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, PR China; Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang City, Hunan Province 421001, PR China.
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9
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Lach D, Zhdan U, Smolinski A, Polanski J. Functional and Material Properties in Nanocatalyst Design: A Data Handling and Sharing Problem. Int J Mol Sci 2021; 22:ijms22105176. [PMID: 34068386 PMCID: PMC8153597 DOI: 10.3390/ijms22105176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 11/16/2022] Open
Abstract
(1) Background: Properties and descriptors are two forms of molecular in silico representations. Properties can be further divided into functional, e.g., catalyst or drug activity, and material, e.g., X-ray crystal data. Millions of real measured functional property records are available for drugs or drug candidates in online databases. In contrast, there is not a single database that registers a real conversion, TON or TOF data for catalysts. All of the data are molecular descriptors or material properties, which are mainly of a calculation origin. (2) Results: Here, we explain the reason for this. We reviewed the data handling and sharing problems in the design and discovery of catalyst candidates particularly, material informatics and catalyst design, structural coding, data collection and validation, infrastructure for catalyst design and the online databases for catalyst design. (3) Conclusions: Material design requires a property prediction step. This can only be achieved based on the registered real property measurement. In reality, in catalyst design and discovery, we can observe either a severe functional property deficit or even property famine.
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Affiliation(s)
- Daniel Lach
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia, Szkolna 9, 40-006 Katowice, Poland; (D.L.); (U.Z.)
| | - Uladzislau Zhdan
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia, Szkolna 9, 40-006 Katowice, Poland; (D.L.); (U.Z.)
| | - Adam Smolinski
- Central Mining Institute, Plac Gwarkow 1, 40-166 Katowice, Poland;
| | - Jaroslaw Polanski
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia, Szkolna 9, 40-006 Katowice, Poland; (D.L.); (U.Z.)
- Correspondence: ; Tel.: +48-32-259-9978
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10
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Chain Transfer to Solvent and Monomer in Early Transition Metal Catalyzed Olefin Polymerization: Mechanisms and Implications for Catalysis. Catalysts 2021. [DOI: 10.3390/catal11020215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Even after several decades of intense research, mechanistic studies of olefin polymerization by early transition metal catalysts continue to reveal unexpected elementary reaction steps. In this mini-review, the recent discovery of two unprecedented chain termination processes is summarized: chain transfer to solvent (CTS) and chain transfer to monomer (CTM), leading to benzyl/tolyl and allyl type chain ends, respectively. Although similar transfer reactions are well-known in radical polymerization, only very recently they have been observed also in olefin insertion polymerization catalysis. In the latter context, these processes were first identified in Ti-catalyzed propene and ethene polymerization; more recently, CTS was also reported in Sc-catalyzed styrene polymerization. In the Ti case, these processes represent a unique combination of insertion polymerization, organic radical chemistry and reactivity of a M(IV)/M(III) redox couple. In the Sc case, CTS occurs via a σ-bond metathesis reactivity, and it is associated with a significant boost of catalytic activity and/or with tuning of polystyrene molecular weight and tacticity. The mechanistic studies that led to the understanding of these chain transfer reactions are summarized, highlighting their relevance in olefin polymerization catalysis and beyond.
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Ratanasak M, Hasegawa JY, Parasuk V. Design and prediction of high potent ansa-zirconocene catalyst for olefin polymerizations: combined DFT calculations and QSPR approach. NEW J CHEM 2021. [DOI: 10.1039/d1nj00655j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Density functional calculations were carried out to predict activities, regio- and stereoselectivity, and to design new ansa-zirconocene catalysts for olefin polymerizations.
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Affiliation(s)
- Manussada Ratanasak
- Institute for Catalysis
- Hokkaido University
- Hokkaido 001-0021
- Japan
- Center of Excellence in Computational Chemistry
| | - Jun-ya Hasegawa
- Institute for Catalysis
- Hokkaido University
- Hokkaido 001-0021
- Japan
| | - Vudhichai Parasuk
- Center of Excellence in Computational Chemistry
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
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12
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Balcells D, Skjelstad BB. tmQM Dataset-Quantum Geometries and Properties of 86k Transition Metal Complexes. J Chem Inf Model 2020; 60:6135-6146. [PMID: 33166143 PMCID: PMC7768608 DOI: 10.1021/acs.jcim.0c01041] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Indexed: 12/19/2022]
Abstract
We report the transition metal quantum mechanics (tmQM) data set, which contains the geometries and properties of a large transition metal-organic compound space. tmQM comprises 86,665 mononuclear complexes extracted from the Cambridge Structural Database, including Werner, bioinorganic, and organometallic complexes based on a large variety of organic ligands and 30 transition metals (the 3d, 4d, and 5d from groups 3 to 12). All complexes are closed-shell, with a formal charge in the range {+1, 0, -1}e. The tmQM data set provides the Cartesian coordinates of all metal complexes optimized at the GFN2-xTB level, and their molecular size, stoichiometry, and metal node degree. The quantum properties were computed at the DFT(TPSSh-D3BJ/def2-SVP) level and include the electronic and dispersion energies, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies, HOMO/LUMO gap, dipole moment, and natural charge of the metal center; GFN2-xTB polarizabilities are also provided. Pairwise representations showed the low correlation between these properties, providing nearly continuous maps with unusual regions of the chemical space, for example, complexes combining large polarizabilities with wide HOMO/LUMO gaps and complexes combining low-energy HOMO orbitals with electron-rich metal centers. The tmQM data set can be exploited in the data-driven discovery of new metal complexes, including predictive models based on machine learning. These models may have a strong impact on the fields in which transition metal chemistry plays a key role, for example, catalysis, organic synthesis, and materials science. tmQM is an open data set that can be downloaded free of charge from https://github.com/bbskjelstad/tmqm.
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Affiliation(s)
- David Balcells
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Bastian Bjerkem Skjelstad
- Institute
for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
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13
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Mdluli V, Diluzio S, Lewis J, Kowalewski JF, Connell TU, Yaron D, Kowalewski T, Bernhard S. High-throughput Synthesis and Screening of Iridium(III) Photocatalysts for the Fast and Chemoselective Dehalogenation of Aryl Bromides. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02247] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Velabo Mdluli
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Stephen Diluzio
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jacqueline Lewis
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jakub F. Kowalewski
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Timothy U. Connell
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - David Yaron
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Tomasz Kowalewski
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Stefan Bernhard
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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14
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Friederich P, Dos Passos Gomes G, De Bin R, Aspuru-Guzik A, Balcells D. Machine learning dihydrogen activation in the chemical space surrounding Vaska's complex. Chem Sci 2020; 11:4584-4601. [PMID: 33224459 PMCID: PMC7659707 DOI: 10.1039/d0sc00445f] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/06/2020] [Indexed: 12/15/2022] Open
Abstract
Homogeneous catalysis using transition metal complexes is ubiquitously used for organic synthesis, as well as technologically relevant in applications such as water splitting and CO2 reduction. The key steps underlying homogeneous catalysis require a specific combination of electronic and steric effects from the ligands bound to the metal center. Finding the optimal combination of ligands is a challenging task due to the exceedingly large number of possibilities and the non-trivial ligand-ligand interactions. The classic example of Vaska's complex, trans-[Ir(PPh3)2(CO)(Cl)], illustrates this scenario. The ligands of this species activate iridium for the oxidative addition of hydrogen, yielding the dihydride cis-[Ir(H)2(PPh3)2(CO)(Cl)] complex. Despite the simplicity of this system, thousands of derivatives can be formulated for the activation of H2, with a limited number of ligands belonging to the same general categories found in the original complex. In this work, we show how DFT and machine learning (ML) methods can be combined to enable the prediction of reactivity within large chemical spaces containing thousands of complexes. In a space of 2574 species derived from Vaska's complex, data from DFT calculations are used to train and test ML models that predict the H2-activation barrier. In contrast to experiments and calculations requiring several days to be completed, the ML models were trained and used on a laptop on a time-scale of minutes. As a first approach, we combined Bayesian-optimized artificial neural networks (ANN) with features derived from autocorrelation and deltametric functions. The resulting ANNs achieved high accuracies, with mean absolute errors (MAE) between 1 and 2 kcal mol-1, depending on the size of the training set. By using a Gaussian process (GP) model trained with a set of selected features, including fingerprints, accuracy was further enhanced. Remarkably, this GP model minimized the MAE below 1 kcal mol-1, by using only 20% or less of the data available for training. The gradient boosting (GB) method was also used to assess the relevance of the features, which was used for both feature selection and model interpretation purposes. Features accounting for chemical composition, atom size and electronegativity were found to be the most determinant in the predictions. Further, the ligand fragments with the strongest influence on the H2-activation barrier were identified.
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Affiliation(s)
- Pascal Friederich
- Chemical Physics Theory Group , Department of Chemistry , University of Toronto , Toronto , Ontario M5S 3H6 , Canada
- Institute of Nanotechnology , Karlsruhe Institute of Technology , Hermann-von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany
- Department of Computer Science , University of Toronto , 214 College St. , Toronto , Ontario M5T 3A1 , Canada
| | - Gabriel Dos Passos Gomes
- Chemical Physics Theory Group , Department of Chemistry , University of Toronto , Toronto , Ontario M5S 3H6 , Canada
- Department of Computer Science , University of Toronto , 214 College St. , Toronto , Ontario M5T 3A1 , Canada
| | - Riccardo De Bin
- Department of Mathematics , University of Oslo , P. O. Box 1053, Blindern , N-0316 , Oslo , Norway
| | - Alán Aspuru-Guzik
- Chemical Physics Theory Group , Department of Chemistry , University of Toronto , Toronto , Ontario M5S 3H6 , Canada
- Department of Computer Science , University of Toronto , 214 College St. , Toronto , Ontario M5T 3A1 , Canada
- Vector Institute for Artificial Intelligence , 661 University Ave. Suite 710 , Toronto , Ontario M5G 1M1 , Canada
- Lebovic Fellow , Canadian Institute for Advanced Research (CIFAR) , 661 University Ave , Toronto , ON M5G 1M1 , Canada
| | - David Balcells
- Hylleraas Centre for Quantum Molecular Sciences , Department of Chemistry , University of Oslo , P. O. Box 1033, Blindern , N-0315 , Oslo , Norway .
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15
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Yang W, Fidelis TT, Sun WH. Prediction of catalytic activities of bis(imino)pyridine metal complexes by machine learning. J Comput Chem 2020; 41:1064-1067. [PMID: 32022293 DOI: 10.1002/jcc.26160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/12/2020] [Accepted: 01/15/2020] [Indexed: 11/07/2022]
Abstract
This work demonstrates the potential of machine learning (ML) method to predict catalytic activity of transition metal complex precatalyst toward ethylene polymerization. For this purpose, 294 complexes and 15 molecular descriptors were selected to build the artificial neural network (ANN) model. The catalytic activity can be well predicted by the obtained ANN model, which was further validated by external complexes. Boruta algorithm was employed to explicitly decipher the importance of descriptors, illustrating the conjugated bond structure, and bulky substitutions are favorable for catalytic activity. The present work indicates that ML could give useful guidance for the new design of homogenous polyolefin catalyst.
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Affiliation(s)
- Wenhong Yang
- Key Laboratory of Engineering Plastics and Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Timothy Tizhe Fidelis
- Key Laboratory of Engineering Plastics and Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Hua Sun
- Key Laboratory of Engineering Plastics and Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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16
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Ehm C, Vittoria A, Goryunov GP, Izmer VV, Kononovich DS, Samsonov OV, Di Girolamo R, Budzelaar PHM, Voskoboynikov AZ, Busico V, Uborsky DV, Cipullo R. An Integrated High Throughput Experimentation/Predictive QSAR Modeling Approach to ansa-Zirconocene Catalysts for Isotactic Polypropylene. Polymers (Basel) 2020; 12:E1005. [PMID: 32349220 PMCID: PMC7284373 DOI: 10.3390/polym12051005] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/11/2020] [Accepted: 04/18/2020] [Indexed: 12/16/2022] Open
Abstract
Compared to heterogenous Ziegler-Natta systems (ZNS), ansa-metallocene catalysts for the industrial production of isotactic polypropylene feature a higher cost-to-performance balance. In particular, the C2-symmetric bis(indenyl) ansa-zirconocenes disclosed in the 1990s are complex to prepare, less stereo- and/or regioselective than ZNS, and lose performance at practical application temperatures. The golden era of these complexes, though, was before High Throughput Experimentation (HTE) could contribute significantly to their evolution. Herein, we illustrate a Quantitative Structure - Activity Relationship (QSAR) model trained on a robust and highly accurate HTE database. The clear-box QSAR model utilizes, in particular, a limited number of chemically intuitive 3D geometric descriptors that screen various regions of space in and around the catalytic pocket in a modular way thus enabling to quantify individual substituent contributions. The main focus of the paper is on the methodology, which should be of rather broad applicability in molecular organometallic catalysis. Then again, it is worth emphasizing that the specific application reported here led us to identify in a comparatively short time novel zirconocene catalysts rivaling or even outperforming all previous homologues which strongly indicates that the metallocene story is not over yet.
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Affiliation(s)
- Christian Ehm
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia, 80126 Napoli, Italy; (A.V.); (R.D.G.); (P.H.M.B.); (V.B.)
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Antonio Vittoria
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia, 80126 Napoli, Italy; (A.V.); (R.D.G.); (P.H.M.B.); (V.B.)
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Georgy P. Goryunov
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia; (G.P.G.); (V.V.I.); (D.S.K.); (O.V.S.); (A.Z.V.)
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Vyatcheslav V. Izmer
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia; (G.P.G.); (V.V.I.); (D.S.K.); (O.V.S.); (A.Z.V.)
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Dmitry S. Kononovich
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia; (G.P.G.); (V.V.I.); (D.S.K.); (O.V.S.); (A.Z.V.)
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Oleg V. Samsonov
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia; (G.P.G.); (V.V.I.); (D.S.K.); (O.V.S.); (A.Z.V.)
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Rocco Di Girolamo
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia, 80126 Napoli, Italy; (A.V.); (R.D.G.); (P.H.M.B.); (V.B.)
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Peter H. M. Budzelaar
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia, 80126 Napoli, Italy; (A.V.); (R.D.G.); (P.H.M.B.); (V.B.)
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Alexander Z. Voskoboynikov
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia; (G.P.G.); (V.V.I.); (D.S.K.); (O.V.S.); (A.Z.V.)
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Vincenzo Busico
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia, 80126 Napoli, Italy; (A.V.); (R.D.G.); (P.H.M.B.); (V.B.)
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Dmitry V. Uborsky
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia; (G.P.G.); (V.V.I.); (D.S.K.); (O.V.S.); (A.Z.V.)
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Roberta Cipullo
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia, 80126 Napoli, Italy; (A.V.); (R.D.G.); (P.H.M.B.); (V.B.)
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
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17
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Affiliation(s)
- Marco Foscato
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Vidar R. Jensen
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
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18
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Yang W, Fidelis TT, Sun WH. Machine Learning in Catalysis, From Proposal to Practicing. ACS OMEGA 2020; 5:83-88. [PMID: 31956754 PMCID: PMC6963892 DOI: 10.1021/acsomega.9b03673] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/10/2019] [Indexed: 05/05/2023]
Abstract
Recently, machine learning (ML) methods have gained popularity and have performed as powerfully predictive tools in various areas of academic and industrious activities. In comparison, their application in catalysis has been underdeveloped. Relying on the rapid development of different algorithms and their implementation, it is the right timing to harvest the potential of ML in catalysis across academy and industry spectra. Herein, we discuss the current applications in the field of homogeneous and heterogeneous catalysis by using various ML approaches. To the best of our knowledge, modern statistical learning techniques will be a strong tool for computational optimization and discovery. This in turn will accurately extract the underlying mechanism in the model that converts readily available data and precatalysts into their promising and useful ones.
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Affiliation(s)
- Wenhong Yang
- Key
Laboratory of Engineering Plastics and Beijing National Laboratory
for Molecular Science, Institute of Chemistry,
Chinese Academy of Sciences, Beijing 100190, China
- CAS
Research/Education Center for Excellence in Molecular Sciences and
International School, University of Chinese
Academy of Sciences, Beijing 100049, China
| | - Timothy Tizhe Fidelis
- Key
Laboratory of Engineering Plastics and Beijing National Laboratory
for Molecular Science, Institute of Chemistry,
Chinese Academy of Sciences, Beijing 100190, China
- CAS
Research/Education Center for Excellence in Molecular Sciences and
International School, University of Chinese
Academy of Sciences, Beijing 100049, China
| | - Wen-Hua Sun
- Key
Laboratory of Engineering Plastics and Beijing National Laboratory
for Molecular Science, Institute of Chemistry,
Chinese Academy of Sciences, Beijing 100190, China
- CAS
Research/Education Center for Excellence in Molecular Sciences and
International School, University of Chinese
Academy of Sciences, Beijing 100049, China
- E-mail:
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19
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Ehm C, Vittoria A, Goryunov GP, Izmer VV, Kononovich DS, Samsonov OV, Budzelaar PHM, Voskoboynikov AZ, Busico V, Uborsky DV, Cipullo R. On the limits of tuning comonomer affinity of ‘Spaleck-type’ ansa-zirconocenes in ethene/1-hexene copolymerization: a high-throughput experimentation/QSAR approach. Dalton Trans 2020; 49:10162-10172. [DOI: 10.1039/d0dt01967d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A change in rate-limiting step imparts a natural limit for comonomer affinity of C2-symmetric zirconocenes.
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20
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Rizkin BA, Hartman RL. Supervised machine learning for prediction of zirconocene-catalyzed α-olefin polymerization. Chem Eng Sci 2019. [DOI: 10.1016/j.ces.2019.115224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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Zhang X, Mao J, Li W, Koike K, Wang J. Improved 3D-QSAR prediction by multiple-conformational alignment: A case study on PTP1B inhibitors. Comput Biol Chem 2019; 83:107134. [DOI: 10.1016/j.compbiolchem.2019.107134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 08/01/2019] [Accepted: 09/18/2019] [Indexed: 10/25/2022]
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22
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Tukur S, Shallangwa GA, Ibrahim A. Theoretical QSAR modelling and molecular docking studies of some 4-hydroxyphenylpyruvate dioxygenase (HPPD) enzyme inhibitors potentially used as herbicides. Heliyon 2019; 5:e02859. [PMID: 31768442 PMCID: PMC6872840 DOI: 10.1016/j.heliyon.2019.e02859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/29/2019] [Accepted: 11/13/2019] [Indexed: 12/01/2022] Open
Abstract
Computational QSAR studies together with molecular docking calculations have been performed on 118 different derivatives of organic molecules potentially used as herbicides. The Becke's three parameter exchange functional (B3) hybrid with Lee, Yang and Parr correlation functional (LYP), termed as B3LYP hybrid function and 6-31G* basis set (B3LYP/6-31G*) were used to develop five models of QSAR using the GFA technique. Models 1, was preferred as the best model because it possesses certain statistical implications (Friedman LOF = 0.52567, R2 = 0.9034, Radjst2= 0.8943, QCV2= 0.87 98 and Rpred.2= 0.8403).” The prepared model was validated internally and externally using training and test inhibitors. The molecular docking studies conducted in this study has actually outline the binding affinities of the 10 selected compounds (5, 25, 26, 27, 29, 35, 52, 55, 98 and 114) which were all in good correlation with their pIC50 values. The binding affinities of the 10 selected compounds range between -5.9 kcal/mol to -10.1 kcal/mol. The compounds 25 and 27 with binding affinities of -10.1 kcal/mol and -9.7 kcal/mol formed the most stable complexes with the receptor (HPPD) as compared to other inhibitors. The complexes of these inhibitors show two most important types of bonding; Hydrogen bonding and hydrophobic bond interaction with the target amino acid residues. The computational QSAR study together with the molecular docking has actually provided a valuable approach for agrochemical researchers in synthesizing and developing new herbicides with high potency against the target enzyme.
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Affiliation(s)
- Saidu Tukur
- Faculty of Physical Sciences, Chemistry Department, Ahmadu Bello University, P.M.B. 1044, Zaria, Kaduna State, Nigeria
| | - Gideon Adamu Shallangwa
- Faculty of Physical Sciences, Chemistry Department, Ahmadu Bello University, P.M.B. 1044, Zaria, Kaduna State, Nigeria
| | - Abdulkadir Ibrahim
- Faculty of Physical Sciences, Chemistry Department, Ahmadu Bello University, P.M.B. 1044, Zaria, Kaduna State, Nigeria
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23
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Parveen R, Cundari TR, Younker JM, Rodriguez G, McCullough L. DFT and QSAR Studies of Ethylene Polymerization by Zirconocene Catalysts. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02925] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Riffat Parveen
- Department of Chemistry and Center of Advanced Scientific Computing and Modeling, University of North Texas, 1155 Union Circle #305070, Denton, Texas 6203-5017, United States
| | - Thomas R. Cundari
- Department of Chemistry and Center of Advanced Scientific Computing and Modeling, University of North Texas, 1155 Union Circle #305070, Denton, Texas 6203-5017, United States
| | - Jarod M. Younker
- ExxonMobil Chemical Company, 5200 Bayway Drive, Baytown, Texas 77520, United States
| | - George Rodriguez
- ExxonMobil Chemical Company, 5200 Bayway Drive, Baytown, Texas 77520, United States
| | - Laughlin McCullough
- ExxonMobil Chemical Company, 5200 Bayway Drive, Baytown, Texas 77520, United States
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24
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A screening DFT study of the para-substituent effect on local hyper-softness in bis(phenoxy-imine) titanium complexes to get insights about their catalytic activity in ethylene polymerization. MOLECULAR CATALYSIS 2019. [DOI: 10.1016/j.mcat.2019.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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25
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Janet JP, Liu F, Nandy A, Duan C, Yang T, Lin S, Kulik HJ. Designing in the Face of Uncertainty: Exploiting Electronic Structure and Machine Learning Models for Discovery in Inorganic Chemistry. Inorg Chem 2019; 58:10592-10606. [PMID: 30834738 DOI: 10.1021/acs.inorgchem.9b00109] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent transformative advances in computing power and algorithms have made computational chemistry central to the discovery and design of new molecules and materials. First-principles simulations are increasingly accurate and applicable to large systems with the speed needed for high-throughput computational screening. Despite these strides, the combinatorial challenges associated with the vastness of chemical space mean that more than just fast and accurate computational tools are needed for accelerated chemical discovery. In transition-metal chemistry and catalysis, unique challenges arise. The variable spin, oxidation state, and coordination environments favored by elements with well-localized d or f electrons provide great opportunity for tailoring properties in catalytic or functional (e.g., magnetic) materials but also add layers of uncertainty to any design strategy. We outline five key mandates for realizing computationally driven accelerated discovery in inorganic chemistry: (i) fully automated simulation of new compounds, (ii) knowledge of prediction sensitivity or accuracy, (iii) faster-than-fast property prediction methods, (iv) maps for rapid chemical space traversal, and (v) a means to reveal design rules on the kilocompound scale. Through case studies in open-shell transition-metal chemistry, we describe how advances in methodology and software in each of these areas bring about new chemical insights. We conclude with our outlook on the next steps in this process toward realizing fully autonomous discovery in inorganic chemistry using computational chemistry.
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Affiliation(s)
- Jon Paul Janet
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Fang Liu
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Aditya Nandy
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.,Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Chenru Duan
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.,Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Tzuhsiung Yang
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Sean Lin
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Heather J Kulik
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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26
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Yang W, Ma Z, Yi J, Ahmed S, Sun WH. Catalytic performance of bis(imino)pyridine Fe/Co complexes toward ethylene polymerization by 2D-/3D-QSPR modeling. J Comput Chem 2019; 40:1374-1386. [PMID: 30697785 DOI: 10.1002/jcc.25792] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/08/2019] [Accepted: 01/11/2019] [Indexed: 01/23/2023]
Abstract
The two-dimensional and three-dimensional quantitative structure-property relationship (2D- and 3D-QSPR) approaches are applied to investigate the catalytic performance for a total data set of 55 bis(imino)pryridine iron and cobalt complexes, including the catalytic activity, molecular weight, and melting temperature of the product. The obtained models for the catalytic performance of interest exhibit good results by both 2D- and 3D-QSPR modeling, meanwhile higher predictive and validation powers observed in the 3D type. The modeling results indicate that the bulky substituents on ortho-position of the singular side phenyl ring and positive charge on para-position of the phenyl ring within the ligand are favorable to catalytic activity, while unfavorable to the molecular weight of product. Based on the obtained QSPR models, four new complexes are designed and predicted with good catalytic activity and very high molecular weight, which are in good agreement with our recent experimental report. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Wenhong Yang
- Key laboratory of Engineering Plastics and Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,CAS Research/Education Center for Excellence in Molecular Sciences and International School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhifeng Ma
- Key laboratory of Engineering Plastics and Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,Department of Chemistry, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Jun Yi
- Key laboratory of Engineering Plastics and Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,Department of Chemistry, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Sadia Ahmed
- Key laboratory of Engineering Plastics and Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,CAS Research/Education Center for Excellence in Molecular Sciences and International School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Hua Sun
- Key laboratory of Engineering Plastics and Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,CAS Research/Education Center for Excellence in Molecular Sciences and International School, University of Chinese Academy of Sciences, Beijing 100049, China
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27
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Zahrt AF, Henle JJ, Rose BT, Wang Y, Darrow WT, Denmark SE. Prediction of higher-selectivity catalysts by computer-driven workflow and machine learning. Science 2019; 363:363/6424/eaau5631. [PMID: 30655414 DOI: 10.1126/science.aau5631] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 12/03/2018] [Indexed: 12/18/2022]
Abstract
Catalyst design in asymmetric reaction development has traditionally been driven by empiricism, wherein experimentalists attempt to qualitatively recognize structural patterns to improve selectivity. Machine learning algorithms and chemoinformatics can potentially accelerate this process by recognizing otherwise inscrutable patterns in large datasets. Herein we report a computationally guided workflow for chiral catalyst selection using chemoinformatics at every stage of development. Robust molecular descriptors that are agnostic to the catalyst scaffold allow for selection of a universal training set on the basis of steric and electronic properties. This set can be used to train machine learning methods to make highly accurate predictive models over a broad range of selectivity space. Using support vector machines and deep feed-forward neural networks, we demonstrate accurate predictive modeling in the chiral phosphoric acid-catalyzed thiol addition to N-acylimines.
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Affiliation(s)
- Andrew F Zahrt
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Jeremy J Henle
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Brennan T Rose
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Yang Wang
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - William T Darrow
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Scott E Denmark
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL 61801, USA.
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28
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Ehm C, Vittoria A, Goryunov GP, Kulyabin PS, Budzelaar PHM, Voskoboynikov AZ, Busico V, Uborsky DV, Cipullo R. Connection of Stereoselectivity, Regioselectivity, and Molecular Weight Capability in rac-R′2Si(2-Me-4-R-indenyl)2ZrCl2 Type Catalysts. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01546] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Christian Ehm
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia, 80126 Napoli, Italy
- DPI, P.O. Box 902, 5600 AX Eindhoven, the Netherlands
| | - Antonio Vittoria
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia, 80126 Napoli, Italy
- DPI, P.O. Box 902, 5600 AX Eindhoven, the Netherlands
| | - Georgy P. Goryunov
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia
- DPI, P.O. Box 902, 5600 AX Eindhoven, the Netherlands
| | - Pavel S. Kulyabin
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia
- DPI, P.O. Box 902, 5600 AX Eindhoven, the Netherlands
| | - Peter H. M. Budzelaar
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia, 80126 Napoli, Italy
- DPI, P.O. Box 902, 5600 AX Eindhoven, the Netherlands
| | - Alexander Z. Voskoboynikov
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia
- DPI, P.O. Box 902, 5600 AX Eindhoven, the Netherlands
| | - Vincenzo Busico
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia, 80126 Napoli, Italy
- DPI, P.O. Box 902, 5600 AX Eindhoven, the Netherlands
| | - Dmitry V. Uborsky
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia
- DPI, P.O. Box 902, 5600 AX Eindhoven, the Netherlands
| | - Roberta Cipullo
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia, 80126 Napoli, Italy
- DPI, P.O. Box 902, 5600 AX Eindhoven, the Netherlands
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29
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Straightforward Design for Phenoxy-Imine Catalytic Activity in Ethylene Polymerization: Theoretical Prediction. Catalysts 2018. [DOI: 10.3390/catal8100422] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The quantitative structure-activity relationship (QSAR) of 18 Ti-phenoxy-imine (FI-Ti)-based catalysts was investigated to clarify the role of the structural properties of the catalysts in polyethylene polymerization activity. The electronic properties of the FI-Ti catalysts were analyzed based on density functional theory with the M06L/6-31G** and LANL2DZ basis functions. The analysis results of the QSAR equation with a genetic algorithm showed that the polyethylene catalytic activity mainly depended on the highest occupied molecular orbital energy level and the total charge of the substituent group on phenylimine ring. The QSAR models showed good predictive ability (R2) and R2 cross validation (R2cv) values of greater than 0.927. The design concept is “head-hat”, where the hats are the phenoxy-imine substituents, and the heads are the transition metals. Thus, for the newly designed series, the phenoxy-imine substituents still remained, while the Ti metal was replaced by Zr or Ni transition metals, entitled FI-Zr and FI-Ni, respectively. Consequently, their polyethylene polymerization activities were predicted based on the obtained QSAR of the FI-Ti models, and it is noteworthy that the FI-Ni metallocene catalysts tend to increase the polyethylene catalytic activity more than that of FI-Zr complexes. Therefore, the new designs of the FI-Ni series are proposed as candidate catalysts for polyethylene polymerization, with their predicted activities in the range of 35,000–48,000 kg(PE)/mol(Cat.)·MPa·h. This combined density functional theory and QSAR analysis is useful and straightforward for molecular design or catalyst screening, especially in industrial research.
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30
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Wang H, Zhang P, Zhou P, Xu R, Tang Y. Factors Affecting Dehydrogenation and Catalytic Activity: Methyl Substituent. Catal Letters 2018. [DOI: 10.1007/s10562-018-2461-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Zaccaria F, Ehm C, Budzelaar PHM, Busico V, Cipullo R. Catalyst Mileage in Olefin Polymerization: The Peculiar Role of Toluene. Organometallics 2018. [DOI: 10.1021/acs.organomet.8b00393] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco Zaccaria
- Università di Napoli Federico II, Dipartimento di Scienze Chimiche, Via Cintia, 80126 Napoli, Italy
| | - Christian Ehm
- Università di Napoli Federico II, Dipartimento di Scienze Chimiche, Via Cintia, 80126 Napoli, Italy
| | - Peter H. M. Budzelaar
- Università di Napoli Federico II, Dipartimento di Scienze Chimiche, Via Cintia, 80126 Napoli, Italy
| | - Vincenzo Busico
- Università di Napoli Federico II, Dipartimento di Scienze Chimiche, Via Cintia, 80126 Napoli, Italy
| | - Roberta Cipullo
- Università di Napoli Federico II, Dipartimento di Scienze Chimiche, Via Cintia, 80126 Napoli, Italy
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32
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Yang Q, Qu Z, Selek D, Zhang S. Study on the Anti-Endometrial Cancer Activity of a Series of 4,6-Diaryl-2-pyrimidinamine Derivatives against Endometrial Carcinoma Ishikawa Cell and Their Molecular Design. ChemistrySelect 2018. [DOI: 10.1002/slct.201801405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Qi Yang
- College of Science; University of Shanghai for Science and Technology; 516 Jungong Rd. Shanghai 200093 china
| | - Ziwei Qu
- School of Medical Instrument and Food Engineering; University of Shanghai for Science and Technology; 516 Jungong Rd. Shanghai 200093 china
| | - Danibai Selek
- The product quality testing institute of yili kazakh autonomous prefecture; xinjiang 835000 china
| | - Shuping Zhang
- College of Science; University of Shanghai for Science and Technology; 516 Jungong Rd. Shanghai 200093 china
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33
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Janet JP, Chan L, Kulik HJ. Accelerating Chemical Discovery with Machine Learning: Simulated Evolution of Spin Crossover Complexes with an Artificial Neural Network. J Phys Chem Lett 2018; 9:1064-1071. [PMID: 29425453 DOI: 10.1021/acs.jpclett.8b00170] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Machine learning (ML) has emerged as a powerful complement to simulation for materials discovery by reducing time for evaluation of energies and properties at accuracy competitive with first-principles methods. We use genetic algorithm (GA) optimization to discover unconventional spin-crossover complexes in combination with efficient scoring from an artificial neural network (ANN) that predicts spin-state splitting of inorganic complexes. We explore a compound space of over 5600 candidate materials derived from eight metal/oxidation state combinations and a 32-ligand pool. We introduce a strategy for error-aware ML-driven discovery by limiting how far the GA travels away from the nearest ANN training points while maximizing property (i.e., spin-splitting) fitness, leading to discovery of 80% of the leads from full chemical space enumeration. Over a 51-complex subset, average unsigned errors (4.5 kcal/mol) are close to the ANN's baseline 3 kcal/mol error. By obtaining leads from the trained ANN within seconds rather than days from a DFT-driven GA, this strategy demonstrates the power of ML for accelerating inorganic material discovery.
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Affiliation(s)
- Jon Paul Janet
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Lydia Chan
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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34
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Ramos J, Vega J, Martínez-Salazar J. Predicting experimental results for polyethylene by computer simulation. Eur Polym J 2018. [DOI: 10.1016/j.eurpolymj.2017.12.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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Yamaguchi S, Nishimura T, Hibe Y, Nagai M, Sato H, Johnston I. Regularized regression analysis of digitized molecular structures in organic reactions for quantification of steric effects. J Comput Chem 2017; 38:1825-1833. [DOI: 10.1002/jcc.24791] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/03/2017] [Accepted: 03/05/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Shigeru Yamaguchi
- RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Takahiro Nishimura
- Department of Chemistry; Graduate School of Science, Kyoto University; Sakyo-ku Kyoto 606-8502 Japan
| | - Yuta Hibe
- Department of Chemistry; Graduate School of Science, Kyoto University; Sakyo-ku Kyoto 606-8502 Japan
| | - Masaki Nagai
- Department of Chemistry; Graduate School of Science, Kyoto University; Sakyo-ku Kyoto 606-8502 Japan
| | - Hirofumi Sato
- Department of Molecular Engineering; Graduate School of Engineering, Kyoto University; Nishikyo-ku Kyoto 610-8510 Japan
| | - Ian Johnston
- Department of Mathematics and Statistics; Boston University; 111 Cummington Mall Boston Massachusetts 02215
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36
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Tanaka R, Nakayama Y, Shiono T. Theoretical investigation of the mechanism of syndiospecific propylene polymerization using ansa-dimethylsilylene(fluorenyl)(amido)titanium complexes. J Organomet Chem 2016. [DOI: 10.1016/j.jorganchem.2016.09.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Minaev B, Baryshnikova A, Sun WH. Spin-dependent effects in ethylene polymerization with bis(imino)pyridine iron(II) complexes. J Organomet Chem 2016. [DOI: 10.1016/j.jorganchem.2016.03.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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38
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Gao X, Han L, Ren Y. In Silico Exploration of 1,7-Diazacarbazole Analogs as Checkpoint Kinase 1 Inhibitors by Using 3D QSAR, Molecular Docking Study, and Molecular Dynamics Simulations. Molecules 2016; 21:molecules21050591. [PMID: 27164065 PMCID: PMC6273173 DOI: 10.3390/molecules21050591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 04/11/2016] [Accepted: 04/28/2016] [Indexed: 12/11/2022] Open
Abstract
Checkpoint kinase 1 (Chk1) is an important serine/threonine kinase with a self-protection function. The combination of Chk1 inhibitors and anti-cancer drugs can enhance the selectivity of tumor therapy. In this work, a set of 1,7-diazacarbazole analogs were identified as potent Chk1 inhibitors through a series of computer-aided drug design processes, including three-dimensional quantitative structure–activity relationship (3D-QSAR) modeling, molecular docking, and molecular dynamics simulations. The optimal QSAR models showed significant cross-validated correlation q2 values (0.531, 0.726), fitted correlation r2 coefficients (higher than 0.90), and standard error of prediction (less than 0.250). These results suggested that the developed models possess good predictive ability. Moreover, molecular docking and molecular dynamics simulations were applied to highlight the important interactions between the ligand and the Chk1 receptor protein. This study shows that hydrogen bonding and electrostatic forces are key interactions that confer bioactivity.
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Affiliation(s)
- Xiaodong Gao
- School of Chemistry and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
| | - Liping Han
- School of Chemistry and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
| | - Yujie Ren
- School of Chemistry and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
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39
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Quantitative structure–property relationships in propene polymerization by zirconocenes with a rac-SiMe2[Ind]2 based ligand framework. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcata.2015.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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40
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Li L, Pan Y, Lei M. The enantioselectivity in asymmetric ketone hydrogenation catalyzed by RuH2(diphosphine)(diamine) complexes: insights from a 3D-QSSR and DFT study. Catal Sci Technol 2016. [DOI: 10.1039/c5cy01225b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 3D-QSSR method was carried out to investigate the enantioselectivity of the asymmetric ketone hydrogenation (AKH) catalyzed by RuH2(diphosphine)(diamine) complexes integrating with DFT method, which could provide a way to design homogeneous transition-metal catalysts.
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Affiliation(s)
- Longfei Li
- State Key Laboratory of Chemical Resource Engineering
- Institute of Materia Medica
- College of Science
- Beijing University of Chemical Technology
- Beijing
| | - Yuhui Pan
- State Key Laboratory of Chemical Resource Engineering
- Institute of Materia Medica
- College of Science
- Beijing University of Chemical Technology
- Beijing
| | - Ming Lei
- State Key Laboratory of Chemical Resource Engineering
- Institute of Materia Medica
- College of Science
- Beijing University of Chemical Technology
- Beijing
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41
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Yang W, Yi J, Sun WH. Revisiting Benzylidenequinolinylnickel Catalysts through the Electronic Effects on Catalytic Activity by DFT Studies. MACROMOL CHEM PHYS 2015. [DOI: 10.1002/macp.201500028] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wenhong Yang
- Key laboratory of Engineering Plastics and Beijing National Laboratory for Molecular Science; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
| | - Jun Yi
- Key laboratory of Engineering Plastics and Beijing National Laboratory for Molecular Science; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
| | - Wen-Hua Sun
- Key laboratory of Engineering Plastics and Beijing National Laboratory for Molecular Science; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
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42
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Bravo I, Alonso-Moreno C, Carrillo-Hermosilla F, López-Solera I, Antiñolo A, Albaladejo J. Toward the Prediction of Activity in the Ethylene Polymerisation of ansa-Bis(indenyl) Zirconocenes: Effect of the Stereochemistry and Hydrogenation of the Indenyl Moiety. Chempluschem 2015; 80:963-972. [PMID: 31973254 DOI: 10.1002/cplu.201500008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Indexed: 11/06/2022]
Abstract
A combined experimental and quantum chemical study has been performed on rac- and meso-[Zr{1-Me2 Si(3-η5 -C9 H5 Et)2 }Cl2 ] (rac- and meso-1) and their hydrogenated forms (rac- and meso-2) to understand ligand effects and guide ligand design for more active ansa-bis(indenyl) zirconocenes for the polymerisation of ethylene. The rac-ansa-zirconocene rac-[Zr(1-Me2 Si{3-Et-(η5 -C9 H9 )}2 )Cl2 ] (rac-2) has been prepared and fully characterised by NMR spectroscopy and elemental analysis. The molecular structure of rac-2 has also been determined by single-crystal XRD. The behaviour of the catalysts was analysed in the polymerisation of ethylene and higher activities were obtained for rac-1 and its hydrogenated form rac-2. The influence of the stereochemistry and hydrogenation of the indenyl ligand on the experimental activities has been evaluated by computational studies. The differences along the reaction pathway are dominated by changes in the relative stabilities of the catalytic intermediates. A hybrid density functional B3LYP study, in the presence of toluene as the solvent, indicates that the rac forms give rise to more active species than their meso counterparts. The hydrogenation of the rac forms is a very promising approach to increase activities in polymerisation, in contrast to the meso forms. Finally, the global mechanism rate constants for the polymerisation reaction for each metallocene were calculated by using the thermodynamic formulation of transition-state theory to complement the computational study.
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Affiliation(s)
- Iván Bravo
- Facultad de Farmacia, Departamento de Química-Física, Universidad de Castilla-La Mancha, Campus de Albacete, Edificio Polivalente, s/n, 02071 Albacete (Spain)
| | - Carlos Alonso-Moreno
- Facultad de Farmacia, Departamento de Química Inorgánica, Orgánica y Bioquímica, Universidad de Castilla-La Mancha, Campus de Albacete, Edificio Polivalente, s/n, 02071 Albacete (Spain)
| | - Fernando Carrillo-Hermosilla
- Facultad de Ciencias y Tecnologías Químicas, Departamento de Química Inorgánica, Orgánica y Bioquímica, Universidad de Castilla-La Mancha, Campus de Ciudad Real, 13071 Ciudad Real (Spain)
| | - Isabel López-Solera
- Facultad de Ciencias y Tecnologías Químicas, Departamento de Química Inorgánica, Orgánica y Bioquímica, Universidad de Castilla-La Mancha, Campus de Ciudad Real, 13071 Ciudad Real (Spain)
| | - Antonio Antiñolo
- Facultad de Ciencias y Tecnologías Químicas, Departamento de Química Inorgánica, Orgánica y Bioquímica, Universidad de Castilla-La Mancha, Campus de Ciudad Real, 13071 Ciudad Real (Spain)
| | - José Albaladejo
- Facultad de Ciencias y Tecnologías Químicas, Departamento de Química-Física, Universidad de Castilla-La Mancha, Campus de Ciudad Real, 13071 Ciudad Real (Spain)
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43
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Yang W, Chen Y, Sun WH. Correlating Cobalt Net Charges with Catalytic Activities of the 2-(Benzimidazolyl)-6-(1-aryliminoethyl)pyridylcobalt Complexes toward Ethylene Polymerization. MACROMOL REACT ENG 2015. [DOI: 10.1002/mren.201400064] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Wenhong Yang
- Key laboratory of Engineering Plastics and Beijing National Laboratory for Molecular Science, Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
| | - Yan Chen
- Key laboratory of Engineering Plastics and Beijing National Laboratory for Molecular Science, Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
| | - Wen-Hua Sun
- Key laboratory of Engineering Plastics and Beijing National Laboratory for Molecular Science, Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
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44
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Manz TA. Deactivation of Ti and Zr half-metallocene complexes activated with B(C6F5)3: a case study in constructing DFT-based QSARs to predict unimolecular rate constants. RSC Adv 2015. [DOI: 10.1039/c5ra00546a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A DFT-based QSAR was constructed to predict the deactivation pathways and rate constants for twenty-seven Ti and Zr half-metallocene complexes activated with B(C6F5)3.
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Affiliation(s)
- Thomas A. Manz
- Department of Chemical & Materials Engineering
- New Mexico State University
- Las Cruces
- USA
- School of Chemical Engineering
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45
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Morton JGM, Al-Shammari H, Sun Y, Zhu J, Stephan DW. 1,1-Olefin-bridged bis-(2-indenyl) metallocenes of titanium and zirconium. Dalton Trans 2014; 43:13219-31. [DOI: 10.1039/c4dt01583e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tetrasubstituted alkenes bearing geminal 2-indenyl substituents were synthesized and metallated to form a new class of ansa titanium and zirconium metallocene complexes containing a single sp2-hybridized carbon bridge.
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Affiliation(s)
| | | | - Yunshan Sun
- Department of Chemistry
- University of Toronto
- Toronto, Canada
| | - Jiangtao Zhu
- Department of Chemistry
- University of Toronto
- Toronto, Canada
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