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Lourenço MP, Hostaš J, Bellinger C, Tchagang A, Salahub DR. Reinforcement learning for in silico determination of adsorbate-substrate structures. J Comput Chem 2024; 45:1289-1302. [PMID: 38357973 DOI: 10.1002/jcc.27322] [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: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Reinforcement learning (RL) methods have helped to define the state of the art in the field of modern artificial intelligence, mostly after the breakthrough involving AlphaGo and the discovery of novel algorithms. In this work, we present a RL method, based on Q-learning, for the structural determination of adsorbate@substrate models in silico, where the minimization of the energy landscape resulting from adsorbate interactions with a substrate is made by actions on states (translations and rotations) chosen from an agent's policy. The proposed RL method is implemented in an early version of the reinforcement learning software for materials design and discovery (RLMaterial), developed in Python3.x. RLMaterial interfaces with deMon2k, DFTB+, ORCA, and Quantum Espresso codes to compute the adsorbate@substrate energies. The RL method was applied for the structural determination of (i) the amino acid glycine and (ii) 2-amino-acetaldehyde, both interacting with a boron nitride (BN) monolayer, (iii) host-guest interactions between phenylboronic acid and β-cyclodextrin and (iv) ammonia on naphthalene. Density functional tight binding calculations were used to build the complex search surfaces with a reasonably low computational cost for systems (i)-(iii) and DFT for system (iv). Artificial neural network and gradient boosting regression techniques were employed to approximate the Q-matrix or Q-table for better decision making (policy) on next actions. Finally, we have developed a transfer-learning protocol within the RL framework that allows learning from one chemical system and transferring the experience to another, as well as from different DFT or DFTB levels.
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Affiliation(s)
- Maicon Pierre Lourenço
- Departamento de Química e Física-Centro de Ciências Exatas, Naturais e da Saúde-CCENS-Universidade Federal do Espírito Santo, Alegre, Brasil
| | - Jiří Hostaš
- Department of Chemistry, Department of Physics and Astronomy, CMS Centre for Molecular Simulation, IQST Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Calgary, Alberta, Canada
- Digital Technologies Research Centre, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Colin Bellinger
- Digital Technologies Research Centre, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Alain Tchagang
- Digital Technologies Research Centre, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Dennis R Salahub
- Department of Chemistry, Department of Physics and Astronomy, CMS Centre for Molecular Simulation, IQST Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Calgary, Alberta, Canada
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Paul S, Das S, Mitra B, Chandra Pariyar G, Ghosh P. β-Cyclodextrin: a green supramolecular catalyst assisted eco-friendly one-pot three-component synthesis of biologically active substituted pyrrolidine-2-one. RSC Adv 2023; 13:5457-5466. [PMID: 36793299 PMCID: PMC9924053 DOI: 10.1039/d2ra08054k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 01/25/2023] [Indexed: 02/16/2023] Open
Abstract
A green, novel and eco-efficient synthetic route towards the synthesis of highly substituted bio-active pyrrolidine-2-one derivatives was demonstrated using β-cyclodextrin, a water-soluble supramolecular solid as a green and eco-benign catalyst at room temperature under water-ethanol solvent medium. The exploration of the green catalyst β-cyclodextrin for the metal-free one-pot three-component synthesis of a wide range of highly functionalized bio-active heterocyclic pyrrolidine-2-one moieties from easily available aldehydes and amines explains the superiority and uniqueness of this protocol.
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Affiliation(s)
- Subhankar Paul
- Department of Chemistry, University of North Bengal District-Darjeeling West Bengal India +91 0353 2699001 +91 0353 2776381
| | - Sharmistha Das
- Department of Chemistry, University of North Bengal District-Darjeeling West Bengal India +91 0353 2699001 +91 0353 2776381
| | - Bijeta Mitra
- Department of Chemistry, University of North Bengal District-Darjeeling West Bengal India +91 0353 2699001 +91 0353 2776381
| | - Gyan Chandra Pariyar
- Department of Food Technology, University of North BengalDistrict-DarjeelingWest BengalIndia
| | - Pranab Ghosh
- Department of Chemistry, University of North Bengal District-Darjeeling West Bengal India +91 0353 2699001 +91 0353 2776381
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Das S, Paul S, Mitra B, Pariyar GC, Ghosh P. PEG-200: A versatile green solvent assisted catalyst-free one-pot three-component synthesis of functionalised N-amino-3-cyano-2-pyridone. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
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Mohammadi M, Ghorbani-Choghamarani A. Complexation of guanidino containing l-arginine with nickel on silica-modified Hercynite MNPs: a novel catalyst for the Hantzsch synthesis of polyhydroquinolines and 2,3-Dihydroquinazolin-4(1H)-ones. RESEARCH ON CHEMICAL INTERMEDIATES 2022. [DOI: 10.1007/s11164-022-04706-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Datta K, Mitra B, Sharma BS, Ghosh P. One‐pot Three‐component Solvent‐free Tandem Annulations for Synthesis of Tetrazolo[1,2‐
a
]pyrimidine and [1,2,4]triazolo[1,5‐
a
]pyrimidine. ChemistrySelect 2022. [DOI: 10.1002/slct.202103602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Kumaresh Datta
- Department of Chemistry University of North Bengal Dist. Darjeeling West Bengal India
| | - Bijeta Mitra
- Department of Chemistry University of North Bengal Dist. Darjeeling West Bengal India
| | - Biswajit Shil Sharma
- Department of Chemistry University of North Bengal Dist. Darjeeling West Bengal India
| | - Pranab Ghosh
- Department of Chemistry University of North Bengal Dist. Darjeeling West Bengal India
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Mohammadi M, Ghorbani-Choghamarani A. Synthesis and characterization of novel hercynite@sulfuric acid and its catalytic applications in the synthesis of polyhydroquinolines and 2,3-dihydroquinazolin-4(1 H)-ones. RSC Adv 2022; 12:2770-2787. [PMID: 35425328 PMCID: PMC8979139 DOI: 10.1039/d1ra07381h] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
Herein, we report the synthesis of hercynite@sulfuric acid as a novel nanomagnetic solid acid catalyst, containing the sulfuric acid catalytic sites on the surface of hercynite MNPs as the catalytic support. The as-synthesized nanocomposite was meticulously characterized using a wide range of physicochemical techniques; including, FT-IR, XRD, EDX, X-ray-mapping, SEM and VSM analysis. The catalytic activity of this nanomagnetic material was considered for the synthesis of the diversely substituted polyhydroquinolines and 2,3-dihydroquinazolin-4(1H)-ones under solvent free conditions and also cyclocondensation reactions in ethanol, respectively affording good to excellent yields. Moreover, it is worth mentioning that the heterogeneity of the catalyst was measured through its excellent reusability and hot-filtration test.
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Affiliation(s)
- Masoud Mohammadi
- Department of Chemistry, Faculty of Science, Ilam University P.O. Box 69315516 Ilam Iran
| | - Arash Ghorbani-Choghamarani
- Department of Organic Chemistry, Faculty of Chemistry, Bu-Ali Sina University Hamedan 6517838683 Iran +98 8138380709 +98 8138282807
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Goud SB, Guin S, Prakash M, Samanta S. Cu(OAc) 2/DABCO-mediated domino reaction of vinyl malononitriles with cyclic sulfamidate imines: access to 6-hydroxyaryl-2-aminonicotinonitriles. Org Biomol Chem 2022; 20:352-357. [PMID: 34931209 DOI: 10.1039/d1ob02095a] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A novel Cu(II)-salt/DABCO-mediated one-pot access to a myriad of highly substituted biologically relevant 2-aminonicotinonitriles possessing a resourceful phenolic moiety with satisfactory yields is reported. This method involves cyclic sulfamidate imines as 1C1N sources and different kinds of acyclic/cyclic vinyl malononitriles as 4C sources for pyridine synthesis via a vinylogous Mannich-cycloaromatization sequence process, creating two new C-N bonds under mild conditions. Importantly, this de novo strategy is applicable to gram-scale syntheses, underlining the method's practicability and allowing for a wide range of substrates with excellent functional group tolerance.
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Affiliation(s)
- S Banuprakash Goud
- Department of Chemistry, Indian Institute of Technology Indore, Simrol, 453552 India.
| | - Soumitra Guin
- Department of Chemistry, Indian Institute of Technology Indore, Simrol, 453552 India.
| | - Meher Prakash
- Department of Chemistry, Indian Institute of Technology Indore, Simrol, 453552 India.
| | - Sampak Samanta
- Department of Chemistry, Indian Institute of Technology Indore, Simrol, 453552 India.
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Enzyme-catalyzed synthesis of bioactive heterocycles. PHYSICAL SCIENCES REVIEWS 2021. [DOI: 10.1515/psr-2021-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Enzymes are proteins that functions as biological catalyst. It is now a known fact that enzyme can catalyze many synthetic operations better than the conventional reagents. Not only in the synthesis of natural products, they can also be applied for construction of varieties of unnatural compounds. In this chapter, Pariyar and Ghosh have discussed in brief synthesis of various biologically active heterocyclic compounds using different enzymes as catalysts. Among various enzymes, laccases, trypsin, α-amylase and Bakers’ yeast are few that are easily available and have been extensively explored for various synthetic strategies. This chapter will definitely serve as valuable source of information to the readers in the field of enzyme-catalyzed reactions.
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Matthee C, Terre'Blanche G, Janse van Rensburg HD, Aucamp J, Legoabe LJ. Chalcone-inspired rA 1 /A 2A adenosine receptor ligands: Ring closure as an alternative to a reactive substructure. Chem Biol Drug Des 2021; 99:416-437. [PMID: 34878728 DOI: 10.1111/cbdd.13999] [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: 09/07/2021] [Revised: 10/21/2021] [Accepted: 10/30/2021] [Indexed: 11/30/2022]
Abstract
Over the past few years, great progress has been made in the development of high-affinity adenosine A1 and/or A2A receptor antagonists-promising agents for the potential treatment of Parkinson's disease. Unfortunately, many of these compounds raise structure-related concerns. The present study investigated the effect of ring closures on the rA1 /A2A affinity of compounds containing a highly reactive α,β-unsaturated carbonyl system, hence providing insight into the potential of heterocycles to address these concerns. A total of 12 heterocyclic compounds were synthesised and evaluated in silico and in vitro. The test compounds performed well upon qualitative assessment of drug-likeness and were generally found to be free from potentially problematic fragments. Most also showed low/weak cytotoxicity. Results from radioligand binding experiments confirm that heterocycles (particularly 2-substituted 3-cyanopyridines) can replace the promiscuous α,β-unsaturated ketone functional group without compromising A1 /A2A affinity. Structure-activity relationships highlighted the importance of hydrogen bonds in binding to the receptors of interest. Compounds 3c (rA1 Ki = 16 nM; rA2A Ki = 65 nM) and 8a (rA1 Ki = 102 nM; rA2A Ki = 37 nM), which both act as A1 antagonists, showed significant dual A1 /A2A affinity and may, therefore, inspire further investigation into heterocycles as potentially safe and potent adenosine receptor antagonists.
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Affiliation(s)
- Chrisna Matthee
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, South Africa
| | - Gisella Terre'Blanche
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, South Africa.,Pharmaceutical Chemistry, School of Pharmacy, North-West University, Potchefstroom, South Africa
| | | | - Janine Aucamp
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, South Africa
| | - Lesetja J Legoabe
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, South Africa
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