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Jung SG, Jung G, Cole JM. Automatic Prediction of Peak Optical Absorption Wavelengths in Molecules Using Convolutional Neural Networks. J Chem Inf Model 2024; 64:1486-1501. [PMID: 38422386 PMCID: PMC10934802 DOI: 10.1021/acs.jcim.3c01792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
Molecular design depends heavily on optical properties for applications such as solar cells and polymer-based batteries. Accurate prediction of these properties is essential, and multiple predictive methods exist, from ab initio to data-driven techniques. Although theoretical methods, such as time-dependent density functional theory (TD-DFT) calculations, have well-established physical relevance and are among the most popular methods in computational physics and chemistry, they exhibit errors that are inherent in their approximate nature. These high-throughput electronic structure calculations also incur a substantial computational cost. With the emergence of big-data initiatives, cost-effective, data-driven methods have gained traction, although their usability is highly contingent on the degree of data quality and sparsity. In this study, we present a workflow that employs deep residual convolutional neural networks (DR-CNN) and gradient boosting feature selection to predict peak optical absorption wavelengths (λmax) exclusively from SMILES representations of dye molecules and solvents; one would normally measure λmax using UV-vis absorption spectroscopy. We use a multifidelity modeling approach, integrating 34,893 DFT calculations and 26,395 experimentally derived λmax data, to deliver more accurate predictions via a Bayesian-optimized gradient boosting machine. Our approach is benchmarked against the state of the art that is reported in the scientific literature; results demonstrate that learnt representations via a DR-CNN workflow that is integrated with other machine learning methods can accelerate the design of molecules for specific optical characteristics.
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Affiliation(s)
- Son Gyo Jung
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K.
- ISIS
Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K.
- Research
Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, U.K.
| | - Guwon Jung
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K.
- Research
Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, U.K.
- Scientific
Computing Department, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K.
| | - Jacqueline M. Cole
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K.
- ISIS
Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K.
- Research
Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, U.K.
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Roy N, Das R, Paira R, Paira P. Different routes for the construction of biologically active diversely functionalized bicyclo[3.3.1]nonanes: an exploration of new perspectives for anticancer chemotherapeutics. RSC Adv 2023; 13:22389-22480. [PMID: 37501776 PMCID: PMC10369265 DOI: 10.1039/d3ra02003g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/09/2023] [Indexed: 07/29/2023] Open
Abstract
Cancer is the second most high-morbidity disease throughout the world. From ancient days, natural products have been known to possess several biological activities, and research on natural products is one of the most enticing areas where scientists are engrossed in the extraction of valuable compounds from various plants to isolate many life-saving medicines, along with their other applications. It has been noticed that the bicyclo[3.3.1]nonane moiety is predominant in most biologically active natural products owing to its exceptional characteristics compared to others. Many derivatives of bicyclo[3.3.1]nonane are attractive to researchers for use in asymmetric catalysis or as potent anticancer entities along with their successful applications as ion receptors, metallocycles, and molecular tweezers. Therefore, this review article discusses several miscellaneous synthetic routes for the construction of bicyclo[3.3.1]nonanes and their heteroanalogues in association with the delineation of their anticancer activities with few selective compounds.
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Affiliation(s)
- Nilmadhab Roy
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology Vellore 632014 Tamilnadu India
- Department of Chemistry, Maharaja Manindra Chandra College 20 Ramkanto Bose Street Kolkata 700 003 India
| | - Rishav Das
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology Vellore 632014 Tamilnadu India
- Department of Chemistry, Maharaja Manindra Chandra College 20 Ramkanto Bose Street Kolkata 700 003 India
| | - Rupankar Paira
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology Vellore 632014 Tamilnadu India
- Department of Chemistry, Maharaja Manindra Chandra College 20 Ramkanto Bose Street Kolkata 700 003 India
| | - Priyankar Paira
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology Vellore 632014 Tamilnadu India
- Department of Chemistry, Maharaja Manindra Chandra College 20 Ramkanto Bose Street Kolkata 700 003 India
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Pisarev SA, Palyulin VA. Conformational effects of 1,5,9-substitution in symmetric bicyclo[3.3.1]nonane analogues. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Pisarev SA, Shulga DA, Palyulin VA, Zefirov NS. Lone pairs vs. covalent bonds: conformational effects in bicyclo[3.3.1]nonane derivatives. Struct Chem 2018. [DOI: 10.1007/s11224-018-1240-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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5
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Christmann M, Hu J, Kitamura M, Stoltz B. Tetrahedron reports on organic chemistry. Tetrahedron 2015. [DOI: 10.1016/s0040-4020(15)00744-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2013. [DOI: 10.1016/s0040-4020(13)01252-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Theoretical investigation of the substituent effects in the conformational isomerism of bromoalkoxycyclohexanes. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.08.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Güizado-Rodríguez M, Ramírez-Galicia G. Electronic effect on the rotational barriers of PN bond in aminophosphanes. A theoretical approach. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Bushmarinov IS, Fedyanin IV, Lyssenko KA, Lapteva VL, Pisarev SA, Palyulin VA, Zefirov NS, Antipin MY. The “Hockey Sticks” Effect Revisited: The Conformational and Electronic Properties of 3,7-Dithia-1,5-diazabicyclo[3.3.1]nonane from the QTAIM Perspective. J Phys Chem A 2011; 115:12738-45. [DOI: 10.1021/jp203730b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- I. S. Bushmarinov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova Str., 28, 119991 Moscow, Russia
| | - I. V. Fedyanin
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova Str., 28, 119991 Moscow, Russia
| | - K. A. Lyssenko
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova Str., 28, 119991 Moscow, Russia
| | - V. L. Lapteva
- Department of Chemistry, Moscow State University, Leninskie gory, 1/3, Moscow 119991 Russia
| | - S. A. Pisarev
- Institute of Physiologically Active Compounds, Russian Academy of Sciences, Severny proezd, 1, Chernogolovka, Moscow region, 142432, Russia
| | - V. A. Palyulin
- Department of Chemistry, Moscow State University, Leninskie gory, 1/3, Moscow 119991 Russia
| | - N. S. Zefirov
- Department of Chemistry, Moscow State University, Leninskie gory, 1/3, Moscow 119991 Russia
| | - M. Yu. Antipin
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova Str., 28, 119991 Moscow, Russia
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Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2011. [DOI: 10.1016/s0040-4020(11)00770-8] [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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Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2010. [DOI: 10.1016/s0040-4020(10)01735-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Tetrahedron reports on organic chemistry. Tetrahedron 2008. [DOI: 10.1016/s0040-4020(08)00897-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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14
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Tetrahedron reports on organic chemistry. Tetrahedron 2007. [DOI: 10.1016/s0040-4020(07)01371-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Tetrahedron reports on organic chemistry. Tetrahedron 2007. [DOI: 10.1016/s0040-4020(07)00834-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Tetrahedron reports on organic chemistry. Tetrahedron 2007. [DOI: 10.1016/s0040-4020(07)00205-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Lectka T, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2006. [DOI: 10.1016/s0040-4020(06)01801-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Lectka T, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2006. [DOI: 10.1016/s0040-4020(06)00771-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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Affiliation(s)
- Per J Garegg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91, Stockholm, Sweden
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Investigation of the stereochemical direction of the cyanoethylation of six-membered heterocyclic ketones as a function of the nature of the heteroatom. Chem Heterocycl Compd (N Y) 1982. [DOI: 10.1007/bf00503187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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