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Stylianakis I, Zervos N, Lii JH, Pantazis DA, Kolocouris A. Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory. J Comput Aided Mol Des 2023; 37:607-656. [PMID: 37597063 PMCID: PMC10618395 DOI: 10.1007/s10822-023-00513-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/03/2023] [Indexed: 08/21/2023]
Abstract
We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.
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Affiliation(s)
- Ioannis Stylianakis
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Nikolaos Zervos
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Jenn-Huei Lii
- Department of Chemistry, National Changhua University of Education, Changhua City, Taiwan
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Antonios Kolocouris
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece.
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece.
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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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Solel E, Ruth M, Schreiner PR. London Dispersion Helps Refine Steric A-Values: The Halogens. J Org Chem 2021; 86:7701-7713. [PMID: 33988377 DOI: 10.1021/acs.joc.1c00767] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Halogens are rarely considered as dispersion energy donors for organic reaction design. Here, we re-examine one of the textbook examples for assessing steric hindrance, the A-value, and demonstrate that even in this system, halogens cannot be treated solely as classic repulsive hard spheres. A significant part of the steric demand of the halogens is compensated by attractive London dispersion (LD) interactions, explaining the experimental lack of a clear trend when going down the halogens' row. Beyond monohalogenated cyclohexanes, dihalo- and perhalocyclohexanes also show significant LD interactions. We also explored several other small organic systems containing halogens. Our findings show that organic chemists should treat halogens as possible sources of LD interactions in reaction design, as these atoms can change the landscape of the potential energy surface and reverse trends of conformer stabilities and reaction selectivities.
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Affiliation(s)
- Ephrath Solel
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Marcel Ruth
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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Bakthadoss M, Surendar M. Cascade annulation reaction (CAR): highly diastereoselective synthesis of pyranopyrazole scaffolds. RSC Adv 2020; 10:19003-19007. [PMID: 35518344 PMCID: PMC9053953 DOI: 10.1039/d0ra03400b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/11/2020] [Indexed: 12/26/2022] Open
Abstract
An unprecedented domino protocol for the novel synthesis of highly diverse and functionalized tetrahydro pyranopyrazole scaffolds using chalcone epoxide has been reported for the first time. This synthetic protocol generates three consecutive stereogenic centres in a highly diastereoselective manner with the formation of vicinal diol and a quaternary carbon centre. A wide range of substrates were utilized for the scope of this methodology and provided very good yields of pyranopyrazoles. The pyranopyrazoles were also transformed into densely functionalized tetrasubstituted olefins. An unprecedented domino protocol for the novel synthesis of highly diverse and functionalized tetrahydro pyranopyrazole scaffolds using chalcone epoxide has been reported.![]()
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Affiliation(s)
| | - Manickam Surendar
- Department of Chemistry
- Pondicherry University
- Pondicherry 605014
- India
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Mazzanti A, Drakopoulos A, Christina T, Kolocouris A. Rotation Barriers of 1‐Adamantyl‐Csp
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Bonds Measured with Dynamic NMR. ChemistrySelect 2019. [DOI: 10.1002/slct.201901042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Andrea Mazzanti
- Department of Industrial Chemistry “Toso Montanari”Alma Mater Studiorum-University of Bologna Viale del Risorgimento 4 40136 Bologna Italy
| | - Antonios Drakopoulos
- Faculty of PharmacyDepartment of Pharmaceutical ChemistryUniversity of Athens, Panepistimioupolis-Zografou 15771 Athens Greece
- current address: Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food ChemistryJulius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Tzitzoglaki Christina
- Faculty of PharmacyDepartment of Pharmaceutical ChemistryUniversity of Athens, Panepistimioupolis-Zografou 15771 Athens Greece
| | - Antonios Kolocouris
- Faculty of PharmacyDepartment of Pharmaceutical ChemistryUniversity of Athens, Panepistimioupolis-Zografou 15771 Athens Greece
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Silva Lopez C, Nieto Faza O, De Proft F, Kolocouris A. Assessing the attractive/repulsive force balance in axial cyclohexane C-Hax···Yaxcontacts: A combined computational analysis in monosubstituted cyclohexanes. J Comput Chem 2016; 37:2647-2658. [DOI: 10.1002/jcc.24496] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 08/26/2016] [Accepted: 09/01/2016] [Indexed: 02/03/2023]
Affiliation(s)
- Carlos Silva Lopez
- Departamento de Química Orgánica; Facultade de Química, Universidade de Vigo; Vigo, 63 Spain310
| | - Olalla Nieto Faza
- Departamento de Química Orgánica; Facultade de Química, Universidade de Vigo; Vigo, 63 Spain310
| | - Frank De Proft
- Eenheid Algemene Chemie, Faculteit Wetenschappen; Vrije Universiteit Brussel; Pleinlaan 2 Brussels B-1050 Belgium
| | - Antonios Kolocouris
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry; National and Kapodistrian University of Athens; Panepistimioupolis-Zografou Athens 15771 Greece
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Kolocouris A, Koch A, Kleinpeter E, Stylianakis I. 2-Substituted and 2,2-disubstituted adamantane derivatives as models for studying substituent chemical shifts and C–Hax⋯Yax cyclohexane contacts—results from experimental and theoretical NMR spectroscopic chemical shifts and DFT structures. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.01.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Ling Y, Ren X, Lai W, Luo J. 4,4,8,8-Tetranitroadamantane-2,6-diyl Dinitrate: A High-Density Energetic Material. European J Org Chem 2015. [DOI: 10.1002/ejoc.201403449] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Friedrich P, Baisch U, Harrington RW, Lyatuu F, Zhou K, Zelder F, McFarlane W, Buckel W, Golding BT. Experimental study of hydrogen bonding potentially stabilizing the 5'-deoxyadenosyl radical from coenzyme B12. Chemistry 2012; 18:16114-22. [PMID: 23080006 DOI: 10.1002/chem.201201840] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 08/21/2012] [Indexed: 01/28/2023]
Abstract
Coenzyme B(12) can assist radical enzymes that accomplish the vicinal interchange of a hydrogen atom with a functional group. It has been proposed that the Co-C bond homolysis of coenzyme B(12) to cob(II)alamin and the 5'-deoxyadenosyl radical is aided by hydrogen bonding of the corrin C19-H to the 3'-O of the ribose moiety of the incipient 5'-deoxyadenosyl radical, which is stabilized by 30 kJ mol(-1) (B. Durbeej et al., Chem. Eur. J. 2009, 15, 8578-8585). The diastereoisomers (R)- and (S)-2,3-dihydroxypropylcobalamin were used as models for coenzyme B(12). A downfield shift of the NMR signal for the C19-H proton was observed for the (R)-isomer (δ=4.45 versus 4.01 ppm for the (S)-isomer) and can be ascribed to an intramolecular hydrogen bond between the C19-H and the oxygen of CHOH. Crystal structures of (R)- and (S)-2,3-dihydroxypropylcobalamin showed C19-H⋅⋅⋅O distances of 3.214(7) Å (R-isomer) and 3.281(11) Å (S-isomer), which suggest weak hydrogen-bond interactions (-ΔG<6 kJ mol(-1)) between the CHOH of the dihydroxypropyl ligand and the C19-H. Exchange of the C19-H, which is dependent on the cobalt redox state, was investigated with cob(I)alamin, cob(II)alamin, and cob(III)alamin by using NMR spectroscopy to monitor the uptake of deuterium from deuterated water in the pH range 3-11. No exchange was found for any of the cobalt oxidation states. 3',5'-Dideoxyadenosylcobalamin, but not the 2',5'-isomer, was found to act as a coenzyme for glutamate mutase, with a 15-fold lower k(cat)/K(M) than 5'-deoxyadenosylcobalamin. This indicates that stabilization of the 5'-deoxyadenosyl radical by a hydrogen bond that involves the C19-H and the 3'-OH group of the cofactor is, at most, 7 kJ mol(-1) (-ΔG). Examination of the crystal structure of glutamate mutase revealed additional stabilizing factors: hydrogen bonds between both the 2'-OH and 3'-OH groups and glutamate 330. The actual strength of a hydrogen bond between the C19-H and the 3'-O of the ribose moiety of the 5'-deoxyadenosyl group is concluded not to exceed 6 kJ mol(-1) (-ΔG).
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Affiliation(s)
- Peter Friedrich
- School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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Kolocouris A, Zervos N, De Proft F, Koch A. Improper Hydrogen Bonded Cyclohexane C–Hax···Yax Contacts: Theoretical Predictions and Experimental Evidence from 1H NMR Spectroscopy of Suitable Axial Cyclohexane Models. J Org Chem 2011; 76:4432-43. [DOI: 10.1021/jo102353f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antonios Kolocouris
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Athens, Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Nikolaos Zervos
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Athens, Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Frank De Proft
- Eenheid Algemene Chemie, Faculteit Wetenschappen, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Andreas Koch
- Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, D-14476 Potsdam (Golm), Germany
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Probing the influence of solvent effects on the conformational behavior of 1,4-diazacyclohexane systems. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.09.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Zervos N, Kolocouris A. Improper hydrogen-bonded cyclohexane C–Hax⋯Yax contacts: experimental evidence from 1H NMR spectroscopy of suitable axial cyclohexane models. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.02.170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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