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Warrington S, Montanaro S, Elsegood MRJ, Nichol GS, Wright IA. Structure-Property Relationships for Potential Inversion From Electron Acceptors Based on Thiophene-Fused Triptycene Quinones, 1,4-Diketones and Their Malononitrile Adducts. Chemistry 2024; 30:e202400782. [PMID: 38517200 DOI: 10.1002/chem.202400782] [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: 02/27/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 03/23/2024]
Abstract
The synthesis and properties of a series of 11,11,12,12-tetracyano-9,10-anthraquinodimethane (TCAQ) inspired electron acceptors based on thiophene-fused quinone and triptycene motifs is presented. This has yielded insights into structure-property relationships for establishing and modulating simultaneous two-electron reduction processes in TCAQ analogues. These new compounds were synthesised using a Friedel-Crafts acylation between triptycene and thiophene-3,4-dicarbonyl chloride. Isomeric para-quinones featuring a [c]-fused thiophene on one side and a β,β- or α,β-fused triptycene on the other were isolated alongside a thiophene-3,4-diketone which bears two triptycene fragments. Knoevenagel condensation of these products with malononitrile produced a quinoidal bis(dicyanomethylene), an oxo-dicyanomethylene and an acyclic bis(dicyanomethylene). This series of new electron accepting molecules has been studied using X-ray crystallography and the implications of their 3D structures on NMR and UV/vis absorbance spectroscopy and cyclic voltammetry results have been ascertained with conclusions underpinned by computational methods.
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Affiliation(s)
- Stefan Warrington
- School of Chemistry, University of Edinburgh Joseph Black Building, David Brewster Road, Edinburgh, EH16 5PL, United Kingdom
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Stephanie Montanaro
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Mark R J Elsegood
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Gary S Nichol
- School of Chemistry, University of Edinburgh Joseph Black Building, David Brewster Road, Edinburgh, EH16 5PL, United Kingdom
| | - Iain A Wright
- School of Chemistry, University of Edinburgh Joseph Black Building, David Brewster Road, Edinburgh, EH16 5PL, United Kingdom
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2
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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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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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Driver RW, Claridge TDW, Scheiner S, Smith MD. Torsional and Electronic Factors Control the C-H⋅⋅⋅O Interaction. Chemistry 2016; 22:16513-16521. [PMID: 27709689 PMCID: PMC5113693 DOI: 10.1002/chem.201602905] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Indexed: 01/07/2023]
Abstract
The precise role of non‐conventional hydrogen bonds such as the C−H⋅⋅⋅O interaction in influencing the conformation of small molecules remains unresolved. Here we survey a series of β‐turn mimetics using X‐ray crystallography and NMR spectroscopy in conjunction with quantum calculation, and conclude that favourable torsional and electronic effects are important for the population of states with conformationally influential C−H⋅⋅⋅O interactions. Our results also highlight the challenge in attempting to deconvolute a myriad of interdependent noncovalent interactions in order to focus on the contribution of a single one. Within a small molecule that is designed to resemble the complexity of the environment within peptides and proteins, the interplay of different steric burdens, hydrogen‐acceptor/‐donor properties and rotational profiles illustrate why unambiguous conclusions based solely on NMR chemical shift data are extremely challenging to rationalize.
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Affiliation(s)
- Russell W Driver
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Timothy D W Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, 84322-0300, USA.
| | - Martin D Smith
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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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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Balaban AT, Young DC, Plavec J, Pečnik K, Pompe M, Dahl JE, Carlson RMK. NMR spectral properties of the tetramantanes - nanometer-sized diamondoids. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:1003-1018. [PMID: 26286373 DOI: 10.1002/mrc.4289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 06/08/2015] [Accepted: 06/12/2015] [Indexed: 06/04/2023]
Abstract
Tetramantanes, and all diamondoid hydrocarbons, possess carbon frameworks that are superimposable upon the cubic diamond lattice. This characteristic is invaluable in assigning their (1)H and (13)C NMR spectra because it translates into repeating structural features, such as diamond-cage isobutyl moieties with distinctively complex methine to methylene signatures in COSY and HMBC data, connected to variable, but systematic linkages of methine and quaternary carbons. In all tetramantane C22H28 isomers, diamond-lattice structures result in long-range (4)JHH, W-coupling in COSY data, except where negated by symmetry; there are two highly symmetrical and one chiral tetramantane (showing seven (4)JHH). Isobutyl-cage methines of lower diamondoids and tetramantanes are the most shielded resonances in their (13)C spectra (<29.5 ppm). The isobutyl methylenes are bonded to additional methines and at least one quaternary carbon in the tetramantanes. W-couplings between these methines and methylenes clarify spin-network interconnections and detailed surface hydrogen stereochemistry. Vicinal couplings of the isobutyl methylenes reveal positions of the quaternary carbons: HMBC data then tie the more remote spin systems together. Diamondoid (13) C NMR chemical shifts are largely determined by α and β effects, however γ-shielding effects are important in [123]tetramantane. (1)H NMR chemical shifts generally correlate with numbers of 1,3-diaxial H-H interactions. Tight van der Waals contacts within [123]tetramantane's molecular groove, however, form improper hydrogen bonds, deshielding hydrogen nuclei inside the groove, while shielding those outside, indicated by Δδ of 1.47 ppm for geminal hydrogens bonded to C-3,21. These findings should be valuable in future NMR studies of diamondoids/nanodiamonds of increasing size.
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Affiliation(s)
- Alexandru T Balaban
- Texas A&M University at Galveston, Department of Marine Sciences, 200 Seawolf Parkway, Galveston, TX, 77553, USA
| | | | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Klemen Pečnik
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Matevž Pompe
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Aškerčeva 5, 1000, Ljubljana, Slovenia
| | - Jeremy E Dahl
- Stanford Institute for Materials and Energy Sciences, Stanford University, 476 Lomita Mall, Stanford, CA, 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Robert M K Carlson
- Stanford Institute for Materials and Energy Sciences, Stanford University, 476 Lomita Mall, Stanford, CA, 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
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Arivazhagan G, Elangovan A, Shanmugam R, Vijayalakshmi R, Kannan P. Spectroscopic studies, NBO analysis and dielectric studies on the behaviour of acetone molecules in non-polar solvent environment. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.03.051] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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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10
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Mo Y. Can QTAIM Topological Parameters Be a Measure of Hydrogen Bonding Strength? J Phys Chem A 2012; 116:5240-6. [DOI: 10.1021/jp3029769] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States
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Vibhute AM, Gonnade RG, Swathi RS, Sureshan KM. Strength from weakness: opportunistic CH⋯O hydrogen bonds differentially dictate the conformational fate in solid and solution states. Chem Commun (Camb) 2012; 48:717-9. [DOI: 10.1039/c1cc15051k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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