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Wu EJ, Kelly AW, Iuzzolino L, Lee AY, Zhu X. Unprecedented Packing Polymorphism of Oxindole: An Exploration Inspired by Crystal Structure Prediction. Angew Chem Int Ed Engl 2024; 63:e202406214. [PMID: 38825853 DOI: 10.1002/anie.202406214] [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: 04/01/2024] [Revised: 05/13/2024] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
Crystal polymorphism, characterized by different packing arrangements of the same compound, strongly ties to the physical properties of a molecule. Determining the polymorphic landscape is complex and time-consuming, with the number of experimentally observed polymorphs varying widely from molecule to molecule. Furthermore, disappearing polymorphs, the phenomenon whereby experimentally observed forms cannot be reproduced, pose a significant challenge for the pharmaceutical industry. Herein, we focused on oxindole (OX), a small rigid molecule with four known polymorphs, including a reported disappearing form. Using crystal structure prediction (CSP), we assessed OX solid-state landscape and thermodynamic stability by comparing predicted structures with experimentally known forms. We then performed melt and solution crystallization in bulk and nanoconfinement to validate our predictions. These experiments successfully reproduced the known forms and led to the discovery of four novel polymorphs. Our approach provided insights into reconstructing disappearing polymorphs and building more comprehensive polymorph landscapes. These results also establish a new record of packing polymorphism for rigid molecules.
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Affiliation(s)
- Emily J Wu
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey, 07065, United States
| | - Andrew W Kelly
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey, 07065, United States
| | - Luca Iuzzolino
- Modeling & Informatics, Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey, 07065, United States
| | - Alfred Y Lee
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey, 07065, United States
| | - Xiaolong Zhu
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey, 07065, United States
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Samigullina AI, Galimullina VR, Kadyrova SF, Krivolapov DB, Mamedov VA, Gubaidullin AT. FEATURES OF THE CRYSTAL STRUCTURES OF THREE POLYMORPHS OF (RS,SR)-1-BENZYL- 3-(α,4-DICHLOROBENZYL)-3-HYDROXYINDOLIN-2-ONE. J STRUCT CHEM+ 2023. [DOI: 10.1134/s0022476623020026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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Salman S, Rekik N, Suleiman J, Abuzir AR. Elucidating the Theoretical Evolution of the IR Spectral Density and the Potential Energy Surfaces of Hydrogen Bonded Complexes: A Quantum Dynamical Study. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Isik IB, Sagdinc SG. Theoretical (Hirshfeld surface, molecular docking, structural, electronic properties, NBO and NLO analyses) and spectroscopic studies of 6-chloro-2-oxindole in monomeric and dimeric forms. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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5
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Sagdinc SG, Akcay BK, Yildiz SZ, Isik IB. Single-crystal X-ray structural characterization, Hirshfeld surface analysis, electronic properties, NBO, and NLO calculations and vibrational analysis of the monomeric and dimeric forms of 5-nitro-2-oxindole. NEW J CHEM 2021. [DOI: 10.1039/d1nj00264c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The information of interactions is given by RDG versus sign(λ2)ρ product of the sign of the second largest eigenvalue of electron density Hessian matrix and electron density) investigated by RDG surface analysis.
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Affiliation(s)
| | - Banu Kevser Akcay
- Department of Physics, Science and Art Faculty
- Kocaeli University
- 41380 Umuttepe
- Turkey
| | - Salih Zeki Yildiz
- Department of Chemistry
- Faculty of Arts and Sciences
- Sakarya University
- 54187 Serdivan
- Turkey
| | - Ilknur Baldan Isik
- Department of Physics, Science and Art Faculty
- Kocaeli University
- 41380 Umuttepe
- Turkey
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Rekik N, Alsaif NAM, Flakus HT, Farooq U, Chand R. A unified quantum model susceptible to elucidate the dissimilarity of IR spectral density of dicarboxylic acid crystals: Phthalic and terephthalic acid crystals cases. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 242:118728. [PMID: 32781405 DOI: 10.1016/j.saa.2020.118728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/29/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
Over the last decades, several approaches have been developed for elucidating the infrared spectral density of dicarboxylic acid crystals, which has been served as prototype for determining hydrogen bonds dynamics. These approaches differ in how accurately the simulated spectra can superimpose the experimental ones. In this study, we present a superdimer quantum approach susceptible to elucidate the infrared spectral properties of some particular dicarboxylic acid crystals using a newly proposed algorithm, which favors the rule of Davydov coupling in the generation of the spectra. The approach, which is herein effectively applied to terephthalic and phthalic acid dimer crystals, ascribes the non-conventional IR spectral properties of these particular acid crystals to the existence of superdimer structure in their lattices. In this superdimer structure, a strong vibronic coupling mechanism, namely Davydov coupling, takes place between the proton stretching vibrations in the (COOH)₂ cycles. This strong coupling exciton, generated by the resonance arising in the two coupled (COOH)₂ cycles of the aromatic rings of the superdimer, in conjunction with the strong anharmonic coupling between the fast and slow modes of each hydrogen bonds provide a strong support basis for a common explanation of the physical properties of these two different crystalline systems. The numerical simulations, involving the implications of the superdimer model, are systematically correlated with the experimental spectra. A decent agreement between the evaluated spectra and the experimental bandshapes of terephthalic and phthalic dicarboxylic acid crystals was obtained using a set of physically sound parameters as inputs in the theoretical formulation. The superdimer quantum approach thereby underscore the potential of the dynamical cooperative interactions between "Davydov coupling" and "strong anharmonic coupling" mechanisms in the generation of the spectral features of terephthalic and phthalic dicarboxylic acid crystals, suggesting that the congregated effects of these two mechanisms can be considered as the most reliable source of the non-conventional IR spectral properties observed. It is therefore expected that this novel algorithm reduces the discrepancies between the simulated spectra compared to the experimental one and simplify the computation of spectra in more complex hydrogen bonded systems.
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Affiliation(s)
- Najeh Rekik
- Physics Department, College of Science, University of Ha'il, Saudi Arabia; Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
| | - Norah A M Alsaif
- Physics Department, Faculty of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Henryk T Flakus
- Institute of Chemistry, University of Silesia, Katowice 40-006, Poland
| | - Umer Farooq
- Physics Department, College of Science, University of Ha'il, Saudi Arabia
| | - Ram Chand
- Physics Department, College of Science, University of Ha'il, Saudi Arabia
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Rekik N, Flakus HT, Hachula B, Salman S, Alshoaibi A, Farooq U. How far the vibrational exciton interactions are responsible for the generation of the infrared spectra of oxindole crystals? SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 237:118302. [PMID: 32416514 DOI: 10.1016/j.saa.2020.118302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/01/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
Oxindole (indolin-2-one, Ox) is a unique and a crucial molecular system in spectroscopic studies. Indole is the core structure of many substances found in the human body (tryptophan, serotonin) and the indole alkaloids have highly differentiated pharmacological properties such as analgesic, anti-fever and anti-inflammatory. The Ox's structural results given in the Cambridge Structural Database revealed the existence of only one crystalline form of Ox, referred to the α-form. However, we have experimentally noticed the existence of two polymorphic forms during the crystallization of Ox. Furthermore, the significant spectral differences that we have observed in the solid state infrared spectra of these two forms additionally confirm the existence of the polymorphism phenomenon. Of the four polymorphic forms of Ox, two of them - α - and β-forms - were of particular interest. In the crystalline lattices of both polymorphs, we observed a similar pattern of molecular arrangements giving rise to the supramolecular synthon according to the terminology of Etter. Moreover, hydrogen bonds in the dimer of the α-form are found to be non-equivalent (non-centrosymmetric dimers), having a length of 2797 Å and 2979 Å, respectively. Comparatively, in the most densely packed crystalline structure of Ox, the β-form, the dimer is formed by a pair of almost identical intermolecular hydrogen bonds and consequently the crystals of β-form exhibited spectral properties typical to centrosymmetric hydrogen bond dimers. In addition, the spectroscopic studies that we have conducted to polymorphic forms of Ox, isotopically diluted with deuterium, show the dramatic influence of isotopic substitution in the hydrogen bridge on the infrared spectra of hydrogen bonding. Thus, the main goal of this work is the proposition of a theoretical approach that can describe the main features of the crystalline infrared spectra of the Ox polymorphs. The proposed approach is based on the phenomenon of the exciton coupling results directly from intermolecular interactions in the vibrationally excited state which leads to the delocalization of the excitation over the molecules in the lattice and to the Davydov splitting effect in the crystalline spectra.
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Affiliation(s)
- Najeh Rekik
- Physics Department, College of Sciences, University of Ha'il, Ha'il, Saudi Arabia; Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
| | - Henryk T Flakus
- Institute of Chemistry, University of Silesia, 9 Szkolna Street, Pl-40-006 Katowice, Poland.
| | - Barbara Hachula
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Saed Salman
- Physics Department, Faculty of Science, King Faisal University, Saudi Arabia
| | - Adil Alshoaibi
- Physics Department, Faculty of Science, King Faisal University, Saudi Arabia
| | - Umer Farooq
- Physics Department, College of Sciences, University of Ha'il, Ha'il, Saudi Arabia
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Hachuła B, Zubko M, Zajdel P, Książek M, Kusz J, Starczewska O, Janek J, Pisarski W. Polymorphs of oxindole as the core structures in bioactive compounds. CrystEngComm 2018. [DOI: 10.1039/c7ce01237c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A new polymorph of oxindole (termed as “δ-form”) has been found and characterized by single-crystal X-ray diffraction.
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Affiliation(s)
- Barbara Hachuła
- Institute of Chemistry
- University of Silesia
- 40-006 Katowice
- Poland
| | - Maciej Zubko
- Institute of Materials Science
- University of Silesia
- 41-500 Chorzów
- Poland
| | - Paweł Zajdel
- Institute of Physics
- University of Silesia
- 40-007 Katowice
- Poland
| | - Maria Książek
- Institute of Physics
- University of Silesia
- 40-007 Katowice
- Poland
| | - Joachim Kusz
- Institute of Physics
- University of Silesia
- 40-007 Katowice
- Poland
| | | | - Joanna Janek
- Institute of Chemistry
- University of Silesia
- 40-006 Katowice
- Poland
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Ravikumar K, Sridhar B, Nanubolu JB, Karthik G, Reddy BVS. Structural consequences of weak interactions in dispirooxindole derivatives. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2015; 71:1001-9. [PMID: 26524175 DOI: 10.1107/s2053229615019610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/16/2015] [Indexed: 11/10/2022]
Abstract
Spiro scaffolds are being increasingly utilized in drug discovery due to their inherent three-dimensionality and structural variations, resulting in new synthetic routes to introduce spiro building blocks into more pharmaceutically active molecules. Multicomponent cascade reactions, involving the in situ generation of carbonyl ylides from α-diazocarbonyl compounds and aldehydes, and 1,3-dipolar cycloadditon with 3-arylideneoxindoles gave a novel class of dispirooxindole derivatives, namely 1,1''-dibenzyl-5'-(4-chlorophenyl)-4'-phenyl-4',5'-dihydrodispiro[indoline-3,2'-furan-3',3''-indoline]-2,2''-dione, C44H33ClN2O3, (I), 1''-acetyl-1-benzyl-5'-(4-chlorophenyl)-4'-phenyl-4',5'-dihydrodispiro[indoline-3,2'-furan-3',3''-indoline]-2,2''-dione, C39H29ClN2O4, (II), 1''-acetyl-1-benzyl-4',5'-diphenyl-4',5'-dihydrodispiro[indoline-3,2'-furan-3',3''-indoline]-2,2''-dione, C39H30N2O4, (III), and 1''-acetyl-1-benzyl-4',5'-diphenyl-4',5'-dihydrodispiro[indoline-3,2'-furan-3',3''-indoline]-2,2''-dione acetonitrile hemisolvate, C39H30N2O4·0.5C2H3N, (IV). All four compounds exist as racemic mixtures of the SSSR and RRRS stereoisomers. In these structures, the two H atoms of the dihydrofuran ring and the two substituted oxindole rings are in a trans orientation, facilitating intramolecular C-H···O and π-π interactions. These weak interactions play a prominent role in the structural stability and aid the highly regio- and diastereoselective synthesis. In each of the four structures, the molecular assembly in the crystal is also governed by weak noncovalent interactions. Compound (IV) is the solvated analogue of (III) and the two compounds show similar structural features.
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Affiliation(s)
- Krishnan Ravikumar
- X-ray Crystallography Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Balasubramanian Sridhar
- X-ray Crystallography Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Jagadeesh Babu Nanubolu
- X-ray Crystallography Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Govindaraju Karthik
- Natural Product Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Basi Venkata Subba Reddy
- Natural Product Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
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Li SS, Huang CY, Hao JJ, Wang CS. Evaluation of the binding energy for hydrogen-bonded complexes containing amides and peptides. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Hachuła B, Flakus HT, Garbacz A, Stolarczyk A. Inter-hydrogen bond coupling in crystals of 3-phenylpyrazole polymorphs investigated by polarized IR spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 123:151-157. [PMID: 24394531 DOI: 10.1016/j.saa.2013.12.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 11/14/2013] [Accepted: 12/05/2013] [Indexed: 06/03/2023]
Abstract
The remarkably strong differences in the fine structure patterns of the νN-H and νN-D bands, temperature and H/D isotopic effects in crystals of two 3-phenylpyrazole (3PhPz) polymorphs, with tetrameric and hexameric hydrogen bond aggregates, were examined by polarized IR spectroscopy, aided by the calculations utilizing the "strong-coupling" model. Experimental and theoretical approaches have suggested that the anti-co-operativity of hydrogen bonds is the main factor responsible for the differences in the spectral properties of both polymorphs. This interaction affects hydrogen-bond geometry of the associates constituting the lattices and in consequence decides about the relative contribution of two different exciton coupling mechanism, "through-space" (SS) and "tail-to-head" (TH), in the spectra generation. The relative contribution of each individual exciton coupling mechanism in the spectra generation is temperature-dependent. In tetramers the TH coupling mechanism dominates at low temperatures, whereas the role of the SS mechanism increases at higher temperatures. For the hexamers the SS mechanism dominates in the wide temperature range. The two types of 3PhPz associates exhibit two different ways of occurring of the H/D isotopic recognition in the crystal hydrogen bonds. In the tetrameric polymorph identical hydrogen isotope atoms exist in entire hydrogen-bonded cycle of 3PhPz. In the case of 3PhPz hexamers, the H/D isotopic recognition mechanism involves pairs of the closely-spaced hydrogen bonds in a cycle.
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Affiliation(s)
- Barbara Hachuła
- Institute of Chemistry, University of Silesia, 9 Szkolna Street, Pl-40-006 Katowice, Poland.
| | - Henryk T Flakus
- Institute of Chemistry, University of Silesia, 9 Szkolna Street, Pl-40-006 Katowice, Poland.
| | - Aleksandra Garbacz
- Institute of Chemistry, University of Silesia, 9 Szkolna Street, Pl-40-006 Katowice, Poland
| | - Agnieszka Stolarczyk
- Department of Physical Chemistry and Technology of Polymers, Faculty of Chemistry, Silesian University of Technology, 9 Marcina Strzody Street, Pl-44-100 Gliwice, Poland
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Li SS, Huang CY, Hao JJ, Wang CS. A polarizable dipole-dipole interaction model for evaluation of the interaction energies for NH···OC and CH···OC hydrogen-bonded complexes. J Comput Chem 2013; 35:415-26. [DOI: 10.1002/jcc.23473] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/30/2013] [Accepted: 10/03/2013] [Indexed: 02/02/2023]
Affiliation(s)
- Shu-Shi Li
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Cui-Ying Huang
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Jiao-Jiao Hao
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Chang-Sheng Wang
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
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