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Tsering D, Dey P, Kapoor KK, Seth SK. An Energetic and Topological Approach to Understanding the Interplay of Noncovalent Interactions in a Series of Crystalline Spiropyrrolizine Compounds. ACS OMEGA 2024; 9:36242-36258. [PMID: 39220545 PMCID: PMC11360030 DOI: 10.1021/acsomega.4c02511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/20/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
Synthesis of quinoline-containing spiropyrrolizine was achieved via a 1,3-dipolar cycloaddition reaction of azomethine ylide (generated in situ from ninhydrin and l-proline) and (E)-2-styrylquinoline. The synthesized compounds were characterized by 1H NMR, 13C NMR, HRMS, and single-crystal XRD analysis. The XRD data revealed that the solid-state structures of the compounds belong to the monoclinic system of the space group P21/c and are stabilized through various weak noncovalent interactions such as C-H···O, C-H···π, and π···π interactions. The noncovalent interactions are characterized and quantified through Hirshfeld surface analysis. Moreover, the interaction energies of the intermolecular noncovalent interactions are calculated through PIXEL calculation. The PIXEL calculation provides precise interaction energy with an energy decomposition scheme. Energy Framework calculations have also been performed to delve deeper into understanding the intermolecular interactions. The intermolecular interactions are further characterized using Bader's theory of "atoms in molecules" (QTAIM) and the "noncovalent" (NCI) interaction plot index. The nature and strength of noncovalent interactions are analyzed from the topological parameters at (3, -1) bond critical points (BCPs).
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Affiliation(s)
- Dolma Tsering
- Department
of Chemistry, University of Jammu, Jammu 180006, India
| | - Pratik Dey
- Department
of Physics, Jadavpur University, Kolkata 700032, India
| | - Kamal K. Kapoor
- Department
of Chemistry, University of Jammu, Jammu 180006, India
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Percino MJ, Udayakumar M, Cerón M, Pérez-Gutiérrez E, Venkatesan P, Thamotharan S. Weak noncovalent interactions in two positional isomers of acrylonitrile derivatives: inputs from PIXEL energy, Hirshfeld surface and QTAIM analyses. Front Chem 2023; 11:1209428. [PMID: 37448855 PMCID: PMC10338114 DOI: 10.3389/fchem.2023.1209428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
A single crystal X-ray diffraction analysis was performed on two positional isomers (m-tolyl and p-tolyl) of acrylonitrile derivatives, namely, (Z)-3-(4-(pyridin-2-yl) phenyl)-2-(m-tolyl) acrylonitrile (1) and (Z)-3-(4-(pyridin-2-yl)phenyl)-2-(p-tolyl) acrylonitrile (2). Compound 1 crystallized in the monoclinic P21/n space group with two crystallographically independent molecules. Compound 2 also possesses two crystallographically independent molecules and crystallized in the triclinic P-1 space group. The Hirshfeld surface analysis revealed that, in both isomers, intermolecular H⋅⋅⋅H/C/N contacts contribute significantly to the crystal packing. More than 40% of the contribution arises from intermolecular C-H⋅⋅⋅C(π) contacts. In both compounds, the relative contribution of these contacts is comparable, indicating that the positional isomeric effects are marginal. The structures in which these isomers are arranged in the solid state are very similar, and the lattice energies are also comparable between the isomers. The Coulomb-London-Pauli-PIXEL (CLP-PIXEL) energy analysis identified the energetically significant dimers. The strength of the intra- and intermolecular interactions was evaluated using the quantum theory of atoms in molecules approach. The UV-Vis absorbance in three different solvents (chloroform, ethanol, and ethyl acetate) for isomers 1 and 2 are very similar. This result is in good agreement with the time-dependent density-functional theory (TD-DFT) calculations.
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Affiliation(s)
- M. Judith Percino
- Instituto de Ciencias, Unidad de Polímeros y Electrónica Orgánica, Benemérita Universidad Autónoma de Puebla, Val3-Ecocampus Valsequillo, Puebla, CP, Mexico
| | - Mani Udayakumar
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
| | - Margarita Cerón
- Instituto de Ciencias, Unidad de Polímeros y Electrónica Orgánica, Benemérita Universidad Autónoma de Puebla, Val3-Ecocampus Valsequillo, Puebla, CP, Mexico
| | - Enrique Pérez-Gutiérrez
- Instituto de Ciencias, Unidad de Polímeros y Electrónica Orgánica, Benemérita Universidad Autónoma de Puebla, Val3-Ecocampus Valsequillo, Puebla, CP, Mexico
| | - Perumal Venkatesan
- Department of Chemistry, Srimad Andavan Arts and Science College (Autonomous), Tiruchirappalli, India
| | - Subbiah Thamotharan
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
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Galvez CE, Piro OE, Echeverría GA, Robles NL, Lezama JOG, Sankaran SV, Thamotharan S, Villecco MB, Loandos MDH, Gil DM. Experimental and theoretical insights into the formation of weak hydrogen bonds and H⋯H bonding interactions in the solid-state structure of two eucalyptol derivatives. NEW J CHEM 2022. [DOI: 10.1039/d2nj00428c] [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
We report the synthesis and X-ray solid-state structure of two eucalyptol derivatives. Both compounds form self-assembled dimers establishing C–H⋯O hydrogen bonds and H⋯H bonding interactions.
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Affiliation(s)
- Carolina E. Galvez
- Cátedra de Química Orgánica II, Instituto de Química Orgánica, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, T4000INI, San Miguel de Tucumán, Argentina
| | - Oscar E. Piro
- Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata e IFLP (CONICET, CCT-La Plata), C. C. 67, 1900, La Plata, Argentina
| | - Gustavo A. Echeverría
- Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata e IFLP (CONICET, CCT-La Plata), C. C. 67, 1900, La Plata, Argentina
| | - Norma Lis Robles
- INQUINOA (CONICET – UNT), Facultad de Ciencias Exactas y Tecnología, Universidad Nacional de Tucumán. Av. Independencia 1800, CP 4000, San Miguel de Tucumán, Argentina
| | - José O. G. Lezama
- INBIOFAL (CONICET – UNT), Instituto de Química Orgánica, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, T4000INI, San Miguel de Tucumán, Argentina
| | - Sankaran Venkatachalam Sankaran
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613 401, India
| | - Subbiah Thamotharan
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613 401, India
| | - Margarita B. Villecco
- Cátedra de Química Orgánica II, Instituto de Química Orgánica, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, T4000INI, San Miguel de Tucumán, Argentina
| | - María del H. Loandos
- Cátedra de Química Orgánica II, Instituto de Química Orgánica, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, T4000INI, San Miguel de Tucumán, Argentina
| | - Diego M. Gil
- INBIOFAL (CONICET – UNT), Instituto de Química Orgánica, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, T4000INI, San Miguel de Tucumán, Argentina
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Al-Wahaibi L, Grandhi DS, Tawfik SS, Al-Shaalan NH, Elmorsy MA, El-Emam AA, Percino MJ, Thamotharan S. Probing the Effect of Halogen Substituents (Br, Cl, and F) on the Non-covalent Interactions in 1-(Adamantan-1-yl)-3-arylthiourea Derivatives: A Theoretical Study. ACS OMEGA 2021; 6:4816-4830. [PMID: 33644590 PMCID: PMC7905817 DOI: 10.1021/acsomega.0c05793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/02/2021] [Indexed: 12/20/2022]
Abstract
The effect of halogen substituents (X = Br, Cl, and F) on the crystal packing and intra- and intermolecular interactions in four adamantane-thiourea hybrid derivatives is investigated using different theoretical tools. The bromo and chloro derivatives exhibit 3D isostructurality as evident from lattice parameters, molecular conformation, and crystal packing. The density functional theory study suggests that the molecular conformation of the parent (unsubstituted) and fluoro derivatives exhibits a stable low energy anti-syn conformation. In contrast, bromo and chloro derivatives adopt stable and relatively high energy minima on their potential energy surfaces. Hirshfeld surface analysis reveals the effect of halogen substituents on the intermolecular contacts. The halogen atoms mainly reduce the contribution of H···H contacts toward crystal packing. PIXEL energy analysis indicates the strong dimer formed by N-H···S hydrogen bonds in all four structures. It also revealed that a vast number of H···H contacts observed in different dimers of these structures either presented along with other conventional interactions or solely stabilize the dimeric topology. The topological parameters for intermolecular interactions in these structures suggest an intermediate bonding character between shared and closed-shell interactions for N-H···S hydrogen bonds in the parent and chloro derivatives. In contrast, the N-H···S hydrogen bond in other structures is of a closed-shell interaction. Among four derivatives, the fluoro derivative is weakly packed in the solid state based on the PIXEL method's lattice energy calculation.
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Affiliation(s)
- Lamya
H. Al-Wahaibi
- Department
of Chemistry, College of Sciences, Princess
Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Divya Sri Grandhi
- Biomolecular
Crystallography Laboratory, Department of Bioinformatics, School of
Chemical and Biotechnology, SASTRA Deemed
University, Thanjavur 613 401, India
| | - Samar S. Tawfik
- Department
of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Nora H. Al-Shaalan
- Department
of Chemistry, College of Sciences, Princess
Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Mohammed A. Elmorsy
- Department
of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Ali A. El-Emam
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - M. Judith Percino
- Unidad
de Polímeros y Electrónica Orgánica, Instituto
de Ciencias, Benemérita Universidad
Autónoma de Puebla, Val3-Ecocampus Valsequillo, Independencia O2 Sur 50, San Pedro Zacachimalpa, Puebla CP 72960, Mexico
| | - Subbiah Thamotharan
- Biomolecular
Crystallography Laboratory, Department of Bioinformatics, School of
Chemical and Biotechnology, SASTRA Deemed
University, Thanjavur 613 401, India
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Interplay of weak intermolecular interactions in two Schiff's bases with organic fluorine derived from 5-nitrothiophene-2-carboxaldehyde: Crystal structures, DFT calculation and in vitro evaluation of bioactivities. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Correlation between structural and optical properties of π-conjugated acrylonitrile derivatives: Insights from X-ray, energy frameworks, TD-DFT and charge density analysis. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mitoraj MP, Sagan F, Szczepanik DW, de Lange JH, Ptaszek AL, van Niekerk DME, Cukrowski I. Origin of Hydrocarbons Stability from a Computational Perspective: A Case Study of Ortho-Xylene Isomers. Chemphyschem 2020; 21:494-502. [PMID: 31990431 DOI: 10.1002/cphc.202000066] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Indexed: 01/12/2023]
Abstract
It is shown herein that intuitive and text-book steric-clash based interpretation of the higher energy "in-in" xylene isomer (as arising solely from the repulsive CH⋅⋅⋅HC contact) with respect to the corresponding global-minimum "out-out" configuration (where the clashing C-H bonds are tilted out) is misleading. It is demonstrated that the two hydrogen atoms engaged in the CH⋅⋅⋅HC contact in "in-in" are involved in attractive interaction so they cannot explain the lower stability of this isomer. We have proven, based on the arsenal of modern bonding descriptors (EDDB, HOMA, NICS, FALDI, ETS-NOCV, DAFH, FAMSEC, IQA), that in order to understand the relative stability of "in-in" versus "out-out" xylenes isomers one must consider the changes in the electronic structure encompassing the entire molecules as arising from the cooperative action of hyperconjugation, aromaticity and unintuitive London dispersion plus charge delocalization based intra-molecular CH⋅⋅⋅HC interactions.
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Affiliation(s)
- Mariusz P Mitoraj
- Department of Theoretical Chemistry Faculty of Chemistry, Jagiellonian University in Krakow, Gronostajowa 2, 30-87, Krakow, Poland
| | - Filip Sagan
- Department of Theoretical Chemistry Faculty of Chemistry, Jagiellonian University in Krakow, Gronostajowa 2, 30-87, Krakow, Poland
| | - Dariusz W Szczepanik
- Department of Theoretical Chemistry Faculty of Chemistry, Jagiellonian University in Krakow, Gronostajowa 2, 30-87, Krakow, Poland
| | - Jurgens H de Lange
- Department of Chemistry Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa
| | - Aleksandra L Ptaszek
- Department of Theoretical Chemistry Faculty of Chemistry, Jagiellonian University in Krakow, Gronostajowa 2, 30-87, Krakow, Poland
| | - Daniel M E van Niekerk
- Department of Chemistry Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa
| | - Ignacy Cukrowski
- Department of Chemistry Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa
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