1
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Siddiqui R, Burguera S, de Las Nieves Piña M, Dhamija S, Titi HM, Frontera A, Bauzá A, Patra R. From Coordination to π-Hole Chemistry of Transition Metals: Metalloporphyrins as a Case of Study. Angew Chem Int Ed Engl 2024:e202409963. [PMID: 38934220 DOI: 10.1002/anie.202409963] [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: 05/27/2024] [Revised: 06/26/2024] [Accepted: 06/26/2024] [Indexed: 06/28/2024]
Abstract
Herein we have evidenced the formation of favorable π-hole Br⋅⋅⋅metal noncovalent interactions (NCIs) involving elements from groups 9, 11 and 12. More in detail, M (M=Co2+, Ni2+, Cu2+ and Zn2+) containing porphyrins have been synthesized and their supramolecular assemblies structurally characterized by means of single crystal X-ray diffraction and Hirshfeld surface analyses, revealing the formation of directional Br⋅⋅⋅M contacts in addition to ancillary hydrogen bond and lone pair-π bonds. Computations at the PBE0-D3/def2-TZVP level of theory revealed the π-hole nature of the Br⋅⋅⋅M interaction. In addition, the physical nature of these NCIs was studied using Quantum Chemistry methodologies, providing evidence of π-hole Spodium and Regium bonds in Zn2+ and Cu2+ porphyrins, in addition to unveiling the presence of a π-hole for group 9 (Co2+). On the other hand, group 10 (Ni2+) acted as both electron donor and acceptor moiety without showing an electropositive π-hole. Owing to the underexplored potential of π-hole interactions in transition metal chemistry, we believe the results reported herein will be useful in supramolecular chemistry, organometallics, and solid-state chemistry by i) putting under the spotlight the π-hole chemistry involving first row transition metals and ii) unlocking a new tool to direct the self-assembly of metalloporphyrins.
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Affiliation(s)
- Rafia Siddiqui
- Amity Institute of Click Chemistry Research and Studies, Amity University, Noida, Uttar Pradesh, India
| | - Sergi Burguera
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122, Palma de Mallorca, Baleares, Spain
| | - María de Las Nieves Piña
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122, Palma de Mallorca, Baleares, Spain
| | - Swati Dhamija
- Amity Institute of Click Chemistry Research and Studies, Amity University, Noida, Uttar Pradesh, India
| | - Hatem M Titi
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QCH3A0B8, Canada
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122, Palma de Mallorca, Baleares, Spain
| | - Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122, Palma de Mallorca, Baleares, Spain
| | - Ranjan Patra
- Amity Institute of Click Chemistry Research and Studies, Amity University, Noida, Uttar Pradesh, India
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2
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Peluso P, Mamane V, Spissu Y, Casu G, Dessì A, Dallocchio R, Sechi B, Palmieri G, Rozzo C. Iodinated 4,4'-Bipyridines with Antiproliferative Activity Against Melanoma Cell Lines. ChemMedChem 2024; 19:e202300662. [PMID: 38489502 DOI: 10.1002/cmdc.202300662] [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: 11/27/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 03/17/2024]
Abstract
In the last decade, biological processes involving halogen bond (HaB) as a leading interaction attracted great interest. However, although bound iodine atoms are considered powerful HaB donors, few iodinated new drugs were reported so far. Recently, iodinated 4,4'-bipyridines showed interesting properties as HaB donors in solution and in the solid state. In this paper, a study on the inhibition activity of seven halogenated 4,4'-bipyridines against malignant melanoma (MM) cell proliferation is described. Explorative dose/response proliferation assays were first performed with three 4,4'-bipyridines by using four MM cell lines and the normal BJ fibroblast cell line as control. Among them, the A375 MM cell line was the most sensitive, as determined by MTT assays, which was selected to evaluate the antiproliferative activity of all 4,4'-bipyridines. Significantly, the presence of an electrophilic iodine impacted the biological activity of the corresponding compounds. The 3,3',5,5'-tetrachloro-2-iodo-4,4'-bipyridine showed significant antiproliferation activity against the A375 cell line, and lower toxicity on BJ fibroblasts. Through in silico studies, the stereoelectronic features of possible sites determining the bioactivity were explored. These results pave the way for the utilization of iodinated 4,4'-bipyridines as templates to design new promising HaB-enabled inhibitors of MM cell proliferation.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
| | - Victor Mamane
- Institut de Chimie de Strasbourg, UMR CNRS 7177, Centre National de la Recherche Scientifique (CNRS), 1 Rue Blaise Pascal, 67008, Strasbourg, France
| | - Ylenia Spissu
- Istituto di Scienze delle Produzioni Alimentari ISPA-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
| | - Giuseppina Casu
- Istituto di Ricerca Genetica e Biomedica IRGB-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
| | - Alessandro Dessì
- Istituto di Chimica Biomolecolare ICB-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
| | - Roberto Dallocchio
- Istituto di Chimica Biomolecolare ICB-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
| | - Barbara Sechi
- Istituto di Chimica Biomolecolare ICB-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
| | - Giuseppe Palmieri
- Istituto di Ricerca Genetica e Biomedica IRGB-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
| | - Carla Rozzo
- Istituto di Ricerca Genetica e Biomedica IRGB-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
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3
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Rajan R, Karthikeyan S, Desikan R. Synthesis, Structural Elucidation, In Silico and In Vitro Studies of New Class of Methylenedioxyphenyl-Based Amide Derivatives as Potential Myeloperoxidase Inhibitors for Cardiovascular Protection. ACS OMEGA 2024; 9:7850-7868. [PMID: 38405500 PMCID: PMC10882620 DOI: 10.1021/acsomega.3c07555] [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: 09/29/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 02/27/2024]
Abstract
Novel methylenedioxyphenyl-based amides, especially N-(4-methoxybenzyl)-6-nitrobenzo-[1,3]-dioxole-5-carboxamide (MDC) and N-(3-acetylphenyl)-6-nitrobenzo-[1,3]-dioxole-5-carboxamide (ADC), potential cardiovascular preventive agents, are successfully synthesized, and their chemical structures are verified by 1H and 13C NMR, Fourier transform infrared (FT-IR), high-resolution mass spectrometry (HRMS), and single-crystal X-ray diffraction (SC-XRD) analyses. Data obtained from SC-XRD reveal that MDC and ADC are both monoclinic molecules with Z = 2 and 4, respectively. From density functional theory (DFT) calculations, 3.54 and 3.96 eV are the energy gaps of the optimized MDC and ADC structures, respectively. MDC and ADC exhibit an electrophilicity index value of more than 1.5 eV, suggesting that they can act as an electrophile, facilitating bond formation with biomolecules. Hirshfeld surface analysis demonstrates that more than 25% of atomic interactions in both MDC and ADC are from H···H interactions. Based on pharmacokinetic predictions, MDC and ADC exhibit drug-like properties, and molecular docking simulations revealed favorable interactions with active site pockets. Both MDC and ADC achieved higher docking scores of -7.74 and -7.79 kcal/mol, respectively, with myeloperoxidase (MPO) protein. From docking results, MPO was found to be most favorable followed by dipeptidyl peptidase-4 (DPP-4) and α-glucosidase (α-GD). Antioxidant, anti-inflammatory, and in vitro enzymatic studies of MDC and ADC indicate that MDC is more selective toward MPO and more potent than ADC. The application of MDC to inhibit myeloperoxidase could be ascertained to reduce the cardiovascular risk factor. This can be supported from the results of computational docking (based on hydrogen bonding and docking score), in vitro antioxidant and anti-inflammatory properties, and MPO enzymatic inhibition (based on the percentage of inhibition and IC50 values).
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Affiliation(s)
- Reshma Rajan
- Department of Chemistry,
School of Advanced Sciences, Vellore Institute
of Technology, Vellore 632014, Tamilnadu, India
| | - Sambantham Karthikeyan
- Department of Chemistry,
School of Advanced Sciences, Vellore Institute
of Technology, Vellore 632014, Tamilnadu, India
| | - Rajagopal Desikan
- Department of Chemistry,
School of Advanced Sciences, Vellore Institute
of Technology, Vellore 632014, Tamilnadu, India
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4
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Scheiner S, Amonov A. Types of noncovalent bonds within complexes of thiazole with CF 4 and SiF 4. Phys Chem Chem Phys 2024; 26:6127-6137. [PMID: 38299682 DOI: 10.1039/d4cp00057a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The five-membered heteroaromatic thiazole molecule contains a number of electron-rich regions that could attract an electrophile, namely the N and S lone pairs that lie in the molecular plane, and π-system areas above the plane. The possibility of each of these sites engaging in a tetrel bond (TB) with CF4 and SiF4, as well as geometries that encompass a CH⋯F H-bond, was explored via DFT calculations. There are a number of minima that occur in the pairing of thiazole with CF4 that are very close in energy, but these complexes are weakly bound by less than 2 kcal mol-1 and the presence of a true TB is questionable. The inclusion of zero-point vibrational energies alters the energetic ordering, which is further modified when entropic effects are added. The preferred geometry would thus be sensitive to the temperature of an experiment. Replacement of CF4 by SiF4 leaves intact most of the configurations, and their tight energetic clustering, the ordering of which is again altered as the temperature rises. But there is one exception in that by far the most tightly bound complex involves a strong Si⋯N TB between SiF4 and the lone pair of the thiazole N, with an interaction energy of 30 kcal mol-1. Even accounting for its high deformation energy and entropic considerations, this structure remains as clearly the most stable at any temperature.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry Utah State University Logan, Utah 84322-0300, USA.
| | - Akhtam Amonov
- Department of Optics and Spectroscopy, Institute of Engineering Physics Samarkand State University 140104, University blv. 15, Samarkand, Uzbekistan
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5
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Peluso P, Chankvetadze B. Recent developments in molecular modeling tools and applications related to pharmaceutical and biomedical research. J Pharm Biomed Anal 2024; 238:115836. [PMID: 37939549 DOI: 10.1016/j.jpba.2023.115836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/21/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023]
Abstract
In modern pharmaceutical and biomedical research, molecular modeling represents a useful tool to explore processes and their mechanistic bases at the molecular level. Integrating experimental and virtual analysis is a fruitful approach to study ligand-receptor interaction in chemical, biochemical and biological environments. In these fields, molecular docking and molecular dynamics are considered privileged techniques for modeling (bio)macromolecules and related complexes. This review aims to present the current landscape of molecular modeling in pharmaceutical and biomedical research by examining selected representative applications published in the last years and highlighting current topics and trends of this field. Thus, a systematic compilation of all published literature has not been attempted herein. After a brief overview of the main theoretical and computational tools used to investigate mechanisms at molecular level, recent applications of molecular modeling in drug discovery, ligand binding and for studying protein conformation and function will be discussed. Furthermore, specific sections will be devoted to the application of molecular modeling for unravelling enantioselective mechanisms underlying the enantioseparation of chiral compounds of pharmaceutical and biomedical interest as well as for studying new forms of noncovalent interactivity identified in biochemical and biological environments. The general aim of this review is to provide the reader with a modern overview of the topic, highlighting advancements and outlooks as well as drawbacks and pitfalls still affecting the applicability of theoretical and computational methods in the field of pharmaceutical and biomedical research.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB-CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy.
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Ave 3, 0179 Tbilisi, Georgia
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6
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Echeverría J, Alvarez S. The borderless world of chemical bonding across the van der Waals crust and the valence region. Chem Sci 2023; 14:11647-11688. [PMID: 37920358 PMCID: PMC10619631 DOI: 10.1039/d3sc02238b] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/01/2023] [Indexed: 11/04/2023] Open
Abstract
The definition of the van der Waals crust as the spherical section between the atomic radius and the van der Waals radius of an element is discussed and a survey of the application of the penetration index between two interacting atoms in a wide variety of covalent, polar, coordinative or noncovalent bonding situations is presented. It is shown that this newly defined parameter permits the comparison of bonding between pairs of atoms in structural and computational studies independently of the atom sizes.
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Affiliation(s)
- Jorge Echeverría
- Instituto de Síntesis Química y Catalisis Homogénea (ISQCH) and Departmento de Química Inorgánica, Facultad de Ciencias, Universidad de Zaragoza Pedro Cerbuna 12 50009 Zaragoza Spain
| | - Santiago Alvarez
- Department de Química Inorgànica i Orgànica, Secció de Química Inorgànica, e Institut de Química Teòrica i Computacional, Universitat de Barcelona Martí i Franquès 1-11 08028 -Barcelona Spain
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7
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Ibrahim MAA, Saeed RRA, Shehata MNI, Moussa NAM, Tawfeek AM, Ahmed MN, Abd El-Rahman MK, Shoeib T. Sigma-Hole and Lone-Pair-Hole Site-Based Interactions of Seesaw Tetravalent Chalcogen-Bearing Molecules with Lewis Bases. ACS OMEGA 2023; 8:32828-32837. [PMID: 37720791 PMCID: PMC10500585 DOI: 10.1021/acsomega.3c03981] [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: 06/06/2023] [Accepted: 07/21/2023] [Indexed: 09/19/2023]
Abstract
For the first time, sigma (σ)- and lone-pair (lp)-hole site-based interactions of SF4 and SeF4 molecules in seesaw geometry with NH3 and FH Lewis bases were herein comparatively investigated. The obtained findings from the electrostatic potential analysis outlined the emergence of sundry holes on the molecular entity of the SF4 and SeF4 molecules, dubbed the σ- and lp-holes. The energetic viewpoint announced splendid negative binding energy values for σ-hole site-based interactions succeeded by lp-hole analogues, which were found to be -9.21 and -0.50 kcal/mol, respectively, for SeF4···NH3 complex as a case study. Conspicuously, a proper concurrence between the strength of chalcogen σ-hole site-based interactions and the chalcogen's atomic size was obtained, whereas a reverse pattern was proclaimed for the lp-hole counterparts. Further, a higher preference for the YF4···NH3 complexes with elevated negative binding energy was promulgated over the YF4···FH ones, indicating the eminent role of Lewis basicity. The indications of the quantum theory of atoms in molecules generally asserted the closed-shell nature of all the considered interactions. The observation of symmetry-adapted perturbation theory revealed the substantial contributing role of the electrostatic forces beyond the occurrence of σ-hole site-based interactions. In comparison, the dispersion forces were specified to govern the lp-hole counterparts. Such emerging findings would be a gate for the fruitful forthcoming applications of chalcogen bonding interactions in crystal engineering and biological systems.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
- School
of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Rehab R. A. Saeed
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Mohammed N. I. Shehata
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A. M. Moussa
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Ahmed M. Tawfeek
- Chemistry
Department, College of Science, King Saud
University, Riyadh 11451, Saudi Arabia
| | - Muhammad Naeem Ahmed
- Department
of Chemistry, The University of Azad Jammu
and Kashmir, Muzaffarabad 13100, Pakistan
| | - Mohamed K. Abd El-Rahman
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Tamer Shoeib
- Department
of Chemistry, The American University in
Cairo, New Cairo 11835, Egypt
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8
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Gobbi S, Martini S, Rozza R, Spinello A, Caciolla J, Rampa A, Belluti F, Zaffaroni N, Magistrato A, Bisi A. Switching from Aromatase Inhibitors to Dual Targeting Flavonoid-Based Compounds for Breast Cancer Treatment. Molecules 2023; 28:3047. [PMID: 37049810 PMCID: PMC10096035 DOI: 10.3390/molecules28073047] [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: 02/23/2023] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023] Open
Abstract
Despite the significant outcomes attained by scientific research, breast cancer (BC) still represents the second leading cause of death in women. Estrogen receptor-positive (ER+) BC accounts for the majority of diagnosed BCs, highlighting the disruption of estrogenic signalling as target for first-line treatment. This goal is presently pursued by inhibiting aromatase (AR) enzyme or by modulating Estrogen Receptor (ER) α. An appealing strategy for fighting BC and reducing side effects and resistance issues may lie in the design of multifunctional compounds able to simultaneously target AR and ER. In this paper, previously reported flavonoid-related potent AR inhibitors were suitably modified with the aim of also targeting ERα. As a result, homoisoflavone derivatives 3b and 4a emerged as well-balanced submicromolar dual acting compounds. An extensive computational study was then performed to gain insights into the interactions the best compounds established with the two targets. This study highlighted the feasibility of switching from single-target compounds to balanced dual-acting agents, confirming that a multi-target approach may represent a valid therapeutic option to counteract ER+ BC. The homoisoflavone core emerged as a valuable natural-inspired scaffold for the design of multifunctional compounds.
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Affiliation(s)
- Silvia Gobbi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Silvia Martini
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, Via Amadeo 42, 20113 Milano, Italy
| | - Riccardo Rozza
- National Research Council of Italy Institute of Materials (CNR-IOM) c/o SISSA, Via Bonomea 265, 34136 Trieste, Italy
| | - Angelo Spinello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Jessica Caciolla
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Angela Rampa
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Federica Belluti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Nadia Zaffaroni
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, Via Amadeo 42, 20113 Milano, Italy
| | - Alessandra Magistrato
- National Research Council of Italy Institute of Materials (CNR-IOM) c/o SISSA, Via Bonomea 265, 34136 Trieste, Italy
| | - Alessandra Bisi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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9
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The influence of N...π pnicogen bonding in π-stacked parallel displaced geometry of nitrobenzene dimers: Evidence using matrix isolation infrared spectroscopy and ab initio computations. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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10
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Saha B, Bhattacharjee M, Boruah SR, N Dutta Purkayastha R, M Gomila R, Chowdhury S, Mandal A, Frontera A. Synthesis, structural characterization, DNA interaction, dye adsorption properties and theoretical studies of copper (II) carboxylates. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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11
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Bellia S, Anderson G, Zeller M, Mirjafari A, Hillesheim PC. 1-Methyl-5-nitro-imidazolium chloride. IUCRDATA 2022; 7:x220878. [PMID: 36337461 PMCID: PMC9635428 DOI: 10.1107/s2414314622008781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/21/2022] Open
Abstract
The title salt, C4H6N3O2 +·Cl-, exhibits multiple hydrogen-bonding inter-actions involving the nitro-imidazolium cation and the chloride anion. Strong hydrogen bonds between the amine hydrogen atom and the chloride anion link the ionic moieties. Of note, with respect to H⋯Cl inter-actions, the central aromatic hydrogen atom displays a shorter inter-action than the other aromatic hydrogen atom. Finally, inter-actions are observed between the nitro moiety and methyl H atoms. While no π-π stacking is observed, anion-π inter-actions are present. The crystal was refined as a two-component twin.
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Affiliation(s)
- Sophia Bellia
- Ave Maria University, Department of Chemistry and Physics, 5050 Ave Maria Blvd, Ave Maria, Florida 34142, USA
| | - Grace Anderson
- Department of Chemistry and Physics, Florida Gulf Coast University, 10501 FGCU Blvd. South, Fort Myers, Florida 33965, USA
| | - Matthias Zeller
- Purdue University, Department of Chemistry, 560 Oval Drive, West Lafayette, Indiana 47907, USA
| | - Arsalan Mirjafari
- Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, USA
| | - Patrick C. Hillesheim
- Ave Maria University, Department of Chemistry and Physics, 5050 Ave Maria Blvd, Ave Maria, Florida 34142, USA
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12
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Jeyaraman Selvaraj N, Sathya U, Gomathi S, Jegan Jennifer S, Mathivathanan L, Abdul Razak I. Synthesis, crystal structure determination and Hirshfeld surface analysis of three new salt forms of creatinine with hydrobromic acid, 3-aminobenzoic acid and 3,5-dinitrobenzoic acid. ACTA CRYSTALLOGRAPHICA SECTION C STRUCTURAL CHEMISTRY 2022; 78:437-448. [DOI: 10.1107/s2053229622006684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 06/28/2022] [Indexed: 11/10/2022]
Abstract
Creatinine, a biologically important compound, is used to analyze kidney function and kidney diseases in the human body. The salt form of creatinine is used in the formation of drug materials like anti-HIV, antifungal, antiprotozoal, antiviral and antitumour compounds. Here we report the solid-state structures of three new crystalline salts, namely, creatininium (2-amino-1-methyl-4-oxo-4,5-dihydro-1H-imidazol-3-ium) bromide, C4H8N3O+·Br−, (I), creatininium 3-aminobenzoate, C4H8N3O+·C7H6NO2
−, (II), and creatininium 3,5-dinitrobenzoate, C4H8N3O+·C7H3N2O6
−, (III). These salts have been synthesized and characterized by single-crystal X-ray diffraction and Hirshfeld surface analysis. The structural chemistry of salts (I)–(III) and their crystal packing are discussed in detail. The primary interaction between the creatinine cation and the acid anion in the three salts is N—H...Br/O hydrogen bonds. In salt (I), the creatinine cation and bromide anion are connected through a pair of N—H...Br hydrogen bonds forming R
4
2(8) and R
4
2(12) ring motifs. In salts (II) and (III), the creatinine cation interacts with the corresponding anion via a pair of N—H...O hydrogen bonds. The crystal structure is further stabilized by C—H...O and O—H...O hydrogen bonds with the ring motifs R
2
2(8), R
2
1(7) and R
2
1(6). Furthermore, the crystal structures are stabilized by π–π, C—H...π, C—O...π and N—O...π stacking interactions. The contributions made by each hydrogen bond in maintaining the crystal structure stability has been quantified by Hirshfeld surface analysis.
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13
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Scheiner S. On the Ability of Nitrogen to Serve as an Electron Acceptor in a Pnicogen Bond. J Phys Chem A 2021; 125:10419-10427. [PMID: 34846149 DOI: 10.1021/acs.jpca.1c09213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Whereas pnicogen atoms like P and As have been shown repeatedly to act as electron acceptors in pnicogen bonds, the same is not true of the more electronegative first-row N atom. Quantum calculations assess whether N can serve in this capacity in such bonds and under what conditions. There is a positive π-hole belt that surrounds the central N atom in the linear arrangement of NNNF, NNN-CN, and NNO, which can engage a NH3 base to form a pnicogen bond with binding energy between 3 and 5 kcal/mol. Within the context of a planar arrangement, the π-hole above the N in NO2OF, N(CN)3, and CF3NO2 is also capable of forming a pnicogen bond, the strongest of which amounts to 11 kcal/mol with NMe3 as base. In their pyramidal geometry, NF3 and N(NO2)3 engage with a base through the σ-hole on the central N, with variable binding energies between 2 and 9 kcal/mol. AIM and NBO provide somewhat different interpretations of the secondary interactions that occur in some of these complexes.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300 United States
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14
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Scheiner S. Maximal occupation by bases of π-hole bands surrounding linear molecules. J Comput Chem 2021; 43:319-330. [PMID: 34859910 DOI: 10.1002/jcc.26792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/19/2022]
Abstract
Linear molecules such as CO2 contain a positive π-hole ring that surrounds C on the molecule's equator. Quantum calculations examine the question as to how many bases can simultaneously bind to this ring. Linear molecules examined are TO2 , where T = C, Si, Ge, Sn; bases are NCH and NH3 . CO2 engages in the weakest of the tetrel bonds, and can bind up to three NCH and two NH3 . Unlike σ-hole tetrel bonds, Si forms the strongest tetrel bonds, with interaction energies as high as 43 kcal/mol with NH3 . But like GeO2 , SiO2 can sustain only two bases in its equatorial ring. The π-hole ring of SnO2 can engage in up to four tetrel bonds with either NCH or NH3 , even though these bonds are weaker than those with GeO2 or SiO2 . As all of these complexes cast TO2 in the role of multiple electron acceptor, the resulting negative cooperativity makes each successive bond weaker than its predecessor as bases are added, as well as reducing the magnitude of the central molecule's π-hole.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA
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15
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Abstract
The list of σ-hole bonds is long and growing, encompassing both H-bonds and its closely related halogen, chalcogen, etc., sisters. These bonds rely on the asymmetric distribution of electron density, whose depletion along the extension of a covalent bond leaves a positive region of electrostatic potential from which these bonds derive their name. However, the density distributions of other molecules contain analogous positive regions that lie out of the molecular plane known as π-holes, which are likewise capable of engaging in noncovalent bonds. Quantum calculations are applied to study such π-hole bonds that involve linear molecules, whose positive region is a circular belt surrounding the molecule, rather than the more restricted area of a σ-hole. These bonds are examined in terms of their most fundamental elements arising from the spatial dispositions of their relevant molecular orbitals and the π-holes in both the total electron density and the electrostatic potential to which they lead. Systems examined comprise tetrel, chalcogen, aerogen, and triel bonds, as well as those involving group II elements, with atoms drawn from various rows of the Periodic Table. The π-hole bonds established by linear molecules tend to be weaker than those of comparable planar systems.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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16
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Núñez-Franco R, Jiménez-Osés G, Jiménez-Barbero J, Cabrera-Escribano F, Franconetti A. Unveiling the role of pyrylium frameworks on π-stacking interactions: a combined ab initio and experimental study. Phys Chem Chem Phys 2021; 24:1965-1973. [PMID: 34633001 DOI: 10.1039/d1cp02622d] [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
A multidisciplinary study is presented to shed light on how pyrylium frameworks, as π-hole donors, establish π-π interactions. The combination of CSD analysis, computational modelling (ab intitio, DFT and MD simulations) and experimental NMR spectroscopy data provides essential information on the key parameters that characterize these intereactions, opening new avenues for further applications of this versatile heterocycle.
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Affiliation(s)
- Reyes Núñez-Franco
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Spain.
| | - Gonzalo Jiménez-Osés
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Spain. .,lkerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Spain. .,lkerbasque, Basque Foundation for Science, 48009 Bilbao, Spain.,Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940 Leioa, Bizkaia, Spain
| | - Francisca Cabrera-Escribano
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, C/Profesor García González 1, 41012 Sevilla, Spain
| | - Antonio Franconetti
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Spain.
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17
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Scheiner S. Dissection of the Origin of π-Holes and the Noncovalent Bonds in Which They Engage. J Phys Chem A 2021; 125:6514-6528. [PMID: 34310147 DOI: 10.1021/acs.jpca.1c05431] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Accompanying the rapidly growing list of σ-hole bonds has come the acknowledgment of parallel sorts of noncovalent bonds which owe their stability in large part to a deficiency of electron density in the area above the molecular plane, known as a π-hole. The origins of these π-holes are probed for a wide series of molecules, comprising halogen, chalcogen, pnicogen, tetrel, aerogen, and spodium bonds. Much like in the case of their σ-hole counterparts, formation of the internal covalent π-bond in the Lewis acid molecule pulls density toward the bond midpoint and away from its extremities. This depletion of density above the central atom is amplified by an electron-withdrawing substituent. At the same time, the amplitude of the π*-orbital is enhanced in the region of the density-depleted π-hole, facilitating a better overlap with the nucleophile's lone pair orbital and a stabilizing n → π* charge transfer. The presence of lone pairs on the central atom acts to attenuate the π-hole and shift its position somewhat, resulting in an overall weakening of the π-hole bond. There is a tendency for π-hole bonds to include a higher fraction of induction energy than σ-bonds with proportionately smaller electrostatic and dispersion components, but this distinction is less a product of the σ- or π-character and more a function of the overall bond strength.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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18
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Babić S, Čižmek L, Maršavelski A, Malev O, Pflieger M, Strunjak-Perović I, Popović NT, Čož-Rakovac R, Trebše P. Utilization of the zebrafish model to unravel the harmful effects of biomass burning during Amazonian wildfires. Sci Rep 2021; 11:2527. [PMID: 33510260 PMCID: PMC7844006 DOI: 10.1038/s41598-021-81789-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/11/2021] [Indexed: 12/26/2022] Open
Abstract
Amazonian wildfires in 2019 have raised awareness about rainforest burning due to increased emissions of particulate matter and carbon. In the context of these emissions, by-products of lignin thermal degradation (i.e. methoxyphenols) are often neglected. Methoxyphenols entering the atmosphere may form intermediates with currently unknown reaction mechanisms and toxicity. This study for the first time provides a comprehensive insight into the impact of lignin degradation products [guaiacol, catechol], and their nitrated intermediates [4-nitrocatechol, 4,6-dinitroguaiacol, 5-nitroguaiacol] on zebrafish Danio rerio. Results revealed 4-nitrocatechol and catechol as the most toxic, followed by 4,6DNG > 5NG > GUA. The whole-organism bioassay integrated with molecular modeling emphasized the potential of methoxyphenols to inhibit tyrosinase, lipoxygenase, and carbonic anhydrase, consequently altering embryonic development (i.e. affected sensorial, skeletal, and physiological parameters, pigmentation formation failure, and non-hatching of larvae). The whole-organism bioassay integrated with in silico approach confirmed the harmful effects of lignin degradation products and their intermediates on aquatic organisms, emphasizing the need for their evaluation within ecotoxicity studies focused on aquatic compartments.
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Affiliation(s)
- Sanja Babić
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.,Center of Excellence for Marine Bioprospecting (BioProCro), Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Lara Čižmek
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.,Center of Excellence for Marine Bioprospecting (BioProCro), Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Aleksandra Maršavelski
- Faculty of Science, Department of Chemistry, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Olga Malev
- Faculty of Science, Department of Biology, University of Zagreb, Roosevelt square 6, Zagreb, Croatia. .,Laboratory for Biological Diversity, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.
| | - Maryline Pflieger
- Faculty of Health Sciences, University of Ljubljana, Zdravstvena pot 5, Ljubljana, Slovenia
| | - Ivančica Strunjak-Perović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.,Center of Excellence for Marine Bioprospecting (BioProCro), Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Natalija Topić Popović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.,Center of Excellence for Marine Bioprospecting (BioProCro), Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Rozelindra Čož-Rakovac
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.,Center of Excellence for Marine Bioprospecting (BioProCro), Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Polonca Trebše
- Faculty of Health Sciences, University of Ljubljana, Zdravstvena pot 5, Ljubljana, Slovenia.
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19
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Mooibroek TJ. DFT and IsoStar Analyses to Assess the Utility of σ- and π-Hole Interactions for Crystal Engineering. Chemphyschem 2021; 22:141-153. [PMID: 33241585 PMCID: PMC7898519 DOI: 10.1002/cphc.202000927] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 11/25/2020] [Indexed: 11/25/2022]
Abstract
The interpretation of 36 charge neutral 'contact pairs' from the IsoStar database was supported by DFT calculations of model molecules 1-12, and bimolecular adducts thereof. The 'central groups' are σ-hole donors (H2 O and aromatic C-I), π-hole donors (R-C(O)Me, R-NO2 and R-C6 F5 ) and for comparison R-C6 H5 (R=any group or atom). The 'contact groups' are hydrogen bond donors X-H (X=N, O, S, or R2 C, or R3 C) and lone-pair containing fragments (R3 C-F, R-C≡N and R2 C=O). Nearly all the IsoStar distributions follow expectations based on the electrostatic potential of the 'central-' and 'contact group'. Interaction energies (ΔEBSSE ) are dominated by electrostatics (particularly between two polarized molecules) or dispersion (especially in case of large contact area). Orbital interactions never dominate, but could be significant (∼30 %) and of the n/π→σ*/π* kind. The largest degree of directionality in the IsoStar plots was typically observed for adducts more stable than ΔEBSSE ≈-4 kcal⋅mol-1 , which can be seen as a benchmark-value for the utility of an interaction in crystal engineering. This benchmark could be met with all the σ- and π-hole donors studied.
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Affiliation(s)
- Tiddo Jonathan Mooibroek
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van Amsterdam, Science Park 9041098 XHAmsterdamThe Netherlands
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20
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Peluso P, Dessì A, Dallocchio R, Sechi B, Gatti C, Chankvetadze B, Mamane V, Weiss R, Pale P, Aubert E, Cossu S. Enantioseparation of 5,5'-Dibromo-2,2'-Dichloro-3-Selanyl-4,4'-Bipyridines on Polysaccharide-Based Chiral Stationary Phases: Exploring Chalcogen Bonds in Liquid-Phase Chromatography. Molecules 2021; 26:molecules26010221. [PMID: 33406753 PMCID: PMC7794968 DOI: 10.3390/molecules26010221] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/26/2020] [Accepted: 12/29/2020] [Indexed: 12/25/2022] Open
Abstract
The chalcogen bond (ChB) is a noncovalent interaction based on electrophilic features of regions of electron charge density depletion (σ-holes) located on bound atoms of group VI. The σ-holes of sulfur and heavy chalcogen atoms (Se, Te) (donors) can interact through their positive electrostatic potential (V) with nucleophilic partners such as lone pairs, π-clouds, and anions (acceptors). In the last few years, promising applications of ChBs in catalysis, crystal engineering, molecular biology, and supramolecular chemistry have been reported. Recently, we explored the high-performance liquid chromatography (HPLC) enantioseparation of fluorinated 3-arylthio-4,4′-bipyridines containing sulfur atoms as ChB donors. Following this study, herein we describe the comparative enantioseparation of three 5,5′-dibromo-2,2′-dichloro-3-selanyl-4,4′-bipyridines on polysaccharide-based chiral stationary phases (CSPs) aiming to understand function and potentialities of selenium σ-holes in the enantiodiscrimination process. The impact of the chalcogen substituent on enantioseparation was explored by using sulfur and non-chalcogen derivatives as reference substances for comparison. Our investigation also focused on the function of the perfluorinated aromatic ring as a π-hole donor recognition site. Thermodynamic quantities associated with the enantioseparation were derived from van’t Hoff plots and local electron charge density of specific molecular regions of the interacting partners were inspected in terms of calculated V. On this basis, by correlating theoretical data and experimental results, the participation of ChBs and π-hole bonds in the enantiodiscrimination process was reasonably confirmed.
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Affiliation(s)
- Paola Peluso
- Institute of Biomolecular Chemistry ICB, CNR, Secondary Branch of Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy; (A.D.); (R.D.); (B.S.)
- Correspondence: (P.P.); (V.M.); Tel.: +39-079-2841218 (P.P.); +33-3-68851612 (V.M.)
| | - Alessandro Dessì
- Institute of Biomolecular Chemistry ICB, CNR, Secondary Branch of Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy; (A.D.); (R.D.); (B.S.)
| | - Roberto Dallocchio
- Institute of Biomolecular Chemistry ICB, CNR, Secondary Branch of Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy; (A.D.); (R.D.); (B.S.)
| | - Barbara Sechi
- Institute of Biomolecular Chemistry ICB, CNR, Secondary Branch of Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy; (A.D.); (R.D.); (B.S.)
| | - Carlo Gatti
- CNR-SCITEC, Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, sezione di via Golgi, via C. Golgi 19, 20133 Milano, Italy;
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Ave 3, 0179 Tbilisi, Georgia;
| | - Victor Mamane
- Strasbourg Institute of Chemistry, UMR CNRS 7177, Team LASYROC, 1 rue Blaise Pascal, University of Strasbourg, 67008 Strasbourg CEDEX, France; (R.W.); (P.P.)
- Correspondence: (P.P.); (V.M.); Tel.: +39-079-2841218 (P.P.); +33-3-68851612 (V.M.)
| | - Robin Weiss
- Strasbourg Institute of Chemistry, UMR CNRS 7177, Team LASYROC, 1 rue Blaise Pascal, University of Strasbourg, 67008 Strasbourg CEDEX, France; (R.W.); (P.P.)
| | - Patrick Pale
- Strasbourg Institute of Chemistry, UMR CNRS 7177, Team LASYROC, 1 rue Blaise Pascal, University of Strasbourg, 67008 Strasbourg CEDEX, France; (R.W.); (P.P.)
| | - Emmanuel Aubert
- Crystallography, Magnetic Resonance and Modelling (CRM2), UMR CNRS 7036, University of Lorraine, Bd des Aiguillettes, 54506 Vandoeuvre-les-Nancy, France;
| | - Sergio Cossu
- Department of Molecular Sciences and Nanosystems DSMN, Venice Ca’ Foscari University, Via Torino 155, 30172 Mestre Venezia, Italy;
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21
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Laolob T, Bunyapraphatsara N, Waranuch N, Pongcharoen S, Punyain W, Chancharunee S, Sakchaisri K, Pratuangdejkul J, Chongruchiroj S, Kielar F, Wichai U. Enhancement of Lipolysis in 3T3-L1 Adipocytes by Nitroarene Capsaicinoid Analogs. Nat Prod Commun 2021. [DOI: 10.1177/1934578x20987949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Transient receptor potential vanilloid 1 (TRPV1) activation by capsaicin binding increased intracellular calcium influx and stimulated adipocyte-to-adipocyte communication, leading to lipolysis. Generally, enhancement of π-stacking capabilities improves certain binding interactions. Notably, nitroarenes exhibit strong binding interactions with aromatic amino acid side chains in proteins. New capsaicinoid analogs were designed by substitution of the OCH3 group with a nitrogen dioxide (NO2) group on the vanillyl ring to investigate how π-stacking interactions in capsaicinoid analogs contribute to lipolysis. Capsaicinoid analogs, nitro capsaicin (5), and nitro dihydrocapsaicin (6) were prepared in moderate yields via coupling of a nitroaromatic amine salt and fatty acids. Oil Red O staining and triglyceride assays with 10 µM loading of capsaicin (CAP), dihydrocapsaicin (DHC), 5, and 6 were performed to investigate their effect on lipolysis in 3T3-L1 adipocytes. Both assay results indicated that 5 and 6 decreased lipid accumulation by 13.6% and 14.7%, respectively, and significantly reduced triglyceride content by 26.9% and 28.4%, respectively, in comparison with the control experiment. Furthermore, the decrease in triglyceride content observed in response to nitroarene capsaicinoid analogs was approximately 2-folds higher than that of CAP and DHC. These results arose from the NO2 group augmented π-π stacking with Tyr511 and the attractive charge interaction with Glu570 affecting binding interactions with TRPV1 receptors.
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Affiliation(s)
- Thanet Laolob
- Department of Chemistry, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | | | - Neti Waranuch
- Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Naresuan University, Phitsanulok, Thailand
| | - Sutatip Pongcharoen
- Department of Medicine, Faculty of Medicine, Naresuan University, Phitsanulok, Thailand
| | - Wikorn Punyain
- Department of Chemistry, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Sirirat Chancharunee
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Krisada Sakchaisri
- Department of Pharmacology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | | | - Sumet Chongruchiroj
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Filip Kielar
- Department of Chemistry and Center of Excellence in Biomaterials, Naresuan University, Phitsanulok, Thailand
| | - Uthai Wichai
- Department of Chemistry and Center of Excellence in Biomaterials, Naresuan University, Phitsanulok, Thailand
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22
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Ursu A, Wang KW, Bush JA, Choudhary S, Chen JL, Baisden JT, Zhang YJ, Gendron TF, Petrucelli L, Yildirim I, Disney MD. Structural Features of Small Molecules Targeting the RNA Repeat Expansion That Causes Genetically Defined ALS/FTD. ACS Chem Biol 2020; 15:3112-3123. [PMID: 33196168 DOI: 10.1021/acschembio.0c00049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genetically defined amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), collectively named c9ALS/FTD, are triggered by hexanucleotide GGGGCC repeat expansions [r(G4C2)exp] within the C9orf72 gene. In these diseases, neuronal loss occurs through an interplay of deleterious phenotypes, including r(G4C2)exp RNA gain-of-function mechanisms. Herein, we identified a benzimidazole derivative, CB096, that specifically binds to a repeating 1 × 1 GG internal loop structure, 5'CGG/3'GGC, that is formed when r(G4C2)exp folds. Structure-activity relationship (SAR) studies and molecular dynamics (MD) simulations were used to define the molecular interactions formed between CB096 and r(G4C2)exp that results in the rescue of disease-associated pathways. Overall, this study reveals a unique structural feature within r(G4C2)exp that can be exploited for the development of lead medicines and chemical probes.
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Affiliation(s)
- Andrei Ursu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Kye Won Wang
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States
| | - Jessica A. Bush
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Shruti Choudhary
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jonathan L. Chen
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jared T. Baisden
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd., Jacksonville, Florida 32224, United States
| | - Tania F. Gendron
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd., Jacksonville, Florida 32224, United States
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd., Jacksonville, Florida 32224, United States
| | - Ilyas Yildirim
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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23
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Factors Impacting σ- and π-Hole Regions as Revealed by the Electrostatic Potential and Its Source Function Reconstruction: The Case of 4,4'-Bipyridine Derivatives. Molecules 2020; 25:molecules25194409. [PMID: 32992941 PMCID: PMC7582854 DOI: 10.3390/molecules25194409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 02/08/2023] Open
Abstract
Positive electrostatic potential (V) values are often associated with σ- and π-holes, regions of lower electron density which can interact with electron-rich sites to form noncovalent interactions. Factors impacting σ- and π-holes may thus be monitored in terms of the shape and values of the resulting V. Further precious insights into such factors are obtained through a rigorous decomposition of the V values in atomic or atomic group contributions, a task here achieved by extending the Bader-Gatti source function (SF) for the electron density to V. In this article, this general methodology is applied to a series of 4,4'-bipyridine derivatives containing atoms from Groups VI (S, Se) and VII (Cl, Br), and the pentafluorophenyl group acting as a π-hole. As these molecules are characterized by a certain degree of conformational freedom due to the possibility of rotation around the two C-Ch bonds, from two to four conformational motifs could be identified for each structure through conformational search. On this basis, the impact of chemical and conformational features on σ- and π-hole regions could be systematically evaluated by computing the V values on electron density isosurfaces (VS) and by comparing and dissecting in atomic/atomic group contributions the VS maxima (VS,max) values calculated for different molecular patterns. The results of this study confirm that both chemical and conformational features may seriously impact σ- and π-hole regions and provide a clear analysis and a rationale of why and how this influence is realized. Hence, the proposed methodology might offer precious clues for designing changes in the σ- and π-hole regions, aimed at affecting their potential involvement in noncovalent interactions in a desired way.
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24
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Domasevitch KV, Senchyk GA, Krautscheid H. Bulk polarity of 3,5,7-trinitro-1-azaadamantane mediated by asymmetric NO 2(lone pair)...NO 2(π-hole) supramolecular bonding. Acta Crystallogr C Struct Chem 2020; 76:598-604. [PMID: 32499458 DOI: 10.1107/s2053229620006762] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/19/2020] [Indexed: 11/10/2022] Open
Abstract
Molecular crystals exhibiting polar symmetry are important paradigms for developing new electrooptical materials. Though accessing bulk polarity still presents a significant challenge, in some cases it may be rationalized as being associated with the specific molecular shapes and symmetries and subtle features of supramolecular interactions. In the crystal structure of 3,5,7-trinitro-1-azaadamantane, C9H12N4O6, the polar symmetry of the molecular arrangement is a result of complementary prerequisites, namely the C3v symmetry of the molecules is suited to the generation of polar stacks and the inherent asymmetry of the principal supramolecular bonding, as is provided by NO2(lone pair)...NO2(π-hole) interactions. These bonds arrange the molecules into a trigonal network. In spite of the apparent simplicity, the structure comprises three unique molecules (Z' = 1/3 + 1/3 + 1/3), two of which are donors and acceptors of three N...O interactions and the third being primarily important for weak C-H...O hydrogen bonding. These distinct structural roles agree with the results of Hirshfeld surface analysis. A set of weak C-H...O and C-H...N hydrogen bonds yields three kinds of stacks. The orientation of the stacks is identical and therefore the polarity of each molecule contributes additively to the net dipole moment of the crystal. This suggests a special potential of asymmetric NO2(lone pair)...NO2(π-hole) interactions for the supramolecular synthesis of acentric materials.
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Affiliation(s)
- Kostiantyn V Domasevitch
- Inorganic Chemistry Department, National Taras Shevchenko University of Kyiv, Volodymyrska Str. 64/13, 01601 Kyiv, Ukraine
| | - Ganna A Senchyk
- Inorganic Chemistry Department, National Taras Shevchenko University of Kyiv, Volodymyrska Str. 64/13, 01601 Kyiv, Ukraine
| | - Harald Krautscheid
- Institute of Inorganic Chemistry, Leipzig University, Johannisallee 29, D-04103 Leipzig, Germany
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25
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Bauzá A, Frontera A, Mooibroek TJ. π-Hole Interactions Involving Nitro Aromatic Ligands in Protein Structures. Chemistry 2019; 25:13436-13443. [PMID: 31453653 PMCID: PMC6856858 DOI: 10.1002/chem.201903404] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Indexed: 01/03/2023]
Abstract
Studying noncanonical intermolecular interactions between a ligand and a protein constitutes an emerging research field. Identifying synthetically accessible molecular fragments that can engage in intermolecular interactions is a key objective in this area. Here, it is shown that so-called "π-hole interactions" are present between the nitro moiety in nitro aromatic ligands and lone pairs within protein structures (water and protein carbonyls and sulfurs). Ample structural evidence was found in a PDB analysis and computations reveal interaction energies of about -5 kcal mol-1 for ligand-protein π-hole interactions. Several examples are highlighted for which a π-hole interaction is implicated in the superior binding affinity or inhibition of a nitro aromatic ligand versus a similar non-nitro analogue. The discovery that π-hole interactions with nitro aromatics are significant within protein structures parallels the finding that halogen bonds are biologically relevant. This has implications for the interpretation of ligand-protein complexation phenomena, for example, involving the more than 50 approved drugs that contain a nitro aromatic moiety.
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Affiliation(s)
- Antonio Bauzá
- Department of ChemistryUniversitat de les Illes BalearsCrta. de Valldemossa km 7.507122Palma (Baleares)Spain
| | - Antonio Frontera
- Department of ChemistryUniversitat de les Illes BalearsCrta. de Valldemossa km 7.507122Palma (Baleares)Spain
| | - Tiddo Jonathan Mooibroek
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
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26
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Intermolecular Non-Covalent Carbon-Bonding Interactions with Methyl Groups: A CSD, PDB and DFT Study. Molecules 2019; 24:molecules24183370. [PMID: 31527496 PMCID: PMC6767229 DOI: 10.3390/molecules24183370] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/05/2019] [Accepted: 09/12/2019] [Indexed: 01/15/2023] Open
Abstract
A systematic evaluation of the CSD and the PDB in conjunction with DFT calculations reveal that non-covalent Carbon-bonding interactions with X-CH3 can be weakly directional in the solid state (P ≤ 1.5) when X = N or O. This is comparable to very weak CH hydrogen bonding interactions and is in line with the weak interaction energies calculated (≤ -1.5 kcal·mol-1) of typical charge neutral adducts such as [Me3N-CH3···OH2] (2a). The interaction energy is enhanced to ≤-5 kcal·mol-1 when X is more electron withdrawing such as in [O2N-CH3··O=Cdme] (20b) and to ≤18 kcal·mol-1 in cationic species like [Me3O+-CH3···OH2]+ (8a).
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