1
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Mu M, Walker KL, Sánchez-Sanz G, Waymouth RM, Trujillo C, Muldoon MJ, García-Melchor M. Insights into the Palladium(II)-Catalyzed Wacker-Type Oxidation of Styrene with Hydrogen Peroxide and tert-Butyl Hydroperoxide. ACS Catal 2024; 14:1567-1574. [PMID: 38327641 PMCID: PMC10845106 DOI: 10.1021/acscatal.3c05630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
Wacker oxidations are ubiquitous in the direct synthesis of carbonyl compounds from alkenes. While the reaction mechanism has been widely studied under aerobic conditions, much less is known about such processes promoted with peroxides. Here, we report an exhaustive mechanistic investigation of the Wacker oxidation of styrene using hydrogen peroxide (H2O2) and tert-butyl hydroperoxide (TBHP) as oxidants by combining density functional theory and microkinetic modeling. Our results with H2O2 uncover a previously unreported reaction pathway that involves an intermolecular proton transfer assisted by the counterion [OTf]- present in the reaction media. Furthermore, we show that when TBHP is used as an oxidant instead of H2O2, the reaction mechanism switches to an intramolecular protonation sourced by the HOtBu moiety generated in situ. Importantly, these two mechanisms are predicted to outcompete the 1,2-hydride shift pathway previously proposed in the literature and account for the level of D incorporation in the product observed in labeling experiments with α-d-styrene and D2O2. We envision that these insights will pave the way for the rational design of more efficient catalysts for the industrial production of chemical feedstocks and fine chemicals.
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Affiliation(s)
- Manting Mu
- School
of Chemistry, Trinity College Dublin, College Green, Dublin 2 Dublin, Ireland
| | - Katherine L. Walker
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Goar Sánchez-Sanz
- Research
IT, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Robert M. Waymouth
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Cristina Trujillo
- School
of Chemistry, Trinity College Dublin, College Green, Dublin 2 Dublin, Ireland
| | - Mark J. Muldoon
- School
of Chemistry and Chemical Engineering, Queen’s
University Belfast, Belfast BT71NN, U.K.
| | - Max García-Melchor
- School
of Chemistry, Trinity College Dublin, College Green, Dublin 2 Dublin, Ireland
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2
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Iribarren I, Mates-Torres E, Trujillo C. Revisiting ion-pair interactions in phase transfer catalysis: from ionic compounds to real catalyst systems. Dalton Trans 2024; 53:1322-1335. [PMID: 38116737 DOI: 10.1039/d3dt03978a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Ion-pairing is a fundamental phenomenon that significantly influences phase-transfer catalysis. In this study, we conduct a comprehensive investigation of ion-pair interactions, aiming to establish a comprehensive understanding of their nature and implications. The study begins with the examination of polar ionic compounds to define the concept of an ion-pair in the context of phase-transfer catalysis. Subsequently, a diverse range of ion-pair catalyst models were explored to gain insight into the factors governing their interactions. Finally, the focus shifts towards the characterisation of real phase-transfer catalysts, bridging the gap between theoretical models and practical applications. Through a combination of computational approaches and theoretical analysis, this work provides valuable insight into the nature of ion-pair interactions within phase-transfer catalysis fields.
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Affiliation(s)
- Iñigo Iribarren
- School of Chemistry, Trinity College Dublin, The University of Dublin, 154-160 Pearse Street, D02 R590 Dublin, Ireland
| | - Eric Mates-Torres
- School of Chemistry, Trinity College Dublin, The University of Dublin, 154-160 Pearse Street, D02 R590 Dublin, Ireland
| | - Cristina Trujillo
- School of Chemistry, Trinity College Dublin, The University of Dublin, 154-160 Pearse Street, D02 R590 Dublin, Ireland
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3
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Sephton T, Charitou A, Trujillo C, Large JM, Butterworth S, Greaney MF. Aryne-Enabled C-N Arylation of Anilines. Angew Chem Int Ed Engl 2023; 62:e202310583. [PMID: 37850515 PMCID: PMC10952162 DOI: 10.1002/anie.202310583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
Anilines are potentially high-value arylating agents, but are limited by the low reactivity of the strong C-N bond. We show that the reactive intermediate benzyne can be used to both activate anilines, and set-up an aryl transfer reaction in a single step. The reaction does not require any transition metal catalysts or stoichiometric organometallics, and establishes a metal-free route to valuable biaryl products by functionalizing the aniline C-N bond.
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Affiliation(s)
- Thomas Sephton
- School of ChemistryUniversity of ManchesterManchesterM13 9PLUK
| | | | | | - Jonathan M. Large
- LifeArc, Accelerator BuildingOpen Innovation CampusStevenageSG1 2FXUK
| | - Sam Butterworth
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences CentreUniversity of ManchesterManchesterM13 9PLUK
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4
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Chanbasha B, Costas M, Echeverría J, Eisenstein O, Greenhalgh M, Kennepohl P, Kirrander A, Linnebank PR, Macgregor SA, Mahmudov KT, Martín-Fernández C, Meeus E, Morris J, Perutz RN, Poater A, Reek JNH, Rouse I, Toste D, Trujillo C, Ward TR, Weinstein JA, Weller AS. Model - state-of-the-art modelling and computational analysis of reactive sites: general discussion. Faraday Discuss 2023; 244:336-355. [PMID: 37477596 DOI: 10.1039/d3fd90015k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
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5
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Lynch DM, Nolan MD, Williams C, Van Dalsen L, Calvert SH, Dénès F, Trujillo C, Scanlan EM. Traceless Thioacid-Mediated Radical Cyclization of 1,6-Dienes. J Org Chem 2023. [PMID: 37418624 PMCID: PMC10367065 DOI: 10.1021/acs.joc.3c00824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Five-membered ring systems are ubiquitous throughout natural products and synthetic therapeutics, and thus, efficient methods to access this essential scaffold are required. Herein, we report the thioacid-mediated, 5-exo-trig cyclization of various 1,6-dienes, with high yields of up to 98%. The labile thioester functionality can be exploited to generate a free thiol residue which can be used as a functional handle or removed entirely to provide the traceless cyclized product.
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Affiliation(s)
- Dylan M Lynch
- Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Mark D Nolan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Conor Williams
- Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Leendert Van Dalsen
- Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Susannah H Calvert
- Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Fabrice Dénès
- Université de Nantes, CEISAM UMR CNRS 6230 UFR des Sciences et des Techniques, 2 rue de la Houssinière BP, 92208 - 44322 Cedex 3 Nantes, France
| | - Cristina Trujillo
- Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
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6
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Garcia MR, Iribarren I, Rozas I, Trujillo C. Simultaneous Hydrogen Bonds with Different Binding Modes: The Acceptor "Rules" but the Donor "Chooses". Chemistry 2023; 29:e202300717. [PMID: 36922745 DOI: 10.1002/chem.202300717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Invited for the cover of this issue is the group of Cristina Trujillo at Trinity College Dublin and the University of Manchester. The image depicts a market run by hydrogen bond acceptors in which hydrogen-bond-donor "customers" are choosing their preferred binding mode "vegetable". Read the full text of the article at 10.1002/chem.202203577.
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Affiliation(s)
- Marianne Rica Garcia
- School of Chemistry, Trinity College Dublin, The University of Dublin, 154-160 Pearse Street, Dublin, 2, Ireland
| | - Iñigo Iribarren
- School of Chemistry, Trinity College Dublin, The University of Dublin, 154-160 Pearse Street, Dublin, 2, Ireland
| | - Isabel Rozas
- School of Chemistry, Trinity College Dublin, The University of Dublin, 154-160 Pearse Street, Dublin, 2, Ireland
| | - Cristina Trujillo
- School of Chemistry, Trinity College Dublin, The University of Dublin, 154-160 Pearse Street, Dublin, 2, Ireland.,Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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7
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Garcia MR, Iribarren I, Rozas I, Trujillo C. Simultaneous Hydrogen Bonds with Different Binding Modes: The Acceptor “Rules” but the Donor “Chooses”. Chemistry 2023. [DOI: 10.1002/chem.202300716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Affiliation(s)
- Marianne Rica Garcia
- School of Chemistry, Trinity College Dublin The University of Dublin 154–160 Pearse Street Dublin 2 Ireland)
| | - Iñigo Iribarren
- School of Chemistry, Trinity College Dublin The University of Dublin 154–160 Pearse Street Dublin 2 Ireland)
| | - Isabel Rozas
- School of Chemistry, Trinity College Dublin The University of Dublin 154–160 Pearse Street Dublin 2 Ireland)
| | - Cristina Trujillo
- School of Chemistry, Trinity College Dublin The University of Dublin 154–160 Pearse Street Dublin 2 Ireland)
- Department of Chemistry The University of Manchester Oxford Road Manchester M13 9PL UK
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8
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Garcia MR, Iribarren I, Rozas I, Trujillo C. Simultaneous Hydrogen Bonds with Different Binding Modes: The Acceptor "Rules" but the Donor "Chooses". Chemistry 2023; 29:e202203577. [PMID: 36701250 DOI: 10.1002/chem.202203577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/26/2023] [Accepted: 01/26/2023] [Indexed: 01/27/2023]
Abstract
This computational work studies the different hydrogen bond (HB) binding modes that can be established between neighbouring HB donors and acceptors in structures with relevance in catalysis and biology. To analyse the electronic effect on the σ-hole, unsubstituted HB donors and ones with two different substituents, an electron withdrawing (EWG), and an electron donating (EDG) group, were studied. Upon complexation, three different binding modes were observed: bifurcated, parallel, and zigzag. It was found that, as a general trend, HBs within a parallel pattern are the strongest followed by those within bifurcated and zigzag binding modes, leading to a "competition" between the last two. Similar patterns and trends have been found in experimental structures found in a search within the CSD. In conclusion, even though the HB acceptors "rule" the pattern and strength of the HB interactions within the dimers, when there is an option for different binding modes within a particular dimer, the HB donors "choose" the type of binding established.
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Affiliation(s)
- Marianne Rica Garcia
- School of Chemistry, Trinity College Dublin, The University of Dublin, 154-160 Pearse Street, D02 R590, Dublin, Ireland
| | - Iñigo Iribarren
- School of Chemistry, Trinity College Dublin, The University of Dublin, 154-160 Pearse Street, D02 R590, Dublin, Ireland
| | - Isabel Rozas
- School of Chemistry, Trinity College Dublin, The University of Dublin, 154-160 Pearse Street, D02 R590, Dublin, Ireland
| | - Cristina Trujillo
- School of Chemistry, Trinity College Dublin, The University of Dublin, 154-160 Pearse Street, D02 R590, Dublin, Ireland.,Department of Chemistry, The University of Manchester, Oxford Road, M13 9PL, Manchester, UK
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9
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Iribarren I, Trujillo C. Efficiency and Suitability when Exploring the Conformational Space of Phase-Transfer Catalysts. J Chem Inf Model 2022; 62:5568-5580. [PMID: 36271836 PMCID: PMC9709918 DOI: 10.1021/acs.jcim.2c00934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this study, a complete exploration of the conformational space of different phase-transfer catalysts by means of computational method benchmarking is presented. For this particular research work, only the most significant and relevant conformational analysis approaches have been chosen to characterize the main Cinchona alkaloid-based phase-transfer catalysts. This particular guiding study aims to rigorously compare the performance of different conformational methods, determining the strengths of each method and providing recommendations regarding suitable and efficient choices of methods for analysis.
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10
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Melnyk N, Iribarren I, Mates‐Torres E, Trujillo C. Theoretical Perspectives in Organocatalysis. Chemistry 2022; 28:e202201570. [PMID: 35792702 PMCID: PMC9804221 DOI: 10.1002/chem.202201570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 01/05/2023]
Abstract
It is clear that the field of organocatalysis is continuously expanding during the last decades. With increasing computational capacity and new techniques, computational methods have provided a more economic approach to explore different chemical systems. This review offers a broad yet concise overview of current state-of-the-art studies that have employed novel strategies for catalyst design. The evolution of the all different theoretical approaches most commonly used within organocatalysis is discussed, from the traditional approach, manual-driven, to the most recent one, machine-driven.
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Affiliation(s)
- Nika Melnyk
- School of ChemistryTrinity College DublinCollege GreenDublin2Ireland
| | - Iñigo Iribarren
- School of ChemistryTrinity College DublinCollege GreenDublin2Ireland
| | - Eric Mates‐Torres
- School of ChemistryTrinity College DublinCollege GreenDublin2Ireland
| | - Cristina Trujillo
- School of ChemistryTrinity College DublinCollege GreenDublin2Ireland
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11
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McLoughlin EC, O'Brien JE, Trujillo C, Meegan MJ, O'Boyle NM. Application of 2D EXSY and qNMR Spectroscopy for Diastereomeric Excess Determination Following Chiral Resolution of β-Lactams. Chemistry 2022:e202200119. [PMID: 35876400 DOI: 10.1002/open.202200119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/04/2022] [Indexed: 11/07/2022]
Abstract
Trans-β-lactam isomers have garnered much attention as anti-cancer microtubule targeting agents. Currently available synthetic methods are available for the preparation of enantiopure β-lactams and favour isomeric cis/trans β-lactam mixtures. Indirect chiral resolution offers the opportunity for isolation of exclusively enantiopure trans-β-lactams. In this study, liquid chromatography chiral resolution of β-lactams derivatized as diastereomer mixtures with a panel of N-protected amino acids is explored, where N-(Boc)-L-proline served as the optimal chiral derivatising reagent. High-performance liquid chromatography failed to adequately determine diastereomeric excess (de) of resolved diastereomers. Variable temperature, 1 H NMR and 2D EXSY spectroscopic analyses of proline-derivatised diastereomers were successfully employed to characterise equilibrating rotamers of resolved diastereomers and determine their de. Integration of resolved resonances corresponding to H3 and H4 of the β-lactam ring served as a quantitative qNMR tool for the calculation of de following resolution.
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Affiliation(s)
- Eavan C McLoughlin
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute and Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, Dublin 2, Ireland
| | - John E O'Brien
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland
| | - Cristina Trujillo
- Trinity Biomedical Sciences Institute, School of Chemistry, Trinity College Dublin, Dublin 2, Ireland
| | - Mary J Meegan
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute and Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, Dublin 2, Ireland
| | - Niamh M O'Boyle
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute and Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, Dublin 2, Ireland
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12
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Smith SN, Trujillo C, Connon SJ. Catalytic, asymmetric azidations at carbonyls: achiral and meso-anhydride desymmetrisation affords enantioenriched γ-lactams. Org Biomol Chem 2022; 20:6384-6393. [PMID: 35861618 DOI: 10.1039/d2ob01040b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An unprecedented organocatalytic process involving the asymmetric addition of azide to meso-anhydrides has been developed, promoted by novel sulfamide-substituted Cinchona alkaloid-based catalysts. Readily available glutaric anhydrides can be smoothly converted to enantioenriched hemi-acyl azides and from there to either γ-amino acids or γ-lactams.
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Affiliation(s)
- Simon N Smith
- Trinity Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, Dublin 2, Ireland.
| | - Cristina Trujillo
- Trinity Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, Dublin 2, Ireland.
| | - Stephen J Connon
- Trinity Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, Dublin 2, Ireland.
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13
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Trujillo C, Cronin SA, Connon SJ. Front Cover: Mechanistic Insights into the Organocatalytic Kinetic Resolution of Oxazinones through Alcoholysis (Eur. J. Org. Chem. 3/2022). European J Org Chem 2022. [DOI: 10.1002/ejoc.202200017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Cristina Trujillo
- Trinity Biomedical Sciences Institute School of Chemistry The University of Dublin Trinity College Dublin 2 Ireland
| | - Sarah A. Cronin
- Trinity Biomedical Sciences Institute School of Chemistry The University of Dublin Trinity College Dublin 2 Ireland
| | - Stephen J. Connon
- Trinity Biomedical Sciences Institute School of Chemistry The University of Dublin Trinity College Dublin 2 Ireland
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14
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Trujillo C, Cronin SA, Connon SJ. Mechanistic Insights into the Organocatalytic Kinetic Resolution of Oxazinones through Alcoholysis. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Cristina Trujillo
- Trinity Biomedical Sciences Institute School of Chemistry The University of Dublin Trinity College Dublin 2 Ireland
| | - Sarah A. Cronin
- Trinity Biomedical Sciences Institute School of Chemistry The University of Dublin Trinity College Dublin 2 Ireland
| | - Stephen J. Connon
- Trinity Biomedical Sciences Institute School of Chemistry The University of Dublin Trinity College Dublin 2 Ireland
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15
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Iribarren I, Sánchez-Sanz G, Elguero J, Alkorta I, Trujillo C. Reactivity of Coinage Metal Hydrides for the Production of H 2 Molecules. ChemistryOpen 2021; 10:722-723. [PMID: 34351077 DOI: 10.1002/open.202100173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Invited for this month's cover picture is the group of Dr. Cristina Trujillo at the Trinity Biomedical Sciences Institute in Dublin (Ireland) and Prof. Ibon Alkorta at the CSIC in Madrid (Spain). The cover picture shows the possibility of reversibly storing hydrogen using metallic compounds as reactants to produce H2 gas and metallic dimers. Computational studies have been carried out to investigate these processes, as shown in the concept art by the Schrödinger equation. It was found that the formation and release of H2 is energetically favorable. These results are a promising starting point for further research of using coinage metals for storing hydrogen in light compounds. Read the full text of their Full Paper at 10.1002/open.202100108.
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Affiliation(s)
- Iñigo Iribarren
- Trinity Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, Dublin 2, Ireland
| | - Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin 2 (Ireland), & School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - José Elguero
- Instituto de Química Médica CSIC, Juan de la Cierva, 3, 28006, Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica CSIC, Juan de la Cierva, 3, 28006, Madrid, Spain
| | - Cristina Trujillo
- Trinity Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, Dublin 2, Ireland
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16
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Iribarren I, Sánchez‐Sanz G, Elguero J, Alkorta I, Trujillo C. Front Cover: Reactivity of Coinage Metal Hydrides for the Production of H
2
Molecules (ChemistryOpen 8/2021). ChemistryOpen 2021. [DOI: 10.1002/open.202100174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Iñigo Iribarren
- Trinity Biomedical Sciences Institute School of Chemistry The University of Dublin Trinity College Dublin 2 Ireland
| | - Goar Sánchez‐Sanz
- Irish Centre of High-End Computing Grand Canal Quay Dublin 2 (Ireland) & School of Chemistry University College Dublin Belfield Dublin 4 Ireland
| | - José Elguero
- Instituto de Química Médica IQM-CSIC Juan de la Cierva, 3 28006 Madrid Spain
| | - Ibon Alkorta
- Instituto de Química Médica IQM-CSIC Juan de la Cierva, 3 28006 Madrid Spain
| | - Cristina Trujillo
- Trinity Biomedical Sciences Institute School of Chemistry The University of Dublin Trinity College Dublin 2 Ireland
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Iribarren I, Sánchez‐Sanz G, Elguero J, Alkorta I, Trujillo C. Reactivity of Coinage Metal Hydrides for the Production of H 2 Molecules. ChemistryOpen 2021; 10:724-730. [PMID: 34319005 PMCID: PMC8340072 DOI: 10.1002/open.202100108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/30/2021] [Indexed: 12/03/2022] Open
Abstract
The formation of molecular hydrogen as well as the possibility of using coinage metal hydrides as a prospective complex to produce hydrogen was presented in this work. Therefore, the reactions involving the interaction between two coinage metal hydrides, MH (M=Cu, Ag and Au, homo and heterodimers), were studied. The free energy profiles corresponding to aforementioned complexation were analysed by means of ab initio methods of quantum chemistry. The characteristics of these intermediates, final complexes and the electron density properties of the established interactions were discussed.
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Affiliation(s)
- Iñigo Iribarren
- Trinity Biomedical Sciences InstituteSchool of ChemistryThe University of DublinTrinity CollegeDublin 2Ireland
| | - Goar Sánchez‐Sanz
- Irish Centre of High-End ComputingGrand Canal QuayDublin 2 (Ireland)& School of ChemistryUniversity College Dublin BelfieldDublin 4Ireland
| | - José Elguero
- Instituto de Química Médica IQM-CSICJuan de la Cierva, 328006MadridSpain
| | - Ibon Alkorta
- Instituto de Química Médica IQM-CSICJuan de la Cierva, 328006MadridSpain
| | - Cristina Trujillo
- Trinity Biomedical Sciences InstituteSchool of ChemistryThe University of DublinTrinity CollegeDublin 2Ireland
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Di Filippo M, Trujillo C, Sánchez-Sanz G, Batsanov AS, Baumann M. Discovery of a photochemical cascade process by flow-based interception of isomerising alkenes. Chem Sci 2021; 12:9895-9901. [PMID: 34349962 PMCID: PMC8317621 DOI: 10.1039/d1sc02879k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/02/2021] [Indexed: 01/08/2023] Open
Abstract
Herein we report the discovery of a new photochemical cascade process through a flow-based strategy for intercepting diradicals generated from simple alkenes. This continuous process delivers a series of unprecedented polycyclic reaction products. Exploring the scope of this novel process revealed that this approach is general and affords a variety of structurally complex reaction products in high yields (up to 81%), short reaction times (7 min) and high throughputs (up to 5.5 mmol h-1). A mechanistic rationale is presented that is supported by computations as well as isolation of key intermediates whose identity is confirmed by X-ray crystallography. The presented photochemical cascade process demonstrates the discovery of new chemical reactivity and complex chemical scaffolds by continuously generating and intercepting high-energy intermediates in a highly practical manner.
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Affiliation(s)
- Mara Di Filippo
- School of Chemistry, University College Dublin, Science Centre South D04 N2E2 Dublin Ireland
| | - Cristina Trujillo
- Trinity Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College Dublin Ireland
| | - Goar Sánchez-Sanz
- School of Chemistry, University College Dublin, Science Centre South D04 N2E2 Dublin Ireland .,Irish Centre for High-End Computing (ICHEC) Grand Canal Quay Dublin 2 D02 HP83 Ireland
| | - Andrei S Batsanov
- Department of Chemistry, Durham University DH1 3LE South Road Durham UK
| | - Marcus Baumann
- School of Chemistry, University College Dublin, Science Centre South D04 N2E2 Dublin Ireland
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Iribarren I, Sánchez-Sanz G, Alkorta I, Elguero J, Trujillo C. Evaluation of Electron Density Shifts in Noncovalent Interactions. J Phys Chem A 2021; 125:4741-4749. [PMID: 34061527 PMCID: PMC8279648 DOI: 10.1021/acs.jpca.1c00830] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/26/2021] [Indexed: 12/12/2022]
Abstract
In the present paper, we report the quantitative evaluation of the electron density shift (EDS) maps within different complexes. Values associated with the total EDS maps exhibited good correlation with different quantities such as interaction energies, Eint, intermolecular distances, bond critical points, and LMOEDA energy decomposition terms. Besides, EDS maps at different cutoffs were also evaluated and related with the interaction energies values. Finally, EDS maps and their corresponding values are found to correlate with Eint within systems with cooperative effects. To our knowledge, this is the first time that the EDS has been quanitatively evaluated.
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Affiliation(s)
- Iñigo Iribarren
- Trinity
Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, Dublin, Dublin 2, Ireland
| | - Goar Sánchez-Sanz
- Irish
Centre For High-End Computing, 7 Floor, The Tower, Grand Canal Quay, Dublin 2 D02 HP83, Ireland
| | - Ibon Alkorta
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
| | - José Elguero
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
| | - Cristina Trujillo
- Trinity
Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, Dublin, Dublin 2, Ireland
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20
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Grover N, Flanagan KJ, Trujillo C, Kingsbury CJ, Senge MO. An Insight into Non-Covalent Interactions on the Bicyclo[1.1.1]pentane Scaffold. European J Org Chem 2021; 2021:1113-1122. [PMID: 33776556 PMCID: PMC7986844 DOI: 10.1002/ejoc.202001564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/03/2020] [Indexed: 12/28/2022]
Abstract
Bicyclo[1.1.1]pentane (BCP) is studied extensively as a bioisosteric component of drugs. Not found in nature, this molecular unit approximates the distance of a para-disubstituted benzene which is replaced in medicines as a method of improving treatments. Predicting interactions of these drugs with specific active sites requires knowledge of the non-covalent interactions engaged by this subunit. Structure determinations and computational analysis (Hirshfeld analysis, 2D fingerprint plots, DFT) of seven BCP derivatives chosen to probe specific and directional interactions. X-ray analysis revealed the presence of various non-covalent interactions including I ⋅⋅⋅ I, I ⋅⋅⋅ N, N-H ⋅⋅⋅ O, C-H ⋅⋅⋅ O, and H-C ⋅⋅⋅ H-C contacts. The preference of halogen bonding (I ⋅⋅⋅ I or I ⋅⋅⋅ N) in BCP 1-4 strictly depends upon the electronic nature and angle between bridgehead substituents. The transannular distance in co-crystals 2 and 4 was longer as compared to monomers 1 and 3. Stronger N-H ⋅⋅⋅ O and weaker C-H ⋅⋅⋅ O contacts were observed for BCP 5 while the O ⋅⋅⋅ H interaction was a prominent contact for BCP 6. The presence of 3D BCP units prevented the π ⋅⋅⋅ π stacking between phenyl rings in 3, 4, and 7. The BCP skeleton was often rotationally averaged, indicating fewer interactions compared to bridgehead functional groups. Using DFT analysis, geometries were optimized and molecular electrostatic potentials were calculated on the BCP surfaces. These interaction profiles may be useful for designing BCP analogs of drugs.
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Affiliation(s)
- Nitika Grover
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College DublinThe University of Dublin152-160 Pearse StreetDublin 2Ireland
| | - Keith J. Flanagan
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College DublinThe University of Dublin152-160 Pearse StreetDublin 2Ireland
| | - Cristina Trujillo
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College DublinThe University of Dublin152-160 Pearse StreetDublin 2Ireland
| | - Christopher J. Kingsbury
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College DublinThe University of Dublin152-160 Pearse StreetDublin 2Ireland
| | - Mathias O. Senge
- Institute for Advanced Study (TUM-IAS)Technical University of Munich, Focus Group – Molecular and Interfacial Engineering of Organic NanosystemsLichtenberg-Str. 2a85748GarchingGermany
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21
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Grover N, Flanagan KJ, Trujillo C, Kingsbury CJ, Senge MO. Cover Feature: An Insight into Non‐Covalent Interactions on the Bicyclo[1.1.1]pentane Scaffold (Eur. J. Org. Chem. 7/2021). European J Org Chem 2021. [DOI: 10.1002/ejoc.202100101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nitika Grover
- School of Chemistry Trinity Biomedical Sciences Institute Trinity College Dublin The University of Dublin 152-160 Pearse Street Dublin 2 Ireland
| | - Keith J. Flanagan
- School of Chemistry Trinity Biomedical Sciences Institute Trinity College Dublin The University of Dublin 152-160 Pearse Street Dublin 2 Ireland
| | - Cristina Trujillo
- School of Chemistry Trinity Biomedical Sciences Institute Trinity College Dublin The University of Dublin 152-160 Pearse Street Dublin 2 Ireland
| | - Christopher J. Kingsbury
- School of Chemistry Trinity Biomedical Sciences Institute Trinity College Dublin The University of Dublin 152-160 Pearse Street Dublin 2 Ireland
| | - Mathias O. Senge
- Institute for Advanced Study (TUM-IAS) Technical University of Munich, Focus Group – Molecular and Interfacial Engineering of Organic Nanosystems Lichtenberg-Str. 2a 85748 Garching Germany
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22
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Alkorta I, Elguero J, Trujillo C, Sánchez-Sanz G. Interaction between Trinuclear Regium Complexes of Pyrazolate and Anions, a Computational Study. Int J Mol Sci 2020; 21:E8036. [PMID: 33126636 PMCID: PMC7663457 DOI: 10.3390/ijms21218036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 01/27/2023] Open
Abstract
The geometry, energy and electron density properties of the 1:1, 1:2 and 1:3 complexes between cyclic (Py-M)3 (M = Au, Ag and Cu) and halide ions (F-, Cl- and Br-) were studied using Møller Plesset (MP2) computational methods. Three different configurations were explored. In two of them, the anions interact with the metal atoms in planar and apical dispositions, while in the last configuration, the anions interact with the CH(4) group of the pyrazole. The energetic results for the 1:2 and 1:3 complexes are a combination of the specific strength of the interaction plus a repulsive component due to the charge:charge coulombic term. However, stable minima structures with dissociation barriers for the anions indicate that those complexes are stable and (Py-M)3 can hold up to three anions simultaneously. A search in the CSD confirmed the presence of (Pyrazole-Cu)3 systems with two anions interacting in apical disposition.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain;
| | - José Elguero
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain;
| | - Cristina Trujillo
- Trinity Biomedical Sciences Institute, School of Chemistry, Trinity Dublin College, D02 R590 Dublin 2, Ireland;
| | - Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin 2, Ireland
- School of Chemistry, University College Dublin, Belfield, D02 HP83 Dublin 4, Ireland
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23
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Sánchez-Sanz G, Trujillo C, Alkorta I, Elguero J. Rivalry between Regium and Hydrogen Bonds Established within Diatomic Coinage Molecules and Lewis Acids/Bases. Chemphyschem 2020; 21:2557-2563. [PMID: 32893396 DOI: 10.1002/cphc.202000704] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/04/2020] [Indexed: 11/09/2022]
Abstract
A theoretical study of the complexes formed by Ag2 and Cu2 with different molecules, XH (FH, ClH, OH2 , SH2 , HCN, HNC, HCCH, NH3 and PH3 ) that can act as hydrogen-bond donors (Lewis acids) or regium-bond acceptors (Lewis bases) was carried out at the CCSD(T)/CBS computational level. The heteronuclear diatomic coinage molecules (AuAg, AuCu, and AgCu) have also been considered. With the exception of some of the hydrogen-bonded complexes with FH, the regium-bonded binary complexes are more stable. The AuAg and AuCu molecules show large dipole moments that weaken the regium bond (RB) with Au and favour those through the Ag and Cu atoms, respectively.
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Affiliation(s)
- Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin, D2, Ireland & School of Chemistry, University College Dublin, Belfield, Dublin, D4, Ireland
| | - Cristina Trujillo
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St., Dublin, D2, Ireland
| | - Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, 28006, Madrid, Spain
| | - José Elguero
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, 28006, Madrid, Spain
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24
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Grover J, Trujillo C, Saad M, Emandi G, Stipaničev N, Bernhard SSR, Guédin A, Mergny JL, Senge MO, Rozas I. Dual-binding conjugates of diaromatic guanidines and porphyrins for recognition of G-quadruplexes. Org Biomol Chem 2020; 18:5617-5624. [PMID: 32648871 DOI: 10.1039/d0ob01264e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The first conceptualised class of dual-binding guanine quadruplex binders has been designed, synthesised and biophysically studied. These compounds combine diaromatic guanidinium systems and neutral tetra-phenylporphyrins (classical binding moiety for guanine quadruplexes) by means of a semi-rigid linker. An extensive screening of a variety of guanine quadruplex structures and double stranded DNA via UV-vis, FRET and CD experiments revealed the preference of the conjugates towards guanine quadruplexes. Additionally, docking studies indicate the potential dual mode of binding.
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Affiliation(s)
- Jagdeep Grover
- School of Chemistry, Trinity Biomedical Science Institute, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.
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25
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Trujillo C, Sánchez-Sanz G, Elguero J, Alkorta I. The Lewis acidities of gold(I) and gold(III) derivatives: a theoretical study of complexes of AuCl and AuCl3. Struct Chem 2020. [DOI: 10.1007/s11224-020-01590-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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26
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Iribarren I, Sánchez-Sanz G, Trujillo C. Anion Recognition by Neutral and Cationic Iodotriazole Halogen Bonding Scaffolds. Molecules 2020; 25:E798. [PMID: 32059506 PMCID: PMC7070532 DOI: 10.3390/molecules25040798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 11/30/2022] Open
Abstract
A computational study of the iodide discrimination by different neutral and cationic iodotriazole halogen bonding hosts was carried out by means of Density Functional Theory. The importance of the size of the scaffold was highlighted and its impact observed in the binding energies and intermolecular X···I distances. Larger scaffolds were found to reduce the electronic repulsion and increase the overlap between the halide electron lone pair and the corresponding I-C antibonding orbital, increasing the halogen bonding interactions. Additionally, the planarity plays an important role within the interaction, and can be tuned using hydroxyl to perform intramolecular hydrogen bonds (IMHB) between the scaffold and the halogen atoms. Structures with IMHB exhibit stronger halogen bond interactions, as evidenced by the shorter intramolecular distances, larger electron density values at the bond critical point and more negative binding energies.
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Affiliation(s)
- Iñigo Iribarren
- Trinity Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, D02 R590 Dublin 2, Ireland;
| | - Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin 2, Ireland & School of Chemistry, University College Dublin, Belfield, D02 HP83 Dublin 4, Ireland;
| | - Cristina Trujillo
- Trinity Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, D02 R590 Dublin 2, Ireland;
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27
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Abstract
A theoretical study of the interactions established between an alkaloid quinine-derived PTC and different anions of interest was performed. Ion pairing competes with an intermolecular hydrogen bond between the PT counteranion and potential HB donors.
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Affiliation(s)
- Iñigo Iribarren
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
| | - Cristina Trujillo
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
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28
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Previtali V, Sánchez‐Sanz G, Trujillo C. Front Cover: Theoretical Investigation of Cyano‐Chalcogen Dimers and Their Importance in Molecular Recognition (ChemPhysChem 23/2019). Chemphyschem 2019. [DOI: 10.1002/cphc.201901098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Viola Previtali
- Center for Nanomedicine & Theranostics, Department of ChemistryTechnical University of Denmark Kemitorvet 207 Kongens Lyngby, DK Denmark
| | - Goar Sánchez‐Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin 2, Ireland & School of ChemistryUniversity College Dublin Belfield Dublin 4 Ireland
| | - Cristina Trujillo
- School of Chemistry Trinity Biomedical Sciences InstituteTrinity College Dublini 152-160 Pearse Street Dublin 2 Ireland
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29
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Previtali V, Sánchez-Sanz G, Trujillo C. Theoretical Investigation of Cyano-Chalcogen Dimers and Their Importance in Molecular Recognition. Chemphyschem 2019; 20:3186-3194. [PMID: 31608563 DOI: 10.1002/cphc.201900899] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/07/2019] [Indexed: 11/10/2022]
Abstract
In this manuscript the different noncovalent interactions established between (HYCN)2 dimers (Y=S, Se and Te) have been studied at the MP2 and CCSD(T) level of theory. Several homodimers have been taken into account, highlighting the capacity of these compounds to act both as electron donor and acceptor. The main properties studied were geometries, binding energy (Eb ), and molecular electrostatic potential (MEP). Given the wide application of chalcogen bonds, and more specifically of cyano-chalcogen moieties in molecular recognition, natural bond orbital (NBO), "atoms-in-molecules" (AIM), and electron density shift (EDS) analysis were also used to analyse the different noncovalent interactions upon complexation. The presence of hydrogen, chalcogen and dipole-dipole interactions was confirmed and their implications on molecular recognition were analysed.
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Affiliation(s)
- Viola Previtali
- Center for Nanomedicine & Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, Kongens Lyngby, DK, Denmark
| | - Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin 2, Ireland & School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cristina Trujillo
- School of Chemistry Trinity Biomedical Sciences Institute, Trinity College Dublini, 152-160 Pearse Street, Dublin 2, Ireland
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30
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Sánchez‐Sanz G, Alkorta I, Elguero J, Trujillo C. Sequestration of CO
2
by Phosphatrane Molecules. Chemphyschem 2019; 20:3195-3200. [DOI: 10.1002/cphc.201900905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/03/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Goar Sánchez‐Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin 2, Ireland & School of ChemistryUniversity College Dublin, Belfield Dublin 4 Ireland
| | - Ibon Alkorta
- Instituto de Química Médica, CSIC Juan de la Cierva, 3 E-28006 Madrid Spain
| | - José Elguero
- Instituto de Química Médica, CSIC Juan de la Cierva, 3 E-28006 Madrid Spain
| | - Cristina Trujillo
- School of Chemistry, Trinity Biomedical Sciences InstituteTrinity College Dublin 152–160 Pearse St. Dublin 2 Ireland
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31
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Sánchez‐Sanz G, Trujillo C, Alkorta I, Elguero J. Understanding Regium Bonds and their Competition with Hydrogen Bonds in Au
2
:HX Complexes. Chemphyschem 2019. [DOI: 10.1002/cphc.201900553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Goar Sánchez‐Sanz
- Irish Centre of High-End Computing Grand Canal Quay Dublin 2 Ireland
- School of ChemistryUniversity College Dublin, Belfield Dublin 4 Ireland
| | - Cristina Trujillo
- School of Chemistry, Trinity Biomedical Sciences InstituteTrinity College Dublin 152–160 Pearse St. Dublin 2 Ireland
| | - Ibon Alkorta
- Instituto de Química Médica, CSIC Juan de la Cierva, 3 E-28006 Madrid Spain
| | - José Elguero
- Instituto de Química Médica, CSIC Juan de la Cierva, 3 E-28006 Madrid Spain
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32
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Trujillo C, Litvajova M, Cronin SA, Craig R, Connon SJ. The Steglich Rearrangement of 2‐Oxindole Derivatives Promoted by Anion‐based Nucleophilic Catalysis. ChemCatChem 2019. [DOI: 10.1002/cctc.201900756] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Cristina Trujillo
- School of Chemistry TrinityBiomedical Sciences Institute Trinity College Dublin 152-160 Pearse Street Dublin 2 Ireland
| | - Mili Litvajova
- School of Chemistry TrinityBiomedical Sciences Institute Trinity College Dublin 152-160 Pearse Street Dublin 2 Ireland
| | - Sarah A. Cronin
- School of Chemistry TrinityBiomedical Sciences Institute Trinity College Dublin 152-160 Pearse Street Dublin 2 Ireland
| | - Ryan Craig
- School of Chemistry TrinityBiomedical Sciences Institute Trinity College Dublin 152-160 Pearse Street Dublin 2 Ireland
| | - Stephen J. Connon
- School of Chemistry TrinityBiomedical Sciences Institute Trinity College Dublin 152-160 Pearse Street Dublin 2 Ireland
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33
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Sánchez‐Sanz G, Trujillo C, Alkorta I, Elguero J. Front Cover: Understanding Regium Bonds and their Competition with Hydrogen Bonds in Au
2
:HX Complexes (ChemPhysChem 12/2019). Chemphyschem 2019. [DOI: 10.1002/cphc.201900554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Goar Sánchez‐Sanz
- Irish Centre of High-End Computing Grand Canal Quay Dublin 2 Ireland
- School of ChemistryUniversity College Dublin Belfield Dublin 4 Ireland
| | - Cristina Trujillo
- School of Chemistry, Trinity Biomedical Sciences InstituteTrinity College Dublin 152–160 Pearse St. Dublin 2 Ireland
| | - Ibon Alkorta
- Instituto de Química Médica, CSIC Juan de la Cierva, 3 E-28006 Madrid Spain
| | - José Elguero
- Instituto de Química Médica, CSIC Juan de la Cierva, 3 E-28006 Madrid Spain
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Sánchez-Sanz G, Trujillo C. Cyclohexane-Based Scaffold Molecules Acting as Anion Transport, Anionophores, via Noncovalent Interactions. J Chem Inf Model 2019; 59:2212-2217. [PMID: 30908020 DOI: 10.1021/acs.jcim.9b00154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A theoretical study of a variety of cyclohexane-based anion transporters interacting with the chloride anion has been conducted using density functional theory. The calculations have been performed in the gas phase but also, in order to describe the solvation effects on the interaction, two different solvents-chloroform and dimethylsulfoxide-have been taken into account. Gas-phase interaction energies within the complexes are found to be up to 400 kJ/mol, while, when solvent effects are considered, the interaction energy values decreased drastically concomitantly with an elongation in the interatomic distances. Atoms in molecules and natural bond analysis corroborate the trends found for the intermolecular energies and Cl···H distances, suggesting strong donations from the Cl- anion into the σ*H-N antibonding orbitals, as well as with noncovalent interaction plots showing large areas of electron density overlap within the chloride anion surroundings.
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Affiliation(s)
- Goar Sánchez-Sanz
- Irish Centre for High-End Computing (ICHEC) , Grand Canal Quay, Dublin 2 , Ireland
| | - Cristina Trujillo
- School of Chemistry , Trinity Biomedical Sciences, Trinity College Dublin , 152-160 Pearse Street , Dublin 2 , Ireland
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35
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Collar AG, Trujillo C, Connon SJ. Highly Enantio- and Diastereoselective Catalytic Asymmetric Tamura Cycloaddition Reactions. Chemistry 2019; 25:7270-7274. [PMID: 31050071 DOI: 10.1002/chem.201900119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Indexed: 12/22/2022]
Abstract
The first broad-scope catalytic asymmetric Tamura cycloaddition reactions are reported. Under the influence of anion-binding bifunctional catalysis a wide range of α,β-unsaturated N-trityl imines undergo reactions with enolisable anhydrides to form highly synthetically useful α-tetralone structures with excellent enantio- and -diastereocontrol. In stark contrast to the previous literature benchmarks, doubly activated or highly electron deficient alkenes are not required. A facile two-step, high yielding sequence can convert the cycloadducts to α-haloketones (challenging to generate catalytically by other means) with the net formation of two new C-C bonds and three new contiguous stereocentres with exquisite stereocontrol. A DFT study has provided insight into the catalyst mode of action and the origins of the observed enantiocontrol.
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Affiliation(s)
- Aarón Gutiérrez Collar
- School of Chemistry Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin, 2, Ireland
| | - Cristina Trujillo
- School of Chemistry Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin, 2, Ireland
| | - Stephen J Connon
- School of Chemistry Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin, 2, Ireland
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36
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Sánchez-Sanz G, Trujillo C, Alkorta I, Elguero J. Understanding Regium Bonds and their Competition with Hydrogen Bonds in Au 2 :HX Complexes. Chemphyschem 2019; 20:1572-1580. [PMID: 30974036 DOI: 10.1002/cphc.201900354] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Indexed: 01/08/2023]
Abstract
A theoretical study of the regium and hydrogen bonds (RB and HB, respectively) in Au2 :HX complexes has been carried out by means of CCSD(T) calculations. The theoretical study shows as overall outcome that in all cases the complexes exhibiting RB are more stable that those with HB. The binding energies for RB complexes range between -24 and -180 kJ ⋅ mol-1, whereas those of the HB complexes are between -6 and -19 kJ ⋅ mol-1 . DFT-SAPT also indicated that HB complexes are governed by electrostatics, but RB complexes present larger contribution of the induction term to the total attractive forces. 197 Au chemical shifts have been calculated using the relativistic ZORA Hamiltonian.
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Affiliation(s)
- Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin, 2, Ireland.,School of Chemistry, University College Dublin Belfield, Dublin, 4, Ireland
| | - Cristina Trujillo
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St., Dublin, 2, Ireland
| | - Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006, Madrid, Spain
| | - José Elguero
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006, Madrid, Spain
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37
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Collar AG, Trujillo C, Lockett-Walters B, Twamley B, Connon SJ. Catalytic Asymmetric γ-Lactam Synthesis from Enolisable Anhydrides and Imines. Chemistry 2019; 25:7275-7279. [PMID: 31050082 DOI: 10.1002/chem.201901028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Indexed: 01/18/2023]
Abstract
An anion-binding approach to the problem of preparing enantioenriched γ-lactams from enolisable anhydrides and imines is reported. A simple bisurea catalyst promotes the cycloaddition between α-aryl succinic anhydrides and either PMP- or benzhydryl-protected aldimines to provide γ-lactams with two contiguous stereocentres (one quaternary) with complete diastereocontrol and high to excellent enantioselectivity for the first time. A DFT study has provided insight into the catalyst mode of action and the origins of the observed stereocontrol.
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Affiliation(s)
- Aarón Gutiérrez Collar
- School of Chemistry Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Cristina Trujillo
- School of Chemistry Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Bruce Lockett-Walters
- School of Chemistry Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Brendan Twamley
- School of Chemistry Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Stephen J Connon
- School of Chemistry Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
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38
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Trujillo C, Flood A, Sánchez-Sanz G, Twamley B, Rozas I. Planarity or Nonplanarity: Modulating Guanidine Derivatives as α2-Adrenoceptors Ligands. J Chem Inf Model 2019; 59:2479-2486. [DOI: 10.1021/acs.jcim.9b00140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cristina Trujillo
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Aoife Flood
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Goar Sánchez-Sanz
- Irish Centre
of
High-End Computing, Grand Canal Quay, Dublin 2, Ireland
| | - Brendan Twamley
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Isabel Rozas
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
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39
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Trujillo C, Rozas I, Elguero J, Alkorta I, Sánchez-Sanz G. Modulating intramolecular chalcogen bonds in aromatic (thio)(seleno)phene-based derivatives. Phys Chem Chem Phys 2019; 21:23645-23650. [DOI: 10.1039/c9cp03694f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Intramolecular chalcogen interactions have been studied for four different derivatives of compounds within two different families, S or Se, to evaluate the effect of these IMChBs in the stability of the interacting and non-interacting systems.
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Affiliation(s)
- Cristina Trujillo
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin 152-160 Pearse Street
- Dublin 2
- Ireland
| | - Isabel Rozas
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin 152-160 Pearse Street
- Dublin 2
- Ireland
| | - José Elguero
- Instituto de Química Médica
- CSIC
- Juan de la Cierva
- 3
- E-28006 Madrid
| | - Ibon Alkorta
- Instituto de Química Médica
- CSIC
- Juan de la Cierva
- 3
- E-28006 Madrid
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40
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Lockett-Walters B, Trujillo C, Twamley B, Connon S. The base-catalysed Tamura cycloaddition reaction: calculation, mechanism, isolation of intermediates and asymmetric catalysis. Chem Commun (Camb) 2019; 55:11283-11286. [DOI: 10.1039/c9cc05064g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A combination of experimental and computational techniques has shown that the mechanism of the base-catalysed Tamura cycloaddition is not a concerted Diels–Alder process.
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Affiliation(s)
- Bruce Lockett-Walters
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
| | - Cristina Trujillo
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
| | - Brendan Twamley
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
| | - Stephen Connon
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
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41
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Aiello ML, Farid U, Trujillo C, Twamley B, Connon SJ. Catalytic Asymmetric Cycloadditions between Aldehydes and Enolizable Anhydrides: cis-Selective Dihydroisocoumarin Formation. J Org Chem 2018; 83:15499-15511. [PMID: 30461274 DOI: 10.1021/acs.joc.8b02332] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the presence of a trityl-substituted cinchona alkaloid-based catalyst, homophthalic, aryl succinic, and glutaconic anhydride derivatives reacted with aromatic and aliphatic aldehydes to produce cis-lactones in up to 90:10 dr and 99% ee. A DFT study has shown how the catalyst is uniquely able to bring about the opposite sense of diastereocontrol to that usually observed.
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Affiliation(s)
- Maria Luisa Aiello
- Trinity Biomedical Sciences Institute, School of Chemistry , The University of Dublin, Trinity College , Dublin 2 , Ireland
| | - Umar Farid
- Trinity Biomedical Sciences Institute, School of Chemistry , The University of Dublin, Trinity College , Dublin 2 , Ireland
| | - Cristina Trujillo
- Trinity Biomedical Sciences Institute, School of Chemistry , The University of Dublin, Trinity College , Dublin 2 , Ireland
| | - Brendan Twamley
- Trinity Biomedical Sciences Institute, School of Chemistry , The University of Dublin, Trinity College , Dublin 2 , Ireland
| | - Stephen J Connon
- Trinity Biomedical Sciences Institute, School of Chemistry , The University of Dublin, Trinity College , Dublin 2 , Ireland
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42
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Boix F, Trujillo C, Muro M. Cell-Mediated Immunity (CMI) as the Instrument to Assess the Response Against the Allograft: Present and Future. Curr Protein Pept Sci 2018; 19:1092-1106. [DOI: 10.2174/1389203719666180730164542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/20/2018] [Accepted: 07/24/2018] [Indexed: 11/22/2022]
Affiliation(s)
- F. Boix
- Immunology Department. Clinic University Hospital ‘Virgen de la Arrixaca` IMIB (Murcian Biomedical Research Institute), Murcia, Spain
| | - C. Trujillo
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
| | - M. Muro
- Immunology Department. Clinic University Hospital ‘Virgen de la Arrixaca` IMIB (Murcian Biomedical Research Institute), Murcia, Spain
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43
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Previtali V, Trujillo C, Amet R, Zisterer DM, Rozas I. Effect of isouronium/guanidinium substitution on the efficacy of a series of novel anti-cancer agents. Medchemcomm 2018; 9:735-743. [PMID: 30108964 DOI: 10.1039/c8md00089a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 03/19/2018] [Indexed: 12/30/2022]
Abstract
Considering our hypothesis that the guanidinium moiety in the protein kinase type III inhibitor 1 interacts with a phosphate of ATP within the hinge region, the nature of the interactions established between a model isouronium and the phosphate groups of ATP was computationally analysed indicating that an isouronium derivative of 1 will interact in a similar manner with ATP. Thus, a number of compounds were prepared to assess the effect of the guanidinium/isouronium substitution on cancer cell growth; additionally, the molecular shortening and conformational change induced by replacing the di-substituted guanidine-linker of 1 by an amide was explored. The effect of these compounds on cell viability was tested in human leukaemia, breast cancer and cervical cancer cell lines and the resulting IC50 values were compared with those of the lead compound 1. Replacement of the di-substituted guanidine-linker by an amide results in the loss of cytotoxicity; however, substitution of the mono-substituted guanidinium by an isouronium cation seems to be beneficial for cell growth inhibition. Additionally, the effect of these compounds on the MAPK/ERK pathway was studied by means of Western blotting and the results indicate that the isouronium derivative 2 decreases the levels of phosphorylated, and thus activated, ERK (pERK) both in leukaemia and breast cancer cells, whereas lead compound 1 only shows an effect on pERK levels in breast cancer cells. This confirms that both compounds could interfere with the MAPK/ERK pathway although other targets cannot be ruled out.
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Affiliation(s)
- Viola Previtali
- School of Chemistry , Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160 Pearse Street , Dublin 2 , Ireland .
| | - Cristina Trujillo
- School of Chemistry , Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160 Pearse Street , Dublin 2 , Ireland .
| | - Rebecca Amet
- School of Biochemistry and Immunology , Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160 Pearse Street , Dublin 2 , Ireland
| | - Daniela M Zisterer
- School of Biochemistry and Immunology , Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160 Pearse Street , Dublin 2 , Ireland
| | - Isabel Rozas
- School of Chemistry , Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160 Pearse Street , Dublin 2 , Ireland .
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Abstract
On the basis of the cyclization reactions reported by Danishefsky et al. of Meldrum's acid hydroxylethyl and anilinoethyl derivatives, the cyclization of the sulfamidomethylene and ureidomethylene derivatives was attempted without success. To understand the lack of reactivity of these compounds versus the successful cyclization of the ethyl derivatives, the corresponding mechanisms of reaction for both processes have been explored by means of MP2/6-311+G(d,p) calculations in an aqueous environment. The conformational analysis of all of these structures revealed that, while for the ethyl derivatives the minimum energy conformation corresponds to that of the cyclization initiating structure, for the methylene analogues the entrance channel conformations are substantially less stable than the energy minimum. Intramolecular hydrogen bonds were found in all of the energy minima as well as in the cyclization initiating conformations as determined by analysis of their electron density. The potential energy surfaces for the successful and unsuccessful cyclization processes were obtained at room temperature and 100 °C. Comparison of both processes allows rationalization that the lack of reactivity of the methylene derivatives can be thermodynamically explained based not only on the strength of the intramolecular hydrogen bond formed in their energy minima but also by the energy penalty needed to reach the entrance channel conformation and by the calculated energy barriers.
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Affiliation(s)
- Cristina Trujillo
- School of Chemistry, Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160 Pearse Street , Dublin 2 , Ireland
| | - Pilar Goya
- Instituto de Química Médica, CSIC , Juan de la Cierva, 3 , E-28006 Madrid , Spain
| | - Isabel Rozas
- School of Chemistry, Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160 Pearse Street , Dublin 2 , Ireland
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45
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Sánchez-Sanz G, Trujillo C, Alkorta I, Elguero J. Modulation of in:out and out:out conformations in [X.X'.X''] phosphatranes by Lewis acids. Phys Chem Chem Phys 2018; 19:20647-20656. [PMID: 28737804 DOI: 10.1039/c7cp03661b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A theoretical study of [X.X'.X'']phosphatrane:Lewis acid complexes has been carried out in order to analyze how the in:out and out:out conformations can be modulated by the interaction with Lewis acids (LA). It has been found that in:out structures are more stable in larger systems i.e. in [4.4.3]:LA and [4.4.4]:LA than in [3.3.3]:LA and [4.3.3]:LA. The results obtained for the relative energies in conjunction with electron density properties showed that upon complexation, in:out conformers become more stable with the increasing acidity of the corresponding Lewis acid. In fact, the binding energies found for in:out complexes are larger than those obtained for out:out complexes. The complexes with the largest relative energy favoring the in:out structure correspond to those with charged Lewis acids, followed by the complexes with ClF. In all cases, the complexes are cooperative, reaching a maximum value of 168.5 kJ mol-1 for the [4.3.3]:F+ complex.
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Affiliation(s)
- Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin 2, Ireland & School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
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46
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Sánchez-Sanz G, Trujillo C. Improvement of Anion Transport Systems by Modulation of Chalcogen Interactions: The influence of solvent. J Phys Chem A 2018; 122:1369-1377. [DOI: 10.1021/acs.jpca.7b10920] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal
Quay, Dublin 2, Ireland
| | - Cristina Trujillo
- School
of Chemistry, Trinity Biomedical Sciences, Trinity College Dublin, 152−160 Pearse Street, Dublin 2, Ireland
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47
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Previtali V, Trujillo C, Boisson JC, Khartabil H, Hénon E, Rozas I. Development of the first model of a phosphorylated, ATP/Mg 2+-containing B-Raf monomer by molecular dynamics simulations: a tool for structure-based design. Phys Chem Chem Phys 2017; 19:31177-31185. [PMID: 29139502 DOI: 10.1039/c7cp05038k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A model of phosphorylated and ATP-containing B-Raf protein kinase is needed as a tool for the structure-based design of new allosteric inhibitors, since no crystal structure of such a system has been resolved. Here, we present the development of such a model as well as a thorough analysis of its structural features. This model was prepared using a systematic molecular dynamics approach considering the presence or absence of both the phosphate group at the Thr599 site and the ATP molecule. Then, different structural features (i.e. DFG motif, Mg2+ binding loop, activation loop, phosphorylation site and αC-helix region) were analysed for each trajectory to validate the aimed 2pBRAF_ATP model. Moreover, the structure and activating interactions of this 2pBRAF_ATP model were found to be in agreement with previously reported information. Finally, the model was further validated by means of a molecular docking study with our previously developed lead compound I confirming that this ATP-containing, phosphorylated protein model is suitable for further structure-based design studies.
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Affiliation(s)
- Viola Previtali
- School of Chemistry Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
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48
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Sánchez-Sanz G, Trujillo C, Alkorta I, Elguero J. Enhancing Intramolecular Chalcogen Interactions in 1-Hydroxy-8-YH-naphthalene Derivatives. J Phys Chem A 2017; 121:8995-9003. [DOI: 10.1021/acs.jpca.7b09678] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Goar Sánchez-Sanz
- Irish Centre of High-End Computing & School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cristina Trujillo
- School
of Chemistry, Trinity Biomedical Sciences, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Ibon Alkorta
- Instituto
de Química Médica, Consejo Superior de Investigaciones Científicas, Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - José Elguero
- Instituto
de Química Médica, Consejo Superior de Investigaciones Científicas, Juan de la Cierva, 3, E-28006 Madrid, Spain
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49
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Flood A, Trujillo C, Sanchez-Sanz G, Kelly B, Muguruza C, Callado LF, Rozas I. Thiophene/thiazole-benzene replacement on guanidine derivatives targeting α 2 -Adrenoceptors. Eur J Med Chem 2017. [DOI: 10.1016/j.ejmech.2017.06.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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50
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Mahmoud S, Planes MD, Cabedo M, Trujillo C, Rienzo A, Caballero-Molada M, Sharma SC, Montesinos C, Mulet JM, Serrano R. TOR complex 1 regulates the yeast plasma membrane proton pump and pH and potassium homeostasis. FEBS Lett 2017; 591:1993-2002. [PMID: 28486745 DOI: 10.1002/1873-3468.12673] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/02/2017] [Accepted: 05/05/2017] [Indexed: 12/16/2022]
Abstract
We have identified in yeast a connection between two master regulators of cell growth: a biochemical connection involving the TORC1 protein kinase (which activates protein synthesis, nutrient uptake, and anabolism) and a biophysical connection involving the plasma membrane proton-pumping H+ -ATPase Pma1 (which drives nutrient and K+ uptake and regulates pH homeostasis). Raising the temperature to nonpermissive values in a TOR thermosensitive mutant decreases Pma1 activity. Rapamycin, a TORC1 inhibitor, inhibits Pma1 dependent on its receptor Fpr1 and on the protein phosphatase Sit4, a TORC1 effector. Mutation of either Sit4 or Tco89, a nonessential subunit of TORC1, decreases proton efflux, K+ uptake, intracellular pH, cell growth, and tolerance to weak organic acids. Tco89 does not affect Pma1 activity but activates K+ transport.
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Affiliation(s)
- Shima Mahmoud
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Spain
| | - María Dolores Planes
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Spain
| | - Marc Cabedo
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Spain
| | - Cristina Trujillo
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Spain
| | - Alessandro Rienzo
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Spain
| | - Marcos Caballero-Molada
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Spain
| | - Sukesh C Sharma
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Spain
| | - Consuelo Montesinos
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Spain
| | - José Miguel Mulet
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Spain
| | - Ramón Serrano
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Spain
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