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Bofill JM, Severi M, Quapp W, Ribas-Ariño J, de P R Moreira I, Albareda G. Optimal Oriented External Electric Fields to Trigger a Barrierless Oxaphosphetane Ring Opening Step of the Wittig Reaction. Chemistry 2024; 30:e202400173. [PMID: 38457260 DOI: 10.1002/chem.202400173] [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: 01/15/2024] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/10/2024]
Abstract
The Wittig reaction is one of the most important processes in organic chemistry for the asymmetric synthesis of olefinic compounds. In view of the increasingly acknowledged potentiality of the electric fields in promoting reactions, here we will consider the effect of the oriented external electric field (OEEF) on the second step of Wittig reaction (i. e. the ring opening oxaphosphetane) in a model system for non-stabilized ylides. In particular, we have determined the optimal direction and strength of the electric field that should be applied to annihilate the reaction barrier of the ring opening through the polarizable molecular electric dipole (PMED) model that we have recently developed. We conclude that the application of the optimal external electric field for the oxaphosphetane ring opening favours a Bestmann-like mechanism.
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Affiliation(s)
- Josep Maria Bofill
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, Universitat de Barcelona, C/Martí i Franquès 1, 08028, Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, C/Martí i Franquès 1, 08028, Barcelona, Spain
| | - Marco Severi
- Department of Chemistry G. Ciamician, University of Bologna, Via F. Selmi 2, 40126, Bologna, Italy
| | - Wolfgang Quapp
- Mathematisches Institut, Universität Leipzig, PF 100920, D-04009, Leipzig, Germany
| | - Jordi Ribas-Ariño
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, C/Martí i Franquès 1, 08028, Barcelona, Spain
- Departament de Ciència de Materials i Química Física, Secció de Química Física, Universitat de Barcelona, C/Martí i Franquès 1, 08028, Barcelona, Spain
| | - Ibério de P R Moreira
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, C/Martí i Franquès 1, 08028, Barcelona, Spain
- Departament de Ciència de Materials i Química Física, Secció de Química Física, Universitat de Barcelona, C/Martí i Franquès 1, 08028, Barcelona, Spain
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Sreenivas K, Rao CN, Khan FA. Intramolecular CH-Hydrogen Bonding During the Dissociation of the Oxaphosphetane Intermediate Facilitates Z/E-Selectivity in Wittig Olefination. ChemistryOpen 2024; 13:e202300171. [PMID: 38060831 PMCID: PMC10924042 DOI: 10.1002/open.202300171] [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: 08/22/2023] [Revised: 10/25/2023] [Indexed: 03/10/2024] Open
Abstract
Herein, DFT studies corroborating experimental results revealed that the shortest intramolecular hydrogen bonding distance of cis/trans-oxaphosphetane (OPA) oxygen with the CH-hydrogen of a triphenylphosphine phenyl ring provides good evidence for the attained olefin Z/E-selectivity in Wittig olefination of the studied examples. 2-Nitrobenzaldehyde, 3-nitrobenzaldehyde, 2-nitro-3-bromobenzaldehyde, 2-nitro-5-bromobenzaldehyde and 2-nitro-5-arylbenzaldehydes provided Z-nitrostilbenes with (2-chloro-4-hydroxy-3-methoxy-5-(methoxycarbonyl)benzyl) triphenylphosphonium chloride as the major products. However, 4-nitrobenzaldehyde and 2-nitro-6-bromobenzaldehydes furnished E-nitrostilbenes as the major products in high yields. Furthermore, the DFT computed intramolecular CH1/CH2-hydrogen bond distances with Cl/NO2 of selected stilbene derivatives were in good agreement with intramolecular hydrogen bond distances measured from single-crystal X-ray diffraction measurements.
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Affiliation(s)
- Kukkamudi Sreenivas
- Department of ChemistryIndian Institute of Technology Hyderabad KandiSangareddyTelangana502 285India
| | - Chintada Nageswara Rao
- Department of Drug Discovery and Biomedical Sciences, College of PharmacyUniversity of South CarolinaColumbiaSC-29208USA
| | - Faiz Ahmed Khan
- Department of ChemistryIndian Institute of Technology Hyderabad, KandiSangareddyTelangana502 285India
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Santos CV, Monteiro SA, Soares ASC, Souto ICA, Moura RT. Decoding Chemical Bonds: Assessment of the Basis Set Effect on Overlap Electron Density Descriptors and Topological Properties in Comparison to QTAIM. J Phys Chem A 2023; 127:7997-8014. [PMID: 37703453 DOI: 10.1021/acs.jpca.3c04504] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Quantum chemical bonding descriptors based on the total and overlap density can provide valuable information about chemical interactions in different systems. However, these descriptors can be sensitive to the basis set used. To address this, different numerical treatments of electron density have been proposed to reduce the basis set dependency. In this work, we introduce overlap properties (OPs) obtained through numerical treatment of the electron density and present the topology of overlap density (TOP) for the first time. We compare the basis set dependency of numerical OP and TOP descriptors with their quantum theory of atoms in molecules (QTAIM) counterparts, considering the total electron density. Three single (C-C, C-O, and C-F) bonds in ethane, methanol, and fluoromethane and two double (C═C and C═O) bonds in ethene and formaldehyde were analyzed. Diatomic molecules Li-X with X = F, Cl, and Br were also analyzed. Eight parameters, including QTAIM descriptors and OP/TOP descriptors, are used to assess the basis dependency at the ωB97X-D level of theory using 28 basis sets from three classes: Pople, Ahlrichs, and Dunning. The study revealed that the topological overlap electron density properties exhibit comparatively lesser dependence on the basis set compared to their total electron density counterparts. Remarkably, these properties retain their chemical significance even with reduced basis set dependency. Similarly, numerical OP descriptors show less basis set dependency than their QTAIM counterparts. The excess of polarization functions increases charge concentration in the interatomic region and influences both QTAIM and OP descriptors. The basis sets Def2TZVP, 6-31++G(d,p), 6-311++G(d,p), cc-pVDZ, cc-pVTZ, and cc-pVQZ demonstrate reduced variability for the tested bond classes in this study, with particular emphasis on the triple-ζ quality Ahlrichs' basis set. We recommend against using basis sets with numerous polarization functions, such as augmented Dunning's and Ahlrichs' quadruple-ζ.
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Affiliation(s)
- Carlos V Santos
- Department of Chemistry, Federal University of Paraiba, Joao Pessoa, Paraiba 58051-970, Brazil
| | - Shirlene A Monteiro
- Department of Chemistry, State University of Paraiba, Campina Grande, Paraiba 58051-970, Brazil
| | - Amanda S C Soares
- Department of Chemistry and Physics, Center of Agrarian Sciences, Federal University of Paraiba, Areia, Paraiba 58397-000, Brazil
| | - Isabeli C A Souto
- Department of Chemistry and Physics, Center of Agrarian Sciences, Federal University of Paraiba, Areia, Paraiba 58397-000, Brazil
| | - Renaldo T Moura
- Department of Chemistry and Physics, Center of Agrarian Sciences, Federal University of Paraiba, Areia, Paraiba 58397-000, Brazil
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
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Valderhaug S, Paškanová N, Tůma J, Herciková J, Eigner V, Liu H, Gorovoy A, Johansen JE, Gautun OR. Synthesis, identification, chiral separation and crystal structure of (3 R,4 R,7 S,8 S)-3,4,7,8-tetrachlorodecane and its stereoisomers. Heliyon 2023; 9:e16987. [PMID: 37346323 PMCID: PMC10279909 DOI: 10.1016/j.heliyon.2023.e16987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/23/2023] Open
Abstract
Chlorinated paraffins (CPs) are a notoriously known class of compounds that stand amongst the most wide-spread persistent organic pollutants. Therefore, their reliable, repeatable, and reproducible quantitative analysis using well-defined reference standards is of utmost importance. In view of the increasing demand for constitutionally and stereochemically defined CP standards, we have synthesized a stereoisomeric mixture of 3,4,7,8-tetrachlorodecane. One stereoisomer - (3R,4R,7S,8S)-3,4,7,8-tetrachlorodecane was separated from the mixture, and enriched fractions of residual stereoisomers were achieved through crystallisation of the residual mother liquors. The molecular structure of the single isolated stereoisomer was confirmed through single-crystal X-ray crystallographic data. One fraction of 3,4,7,8-tetrachlorodecane stereoisomers was successfully separated on a chiral stationary phase using supercritical fluid chromatography hyphenated to mass spectrometry (column: Chiral ART Amylose-C; mobile phase: CO2/MeOH (96/4 v/v) with 0.1% diethylamine). The reported separation of stereoisomers is unprecedented in CP analysis so far.
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Affiliation(s)
- Solveig Valderhaug
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, NO-7491, Trondheim, Norway
- Chiron AS, Stiklestadveien 1, NO-7041 Trondheim, Norway
| | - Natalie Paškanová
- Department of Organic Chemistry, University of Chemistry and Technology, Technická 5, 16628, Prague, Czech Republic
| | - Jiří Tůma
- Chiron AS, Stiklestadveien 1, NO-7041 Trondheim, Norway
- Department of Organic Chemistry, University of Chemistry and Technology, Technická 5, 16628, Prague, Czech Republic
| | - Jana Herciková
- Department of Organic Chemistry, University of Chemistry and Technology, Technická 5, 16628, Prague, Czech Republic
| | - Václav Eigner
- Department of Solid State Chemistry, University of Chemistry and Technology, Technická 5, 16628, Prague, Czech Republic
| | - Huiling Liu
- Chiron AS, Stiklestadveien 1, NO-7041 Trondheim, Norway
| | | | | | - Odd Reidar Gautun
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, NO-7491, Trondheim, Norway
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Gómez S, Rojas-Valencia N, Toro-Labbé A, Restrepo A. The transition state region in nonsynchronous concerted reactions. J Chem Phys 2023; 158:084109. [PMID: 36859077 DOI: 10.1063/5.0133487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
The critical and vanishing points of the reaction force F(ξ) = -dV(ξ)/dξ yield five important coordinates (ξR, ξR* , ξTS, ξP* , ξP) along the intrinsic reaction coordinate (IRC) for a given concerted reaction or reaction step. These points partition the IRC into three well-defined regions, reactants (ξR→ξR* ), transition state (ξR* →ξP* ), and products (ξP* →ξP), with traditional roles of mostly structural changes associated with the reactants and products regions and mostly electronic activity associated with the transition state (TS) region. Following the evolution of chemical bonding along the IRC using formal descriptors of synchronicity, reaction electron flux, Wiberg bond orders, and their derivatives (or, more precisely, the intensity of the electron activity) unambiguously indicates that for nonsynchronous reactions, electron activity transcends the TS region and takes place well into the reactants and products regions. Under these circumstances, an extension of the TS region toward the reactants and products regions may occur.
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Affiliation(s)
- Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Natalia Rojas-Valencia
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago de Chile 7820436, Chile
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
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Li H, Liu Z, Dong Y, Wang YX, Zhu XL. Design, Synthesis, and Fungicidal Evaluation of Novel N-Methoxy Pyrazole-4-Carboxamides as Potent Succinate Dehydrogenase Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2610-2615. [PMID: 36696251 DOI: 10.1021/acs.jafc.2c07031] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Succinate dehydrogenase (SDH, EC 1.3.5.1, also known as complex II) has been recognized as one of the most promising targets of fungicides. Here, based on the binding mode of pydiflumetofen with SDH, the carbon-carbon double bond was introduced into the chemical of pydiflumetofen and then produced the target compounds 6a-6o. The enzymatic inhibitory activity and structure-activity relationship (SAR) study showed that the 2-position and 4-position in terminal benzene were positive to increasing activity. Furthermore, fungicidal activity results in greenhouses indicated that compound 6o showed good control effects against wheat powdery mildew (WPM), cucumber powdery mildew (CPM), and southern corn rust (SCR), showing its broad-spectrum property. Especially, compound 6o exhibited 95 and 75% control effects against CPM and SCR at 6.25 mg/L, respectively, which are better than pydiflumetofen (80% control effects against CPM and 15% against SCR), indicating its potency that is worthy of further development.
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Affiliation(s)
- Hua Li
- Henan Joint International Research Laboratory of Veterinary Biologics Research and Application, Anyang Institute of Technology, Anyang, Henan 455000, P.R. China
- Key Laboratory of Pesticide and Chemical Biology of the Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan, Hubei 430079, P.R. China
| | - Zheng Liu
- Key Laboratory of Pesticide and Chemical Biology of the Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan, Hubei 430079, P.R. China
| | - Ying Dong
- Key Laboratory of Pesticide and Chemical Biology of the Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan, Hubei 430079, P.R. China
| | - Yu-Xia Wang
- Key Laboratory of Pesticide and Chemical Biology of the Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan, Hubei 430079, P.R. China
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide and Chemical Biology of the Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan, Hubei 430079, P.R. China
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7
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Moreno N, Hadad CZ, Restrepo A. Microsolvation of electrons by a handful of ammonia molecules. J Chem Phys 2022; 157:134301. [PMID: 36209021 DOI: 10.1063/5.0107245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Microsolvation of electrons in ammonia is studied here via anionic NH3 n - clusters with n = 2-6. Intensive samplings of the corresponding configurational spaces using second-order perturbation theory with extended basis sets uncover rich and complex energy landscapes, heavily populated by many local minima in tight energy windows as calculated from highly correlated coupled cluster methods. There is a marked energetical preference for structures that place the excess electron external to the molecular frame, effectively coordinating it with the three protons from a single ammonia molecule. Overall, as the clusters grow in size, the lowest energy dimer serves as the basic motif over which additional ammonia molecules are attached via unusually strong charge-assisted hydrogen bonds. This is a priori quite unexpected because, on electrostatic grounds, the excess electron would be expected to be in contact with as many protons as possible. Accordingly, a full quantum mechanical treatment of the bonding interactions under the tools provided by the quantum theory of atoms in molecules is carried out in order to dissect and understand the nature of intermolecular contacts. Vertical detachment energies reveal bound electrons even for n = 2.
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Affiliation(s)
- Norberto Moreno
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Cacier Z Hadad
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
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Correa E, Montaño D, Restrepo A. Cation ⋯anion bonding interactions in 1–Ethyl–3–Methylimidazolium based ionic liquids. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Preparation and DFT studies of chiral Cu (I)-complexes of biphenyl bisoxazolines and their application in enantioselective Kharasch-Sosnovsky reaction. Sci Rep 2022; 12:15038. [PMID: 36057728 PMCID: PMC9440904 DOI: 10.1038/s41598-022-18922-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/22/2022] [Indexed: 11/09/2022] Open
Abstract
Effect of a range of t-butyl perbenzoates bearing electron-withdrawing and electron-donating substitutions on the phenyl ring and HZSM-5 as a porous additive at 0 °C in enantioselective allylic C-H bond oxidation of cyclic and acyclic olefins in the presence of Cu (I)-(S,aS,S) complexes of biphenyl bisoxazoline ligands, produced easily through the chelation-induced process, were investigated. The enantioenriched allylic esters were obtained in reasonable times with excellent enantioselectivities and yields using electron-withdrawing substituted peresters in the presence of Cu (I)-(S,aS,S)-1a complex, containing phenyl groups at the stereogenic centers of the oxazoline moieties. To reach a better insight on geometry, chemical activity, enantioselectivity, and thermodynamic stability of the Cu (I)-BOX complexes, DFT calculations with B3LYP-D3/6-31G (d, p) level of theory were applied to them. Moreover, NBO analysis was used to illustrate interactions between orbitals.
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Abstract
The reactivity of phosphorus and sulfur ylides toward carbonyl compounds constitutes a well-known dichotomy that is a common educational device in organic chemistry─the former gives olefins, while the latter gives epoxides. Herein, we report a stereodivergent carbonyl olefination that challenges this dichotomy, showcasing thiouronium ylides as valuable olefination reagents. With this method, aldehydes are converted to Z-alkenes with high stereoselectivity and broad substrate scope, while N-tosylimines provide a similarly proficient entry to E-alkenes. In-depth computational and experimental studies clarified the mechanistic details of this unusual reactivity.
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Disease Prevention and Treatment Using β-Carotene: the Ultimate Provitamin A. REVISTA BRASILEIRA DE FARMACOGNOSIA : ORGAO OFICIAL DA SOCIEDADE BRASILEIRA DE FARMACOGNOSIA 2022; 32:491-501. [PMID: 35669276 PMCID: PMC9150880 DOI: 10.1007/s43450-022-00262-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/06/2022] [Indexed: 12/14/2022]
Abstract
Humans being unable to synthesize beta-carotene, the provitamin A, depend on external sources as its supplement. Health benefits and dietary requirements of beta-carotene are interrelated. This orange-red coloured pigment has been enormously examined for its capacity to alleviate several chronic diseases including various types of cancer, cystic fibrosis, as well as COVID-19. However, this class of phytoconstituents has witnessed a broad research gap due to several twin conclusions that have been reported. Natural sources for these compounds along with their extraction methods have been mentioned. The current communication aims at contributing to the global scientific literature on beta-carotene’s application in prevention and treatment of lifestyle diseases.
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Phelps R, Orr-Ewing AJ. Direct Observation of the Dynamics of Ylide Solvation by Hydrogen-bond Donors Using Time-Resolved Infrared Spectroscopy. J Am Chem Soc 2022; 144:9330-9343. [PMID: 35580274 PMCID: PMC9164226 DOI: 10.1021/jacs.2c01208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photoexcitation of α-diazocarbonyl compounds produces singlet carbene intermediates that react with nucleophilic solvent molecules to form ylides. The zwitterionic nature of these newly formed ylides induces rapid changes in their interactions with the surrounding solvent. Here, ultrafast time-resolved infrared absorption spectroscopy is used to study the ylide-forming reactions of singlet carbene intermediates from the 270 nm photoexcitation of ethyl diazoacetate in various solvents and the changes in the subsequent ylide-solvent interactions. The results provide direct spectroscopic observation of the competition between ylide formation and C-H insertion in reactions of the singlet carbene with nucleophilic solvent molecules. We further report the specific solvation dynamics of the tetrahydrofuran (THF)-derived ylide (with a characteristic IR absorption band at 1636 cm-1) by various hydrogen-bond donors and the coordination by lithium cations. Hydrogen-bonded ylide bands shift to a lower wavenumber by -19 cm-1 for interactions with ethanol, -14 cm-1 for chloroform, -10 cm-1 for dichloromethane, -9 cm-1 for acetonitrile or cyclohexane, and -16 cm-1 for Li+ coordination, allowing the time evolution of the ylide-solvent interactions to be tracked. The hydrogen-bonded ylide bands grow with rate coefficients that are close to the diffusional limit. We further characterize the specific interactions of ethanol with the THF-derived ylide using quantum chemical (MP2) calculations and DFT-based atom-centered density matrix propagation trajectories, which show preferential coordination to the α-carbonyl group. This coordination alters the hybridization character of the ylidic carbon atom, with the greatest change toward sp2 character found for lithium-ion coordination.
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Affiliation(s)
- Ryan Phelps
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
| | - Andrew J Orr-Ewing
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
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13
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Analysis of Conformational Preferences in Caffeine. Molecules 2022; 27:molecules27061937. [PMID: 35335301 PMCID: PMC8949453 DOI: 10.3390/molecules27061937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 12/10/2022] Open
Abstract
High level DLPNO−CCSD(T) electronic structure calculations with extended basis sets over B3LYP−D3 optimized geometries indicate that the three methyl groups in caffeine overcome steric hindrance to adopt uncommon conformations, each one placing a C−H bond on the same plane of the aromatic system, leading to the C−H bonds eclipsing one carbonyl group, one heavily delocalized C−N bond constituent of the fused double ring aromatic system, and one C−H bond from the imidazole ring. Deletion of indiscriminate and selective non-Lewis orbitals unequivocally show that hyperconjugation in the form of a bidirectional −CH3 ⇆ aromatic system charge transfer is responsible for these puzzling conformations. The structural preferences in caffeine are exclusively determined by orbital interactions, ruling out electrostatics, induction, bond critical points, and density redistribution because the steric effect, the allylic effect, the Quantum Theory of Atoms in Molecules (QTAIM), and the non-covalent interactions (NCI), all predict wrong energetic orderings. Tiny rotational barriers, not exceeding 1.3 kcal/mol suggest that at room conditions, each methyl group either acts as a free rotor or adopts fluxional behavior, thus preventing accurate determination of their conformations. In this context, our results supersede current experimental ambiguity in the assignation of methyl conformation in caffeine and, more generally, in methylated xanthines and their derivatives.
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Santos-Jr CV, A. F. de Souza M, Kraka E, Moura Jr RT. Analysis of spectator chemical bonds in SN2@C and @Si reaction mechanisms in the gas phase. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2021.139282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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15
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Guillade L, Mora P, Villar P, Alvarez R, R de Lera A. Total synthesis of nahuoic acid A via a putative biogenetic intramolecular Diels-Alder (IMDA) reaction. Chem Sci 2021; 12:15157-15169. [PMID: 34909158 PMCID: PMC8612404 DOI: 10.1039/d1sc04524e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/26/2021] [Indexed: 11/21/2022] Open
Abstract
Inspired by the biogenetic proposal of an intramolecular Diels–Alder (IMDA) cycloaddition, the total synthesis of natural product nahuoic acid A, a cofactor-competitive inhibitor of the epigenetic enzyme lysine methyl transferase SETD8, has been carried out. A non-conjugated pentaenal precursor was synthesized with high levels of stereoselectivity at seven stereogenic centers and with the appropriate control of double bond geometries. Although the IMDA reaction of the non-conjugated pentaenal using Me2AlCl for catalysis at −40 °C selectively afforded the trans-fused diastereomer corresponding to the Re-endo mode of cycloaddition, under thermal reaction conditions it gave rise to a mixture of diastereomers, that preferentially formed through the exo mode, including the cis-fused angularly-methylated octahydronaphthalene diastereomer precursor of nahuoic acid A. The natural product could be obtained upon oxidation and overall deprotection of the hydroxyl groups present in the Si-exo IMDA diastereomer. The total synthesis of natural product nahuoic acid A, a cofactor-competitive inhibitor of the epigenetic enzyme lysine methyl transferase SETD8, has been carried out based on the biogenetic proposal of an intramolecular Diels–Alder (IMDA) cycloaddition.![]()
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Affiliation(s)
- Lucía Guillade
- Departamento de Química Orgánica, Facultade de Química, CINBIO, IIS Galicia Sur, Universidade de Vigo 36310 Vigo Spain
| | - Paula Mora
- Departamento de Química Orgánica, Facultade de Química, CINBIO, IIS Galicia Sur, Universidade de Vigo 36310 Vigo Spain
| | - Pedro Villar
- Departamento de Química Orgánica, Facultade de Química, CINBIO, IIS Galicia Sur, Universidade de Vigo 36310 Vigo Spain
| | - Rosana Alvarez
- Departamento de Química Orgánica, Facultade de Química, CINBIO, IIS Galicia Sur, Universidade de Vigo 36310 Vigo Spain
| | - Angel R de Lera
- Departamento de Química Orgánica, Facultade de Química, CINBIO, IIS Galicia Sur, Universidade de Vigo 36310 Vigo Spain
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Bal A, Mal P. A Click Reaction Enabled by Phosphorus‐Oxygen Bond for Synthesis of Triazoles. ChemistrySelect 2021. [DOI: 10.1002/slct.202102758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ankita Bal
- School of Chemical Sciences Institute of Science Education and Research (NISER), HBNI, Bhubaneswar, PO Bhimpur-Padanpur Via Jatni, District Khurda Odisha 752050 India
| | - Prasenjit Mal
- School of Chemical Sciences Institute of Science Education and Research (NISER), HBNI, Bhubaneswar, PO Bhimpur-Padanpur Via Jatni, District Khurda Odisha 752050 India
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17
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Chen QH, Wu BK, Pan D, Sang LX, Chang B. Beta-carotene and its protective effect on gastric cancer. World J Clin Cases 2021; 9:6591-6607. [PMID: 34447808 PMCID: PMC8362528 DOI: 10.12998/wjcc.v9.i23.6591] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/16/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
Beta-carotene is an important natural pigment that is very beneficial to human health. It is widely found in vegetables and fruits. The three main functions are antioxidant effects, cell gap junction-related functions and immune-related functions. Because of its diverse functions, beta-carotene is believed to prevent and treat many chronic diseases. Gastric cancer is one of the most important diseases it can treat. Gastric cancer is a type of cancer with a high incidence. Its etiology varies, and the pathogenesis is complex. Gastric cancer seriously affects human health. The role of beta-carotene, a natural nutrient, in gastric cancer has been explored by many researchers, including molecular mechanisms and epidemiological studies. Molecular studies have mainly focused on oxidative stress, cell cycle, signal transduction pathways and immune-related mechanisms of beta-carotene in gastric cancer. Many epidemiological surveys and cohort studies of patients with gastric cancer have been conducted, and the results of these epidemiological studies vary due to the use of different research methods and analysis of different regions. This paper will summarize the results of these studies, mainly in terms of molecular mechanisms and epidemiological research results, which will provide a systematic basis for future studies of the treatment and prognosis of gastric cancer. This paper will help researchers identify new research directions.
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Affiliation(s)
- Qian-Hui Chen
- Department of Intensive Care Unit, First Affiliated Hospital of China Medical University, Shenyang 110001, Liaoning Province, China
| | - Bao-Kang Wu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China
| | - Dan Pan
- Department of Geriatrics, First Affiliated Hospital of China Medical University, Shenyang 110001, Liaoning Province, China
| | - Li-Xuan Sang
- Department of Geriatrics, First Affiliated Hospital of China Medical University, Shenyang 110001, Liaoning Province, China
| | - Bing Chang
- Department of Gastroenterology, First Affiliated Hospital of China Medical University, Shenyang 110001, Liaoning Province, China
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18
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Tobón P, Gómez S, Restrepo A, Núñez-Zarur F. Role of Substrate Substituents in Alkene Metathesis Mediated by a Ru Alkylidene Catalyst. Organometallics 2021. [DOI: 10.1021/acs.organomet.0c00482] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Paola Tobón
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 50010, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 50010, Colombia
| | - Francisco Núñez-Zarur
- Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, 050026 Medellín, Colombia
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19
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Alvarez R, de Lera AR. Natural polyenic macrolactams and polycyclic derivatives generated by transannular pericyclic reactions: optimized biogenesis challenging chemical synthesis. Nat Prod Rep 2020; 38:1136-1220. [PMID: 33283831 DOI: 10.1039/d0np00050g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Covering from 1992 to the end of 2020-11-20.Genetically-encoded polyenic macrolactams, which are constructed by Nature using hybrid polyketide synthase/nonribosomal peptide synthase (PKSs/NRPSs) assembly lines, are part of the large collection of natural products isolated from bacteria. Activation of cryptic (i.e., silent) gene clusters in these microorganisms has more recently allowed to generate and eventually isolate additional members of the family. Having two unsaturated fragments separated by short saturated chains, the primary macrolactam is posited to undergo transannular reactions and further rearrangements thus leading to the generation of a structurally diverse collection of polycyclic (natural) products and oxidized derivatives. The review will cover the challenges that scientists face on the isolation of these unstable compounds from the cultures of the producing microorganisms, their structural characterization, biological activities, optimized biogenetic routes, as well as the skeletal rearrangements of the primary structures of the natural macrolactams derived from pericyclic reactions of the polyenic fragments. The efforts of the synthetic chemists to emulate Nature on the successful generation and structural confirmation of these natural products will also be reported.
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Affiliation(s)
- Rosana Alvarez
- Department of Organic Chemistry and Center for Biomedical Research (CINBIO), IBIV, Universidade de Vigo, 36310 Vigo, Spain.
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20
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García López J, Sansores Peraza PM, Iglesias MJ, Roces L, García-Granda S, López Ortiz F. Spiro[1,2]oxaphosphetanes of Nonstabilized and Semistabilized Phosphorus Ylide Derivatives: Synthesis and Kinetic and Computational Study of Their Thermolysis. J Org Chem 2020; 85:14570-14591. [DOI: 10.1021/acs.joc.0c01270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jesús García López
- Área de Quı́mica Orgánica, Centro de Investigación CIAIMBITAL, Universidad de Almerı́a, 04120 Almería, Spain
| | - Pablo M. Sansores Peraza
- Área de Quı́mica Orgánica, Centro de Investigación CIAIMBITAL, Universidad de Almerı́a, 04120 Almería, Spain
| | - María José Iglesias
- Área de Quı́mica Orgánica, Centro de Investigación CIAIMBITAL, Universidad de Almerı́a, 04120 Almería, Spain
| | - Laura Roces
- Departamento de Quı́mica Fı́sica y Analı́tica, Universidad de Oviedo-CINN, C/Julián Clavería 8, 33006 Oviedo, Spain
- Servicios Cientı́fico Técnicos, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Santiago García-Granda
- Departamento de Quı́mica Fı́sica y Analı́tica, Universidad de Oviedo-CINN, C/Julián Clavería 8, 33006 Oviedo, Spain
| | - Fernando López Ortiz
- Área de Quı́mica Orgánica, Centro de Investigación CIAIMBITAL, Universidad de Almerı́a, 04120 Almería, Spain
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21
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Gómez S, Ramírez-Malule H, Cardona-G W, Osorio E, Restrepo A. Double-Ring Epimerization in the Biosynthesis of Clavulanic Acid. J Phys Chem A 2020; 124:9413-9426. [PMID: 33135896 DOI: 10.1021/acs.jpca.0c05427] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
All reaction steps during the biosynthesis of suicidal clavulanic acid (coformulated with β-lactam antibiotics and used to fight bacterial infections) are known, except for the crucial 3S,5S → 3R,5R double epimerization needed to produce a biologically active stereoisomer, for which mechanistic hypothesis is subject to debate. In this work, we provide evidence for a reaction channel for the double inversion of configuration that involves a total of six reaction steps. When mediated by an enzyme with a terminal S-H bond, this highly complex reaction is spontaneous in the absence of solvents. Polarizable continuum models introduce reaction barriers in aqueous environments because of the strong destabilization of the first transition state. Molecular geometries and electronic structures in both cases indicate that solvent-free spontaneity and aqueous medium barriers are both firmly rooted in a substantial reorganization of the electron density right at the onset of the reaction, mostly involving a cyclic evolution/involution of large regions of π delocalization used to stabilize the excess charge left after the initial proton abstraction.
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Affiliation(s)
- Sara Gómez
- Instituto de Quı́mica, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 50010 Medellı́n, Colombia.,Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Howard Ramírez-Malule
- Escuela de Ingenierı́a Quı́mica, Universidad del Valle, A.A. 25360, 76001 Cali, Colombia
| | - Wilson Cardona-G
- Instituto de Quı́mica, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 50010 Medellı́n, Colombia
| | - Edison Osorio
- Facultad de Ciencias Naturales y Matemáticas, Universidad de Ibagué, Carrera 22 Calle 67, 73001 Ibagué, Colombia
| | - Albeiro Restrepo
- Instituto de Quı́mica, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 50010 Medellı́n, Colombia
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22
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Rojas-Valencia N, Gómez S, Guerra D, Restrepo A. A detailed look at the bonding interactions in the microsolvation of monoatomic cations. Phys Chem Chem Phys 2020; 22:13049-13061. [PMID: 32478372 DOI: 10.1039/d0cp00428f] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Global and local descriptors of the properties of intermolecular bonding, formally derived from independent methodologies (QTAIM, NCI, NBO, density differences) afford a highly complex picture of the bonding interactions responsible for microsolvation of monoatomic cations. In all cases, the dominant factor dictating geometries and interaction strengths is the electrophilic power of the metal cation. The formal charge disrupts the hydrogen bonding network otherwise present in pristine water clusters, making the hydrogen bonds considerably stronger, even inducing some degree of covalency. All MO interactions are highly ionic, with strengths than in some cases approach that of the reference LiCl bond. Accumulation of electron density in the region connecting MO is observed, thus, ionic bonding in the microsolvation of monoatomic cations is not as simple as an electrostatic interaction between opposing charges.
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Affiliation(s)
- Natalia Rojas-Valencia
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia. and Escuela de Ciencias y Humanidades, Departamento de Ciencias Básicas, Universidad Eafit, AA 3300, Medellín, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, Pisa, 56126, Italy
| | - Doris Guerra
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
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23
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Chamorro E, Duque-Noreña M, Gutierrez-Sánchez N, Rincón E, Domingo LR. A Close Look to the Oxaphosphetane Formation along the Wittig Reaction: A [2+2] Cycloaddition? J Org Chem 2020; 85:6675-6686. [DOI: 10.1021/acs.joc.0c00697] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eduardo Chamorro
- Departamento de Ciencias Quı́micas, Facultad de Ciencias Exactas, Universidad Andres Bello, Avenida República 275, Santiago 8370146, Chile
| | - Mario Duque-Noreña
- Departamento de Ciencias Quı́micas, Facultad de Ciencias Exactas, Universidad Andres Bello, Avenida República 275, Santiago 8370146, Chile
| | - Nestor Gutierrez-Sánchez
- Departamento de Ciencias Quı́micas, Facultad de Ciencias Exactas, Universidad Andres Bello, Avenida República 275, Santiago 8370146, Chile
| | - Elizabeth Rincón
- Facultad de Ciencias, Instituto de Ciencias Quı́micas, Universidad Austral de Chile, Las encinas 220, Valdivia 5110033, Chile
| | - Luis R. Domingo
- Department of Organic Chemistry, Research Building Jeroni Muñoz, University of Valencia, Dr. Moliner 50, Burjassot, Valencia ESP-46100, Spain
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