1
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Charlier C, Gavalda S, Grga J, Perrot L, Gabrielli V, Löhr F, Schörghuber J, Lichtenecker R, Arnal G, Marty A, Tournier V, Lippens G. Exploring the pH dependence of an improved PETase. Biophys J 2024; 123:1542-1552. [PMID: 38664965 PMCID: PMC11213969 DOI: 10.1016/j.bpj.2024.04.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/20/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
Enzymatic recycling of plastic and especially of polyethylene terephthalate (PET) has shown great potential to reduce its negative impact on our society. PET hydrolases (PETases) have been optimized using rational design and machine learning, but the mechanistic details of the PET depolymerization process remain unclear. Belonging to the carboxylic-ester hydrolase family with a canonical Ser-His-Asp catalytic triad, their observed alkaline pH optimum is generally thought to be related to the protonation state of the catalytic His. Here, we explore this aspect in the context of LCCICCG, an optimized PETase, derived from the leaf-branch compost cutinase enzyme. We use NMR to identify the dominant tautomeric structure of the six histidines. Five show surprisingly low pKa values below 4.0, whereas the catalytic H242 in the active enzyme displays a pKa value that varies from 4.9 to 4.7 when temperatures increase from 30°C to 50°C. Whereas the hydrolytic activity of the enzyme toward a soluble substrate can be modeled by the corresponding protonation/deprotonation curve, an important discrepancy is found when the substrate is the solid plastic. This opens the way to further mechanistic understanding of the PETase activity and underscores the importance of studying the enzyme at the liquid-solid interface.
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Affiliation(s)
- Cyril Charlier
- Toulouse Biotechnology Institute (TBI), University of Toulouse, CNRS, INRAE, INSA Toulouse, Toulouse Cedex, France
| | - Sabine Gavalda
- Carbios, Parc Cataroux - Bâtiment B80, Clermont-Ferrand, France
| | - Jelena Grga
- Toulouse Biotechnology Institute (TBI), University of Toulouse, CNRS, INRAE, INSA Toulouse, Toulouse Cedex, France
| | - Laura Perrot
- Toulouse Biotechnology Institute (TBI), University of Toulouse, CNRS, INRAE, INSA Toulouse, Toulouse Cedex, France
| | - Valeria Gabrielli
- Toulouse Biotechnology Institute (TBI), University of Toulouse, CNRS, INRAE, INSA Toulouse, Toulouse Cedex, France
| | - Frank Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe, University Frankfurt, Frankfurt am Main, Germany
| | - Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, Vienna, Austria
| | - Roman Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, Vienna, Austria; MAG-LAB, Vienna, Austria
| | - Grégory Arnal
- Carbios, Parc Cataroux - Bâtiment B80, Clermont-Ferrand, France
| | - Alain Marty
- Carbios, Parc Cataroux - Bâtiment B80, Clermont-Ferrand, France
| | | | - Guy Lippens
- Toulouse Biotechnology Institute (TBI), University of Toulouse, CNRS, INRAE, INSA Toulouse, Toulouse Cedex, France.
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2
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Belleflamme M, Hommes J, Dervisoglu R, Bartalucci E, Wiegand T, Beine AK, Leitner W, Vorholt AJ. Catalytic Upgrading of Acetaldehyde to Acetoin Using a Supported N-Heterocyclic Carbene Catalyst. CHEMSUSCHEM 2024:e202400647. [PMID: 38853691 DOI: 10.1002/cssc.202400647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024]
Abstract
We report the catalytic synthesis of 3-hydroxy-2-butanon (acetoin) from acetaldehyde as a key step in the synthesis of C4-molecules from ethanol. Facile C-C bond formation at the α-carbon of the C2 building block is achieved using an N-heterocyclic carbene (NHC) catalyst. The immobilization of the catalyst on a Merrifield's peptide resin and its spectroscopic characterisation using solid-state Nuclear Magnetic Resonance (NMR) is described herein. The immobilization of the NHC catalyst allows for process intensification steps and the reported catalytic system was subjected to batch recycling as well as continuous flow experiments. The robustness of the catalytic system was shown over a maximum of 10 h time-on-stream. Overall, high selectivity S>90 % was observed. The observed deactivation of the catalyst with increasing time-on-stream is explained by ex-situ 1H solution-state, as well as 13C and 15N solid-state NMR spectra allowing us to develop a deeper understanding of the underlying decomposition mechanism of the catalyst.
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Affiliation(s)
- Maurice Belleflamme
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute for Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Jerome Hommes
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
- Department for Biochemical and Chemical Engineering, Laboratory of Industrial Chemistry, TU Dortmund University, Emil-Figge-Str. 66, 44227, Dortmund, Germany
| | - Riza Dervisoglu
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Ettore Bartalucci
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute for Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Thomas Wiegand
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute for Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Anna Katharina Beine
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
- Department of Mechanical Engineering, University of Siegen, Paul-Bonatz-Str. 9-11, 57076, Siegen, Germany
| | - Walter Leitner
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute for Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Andreas J Vorholt
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
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3
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Muthusamy AR, Singh A, Sundaram MSS, Wagh Y, Jegorov A, Jain AK. In-Silico Aided Screening and Characterization Results in Stability Enhanced Novel Roxadustat Co-Crystal. J Pharm Sci 2024; 113:1190-1201. [PMID: 37875213 DOI: 10.1016/j.xphs.2023.10.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 10/26/2023]
Abstract
Roxadustat (RXD) is an approved drug substances for the treatment of renal anemia. It has poor aqueous solubility and photochemical stability. This study employs a comprehensive approach to enhance the stability and physicochemical properties RXD through coformer selection and characterization. The investigation integrates delta pKa analysis, molecular complementary assessment, molecular electrostatic potential surface analysis, and machine learning techniques to predict potential co-crystal formation and binding interactions between drug molecules and coformers. The co-crystal screening which lead to in a novel RXD-nicotinamide co-crystal (RXD-NA). Experimental characterization underscores the physical and chemical stability of the co-crystals. To elucidate the supramolecular synthons and understand the intermolecular interactions in the RXD-NA co-crystal, Hirshfeld surfaces analysis, quantum theory of atoms in molecules (QTAIM) analysis and non-covalent interaction (NCI) analysis were performed. Computational analysis of photo-isomer formation aligns with experimental observations, further enhancing our understanding of RXD-coformer interactions. RXD-NA co-crystal was found photo-chemically stable as compared to free base API drug substance. This integrated methodology provides a systematic framework for informed co-crystal design, holding promise for optimizing RXD formulations based on molecular interactions and stability considerations. Consequently, this study contributes valuable insights to the field of rational drug design and formulation optimization.
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Affiliation(s)
- Anantha Rajmohan Muthusamy
- Department of Physical R&D, Teva API India Pvt. Ltd. Ecotech-II, Udyog Vihar, Greater Noida, Uttar Pradesh 201306, India.
| | - Amit Singh
- Department of Physical R&D, Teva API India Pvt. Ltd. Ecotech-II, Udyog Vihar, Greater Noida, Uttar Pradesh 201306, India
| | | | - Yogesh Wagh
- Department of Physical R&D, Teva API India Pvt. Ltd. Ecotech-II, Udyog Vihar, Greater Noida, Uttar Pradesh 201306, India
| | - Alexandr Jegorov
- Teva Czech Industries, Branisovska 31, Ceske Budejice, 37005, Czech Republic
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4
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Tupikina EY, Titova AA, Kaplanskiy MV, Chakalov ER, Kostin MA, Tolstoy PM. Estimations of OH·N hydrogen bond length from positions and intensities of IR bands. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 275:121172. [PMID: 35366525 DOI: 10.1016/j.saa.2022.121172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/02/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
In this computational work applicability of IR spectral parameters for evaluations of OH···N hydrogen bond length is discussed. For a set of 124 complexes with OH···N hydrogen bond formed by combinations of methanol/acetic acid and pyridine (and their fluorine substituted versions) geometries, energies and IR parameters were calculated at MP2/def2-TZVP level of theory. For a number of IR parameters (the shift of proton donor group stretching vibration Δνs, increase of its intensity I, the low-frequency hydrogen bond stretching vibration νσ, bending in-plane δ and out-of-plane γ vibrations) equations linking them with interatomic distances are proposed, the robustness and accuracy of such equations are discussed. The enthalpy of OH···N hydrogen bond formation ΔH was also linked with electron density parameters in (3; -1) critical point.
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Affiliation(s)
- E Yu Tupikina
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia.
| | - A A Titova
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - M V Kaplanskiy
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - E R Chakalov
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - M A Kostin
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia; Department of Physics, St. Petersburg State University, St. Petersburg, Russia
| | - P M Tolstoy
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia.
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5
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Lombe BK, Winand L, Diettrich J, Töbermann M, Hiller W, Kaiser M, Nett M. Discovery, Biosynthetic Origin, and Heterologous Production of Massinidine, an Antiplasmodial Alkaloid. Org Lett 2022; 24:2935-2939. [PMID: 35412834 DOI: 10.1021/acs.orglett.2c00963] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bacteria of the genus Massilia represent an underexplored source of bioactive natural products. Here, we report the discovery of massinidine (1), a guanidine alkaloid with antiplasmodial activity, from these microbes. The unusual scaffold of massinidine is shown to originate from l-phenylalanine, acetate, and l-arginine. Massinidine biosynthesis genes were identified in the native producer and validated through heterologous expression in Myxococcus xanthus. Bioinformatic analyses indicate that the potential for massinidine biosynthesis is distributed in various proteobacteria.
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Affiliation(s)
- Blaise Kimbadi Lombe
- Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Lea Winand
- Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Jan Diettrich
- Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Melanie Töbermann
- Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Wolf Hiller
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Marcel Kaiser
- Parasite Chemotherapy Unit, Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland.,University of Basel, 4001 Basel, Switzerland
| | - Markus Nett
- Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
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6
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Alguacil A, Scalambra F, Romerosa A. Insights into the κ-P,N Coordination of 1,3,5-Triaza-7-phosphaadamantane and Derivatives: κ-P,N-Heterometallic Complexes and a 15N Nuclear Magnetic Resonance Survey. Inorg Chem 2022; 61:5779-5791. [PMID: 35378037 PMCID: PMC9019812 DOI: 10.1021/acs.inorgchem.1c03831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Complexes {[(PTA)2CpRu-μ-CN-1κC:2κ2N-RuCp(PTA)2-ZnCl3]}·2DMSO (13) {[ZnCl2(H2O)]-(PTA-1κP:2κ2N)(PTA)CpRu-μ-CN-1κC:2κ2N-RuCp(PTA)(PTA-1κP:2κ2N)-[ZnCl2(H2O)]}Cl (14), [RuCp(HdmoPTA)(PPh3)(PTA)](CF3SO3)2 (20), [RuCp(HdmoPTA)(HPTA)(PPh3)](CF3SO3)3 (21), and [RuCp(dmoPTA)(PPh3)(PTA)](CF3SO3) (22) were obtained
and characterized, and their crystal structure together with that
of the previously published complex 18 is reported. The
behavior of the 1,3,5-triaza-7-phosphatricyclo[3.3.1.13,7]decane (PTA)
and 3,7-dimethyl-1,3,7-triaza-5-phosphabicyclo[3.3.1]nonane (dmoPTA)
ligands against protonation and κN-coordination
is discussed, on the basis of 15N nuclear magnetic resonance
data collected on 22 different compounds, including PTA (1), HdmoPTA (7H), and some common derivatives as free
ligands (2–6 and 8), along with mono-
and polymetallic complexes containing PTA and/or HdmoPTA (9–22). 15N detection via 1H–15N heteronuclear multiple bond correlation allowed the construction
of a small library of 15N chemical shifts that shed light
on important features regarding κN-coordination
in PTA and its derivatives. To shed light
on the behavior of the triazaphosphines 1,3,5-triaza-7-phosphatricyclo[3.3.1.13,7]decane
(PTA) and 3,7-dimethyl-1,3,7-triaza-5-phosphabicyclo[3.3.1]nonane
(dmoPTA) upon κN coordination and N protonation, the 15N chemical shifts of 22 compounds, including PTA and a representative
variety of its derivatives, piano-stool complexes, were collected
by 1H−15N heteronuclear multiple bond
correlation nuclear magnetic resonance. New heterometallic complexes
containing PTA were also synthesized and fully characterized.
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Affiliation(s)
- Andrés Alguacil
- Área de Química Inorgánica-CIESOL, Universidad de Almería, 04120 Almería, Spain
| | - Franco Scalambra
- Área de Química Inorgánica-CIESOL, Universidad de Almería, 04120 Almería, Spain
| | - Antonio Romerosa
- Área de Química Inorgánica-CIESOL, Universidad de Almería, 04120 Almería, Spain
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7
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Single-Crystal X-ray and Solid-State NMR Characterisation of AND-1184 and Its Hydrochloride Form. MATERIALS 2021; 14:ma14237175. [PMID: 34885329 PMCID: PMC8658117 DOI: 10.3390/ma14237175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/08/2021] [Accepted: 11/22/2021] [Indexed: 12/05/2022]
Abstract
In this study, we report on a structural investigation of AND-1184, with the chemical name N-[3-[4-(6-fluoro-1,2-benzoxazol-3-yl)piperidin-1-yl]propyl]-3-methylbenzenesulfonamide (MBS), and its hydrochloride form (MBSHCl); AND-1184 is a potential API for the treatment of dementia. The single-crystal X-ray investigation of both forms results in monoclinic crystal systems with P21/c and C2/c symmetry for MBS and MBSHCl, respectively. This solid-state NMR study, combined with quantum-chemical calculations, allowed us to assign all 13C and most 1H signals. The MBS structure was defined as a completely rigid system without significant dynamic behaviours, whereas MBSHCl exhibited limited dynamic motion of the aromatic part of the molecule.
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8
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Sakai KI, Miyamoto N, Ogawa M, Kawano K, Akutagawa T. Photoinduced Generation of the π-Conjugated Zwitterionic State in the ESIPT Fluorophore of 2,4-Bisimidazolylphenol. J Phys Chem A 2021; 125:4784-4792. [PMID: 34060839 DOI: 10.1021/acs.jpca.1c02353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate that 2,4-bis(4,5-diphenyl-1H-imidazol-2-yl)phenol (2,4-bImP) undergoes photoinduced conversion into the so-called "π-conjugated zwitterion" after causing an excited-state intramolecular proton transfer (ESIPT) reaction. The powder sample of 2,4-bImP exhibits largely Stokes-shifted fluorescence characteristics to ESIPT fluorophores. On the other hand, its originally colorless solutions become colored when exposed to UV light for several minutes, whose color depends on the type of solvent. In particular, the CHCl3 solution rapidly turns dark green with the absorption maximum around 700 nm, and the colored solution is nearly restored to original by alternating addition of acid and base. To explain such drastic and reversible color changes, we hypothesized that the occurrence of ESIPT (i.e., deprotonation of the phenol and protonation of the imidazolyl group at its 2-position) triggered the charge-separated structure between the negatively charged phenolate and the positively charged imidazoliumyl group at its 4-position, which allowed resonance with the neutral p-quinoid structure. The formation of this π-conjugated zwitterion was strongly supported by the results of 1H and 15N NMR and Raman measurements.
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Affiliation(s)
- Ken-Ichi Sakai
- Department of Applied Chemistry and Bioscience, Chitose Institute of Science and Technology (CIST), Chitose 066-8655, Japan
| | - Naoya Miyamoto
- Department of Applied Chemistry and Bioscience, Chitose Institute of Science and Technology (CIST), Chitose 066-8655, Japan
| | - Mayu Ogawa
- Department of Applied Chemistry and Bioscience, Chitose Institute of Science and Technology (CIST), Chitose 066-8655, Japan
| | - Keiichi Kawano
- Department of Applied Chemistry and Bioscience, Chitose Institute of Science and Technology (CIST), Chitose 066-8655, Japan
| | - Tomoyuki Akutagawa
- Polymer Hybrid Materials Research Center, Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, Sendai 980-8577, Japan
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9
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Ji X, Gonnella NC, Xin D. Deconvolution of fast exchange equilibrium states in NMR spectroscopy using virtual reference standards and probability theory. Org Biomol Chem 2020; 18:6927-6934. [PMID: 32936188 DOI: 10.1039/d0ob01459a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A methodology for deconvolution of fast exchange equilibrium states in NMR spectroscopy (DFEQNMR) was developed based on DFT-GIAO NMR chemical shift prediction and a probability theory algorithm. Proof-of-concept studies were performed to estimate the protonation state of N-containing organic molecules involving fast proton exchange equilibrium and evaluate the solution tautomerism of a purine derivative. DFT-GIAO calculations were optimized to achieve good accuracy in 13C, 1H and 15N chemical shift prediction for protonated species. The probability theory algorithm enabled the determination of solution species ratios and yielded 95% confidence regions by comparing experimental and simulated chemical shift data sets. The calculation showed good accuracy for model partial salts with various functionalities and application in structure elucidation of complex natural product partial salts was also demonstrated. This method showed promising potential in acquisition of important insight into fast exchange equilibrium systems with only one experimental NMR chemical shift data set.
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Affiliation(s)
- Xiaozhou Ji
- Department of Chemistry, Texas A&M University, College Station, TX, USA
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10
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Morgan KD, Williams DE, Patrick BO, Remigy M, Banuelos CA, Sadar MD, Ryan KS, Andersen RJ. Incarnatapeptins A and B, Nonribosomal Peptides Discovered Using Genome Mining and 1H/ 15N HSQC-TOCSY. Org Lett 2020; 22:4053-4057. [PMID: 32283033 DOI: 10.1021/acs.orglett.0c00818] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methods for the focused isolation of low-abundance natural products with specific chemical substructures could expand known bioactive chemical diversity for drug discovery. Here we report the combined use of genome mining and an 15N NMR-based screening method for the targeted isolation of the low-abundance piperazic-acid-containing peptides incarnatapeptins A (1) and B (3). Incarnatapeptin B (3) shows in vitro cytotoxicity to LNCaP prostate cancer cells.
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Affiliation(s)
| | | | | | | | - Carmen A Banuelos
- Department of Genome Sciences, BC Cancer, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Marianne D Sadar
- Department of Genome Sciences, BC Cancer, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
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11
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Semenov VA, Samultsev DO, Krivdin LB. Calculation of 15N NMR Chemical Shifts in a Diversity of Nitrogen-Containing Compounds Using Composite Method Approximation at the DFT, MP2, and CCSD Levels. J Phys Chem A 2019; 123:8417-8426. [PMID: 31465226 DOI: 10.1021/acs.jpca.9b06780] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computations of 15N NMR chemical shifts in 93 diverse nitrogen-containing compounds representing almost all known classes are performed at the density functional theory (DFT), second-order Møller-Plesset perturbation theory (MP2), and coupled cluster singles and doubles (CCSD) levels using the composite method approximation (CMA) in comparison with experimental results. It is shown that the CMA-DFT and CMA-CCSD methods provided the best performance characterized by a normalized mean absolute error of 1.1-1.3% as compared to 2.3% for the CMA-MP2 results. Taking into account solvent effects within the conductor-like polarizable continuum model decreased the normalized mean absolute error by 0.4% for the CMA-DFT and by 0.2% for the CMA-CCSD calculations.
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Affiliation(s)
- Valentin A Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry , Siberian Branch of the Russian Academy of Sciences , Favorsky St. 1 , 664033 Irkutsk , Russia
| | - Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry , Siberian Branch of the Russian Academy of Sciences , Favorsky St. 1 , 664033 Irkutsk , Russia
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry , Siberian Branch of the Russian Academy of Sciences , Favorsky St. 1 , 664033 Irkutsk , Russia
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12
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Semenov VA, Samultsev DO, Krivdin LB. DFT computational schemes for 15 N NMR chemical shifts of the condensed nitrogen-containing heterocycles. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:346-358. [PMID: 30769377 DOI: 10.1002/mrc.4851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/08/2019] [Accepted: 02/12/2019] [Indexed: 06/09/2023]
Abstract
A systematic density functional theory (DFT) study of the accuracy factors (functionals, basis sets, and solvent effects) for the computation of 15 N NMR chemical shifts has been performed in the series of condensed nitrogen-containing heterocycles. The behavior of the most representative functionals was examined based on the benchmark calculations of 15 N NMR chemical shifts in the reference set of compounds. It was found that the best agreement with experiment was achieved with OLYP functional in combination with aug-pcS-3(N)//pc-2 locally dense basis set scheme providing mean absolute error of 5.2 ppm in the range of about 300 ppm. Taking into account solvent effects was performed within a general Tomasi's polarizable continuum model scheme. It was also found that computationally demanding supermolecular solvation model computations essentially improved some "difficult" cases, as was illustrated with phenanthroline dissolved in methanol. Based on the performed calculations, some 200 unknown 15 N NMR chemical shifts were predicted with a high level of confidence for about 50 real-life condensed nitrogen-containing heterocycles, which could serve as a practical guide in structural elucidation of this class of compounds.
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Affiliation(s)
- Valentin A Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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13
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Vérité PM, Hédé S, Jacquemin D. A theoretical elucidation of the mechanism of tuneable fluorescence in a full-colour emissive ESIPT dye. Phys Chem Chem Phys 2019; 21:17400-17409. [DOI: 10.1039/c9cp03759d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We reinvestigate with ab initio tools the origin of the diverse colours in a complex multi-ESIPT dye, and we propose a new assignment for the blue fluorescence.
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Affiliation(s)
- Pauline M. Vérité
- Laboratoire CEISAM-UMR CNRS 6230
- Université de Nantes
- 44322 Nantes Cedex 3
- France
| | - Simon Hédé
- Laboratoire CEISAM-UMR CNRS 6230
- Université de Nantes
- 44322 Nantes Cedex 3
- France
| | - Denis Jacquemin
- Laboratoire CEISAM-UMR CNRS 6230
- Université de Nantes
- 44322 Nantes Cedex 3
- France
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14
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Priotti J, García A, Leonardi D, Ferreira MJ, Lamas MC, Nunes TG. Succinyl-β-cyclodextrin: Influence of the substitution degree on albendazole inclusion complexes probed by NMR. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2018; 92:694-702. [PMID: 30184797 DOI: 10.1016/j.msec.2018.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 02/03/2023]
Abstract
Succinyl-β-CD derivatives were obtained by green synthesis with degrees of substitution (DS) 1.3 and 2.9. The spray-drying technique was used to obtain albendazole (ABZ):succinyl-β-CD inclusion complexes. Phase solubility diagrams indicated that both succinyl-β-CD derivatives formed 1:1 molar ratio ABZ complexes, but the complex with DS 2.9 has a lower formation constant. The presence of stable inclusion complexes in aqueous solution was confirmed by NMR. For both complexes the aromatic moiety is encapsulated into the host cavity. In the solid-state, 13C and 15N NMR spectral differences between ABZ and ABZ included in spray-dried systems showed that strong structural changes occurred in the systems. At least two different ABZ amorphous species were identified based on DS. ABZ species were stable over more than six months based on spectral data. Finally, the influence of DS in the number and type of the inclusion complexes was elucidated.
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Affiliation(s)
- J Priotti
- IQUIR-CONICET, Suipacha 570, 2000 Rosario, Argentina
| | - A García
- Área Técnica Farmacéutica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, 2000 Rosario, Argentina
| | - D Leonardi
- IQUIR-CONICET, Suipacha 570, 2000 Rosario, Argentina; Área Técnica Farmacéutica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, 2000 Rosario, Argentina
| | - M J Ferreira
- CQE, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - M C Lamas
- IQUIR-CONICET, Suipacha 570, 2000 Rosario, Argentina; Área Técnica Farmacéutica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, 2000 Rosario, Argentina.
| | - T G Nunes
- CQE, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
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15
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Semenov VA, Samultsev DO, Krivdin LB. GIAO-DFT calculation of 15 N NMR chemical shifts of Schiff bases: Accuracy factors and protonation effects. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:727-739. [PMID: 29427330 DOI: 10.1002/mrc.4721] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 06/08/2023]
Abstract
15 N NMR chemical shifts in the representative series of Schiff bases together with their protonated forms have been calculated at the density functional theory level in comparison with available experiment. A number of functionals and basis sets have been tested in terms of a better agreement with experiment. Complimentary to gas phase results, 2 solvation models, namely, a classical Tomasi's polarizable continuum model (PCM) and that in combination with an explicit inclusion of one molecule of solvent into calculation space to form supermolecule 1:1 (SM + PCM), were examined. Best results are achieved with PCM and SM + PCM models resulting in mean absolute errors of calculated 15 N NMR chemical shifts in the whole series of neutral and protonated Schiff bases of accordingly 5.2 and 5.8 ppm as compared with 15.2 ppm in gas phase for the range of about 200 ppm. Noticeable protonation effects (exceeding 100 ppm) in protonated Schiff bases are rationalized in terms of a general natural bond orbital approach.
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Affiliation(s)
- Valentin A Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, 664033, Russia
| | - Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, 664033, Russia
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, 664033, Russia
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16
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Semenov VA, Samultsev DO, Krivdin LB. Substitution effects in the 15 N NMR chemical shifts of heterocyclic azines evaluated at the GIAO-DFT level. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:767-774. [PMID: 29504638 DOI: 10.1002/mrc.4731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/18/2018] [Accepted: 02/20/2018] [Indexed: 06/08/2023]
Abstract
A systematic study of the accuracy factors for the computation of 15 N NMR chemical shifts in comparison with available experiment in the series of 72 diverse heterocyclic azines substituted with a classical series of substituents (CH3 , F, Cl, Br, NH2 , OCH3 , SCH3 , COCH3 , CONH2 , COOH, and CN) providing marked electronic σ- and π-electronic effects and strongly affecting 15 N NMR chemical shifts is performed. The best computational scheme for heterocyclic azines at the DFT level was found to be KT3/pcS-3//pc-2 (IEF-PCM). A vast amount of unknown 15 N NMR chemical shifts was predicted using the best computational protocol for substituted heterocyclic azines, especially for trizine, tetrazine, and pentazine where experimental 15 N NMR chemical shifts are almost totally unknown throughout the series. It was found that substitution effects in the classical series of substituents providing typical σ- and π-electronic effects followed the expected trends, as derived from the correlations of experimental and calculated 15 N NMR chemical shifts with Swain-Lupton's F and R constants.
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Affiliation(s)
- Valentin A Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| | - Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
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17
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Tsuchiya S, Sakai KI, Kawano K, Nakane Y, Kikuchi T, Akutagawa T. Color Changes of a Full-Color Emissive ESIPT Fluorophore in Response to Recognition of Certain Acids and Their Conjugate Base Anions. Chemistry 2018; 24:5868-5875. [DOI: 10.1002/chem.201705622] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Saki Tsuchiya
- Department of Applied Chemistry and Bioscience; Chitose Institute of Science and Technology (CIST); Chitose 066-8655 Japan
| | - Ken-ichi Sakai
- Department of Applied Chemistry and Bioscience; Chitose Institute of Science and Technology (CIST); Chitose 066-8655 Japan
| | - Keiichi Kawano
- Department of Applied Chemistry and Bioscience; Chitose Institute of Science and Technology (CIST); Chitose 066-8655 Japan
| | - Yuta Nakane
- Polymer Hybrid Materials Research Center; Institute of Multidisciplinary Research for Advanced Materials (IMRAM); Tohoku University; Sendai 980-8577 Japan
| | - Takemitsu Kikuchi
- Polymer Hybrid Materials Research Center; Institute of Multidisciplinary Research for Advanced Materials (IMRAM); Tohoku University; Sendai 980-8577 Japan
| | - Tomoyuki Akutagawa
- Polymer Hybrid Materials Research Center; Institute of Multidisciplinary Research for Advanced Materials (IMRAM); Tohoku University; Sendai 980-8577 Japan
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18
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Calculation of 15N NMR chemical shifts of amines in the framework of the density functional theory. Russ Chem Bull 2018. [DOI: 10.1007/s11172-017-2009-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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19
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Samultsev DO, Rusakov YY, Krivdin LB. On the long-range relativistic effects in the 15 N NMR chemical shifts of halogenated azines. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:990-995. [PMID: 28557069 DOI: 10.1002/mrc.4618] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 05/23/2017] [Accepted: 05/24/2017] [Indexed: 06/07/2023]
Abstract
Long-range β- and γ-relativistic effects of halogens in 15 N NMR chemical shifts of 20 halogenated azines (pyridines, pyrimidines, pyrazines, and 1,3,5-triazines) are shown to be unessential for fluoro-, chloro-, and bromo-derivatives (1-2 ppm in average). However, for iodocontaining compounds, β- and γ-relativistic effects are important contributors to the accuracy of the 15 N calculation. Taking into account long-range relativistic effects slightly improves the agreement of calculation with experiment. Thus, mean average errors (MAE) of 15 N NMR chemical shifts of the title compounds calculated at the non-relativistic and full 4-component relativistic levels in gas phase are accordingly 7.8 and 5.5 ppm for the range of about 150 ppm. Taking into account solvent effects within the polarizable continuum model scheme marginally improves agreement of computational results with experiment decreasing MAEs from 7.8 to 7.4 ppm and from 5.5 to 5.3 ppm at the non-relativistic and relativistic levels, respectively. The best result (MAE: 5.3 ppm) is achieved at the 4-component relativistic level using Keal and Tozer's KT3 functional used in combination with Dyall's relativistic basis set dyall.av3z with taking into account solvent effects within the polarizable continuum solvation model. The long-range relativistic effects play a major role (of up to dozen of parts per million) in 15 N NMR chemical shifts of halogenated nitrogen-containing heterocycles, which is especially crucial for iodine derivatives. This effect should apparently be taken into account for practical purposes.
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Affiliation(s)
- Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, 664033, Russia
| | - Yury Yu Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, 664033, Russia
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, 664033, Russia
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20
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Samultsev DO, Semenov VA, Krivdin LB. On the accuracy factors and computational cost of the GIAO-DFT calculation of 15 N NMR chemical shifts of amides. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:1015-1021. [PMID: 28600816 DOI: 10.1002/mrc.4625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/04/2017] [Accepted: 06/06/2017] [Indexed: 06/07/2023]
Abstract
The main factors affecting the accuracy and computational cost of Gauge-independent Atomic Orbital-density functional theory (GIAO-DFT) calculation of 15 N NMR chemical shifts in the benchmark series of 16 amides are considered. Among those are the choice of the DFT functional and basis set, solvent effects, internal reference conversion factor and applicability of the locally dense basis set (LDBS) scheme. Solvent effects are treated within the polarizable continuum model (PCM) scheme as well as at supermolecular level with solvent molecules considered in explicit way. The best result is found for Keal and Tozer's KT3 functional used in combination with Jensen's pcS-3 basis set with taking into account solvent effects within the polarizable continuum model. The proposed LDBS scheme implies pcS-3 on nitrogen and pc-2 elsewhere in the molecule. The resulting mean average error for the calculated 15 N NMR chemical shifts is about 6 ppm. The application of the LDBS approach tested in a series of 16 amides results in a dramatic decrease in computational cost (more than an order of magnitude in time scale) with insignificant loss of accuracy.
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Affiliation(s)
- Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, 664033, Irkutsk, Russia
| | - Valentin A Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, 664033, Irkutsk, Russia
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, 664033, Irkutsk, Russia
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21
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Krivdin LB. Calculation of 15N NMR chemical shifts: Recent advances and perspectives. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:98-119. [PMID: 29157495 DOI: 10.1016/j.pnmrs.2017.08.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/21/2017] [Accepted: 08/21/2017] [Indexed: 06/07/2023]
Abstract
Recent advances in computation of 15N NMR chemical shifts are reviewed, concentrating mainly on practical aspects of computational protocols and accuracy factors. The review includes the discussion of the level of theory, the choice of density functionals and basis sets together with taking into account solvent effects, rovibrational corrections and relativistic effects. Computational aspects of 15N NMR are illustrated for the series of neutral and protonated open-chain nitrogen-containing compounds and nitrogen heterocycles, coordination and intermolecular complexes.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia.
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22
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Camp AM, Kita MR, Grajeda J, White PS, Dickie DA, Miller AJM. Mapping the Binding Modes of Hemilabile Pincer-Crown Ether Ligands in Solution Using Diamagnetic Anisotropic Effects on NMR Chemical Shift. Inorg Chem 2017; 56:11141-11150. [PMID: 28872310 DOI: 10.1021/acs.inorgchem.7b01485] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A protocol for identifying ligand binding modes in a series of iridium pincer complexes bearing hemilabile aza-crown ether ligands has been developed using readily accessible NMR methods. The approach was tested on a collection of 13 structurally diverse pincer-crown ether complexes that include several newly characterized species. New synthetic routes enable facile interconversion of coordination modes and supporting ligands. Detailed structural assignments of five complexes reveal that the difference in chemical shift (Δδ) between geminal protons in the crown ether is influenced by diamagnetic anisotropy arising from halides and other ligands in the primary coordination sphere. The average difference in chemical shift between diastereotopic geminal protons in the crown ether macrocycle (Δδavg), as determined through a single 1H-13C HSQC experiment, provides information on the pincer ligand binding mode by establishing whether the macrocycle is in close proximity to the metal center. The Δδavg values for binding modes that involve chelating ether(s) bound to iridium are roughly 2-fold larger than those for tridentate complexes with no Ir-O bonds.
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Affiliation(s)
- Andrew M Camp
- Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-3290, United States
| | - Matthew R Kita
- Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-3290, United States
| | - Javier Grajeda
- Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-3290, United States
| | - Peter S White
- Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-3290, United States
| | - Diane A Dickie
- Department of Chemistry, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
| | - Alexander J M Miller
- Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-3290, United States
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23
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Xin D, Sader CA, Fischer U, Wagner K, Jones PJ, Xing M, Fandrick KR, Gonnella NC. Systematic investigation of DFT-GIAO 15N NMR chemical shift prediction using B3LYP/cc-pVDZ: application to studies of regioisomers, tautomers, protonation states and N-oxides. Org Biomol Chem 2017; 15:928-936. [PMID: 28050610 DOI: 10.1039/c6ob02450e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The calculation of 15N NMR chemical shifts has been systematically investigated using density functional theory-gauge including/invariant atomic orbitals (DFT-GIAO) approximation at the B3LYP/cc-pVDZ level of theory. General linear regression terms for 15N chemical shift predictions were calculated for nitromethane and liquid ammonia references in DMSO. Both aliphatic and aromatic nitrogens were studied using a diverse set of molecular scaffolds. Statistical error analysis between experiment and prediction revealed that, with the exception of primary amines, 95% of linear scaled N-15 chemical shifts are within a ±9.56 ppm range. Comparison of the 15N calculated isotropic chemical shifts with the experimentally determined chemical shifts provided accurate assignment of the correct structure in cases where experimental data was ambiguous or inconclusive. Application of 15N prediction proved to be highly effective in identifying the correct regio-isomer, oxidation state, protonation state and preferred tautomer in solution.
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Affiliation(s)
- Dongyue Xin
- Material and Analytical Sciences, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA.
| | - Charles Avery Sader
- Material and Analytical Sciences, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA.
| | - Udo Fischer
- Boehringer Ingelheim Pharma GmbH & Co.KG, Germany
| | - Klaus Wagner
- Boehringer Ingelheim Pharma GmbH & Co.KG, Germany
| | - Paul-James Jones
- Information Technology, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA
| | - Minli Xing
- Material and Analytical Sciences, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA.
| | - Keith R Fandrick
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA
| | - Nina C Gonnella
- Material and Analytical Sciences, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA.
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24
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Schwamm RJ, Vianello R, Maršavelski A, García MÁ, Claramunt RM, Alkorta I, Saame J, Leito I, Fitchett CM, Edwards AJ, Coles MP. (15)N NMR Spectroscopy, X-ray and Neutron Diffraction, Quantum-Chemical Calculations, and UV/vis-Spectrophotometric Titrations as Complementary Techniques for the Analysis of Pyridine-Supported Bicyclic Guanidine Superbases. J Org Chem 2016; 81:7612-25. [PMID: 27494395 DOI: 10.1021/acs.joc.6b01330] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pyridine substituted with one and two bicyclic guanidine groups has been studied as a potential source of superbases. 2-{hpp}C5H4N (I) and 2,6-{hpp}2C5H3N (II) (hppH = 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine) were protonated using [HNEt3][BPh4] to afford [I-H][BPh4] (1a), [II-H][BPh4] (2), and [II-H2][BPh4]2 (3). Solution-state (1)H and (15)N NMR spectroscopy shows a symmetrical cation in 2, indicating a facile proton-exchange process in solution. Solid-state (15)N NMR data differentiates between the two groups, indicating a mixed guanidine/guanidinium. X-ray diffraction data are consistent with protonation at the imine nitrogen, confirmed for 1a by single-crystal neutron diffraction. The crystal structure of 1a shows association of two [I-H](+) cations within a cage of [BPh4](-) anions. Computational analysis performed in the gas phase and in MeCN solution shows that the free energy barrier to transfer a proton between imino centers in [II-H](+) is 1 order of magnitude lower in MeCN than in the gas phase. The results provide evidence that linking hpp groups with the pyridyl group stabilizes the protonation center, thereby increasing the intrinsic basicity in the gas phase, while the bulk prevents efficient cation solvation, resulting in diminished pKa(MeCN) values. Spectrophotometrically measured pKa values are in excellent agreement with calculated values and confirm that I and II are superbases in solution.
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Affiliation(s)
- Ryan J Schwamm
- School of Chemical and Physical Sciences, Victoria University of Wellington , P.O. Box 600, Wellington 6012, New Zealand
| | - Robert Vianello
- Computational Organic Chemistry and Biochemistry Group, Ruder Bošković Institute , Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Aleksandra Maršavelski
- Computational Organic Chemistry and Biochemistry Group, Ruder Bošković Institute , Bijenička cesta 54, 10000 Zagreb, Croatia
| | - M Ángeles García
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias, UNED , Paseo Senda del Rey 9, 28040 Madrid, Spain
| | - Rosa M Claramunt
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias, UNED , Paseo Senda del Rey 9, 28040 Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (IQM-CSIC) , Juan de la Cierva 3, 28006 Madrid, Spain
| | - Jaan Saame
- Institute of Chemistry, University of Tartu , 14a Ravila Street, 50411, Tartu, Estonia
| | - Ivo Leito
- Institute of Chemistry, University of Tartu , 14a Ravila Street, 50411, Tartu, Estonia
| | | | - Alison J Edwards
- Bragg Institute, Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2234, Australia
| | - Martyn P Coles
- School of Chemical and Physical Sciences, Victoria University of Wellington , P.O. Box 600, Wellington 6012, New Zealand
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25
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Semenov VA, Samultsev DO, Rulev AY, Krivdin LB. Theoretical and experimental (15)N NMR study of enamine-imine tautomerism of 4-trifluoromethyl[b]benzo-1,4-diazepine system. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:1031-1034. [PMID: 26290420 DOI: 10.1002/mrc.4296] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 06/04/2023]
Abstract
The tautomeric structure of 4-trifluoromethyl[b]benzo-1,4-diazepine system in solution has been evaluated by means of the calculation of (15)N NMR chemical shifts of individual tautomers in comparison with the averaged experimental shifts to show that the enamine-imine equilibrium is entirely shifted toward the imine form. The adequacy of the theoretical level used for the computation of (15)N NMR chemical shifts in this case has been verified based on the benchmark calculations in the series of the push-pull and captodative enamines together with related azomethynes, which demonstrated a good to excellent agreement with experiment.
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Affiliation(s)
- Valentin A Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| | - Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| | - Alexander Yu Rulev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
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