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Raczyńska ED, Gal JF, Maria PC. Strong Bases and beyond: The Prominent Contribution of Neutral Push-Pull Organic Molecules towards Superbases in the Gas Phase. Int J Mol Sci 2024; 25:5591. [PMID: 38891779 PMCID: PMC11172071 DOI: 10.3390/ijms25115591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
In this review, the principles of gas-phase proton basicity measurements and theoretical calculations are recalled as a reminder of how the basicity PA/GB scale, based on Brønsted-Lowry theory, was constructed in the gas-phase (PA-proton affinity and/or GB-gas-phase basicity in the enthalpy and Gibbs energy scale, respectively). The origins of exceptionally strong gas-phase basicity of some organic nitrogen bases containing N-sp3 (amines), N-sp2 (imines, amidines, guanidines, polyguanides, phosphazenes), and N-sp (nitriles) are rationalized. In particular, the role of push-pull nitrogen bases in the development of the gas-phase basicity in the superbasicity region is emphasized. Some reasons for the difficulties in measurements for poly-functional nitrogen bases are highlighted. Various structural phenomena being in relation with gas-phase acid-base equilibria that should be considered in quantum-chemical calculations of PA/GB parameters are discussed. The preparation methods for strong organic push-pull bases containing a N-sp2 site of protonation are briefly reviewed. Finally, recent trends in research on neutral organic superbases, leaning toward catalytic and other remarkable applications, are underlined.
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Affiliation(s)
- Ewa Daniela Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Jean-François Gal
- Institut de Chimie de Nice, UMR 7272, Université Côte d’Azur, Parc Valrose, 06108 Nice, France;
| | - Pierre-Charles Maria
- Institut de Chimie de Nice, UMR 7272, Université Côte d’Azur, Parc Valrose, 06108 Nice, France;
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2
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Valadbeigi Y, Taheri R. Superbasicity of imines with bicyclo[5.1.0]octa-1,3,5,7-tetraene scaffold due to electron delocalization in the conjugated acids. COMPUT THEOR CHEM 2023. [DOI: 10.1016/j.comptc.2023.114076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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3
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Khazali M, Rouhani M, Saeidian H. Utilizing the synergistic effect between imidazole aromaticity and guanidine structure for the computational design of novel uncharged organic superbases. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134348] [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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4
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Super/hyperbasicity of novel diquinonimino derivatives of guanidine in gas phase. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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Vermersch F, Yazdani S, Junor GP, Grotjahn DB, Jazzar R, Bertrand G. Stable Singlet Carbenes as Organic Superbases. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202111588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- François Vermersch
- UCSD-CNRS Joint Research Laboratory (IRL 3555) Department of Chemistry and Biochemistry University of California San Diego, La Jolla CA 92093-0358 USA
| | - Sima Yazdani
- UCSD-CNRS Joint Research Laboratory (IRL 3555) Department of Chemistry and Biochemistry University of California San Diego, La Jolla CA 92093-0358 USA
- Department of Chemistry and Biochemistry San Diego State University 5500 Campanile Drive San Diego CA 92182-1030 USA
| | - Glen P. Junor
- UCSD-CNRS Joint Research Laboratory (IRL 3555) Department of Chemistry and Biochemistry University of California San Diego, La Jolla CA 92093-0358 USA
| | - Douglas B. Grotjahn
- Department of Chemistry and Biochemistry San Diego State University 5500 Campanile Drive San Diego CA 92182-1030 USA
| | - Rodolphe Jazzar
- UCSD-CNRS Joint Research Laboratory (IRL 3555) Department of Chemistry and Biochemistry University of California San Diego, La Jolla CA 92093-0358 USA
| | - Guy Bertrand
- UCSD-CNRS Joint Research Laboratory (IRL 3555) Department of Chemistry and Biochemistry University of California San Diego, La Jolla CA 92093-0358 USA
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Vermersch F, Yazdani S, Junor GP, Grotjahn DB, Jazzar R, Bertrand G. Stable Singlet Carbenes as Organic Superbases. Angew Chem Int Ed Engl 2021; 60:27253-27257. [PMID: 34729888 DOI: 10.1002/anie.202111588] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/18/2021] [Indexed: 11/10/2022]
Abstract
A simple experimental procedure for scaling carbene Brønsted basicity is described. The results highlight the strong basicity of pyrazol-4-ylidenes, a type of mesoionic carbene, also named cyclic-bentallenes (CBA). They are more basic (pKaH >42.7 in acetonitrile) than the popular proazaphosphatrane Verkade bases, and even the Schwesinger phosphazene superbase P4 (t Bu). The basicity of these compounds can readily be tuned, and they are accessible in multigram quantities. These results open new avenues for carbon centered superbases.
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Affiliation(s)
- François Vermersch
- UCSD-CNRS Joint Research Laboratory (IRL 3555), Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0358, USA
| | - Sima Yazdani
- UCSD-CNRS Joint Research Laboratory (IRL 3555), Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0358, USA.,Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-1030, USA
| | - Glen P Junor
- UCSD-CNRS Joint Research Laboratory (IRL 3555), Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0358, USA
| | - Douglas B Grotjahn
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-1030, USA
| | - Rodolphe Jazzar
- UCSD-CNRS Joint Research Laboratory (IRL 3555), Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0358, USA
| | - Guy Bertrand
- UCSD-CNRS Joint Research Laboratory (IRL 3555), Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0358, USA
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7
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Vazdar K, Margetić D, Kovačević B, Sundermeyer J, Leito I, Jahn U. Design of Novel Uncharged Organic Superbases: Merging Basicity and Functionality. Acc Chem Res 2021; 54:3108-3123. [PMID: 34308625 DOI: 10.1021/acs.accounts.1c00297] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
ConspectusOne of the constant challenges of synthetic chemistry is the molecular design and synthesis of nonionic, metal-free superbases as chemically stable neutral organic compounds of moderate molecular weight, intrinsically high thermodynamic basicity, adaptable kinetic basicity, and weak or tunable nucleophilicity at their nitrogen, phosphorus, or carbon basicity centers. Such superbases can catalyze numerous reactions, ranging from C-C bond formation to cycloadditions and polymerization, to name just a few. Additional benefits of organic superbases, as opposed to their inorganic counterparts, are their solubility in organic reaction media, mild reaction conditions, and higher selectivity. Approaching such superbasic compounds remains a continuous challenge. However, recent advances in synthetic methodology and theoretical understanding have resulted in new design principles and synthetic strategies toward superbases. Our computational contributions have demonstrated that the gas-phase basicity region of 350 kcal mol-1 and even beyond is easily reachable by organosuperbases. However, despite record-high basicities, the physical limitations of many of these compounds become quickly evident. The typically large molecular weight of these molecules and their sensitivity to ordinary reaction conditions prevent them from being practical, even though their preparation is often not too difficult. Thus, obviously structural limitations with respect to molecular weight and structural complexity must be imposed on the design of new synthetically useful organic superbases, but strategies for increasing their basicity remain important.The contemporary design of novel organic superbases is illustrated by phosphazenyl phosphanes displaying gas-phase basicities (GB) above 300 kcal mol-1 but having molecular weights well below 1000 g·mol-1. This approach is based on a reconsideration of phosphorus(III) compounds, which goes along with increasing their stability in solution. Another example is the preparation of carbodiphosphoranes incorporating pyrrolidine, tetramethylguanidine, or hexamethylphosphazene as a substituent. With gas-phase proton affinities of up to 300 kcal mol-1, they are among the top nonionic carbon bases on the basicity scale. Remarkably, the high basicity of these compounds is achieved at molecular weights of around 600 g·mol-1. Another approach to achieving high basicity through the cooperative effect of multiple intramolecular hydrogen bonding, which increases the stabilization of conjugate acids, has recently been confirmed.This Account focuses on our efforts to produce superbasic molecules that embody many desirable traits, but other groups' approaches will also be discussed. We reveal the crucial structural features of superbases and place them on known basicity scales. We discuss the emerging potential and current limits of their application and give a general outlook into the future.
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Affiliation(s)
- Katarina Vazdar
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, v.v.i. Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | | | | | - Jörg Sundermeyer
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Ivo Leito
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Ullrich Jahn
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, v.v.i. Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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8
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Valadbeigi Y. Acidity enhancement of sulfonic acid derivatives by hydrogen bond networks. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2020.113054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Valadbeigi Y. Effects of intramolecular hydrogen bond and electron delocalization on the basicity of proton sponges and superbases with benzene, pyridine, pyrazine and pyrimidine scaffolds. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Valadbeigi Y. Proton sponges and superbases with nitrogen, phosphorus, arsenic, oxygen, sulfur, and selenium as proton acceptor sites. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Saadat K, Shiri A, Kovačević B. Step Forward to Stronger Neutral Organic Superbases: Fused Troponimines. J Org Chem 2020; 85:11375-11381. [DOI: 10.1021/acs.joc.0c01466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kayvan Saadat
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, 91775-1436 Mashhad, Iran
| | - Ali Shiri
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, 91775-1436 Mashhad, Iran
| | - Borislav Kovačević
- Group for Computational Life Science, Division of Chemistry, Ruder Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
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12
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Harnessing aromaticity and intramolecular hydrogen bonding to tailor organosuperbases by using 2,4,6-cycloheptatriene-1-imine scaffold. Struct Chem 2020. [DOI: 10.1007/s11224-020-01520-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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13
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Saeidian H, Mirjafary Z. Engineering non-ionic carbon super- and hyperbases by a computational DFT approach: substituted allenes have unprecedented cation affinities. NEW J CHEM 2020. [DOI: 10.1039/d0nj02207a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
DFT calculations reveal that allenes substituted by a cyclopropene or a methylenecyclopropene group, offer suitable scaffolds for tailoring powerful carbon bases. The protonation at C(sp) site provide superbases with PAs = 879–1218 kJ mol−1.
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Affiliation(s)
- Hamid Saeidian
- Department of Science
- Payame Noor University (PNU)
- Tehran
- Iran
| | - Zohreh Mirjafary
- Department of Chemistry
- Science and Research Branch
- Islamic Azad University
- Tehran
- Iran
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14
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Ullrich S, Barić D, Xie X, Kovačević B, Sundermeyer J. Basicity Enhancement by Multiple Intramolecular Hydrogen Bonding in Organic Superbase N,N′,N″,N‴-Tetrakis(3-(dimethylamino)propyl)triaminophosphazene. Org Lett 2019; 21:9142-9146. [DOI: 10.1021/acs.orglett.9b03521] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sebastian Ullrich
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Danijela Barić
- The Group for Computational Life Sciences, Ruđer Bošković Institute, Bijenička c. 54, HR-10000 Zagreb, Croatia
| | - Xiulan Xie
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Borislav Kovačević
- The Group for Computational Life Sciences, Ruđer Bošković Institute, Bijenička c. 54, HR-10000 Zagreb, Croatia
| | - Jörg Sundermeyer
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
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15
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Ullrich S, Kovačević B, Xie X, Sundermeyer J. Phosphazenyl Phosphines: The Most Electron‐Rich Uncharged Phosphorus Brønsted and Lewis Bases. Angew Chem Int Ed Engl 2019; 58:10335-10339. [DOI: 10.1002/anie.201903342] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/29/2019] [Indexed: 01/15/2023]
Affiliation(s)
- Sebastian Ullrich
- Fachbereich ChemiePhilipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Germany
| | - Borislav Kovačević
- The Group for Computational Life SciencesRudjer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | - Xiulan Xie
- Fachbereich ChemiePhilipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Germany
| | - Jörg Sundermeyer
- Fachbereich ChemiePhilipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Germany
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16
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Ullrich S, Kovačević B, Xie X, Sundermeyer J. Phosphazenylphosphine: Die elektronenreichsten ungeladenen Brønsted‐ und Lewis‐Phosphor‐Basen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903342] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Sebastian Ullrich
- Fachbereich ChemiePhilipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Deutschland
| | - Borislav Kovačević
- The Group for Computational Life SciencesRudjer Bošković Institute Bijenička 54 HR-10000 Zagreb Kroatien
| | - Xiulan Xie
- Fachbereich ChemiePhilipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Deutschland
| | - Jörg Sundermeyer
- Fachbereich ChemiePhilipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Deutschland
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17
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Affiliation(s)
- Steven M. Bachrach
- Department of Chemistry and School of Science, Monmouth University, 400 Cedar Avenue, West Long Branch, New Jersey 07764, United States
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18
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Masumian E, Nowroozi A. Comparative study of resonance-inhibited hydrogen bonded (RIHB) systems with different atoms involved: the leading role of σ-planarity. Mol Phys 2019. [DOI: 10.1080/00268976.2018.1557350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Ehsan Masumian
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | - Alireza Nowroozi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
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19
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Despotović I. Basicity of Some Pyridinophanes in Gas Phase and Acetonitrile – a DFT Study. ChemistrySelect 2018. [DOI: 10.1002/slct.201801449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ines Despotović
- Division of Physical ChemistryRuđer Bošković Institute, Bijenička 54 HR-10002 Zagreb Croatia
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20
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Singh A, Ojha AK, Jang HM. Strategic Design and Utilization of Molecular Flexibility for Straddling the Application of Organic Superbases: A DFT Study. ChemistrySelect 2018. [DOI: 10.1002/slct.201702912] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ajeet Singh
- Department of Physics; Motilal Nehru National Institute of Technology Allahabad; Allahabad- 211004 India
- Division of Advanced Materials Science; Pohang University of Science and Technology (POSTECH); Pohang 790-784 Republic of Korea
| | - Animesh K. Ojha
- Department of Physics; Motilal Nehru National Institute of Technology Allahabad; Allahabad- 211004 India
| | - Hyun Myung Jang
- Division of Advanced Materials Science; Pohang University of Science and Technology (POSTECH); Pohang 790-784 Republic of Korea
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21
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Kögel JF, Kovačević B, Ullrich S, Xie X, Sundermeyer J. Chelating P2-Bis-phosphazenes with a (R
,R
)-1,2-Diaminocyclohexane Skeleton: Two New Chiral Superbases. Chemistry 2017; 23:2591-2598. [DOI: 10.1002/chem.201604522] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/06/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Julius F. Kögel
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Straße 35032 Marburg Germany
- Current address: FB Biologie/Chemie; Universität Bremen; Leobener Str. im NW2 28359 Bremen Germany
| | - Borislav Kovačević
- Group for Computational Life Sciences; Rudjer Bošković Institute; Bijenička c. 54 HR-10000 Zagreb Croatia
| | - Sebastian Ullrich
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Straße 35032 Marburg Germany
| | - Xiulan Xie
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Straße 35032 Marburg Germany
| | - Jörg Sundermeyer
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Straße 35032 Marburg Germany
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Raczyńska ED, Gal JF, Maria PC. Enhanced Basicity of Push-Pull Nitrogen Bases in the Gas Phase. Chem Rev 2016; 116:13454-13511. [PMID: 27739663 DOI: 10.1021/acs.chemrev.6b00224] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogen bases containing one or more pushing amino-group(s) directly linked to a pulling cyano, imino, or phosphoimino group, as well as those in which the pushing and pulling moieties are separated by a conjugated spacer (C═X)n, where X is CH or N, display an exceptionally strong basicity. The n-π conjugation between the pushing and pulling groups in such systems lowers the basicity of the pushing amino-group(s) and increases the basicity of the pulling cyano, imino, or phosphoimino group. In the gas phase, most of the so-called push-pull nitrogen bases exhibit a very high basicity. This paper presents an analysis of the exceptional gas-phase basicity, mostly in terms of experimental data, in relation with structure and conjugation of various subfamilies of push-pull nitrogen bases: nitriles, azoles, azines, amidines, guanidines, vinamidines, biguanides, and phosphazenes. The strong basicity of biomolecules containing a push-pull nitrogen substructure, such as bioamines, amino acids, and peptides containing push-pull side chains, nucleobases, and their nucleosides and nucleotides, is also analyzed. Progress and perspectives of experimental determinations of GBs and PAs of highly basic compounds, termed as "superbases", are presented and benchmarked on the basis of theoretical calculations on existing or hypothetical molecules.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW) , ul. Nowoursynowska 159c, 02-776 Warszawa, Poland
| | - Jean-François Gal
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
| | - Pierre-Charles Maria
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
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23
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Pairas GN, Tsoungas PG. H-Bond: Τhe Chemistry-Biology H-Bridge. ChemistrySelect 2016; 1:4520-4532. [PMID: 32328512 PMCID: PMC7169486 DOI: 10.1002/slct.201600770] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 07/29/2016] [Indexed: 12/19/2022]
Abstract
H-bonding, as a non covalent stabilizing interaction of diverse nature, has a central role in the structure, function and dynamics of chemical and biological processes, pivotal to molecular recognition and eventually to drug design. Types of conventional and non conventional (H-H, dihydrogen, H- π, CH- π, anti- , proton coordination and H-S) H-bonding interactions are discussed as well as features emerging from their interplay, such as cooperativity (σ- and π-) effects and allostery. Its utility in many applications is described. Catalysis, proton and electron transfer processes in various materials or supramolecular architectures of preorganized hosts for guest binding, are front-line technology. The H-bond-related concept of proton transfer (PT) addresses energy issues or deciphering the mechanism of many natural and synthetic processes. PT is also of paramount importance in the functions of cells and is assisted by large complex proteins embedded in membranes. Both intermolecular and intramolecular PT in H-bonded systems has received attention, theoretically and experimentally, using prototype molecules. It is found in rearrangement reactions, protein functions, and enzyme reactions or across proton channels and pumps. Investigations on the competition between intra- and intermolecular H bonding are discussed. Of particular interest is the H-bond furcation, a common phenomenon in protein-ligand binding. Multiple H-bonding (H-bond furcation) is observed in supramolecular structures.
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Affiliation(s)
- George N. Pairas
- Department of PharmacyLaboratory of Medicinal ChemistryUniversity of PatrasGR-265 04PatrasGreece
| | - Petros G. Tsoungas
- Laboratory of BiochemistryHellenic Pasteur Institute127 Vas. Sofias Ave.GR-115 21AthensGreece
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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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Kaljurand I, Saame J, Rodima T, Koppel I, Koppel IA, Kögel JF, Sundermeyer J, Köhn U, Coles MP, Leito I. Experimental Basicities of Phosphazene, Guanidinophosphazene, and Proton Sponge Superbases in the Gas Phase and Solution. J Phys Chem A 2016; 120:2591-604. [DOI: 10.1021/acs.jpca.6b01552] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ivari Kaljurand
- Institute
of Chemistry, University of Tartu, Ravila 14a Str, 50411 Tartu, Estonia
| | - Jaan Saame
- Institute
of Chemistry, University of Tartu, Ravila 14a Str, 50411 Tartu, Estonia
| | - Toomas Rodima
- Institute
of Chemistry, University of Tartu, Ravila 14a Str, 50411 Tartu, Estonia
| | - Ivar Koppel
- Institute
of Computer Sciences, University of Tartu, J. Liivi 2 Str, 50409 Tartu, Estonia
| | - Ilmar A. Koppel
- Institute
of Chemistry, University of Tartu, Ravila 14a Str, 50411 Tartu, Estonia
| | - Julius F. Kögel
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Jörg Sundermeyer
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Uwe Köhn
- Institut
für Organische Chemie und Makromolekulare Chemie, Friedrich-Schiller-Universität Jena, Humboldtstraße 10, 07743 Jena, Germany
| | - Martyn P. Coles
- School
of Chemical and Physical Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Ivo Leito
- Institute
of Chemistry, University of Tartu, Ravila 14a Str, 50411 Tartu, Estonia
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26
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Berlinck RGS, Romminger S. The chemistry and biology of guanidine natural products. Nat Prod Rep 2016; 33:456-90. [DOI: 10.1039/c5np00108k] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The present review discusses the isolation, structure determination, synthesis, biosynthesis and biological activities of secondary metabolites bearing a guanidine group.
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Affiliation(s)
| | - Stelamar Romminger
- Instituto de Química de São Carlos
- Universidade de São Paulo
- São Carlos
- Brazil
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27
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Sánchez-Sanz G, Trujillo C, Alkorta I, Elguero J. Modulating intramolecular P⋯N pnictogen interactions. Phys Chem Chem Phys 2016; 18:9148-60. [DOI: 10.1039/c6cp00227g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The strength of P⋯N intramolecular pnictogen interactions can be modulated, enhanced or diminished upon substitution of different electron withdrawing or donor groups.
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Affiliation(s)
| | - Cristina Trujillo
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
| | - Ibon Alkorta
- Instituto de Química Médica
- CSIC
- E-28006 Madrid
- Spain
| | - José Elguero
- Instituto de Química Médica
- CSIC
- E-28006 Madrid
- Spain
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28
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Khamaru K, Ganguly B. In silico design of adamantane derived organic superbases with an extended hydrogen bond network and their use as molecular containers for the storage of H2 and CO2. RSC Adv 2015. [DOI: 10.1039/c5ra19206d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
DFT calculations predicted that amine substituted adamantane derivatives can function as organic superbases and can be used for gas storage.
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Affiliation(s)
- Krishnendu Khamaru
- Computation and Simulation Unit
- Analytical Discipline & Centralized Instrument Facility, and Academy of Scientific and Innovative Research
- CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar
- India
| | - Bishwajit Ganguly
- Computation and Simulation Unit
- Analytical Discipline & Centralized Instrument Facility, and Academy of Scientific and Innovative Research
- CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar
- India
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29
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Barić D, Dragičević I, Kovačević B. Cyclopropenimine as a hydrogen bond acceptor—towards the strongest non-phosphorus superbases. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.09.068] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Glasovac Z, Eckert-Maksić M. Effect of Intramolecular Hydrogen Bonds on the Gas-Phase Basicity of Guanidines. Aust J Chem 2014. [DOI: 10.1071/ch14182] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Three series of novel trisubstituted guanidines containing at least one hydrogen bond accepting (HBA) group were modelled using B3LYP/6–311+G(2df,p)//B3LYP/6–31G(d) calculations. Their structure was modified by incorporating a variety of different HBA groups covering a wide range of hydrogen bond strengths. Calculated gas-phase basicities (GBs) ranged from 1035 to 1181 kJ mol–1 depending on the nature of the substituent. To rationalise changes in the GB, a correlation of GB against two independent variables (pKHB and σ4B) was conducted where pKHB served as the descriptor of the hydrogen bond strength and σ4B was introduced to describe changes in the GBs in the open-chain model systems, i.e. in the absence of intramolecular hydrogen bond (IMHB), caused by the electronic effect of the propyl-HBA substituent. A very good correlation of the calculated gas-phase basicities against these two independent variables was established for all three sets of the bases.
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31
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Sánchez-Sanz G, Trujillo C, Alkorta I, Elguero J. Intramolecular pnicogen interactions in phosphorus and arsenic analogues of proton sponges. Phys Chem Chem Phys 2014; 16:15900-9. [DOI: 10.1039/c4cp01072h] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A computational study of the intramolecular pnicogen bond in 1,8-bis-substituted naphthalene derivatives (ZXH and ZX2 with Z = P, As and X = H, F, Cl, and Br), structurally related to proton sponges, has been carried out.
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Affiliation(s)
- Goar Sánchez-Sanz
- School of Physics & Complex and Adaptive Systems Laboratory
- University College Dublin
- Dublin 4, Ireland
| | - Cristina Trujillo
- Institute of Organic Chemistry and Biochemistry
- Gilead Sciences Research Center & IOCB
- Academy of Sciences of the Czech Republic
- 166 10 Praha 6, Czech Republic
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC)
- 28006-Madrid, Spain
| | - José Elguero
- Instituto de Química Médica (CSIC)
- 28006-Madrid, Spain
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32
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Bachrach SM. Amine Superbases Stabilized by Extended Hydrogen Bond Networks. J Org Chem 2013; 78:10909-16. [DOI: 10.1021/jo4018974] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Steven M. Bachrach
- Department of Chemistry, Trinity University, 1 Trinity Place, San Antonio, Texas 78212, United States
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