1
|
Jia XB, Wang J, Liu YF, Zhu YF, Li JY, Li YJ, Chou SL, Xiao Y. Facilitating Layered Oxide Cathodes Based on Orbital Hybridization for Sodium-Ion Batteries: Marvelous Air Stability, Controllable High Voltage, and Anion Redox Chemistry. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307938. [PMID: 37910130 DOI: 10.1002/adma.202307938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/17/2023] [Indexed: 11/03/2023]
Abstract
Layered oxides have become the research focus of cathode materials for sodium-ion batteries (SIBs) due to the low cost, simple synthesis process, and high specific capacity. However, the poor air stability, unstable phase structure under high voltage, and slow anionic redox kinetics hinder their commercial application. In recent years, the concept of manipulating orbital hybridization has been proposed to simultaneously regulate the microelectronic structure and modify the surface chemistry environment intrinsically. In this review, the hybridization modes between atoms in 3d/4d transition metal (TM) orbitals and O 2p orbitals near the region of the Fermi energy level (EF) are summarized based on orbital hybridization theory and first-principles calculations as well as various sophisticated characterizations. Furthermore, the underlying mechanisms are explored from macro-scale to micro-scale, including enhancing air stability, modulating high working voltage, and stabilizing anionic redox chemistry. Meanwhile, the origin, formation conditions, and different types of orbital hybridization, as well as its application in layered oxide cathodes are presented, which provide insights into the design and preparation of cathode materials. Ultimately, the main challenges in the development of orbital hybridization and its potential for the production application are also discussed, pointing out the route for high-performance practical sodium layered oxide cathodes.
Collapse
Affiliation(s)
- Xin-Bei Jia
- Institute for Carbon Neutralization, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China
- Wenzhou Key Laboratory of Sodium-Ion Batteries, Wenzhou University Technology Innovation Institute for Carbon Neutralization, Wenzhou, 325035, China
| | - Jingqiang Wang
- Institute for Carbon Neutralization, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China
- Wenzhou Key Laboratory of Sodium-Ion Batteries, Wenzhou University Technology Innovation Institute for Carbon Neutralization, Wenzhou, 325035, China
| | - Yi-Feng Liu
- Institute for Carbon Neutralization, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China
- Wenzhou Key Laboratory of Sodium-Ion Batteries, Wenzhou University Technology Innovation Institute for Carbon Neutralization, Wenzhou, 325035, China
| | - Yan-Fang Zhu
- Institute for Carbon Neutralization, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China
- Wenzhou Key Laboratory of Sodium-Ion Batteries, Wenzhou University Technology Innovation Institute for Carbon Neutralization, Wenzhou, 325035, China
| | - Jia-Yang Li
- Institute for Carbon Neutralization, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China
- Wenzhou Key Laboratory of Sodium-Ion Batteries, Wenzhou University Technology Innovation Institute for Carbon Neutralization, Wenzhou, 325035, China
| | - Yan-Jiang Li
- Institute for Carbon Neutralization, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China
- Wenzhou Key Laboratory of Sodium-Ion Batteries, Wenzhou University Technology Innovation Institute for Carbon Neutralization, Wenzhou, 325035, China
| | - Shu-Lei Chou
- Institute for Carbon Neutralization, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China
- Wenzhou Key Laboratory of Sodium-Ion Batteries, Wenzhou University Technology Innovation Institute for Carbon Neutralization, Wenzhou, 325035, China
| | - Yao Xiao
- Institute for Carbon Neutralization, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, 325035, China
- Wenzhou Key Laboratory of Sodium-Ion Batteries, Wenzhou University Technology Innovation Institute for Carbon Neutralization, Wenzhou, 325035, China
| |
Collapse
|
2
|
Kang D, Kim J. Enamine N-oxides: Design, Synthesis, and Function in Bioorthogonal Reactions. Synlett 2024; 35:145-154. [PMID: 38947226 PMCID: PMC11210832 DOI: 10.1055/a-2127-1086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Enamine N-oxides act as a chemical linchpin bridging two bioorthogonal associative and dissociative reactions. This article describes the design of enamine N-oxides; their synthesis through the retro-Cope elimination reaction; the use of solvent, hyperconjugation, strain, and rehybridization effects to achieve bioorthogonal reactivity; and their rapid reductive cleavage with diboron reagents. The coordinated assembly and disassembly of the enamine N-oxide motif constitutes a powerful chemical operation that enables the attachment and detachment of small molecules from biomacromolecules in a biological setting.
Collapse
Affiliation(s)
- Dahye Kang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Justin Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| |
Collapse
|
3
|
Chugunova E, Gazizov AS, Islamov D, Matveeva V, Burilov A, Akylbekov N, Dobrynin A, Zhapparbergenov R, Appazov N, Chabuka BK, Christopher K, Tonkoglazova DI, Alabugin IV. An Unusual Rearrangement of Pyrazole Nitrene and Coarctate Ring-Opening/Recyclization Cascade: Formal CH-Acetoxylation and Azide/Amine Conversion without External Oxidants and Reductants. Molecules 2023; 28:7335. [PMID: 37959754 PMCID: PMC10648078 DOI: 10.3390/molecules28217335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
We report an unusual transformation where the transient formation of a nitrene moiety initiates a sequence of steps leading to remote oxidative C-H functionalization (R-CH3 to R-CH2OC(O)R') and the concomitant reduction of the nitrene into an amino group. No external oxidants or reductants are needed for this formal molecular comproportionation. Detected and isolated intermediates and computational analysis suggest that the process occurs with pyrazole ring opening and recyclization.
Collapse
Affiliation(s)
- Elena Chugunova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Akad. Arbuzov St. 8, Kazan 420088, Russia; (A.S.G.); (D.I.); (V.M.); (A.B.); (A.D.); (I.V.A.)
| | - Almir S. Gazizov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Akad. Arbuzov St. 8, Kazan 420088, Russia; (A.S.G.); (D.I.); (V.M.); (A.B.); (A.D.); (I.V.A.)
| | - Daut Islamov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Akad. Arbuzov St. 8, Kazan 420088, Russia; (A.S.G.); (D.I.); (V.M.); (A.B.); (A.D.); (I.V.A.)
| | - Victoria Matveeva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Akad. Arbuzov St. 8, Kazan 420088, Russia; (A.S.G.); (D.I.); (V.M.); (A.B.); (A.D.); (I.V.A.)
| | - Alexander Burilov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Akad. Arbuzov St. 8, Kazan 420088, Russia; (A.S.G.); (D.I.); (V.M.); (A.B.); (A.D.); (I.V.A.)
| | - Nurgali Akylbekov
- Laboratory of Engineering Profile “Physical and Chemical Methods of Analysis”, Korkyt Ata Kyzylorda University, Aitekebie Str. 29A, Kyzylorda 120014, Kazakhstan; (N.A.); (R.Z.)
| | - Alexey Dobrynin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Akad. Arbuzov St. 8, Kazan 420088, Russia; (A.S.G.); (D.I.); (V.M.); (A.B.); (A.D.); (I.V.A.)
| | - Rakhmetulla Zhapparbergenov
- Laboratory of Engineering Profile “Physical and Chemical Methods of Analysis”, Korkyt Ata Kyzylorda University, Aitekebie Str. 29A, Kyzylorda 120014, Kazakhstan; (N.A.); (R.Z.)
| | - Nurbol Appazov
- Laboratory of Engineering Profile “Physical and Chemical Methods of Analysis”, Korkyt Ata Kyzylorda University, Aitekebie Str. 29A, Kyzylorda 120014, Kazakhstan; (N.A.); (R.Z.)
- Zhakhaev Kazakh Scientific Research Institute of Rice Growing, Abay Av. 25B, Kyzylorda 120008, Kazakhstan
| | - Beauty K. Chabuka
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-3290, USA; (B.K.C.); (K.C.); (D.I.T.)
| | - Kimberley Christopher
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-3290, USA; (B.K.C.); (K.C.); (D.I.T.)
| | - Daria I. Tonkoglazova
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-3290, USA; (B.K.C.); (K.C.); (D.I.T.)
| | - Igor V. Alabugin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Akad. Arbuzov St. 8, Kazan 420088, Russia; (A.S.G.); (D.I.); (V.M.); (A.B.); (A.D.); (I.V.A.)
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-3290, USA; (B.K.C.); (K.C.); (D.I.T.)
| |
Collapse
|
4
|
Vil’ VA, Barsegyan YA, Kuhn L, Terent’ev AO, Alabugin IV. Creating, Preserving, and Directing Carboxylate Radicals in Ni-Catalyzed C(sp 3)–H Acyloxylation of Ethers, Ketones, and Alkanes with Diacyl Peroxides. Organometallics 2023. [DOI: 10.1021/acs.organomet.2c00663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Affiliation(s)
- Vera A. Vil’
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prospect, Moscow 119991, Russian Federation
| | - Yana A. Barsegyan
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prospect, Moscow 119991, Russian Federation
| | - Leah Kuhn
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Fl 32306, United States
| | - Alexander O. Terent’ev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prospect, Moscow 119991, Russian Federation
| | - Igor V. Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Fl 32306, United States
| |
Collapse
|
5
|
Fuchibe K, Ichikawa J. Generation of difluorocarbenes and introduction of fluorinated one carbon units into carbonyl and related compounds. Chem Commun (Camb) 2023; 59:2532-2540. [PMID: 36723345 DOI: 10.1039/d2cc03950h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Difluorocarbene is a simple and versatile one-carbon unit for synthesizing acyclic and cyclic organofluorine compounds. However, the use of difluorocarbene in organic synthesis has been relatively limited because of the harsh conditions required for its generation, the toxicity of the precursors, and undesired dimerization. This feature article provides an account of (i) the generation of free and metal difluorocarbenes from trimethylsilyl 2,2-difluoro-2-(fluorosulfonyl)acetate (TFDA) or BrCF2CO2Li/Na and (ii) their application to the facile synthesis of valuable organofluorine compounds. The difluorocarbenes thus generated react with (thio)carbonyl compounds and silyl dienol ethers to provide a wide variety of products such as (a) difluoromethyl (thio)ethers, (b) fluorinated thiophenes, (c) fluorinated thia/oxazoles, (d) fluorinated cyclopentanones and (e) difluoroalkenes.
Collapse
Affiliation(s)
- Kohei Fuchibe
- Division of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan.
| | - Junji Ichikawa
- Division of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan.
| |
Collapse
|
6
|
Charlton NC, Mastyugin M, Török B, Török M. Structural Features of Small Molecule Antioxidants and Strategic Modifications to Improve Potential Bioactivity. Molecules 2023; 28:molecules28031057. [PMID: 36770724 PMCID: PMC9920158 DOI: 10.3390/molecules28031057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
This review surveys the major structural features in various groups of small molecules that are considered to be antioxidants, including natural and synthetic compounds alike. Recent advances in the strategic modification of known small molecule antioxidants are also described. The highlight is placed on changing major physicochemical parameters, including log p, bond dissociation energy, ionization potential, and others which result in improved antioxidant activity.
Collapse
|
7
|
Kang D, Wahl C, Kim J. Synthesis of push-pull-activated ynol ethers and their evaluation in the bioorthogonal hydroamination reaction. Org Biomol Chem 2022; 20:9217-9221. [PMID: 36367436 PMCID: PMC9769999 DOI: 10.1039/d2ob01917e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
A new class of push-pull-activated alkynes featuring di- and trifluorinated ynol ethers was synthesized. The difluorinated ynol ether exhibited an optimal balance of stability and reactivity, displaying a substantially improved half-life in the presence of aqueous thiols over the previously reported 1-haloalkyne analogs while reacting just as fast in the hydroamination reaction with N,N-diethylhydroxylamine. The trifluorinated ynol ether reacted significantly faster, exhibiting a second order rate constant of 0.56 M-1 s-1 in methanol, but it proved too unstable toward thiols. These fluorinated ynol ethers further demonstrate the importance of the hyperconjugation-rehybridization effect in activating alkynes and demonstrate how substituent effects can both activate and stabilize alkynes for bioorthogonal reactivity.
Collapse
Affiliation(s)
- Dahye Kang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Conrad Wahl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
| | - Justin Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| |
Collapse
|
8
|
Seeman JI, Tantillo DJ. Understanding chemistry: from "heuristic (soft) explanations and reasoning by analogy" to "quantum chemistry". Chem Sci 2022; 13:11461-11486. [PMID: 36320403 PMCID: PMC9575397 DOI: 10.1039/d2sc02535c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/06/2022] [Indexed: 12/02/2022] Open
Abstract
"Soft theories," i.e., "heuristic models based on reasoning by analogy" largely drove chemistry understanding for 150 years or more. But soft theories have their limitations and with the expansion of chemistry in the mid-20th century, more and more inexplicable (by soft theory) experimental results were being obtained. In the past 50 years, quantum chemistry, most often in the guise of applied theoretical chemistry including computational chemistry, has provided (a) the underlying "hard evidence" for many soft theories and (b) the explanations for chemical phenomena that were unavailable by soft theories. In this publication, we define "hard theories" as "theories derived from quantum chemistry." Both soft and hard theories can be qualitative and quantitative, and the "Houk quadrant" is proposed as a helpful categorization tool. Furthermore, the language of soft theories is often used appropriately to describe quantum chemical results. A valid and useful way of doing science is the appropriate use and application of both soft and hard theories along with the best nomenclature available for successful communication of results and ideas.
Collapse
Affiliation(s)
- Jeffrey I Seeman
- Department of Chemistry, University of Richmond Richmond VA 23173 USA
| | - Dean J Tantillo
- Department of Chemistry, University of California - Davis Davis CA 95616 USA
| |
Collapse
|
9
|
Masnabadi N, Thalji MR, Alhasan HS, Mahmoodi Z, Soldatov AV, Ali GAM. Structural, Electronic, Reactivity, and Conformational Features of 2,5,5-Trimethyl-1,3,2-diheterophosphinane-2-sulfide, and Its Derivatives: DFT, MEP, and NBO Calculations. Molecules 2022; 27:molecules27134011. [PMID: 35807257 PMCID: PMC9268642 DOI: 10.3390/molecules27134011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/11/2022] [Accepted: 06/17/2022] [Indexed: 01/18/2023] Open
Abstract
In this study, we used density functional theory (DFT) and natural bond orbital (NBO) analysis to determine the structural, electronic, reactivity, and conformational features of 2,5,5-trimethyl-1,3,2-di-heteroatom (X) phosphinane-2-sulfide derivatives (X = O (compound 1), S (compound 2), and Se (compound 3)). We discovered that the features improve dramatically at 6-31G** and B3LYP/6-311+G** levels. The level of theory for the molecular structure was optimized first, followed by the frontier molecular orbital theory development to assess molecular stability and reactivity. Molecular orbital calculations, such as the HOMO–LUMO energy gap and the mapping of molecular electrostatic potential surfaces (MEP), were performed similarly to DFT calculations. In addition, the electrostatic potential of the molecule was used to map the electron density on a surface. In addition to revealing molecules’ size and shape distribution, this study also shows the sites on the surface where molecules are most chemically reactive.
Collapse
Affiliation(s)
- Nasrin Masnabadi
- Department of Chemistry, Roudehen Branch, Islamic Azad University, Roudehen P.O. Box 189, Iran
- Correspondence: or (N.M.); or (G.A.M.A.)
| | - Mohammad R. Thalji
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Korea;
| | - Huda S. Alhasan
- Environmental Research and Studies Center, University of Babylon, Babil 51002, Iraq;
| | - Zahra Mahmoodi
- Department of Chemistry, University of Applied Science and Technology, Center of Arya Gach Poldokhtar, Tehran P.O. Box 68, Iran;
| | - Alexander V. Soldatov
- The Smart Materials Research Institute, Southern Federal University, Sladkova Str. 178/24, Rostov-on-Don 344006, Russia;
| | - Gomaa A. M. Ali
- Chemistry Department, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt
- Correspondence: or (N.M.); or (G.A.M.A.)
| |
Collapse
|
10
|
Kuhn L, Vil' VA, Barsegyan YA, Terent'ev AO, Alabugin IV. Carboxylate as a Non-innocent L-Ligand: Computational and Experimental Search for Metal-Bound Carboxylate Radicals. Org Lett 2022; 24:3817-3822. [PMID: 35609004 DOI: 10.1021/acs.orglett.2c01356] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We show that the carboxylate radical acts as an L-ligand with certain high-spin transition metal centers. Such coordination preserves the O-radical character needed for C-H activation via hydrogen atom transfer. Capture of the new C-radical by the metal and subsequent reductive elimination leads to formal C-H acyloxylation. Decarboxylation of the RCO2 radical is minimized through hybridization effects introduced by spiro-cyclopropyl moiety.
Collapse
Affiliation(s)
- Leah Kuhn
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Vera A Vil'
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prospect, Moscow, 119991, Russian Federation
| | - Yana A Barsegyan
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prospect, Moscow, 119991, Russian Federation
| | - Alexander O Terent'ev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prospect, Moscow, 119991, Russian Federation
| | - Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| |
Collapse
|
11
|
Akyeva AY, Kansuzyan AV, Vukich KS, Kuhn L, Saverina EA, Minyaev ME, Pechennikov VM, Egorov MP, Alabugin IV, Vorobyev SV, Syroeshkin MA. Remote Stereoelectronic Effects in Pyrrolidone- and Caprolactam-Substituted Phenols: Discrepancies in Antioxidant Properties Evaluated by Electrochemical Oxidation and H-Atom Transfer Reactivity. J Org Chem 2022; 87:5371-5384. [PMID: 35363496 DOI: 10.1021/acs.joc.2c00207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New antioxidants are commonly evaluated via two main approaches, i.e., the ability to donate an electron and the ability to intercept free radicals. We compared these approaches by evaluating the properties of 11 compounds containing both antioxidant moieties (mono- and polyphenols) and auxiliary pharmacophores (pyrrolidone and caprolactam). Several common antioxidants, such as butylated hydroxytoluene (BHT), 2,3,5-trimethylphenol (TMP), quercetin, and dihydroquercetin, were added for comparison. The antioxidant properties of these compounds were determined by their rates of reaction with 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical and their oxidation potentials from cyclic voltammetry. Although these methods test different chemical properties, their results correlate reasonably well. However, several exceptions exist where the two methods give opposite predictions! One of them is the different behavior of mono- and polyphenols: polyphenols can react with DPPH more than an order of magnitude faster than monophenols of a similar oxidation potential. The second exception stems from the size of a "bystander" lactam ring at the benzylic position. Although the phenols with a seven-membered lactam ring are harder to oxidize, the sterically nonhindered compounds react with DPPH about 2× faster than the analogous five-membered lactams. The limitations of computational methods, especially those based on a single parameter, are also evaluated and discussed.
Collapse
Affiliation(s)
- Anna Ya Akyeva
- N.D. Zelinsky Institute of Organic Chemistry, 119991 Moscow Russia
| | | | - Katarina S Vukich
- N.D. Zelinsky Institute of Organic Chemistry, 119991 Moscow Russia.,I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Leah Kuhn
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | | | | | | | - Mikhail P Egorov
- N.D. Zelinsky Institute of Organic Chemistry, 119991 Moscow Russia
| | - Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Stepan V Vorobyev
- Gubkin Russian State University of Oil and Gas, 65 Leninsky Prospect, 119991 Moscow, Russia
| | | |
Collapse
|
12
|
Tsipis A. Robust Fluorine Effects on Molecular Conformations of 2-Amino-2-Fluorotetrahydro-2 H-Pyrans: Fluorine-Perlin-like vs Perlin Effects. NEW J CHEM 2022. [DOI: 10.1039/d2nj02380f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformational behavior of a wide variety of amino substituents (totally 13) in 2-amino-2-fluorotetrahydro-2H-pyrans and 2-amino-tetrahydro-2H-pyrans are thoroughly explored employing Density Functional Theory and Natural Bond Orbital methods. Calculations demonstrated...
Collapse
|
13
|
Alabugin IV, Kuhn L, Krivoshchapov NV, Mehaffy P, Medvedev MG. Anomeric effect, hyperconjugation and electrostatics: lessons from complexity in a classic stereoelectronic phenomenon. Chem Soc Rev 2021; 50:10212-10252. [PMID: 34542133 DOI: 10.1039/d1cs00564b] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the interplay of multiple components (steric, electrostatic, stereoelectronic, dispersive, etc.) that define the overall energy, structure, and reactivity of organic molecules can be a daunting task. The task becomes even more difficult when multiple approaches based on different physical premises disagree in their analysis of a multicomponent molecular system. Herein, we will use a classic conformational "oddity", the anomeric effect, to discuss the value of identifying the key contributors to reactivity that can guide chemical predictions. After providing the background related to the relevant types of hyperconjugation and a brief historic outline of the origins of the anomeric effect, we outline variations of its patterns and provide illustrative examples for the role of the anomeric effect in structure, stability, and spectroscopic properties. We show that the complete hyperconjugative model remains superior in explaining the interplay between structure and reactivity. We will use recent controversies regarding the origin of the anomeric effect to start a deeper discussion relevant to any electronic effect. Why are such questions inherently controversial? How to describe a complex quantum system using a model that is "as simple as possible, but no simpler"? What is a fair test for such a model? Perhaps, instead of asking "who is right and who is wrong?" one should ask "why do we disagree?". Stereoelectronic thinking can reconcile quantum complexity with chemical intuition and build the conceptual bridge between structure and reactivity. Even when many factors contribute to the observed structural and conformational trends, electron delocalization is a dominating force when the electronic demand is high (i.e., bonds are breaking as molecules distort from their equilibrium geometries). In these situations, the role of orbital interactions increases to the extent where they can define reactivity. For example, negative hyperconjugation can unleash the "underutilized" stereoelectronic power of unshared electrons (i.e., the lone pairs) to stabilize a developing positive charge at an anomeric carbon. This analysis paves the way for the broader discussion of the omnipresent importance of negative hyperconjugation in oxygen-containing functional groups. From that point of view, the stereoelectronic component of the anomeric effect plays a unique role in guiding reaction design.
Collapse
Affiliation(s)
- Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University, USA.
| | - Leah Kuhn
- Department of Chemistry and Biochemistry, Florida State University, USA.
| | - Nikolai V Krivoshchapov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation. .,Lomonosov Moscow State University, Leninskie Gory 1 (3), Moscow, 119991, Russian Federation
| | - Patricia Mehaffy
- Department of Chemistry and Biochemistry, Florida State University, USA.
| | - Michael G Medvedev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation. .,A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilova St., 119991 Moscow, Russian Federation
| |
Collapse
|
14
|
Alabugin IV, Kuhn L, Medvedev MG, Krivoshchapov NV, Vil' VA, Yaremenko IA, Mehaffy P, Yarie M, Terent'ev AO, Zolfigol MA. Stereoelectronic power of oxygen in control of chemical reactivity: the anomeric effect is not alone. Chem Soc Rev 2021; 50:10253-10345. [PMID: 34263287 DOI: 10.1039/d1cs00386k] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although carbon is the central element of organic chemistry, oxygen is the central element of stereoelectronic control in organic chemistry. Generally, a molecule with a C-O bond has both a strong donor (a lone pair) and a strong acceptor (e.g., a σ*C-O orbital), a combination that provides opportunities to influence chemical transformations at both ends of the electron demand spectrum. Oxygen is a stereoelectronic chameleon that adapts to the varying situations in radical, cationic, anionic, and metal-mediated transformations. Arguably, the most historically important stereoelectronic effect is the anomeric effect (AE), i.e., the axial preference of acceptor groups at the anomeric position of sugars. Although AE is generally attributed to hyperconjugative interactions of σ-acceptors with a lone pair at oxygen (negative hyperconjugation), recent literature reports suggested alternative explanations. In this context, it is timely to evaluate the fundamental connections between the AE and a broad variety of O-functional groups. Such connections illustrate the general role of hyperconjugation with oxygen lone pairs in reactivity. Lessons from the AE can be used as the conceptual framework for organizing disjointed observations into a logical body of knowledge. In contrast, neglect of hyperconjugation can be deeply misleading as it removes the stereoelectronic cornerstone on which, as we show in this review, the chemistry of organic oxygen functionalities is largely based. As negative hyperconjugation releases the "underutilized" stereoelectronic power of unshared electrons (the lone pairs) for the stabilization of a developing positive charge, the role of orbital interactions increases when the electronic demand is high and molecules distort from their equilibrium geometries. From this perspective, hyperconjugative anomeric interactions play a unique role in guiding reaction design. In this manuscript, we discuss the reactivity of organic O-functionalities, outline variations in the possible hyperconjugative patterns, and showcase the vast implications of AE for the structure and reactivity. On our journey through a variety of O-containing organic functional groups, from textbook to exotic, we will illustrate how this knowledge can predict chemical reactivity and unlock new useful synthetic transformations.
Collapse
Affiliation(s)
- Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
| | - Leah Kuhn
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
| | - Michael G Medvedev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation.,A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilova St., 119991 Moscow, Russian Federation
| | - Nikolai V Krivoshchapov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation.,Lomonosov Moscow State University, Leninskie Gory 1 (3), Moscow, 119991, Russian Federation
| | - Vera A Vil'
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation
| | - Ivan A Yaremenko
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation
| | - Patricia Mehaffy
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
| | - Meysam Yarie
- Department of Organic Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan 65167, Iran
| | - Alexander O Terent'ev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation
| | - Mohammad Ali Zolfigol
- Department of Organic Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan 65167, Iran
| |
Collapse
|
15
|
Kang D, Cheung ST, Kim J. Bioorthogonal Hydroamination of Push-Pull-Activated Linear Alkynes. Angew Chem Int Ed Engl 2021; 60:16947-16952. [PMID: 34019705 DOI: 10.1002/anie.202104863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/16/2021] [Indexed: 01/14/2023]
Abstract
A bioorthogonal reaction between N,N-dialkylhydroxylamines and push-pull-activated halogenated alkynes is described. We explore the use of rehybridization effects in activating alkynes, and we show that electronic effects, when competing stereoelectronic and inductive factors are properly balanced, sufficiently activate a linear alkyne in the uncatalyzed conjugative retro-Cope elimination reaction while adequately protecting it against cellular nucleophiles. This design preserves the low steric profile of an alkyne and pairs it with a comparably unobtrusive hydroxylamine. The kinetics are on par with those of the fastest strain-promoted azide-alkyne cycloaddition reactions, the products regioselectively formed, the components sufficiently stable and easily installed, and the reaction suitable for cellular labeling.
Collapse
Affiliation(s)
- Dahye Kang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sheldon T Cheung
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Justin Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| |
Collapse
|
16
|
Kang D, Cheung ST, Kim J. Bioorthogonal Hydroamination of Push–Pull‐Activated Linear Alkynes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dahye Kang
- Department of Cancer Biology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA 02115 USA
| | - Sheldon T. Cheung
- Department of Cancer Biology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA 02115 USA
| | - Justin Kim
- Department of Cancer Biology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA 02115 USA
| |
Collapse
|
17
|
Datta S, Limpanuparb T. Steric effects vs. electron delocalization: a new look into the stability of diastereomers, conformers and constitutional isomers. RSC Adv 2021; 11:20691-20700. [PMID: 35479364 PMCID: PMC9033979 DOI: 10.1039/d1ra02877d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/24/2021] [Indexed: 01/22/2023] Open
Abstract
A quantum chemical investigation of the stability of compounds with identical formulas was carried out on 23 classes of compounds made of C, N, P, O and S atoms as core structures and halogens H, F, Cl, Br and I as substituents. All possible structures were generated and investigated by quantum mechanical methods. The prevalence of a formula in which its Z configuration, gauche conformation or meta isomer is the most stable form is calculated and discussed. Quantitative and qualitative models to explain the stability of the 23 classes of halogenated compounds were also proposed. The prevalence of a chemical formula in which its Z configuration, gauche conformation or meta isomer is the most stable form is derived from over ten thousand chemical structures. The instance of steric prediction failure is surprisingly common.![]()
Collapse
Affiliation(s)
- Sopanant Datta
- Science Division, Mahidol University International College, Mahidol University Salaya Nakhon Pathom 73170 Thailand
| | - Taweetham Limpanuparb
- Science Division, Mahidol University International College, Mahidol University Salaya Nakhon Pathom 73170 Thailand
| |
Collapse
|
18
|
Mapping C−H⋅⋅⋅M Interactions in Confined Spaces: (α‐ICyD
Me
)Au, Ag, Cu Complexes Reveal “Contra‐electrostatic H Bonds” Masquerading as Anagostic Interactions**. Chemistry 2021; 27:8127-8142. [DOI: 10.1002/chem.202100263] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Indexed: 12/18/2022]
|
19
|
Yaremenko IA, Belyakova YY, Radulov PS, Novikov RA, Medvedev MG, Krivoshchapov NV, Korlyukov AA, Alabugin IV, Terent'ev AO. Marriage of Peroxides and Nitrogen Heterocycles: Selective Three-Component Assembly, Peroxide-Preserving Rearrangement, and Stereoelectronic Source of Unusual Stability of Bridged Azaozonides. J Am Chem Soc 2021; 143:6634-6648. [PMID: 33877842 DOI: 10.1021/jacs.1c02249] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Stable bridged azaozonides can be selectively assembled via a catalyst-free three-component condensation of 1,5-diketones, hydrogen peroxide, and an NH-group source such as aqueous ammonia or ammonium salts. This procedure is scalable and can produce gram quantities of bicyclic stereochemically rich heterocycles. The new azaozonides are thermally stable and can be stored at room temperature for several months without decomposition and for at least 1 year at -10 °C. The chemical stability of azaozonides was explored for their subsequent selective transformations including the first example of an aminoperoxide rearrangement that preserves the peroxide group. The amino group in aminoperoxides has remarkably low nucleophilicity and does not participate in the usual amine alkylation and acylation reactions. These observations and the 15 pKa units decrease in basicity in comparison with a typical dialkyl amine are attributed to the strong hyperconjugative nN→σ*C-O interaction with the two antiperiplanar C-O bonds. Due to the weakness of the complementary nO→σ*C-N donation from the peroxide oxygens (a consequence of "inverse α-effect"), this interaction depletes electron density from the NH moiety, protects it from oxidation, and makes it similar in properties to an amide.
Collapse
Affiliation(s)
- Ivan A Yaremenko
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prospekt, 119991 Moscow, Russian Federation
| | - Yulia Yu Belyakova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prospekt, 119991 Moscow, Russian Federation
| | - Peter S Radulov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prospekt, 119991 Moscow, Russian Federation
| | - Roman A Novikov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prospekt, 119991 Moscow, Russian Federation
| | - Michael G Medvedev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prospekt, 119991 Moscow, Russian Federation
| | - Nikolai V Krivoshchapov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prospekt, 119991 Moscow, Russian Federation
| | - Alexander A Korlyukov
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilova Street, 119991 Moscow, Russian Federation
| | - Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Alexander O Terent'ev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prospekt, 119991 Moscow, Russian Federation
| |
Collapse
|
20
|
Dunning TH, Xu LT, Cooper DL, Karadakov PB. Spin-Coupled Generalized Valence Bond Theory: New Perspect ives on the Electronic Structure of Molecules and Chemical Bonds. J Phys Chem A 2021; 125:2021-2050. [PMID: 33677960 DOI: 10.1021/acs.jpca.0c10472] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Spin-Coupled Generalized Valence Bond (SCGVB) theory provides the foundation for a comprehensive theory of the electronic structure of molecules. SCGVB theory offers a compelling orbital description of the electronic structure of molecules as well as an efficient and effective zero-order wave function for calculations striving for quantitative predictions of molecular structures, energetics, and other properties. The orbitals in the SCGVB wave function are usually semilocalized, and for most molecules, they can be interpreted using concepts familiar to all chemists (hybrid orbitals, localized bond pairs, lone pairs, etc.). SCGVB theory also provides new perspectives on the nature of the bonds in molecules such as C2, Be2 and SF4/SF6. SCGVB theory contributes unparalleled insights into the underlying cause of the first-row anomaly in inorganic chemistry as well as the electronic structure of organic molecules and the electronic mechanisms of organic reactions. The SCGVB wave function accounts for nondynamical correlation effects and, thus, corrects the most serious deficiency in molecular orbital (RHF) wave functions. Dynamical correlation effects, which are critical for quantitative predictions, can be taken into account using the SCGVB wave function as the zero-order wave function for multireference configuration interaction or coupled cluster calculations.
Collapse
Affiliation(s)
- Thom H Dunning
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Lu T Xu
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - David L Cooper
- Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, U.K
| | | |
Collapse
|
21
|
Matić M, Denegri B. DFT‐PCM Study on Solvolytic Behaviour of
N
‐alkyl‐X‐pyridinium Ions. ChemistrySelect 2021. [DOI: 10.1002/slct.202004231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mirela Matić
- University of Zagreb Faculty of Pharmacy and Biochemistry Ante Kovačića 1 10000 Zagreb Croatia
| | - Bernard Denegri
- University of Zagreb Faculty of Pharmacy and Biochemistry Ante Kovačića 1 10000 Zagreb Croatia
| |
Collapse
|
22
|
Deb T, Tu J, Franzini RM. Mechanisms and Substituent Effects of Metal-Free Bioorthogonal Reactions. Chem Rev 2021; 121:6850-6914. [DOI: 10.1021/acs.chemrev.0c01013] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Titas Deb
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Julian Tu
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Raphael M. Franzini
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| |
Collapse
|
23
|
Walton JC. Dissociations of free radicals to generate protons, electrophiles or nucleophiles: role in DNA strand breaks. Chem Soc Rev 2021; 50:7496-7512. [PMID: 34019058 DOI: 10.1039/d1cs00193k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The concept behind the research described in this article was that of marrying the 'soft' methods of radical generation with the effectiveness and flexibility of nucleophile/electrophile synthetic procedures. Classic studies with pulse radiolysis and laser flash photolysis had shown that free radicals could be more acidic than their closed shell counterparts. QM computations harmonised with this and helped to define which radical centres and which structural types were most effective. Radicals based on the sulfonic acid moiety and on the Meldrum's acid moiety (2,2-dimethyl-1,3-dioxane-4,6-dione) were found to be extreme examples in the superacid class. The ethyne unit could be used as a very effective spacer between the radical centre and the site of proton donation. The key factor in promoting acidity was understood to be the thermodynamic stabilisation of the conjugate anion-radicals released on deprotonation. Solvation played a key part in promoting this and theoretical microhydration studies provided notable support. A corollary was that heterolytic dissociations of free radicals to yield either electrophiles or nucleophiles were also enhanced relative to non-radical models. The most effective radical types for spontaneous releases of both these types of reagents were identified. Ethyne units were again effective as spacers. The enhancement of release of phosphate anions by adjacent radical centres was an important special case. Reactive oxygen species and also diradicals from endiyne antibiotics generate C4'-deoxyribose radicals from nucleotides. Radicals of these types spontaneously release phosphate and triphosphate and this is a contributor to DNA and RNA strand breaks.
Collapse
Affiliation(s)
- John C Walton
- EaStCHEM School of Chemistry, University of St. Andrews, St. Andrews, Fife KY16 9ST, UK.
| |
Collapse
|
24
|
Jung ST, Nickisch R, Reinsperger T, Luy B, Podlech J. Stereoelectronic effects: Perlin effects in cyclohexane‐derived compounds. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Sebastian T. Jung
- Institute for Organic Chemistry Karlsruher Institute of Technology (KIT) Karlsruhe Germany
| | - Roman Nickisch
- Institute for Organic Chemistry Karlsruher Institute of Technology (KIT) Karlsruhe Germany
| | - Tony Reinsperger
- Institute for Organic Chemistry Karlsruher Institute of Technology (KIT) Karlsruhe Germany
- Institute for Biological Interfaces 4—Magnetic Resonance Karlsruher Institute of Technology (KIT) Eggenstein‐Leopoldshafen Germany
| | - Burkhard Luy
- Institute for Organic Chemistry Karlsruher Institute of Technology (KIT) Karlsruhe Germany
- Institute for Biological Interfaces 4—Magnetic Resonance Karlsruher Institute of Technology (KIT) Eggenstein‐Leopoldshafen Germany
| | - Joachim Podlech
- Institute for Organic Chemistry Karlsruher Institute of Technology (KIT) Karlsruhe Germany
| |
Collapse
|
25
|
Voronova ED, Golub IE, Pavlov A, Belkova NV, Filippov OA, Epstein LM, Shubina ES. Dichotomous Si-H Bond Activation by Alkoxide and Alcohol in Base-Catalyzed Dehydrocoupling of Silanes. Inorg Chem 2020; 59:12240-12251. [PMID: 32805120 DOI: 10.1021/acs.inorgchem.0c01293] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The activation of silanes in dehydrogenative coupling with alcohols under general base catalysis was studied experimentally (using multinuclear NMR, IR, and UV-visible spectroscopies) and computationally (at DFT M06/6-311++G(d,p) theory level) on the example of Ph4-nSiHn (n = 1-3) interaction with (CF3)2CHOH in the presence of Et3N. The effect of the phenyl groups' number and H- substitution by the electron-withdrawing (CF3)2CHO- group on Si-H bond hydricity (quantified as hydride-donating ability, HDA) and Lewis acidity of silicon atom (characterized by maxima of molecular electrostatic potential) was accessed. Our results show the coordination of Lewis base (Y = Me3N, ROH, OR-) leads to the increased hydricity of pentacoordinate hypervalent Ph4-nSi(Y)Hn complexes and a decrease of the reaction barrier for H2 release. The formation of tertiary complexes [Ph4-nSi(Y)Hn]···HOR is a critical prerequisite for the dehydrocoupling with alkoxides being ideal activators. The latter can be external or internal, generated by in situ HOR deprotonation. The mutual effect of tetrel interaction and dihydrogen bonding in tertiary complexes (RO-)Ph4-nSiHn···HOR leads to dichotomous activation of Si-H bond promoting the proton-hydride transfer and H2 release.
Collapse
Affiliation(s)
- Evgenia D Voronova
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28 Vavilova St., 119991 Moscow, Russia
| | - Igor E Golub
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28 Vavilova St., 119991 Moscow, Russia
| | - Alexander Pavlov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28 Vavilova St., 119991 Moscow, Russia
| | - Natalia V Belkova
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28 Vavilova St., 119991 Moscow, Russia
| | - Oleg A Filippov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28 Vavilova St., 119991 Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklay Str., Moscow 117997, Russia
| | - Lina M Epstein
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28 Vavilova St., 119991 Moscow, Russia
| | - Elena S Shubina
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28 Vavilova St., 119991 Moscow, Russia
| |
Collapse
|
26
|
Vidhani DV, Gillett JR, Cusido Y, Alabugin IV. [1,5]-Sigmatropic Shifts Regulated by Built-in Frustration. J Phys Chem A 2020; 124:6016-6028. [DOI: 10.1021/acs.jpca.0c03933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Dinesh V. Vidhani
- Department of Math & Natural Science, Miami Dade College, Miami, Florida, United States
| | - Jared R. Gillett
- Department of Chemistry & Biochemistry, University of Wisconsin, La Crosse, Wisconsin, United States
| | - Yanet Cusido
- Department of Math & Natural Science, Miami Dade College, Miami, Florida, United States
| | - Igor V. Alabugin
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida, United States
| |
Collapse
|
27
|
|
28
|
Xu LT, Dunning TH. Orbital Hybridization in Modern Valence Bond Wave Functions: Methane, Ethylene, and Acetylene. J Phys Chem A 2019; 124:204-214. [PMID: 31825639 DOI: 10.1021/acs.jpca.9b11054] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The concept of hybrid orbitals is one of the key theoretical concepts used by chemists to explain the structures and other properties of molecules. Recent work found that the hybrid orbitals from modern ab initio valence bond wave functions differ significantly from traditional hybrid orbitals. We report a detailed analysis of the orbitals of methane, ethylene, and acetylene from spin-coupled generalized valence bond (SCGVB) wave functions, a variationally optimized valence bond wave function that places no constraints on the orbitals and spin function. The carbon-centered orbitals in the SCGVB wave functions are found to be 2s-2p hybrid orbitals largely localized on the carbon atom and pointed directly at the hydrogen atoms to which they are bonded. However, the SCGVB orbitals for methane, ethylene, and acetylene differ markedly from the sp3, sp2, and sp hybrid orbitals traditionally associated with these molecules. It is now clear that the orbitals in modern valence bond wave functions do not follow the hybridization rules of traditional valence bond theory. These findings imply that, in modern valence bond theories, other factors are responsible for the structures and properties of molecules that are traditionally attributed to orbital hybridization.
Collapse
Affiliation(s)
- Lu T Xu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Thom H Dunning
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| |
Collapse
|
29
|
Champion C, Barigye SJ, Wei W, Liu Z, Labute P, Moitessier N. Atom Type Independent Modeling of the Conformational Energy of Benzylic, Allylic, and Other Bonds Adjacent to Conjugated Systems. J Chem Inf Model 2019; 59:4750-4763. [PMID: 31589815 DOI: 10.1021/acs.jcim.9b00581] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Applications of computational methods to predict binding affinities for protein/drug complexes are routinely used in structure-based drug discovery. Applications of these methods often rely on empirical force fields (FFs) and their associated parameter sets and atom types. However, it is widely accepted that FFs cannot accurately cover the entire chemical space of drug-like molecules, due to the restrictive cost of parametrization and the poor transferability of existing parameters. To address these limitations, initiatives have been carried out to develop more transferable methods, in order to allow for more rigorous descriptions of any drug-like molecule. We have previously reported H-TEQ, a method which does not rely on atom types and incorporates well established chemical principles to assign parameters to organic molecules. The previous implementation of H-TEQ (a torsional barrier prediction method) only covered saturated and lone pair containing molecules; here, we report our efforts to incorporate conjugated systems into our model. The next step was the evaluation of the introduction of unsaturations. The developed model (H-TEQ3.0) has been validated on a wide variety of molecules containing heteroaromatic groups, alkyls, and fused ring systems. Our method performs on par with one of the most commonly used FFs (GAFF2), without relying on atom types or any prior parametrization.
Collapse
Affiliation(s)
- Candide Champion
- Department of Chemistry , McGill University , 801 Sherbrooke Street W. , Montréal , QC , Canada H3A 0B8
| | - Stephen J Barigye
- Department of Chemistry , McGill University , 801 Sherbrooke Street W. , Montréal , QC , Canada H3A 0B8
| | - Wanlei Wei
- Department of Chemistry , McGill University , 801 Sherbrooke Street W. , Montréal , QC , Canada H3A 0B8
| | - Zhaomin Liu
- Department of Chemistry , McGill University , 801 Sherbrooke Street W. , Montréal , QC , Canada H3A 0B8
| | - Paul Labute
- Chemical Computing Group Inc. , 1010 Sherbrooke Street W. , Montréal , QC , Canada H3A 2R7
| | - Nicolas Moitessier
- Department of Chemistry , McGill University , 801 Sherbrooke Street W. , Montréal , QC , Canada H3A 0B8
| |
Collapse
|
30
|
Marín M, Moreno JJ, Alcaide MM, Álvarez E, López-Serrano J, Campos J, Nicasio MC, Carmona E. Evaluating stereoelectronic properties of bulky dialkylterphenyl phosphine ligands. J Organomet Chem 2019. [DOI: 10.1016/j.jorganchem.2019.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
31
|
Jovanovic M, Michl J. Effect of Conformation on Electron Localization and Delocalization in Infinite Helical Chains [X(CH 3) 2] ∞ (X = Si, Ge, Sn, and Pb). J Am Chem Soc 2019; 141:13101-13113. [PMID: 31306578 DOI: 10.1021/jacs.9b04780] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An intuitive explanation of the effects of conformation (backbone dihedral angle) on electron delocalization in infinite saturated regular helices [(CH3)2]∞Si, [(CH3)2Ge]∞, [(CH3)2Sn]∞, and [(CH3)2Pb]∞ is offered in terms of the simple Ladder C model and confirmed by density functional theory calculations. The effective hole mass, which ranges from near zero to infinity as a function of conformation, is used as a measure of the degree of delocalization and relates to the effects of chain length extension in finite systems. The position of the Fermi level in reciprocal space has a simple counterpart in systems of finite length and is used to characterize the dominant mechanism, σ conjugation (geminal interactions) or σ hyperconjugation (vicinal interactions, through-bond coupling). Constructive or destructive interference of the two mechanisms produces three different delocalization regimes as a function of the backbone dihedral angle and analogy is drawn to polycyclic π-electron systems consisting of fused Hückel or Möbius four-membered rings.
Collapse
Affiliation(s)
- Milena Jovanovic
- Department of Chemistry , University of Colorado , Boulder , Colorado 80309-0215 , United States.,Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 1 , 16610 Prague 6 , Czech Republic
| | - Josef Michl
- Department of Chemistry , University of Colorado , Boulder , Colorado 80309-0215 , United States.,Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 1 , 16610 Prague 6 , Czech Republic
| |
Collapse
|
32
|
Kasznel AJ, Harris T, Porter NJ, Zhang Y, Chenoweth DM. Aza-proline effectively mimics l-proline stereochemistry in triple helical collagen. Chem Sci 2019; 10:6979-6983. [PMID: 31588264 PMCID: PMC6761869 DOI: 10.1039/c9sc02211b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/19/2019] [Indexed: 11/22/2022] Open
Abstract
Chenoweth and co-workers provide an atomic resolution crystal structure and computational analysis illustrating that aza-proline mimics l-proline stereochemistry in collagen.
The prevalence of l-amino acids in biomolecules has been shown to have teleological importance in biomolecular structure and self-assembly. Recently, biophysical studies have demonstrated that natural l-amino acids can be replaced with non-natural achiral aza-amino acids in folded protein structures such as triple helical collagen. However, the structural consequences of achiral aza-amino acid incorporation has not been elucidated in the context of any relevant folded biomolecule. Herein, we use X-ray crystallography to provide the first atomic resolution crystal structure of an achiral aza-amino acid residue embedded within a folded protein structure, definitively illustrating that achiral aza-proline has the capacity to effectively mimic the stereochemistry of natural amino acids within the context of triple helical collagen. We further corroborate this finding with density functional theory computational analysis showing that the natural l-amino acid stereochemistry for aza-proline is energetically favored when arranged in the aza-proline-hydroxyproline-glycine motif. In addition to providing fundamental insight into peptide and protein structure, the incorporation of achiral stereochemical mimics such as aza-amino acids could have far reaching impacts in areas ranging from synthetic materials to drug design.
Collapse
Affiliation(s)
- Alexander J Kasznel
- Department of Chemistry , University of Pennsylvania , 231 S. 34th St. , Philadelphia , PA 19104-6323 , USA . .,Department of Bioengineering , University of Pennsylvania , 210 S. 33rd St. , Philadelphia , PA 19104-6323 , USA
| | - Trevor Harris
- Department of Chemistry , University of Pennsylvania , 231 S. 34th St. , Philadelphia , PA 19104-6323 , USA .
| | - Nicholas J Porter
- Department of Chemistry , University of Pennsylvania , 231 S. 34th St. , Philadelphia , PA 19104-6323 , USA .
| | - Yitao Zhang
- Department of Chemistry , University of Pennsylvania , 231 S. 34th St. , Philadelphia , PA 19104-6323 , USA .
| | - David M Chenoweth
- Department of Chemistry , University of Pennsylvania , 231 S. 34th St. , Philadelphia , PA 19104-6323 , USA .
| |
Collapse
|
33
|
On the Origin of Alkali-Catalyzed Aromatization of Phenols. Polymers (Basel) 2019; 11:polym11071119. [PMID: 31269629 PMCID: PMC6680450 DOI: 10.3390/polym11071119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/17/2019] [Accepted: 06/25/2019] [Indexed: 11/24/2022] Open
Abstract
To gain an insight of the chemistry in the alkali-promoted aromatization of oxygen-containing heavily aromatic polymers or biomass; thermal degradations of sodium phenolates with different substituents have been investigated. The -ONa group strongly destabilizes the phenolates. The thermal stability of phenolates is largely in parallel with bond strengths of Ar substituents. De-substituents and the removal of aromatic hydrogens are dominant reactions in the main degradation step. CO is formed only at a very late stage. This degradation pattern is completely different from that of phenol. To account for this distinctive decomposition; a mechanism involving an unprecedented formation of an aromatic carbon radical anion generated from the homolytic cleavage of Ar substituent (or Ar–H) in keto forms has been proposed. The homolytic cleavage of Ar substituent (or Ar–H) is facilitated by the strong electron-donating ability of the oxygen anion. A set of free-radical reactions involved in the alkali-catalyzed aromatization have been established.
Collapse
|
34
|
Kreuzahler M, Haberhauer G. Gold(I)-Catalyzed Chloroalkynylation of 1,1-Disubstituted Alkenes via 1,3-Chlorine Shift: A Combined Experimental and Theoretical Study. J Org Chem 2019; 84:8210-8224. [PMID: 31192596 DOI: 10.1021/acs.joc.9b01371] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Mathis Kreuzahler
- Institut für Organische Chemie, Universität Duisburg-Essen, Universitätsstr. 7, D-45117 Essen, Germany
| | - Gebhard Haberhauer
- Institut für Organische Chemie, Universität Duisburg-Essen, Universitätsstr. 7, D-45117 Essen, Germany
| |
Collapse
|
35
|
Harris T, Alabugin IV. Strain and stereoelectronics in cycloalkyne click chemistry. MENDELEEV COMMUNICATIONS 2019. [DOI: 10.1016/j.mencom.2019.05.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
36
|
dos Passos Gomes G, Wimmer A, Smith JM, König B, Alabugin IV. CO2 or SO2: Should It Stay, or Should It Go? J Org Chem 2019; 84:6232-6243. [DOI: 10.1021/acs.joc.9b00503] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Gabriel dos Passos Gomes
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32309, United States
| | - Alexander Wimmer
- Institut für Organische Chemie, Universität Regensburg, Universitätsstraße 31, Regensburg 93040, Germany
| | - Joel M. Smith
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32309, United States
| | - Burkhard König
- Institut für Organische Chemie, Universität Regensburg, Universitätsstraße 31, Regensburg 93040, Germany
| | - Igor V. Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32309, United States
| |
Collapse
|
37
|
Carvalho LC, Bueno MA, de Oliveira BG. The interplay and strength of the π⋯HF, C⋯HF, F⋯HF and F⋯HC hydrogen bonds upon the formation of multimolecular complexes based on C 2H 2⋯HF and C 2H 4⋯HF small dimers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 213:438-455. [PMID: 30738351 DOI: 10.1016/j.saa.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/20/2018] [Accepted: 01/01/2019] [Indexed: 06/09/2023]
Abstract
The conception of this theoretical research was idealized aiming to unveil the intermolecular structures of complexes formed by acetylene or ethylene and hydrofluoric acid. At light of computational calculations by using the B3LYP/6-311++G(d,p) method, the geometries of the C2H2⋯(HF), C2H2⋯2(HF), C2H2⋯4(HF), C2H4⋯(HF), C2H4⋯2(HF) and C2H4⋯4(HF) hydrogen-bonded complexes were fully optimized. Moreover, the Post-Hartree-Fock calculations MP2/6-311++G(d,p), MP2/aug-cc-pVTZ, MP4(SDQ)/6-311++G(d,p) and CCSD/6-311++G(d,p) also were also used. The infrared spectra were analyzed in order to identify the new vibrational modes and frequencies of the proton donors shifted to red region. Through the modeling of charge-fluxes on the basis of the Quantum Theory of Atoms In Molecules (QTAIM) and, by contradicting the expectation of the hydrofluorination mechanisms of acetylene or ethylene, C⋯HF was recognized as a new type of hydrogen bond instead of the already well known π⋯H. The calculations of the Natural Bonding Orbital (NBO) and Charges derived from the Electrostatic Potential Grid-based (ChElPG) were also applied to interpret the shifting frequencies as well as measuring of the punctual charge-transfer after the formation of the complexes. Finally, the determination of the stabilization energy was carried out through the arguments of the Fock matrix in NBO basis and through the supermolecule approach. Also it is worthwhile to notice that some algebraic formulations were used for determining the electronic cooperative effect (CE).
Collapse
|
38
|
Naturally occurring of α,β-diepoxy-containing compounds: origin, structures, and biological activities. Appl Microbiol Biotechnol 2019; 103:3249-3264. [PMID: 30852659 DOI: 10.1007/s00253-019-09711-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/19/2019] [Accepted: 02/22/2019] [Indexed: 01/12/2023]
Abstract
Diepoxy-containing compounds are widely distributed in nature. These metabolites are found in plants and marine organisms and are also produced by many microorganisms, fungi, or fungal endophytes. Many of these metabolites are antibiotics and exhibit a wide variety of biological activities. More than 80 α,β-diepoxy-containing compounds are presented in this article, which belong to different classes of chemical compounds including lipids, terpenoids, alkaloids, quinones, hydroquinones, and pyrones. The main activities that characterize α,β-diepoxy-containing compounds are antineoplastic with confidence up to 99%, antifungal with confidence up to 94%, antiinflammatory with confidence up to 92%, or antibacterial with confidence up to 78%. In addition, these metabolites can be used as a lipid metabolism regulator with a certainty of up to 81%, antiviral (Arbovirus) activity with a certainty of up to 71%, or antiallergic activity with confidence up to 69%. These data on the biological activity of diepoxy-containing compounds are of considerable interest to pharmacologists, chemists, and medical professionals who are involved in phytomedicine and related areas of science and industry.
Collapse
|
39
|
Nepel A, Viesser RV, Tormena CF. 1 J CH Coupling in Benzaldehyde Derivatives: Ortho Substitution Effect. ACS OMEGA 2019; 4:1494-1503. [PMID: 31459414 PMCID: PMC6648193 DOI: 10.1021/acsomega.8b03035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/08/2019] [Indexed: 05/30/2023]
Abstract
The natural J-coupling (NJC) method is applied to analyze the Fermi contact contribution of the NMR spin-spin coupling constant decomposing this contribution in terms of natural localized molecular orbitals. We investigated the influence of the basis set on the NJC analysis for the formyl group coupling constant (1 J CHf) of benzaldehyde derivatives. NJC and other NBO analyses, like steric and natural Coulombic energy, were chosen to explain the influence of electron-donating and electron-withdrawing groups on 1 J CHf for some substituted benzaldehydes (Me, OH, OMe, F, Cl, Br, I, and NO2). For the ortho derivatives, electronegative substituents near the C-Hf bond increase the 1 J CHf coupling. This effect could be related to an increase in formyl carbon s character and changes in the carbon and hydrogen natural charges. This indicates that the substituents in ortho have a proximity effect on 1 J CHf coupling mainly of electrostatic origin instead of the expected hyperconjugative interactions.
Collapse
|
40
|
Pozharskii AF, Ozeryanskii VA, Filatova EA, Dyablo OV, Pogosova OG, Borodkin GS, Filarowski A, Steglenko DV. Neutral Pyrrole Nitrogen Atom as a π- and Mixed n,π-Donor in Hydrogen Bonding. J Org Chem 2019; 84:726-737. [PMID: 30576143 DOI: 10.1021/acs.joc.8b02562] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
9-Dimethylaminobenzo[ g]indoles 3-6 and 1-dimethylamino-8-(pyrrolyl-1)naphthalene 7 were examined as possible models for establishing the ability of the pyrrole nitrogen atom to participate in [NHN]+ hydrogen bonding as a proton acceptor. Indoles 3-5 (to a lesser extent 6) form rather stable tetrafluoroborates, with the proton mostly located on the NMe2 group but simultaneously engaged in the formation of a charged intramolecular [NHN]+ hydrogen bond (IHB) with the pyrrole N atom. The theoretically estimated energies of IHB in salts 3H+BF4--6H+BF4- vary between 7.0-10.7 and 6.2-7.0 kcal mol-1 in vapor and MeCN, respectively. The pyrrole N atom undergoes a perceptible pyramidalization but still remains involved in the 6π-electron aromatic system, suggesting that the hydrogen bonding in salts 3H+BF4--6H+BF4- represents a previously unknown mixed NH···N(n,π) interaction. Despite the favorable orientation of the N-H bond and the pyrrole ring in salt 7H+BF4-, no signs of NH···N(n) bonding in it were noticed, and the existing interaction was classified as pure NH···N(π). The results obtained may be useful in studies of secondary protein structures, especially those α-helix sections which contain tryptophan residues.
Collapse
Affiliation(s)
- Alexander F Pozharskii
- Department of Organic Chemistry , Southern Federal University , Zorge str. 7 , 344090 Rostov-on-Don , Russian Federation
| | - Valery A Ozeryanskii
- Department of Organic Chemistry , Southern Federal University , Zorge str. 7 , 344090 Rostov-on-Don , Russian Federation
| | - Ekaterina A Filatova
- Department of Organic Chemistry , Southern Federal University , Zorge str. 7 , 344090 Rostov-on-Don , Russian Federation
| | - Olga V Dyablo
- Department of Organic Chemistry , Southern Federal University , Zorge str. 7 , 344090 Rostov-on-Don , Russian Federation
| | - Olga G Pogosova
- Department of Organic Chemistry , Southern Federal University , Zorge str. 7 , 344090 Rostov-on-Don , Russian Federation
| | - Gennady S Borodkin
- Institute of Physical and Organic Chemistry , Southern Federal University , Stachki Avenue 194/2 , 344090 Rostov-on-Don , Russian Federation
| | - Aleksander Filarowski
- Faculty of Chemistry , University of Wroclaw , F. Joliot-Curie 14 , 50-383 Wroclaw , Poland.,Department of Physics , Industrial University of Tyumen , Volodarskogo 38 , 625000 Tyumen , Russian Federation
| | - Dmitriy V Steglenko
- Department of Organic Chemistry , Southern Federal University , Zorge str. 7 , 344090 Rostov-on-Don , Russian Federation.,Institute of Physical and Organic Chemistry , Southern Federal University , Stachki Avenue 194/2 , 344090 Rostov-on-Don , Russian Federation
| |
Collapse
|
41
|
Oxetane-containing metabolites: origin, structures, and biological activities. Appl Microbiol Biotechnol 2019; 103:2449-2467. [PMID: 30610285 DOI: 10.1007/s00253-018-09576-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 12/09/2018] [Accepted: 12/10/2018] [Indexed: 01/21/2023]
Abstract
Cyclobutanes containing one oxygen atom in a molecule are called oxetane-containing compounds (OCC). More than 600 different OCC are found in nature; they are produced by microorganisms, and also found in marine invertebrates and algae. The greatest number of them is found in plants belonging to the genus Taxus. Oxetanes are high-energy oxygen-containing non-aromatic heterocycles that are of great interest as new potential pharmacophores with a significant spectrum of biological activities. The biological activity of OCC that is produced by bacteria and Actinomycetes demonstrates antineoplastic, antiviral (arbovirus), and antifungal activity with confidence an angiogenesis stimulator, respiratory analeptic, and antiallergic activity dominate with confidence from 81 to 99%.
Collapse
|
42
|
Janiszewski A, Fax J, Haberhauer G. Dimerization of substituted 4-aryl-1,3-diacetylenes – quantum chemical calculations and kinetic studies. Org Chem Front 2019. [DOI: 10.1039/c9qo00119k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Thermal dimerization of 4-aryl-1,3-diacetylenes resulting in diradical intermediates were investigated by experimental and quantum chemical studies.
Collapse
Affiliation(s)
| | - Jonas Fax
- Institut für Organische Chemie
- Universität Duisburg-Essen
- D-45117 Essen
- Germany
| | - Gebhard Haberhauer
- Institut für Organische Chemie
- Universität Duisburg-Essen
- D-45117 Essen
- Germany
| |
Collapse
|
43
|
Zenkevich IG, Todua NG, Mikaia AI. Unusual Regularity in GC Retention of Simple Amino Acid Derivatives. CURRENT CHROMATOGRAPHY 2019; 6:10.2174/2213240606666190709100858. [PMID: 31579276 PMCID: PMC6774356 DOI: 10.2174/2213240606666190709100858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/04/2019] [Accepted: 06/27/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Application of simple regularities and general principles along with direct use of reference gas chromatography retention index data for reliable structure determination of compounds can be enhanced by determination of new regularities that are specific to certain structural elements. OBJECTIVE Revelation and interpretation of an anomaly in the elution order of alkyl esters of alkoxycarbonyl derivatives of glycine and alanine on standard and semi-standard non-polar phases. METHOD Preliminary derivatization of amino acids to alkyl esters of N-alkoxycarbonyl analogs and interpretation of their gas chromatographic characteristics. RESULTS Alkyl esters of N-alkoxycarbonyl derivatives of alanine (Alkyl = C2H5, n- and iso-C3H7) elute prior to the same derivatives of glycine, despite the presence of an additional methyl group at C(2) in the molecule. Elution order is reversed for methyl esters of N-methoxycarbonyl derivatives. CONCLUSION It is established that the peculiar behavior of alkyl esters of N-alkoxycarbonyl derivatives of glycine and alanine agrees with the concepts of gas chromatography and the known retention index regularities of organic compounds. A decrease of retention index values is a result of an introduction of an additional methyl group to a carbon atom connected to two polar fragments in a molecule like CH2XY. The dependence of the difference of retention index values for homologs of the types of CH3-CHXY and CH2XY vs. the total mass of fragments (X + Y) is similar to those for other sub-groups of analytes.
Collapse
Affiliation(s)
- Igor G. Zenkevich
- Institute for Chemistry, St. Petersburg State University, Universtitetskii Prospect, 26, St. Petersburg 198504, Russia
- National Institute of Standards & Technology, Gaithersburg, 100 Bureau Drive, 221/A345, Gaithersburg, MD 20899-8362, USA
| | - Nino G. Todua
- National Institute of Standards & Technology, Gaithersburg, 100 Bureau Drive, 221/A345, Gaithersburg, MD 20899-8362, USA
- Strativia, LLC, 1401 Mercantile Ln #501, Largo, MD 20774, USA
| | - Anzor I. Mikaia
- National Institute of Standards & Technology, Gaithersburg, 100 Bureau Drive, 221/A345, Gaithersburg, MD 20899-8362, USA
| |
Collapse
|
44
|
Veenboer RMP, Azofra LM, Gasperini D, Collado A, Cordes DB, Slawin AMZ, Cavallo L, Nolan SP. Regression analysis of properties of [Au(IPr)(CHR2)] complexes. Dalton Trans 2019; 48:7693-7703. [DOI: 10.1039/c9dt00841a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New [Au(IPr)(CHR2)] complexes have been synthesised through protonolysis reactions of [Au(IPr)(OH)] with moderately acidic substrates, CH2R2.
Collapse
Affiliation(s)
| | - Luis Miguel Azofra
- CIDIA-FEAM (Unidad Asociada al Consejo Superior de Investigaciones Científicas
- CSIC
- avalada por el Instituto de Ciencia de Materiales de Sevilla
- Universidad de Sevilla)
- Instituto de Estudios Ambientales y Recursos Naturales (i-UNAT)
| | | | - Alba Collado
- Departamento de Química Orgánica and Centro de Innovación en Química Avanzada (ORFEO-CINQA)
- Facultad de Ciencias Químicas
- Universidad Complutense
- Madrid
- Spain
| | - David B. Cordes
- EaStCHEM
- School of Chemistry
- University of St Andrews
- St Andrews
- UK
| | | | - Luigi Cavallo
- KAUST Catalysis Center (KCC)
- King Abdullah University of Science and Technology (KAUST)
- Thuwal 23955-6900
- Saudi Arabia
| | - Steven P. Nolan
- Department Chemistry and Center for Sustainable Chemistry
- Ghent University
- 9000 Ghent
- Belgium
- Department of Chemistry
| |
Collapse
|
45
|
Brüllingen E, Neudörfl JM, Goldfuss B. Ligand's electronegativity controls the sense of enantioselectivity in BIFOP-X palladium-catalyzed allylic alkylations. NEW J CHEM 2019. [DOI: 10.1039/c9nj02798j] [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
Palladium-catalyzed allylic alkylations of Na(CH(CO2Me)2 with 1,3-diphenylallyl acetate, employing BIFOP-X (X = H, D, Cl, CN, N3) ligands, yield the C–C coupling product (up to 91% yield, 70% ee). A NBO effect reveals a change of stereochemistry.
Collapse
Affiliation(s)
- Eric Brüllingen
- Department of Chemistry
- University of Cologne
- Organic Chemistry
- 50939 Cologne
- Germany
| | - Jörg-Martin Neudörfl
- Department of Chemistry
- University of Cologne
- Organic Chemistry
- 50939 Cologne
- Germany
| | - Bernd Goldfuss
- Department of Chemistry
- University of Cologne
- Organic Chemistry
- 50939 Cologne
- Germany
| |
Collapse
|
46
|
Pisarev SA, Shulga DA, Palyulin VA, Zefirov NS. Lone pairs vs. covalent bonds: conformational effects in bicyclo[3.3.1]nonane derivatives. Struct Chem 2018. [DOI: 10.1007/s11224-018-1240-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
47
|
Antonov AS, Pozharskii AF, Tolstoy PM, Filarowski A, Khoroshilova OV. 1,8-Bis(dimethylamino)naphthyl-2-ketimines: Inside vs outside protonation. Beilstein J Org Chem 2018; 14:2940-2948. [PMID: 30546478 PMCID: PMC6278759 DOI: 10.3762/bjoc.14.273] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/15/2018] [Indexed: 11/26/2022] Open
Abstract
The structure and protonation behaviour of four ortho-arylketimines of 1,8-bis(dimethylamonio)naphthalene with a different number of methoxy groups in an aromatic substituent were investigated in solution by NMR (acetone, DMSO, MeCN), in solid state by X-ray analysis and in the gas phase by DFT calculations. Both mono- and diprotonated species were considered. It has been shown that E-isomers of neutral imines can be stabilised by an intramolecular C=N−H···OMe hydrogen bond with a neighbouring methoxy group. Electron-donating OMe groups dramatically increase the basicity of the imino nitrogen, forcing the latter to abstract a proton from the proton sponge moiety in monoprotonated forms. The participation of the out-inverted and protonated 1-NMe2 group in the Me2N−H···NH=C hydrogen bond is experimentally demonstrated. It was shown that the number and position of OMe groups in the aromatic substituents strongly affects the rate of the internal hindered rotation of the NH2+ fragment in dications.
Collapse
Affiliation(s)
- A S Antonov
- Department of Organic Chemistry, Southern Federal University, Zorge str. 7, 344090 Rostov-on-Don, Russian Federation.,Institute of Chemistry, St. Petersburg State University, Universitetskii pr. 26, 198504 St. Petersburg, Russian Federation
| | - A F Pozharskii
- Department of Organic Chemistry, Southern Federal University, Zorge str. 7, 344090 Rostov-on-Don, Russian Federation
| | - P M Tolstoy
- Institute of Chemistry, St. Petersburg State University, Universitetskii pr. 26, 198504 St. Petersburg, Russian Federation
| | - A Filarowski
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland.,Department of Physics, Industrial University of Tyumen, Volodarskogo 38, 625-000 Tyumen, Russian Federation
| | - O V Khoroshilova
- Institute of Chemistry, St. Petersburg State University, Universitetskii pr. 26, 198504 St. Petersburg, Russian Federation
| |
Collapse
|
48
|
Schaub TA, Margraf JT, Zakharov L, Reuter K, Jasti R. Strain‐Promoted Reactivity of Alkyne‐Containing Cycloparaphenylenes. Angew Chem Int Ed Engl 2018; 57:16348-16353. [DOI: 10.1002/anie.201808611] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/27/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Tobias A. Schaub
- Department of Chemistry & Biochemistry and Material Science Institute University of Oregon Eugene OR 97403 USA
| | - Johannes T. Margraf
- Chair of Theoretical Chemistry Technical University of Munich 85747 Garching Germany
| | - Lev Zakharov
- Department of Chemistry & Biochemistry and Material Science Institute University of Oregon Eugene OR 97403 USA
| | - Karsten Reuter
- Chair of Theoretical Chemistry Technical University of Munich 85747 Garching Germany
| | - Ramesh Jasti
- Department of Chemistry & Biochemistry and Material Science Institute University of Oregon Eugene OR 97403 USA
| |
Collapse
|
49
|
Schaub TA, Margraf JT, Zakharov L, Reuter K, Jasti R. Strain‐Promoted Reactivity of Alkyne‐Containing Cycloparaphenylenes. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808611] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Tobias A. Schaub
- Department of Chemistry & Biochemistry and Material Science Institute University of Oregon Eugene OR 97403 USA
| | - Johannes T. Margraf
- Chair of Theoretical Chemistry Technical University of Munich 85747 Garching Germany
| | - Lev Zakharov
- Department of Chemistry & Biochemistry and Material Science Institute University of Oregon Eugene OR 97403 USA
| | - Karsten Reuter
- Chair of Theoretical Chemistry Technical University of Munich 85747 Garching Germany
| | - Ramesh Jasti
- Department of Chemistry & Biochemistry and Material Science Institute University of Oregon Eugene OR 97403 USA
| |
Collapse
|
50
|
Heteroatom Substitution at Amide Nitrogen-Resonance Reduction and HERON Reactions of Anomeric Amides. Molecules 2018; 23:molecules23112834. [PMID: 30384496 PMCID: PMC6278557 DOI: 10.3390/molecules23112834] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 12/25/2022] Open
Abstract
This review describes how resonance in amides is greatly affected upon substitution at nitrogen by two electronegative atoms. Nitrogen becomes strongly pyramidal and resonance stabilisation, evaluated computationally, can be reduced to as little as 50% that of N,N-dimethylacetamide. However, this occurs without significant twisting about the amide bond, which is borne out both experimentally and theoretically. In certain configurations, reduced resonance and pronounced anomeric effects between heteroatom substituents are instrumental in driving the HERON (Heteroatom Rearrangement On Nitrogen) reaction, in which the more electronegative atom migrates from nitrogen to the carbonyl carbon in concert with heterolysis of the amide bond, to generate acyl derivatives and heteroatom-substituted nitrenes. In other cases the anomeric effect facilitates SN1 and SN2 reactivity at the amide nitrogen.
Collapse
|