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Cortés I, Sarotti AM. E/ Z configurational determination of oximes and related derivatives through quantum mechanics NMR calculations: scope and limitations of the leading probabilistic methods. Org Biomol Chem 2023; 21:2935-2940. [PMID: 36942946 DOI: 10.1039/d3ob00291h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Oximes and related derivatives featuring a CN double bond are important in many areas of chemistry. Different methods for the determination of the E/Z configuration have been developed, each with its own scope and limitations. While some cannot be used when only one isomer is available, others require special NMR experiments. Here, three popular computational methodologies (DP4, DP4+, and ML-J-DP4) have been thoroughly studied using a challenging test set. Although DP4+ provides the best confidence, its computational cost might be high. On the other hand, ML-J-DP4 shows excellent performance in most cases in a fraction of CPU time. A detailed analysis of the structural factors affecting the NMR prediction and sense of the assignment is also provided.
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Affiliation(s)
- Iván Cortés
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina.
| | - Ariel M Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina.
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2
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Krivdin LB. Carbon-carbon spin-spin coupling constants: Practical applications of theoretical calculations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 105:54-99. [PMID: 29548367 DOI: 10.1016/j.pnmrs.2018.03.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 06/08/2023]
Abstract
Practical applications of theoretical calculations of carbon-carbon spin-spin coupling constants in particular classes of organic and bioorganic molecules are reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives as well as on carbohydrates and natural compounds.
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Affiliation(s)
- Leonid B Krivdin
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia.
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Muramatsu W, Tsuji H, Yamamoto H. Catalytic Peptide Synthesis: Amidation of N-Hydroxyimino Esters. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04244] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Wataru Muramatsu
- Molecular Catalyst Research
Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Hiroaki Tsuji
- Molecular Catalyst Research
Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Hisashi Yamamoto
- Molecular Catalyst Research
Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
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Powell J, Valenti D, Bobnar H, Drain E, Elliott B, Frank S, McCullough T, Moore S, Kettring A, Iuliucci R, Harper JK. Evaluating the accuracy of theoretical one-bond 13 C─ 13 C scalar couplings and their ability to predict structure in a natural product. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:979-989. [PMID: 28557141 DOI: 10.1002/mrc.4616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/17/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
This study explores the feasibility of using a combination of experimental and theoretical 1-bond 13 C─13 C scalar couplings (1 JCC ) to establish structure in organic compounds, including unknowns. Historically, n JCC and n JCH studies have emphasized 2 and 3-bond couplings, yet 1 JCC couplings exhibit significantly larger variations. Moreover, recent improvements in experimental measurement and data processing methods have made 1 JCC data more available. Herein, an approach is evaluated in which a collection of theoretical structures is created from a partial nuclear magnetic resonance structural characterization. Computed 1 JCC values are compared to experimental data to identify candidates giving the best agreement. This process requires knowledge of the error in theoretical methods, thus the B3LYP, B3PW91, and PBE0 functionals are evaluated by comparing to 27 experimental values from INADEQUATE. Respective errors of ±1.2, ±3.8, and ±2.3 Hz are observed. An initial test of this methodology involves the natural product 5-methylmellein. In this case, only a single candidate matches experimental data with high statistical confidence. This analysis establishes the intramolecular hydrogen-bonding arrangement, ring heteroatom identity, and conformation at one position. This approach is then extended to hydroheptelidic acid, a natural product not fully characterized in prior studies. The experimental/theoretical approach proposed herein identifies a single best-fit structure from among 26 candidates and establishes, for the first time, 1 configuration and 3 conformations to complete the characterization. These results suggest that accurate and complete structural characterizations of many moderately sized organic structures (<800 Da) may be possible using only 1 JCC data.
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Affiliation(s)
- Jacob Powell
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL, 32816, USA
| | - Domenic Valenti
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL, 32816, USA
| | - Harley Bobnar
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Erika Drain
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Blaine Elliott
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Sydney Frank
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Tyler McCullough
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Sean Moore
- Burnett School of Biomedical Sciences, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Andrew Kettring
- Burnett School of Biomedical Sciences, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Robbie Iuliucci
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - James K Harper
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL, 32816, USA
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Kucuk I, Kaya Y, Kaya AA. Structural, spectroscopic (FT-IR, NMR, UV–visible), nonlinear optical (NLO), cytotoxic and molecular docking studies of 4-nitro-isonitrosoacetophenone (ninapH) by DFT method. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.03.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kaya Y. Quantum Chemical Studies of the Substituent Effect on the Reaction of Carbonyl Oxime with Amine. J Phys Chem A 2016; 120:5736-44. [DOI: 10.1021/acs.jpca.6b05147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yunus Kaya
- Faculty of Natural Sciences, Architecture,
and Engineering, Department of Chemistry, Bursa Technical University, TR-16190 Bursa, Turkey
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Kaya Y, Icsel C, Yilmaz VT, Buyukgungor O. Structural, spectroscopic and quantum chemical studies of acetyl hydrazone oxime and its palladium(II) and platinum(II) complexes. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.04.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kaya Y, Icsel C, Yilmaz VT, Buyukgungor O. Palladium(II) and platinum(II) complexes of a new imineoxime ligand – Structural, spectroscopic and DFT/time-dependent (TD) DFT studies. J Organomet Chem 2014. [DOI: 10.1016/j.jorganchem.2013.12.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Kaya Y, Icsel C, Yilmaz VT, Buyukgungor O. A palladium(II) complex containing both carbonyl and imine oxime ligands: crystal structure, experimental and theoretical UV-vis, IR and NMR studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 108:133-140. [PMID: 23466323 DOI: 10.1016/j.saa.2013.01.054] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/22/2013] [Accepted: 01/23/2013] [Indexed: 06/01/2023]
Abstract
A new palladium(II) complex, [Pd(ppeieo)(inap)]·DMSO (ppeieo=(1E,2E)-phenyl-[(1-phenylethyl)imino]-ethanal oxime and inap=isonitrosoacetophenone) has been synthesized and characterized by elemental analysis, UV-vis, IR, NMR. X-ray diffraction analysis of the DMSO solvate of the complex shows that the palladium(II) ion is coordinated in a distorted square-planar geometry by ppeieo and inap, which is formed during the hydrolysis of ppeieo. DFT (B3LYP/LANL2DZ) calculations on the complex have been carried out to correlate geometry and spectroscopic properties such as electronic, vibrational and NMR chemical shifts. The complete vibrational frequency assignments were made and the calculation results were applied to simulate infrared spectra of the title compound which shows good agreement with observed spectra. The calculated HOMO and LUMO energies show that several transitions including the π→π(*) and charge transfer occur within the molecule. The chemical shifts reasonably correspond to the calculated spectra.
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Affiliation(s)
- Yunus Kaya
- Department of Chemistry, Faculty of Arts and Sciences, Uludag University, 16059 Bursa, Turkey
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Kaya Y, Yilmaz VT, Arslan T, Buyukgungor O. Experimental and theoretical DFT studies of structure, spectroscopic and fluorescence properties of a new imine oxime derivative. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.05.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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