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Kwon J, Reeves HL, Wang LP, Freedberg DI. Revealing elusive conformations of sucrose from hydrogen bond J-coupling in H 2O: A combined NMR and quantum mechanics study. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:742-753. [PMID: 38981694 DOI: 10.1002/mrc.5473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/11/2024] [Accepted: 06/18/2024] [Indexed: 07/11/2024]
Abstract
Hydrogen bonding is a crucial feature of biomolecules, but its characterization in glycans dissolved in aqueous solutions is challenging due to rapid hydrogen exchange between hydroxyl groups and H2O. In principle, the scalar (J) coupling constant can reveal the relative orientation of the atoms in the molecule. In contrast to J-coupling through H-bonds reported in proteins and nucleic acids, research on J-coupling through H-bonds in glycans dissolved in water is lacking. Here, we use sucrose as a model system for H-bonding studies; its structure, which consists of glucose (Glc) and fructose (Frc), is well-studied, and it is readily available. We apply the in-phase, antiphase-HSQC-TOCSY and quantify previously unreported through H-bond J-values for Frc-OH1-Glc-OH2 in H2O. While earlier reports of Brown and Levy indicate this H-bond as having only a single direction, our reported findings indicate the potential presence of two involving these same atoms, namely, G2OH ➔ F1O and F1OH ➔ G2O (where F and G stand for Frc and Glc, respectively). The calculated density functional theory J-values for the G2OH ➔ F1O agree with the experimental values. Additionally, we detected four other possible H-bonds in sucrose, which require different phi, psi (ϕ, ψ) torsion angles. The ϕ, ψ values are consistent with previous predictions of du Penhoat et al. and Venable et al. Our results will provide new insights into the molecular structure of sucrose and its interactions with proteins.
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Affiliation(s)
- Jeahoo Kwon
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Hannah L Reeves
- Department of Chemistry, University of California at Davis, Davis, California, USA
| | - Lee-Ping Wang
- Department of Chemistry, University of California at Davis, Davis, California, USA
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
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2
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Chaloupecká E, Kurfiřt M, Červenková Šťastná L, Karban J, Dračínský M. Exploring long-range fluorine-carbon J-coupling for conformational analysis of deoxyfluorinated disaccharides: A combined computational and NMR study. Bioorg Chem 2024; 147:107388. [PMID: 38678775 DOI: 10.1016/j.bioorg.2024.107388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
In this study, we investigated the potential of long-range fluorine-carbon J-coupling for determining the structures of deoxyfluorinated disaccharides. Three disaccharides, previously synthesized as potential galectin inhibitors, exhibited through-space fluorine-carbon J-couplings. In our independent conformational analysis of these disaccharide derivatives, we employed a combination of density functional theory (DFT) calculations and nuclear magnetic resonance (NMR) experiments. By comparing the calculated nuclear shieldings with the experimental carbon chemical shifts, we were able to identify the most probable conformers for each compound. A model comprising fluoromethane and methane molecules was used to study the relationship between molecular arrangements and intermolecular through-space J-coupling. Our study demonstrates the important effect of internuclear distance and molecular orientation on the magnitude of fluorine-carbon coupling. The experimental values for the fluorine-carbon through-space couplings (TSCs) of the disaccharides corresponded with values calculated for the most probable conformers identified by the conformational analysis. These results unlock the broader application of fluorine-carbon TSCs as powerful tools for conformational analysis of flexible molecules, offering valuable insights for future structural investigations.
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Affiliation(s)
- Ema Chaloupecká
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Martin Kurfiřt
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, Rozvojová 1/135, 165 00 Prague 6, Czech Republic; University of Chemistry and Technology, Technická 3, 166 28 Prague 6, Czech Republic
| | - Lucie Červenková Šťastná
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, Rozvojová 1/135, 165 00 Prague 6, Czech Republic
| | - Jindřich Karban
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, Rozvojová 1/135, 165 00 Prague 6, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic.
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3
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Rusakova IL, Rusakov YY, Krivdin LB. Computational 199 Hg NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:929-953. [PMID: 35737297 DOI: 10.1002/mrc.5296] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Theoretical background and fundamental results dealing with the computation of mercury chemical shifts and spin-spin coupling constants are reviewed with a special emphasis on their stereochemical behavior and applications.
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Affiliation(s)
- Irina L Rusakova
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yuriy Yu Rusakov
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Leonid B Krivdin
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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4
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Quantum Chemical Approaches to the Calculation of NMR Parameters: From Fundamentals to Recent Advances. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8050050] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Quantum chemical methods for the calculation of indirect NMR spin–spin coupling constants and chemical shifts are always in progress. They never stay the same due to permanently developing computational facilities, which open new perspectives and create new challenges every now and then. This review starts from the fundamentals of the nonrelativistic and relativistic theory of nuclear magnetic resonance parameters, and gradually moves towards the discussion of the most popular common and newly developed methodologies for quantum chemical modeling of NMR spectra.
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5
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Saeed A, Shabir G, Channar PA, Flörke U, Hökelek T, Erben MF. COMPUTATIONAL INVESTIGATIONS, HIRSHFELD SURFACE ANALYSIS, INTERACTION ENERGY CALCULATIONS, AND ENERGY FRAMEWORK CRYSTAL STRUCTURE OF METHYL 2-AMINO-5-HYDROXYBENZOATE. J STRUCT CHEM+ 2021. [DOI: 10.1134/s0022476621110111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Predicting scalar coupling constants by graph angle-attention neural network. Sci Rep 2021; 11:18686. [PMID: 34548513 PMCID: PMC8455698 DOI: 10.1038/s41598-021-97146-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/17/2021] [Indexed: 01/20/2023] Open
Abstract
Scalar coupling constant (SCC), directly measured by nuclear magnetic resonance (NMR) spectroscopy, is a key parameter for molecular structure analysis, and widely used to predict unknown molecular structure. Restricted by the high cost of NMR experiments, it is impossible to measure the SCC of unknown molecules on a large scale. Using density functional theory (DFT) to theoretically calculate the SCC of molecules is incredibly challenging, due to the cost of substantial computational time and space. Graph neural networks (GNN) of artificial intelligence (AI) have great potential in constructing molecul
ar-like topology models, which endows them the ability to rapidly predict SCC through data-driven machine learning methods, and avoiding time-consuming quantum chemical calculations. With a priori knowledge of angles, we propose a graph angle-attention neural network (GAANN) model to predict SCC by means of some easily accessible related information. GAANN, with a multilayer message-passing network and a self-attention mechanism, can accurately simulate the molecular-like topological structure and predict molecular properties. Our simulations show that the prediction accuracy by GAANN, with the log(MAE) = −2.52, is close to that by DFT calculations. Different from conventional AI methods, GAANN combining the AI method with quantum chemistry theory (Karplus equation) has a strong physicochemical interpretability about angles. From an AI perspective, we find that bond angle has the highest correlation with the SCC among all angle features (dihedral angle, bond angle, geometric angles) about multiple coupling types in the small molecule datasets.
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7
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NMR Properties of the Cyanide Anion, a Quasisymmetric Two-Faced Hydrogen Bonding Acceptor. Symmetry (Basel) 2021. [DOI: 10.3390/sym13071298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The isotopically enriched cyanide anion, (13C≡15N)−, has a great potential as the NMR probe of non-covalent interactions. However, hydrogen cyanide is highly toxic and can decompose explosively. It is therefore desirable to be able to theoretically estimate any valuable results of certain experiments in advance in order to carry out experimental studies only for the most suitable molecular systems. We report the effect of hydrogen bonding on NMR properties of 15N≡13CH···X and 13C≡15NH···X hydrogen bonding complexes in solution, where X = 19F, 15N, and O=31P, calculated at the ωB97XD/def2tzvp and the polarizable continuum model (PCM) approximations. In many cases, the isotropic 13C and 15N chemical shieldings of the cyanide anion are not the most informative NMR properties of such complexes. Instead, the anisotropy of these chemical shieldings and the values of scalar coupling constants, including those across hydrogen bonds, can be used to characterize the geometry of such complexes in solids and solutions. 1J(15N13C) strongly correlates with the length of the N≡C bond.
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8
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Actual Symmetry of Symmetric Molecular Adducts in the Gas Phase, Solution and in the Solid State. Symmetry (Basel) 2021. [DOI: 10.3390/sym13050756] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
This review discusses molecular adducts, whose composition allows a symmetric structure. Such adducts are popular model systems, as they are useful for analyzing the effect of structure on the property selected for study since they allow one to reduce the number of parameters. The main objectives of this discussion are to evaluate the influence of the surroundings on the symmetry of these adducts, steric hindrances within the adducts, competition between different noncovalent interactions responsible for stabilizing the adducts, and experimental methods that can be used to study the symmetry at different time scales. This review considers the following central binding units: hydrogen (proton), halogen (anion), metal (cation), water (hydrogen peroxide).
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9
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Navarro-Vázquez A. How large a 3 J HCCH coupling can be? Prediction of giant vicinal couplings in quinonoid systems. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:763-768. [PMID: 32384586 DOI: 10.1002/mrc.5037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
Second-order polarization propagator approximation (SOPPA) and density functional theory (DFT) B3LYP computations revealed the presence of giant 3 JHCCH couplings, up to more than 60 Hz, in conjugated quinonoid systems, very far above the typical limit of ~15 Hz. Strong hyperconjugative interactions of the C-H σ orbitals with the quinonoid 8-e- π system, which allows effective propagation of the spin polarization, seem to be responsible for those extraordinarily large couplings. Computation on several model systems showed the additive nature of the contributions from the available coupling paths to the total coupling.
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Affiliation(s)
- Armando Navarro-Vázquez
- Department of Fundamental Chemistry, CCEN, Federal University of Pernambuco, Recife, Pernambuco, Brazil
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10
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Mobley TA. Relativistic DFT Calculations of 1JWH and 1JWC Provide Detailed Structural Insight of Cyclopentadienyl Binding in Cp 2WH 2. J Phys Chem A 2020; 124:966-975. [PMID: 31922415 DOI: 10.1021/acs.jpca.9b11540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Experimental measurements of the one-bond scalar coupling of Cp2WH2 in tetrahydrofuran (1JWH = 73.4 Hz and 1JWC = 4.8 Hz) are compared to density functional theory calculations of the same based upon geometries minimized utilizing a variety of approximate functionals typically utilized to calculate organometallic geometries. One difference between the various functionals is the Cp-W distance, and dCpW is linearly correlated to the calculated values for both 1JWH and 1JWC. Differences in the structures of the Cp2WH2 reported in the literature are compared to the calculated geometries, utilizing calculated values of 1JWH to provide insight into the differences. The distance between the tungsten and attached hydride as well as the angle of the cyclopentadienyl plane with respect to the tungsten cyclopentadienyl centroid vector also have a strong effect on 1JWH. A natural bond orbital (NBO) analysis of the orbital origins of 1JWH indicates that the W-H σ-bonding orbital is the primary contributor to the coupling constant.
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Affiliation(s)
- T Andrew Mobley
- Grinnell College , 1116 8th Avenue , Grinnell , Iowa 50112 , United States
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11
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Koch A, Stamboliyska B, Mikhova B, Breznica-Selmani P, Mladenovska K, Popovski E. Calculations of 13 C NMR chemical shifts and F-C coupling constants of ciprofloxacin. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:S75-S84. [PMID: 30605227 DOI: 10.1002/mrc.4827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 06/09/2023]
Abstract
Ciprofloxacin is a widely used fluoroquinolone antibiotic. In this work, a comprehensive evaluation of MP2 and DFT with different functionals and basis sets was carried out to select the most suitable level of theory for the study of the NMR properties of ciprofloxacin. Their relative predictive capabilities were evaluated comparing the theoretically predicted and experimental spectral data. Our computational results indicated that in contrast to the solid state, the molecule of ciprofloxacin does not exist as a zwitterion in gaseous state. The results of the calculations of the chemical shifts most close to the experimental were obtained with B3LYP/aug-cc-pVDZ. The F-C coupling constants were calculated systematically with different DFT methods and several basis sets. In general, the calculations of the coupling constants with the BHandH computational method including the applied in this work 6-311++G**, EPRII, and EPRIII basis sets showed a good reproducibility of the experimental values of the coupling constants.
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Affiliation(s)
- Andreas Koch
- Department of Chemistry, University of Potsdam, Potsdam, Germany
| | - Bistra Stamboliyska
- Institute of Organic Chemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Bozhana Mikhova
- Institute of Organic Chemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | - Kristina Mladenovska
- Faculty of Pharmacy, University "Ss Cyril and Methodius", Skopje, Republic of Macedonia
| | - Emil Popovski
- Institute of Chemistry, Faculty of Natural Sciences and Mathematics, University "Ss. Cyril and Methodius", Skopje, Republic of Macedonia
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12
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Dračínský M, Buchta M, Buděšínský M, Vacek-Chocholoušová J, Stará IG, Starý I, Malkina OL. Dihydrogen contacts observed by through-space indirect NMR coupling. Chem Sci 2018; 9:7437-7446. [PMID: 30319744 PMCID: PMC6180313 DOI: 10.1039/c8sc02859a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 08/11/2018] [Indexed: 11/21/2022] Open
Abstract
"Through-space" indirect spin-spin couplings between hydrogen atoms formally separated by up to 18 covalent bonds have been detected by NMR experiments in model helical molecules. It is demonstrated that this coupling can provide crucial structural information on the molecular conformation in solution. The coupling pathways have been visualised and analysed by computational methods. The conformational dependence of the coupling is explained in terms of orbital interactions.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Michal Buchta
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Jana Vacek-Chocholoušová
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Irena G Stará
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Ivo Starý
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Olga L Malkina
- Institute of Inorganic Chemistry , Slovak Academy of Sciences , Dúbravská cesta 9 , SK-84536 Bratislava , Slovakia .
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13
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Gooneie A, Schuschnigg S, Holzer C. A Review of Multiscale Computational Methods in Polymeric Materials. Polymers (Basel) 2017; 9:E16. [PMID: 30970697 PMCID: PMC6432151 DOI: 10.3390/polym9010016] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/07/2016] [Accepted: 12/22/2016] [Indexed: 11/17/2022] Open
Abstract
Polymeric materials display distinguished characteristics which stem from the interplay of phenomena at various length and time scales. Further development of polymer systems critically relies on a comprehensive understanding of the fundamentals of their hierarchical structure and behaviors. As such, the inherent multiscale nature of polymer systems is only reflected by a multiscale analysis which accounts for all important mechanisms. Since multiscale modelling is a rapidly growing multidisciplinary field, the emerging possibilities and challenges can be of a truly diverse nature. The present review attempts to provide a rather comprehensive overview of the recent developments in the field of multiscale modelling and simulation of polymeric materials. In order to understand the characteristics of the building blocks of multiscale methods, first a brief review of some significant computational methods at individual length and time scales is provided. These methods cover quantum mechanical scale, atomistic domain (Monte Carlo and molecular dynamics), mesoscopic scale (Brownian dynamics, dissipative particle dynamics, and lattice Boltzmann method), and finally macroscopic realm (finite element and volume methods). Afterwards, different prescriptions to envelope these methods in a multiscale strategy are discussed in details. Sequential, concurrent, and adaptive resolution schemes are presented along with the latest updates and ongoing challenges in research. In sequential methods, various systematic coarse-graining and backmapping approaches are addressed. For the concurrent strategy, we aimed to introduce the fundamentals and significant methods including the handshaking concept, energy-based, and force-based coupling approaches. Although such methods are very popular in metals and carbon nanomaterials, their use in polymeric materials is still limited. We have illustrated their applications in polymer science by several examples hoping for raising attention towards the existing possibilities. The relatively new adaptive resolution schemes are then covered including their advantages and shortcomings. Finally, some novel ideas in order to extend the reaches of atomistic techniques are reviewed. We conclude the review by outlining the existing challenges and possibilities for future research.
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Affiliation(s)
- Ali Gooneie
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
| | - Stephan Schuschnigg
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
| | - Clemens Holzer
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
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14
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Sosnovskikh VY, Safrygin AV, Irgashev RA, Ezhikova MA, Kodess MI. Synthesis of 4-arylamino-3-(trifluoromethyl)pyridazines and pyridazino[3,4-b]quinoxalines (as by-products) from 3-aroylmethyl-2-(trifluoromethyl)quinoxalines and hydrazine hydrate. RSC Adv 2016. [DOI: 10.1039/c5ra27032d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A number of 4-arylamino-3-(trifluoromethyl)pyridazines were obtained in good yields via the novel reaction of 3-aroylmethyl-2-(trifluoromethyl)quinoxalines with an excess of hydrazine hydrate in refluxing n-butanol with or without acetic acid.
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Affiliation(s)
| | - Alexander V. Safrygin
- Institute of Natural Sciences
- Ural Federal University
- 620000 Ekaterinburg
- Russian Federation
| | - Roman A. Irgashev
- Institute of Natural Sciences
- Ural Federal University
- 620000 Ekaterinburg
- Russian Federation
- Institute of Organic Synthesis
| | - Marina A. Ezhikova
- Institute of Organic Synthesis
- Ural Branch of the Russian Academy of Sciences
- 620990 Ekaterinburg
- Russian Federation
| | - Mikhail I. Kodess
- Institute of Natural Sciences
- Ural Federal University
- 620000 Ekaterinburg
- Russian Federation
- Institute of Organic Synthesis
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16
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Bieler NS, Hünenberger PH. On the ambiguity of conformational states: A B&S-LEUS simulation study of the helical conformations of decaalanine in water. J Chem Phys 2015; 142:165102. [DOI: 10.1063/1.4918548] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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17
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Ghosh A, Chaudhuri P. NMR spin–spin coupling constants in microhydrated ortho-aminobenzoic acid. Mol Phys 2015. [DOI: 10.1080/00268976.2014.955065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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Pérez-Torralba M, Claramunt RM, Angeles García M, López C, Torralba MC, Rosario Torres M, Alkorta I, Elguero J. Structure of 1,5-benzodiazepinones in the solid state and in solution: Effect of the fluorination in the six-membered ring. Beilstein J Org Chem 2013; 9:2156-67. [PMID: 24204428 PMCID: PMC3817505 DOI: 10.3762/bjoc.9.253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 09/24/2013] [Indexed: 12/22/2022] Open
Abstract
Two novel tetrafluorinated 1,5-benzodiazepinones were synthesized and their X-ray structures determined. 6,7,8,9-Tetrafluoro-4-methyl-1,3-dihydro-2H-1,5-benzodiazepin-2-one crystallizes in the monoclinic P21/c space group and 6,7,8,9-tetrafluoro-1,4-dimethyl-1,3-dihydro-2H-1,5-benzodiazepin-2-one in the triclinic P−1 space group. Density functional theory studies at the B3LYP/6-311++G(d,p) level were carried out on these compounds and on four non-fluorinated derivatives, allowing to calculate geometries, tautomeric energies and ring-inversion barriers, that were compared with the experimental results obtained by static and dynamic NMR in solution and in solid state.
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Affiliation(s)
- Marta Pérez-Torralba
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias, UNED, Paseo Senda del Rey 9, 28040-Madrid, Spain
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da Silva AM, Ghosh A, Chaudhuri P. Effect of Hydrogen Bond Formation on the NMR Properties of Glycine–HCN Complexes. J Phys Chem A 2013; 117:10274-85. [DOI: 10.1021/jp4056818] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arnaldo Machado da Silva
- Departamento
de Física, Universidade Federal do Amazonas, 69077-000 Manaus, AM, Brazil
- Departamento
de Física, Universidade Federal de São Carlos, São Paulo 13565-905, Brazil
| | - Angsula Ghosh
- Departamento
de Física, Universidade Federal do Amazonas, 69077-000 Manaus, AM, Brazil
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20
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NMR chemical shielding and spin–spin coupling constants across hydrogen bonds in uracil–α-hydroxy-N-nitrosamine complexes. Struct Chem 2013. [DOI: 10.1007/s11224-013-0264-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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Lomas JS. 1H NMR spectra of alkane-1,3-diols in benzene: GIAO/DFT shift calculations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:469-481. [PMID: 23784999 DOI: 10.1002/mrc.3973] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 05/07/2013] [Accepted: 05/07/2013] [Indexed: 06/02/2023]
Abstract
The proton nuclear magnetic resonance (NMR) spectra of propane-1,3-diol, 2-methylpropane-1,3-diol, 2,2-dimethylpropane-1,3-diol, butane-1,3-diol, 3-methylbutane-1,3-diol, pentane-2,4-diols (dl and meso), 2-methylpentane-2,4-diol and cyclohexane-1,3-diols (cis and trans) in benzene have been analysed. The conformer distribution and the NMR shifts of these diols have been computed on the basis of density functional theory, the solvent being included by means of the integral equation formalism phase continuum model (IEFPCM) implemented in Gaussian 09. Relative Gibbs energies of all conformers are calculated at the Perdew, Burke and Ernzerhof (PBE)0/6-311 + G(d,p) level, and NMR shifts by the gauge-including atomic orbital method with the PBE0/6-311 + G(d,p) geometry and the cc-pVTZ basis set. Vicinal coupling constants for 1,2- and 1,3-diols are rationalised in terms of relative conformer populations and geometries. The NMR shifts of hydrogen-bonded protons in individual conformers of alkane-1,n-diols show a very rough correlation with the OH⋯OH distances. The computed overall NMR shifts for CH protons in 1,2- and 1,3-diols are systematically high but correlate very well with the experimental values, with a gradient of 1.07 ± 0.01. Some values for nonequivalent methylene protons in 1,3-diols are reversed, calculation giving enhanced values for the proton anti to the COH bonds. Errors in the NMR shifts computed for the OH protons of nonsymmetrical diols appear to be related to relative populations of conformers where one or other of the OH groups is the donor. Some results based on the second-order Møller-Plesset approach, the Becke three-parameter Lee-Yang-Parr method and on the IEFPCM solvation model implemented in Gaussian 03 are included.
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Affiliation(s)
- John S Lomas
- Univ Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086, F-75205, Paris, France
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Rusakov YY, Krivdin LB. Modern quantum chemical methods for calculating spin–spin coupling constants: theoretical basis and structural applications in chemistry. RUSSIAN CHEMICAL REVIEWS 2013. [DOI: 10.1070/rc2013v082n02abeh004350] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Bifulco G, Riccio R, Martin GE, Buevich AV, Williamson RT. Quantum Chemical Calculations of 1JCC Coupling Constants for the Stereochemical Determination of Organic Compounds. Org Lett 2013; 15:654-7. [DOI: 10.1021/ol3034803] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Giuseppe Bifulco
- Dipartimento di Farmacia, Università di Salerno, Via Ponte Don Melillo, 84084 Fisciano (SA), Italy, Merck Research Laboratories Discovery and Preclinical Sciences, Process and Analytical Chemistry − Structure Elucidation Group Summit, New Jersey 07901, Kenilworth, New Jersey 07033, and Rahway, New Jersey 07065, United States
| | - Raffaele Riccio
- Dipartimento di Farmacia, Università di Salerno, Via Ponte Don Melillo, 84084 Fisciano (SA), Italy, Merck Research Laboratories Discovery and Preclinical Sciences, Process and Analytical Chemistry − Structure Elucidation Group Summit, New Jersey 07901, Kenilworth, New Jersey 07033, and Rahway, New Jersey 07065, United States
| | - Gary E. Martin
- Dipartimento di Farmacia, Università di Salerno, Via Ponte Don Melillo, 84084 Fisciano (SA), Italy, Merck Research Laboratories Discovery and Preclinical Sciences, Process and Analytical Chemistry − Structure Elucidation Group Summit, New Jersey 07901, Kenilworth, New Jersey 07033, and Rahway, New Jersey 07065, United States
| | - Alexei V. Buevich
- Dipartimento di Farmacia, Università di Salerno, Via Ponte Don Melillo, 84084 Fisciano (SA), Italy, Merck Research Laboratories Discovery and Preclinical Sciences, Process and Analytical Chemistry − Structure Elucidation Group Summit, New Jersey 07901, Kenilworth, New Jersey 07033, and Rahway, New Jersey 07065, United States
| | - R. Thomas Williamson
- Dipartimento di Farmacia, Università di Salerno, Via Ponte Don Melillo, 84084 Fisciano (SA), Italy, Merck Research Laboratories Discovery and Preclinical Sciences, Process and Analytical Chemistry − Structure Elucidation Group Summit, New Jersey 07901, Kenilworth, New Jersey 07033, and Rahway, New Jersey 07065, United States
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Dračínský M, Jansa P, Bouř P. Computational and Experimental Evidence of Through-Space NMR Spectroscopic J Coupling of Hydrogen Atoms. Chemistry 2011; 18:981-6. [DOI: 10.1002/chem.201102272] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Indexed: 11/06/2022]
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Electron-density descriptors as predictors in quantitative structure--activity/property relationships and drug design. Future Med Chem 2011; 3:969-94. [PMID: 21707400 DOI: 10.4155/fmc.11.65] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The use of electron density-based molecular descriptors in drug research, particularly in quantitative structure--activity relationships/quantitative structure--property relationships studies, is reviewed. The exposition starts by a discussion of molecular similarity and transferability in terms of the underlying electron density, which leads to a qualitative introduction to the quantum theory of atoms in molecules (QTAIM). The starting point of QTAIM is the topological analysis of the molecular electron-density distributions to extract atomic and bond properties that characterize every atom and bond in the molecule. These atomic and bond properties have considerable potential as bases for the construction of robust quantitative structure--activity/property relationships models as shown by selected examples in this review. QTAIM is applicable to the electron density calculated from quantum-chemical calculations and/or that obtained from ultra-high resolution x-ray diffraction experiments followed by nonspherical refinement. Atomic and bond properties are introduced followed by examples of application of each of these two families of descriptors. The review ends with a study whereby the molecular electrostatic potential, uniquely determined by the density, is used in conjunction with atomic properties to elucidate the reasons for the biological similarity of bioisosteres.
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Lorand JP. CH hydrogen bonding: 3. Hammett correlations for phenylacetonitriles and tetrafluorobenzenes with HMPA. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1740] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Wrackmeyer B, Klimkina EV, Milius W, Bauer T, Kempe R. Synthesis and reactivity of 4,5-[1,2-dicarba-closo-dodecaborano(12)]-1,3-diselenacyclopentane: opening of the icosahedron to give a zwitterionic intermediate and conversion into 7,8-dicarba-nido-undecaborate(1-). Chemistry 2011; 17:3238-51. [PMID: 21308806 DOI: 10.1002/chem.201002277] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Indexed: 12/21/2022]
Abstract
The reaction of the 1,2-diselenolato-1,2-dicarba-closo-dodecaborane(12) dianion [1,2-(1,2-C(2)B(10)H(10))Se(2)](2-) with dichloromethane (CH(2)Cl(2) or CD(2)Cl(2)) in the presence of donor solvents gave 4,5-[1,2-dicarba-closo-dodecaborano(12)]-1,3-diselenacyclopentane, the title compound, which was characterized by X-ray structural analysis and NMR spectroscopy ((1)H, (11)B, (13)C, and (77)Se). In the presence of pyridine, opening of the icosahedron took place, and a zwitterionic intermediate was isolated and fully characterized in the solid state by X-ray diffraction and in solution by multinuclear magnetic resonance techniques. Although such types of intermediates, prior to deboronation of the ortho-carborane cage, have been proposed several times, this is first example for which the structure has been confirmed unambiguously. This intermediate possesses a nido structure and contains a 7,8-dicarba-nido-undecaborate(1-) anion and a boronium cation, the latter with two pyridine rings linked to the boron atom, which has been extruded from the cage. It was shown that this process is reversible as long as the deboronation is not complete. The formation of the intermediate is accompanied by deboronation, which leads to the 7,8-dicarba-nido-undecaborate(1-) anion. The latter was prepared independently by conventional routes from the title compound, isolated as crystalline material as the tetrabutyl ammonium salt, and characterized by X-ray structural analysis and multinuclear magnetic resonance spectroscopy ((1)H, (11)B, (13)C, and (77)Se).
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Affiliation(s)
- Bernd Wrackmeyer
- Anorganische Chemie II, Universität Bayreuth, Universitätsstrasse 30, NW I, 95440 Bayreuth, Germany.
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29
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A theoretical study of the stationary structures of the methane surface with special emphasis on NMR properties. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.02.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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Afonin AV, Vashchenko AV. Theoretical study of bifurcated hydrogen bonding effects on the 1J(N,H), 1hJ(N,H), 2hJ(N,N) couplings and 1H, 15N shieldings in model pyrroles. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:309-317. [PMID: 20198609 DOI: 10.1002/mrc.2579] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
According to the density functional theory calculations, the X...H...N (X=N, O) intramolecular bifurcated (three-centered) hydrogen bond with one hydrogen donor and two hydrogen acceptors causes a significant decrease of the (1h)J(N,H) and (2h)J(N,N) coupling constants across the N-H...N hydrogen bond and an increase of the (1)J(N,H) coupling constant across the N-H covalent bond in the 2,5-disubstituted pyrroles. This occurs due to a weakening of the N-H...N hydrogen bridge resulting in a lengthening of the N...H distance and a decrease of the hydrogen bond angle at the bifurcated hydrogen bond formation. The gauge-independent atomic orbital calculations of the shielding constants suggest that a weakening of the N-H...N hydrogen bridge in case of the three-centered hydrogen bond yields a shielding of the bridge proton and deshielding of the acceptor nitrogen atom. The atoms-in-molecules analysis shows that an attenuation of the (1h)J(N,H) and (2h)J(N,N) couplings in the compounds with bifurcated hydrogen bond is connected with a decrease of the electron density rho(H...N) at the hydrogen bond critical point and Laplacian of this electron density nabla(2)rho(H...N). The natural bond orbital analysis suggests that the additional N-H...X interaction partly inhibits the charge transfer from the nitrogen lone pair to the sigma*(N-H) antibonding orbital across hydrogen bond weakening of the (1h)J(N,H) and (2h)J(N,N) trans-hydrogen bond couplings through Fermi-contact mechanism. An increase of the nitrogen s-character percentage of the N-H bond in consequence of the bifurcated hydrogen bonding leads to an increase of the (1)J(N,H) coupling constant across the N-H covalent bond and deshielding of the hydrogen donor nitrogen atom.
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Affiliation(s)
- Andrei V Afonin
- Institute of Chemistry, Siberian Branch of the Russian Academy of Science, Favorski St. 1, 664033 Irkutsk, Russia.
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Palermo G, Riccio R, Bifulco G. Effect of Electronegative Substituents and Angular Dependence on the Heteronuclear Spin−Spin Coupling Constant 3JC−H: An Empirical Prediction Equation Derived by Density Functional Theory Calculations. J Org Chem 2010; 75:1982-91. [DOI: 10.1021/jo902704u] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giulia Palermo
- Dipartimento di Scienze Farmaceutiche, University of Salerno, Via Ponte Don Melillo, 84084 Fisciano, Salerno, Italy
| | - Raffaele Riccio
- Dipartimento di Scienze Farmaceutiche, University of Salerno, Via Ponte Don Melillo, 84084 Fisciano, Salerno, Italy
| | - Giuseppe Bifulco
- Dipartimento di Scienze Farmaceutiche, University of Salerno, Via Ponte Don Melillo, 84084 Fisciano, Salerno, Italy
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Taha HA, Castillo N, Sears DN, Wasylishen RE, Lowary TL, Roy PN. Conformational Analysis of Arabinofuranosides: Prediction of 3JH,H Using MD Simulations with DFT-Derived Spin−Spin Coupling Profiles. J Chem Theory Comput 2009; 6:212-22. [DOI: 10.1021/ct900477x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Hashem A. Taha
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Norberto Castillo
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Devin N. Sears
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Roderick E. Wasylishen
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Todd L. Lowary
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Pierre-Nicholas Roy
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
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Vokáčová Z, Bickelhaupt FM, Šponer J, Sychrovský V. Structural Interpretation of J Coupling Constants in Guanosine and Deoxyguanosine: Modeling the Effects of Sugar Pucker, Backbone Conformation, and Base Pairing. J Phys Chem A 2009; 113:8379-86. [DOI: 10.1021/jp902473v] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Zuzana Vokáčová
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo Square 2, 166 10 Prague 6, Czech Republic, Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - F. Matthias Bickelhaupt
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo Square 2, 166 10 Prague 6, Czech Republic, Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - JiYí Šponer
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo Square 2, 166 10 Prague 6, Czech Republic, Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo Square 2, 166 10 Prague 6, Czech Republic, Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
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Del Bene JE, Alkorta I, Elguero J. A Systematic Comparison of Second-Order Polarization Propagator Approximation and Equation-of-Motion Coupled Cluster Singles and Doubles C−C, C−N, N−N, C−H, and N−H Spin−Spin Coupling Constants. J Phys Chem A 2009; 113:12411-20. [DOI: 10.1021/jp902089g] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Janet E. Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, and Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - Ibon Alkorta
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, and Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - José Elguero
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, and Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
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Alkorta I, Blanco F, Elguero J. A theoretical structural analysis of the factors that affect (1)J(NH), (1h)J(NH) and (2h)J(NN) in N-H...N hydrogen-bonded complexes. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:249-256. [PMID: 19097158 DOI: 10.1002/mrc.2382] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Calculations of (1)J(NH), (1h)J(NH) and (2h)J(NN) spin-spin coupling constants of 27 complexes presenting N-H...N hydrogen bonds have allowed to analyze these through hydrogen-bond coupling as a function of the hybridization of both nitrogen atoms and the charge (+1, 0, - 1) of the complex. The main conclusions are that the hybridization of N atom of the hydrogen bond donor is much more important than that of the hydrogen bond acceptor. Positive and negative charges (cationic and anionic complexes) exert opposite effects while the effect of the transition states 'proton-in-the-middle' is considerable.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain.
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Joyce SA, Yates JR, Pickard CJ, Brown SP. Density Functional Theory Calculations of Hydrogen-Bond-Mediated NMR J Coupling in the Solid State. J Am Chem Soc 2008; 130:12663-70. [DOI: 10.1021/ja800419m] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Siân A. Joyce
- Tyndall National Institute, Lee Maltings, Prospect Row, Cork, Ireland, TCM Group, Cavendish Laboratory, University of Cambridge, 19 J. J. Thomson Avenue, Cambridge CB3 OHE, U.K., School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, U.K., and Department of Physics, University of Warwick, Coventry CV4 7AL, U.K
| | - Jonathan R. Yates
- Tyndall National Institute, Lee Maltings, Prospect Row, Cork, Ireland, TCM Group, Cavendish Laboratory, University of Cambridge, 19 J. J. Thomson Avenue, Cambridge CB3 OHE, U.K., School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, U.K., and Department of Physics, University of Warwick, Coventry CV4 7AL, U.K
| | - Chris J. Pickard
- Tyndall National Institute, Lee Maltings, Prospect Row, Cork, Ireland, TCM Group, Cavendish Laboratory, University of Cambridge, 19 J. J. Thomson Avenue, Cambridge CB3 OHE, U.K., School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, U.K., and Department of Physics, University of Warwick, Coventry CV4 7AL, U.K
| | - Steven P. Brown
- Tyndall National Institute, Lee Maltings, Prospect Row, Cork, Ireland, TCM Group, Cavendish Laboratory, University of Cambridge, 19 J. J. Thomson Avenue, Cambridge CB3 OHE, U.K., School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, U.K., and Department of Physics, University of Warwick, Coventry CV4 7AL, U.K
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Alkorta I, Elguero J, Denisov GS. A review with comprehensive data on experimental indirect scalar NMR spin-spin coupling constants across hydrogen bonds. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:599-624. [PMID: 18357569 DOI: 10.1002/mrc.2209] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Scalar NMR spin-spin coupling constants across hydrogen bonds are fundamental in structural studies and as test grounds for theoretical calculations. Since they are scattered among many articles of different kinds, it seems useful to collect them in the most comprehensive way.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain.
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Giribet CG, Azúa MCRD. CLOPPA-IPPP analysis of cooperative effects in hydrogen-bonded molecular complexes. Application to intermolecular 2hJ(N,C) spin-spin coupling constants in linear (CNH)n complexes. J Phys Chem A 2008; 112:4386-93. [PMID: 18410158 DOI: 10.1021/jp712113y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cooperative effects on NMR indirect nuclear coupling constants are analyzed by means of the IPPP-CLOPPA approach (where CLOPPA is the Contributions from Localized Orbitals within the Polarization Propagator Approach and IPPP is the Inner Projections of the Polarization Propagator). The decomposition of the J coupling allows one to classify these effects as those due to changes in the geometric structure and those that directly involve the transmission mechanisms. This latter contribution admits a further classification, taking into account its electronic origin. As an example, the cooperative effects on intermolecular 2hJ(N,C) couplings of the linear complexes (CNH)n (n = 2, 3, 4) are discussed.
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Affiliation(s)
- Claudia G Giribet
- Department of Physics, Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Ciudad Universitaria, Pab. I, (1428) Buenos Aires, Argentina. giribet@ df.uba.ar
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Del Bene JE, Alkorta I, Elguero J. Spin-spin coupling across intramolecular N-H(+)-N hydrogen bonds in models for proton sponges: an ab initio investigation. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:457-463. [PMID: 18297741 DOI: 10.1002/mrc.2199] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Ab initio calculations have been performed to obtain structures and coupling constants (1)J(N-H), (1h)J(H-N), and (2h)J(N-N) for models of proton sponges with symmetric and asymmetric N-H(+)-N intramolecular hydrogen bonds (IMHBs). For a given model, the asymmetric structure has a lower energy, a longer N-N distance, and a hydrogen bond which has a greater deviation from linearity. The computed values of (2h)J(N-N) for the models are significantly less than predicted values based on the distance dependence of (2h)J(N-N) for complexes with intermolecular N-H(+)-N hydrogen bonds. However, the reduced values of (2h)J(N-N) cannot be attributed solely to the distortion of the hydrogen bond in the models, but also reflect differences in s electron populations at the nitrogens in both the ground state and the excited states which couple to it through the Fermi-contact (FC) operator. Values of (2h)J(N-N) for IMHBs can be related quadratically to the N-N distances in the models, and demonstrate that there is no discrepancy between computed values of (2h)J(N-N) at the short N-N distances found in these systems and experimental data for proton sponges.
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Affiliation(s)
- Janet E Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, USA.
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Alkorta I, Provasi PF, Aucar GA, Elguero J. A computational study of 2J(HH)(gem) indirect spin-spin coupling constants in simple hydrides of the second and third periods. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:356-361. [PMID: 18273860 DOI: 10.1002/mrc.2181] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Several theoretical methods have been used to compute (2)J(HH) in neutral, anionic and cationic HXH hydrides, X being the 14 nuclei from Li to Cl (28 molecules). Since the calculations also provide (1)J(XH) spin-spin coupling constants (SSCC), these have also been analyzed. The best results were obtained using Second-order polarization propagator approximation (SOPPA)/sadJ. The geminal coupling constants appear to be dependent on the electronegativity of the X-atom.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain.
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Vokacova Z, Sponer J, Sponer JE, Sychrovský V. Theoretical study of the scalar coupling constants across the noncovalent contacts in RNA base pairs: the cis- and trans-watson-crick/sugar edge base pair family. J Phys Chem B 2007; 111:10813-24. [PMID: 17713941 DOI: 10.1021/jp072822p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The structure and function of RNA molecules are substantially affected by non-Watson-Crick base pairs actively utilizing the 2'-hydroxyl group of ribose. Here we correlate scalar coupling constants across the noncovalent contacts calculated for the cis- and trans-WC/SE (Watson-Crick/sugar edge) RNA base pairs with the geometry of base to base and sugar to base hydrogen bond(s). 23 RNA base pairs from the 32 investigated were found in RNA crystal structures, and the calculated scalar couplings are therefore experimentally relevant with regard to the binding patterns occurring in this class of RNA base pairs. The intermolecular scalar couplings 1hJ(N,H), 2hJ(N,N), 2hJ(C,H), and 3hJ(C,N) were calculated for the N-H...N and N-H...O=C base to base contacts and various noncovalent links between the sugar hydroxyl and RNA base. Also, the intramolecular 1J(N,H) and 2J(C,H) couplings were calculated for the amino or imino group of RNA base and the ribose 2'-hydroxyl group involved in the noncovalent interactions. The calculated scalar couplings have implications for validation of local geometry, show specificity for the amino and imino groups of RNA base involved in the linkage, and can be used for discrimination between the cis- and trans-WC/SE base pairs. The RNA base pairs within an isosteric subclass of the WC/SE binding patterns can be further sorted according to the scalar couplings calculated across different local noncovalent contacts. The effect of explicit water inserted in the RNA base pairs on the magnitude of the scalar couplings was calculated, and the data for discrimination between the water-inserted and direct RNA base pairs are presented. The calculated NMR data are significant for structural interpretation of the scalar couplings in the noncanonical RNA base pairs.
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Affiliation(s)
- Zuzana Vokacova
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo Square 2, 166 10 Prague 6, Czech Republic
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Del Bene JE, Elguero J. Systematic ab initio study of 15N-15N and 15N-1H spin-spin coupling constants across N-H+-N hydrogen bonds: predicting N-N and N-H coupling constants and relating them to hydrogen bond type. J Phys Chem A 2007; 110:7496-502. [PMID: 16759141 DOI: 10.1021/jp0613642] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A systematic ab initio EOM-CCSD study of 15N-15N and 15N-1H spin-spin coupling constants has been carried out for a series of complexes formed from 11 nitrogen bases with experimentally measured proton affinities. When these complexes are arranged in order of increasing proton affinity of the proton-acceptor base and, for each proton acceptor, increasing order of proton affinity of the protonated N-H donor, trends in distances and signs of coupling constants are evident that are indicative of the nature of the hydrogen bond. All two-bond spin-spin coupling constants (2hJ(N-N)) are positive and decrease as the N-N distance increases. All one-bond N-H coupling constants (1J(N-H)) are negative (1K(N-H) are positive). 1J(N-H) is related to the N-H distance and the hybridization of the donor N atom. One-bond H...N coupling constants (1hJ(H-N)) are positive (1hK(H-N) are negative) for traditional hydrogen bonds, but 1hJ(H-N) becomes negative when the hydrogen bond acquires sufficient proton-shared character. The N-N and H...N distances at which 1hJ(H-N) changes sign are approximately 2.71 and 1.62 A, respectively. Predictions are made of the values of 2hJ(N-N) and 1J(N-H), and the signs of 1hJ(H-N), for those complexes that are too large for EOM-CCSD calculations.
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Affiliation(s)
- Janet E Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, USA.
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Sychrovský V, Sponer J, Trantírek L, Schneider B. Indirect NMR spin-spin coupling constants 3J(P,C) and 2J(P,H) across the P-O...H-C link can be used for structure determination of nucleic acids. J Am Chem Soc 2007; 128:6823-8. [PMID: 16719462 DOI: 10.1021/ja0551180] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Calculated indirect NMR spin-spin coupling constants (3)J(P,C) and (2)J(P,H) were correlated with the local structure of the P-O...H-C linkage between the nucleic acid (NA) backbone phosphate and the H-C group(s) of a nucleic acid base. The calculations were carried out for selected nucleotides from the large ribosomal subunit (Ban et al. Science 2000, 289, 905) with the aim of identifying NMR parameters suitable for detection of certain noncanonical RNA structures. As calculations in the model system, dimethyl-phosphate-guanine, suggest, the calculated indirect spin-spin couplings across the linkage are sensitive to the mutual orientation and distance between the phosphate and nucleic acid base. A short distance between the nucleic acid base and phosphate group and the angles C...P-O and P...C-H smaller than 50 degrees are prerequisites for a measurable spin-spin interaction of either coupling (|J| > 1 Hz). A less favorable arrangement of the P-O...H-C motif, e.g., in nucleotides of the canonical A-RNA, results in an effective dumping of both spin-spin interactions and insignificant values of the NMR coupling constants. The present work indicates that quantum chemical calculations of the indirect spin-spin couplings across the P-O...H-C motif can help detect some rare but important backbone topologies, as seen for example in the reverse kink-turn. Measuring of (3)J(P,C) and (2)J(P,H) couplings can therefore provide critical constraints on the NA base and phosphate geometry and help to determine the structure of NAs.
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Affiliation(s)
- Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2., 166 10 Prague 6, Czech Republic
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Katritzky AR, Akhmedov NG, Doskocz J, Mohapatra PP, Hall CD, Güven A. NMR spectra, GIAO and charge density calculations of five-membered aromatic heterocycles. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45:532-43. [PMID: 17534885 DOI: 10.1002/mrc.1967] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The B3LYP/6-31+G(d) molecular geometry optimized structures of 17 five-membered heterocycles were employed together with the gauge including atomic orbitals (GIAO) density functional theory (DFT) method at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p) and B3LYP/6-311+G(2d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants. The method of geometry optimization for pyrrole (1), N-methylpyrrole (2) and thiophene (7) using the larger 6-311++G(d,p) basis sets at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,p) and B3LYP/cc-pVTZ levels of theory gave little difference between calculated and experimental values of coupling constants. In general, the (1)H and 13C chemical shifts for all compounds are in good agreement with theoretical calculations using the smaller 6-31 basis set. The values of nJHH(n=3, 4, 5) and rmnJ(CH)(n=1, 2, 3, 4) were predicted well using the larger 6-31+G(d,p) and 6-311++G(d,p) basis sets and at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,2p) levels of theory. The computed atomic charges [Mülliken; Natural Bond Orbital Analysis (NBO); Merz-Kollman (MK); CHELP and CHELPG] for the B3LYP/6-311++G(d,p) geometry optimized structures of 1-17 were used to explore correlations with the experimental proton and carbon chemical shifts.
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Affiliation(s)
- Alan R Katritzky
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA.
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Afonin AV, Ushakov IA, Mikhaleva AI, Trofimov BA. Bifurcated hydrogen-bonding effect on the shielding and coupling constants in trifluoroacetyl pyrroles as studied by 1H, 13C and 15N NMR spectroscopy and DFT calculations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45:220-30. [PMID: 17221917 DOI: 10.1002/mrc.1949] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
According to the (1)H, (13)C and (15)N NMR spectroscopic data and DFT calculations, bifurcated N--H...N and N--H...O intramolecular hydrogen bond is shown to be present in 2-trifluoroacetyl-5-(2'-pyridyl)-pyrrole. This bifurcated hydrogen bond causes an increase in the absolute size of the (1)J(N,H) coupling constant by about 6 Hz, and the deshielding of the bridge proton by 2 ppm. DFT calculations show that the influence of the N--H...N and N--H...O intramolecular hydrogen bonds on the (1)J(N,H) coupling and proton shielding is almost additive, although the components of the bifurcated hydrogen bond slightly weaken each other. In 2-trifluoroacetyl-5-(2'-pyridyl)-pyrrole, the coupling constants involving the fluorine and the N--H covalent bond nuclei depend dramatically on the spatial position of the pyridine ring. The pyridine ring rotation operates as a quantum switch controlling the spin information transfer between the (19)F and (15)N nuclei, as well as the proton.
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Affiliation(s)
- Andrei V Afonin
- Institute of Chemistry, Favorsky St. 1, 664033 Irkutsk, Russia.
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San Fabián J, Westra Hoekzema AJA. Vicinal fluorine-fluorine coupling constants: Fourier analysis. J Chem Phys 2007; 121:6268-76. [PMID: 15446920 DOI: 10.1063/1.1785141] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Stereochemical dependences of vicinal fluorine-fluorine nuclear magnetic resonance coupling constants (3JFF) have been studied with the multiconfigurational self-consistent field in the restricted active space approach, with the second-order polarization propagator approximation (SOPPA), and with density functional theory. The SOPPA results show the best overall agreement with experimental couplings. The relationship with the dihedral angle between the coupled fluorines has been studied by Fourier analysis, the result is very different from that of proton-proton couplings. The Fourier coefficients do not resemble those of a typical Karplus equation. The four nonrelativistic contributions to the coupling constants of 1,2-difluoroethane configurations have been studied separately showing that up to six Fourier coefficients are required to reproduce the calculated values satisfactorily. Comparison with Fourier coefficients for matching hydrogen fluoride dimer configurations suggests that the higher order Fourier coefficients (Cn> or =3) originate mainly from through-space Fermi contact interaction. The through-space interaction is the main reason 3JFF do not follow the Karplus equation.
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Affiliation(s)
- J San Fabián
- Facultad de Ciencias C-2, Universidad Autónoma de Madrid, Madrid E-28049, Spain.
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Katritzky AR, Akhmedov NG, Doskocz J, Hall CD, Akhmedova RG, Majumder S. Structural elucidation of nitro-substituted five-membered aromatic heterocycles utilizing GIAO DFT calculations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45:5-23. [PMID: 17042032 DOI: 10.1002/mrc.1894] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The GIAO (Gauge Including Atomic Orbitals) DFT (Density Functional Theory) method is applied at the B3LYP/6-31+G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311++G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311+G (2d,p)//B3LYP/6-31+G(d) and B3LYP/6-311++G(d,p)//B3LYP/6-311++G(d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants for 25 nitro-substituted five-membered heterocycles. Difference (1D NOE) spectra in combination with long-range gHMBC experiments were used as tools for the structural elucidation of nitro-substituted five-membered heterocycles. The assigned NMR data (chemical shifts and coupling constants) for all compounds were found to be in good agreement with theoretical calculations using the GIAO DFT method. The magnitudes of one-bond (1JCH) and long-range (nJCH, n>1) coupling constants were utilized for unambiguous differentiation between regioisomers of nitro-substituted five-membered heterocycles.
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Affiliation(s)
- Alan R Katritzky
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA.
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Hatnean JA, Raturi R, Lefebvre J, Leznoff DB, Lawes G, Johnson SA. Assembly of Triangular Trimetallic Complexes by Triamidophosphine Ligands: Spin-Frustrated Mn2+ Plaquettes and Diamagnetic Mg2+ Analogues with a Combined Through-Space, Through-Bond Pathway for 31P-31P Spin−Spin Coupling. J Am Chem Soc 2006; 128:14992-9. [PMID: 17105311 DOI: 10.1021/ja065597i] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reactions of 2 equiv of the ligand precursor P(CH2NHPh)3 or P[CH2NH-3,5-(CF3)2C6H3]3 with 3 equiv of Mn[N(SiMe3)2]2 provide high-yielding routes to the triangular trinuclear Mn(II) complexes [P(CH2NPh)3]2Mn3(THF)3.1.5THF and [P(CH2N-3,5-(CF3)2C6H3)3]2Mn3(THF)3. The solid-state structures of these paramagnetic complexes have approximate C3 symmetry. The magnetic moments from 300 to 1.8 K could be fit as a magnetic Jahn-Teller distorted isosceles triangle. These complexes exhibit spin frustration and possess an S = 1/2 ground state, as revealed by a plot of magnetization versus field at 1.8 K; at fields above 3.8 T, the occupation of an excited state with S = 3/2 becomes significant. The diamagnetic magnesium analogues were prepared by the reaction of the ligand precursor P(CH2NHPh)3, P[CH2NH-3,5-(CF3)2C6H3]3, or P(CH2NH-3,5-Me2C6H3)3 with nBu2Mg. The solid-state structures of [P(CH2NPh)3]2Mg3(THF)3.1.5THF and [P(CH2N-3,5-(CF3)2C6H3)3]2Mg3(THF)3 were determined. Solution 1H NMR spectroscopy was used to demonstrate that the solid-state structures are maintained in solution. The aryl group of the terminal amido donor exhibits slow rotation on the NMR time scale, and this was found to be an electronic effect. Solution 31P{1H} NMR spectroscopy revealed an unexpected 15 Hz coupling between phosphorus nuclei in these complexes. Calculations on a model complex using density functional theory demonstrates that this coupling occurs via a combined through-space, through-bond pathway.
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Affiliation(s)
- Jillian A Hatnean
- Department of Chemistry & Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4
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49
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Giribet CG, Ruiz de Azúa MC. The Sign and Magnitude of 2hJ(F,F) and 1hJ(F,H) in FH···FH. A CLOPPA Analysis of Their Distance Dependence. J Phys Chem A 2006; 110:11575-83. [PMID: 17020272 DOI: 10.1021/jp060095c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sign change of the intermolecular (2h)J(F,F) coupling in the (HF)2 dimer as a function of the F-F distance is discussed by means of the CLOPPA method. It is found that it is due to the competition of positive and negative contributions involving the interaction of the sigma lone pair of the acceptor nucleus with vacant molecular orbitals localized in the F-H...F moiety and with other molecular orbitals localized in the donor molecule. The origin of the sign of each contribution is fully determined by analyzing the response of the electronic system to the magnetic perturbation at the acceptor F nucleus. (2h)J(F,F) coupling in the FH...F-, which is positive for all F-F distances, is also analyzed in order to look for the differences with the former case.
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Affiliation(s)
- Claudia G Giribet
- Department of Physics, Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Ciudad Universitaria, Pab. I, (1428) Buenos Aires, Argentina.
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Jimeno ML, Alkorta I, Elguero J, Del Bene JE. Computed coupling constants in X(CH3)nH(4-n) moieties where X = 13C and 15N+, and n = 0-4: comparisons with experimental data. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44:698-707. [PMID: 16671054 DOI: 10.1002/mrc.1840] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Seventy-three unique spin-spin coupling constants have been analyzed for the ten species in the two series X(CH3)nH(4-n), where the central atom X is 13C or 15N+. Thirty-seven experimental values have been obtained from the literature, and several new coupling constants have been measured for the methyl-substituted ammonium ions. Both DFT with the B3LYP functional and ab initio EOM-CCSD calculations have been carried out on these same systems. Coupling constants computed by these two methods are in agreement with experimental values. Some problems related to coupling constants for the cationic ammonium systems have been resolved when these were recomputed at EOM-CCSD for complexes in which NH4+ is hydrogen-bonded to H2O molecules.
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Affiliation(s)
- María-Luisa Jimeno
- Centro de Química Orgánica "Manuel Lora-Tamayo", CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
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