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Lomas JS. 1H NMR spectra of alcohols and diols in chloroform: DFT/GIAO calculation of chemical shifts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2014; 52:745-754. [PMID: 25199903 DOI: 10.1002/mrc.4130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/10/2014] [Accepted: 07/29/2014] [Indexed: 06/03/2023]
Abstract
Proton nuclear magnetic resonance (NMR) shifts of aliphatic alcohols in chloroform have been computed on the basis of density functional theory, the solvent being included by the integral-equation-formalism polarisable continuum model of Gaussian 09. Relative 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. The 208 computed CH proton NMR shifts for 34 alcohols correlate very well with the experimental values, with a gradient of 1.00 ± 0.01 and intercept close to zero; the overall root mean square difference (RMSD) is 0.08 ppm. Shifts for CH protons of diols in chloroform are well correlated with the theoretical values for (isotropic) benzene, with similar gradient and intercept (1.02 ± 0.01, -0.13 ppm), but the overall RMSD is slightly higher, 0.12 ppm. This approach generally gives slightly better results than the CHARGE model of Abraham et al. The shifts of unsaturated alcohols in benzene have been re-examined with Gaussian 09, but the overall fit for CH protons is not improved, and OH proton shifts are worse. Shifts of vinyl protons in alkenols are systematically overestimated, and the correlation of computed shifts against the experimental data for unsaturated alcohols follows a quadratic equation. Splitting the 20 compounds studied into two sets, and applying empirical scaling based on the quadratic for the first set to the second set, gives an RMSD of 0.10 ppm. A multi-standard approach gives a similar result.
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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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52
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Lomas JS. 1H NMR spectra of butane-1,4-diol and other 1,4-diols: DFT calculation of shifts and coupling constants. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2014; 52:87-97. [PMID: 24519848 DOI: 10.1002/mrc.4039] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 12/03/2013] [Accepted: 12/09/2013] [Indexed: 06/03/2023]
Abstract
The proton nuclear magnetic resonance (NMR) spectra of butane-1,4-diol, pentane-1,4-diol, (S,S)-hexane-2,5-diol, 2,5-dimethylhexane-2,5-diol and cyclohexane-1,4-diols (cis and trans) in benzene and some other solvents have been analysed. The conformer distribution and the NMR shifts of these diols in benzene have been computed on the basis of the density functional theory, the solvent being included by means of the integral-equation-formalism polarizable continuum model 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 three-bond coupling constants for the acyclic diols are calculated from the relative conformer populations, the geometries and generalized Karplus equations developed by Altona's group; these correlate well with the experimental values. The solvent dependence of coupling constants for butane-1,4-diol is attributed to conformational change. Coupling constants for the rigid cyclohexane-1,4-diols do not change with solvent and are readily explained in terms of their 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-diols, 1,3-diols and 1,4-diols are systematically high but correlate very well with the experimental values, with a gradient of 1.07 ± 0.01; those for OH protons correlate less well.
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Affiliation(s)
- John S Lomas
- Université Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086, F-75205, Paris, France
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53
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Rozhenko AB, Schoeller WW, Leszczynski J. On the stability of perfluoroalkyl-substituted singlet carbenes: a coupled-cluster quantum chemical study. J Phys Chem A 2014; 118:1479-88. [PMID: 24471524 DOI: 10.1021/jp408778x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A series of trifluoromethyl-substituted carbenes R-C(:)-CF3 (R = NMe2, OMe, F, PMe2, P(NMe2)2, P(N(Pr-i)2)2, SMe, Cl); (dimethylamino)(perfluoroalkyl)carbenes Me2N-C(:)-R (R = CF3, C2F5, n-C3F7, i-C3F7, and t-C4F9) and symmetrically substituted carbenes R-C(:)-R (R = NMe2, OMe, F, PMe2, SMe, Cl) have been investigated by means of quantum chemistry methods. Different levels of approximation were used, including the CCSD(T) approach also known in quantum chemistry as the "golden standard", in combination with three different basis sets (TZVP, cc-pVDZ, cc-pVTZ). Relative stabilities of carbenes have been estimated using the differences between the singlet and triplet ground state energies (ΔEST) and energies of the hydrogenation reaction for the singlet and triplet ground states of the carbenes. The latter seem to correlate better with stability of carbenes than the ΔEST values. The (13)C NMR chemical shifts of the methylidene carbon indicate the more high-field chemical shift values in the known, isolable carbenes compared to the unstable ones. This is the first report on the expected chemical shifts in the highly unstable singlet carbenes. Using these criteria, some carbene structures from the studied series (as, for instance, Me2N-C(:)-CF3, Me2N-C(:)-C3F7-i) are proposed as good candidates for the experimental preparation.
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Affiliation(s)
- Alexander B Rozhenko
- Institute of Organic Chemistry of NAS of Ukraine , Murmans'ka str. 5, Kyiv 02094, Ukraine
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54
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San Fabián J, García de la Vega JM, Suardíaz R, Fernández-Oliva M, Pérez C, Crespo-Otero R, Contreras RH. Computational NMR coupling constants: shifting and scaling factors for evaluating 1JCH. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:775-787. [PMID: 24123317 DOI: 10.1002/mrc.4014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/28/2013] [Accepted: 09/02/2013] [Indexed: 06/02/2023]
Abstract
Optimized shifting and/or scaling factors for calculating one-bond carbon-hydrogen spin-spin coupling constants have been determined for 35 combinations of representative functionals (PBE, B3LYP, B3P86, B97-2 and M06-L) and basis sets (TZVP, HIII-su3, EPR-III, aug-cc-pVTZ-J, ccJ-pVDZ, ccJ-pVTZ, ccJ-pVQZ, pcJ-2 and pcJ-3) using 68 organic molecular systems with 88 (1)JCH couplings including different types of hybridized carbon atoms. Density functional theory assessment for the determination of (1)JCH coupling constants is examined, comparing the computed and experimental values. The use of shifting constants for obtaining the calculated coupling improves substantially the results, and most models become qualitatively similar. Thus, for the whole set of couplings and for all approaches excluding those using the M06 functional, the root-mean-square deviations lie between 4.7 and 16.4 Hz and are reduced to 4-6.5 Hz when shifting constants are considered. Alternatively, when a specific rovibrational contribution of 5 Hz is subtracted from the experimental values, good results are obtained with PBE, B3P86 and B97-2 functionals in combination with HIII-su3, aug-cc-pVTZ-J and pcJ-2 basis sets.
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Affiliation(s)
- J San Fabián
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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55
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Santos-Carballal D, Suardíaz R, Crespo-Otero R, González L, Pérez CS. Conformational and NMR study of some furan derivatives by DFT methods. J Mol Model 2013; 19:4591-601. [PMID: 23975160 DOI: 10.1007/s00894-013-1964-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 07/25/2013] [Indexed: 11/27/2022]
Abstract
4'-substituted neutral/protonated furfurylidenanilines and trans-styrylfurans are able to exist in two different conformations related to the rotation around the furan ring-bridge double bond. In this work, the equilibrium geometry and the corresponding rotational barrier of the benzene ring for each furan derivative conformation were calculated by DFT methods. The trend and shape of the rotational barrier are rationalized within natural bond orbitals as well as atoms-in-molecules approach. For the corresponding equilibrium geometries, (1)H and (13)C substituent induced shifts (SIS) were calculated and compared with experimental values. Calculated shielding constants are shown to be sensitive to the substituent effect through a linear fit with substituent's Hammett constants. An alternative approach was followed for assessing the effect of substituents over SIS through comparing the differences in isotropic shielding constants with NBO charges as well as with (1)H and (13)C experimental chemical shifts.
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Affiliation(s)
- David Santos-Carballal
- Departamento de Química Física, Facultad de Química, Universidad de La Habana, Ciudad de La Habana, Cuba
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Davis JC, Bühl M, Koch KR. Probing isotope shifts in 103Rh and 195Pt NMR spectra with density functional theory. J Phys Chem A 2013; 117:8054-64. [PMID: 23862753 DOI: 10.1021/jp405453c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Zero-point vibrationally averaged (rg(0)) structures were computed at the PBE0/SDD/6-31G* level for the [Pt(35)Cln(37)Cl5-n(H2(18)O)](-) (n = 0-5), cis-Pt(35)Cln(37)Cl4-n(H2(18)O)(H2(16)O) (n = 0-4), fac-[Pt(35)Cln(37)Cl3-n(H2(18)O)(H2(16)O)2](+) (n = 0-3), [Pt(35)Cln(37)Cl5-n((16/18)OH)](2-) (n = 0-5), cis-[Pt(35)Cln(37)Cl4-n((16/18)OH)2](2-) (n = 0-4), fac-[Pt(35)Cln(37)Cl3-n((16/18)OH)3](2-) (n = 0-3), cis-[Pt(35)Cln(37)Cl2-n((16/18)OH)4](2-) (n = 0-2), [Pt(35)Cln(37)Cl1-n((16/18)OH)5](2-) (n = 0-1), [Rh(35)Cln(37)Cl5-n(H2O)](2-) (n = 0-5), cis-[Rh(35)Cln(37)Cl4-n(H2O)2](-) (n = 0-4), and fac-Rh(35)Cln(37)Cl3-n(H2O)3 (n = 0-3) isotopologues and isotopomers. Magnetic shielding constants, computed at the ZORA-SO/PW91/QZ4P/TZ2P level, were used to evaluate the corresponding (35/37)Cl isotope shifts on the (195)Pt and (103)Rh NMR spectra, which are known experimentally. While the observed effects are reproduced reasonably well computationally in terms of qualitative trends and the overall order of magnitude (ca. 1 ppm), quantitative agreement with experiment is not yet achieved. Only small changes in M-Cl and M-O bonds upon isotopic substitution, on the order of femtometers, are necessary to produce the observed isotope shifts.
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Affiliation(s)
- John C Davis
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, United Kingdom
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57
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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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Ebrahimi H, Hadi J, Al-Ansari H. A new series of Schiff bases derived from sulfa drugs and indole-3-carboxaldehyde: Synthesis, characterization, spectral and DFT computational studies. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.01.063] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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59
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Giese TJ, Chen H, Dissanayake T, Giambaşu GM, Heldenbrand H, Huang M, Kuechler ER, Lee TS, Panteva MT, Radak BK, York DM. A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields. J Chem Theory Comput 2013; 9:1417-1427. [PMID: 23814506 DOI: 10.1021/ct3010134] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We introduce a new hybrid molecular orbital/density-functional modified divide-and-conquer (mDC) approach that allows the linear-scaling calculation of very large quantum systems. The method provides a powerful framework from which linear-scaling force fields for molecular simulations can be developed. The method is variational in the energy, and has simple, analytic gradients and essentially no break-even point with respect to the corresponding full electronic structure calculation. Furthermore, the new approach allows intermolecular forces to be properly balanced such that non-bonded interactions can be treated, in some cases, to much higher accuracy than the full calculation. The approach is illustrated using the second-order self-consistent charge density-functional tight-binding model (DFTB2). Using this model as a base Hamiltonian, the new mDC approach is applied to a series of water systems, where results show that geometries and interaction energies between water molecules are greatly improved relative to full DFTB2. In order to achieve substantial improvement in the accuracy of intermolecular binding energies and hydrogen bonded cluster geometries, it was necessary to extend the DFTB2 model to higher-order atom-centered multipoles for the second-order self-consistent intermolecular electrostatic term. Using generalized, linear-scaling electrostatic methods, timings demonstrate that the method is able to calculate a water system of 3000 atoms in less than half of a second, and systems of up to one million atoms in only a few minutes using a conventional desktop workstation.
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Affiliation(s)
- Timothy J Giese
- BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087 USA
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Vícha J, Patzschke M, Marek R. A relativistic DFT methodology for calculating the structures and NMR chemical shifts of octahedral platinum and iridium complexes. Phys Chem Chem Phys 2013; 15:7740-54. [DOI: 10.1039/c3cp44440f] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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61
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Lomas JS. 1H NMR spectra of ethane-1,2-diol and other vicinal diols in benzene: GIAO/DFT shift calculations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:32-41. [PMID: 23169263 DOI: 10.1002/mrc.3899] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/16/2012] [Accepted: 10/16/2012] [Indexed: 06/01/2023]
Abstract
The proton NMR spectra of several 1,2-diols in benzene have been analysed so as to associate each magnetically nonequivalent proton with its chemical shift. The shifts and coupling constants of the OH and methylene protons of ethane-1,2-diol have been determined in a wide range of solvents. The conformer distribution and the proton NMR shifts of these 1,2-diols in benzene have been computed on the basis of density functional theory. The solvent is included using the integral-equation-formalism polarizable continuum model implemented in Gaussian 09. Relative Gibbs energies for all stable conformers are calculated at the Perdew, Burke and Enzerhof (PBE)0/6-311 + G(d,p) level, and shifts are calculated using the gauge-including atomic orbital method with the PBE0/6-311 + G(d,p) geometry but using the cc-pVTZ basis set. Previous calculations on ethane-1,2-diol and propane-1,2-diol have been corrected and extended. New calculations on tert-butylethane-1,2-diol, phenylethane-1,2-diol, butane-2,3-diols (dl and meso) and cyclohexane-1,2-diols (cis and trans) are presented. Overall, the computed NMR shifts are in good agreement with experimental values for the OH protons but remain systematically high for CH protons. Some results based on the Gaussian 03 solvation model are included for comparison.
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Affiliation(s)
- John S Lomas
- ITODYS, Université Paris Diderot, Sorbonne Paris Cité, UMR 7086, F-75205, Paris, France
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Zhu T, He X, Zhang JZH. Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation. Phys Chem Chem Phys 2012; 14:7837-45. [PMID: 22314755 DOI: 10.1039/c2cp23746f] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Fragment density functional theory (DFT) calculation of NMR chemical shifts for several proteins (Trp-cage, Pin1 WW domain, the third IgG-binding domain of Protein G (GB3) and human ubiquitin) has been carried out. The present study is based on a recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach but the solvent effects are included by using the PB (Poisson-Boltzmann) model. Our calculated chemical shifts of (1)H and (13)C for these four proteins are in excellent agreement with experimentally measured values and represent clear improvement over that from the gas phase calculation. However, although the inclusion of the solvent effect also improves the computed chemical shifts of (15)N, the results do not agree with experimental values as well as (1)H and (13)C. Our study also demonstrates that AF-QM/MM calculated results accurately reproduce the separation of α-helical and β-sheet chemical shifts for (13)C(α) atoms in proteins, and using the (1)H chemical shift to discriminate the native structure of proteins from decoys is quite remarkable.
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Affiliation(s)
- Tong Zhu
- State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, China 200062
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Mazzanti A, Casarini D. Recent trends in conformational analysis. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.96] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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