51
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Horbatenko Y, Vyboishchikov SF. Dynamic Behavior of Hydrogen in Transition Metal Bis(silyl) Hydride Complexes. Organometallics 2013. [DOI: 10.1021/om300981y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yevhen Horbatenko
- Institut de Química
Computacional i Catàlisi
and Departament de Química, Campus de Montilivi, Universitat de Girona, 17071, Girona, Spain
| | - Sergei F. Vyboishchikov
- Institut de Química
Computacional i Catàlisi
and Departament de Química, Campus de Montilivi, Universitat de Girona, 17071, Girona, Spain
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52
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Substituent effects on indirect carbon-carbon couplings, J
(CC), in substituted thiophenes, pyrroles, and furans studied by experiment and theory. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.2955] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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53
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García de la Vega J, San Fabián J. Analysis of Contributions to Spin–Spin Coupling Constants by the Natural J-Coupling Method. SCIENCE AND TECHNOLOGY OF ATOMIC, MOLECULAR, CONDENSED MATTER & BIOLOGICAL SYSTEMS 2013. [DOI: 10.1016/b978-0-444-59411-2.00006-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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54
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Hedegård ED, Kongsted J, Sauer SPA. Improving the calculation of Electron Paramagnetic Resonance hyperfine coupling tensors for d-block metals. Phys Chem Chem Phys 2012; 14:10669-76. [PMID: 22785432 DOI: 10.1039/c2cp40969k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Calculation of hyperfine coupling constants (HFCs) of Electron Paramagnetic Resonance from first principles can be a beneficial complement to experimental data in cases where the molecular structure is unknown. We have recently investigated basis set convergence of HFCs in d-block complexes and obtained a set of basis functions for the elements Sc-Zn, which were saturated with respect to both the Fermi contact and spin-dipolar components of the hyperfine coupling tensor [Hedegård et al., J. Chem. Theory Comput., 2011, 7, 4077-4087]. Furthermore, a contraction scheme was proposed leading to very accurate, yet efficient basis sets for the elements Sc-Zn. Here this scheme is tested against a larger test set of molecules and a wider range of DFT functionals. We further investigate the regular aug-cc-pVTZ and core-valence correlation aug-cc-pCVTZ basis sets as well as another core-property basis set, CP(PPP). While aug-cc-pVTZ-J provides hyperfine coupling constants that are almost identical to the converged series (aug-cc-pVTZ-Juc), we observe that not only the regular but also the core-valence correlation basis sets provide results far from the converged results. The usage of specialized core-basis sets leads to a large and highly significant improvement of the calculated hyperfine couplings in comparison with experimental data.
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Affiliation(s)
- Erik D Hedegård
- University of Southern Denmark, Institute for Physics, Chemistry and Pharmacy, Campusvej 55, Odense, Denmark.
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55
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de Oliveira P, Gomes M, Pires J. Core–valence Gaussian basis sets of double and triple zeta quality for Li to Ar. Applications in calculations of indirect nuclear spin–spin coupling constants. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.07.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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56
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Rusakova IL, Krivdin LB, Rusakov YY, Trofimov AB. Algebraic-diagrammatic construction polarization propagator approach to indirect nuclear spin–spin coupling constants. J Chem Phys 2012; 137:044119. [DOI: 10.1063/1.4737181] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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57
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Afonin AV, Pavlov DV, Ushakov IA, Keiko NA. Stereospecificity of (1) H, (13) C and (15) N shielding constants in the isomers of methylglyoxal bisdimethylhydrazone: problem with configurational assignment based on (1) H chemical shifts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50:502-510. [PMID: 22615146 DOI: 10.1002/mrc.3828] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 04/02/2012] [Accepted: 04/26/2012] [Indexed: 06/01/2023]
Abstract
In the (13) C NMR spectra of methylglyoxal bisdimethylhydrazone, the (13) C-5 signal is shifted to higher frequencies, while the (13) C-6 signal is shifted to lower frequencies on going from the EE to ZE isomer following the trend found previously. Surprisingly, the (1) H-6 chemical shift and (1) J(C-6,H-6) coupling constant are noticeably larger in the ZE isomer than in the EE isomer, although the configuration around the -CH═N- bond does not change. This paradox can be rationalized by the C-H⋯N intramolecular hydrogen bond in the ZE isomer, which is found from the quantum-chemical calculations including Bader's quantum theory of atoms in molecules analysis. This hydrogen bond results in the increase of δ((1) H-6) and (1) J(C-6,H-6) parameters. The effect of the C-H⋯N hydrogen bond on the (1) H shielding and one-bond (13) C-(1) H coupling complicates the configurational assignment of the considered compound because of these spectral parameters. The (1) H, (13) C and (15) N chemical shifts of the 2- and 8-(CH(3) )(2) N groups attached to the -C(CH(3) )═N- and -CH═N- moieties, respectively, reveal pronounced difference. The ab initio calculations show that the 8-(CH(3) )(2) N group conjugate effectively with the π-framework, and the 2-(CH(3) )(2) N group twisted out from the plane of the backbone and loses conjugation. As a result, the degree of charge transfer from the N-2- and N-8- nitrogen lone pairs to the π-framework varies, which affects the (1) H, (13) C and (15) N shieldings.
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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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58
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Kjaer H, Nielsen MR, Pagola GI, Ferraro MB, Lazzeretti P, P. A. Sauer S. Nuclear magnetic resonance J coupling constant polarizabilities of hydrogen peroxide: A basis set and correlation study. J Comput Chem 2012; 33:1845-53. [DOI: 10.1002/jcc.23013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 04/03/2012] [Accepted: 04/19/2012] [Indexed: 11/10/2022]
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59
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Abraham RJ, Leonard P, Tormena CF. (1) H NMR Spectra. Part 28: Proton chemical shifts and couplings in three-membered rings. A ring current model for cyclopropane and a novel dihedral angle dependence for (3) J(HH) couplings involving the epoxy proton. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50:305-313. [PMID: 22407746 DOI: 10.1002/mrc.3808] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 01/30/2012] [Accepted: 02/08/2012] [Indexed: 05/31/2023]
Abstract
The (1) H chemical shifts of selected three-membered ring compounds in CDCl(3) solvent were obtained. This allowed the determination of the substituent chemical shifts of the substituents in the three-membered rings and the long-range effect of these rings on the distant protons. The substituent chemical shifts of common substituents in the cyclopropane ring differ considerably from the same substituents in acyclic fragments and in cyclohexane and were modelled in terms of a three-bond (γ)-effect. For long-range protons (more than three bonds removed), the substituent effects of the cyclopropane ring were analysed in terms of the cyclopropane magnetic anisotropy and steric effect. The cyclopropane magnetic anisotropy (ring current) shift was modelled by (a) a single equivalent dipole perpendicular to and at the centre of the cyclopropane ring and (b) by three identical equivalent dipoles perpendicular to the ring placed at each carbon atom. Model (b) gave a more accurate description of the (1) H chemical shifts and was the selected model. After parameterization, the overall root mean square error for the dataset of 289 entries was 0.068 ppm. The anisotropic effects are significant for the cyclopropane protons (ca 1 ppm) but decrease rapidly with distance. The heterocyclic rings of oxirane, thiirane and aziridine do not possess a ring current. (3) J(HH) couplings of the epoxy ring proton with side-chain protons were obtained and shown to be dependent on both the H-C-C-H and H-C-C-O orientations. Both density functional theory calculations and a simple Karplus-type equation gave general agreement with the observed couplings (root mean square error 0.5 Hz over a 10-Hz range).
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Affiliation(s)
- Raymond J Abraham
- Department of Chemistry, University of Liverpool, Crown St, Liverpool, L69 7ZD, UK.
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60
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Kupka T, Nieradka M, Stachów M, Pluta T, Nowak P, Kjær H, Kongsted J, Kaminsky J. Basis Set Convergence of Indirect Spin–Spin Coupling Constants in the Kohn–Sham Limit for Several Small Molecules. J Phys Chem A 2012; 116:3728-38. [DOI: 10.1021/jp212588h] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Teobald Kupka
- Faculty of Chemistry, University of Opole, 45-052 Opole, Poland
| | | | - Michał Stachów
- Faculty of Chemistry, University of Opole, 45-052 Opole, Poland
| | - Tadeusz Pluta
- Institute of Chemistry, University of Silesia, 40-007 Katowice, Poland
| | - Piotr Nowak
- Technical University of Opole, Opole, Poland
| | - Hanna Kjær
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Jakub Kaminsky
- Institute of Organic Chemistry and Biochemistry, 166 10 Prague, Czech Republic
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61
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Tian C, Nie W, Borzov MV, Su P. High-Yield Thermolytic Conversion of Imidazolium Salts into Arduengo Carbene Adducts with BF3 and PF5. Organometallics 2012. [DOI: 10.1021/om201086d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chong Tian
- Key Laboratory of Synthetic
and Natural Chemistry of the Ministry of Education, College of Chemistry and Material Science, North-West University, Taibai Bei avenue
229, Xi’an 710069, People's Republic of China
| | - Wanli Nie
- Key Laboratory of Synthetic
and Natural Chemistry of the Ministry of Education, College of Chemistry and Material Science, North-West University, Taibai Bei avenue
229, Xi’an 710069, People's Republic of China
| | - Maxim V. Borzov
- Key Laboratory of Synthetic
and Natural Chemistry of the Ministry of Education, College of Chemistry and Material Science, North-West University, Taibai Bei avenue
229, Xi’an 710069, People's Republic of China
| | - Pengfei Su
- Xi’an Modern Chemistry Research Institute, East Zhangba road 168,
Xi’an 710065, People's Republic of China
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62
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Nath N, Lokesh, Suryaprakash N. Measurement and applications of long-range heteronuclear scalar couplings: recent experimental and theoretical developments. Chemphyschem 2012; 13:645-60. [PMID: 22302693 DOI: 10.1002/cphc.201100748] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 12/04/2011] [Indexed: 12/11/2022]
Abstract
The use of long-range heteronuclear couplings, in association with (1)H-(1)H scalar couplings and NOE restraints, has acquired growing importance for the determination of the relative stereochemistry, and structural and conformational information of organic and biological molecules. However, the routine use of such couplings is hindered by the inherent difficulties in their measurement. Prior to the advancement in experimental techniques, both long-range homo- and heteronuclear scalar couplings were not easily accessible, especially for very large molecules. The development of a large number of multidimensional NMR experimental methodologies has alleviated the complications associated with the measurement of couplings of smaller strengths. Subsequent application of these methods and the utilization of determined J-couplings for structure calculations have revolutionized this area of research. Problems in organic, inorganic and biophysical chemistry have also been solved by utilizing the short- and long-range heteronuclear couplings. In this minireview, we discuss the advantages and limitations of a number of experimental techniques reported in recent times for the measurement of long-range heteronuclear couplings and a few selected applications of such couplings. This includes the study of medium- to larger-sized molecules in a variety of applications, especially in the study of hydrogen bonding in biological systems. The utilization of these couplings in conjunction with theoretical calculations to arrive at conclusions on the hyperconjugation, configurational analysis and the effect of the electronegativity of the substituents is also discussed.
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Affiliation(s)
- Nilamoni Nath
- NMR Research Centre, Indian Institute of Science, Bangalore, India
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63
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Hopmann KH, Šebestík J, Novotná J, Stensen W, Urbanová M, Svenson J, Svendsen JS, Bouř P, Ruud K. Determining the Absolute Configuration of Two Marine Compounds Using Vibrational Chiroptical Spectroscopy. J Org Chem 2012; 77:858-69. [DOI: 10.1021/jo201598x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Jaroslav Šebestík
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166
10 Prague, Czech Republic
| | | | - Wenche Stensen
- Lytix Biopharma AS, Tromsø Research
Park, N-9294 Tromsø, Norway
| | | | | | | | - Petr Bouř
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166
10 Prague, Czech Republic
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64
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Faber R, Sauer SPA. On the discrepancy between theory and experiment for the F–F spin–spin coupling constant of difluoroethyne. Phys Chem Chem Phys 2012; 14:16440-7. [DOI: 10.1039/c2cp42198d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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65
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Jarmelo S, Marques DAS, Simões PN, Carvalho RA, Batista CMSG, Araujo-Andrade C, Gil MH, Fausto R. Experimental (IR/Raman and 1H/13C NMR) and Theoretical (DFT) Studies of the Preferential Conformations Adopted by l-Lactic Acid Oligomers and Poly(l-lactic acid) Homopolymer. J Phys Chem B 2011; 116:9-21. [DOI: 10.1021/jp205033c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S. Jarmelo
- Department of Chemistry, University of Coimbra, Coimbra 3004-535, Portugal
- Department of Chemical Engineering, University of Coimbra, Coimbra 3030-290, Portugal
| | - D. A. S. Marques
- Department of Chemical Engineering, University of Coimbra, Coimbra 3030-290, Portugal
| | - P. N. Simões
- Department of Chemical Engineering, University of Coimbra, Coimbra 3030-290, Portugal
| | - R. A. Carvalho
- Department of Life Sciences and Center for Neurosciences, University of Coimbra, Coimbra 3001-401, Portugal
| | - C. M. S. G. Batista
- Department of Chemical Engineering, University of Coimbra, Coimbra 3030-290, Portugal
| | - C. Araujo-Andrade
- Centro de Investigaciones en Óptica, A. C., Loma del Bosque No. 115, Col. Lomas del Campestre, 37150, León, Guanajuato 37150, Mexico
| | - M. H. Gil
- Department of Chemical Engineering, University of Coimbra, Coimbra 3030-290, Portugal
| | - R. Fausto
- Department of Chemistry, University of Coimbra, Coimbra 3004-535, Portugal
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66
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Kjær H, Sauer SPA. Pople Style Basis Sets for the Calculation of NMR Spin-Spin Coupling Constants: the 6-31G-J and 6-311G-J Basis Sets. J Chem Theory Comput 2011; 7:4070-6. [PMID: 26598352 DOI: 10.1021/ct200546q] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a modification of the small and popular Pople basis sets, 6-31G and 6-311G, for density functional theory calculations of Fermi contact dominated NMR indirect nuclear spin-spin coupling constants. These new basis sets, 6-31G-J and 6-311G-J, contain twice the number of contracted s-type functions but the same number of contracted p-type functions as the original Pople basis set. For our test set of 12 one-, two- and three-bond coupling constants, the new basis sets augmented with the standard diffuse and polarization functions, i.e., the 6-31+G*-J and 6-311++G**-J basis sets, lead to a maximum deviation of 5 and 2 Hz, respectively, compared to results obtained with the 6 or more times larger aug-pcJ-4 basis set. In correlated wave function calculations using the second-order polarization propagator approximation, the deviations with respect to the aug-ccJ-pVQZ basis set are 8 and 3 Hz and thus slightly larger.
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Affiliation(s)
- Hanna Kjær
- Department of Chemistry, University of Copenhagen , DK-2100 Copenhagen Ø, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen , DK-2100 Copenhagen Ø, Denmark
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67
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Afonin AV, Pavlov DV, Albanov AI, Levanova EP, Levkovskaya GG. Study of stereospecificity of 1H, 13C, 15N and 77Se shielding constants in the configurational isomers of the selenophene-2-carbaldehyde azine by NMR spectroscopy and MP2-GIAO calculations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2011; 49:740-748. [PMID: 22002712 DOI: 10.1002/mrc.2824] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 08/10/2011] [Accepted: 08/21/2011] [Indexed: 05/31/2023]
Abstract
In the (1)H and (13)C NMR spectra of selenophene-2-carbaldehyde azine, the (1)H-5, (13)C-3 and (13)C-5 signals of the selenophene ring are shifted to higher frequencies, whereas those of the (1)H-1, (13)C-1, (13)C-2 and (13)C-4 are shifted to lower frequencies on going from the EE to ZZ isomer or from the E moiety to the Z moiety of EZ isomer. The (15)N chemical shift is significantly larger in the EE isomer relative to the ZZ isomer and in the E moiety relative to the Z moiety of EZ isomer. A very pronounced difference (60-65 mg/g) between the (77)Se resonance positions is revealed in the studied azine isomers, the (77)Se peak being shifted to higher frequencies in the ZZ isomer and in the Z moiety of EZ isomer. The trends in the changes of the measured chemical shifts are reasonably reproduced by the GIAO calculations at the MP2 level of the (1)H, (13)C, (15)N and (77)Se shielding constants in the energy-favorable conformation with the syn orientation of both selenophene rings relative to the C = N groups. The NBO analysis suggests that such an arrangement of the selenophene rings may take place because of a higher energy of some intramolecular interactions.
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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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68
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Salvador P, Tsai IH(M, Dannenberg JJ. J-coupling constants for a trialanine peptide as a function of dihedral angles calculated by density functional theory over the full Ramachandran space. Phys Chem Chem Phys 2011; 13:17484-93. [PMID: 21897927 PMCID: PMC3538093 DOI: 10.1039/c1cp20520j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We present 13 (3)J, seven (2)J and four (1)J coupling constants (24 in all) calculated using B3LYP/D95** as a function of the φ and ψ Ramachandran dihedral angles of the acetyl(Ala)(3)NH(2) capped trialanine peptide over the entire Ramachandran space. With the exception of three of these J couplings, all show significant dependence upon both dihedral angles. For each J coupling considered, a two dimensional grid with respect to φ and ψ angles can be used to interpolate the values for any pair of φ and ψ values. Such simple interpolation is shown to be very accurate. Most of these calculated J couplings should prove useful for improving the accuracy of the determination of peptide and protein structures from NMR measurements in solution over that provided by the common procedure of treating the J couplings as functions of a single dihedral angle by means of Karplus-type fittings.
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Affiliation(s)
| | - I-Hsien (Midas) Tsai
- Department of Chemistry, City University of New York - Hunter College and the Graduate School, 695 Park Avenue, New York NY 10065; Institute of Computational Chemistry and Department of Chemistry, University of Girona, 17071 Girona (Catalonia)
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69
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Kupka T, Stachów M, Nieradka M, Kaminsky J, Pluta T, Sauer SPA. From CCSD(T)/aug-cc-pVTZ-J to CCSD(T) complete basis set limit isotropic nuclear magnetic shieldings via affordable DFT/CBS calculations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2011; 49:231-236. [PMID: 21387405 DOI: 10.1002/mrc.2738] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 01/12/2011] [Accepted: 01/13/2011] [Indexed: 05/30/2023]
Abstract
It is shown that a linear correlation exists between nuclear shielding constants for nine small inorganic and organic molecules (N(2), CO, CO(2), NH(3), CH(4), C(2)H(2), C(2)H(4), C(2)H(6) and C(6)H(6)) calculated with 47 methods (42 DFT methods, RHF, MP2, SOPPA, SOPPA(CCSD), CCSD(T)) and the aug-cc-pVTZ-J basis set and corresponding complete basis set results, estimated from calculations with the family of polarization-consistent pcS-n basis sets. This implies that the remaining basis set error of the aug-cc-pVTZ-J basis set is very similar in DFT and CCSD(T) calculations. As the aug-cc-pVTZ-J basis set is significantly smaller, CCSD(T)/aug-cc-pVTZ-J calculations allow in combination with affordable DFT/pcS-n complete basis set calculations the prediction of nuclear shieldings at the CCSD(T) level of nearly similar accuracy as those, obtained by fitting results obtained from computationally demanding pcS-n calculations at the CCSD(T) limit. A significant saving of computational efforts can thus be achieved by scaling inexpensive CCSD(T)/aug-cc-pVTZ-J calculations of nuclear isotropic shieldings with affordable DFT complete basis set limit corrections.
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Affiliation(s)
- Teobald Kupka
- Faculty of Chemistry, University of Opole, 45-052 Opole, Poland.
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70
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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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71
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Benda L, Schneider B, Sychrovský V. Calculating the Response of NMR Shielding Tensor σ(31P) and 2J(31P,13C) Coupling Constants in Nucleic Acid Phosphate to Coordination of the Mg2+ Cation. J Phys Chem A 2011; 115:2385-95. [DOI: 10.1021/jp1114114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ladislav Benda
- 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
| | - Bohdan Schneider
- Institute of Biotechnology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague 4, 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
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72
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Graves KS, Thamattoor DM, Rablen PR. Experimental and theoretical study of the 2-alkoxyethylidene rearrangement. J Org Chem 2011; 76:1584-91. [PMID: 21338136 DOI: 10.1021/jo1020536] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rearrangement of 2-ethoxyethylidene, generated photochemically from a nonnitrogenous precursor, leads to ethyl vinyl ether. Although this product could result, in principle, from a 1,2-hydrogen shift and/or a 1,2-ethoxy shift in the carbene, a deuterium labeling study indicates an essentially exclusive preference for hydrogen migration. The experimental results are in agreement with CCSD and W1BD calculations for the simpler 2-methoxyethylidene system that show a prohibitively large barrier for the methoxy shift and a negligible barrier for the hydride shift.
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Affiliation(s)
- Kimberly S Graves
- Department of Chemistry, Colby College, Waterville, Maine 04901, USA
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73
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Suardíaz R, Crespo-Otero R, Pérez C, Fabián JS, de la Vega JMG. Communication: Accurate determination of side-chain torsion angle χ1 in proteins: Phenylalanine residues. J Chem Phys 2011; 134:061101. [DOI: 10.1063/1.3553204] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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74
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Abraham RJ, Leonard P, Tormena CF. A 1H NMR and theoretical investigation of the conformations of some monosubstituted cyclobutanes. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2011; 49:23-29. [PMID: 21162138 DOI: 10.1002/mrc.2705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 10/27/2010] [Accepted: 10/29/2010] [Indexed: 05/30/2023]
Abstract
The complete analysis of the complex (1)H NMR spectra of some monosubstituted cyclobutanes was achieved to give all the (1)H chemical shifts and (n)J(HH) (n = 2, 3 and 4) coupling constants in these molecules. The substituent chemical shifts of the substituents in the cyclobutane ring differ significantly from those in acyclic systems. For example, the OH and the NH(2) groups in cyclobutanol and cyclobutylamine produce a large shielding of the hydrogens of the opposite CH(2) group of the ring compared with little effect on the comparable methylene protons of butane. These effects and the other (1)H shifts in the cyclobutanes were modelled successfully in the CHARGE program. The RMS error (calculated vs observed shifts) for the 34 (1)H shifts recorded was 0.053 ppm. The conformational equilibrium in these compounds between the axial and the equatorial conformers was obtained by comparing the observed and the calculated (4)J(HH) couplings. These couplings in cyclobutanes, in contrast to the corresponding (3)J(HH) couplings, show a pronounced orientation dependence; (4)J(eq-eq) is ca 5 Hz and (4)J(ax-ax) ca 0 Hz. The couplings in the individual conformers were calculated at the B3LYP/EPR-III level. The conformer energy differences ΔG(ax-eq) vary from 1.1 kcal mol(-1) for OH to 0.2 kcal mol(-1) for the CH(2)OH substituent. The values of the conformer energy differences are compared with the previous IR data and the corresponding theoretical values from molecular mechanics (MM) and DFT theory. Generally, good agreement is observed although both the MM and the DFT calculations deviate significantly from the observed values for some substituents.
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Affiliation(s)
- Raymond J Abraham
- Chemistry Department, University of Liverpool, Crown St, Liverpool L69 7ZD, UK.
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75
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Provasi PF, Sauer SPA. Optimized basis sets for the calculation of indirect nuclear spin-spin coupling constants involving the atoms B, Al, Si, P, and Cl. J Chem Phys 2010; 133:054308. [PMID: 20707533 DOI: 10.1063/1.3465553] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The aug-cc-pVTZ-J series of basis sets for indirect nuclear spin-spin coupling constants has been extended to the atoms B, Al, Si, P, and Cl. The basis sets were obtained according to the scheme previously described by Provasi et al. [J. Chem. Phys. 115, 1324 (2001)]. First, the completely uncontracted correlation consistent aug-cc-pVTZ basis sets were extended with four tight s and three tight d functions. Second, the s and p basis functions were contracted with the molecular orbital coefficients of self-consistent-field calculations performed with the uncontracted basis sets on the simplest hydrides of each atom. As a first illustration, we have calculated the one-bond indirect spin-spin coupling constants in BH(4)(-), BF, AlH, AlF, SiH(4), SiF(4), PH(3), PF(3), H(2)S, SF(6), HCl, and ClF at the level of density functional theory using the Becke three parameter Lee-Yang-Parr and the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes.
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Affiliation(s)
- Patricio F Provasi
- Department of Physics, University of Northeastern, Av. Libertad 5500, W 3404 AAS Corrientes, Argentina.
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76
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Afonin AV, Ushakov IA, Vashchenko AV, Kondrashov EV, Rulev AY. GIAO, DFT, AIM and NBO analysis of the N-H...O intramolecular hydrogen-bond influence on the 1J(N,H) coupling constant in push-pull diaminoenones. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:661-670. [PMID: 20661903 DOI: 10.1002/mrc.2643] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In the series of diaminoenones, large high-frequency shifts of the (1)H NMR of the N-H group in the cis-position relative to the carbonyl group suggests strong N-H...O intramolecular hydrogen bonding comprising a six-membered chelate ring. The N-H...O hydrogen bond causes an increase of the (1)J(N,H) coupling constant by 2-4 Hz and high-frequency shift of the (15)N signal by 9-10 ppm despite of the lengthening of the relevant N-H bond. These experimental trends are substantiated by gauge-independent atomic orbital and density functional theory calculations of the shielding and coupling constants in the 3,3-bis(isopropylamino)-1-(aryl)prop-2-en-1-one (12) for conformations with the Z- and E-orientations of the carbonyl group relative to the N-H group. The effects of the N-H...O hydrogen-bond on the NMR parameters are analyzed with the atoms-in-molecules (AIM) and natural bond orbital (NBO) methods. The AIM method indicates a weakening of the N-H...O hydrogen bond as compared with that of 1,1-di(pyrrol-2-yl)-2-formylethene (13) where N-H...O hydrogen bridge establishes a seven-membered chelate ring, and the corresponding (1)J(N,H) coupling constant decreases. The NBO method reveals that the LP(O) --> sigma*(N-H) hyperconjugative interaction is weakened on going from the six-membered chelate ring to the seven-membered one due to a more bent hydrogen bond in the former case. A dominating effect of the N-H bond rehybridization, owing to an electrostatic term in the hydrogen bonding, seems to provide an increase of the (1)J(N,H) value as a consequence of the N-H...O hydrogen bonding in the studied diaminoenones.
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77
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Afonin AV, Ushakov IA, Pavlov DV, Ivanov AV, Mikhaleva AI. Study of conformations and hydrogen bonds in the configurational isomers of pyrrole-2-carbaldehyde oxime by 1H, 13C and 15N NMR spectroscopy combined with MP2 and DFT calculations and NBO analysis. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:685-692. [PMID: 20623827 DOI: 10.1002/mrc.2650] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The (1)H, (13)C and (15)N NMR studies have shown that the E and Z isomers of pyrrole-2-carbaldehyde oxime adopt preferable conformation with the syn orientation of the oxime group with respect to the pyrrole ring. The syn conformation of E and Z isomers of pyrrole-2-carbaldehyde oxime is stabilized by the N-H...N and N-H...O intramolecular hydrogen bonds, respectively. The N-H...N hydrogen bond in the E isomer causes the high-frequency shift of the bridge proton signal by about 1 ppm and increase the (1)J(N, H) coupling by approximately 3 Hz. The bridge proton shows further deshielding and higher increase of the (1)J(N, H) coupling constant due to the strengthening of the N-H...O hydrogen bond in the Z isomer. The MP2 calculations indicate that the syn conformation of E and Z isomers is by approximately 3.5 kcal/mol energetically less favorable than the anti conformation. The calculations of (1)H shielding and (1)J(N, H) coupling in the syn and anti conformations allow the contribution to these constants from the N-H...N and N-H...O hydrogen bondings to be estimated. The NBO analysis suggests that the N-H...N hydrogen bond in the E isomer is a pure electrostatic interaction while the charge transfer from the oxygen lone pair to the antibonding orbital of the N-H bond through the N-H...O hydrogen bond occurs in the Z isomer.
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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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78
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Pennanen TS, Lantto P, Hakala M, Vaara J. Nuclear magnetic resonance parameters in water dimer. Theor Chem Acc 2010. [DOI: 10.1007/s00214-010-0782-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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79
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Ethynylmonocarba-closo-dodecaborates: M[12-HCC-closo-1-CB11H11] and M[7,12-(HCC)2-closo-1-CB11H10] (M=Cs+, [Et4N]+). J Organomet Chem 2010. [DOI: 10.1016/j.jorganchem.2010.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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80
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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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81
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Kupka T, Stachów M, Nieradka M, Kaminsky J, Pluta T. Convergence of Nuclear Magnetic Shieldings in the Kohn-Sham Limit for Several Small Molecules. J Chem Theory Comput 2010; 6:1580-9. [PMID: 26615692 DOI: 10.1021/ct100109j] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Convergence patterns and limiting values of isotropic nuclear magnetic shieldings were studied for several small molecules (N2, CO, CO2, NH3, CH4, C2H2, C2H4, C2H6, and C6H6) in the Kohn-Sham limit. Individual results of calculations using dedicated families of Jensen's basis sets (pcS-n and pcJ-n) were fitted toward the complete basis set limit (CBS) using a simple two-parameter formula. Several density functionals were used; calculated vibrational corrections (ZPV) applied; and, for comparison purposes, similar calculations performed using RHF, MP2, SOPPA, SOPPA(CCSD), and CCSD(T) methods and additionally, the aug-cc-pVTZ-J basis set. Finally, the CBS estimated results were critically compared with earlier reported literature data and experimental results. Among 42 studied DFT methods, the KTn and "pure" functionals produced the most accurate heavy atom isotropic nuclear shieldings.
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Affiliation(s)
- Teobald Kupka
- University of Opole, Faculty of Chemistry, Poland, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic, and University of Silesia, Institute of Chemistry, Katowice, Poland
| | - Michał Stachów
- University of Opole, Faculty of Chemistry, Poland, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic, and University of Silesia, Institute of Chemistry, Katowice, Poland
| | - Marzena Nieradka
- University of Opole, Faculty of Chemistry, Poland, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic, and University of Silesia, Institute of Chemistry, Katowice, Poland
| | - Jakub Kaminsky
- University of Opole, Faculty of Chemistry, Poland, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic, and University of Silesia, Institute of Chemistry, Katowice, Poland
| | - Tadeusz Pluta
- University of Opole, Faculty of Chemistry, Poland, Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic, and University of Silesia, Institute of Chemistry, Katowice, Poland
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82
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Yachmenev A, Yurchenko SN, Paidarová I, Jensen P, Thiel W, Sauer SPA. Thermal averaging of the indirect nuclear spin-spin coupling constants of ammonia: The importance of the large amplitude inversion mode. J Chem Phys 2010; 132:114305. [DOI: 10.1063/1.3359850] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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83
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Rusakov YY, Krivdin LB, Sauer SPA, Levanova EP, Levkovskaya GG. Structural trends of 77Se-1H spin-spin coupling constants and conformational behavior of 2-substituted selenophenes. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:44-52. [PMID: 19877126 DOI: 10.1002/mrc.2537] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Experimental measurements and second-order polarization propagator approach (SOPPA) calculations of (77)Se-(1)H spin-spin coupling constants together with theoretical energy-based conformational analysis in the series of 2-substituted selenophenes have been carried out. A new basis set optimized for the calculation of (77)Se-(1)H spin-spin coupling constants has been introduced by extending the aug-cc-pVTZ-J basis for selenium. Most of the spin-spin coupling constants under study, especially vicinal (77)Se-(1)H couplings, demonstrated a remarkable stereochemical behavior with respect to the internal rotation of the substituent in the 2-position of the selenophene ring, which is of major importance in the stereochemical studies of the related organoselenium compounds.
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Affiliation(s)
- Yury Yu Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia
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84
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85
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Kupka T. H2O, H2, HF, F2 and F2O nuclear magnetic shielding constants and indirect nuclear spin-spin coupling constants (SSCCs) in the BHandH/pcJ-n and BHandH/XZP Kohn-Sham limits. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:959-970. [PMID: 19681101 DOI: 10.1002/mrc.2500] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Good performance of segmented contracted basis sets XZP, where X = D, T, Q and 5, for obtaining H(2)O, H(2), HF, F(2) and F(2)O nuclear isotropic shielding constants in the BHandH Kohn-Sham basis set limit was shown. The results of two- and three-parameter complete basis set limit extrapolation schemes were compared with experimental results, earlier literature data and benchmark ab initio results. Similar convergence patterns of shieldings obtained from calculations using general purpose XZP basis sets and from polarization-consistent basis sets pcS-n and pcJ-n, where n = 0, 1, 2, 3 and 4, designed to accurately predict magnetic properties were observed. On the contrary, the SSCCs were more sensitive to the XZP basis set size and generally less accurate than those estimated using pcJ-n basis set family. The BHandH density functional markedly outperforms B3LYP method in predicting heavy atom shieldings and SSCCs values in the studied systems.
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Affiliation(s)
- Teobald Kupka
- Department of Chemistry, University of Opole, 48, Oleska Street, 45-052 Opole, Poland.
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86
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Kupka T. Complete basis set prediction of methanol isotropic nuclear magnetic shieldings and indirect nuclear spin-spin coupling constants (SSCC) using polarization-consistent and XZP basis sets and B3LYP and BHandH density functionals. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:674-683. [PMID: 19431153 DOI: 10.1002/mrc.2448] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Efficient B3LYP and BHandH density functionals were used to estimate methanol's nuclear magnetic isotropic shieldings and spin-spin coupling constants in the basis set limit. Polarization-consistent pcS-n and pcJ-n (n = 0, 1, 2, 3 and 4), and segmented contracted XZP, where X = D, T, Q and 5, basis sets were used and the results fitted with simple mathematical formulas. The performance of the methods was assessed from comparison with experiment and higher level calculations. 1J(CH) and 3J(HH) values were determined from very diluted solutions in deuterochloroform and compared with theoretical predictions. The agreement between complete basis set (CBS) density functional theory (DFT) predicted isotropic shieldings and spin-spin values and experiment was good. The BHandH/pcS-n methanol shieldings obtained using structures optimized at the same level of theory are approaching the accuracy of the advanced coupled-cluster-singles-doubles-approximate triples (CCSD(T)) calculations.
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Affiliation(s)
- Teobald Kupka
- Department of Chemistry, University of Opole, 45-052 Opole, Poland.
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87
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1,2-, 1,7- and 1,12-Dicarba-closo-dodecaborane(12) Derivatives Revisited by13C NMR Spectroscopy and DFT Calculations. First Observation of Isotope-Induced Chemical Shifts1Δ10/11B(13C), and the Signs and Magnitudes of Coupling Constants1J(13C,13C) and1J(13C,11B). Z Anorg Allg Chem 2009. [DOI: 10.1002/zaac.200900022] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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88
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Pérez-Hernández N, Alvarez-Cisneros C, Cerda-García-Rojas CM, Morales-Ríos MS, Joseph-Nathan P. Benzylic coupling constants in toluene derivatives by J doubling in the frequency domain and DFT calculations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:437-442. [PMID: 19229891 DOI: 10.1002/mrc.2411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The recently modified J doubling in the frequency domain method (MJDFDM) allowed the determination of (4, 5, 6)J(H, CH(3) ) in toluene, a series of 4-mono- and 3,5-disubstituted toluene derivatives, as well as in 4-picoline. The methyl and aromatic signals were subjected to successive deconvolution processes, which at the end led to singlet signals and afforded the corresponding coupling constant values with a high degree of accuracy. Density functional theory calculation of benzylic coupling constants by addition of the Fermi contact, the spin-dipole, the diamagnetic spin-orbit, and the paramagnetic spin-orbit terms revealed good agreement between predicted and measured values when the B3LYP/aug-cc-pVTZ level of theory was used. Evaluation of the substituent effect over the coupling constant was made for all studied compounds and some limitations of the methodology were evidenced.
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Affiliation(s)
- Nury Pérez-Hernández
- Escuela de Medicina, Universidad Autónoma del Estado de Hidalgo, Apartado 1-622, Pachuca, Hidalgo 42001, México
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89
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Experimental and theoretical investigation of 5-para-nitro-benzylidene-thiazolidine-2-thione-4-one molecule. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2008.12.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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90
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Mendoza-Espinoza JA, López-Vallejo F, Fragoso-Serrano M, Pereda-Miranda R, Cerda-García-Rojas CM. Structural reassignment, absolute configuration, and conformation of hypurticin, a highly flexible polyacyloxy-6-heptenyl-5,6-dihydro-2H-pyran-2-one. JOURNAL OF NATURAL PRODUCTS 2009; 72:700-708. [PMID: 19265396 DOI: 10.1021/np800447k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The structural reassignment, absolute configuration, and conformational behavior of the highly flexible natural product hypurticin (pectinolide E), 6S-[3'S,5'R,6'S-triacetoxy-1Z-heptenyl]-5S-acetoxy-5,6-dihydro-2H-pyran-2-one (1), were ascertained by a molecular modeling protocol, which includes extensive conformational searching, geometry optimization by DFT B3LYP/DGDZVP calculations, and comparison between the theoretical (DFT) and experimental (1)H-(1)H NMR coupling constants. Hyptolide (2), a related cytotoxic 5,6-dihydro-2H-pyran-2-one that increased the S phase of the HeLa cell cycle, was employed as a reference substance to validate the theoretical protocol designed to characterize the 3D properties of compound 1. The related synthetic derivative, tri-O-acetyl-3,6-dideoxy-d-glucose diphenyldithioacetal (14), was prepared by a six-step reaction sequence starting from d-glucose and served as an enantiopure building block to reinforce the structural and configurational assignment of 1. This protocol proved to be an important tool for the structural characterization of highly flexible bioactive polyoxygenated natural products.
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Affiliation(s)
- José Alberto Mendoza-Espinoza
- Departamento de Química y Programa de Posgrado en Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, DF, Mexico
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91
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92
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Khan E, Kempe R, Wrackmeyer B. Synthesis and molecular structures of 1-chloro-1-silacyclopent-2-enes. Combination of 1,2-hydroboration, 1,1-organoboration and protodeborylation. Appl Organomet Chem 2009. [DOI: 10.1002/aoc.1482] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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93
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Kupka T. Prediction of water's isotropic nuclear shieldings and indirect nuclear spin-spin coupling constants (SSCCs) using correlation-consistent and polarization-consistent basis sets in the Kohn-Sham basis set limit. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:210-221. [PMID: 19086009 DOI: 10.1002/mrc.2369] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Density functional theory (DFT) was used to estimate water's isotropic nuclear shieldings and indirect nuclear spin-spin coupling constants (SSCCs) in the Kohn-Sham (KS) complete basis set (CBS) limit. Correlation-consistent cc-pVxZ and cc-pCVxZ (x = D, T, Q, 5, and 6), and their modified versions (ccJ-pVxZ, unc-ccJ-pVxZ, and aug-cc-pVTZ-J) and polarization-consistent pc-n and pcJ-n (n = 0, 1, 2, 3, and 4) basis sets were used, and the results fitted with a simple mathematical formula. The performance of over 20 studied density functionals was assessed from comparison with the experiment. The agreement between the CBS DFT-predicted isotropic shieldings, spin-spin values, and the experimental values was good and similar for the modified correlation-consistent and polarization-consistent basis sets. The BHandH method predicted the most accurate (1)H, (17)O isotropic shieldings and (1)J(OH) coupling constant (deviations from experiment of about -0.2 and -1 ppm and 0.6 Hz, respectively). The performance of BHandH for predicting water isotropic shieldings and (1)J(OH) is similar to the more advanced methods, second-order polarization propagator approximation (SOPPA) and SOPPA(CCSD), in the basis set limit.
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Affiliation(s)
- Teobald Kupka
- Institute of Chemistry, University of Opole, 45-052 Opole, Poland.
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94
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Gauze GF, Basso EA, Contreras RH, Tormena CF. Effect of Sulfur Oxidation on the Transmission Mechanism of 4JHH NMR Coupling Constants in 1,3-Dithiane. J Phys Chem A 2009; 113:2647-51. [DOI: 10.1021/jp810981z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gisele F. Gauze
- Departamento de Química, Universidade Estadual de Maringá, CEP-87020-900, Maringá, PR, Brazil, Department of Physics, FCEyN, University of Buenos Aires and CONICET, Buenos Aires, Argentina, and Department of Organic Chemistry, Chemistry Institute, P.O. Box 6154, University of Campinas, UNICAMP, CEP: 13084-971 Campinas, SP, Brazil
| | - Ernani A. Basso
- Departamento de Química, Universidade Estadual de Maringá, CEP-87020-900, Maringá, PR, Brazil, Department of Physics, FCEyN, University of Buenos Aires and CONICET, Buenos Aires, Argentina, and Department of Organic Chemistry, Chemistry Institute, P.O. Box 6154, University of Campinas, UNICAMP, CEP: 13084-971 Campinas, SP, Brazil
| | - Rubén H. Contreras
- Departamento de Química, Universidade Estadual de Maringá, CEP-87020-900, Maringá, PR, Brazil, Department of Physics, FCEyN, University of Buenos Aires and CONICET, Buenos Aires, Argentina, and Department of Organic Chemistry, Chemistry Institute, P.O. Box 6154, University of Campinas, UNICAMP, CEP: 13084-971 Campinas, SP, Brazil
| | - Cláudio F. Tormena
- Departamento de Química, Universidade Estadual de Maringá, CEP-87020-900, Maringá, PR, Brazil, Department of Physics, FCEyN, University of Buenos Aires and CONICET, Buenos Aires, Argentina, and Department of Organic Chemistry, Chemistry Institute, P.O. Box 6154, University of Campinas, UNICAMP, CEP: 13084-971 Campinas, SP, Brazil
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95
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Afonin AV, Ushakov IA, Vashchenko AV, Simonenko DE, Ivanov AV, Vasil'tsov AM, Mikhaleva AI, Trofimov BA. C-H...N and C-H...O intramolecular hydrogen bonding effects in the 1H, 13C and 15N NMR spectra of the configurational isomers of 1-vinylpyrrole-2-carbaldehyde oxime substantiated by DFT calculations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:105-112. [PMID: 19006103 DOI: 10.1002/mrc.2358] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
According to the (1)H, (13)C and (15)N NMR spectroscopic data and DFT calculations, the E-isomer of 1-vinylpyrrole-2-carbaldehyde adopts preferable conformation with the anti-orientation of the vinyl group relative to the carbaldehyde oxime group and with the syn-arrangement of the carbaldehyde oxime group with reference to the pyrrole ring. This conformation is stabilized by the C-H...N intramolecular hydrogen bond between the alpha-hydrogen of the vinyl group and the oxime group nitrogen, which causes a pronounced high-frequency shift of the alpha-hydrogen signal in (1)H NMR (approximately 0.5 ppm) and an increase in the corresponding one-bond (13)C-(1)H coupling constant (ca 4 Hz). In the Z-isomer, the carbaldehyde oxime group turns to the anti-position with respect to the pyrrole ring. The C-H...O intramolecular hydrogen bond between the H-3 hydrogen of the pyrrole ring and the oxime group oxygen is realized in this case. Due to such hydrogen bonding, the H-3 hydrogen resonance is shifted to a higher frequency by about 1 ppm and the one-bond (13)C-(1)H coupling constant for this proton increases by approximately 5 Hz.
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Affiliation(s)
- Andrei V Afonin
- Irkutsk Institute of Chemistry, Favorsky Street 1, 664033 Irkutsk, Russia.
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96
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Contreras RH, Provasi PF, dos Santos FP, Tormena CF. Stereochemical dependence of NMR geminal spin-spin coupling constants. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:113-120. [PMID: 18991325 DOI: 10.1002/mrc.2359] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this work it was sought to explore the versatility of geminal spin-spin coupling constants, (2)J(XY) SSCCs, as probes for stereochemical studies. A set of compounds, where their experimental (2)J(XY) SSCCs through the X-C-Y molecular fragment are predicted to be sensitive to hyperconjugative interactions involving either bonding or antibonding orbitals containing the C carbon atom ('coupling pathway'), were analyzed. SSCC calculations were performed for some selected examples using the second order polarization propagator approximation (SOPPA) method or within the DFT-B3LYP framework. Hyperconjugative interactions were calculated within the Natural Bond Orbital (NBO) approach. Results are condensed in two qualitative rules: Rule I(M)-hyperconjugative interactions transferring charge into the coupling pathway yield a positive increase to the Fermi contact (FC), contribution to (2)K(XY) reduced spin-spin coupling constants (RSSCC), and Rule II(M)-hyperconjugative interactions transferring charge from the coupling pathway yield a negative increase to the FC contribution to (2)K(XY) RSSCC.
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Affiliation(s)
- Rubén H Contreras
- Department of Physics, FCEyN, University of Buenos Aires and CONICET, Buenos Aires, Argentina
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97
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Provasi PF, A. Sauer SP. Analysis of isotope effects in NMR one-bond indirect nuclear spin–spin coupling constants in terms of localized molecular orbitals. Phys Chem Chem Phys 2009; 11:3987-95. [DOI: 10.1039/b819376b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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98
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Alkorta I, Elguero J. How Aromaticity Affects the Chemical and Physicochemical Properties of Heterocycles: A Computational Approach. TOPICS IN HETEROCYCLIC CHEMISTRY 2008. [DOI: 10.1007/978-3-540-68343-8_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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99
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Finze M. Carba-closo-dodecaborates with One or Two Alkynyl Substituents Bonded to Boron. Inorg Chem 2008; 47:11857-67. [PMID: 18998671 DOI: 10.1021/ic801610b] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maik Finze
- Institut für Anorganische Chemie and Strukturchemie II, Heinrich-Heine-Universität Düsseldorf, Universitätsstraβe 1, 40225 Düsseldorf, Germany
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100
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Pedersoli S, Tormena CF, dos Santos FP, Contreras RH, Rittner R. Stereochemical behavior of 1JCH and 2JCH NMR coupling constants in α-substituted acetamides. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.04.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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