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Afonin AV, Rusinska-Roszak D. Quantification of hydrogen bond energy based on equations using spectroscopic, structural, QTAIM-based, and NBO-based descriptors which calibrated by the molecular tailoring approach. J Mol Model 2023; 30:18. [PMID: 38159168 PMCID: PMC10757697 DOI: 10.1007/s00894-023-05811-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
CONTEXT Hydrogen bonds critically influence the structure and properties of both organic molecules and biomolecules, as well as supramolecular assemblies. For this reason, the development and elaboration of methods for quantitative assessment of hydrogen bond energy is an urgent challenge. In this study, using a large series of hydroxycarbonyl aliphatic compounds with the O‒H···O = C intramolecular hydrogen bond, a bank of hydrogen bond descriptors was created, including spectroscopic, structural, QTAIM-based, and NBO-based parameters. It was shown that the O‒H vibration frequency, OH chemical shift as the spectroscopic descriptors, the O···H hydrogen bond length, O···O distance, and O‒H covalent bond length as the structural descriptors, the electron density and its Laplacian, electron potential energy density in the hydrogen bond critical point, the electron density at the ring critical point as the QTAIM-based descriptors change in a correlated manner. The same correlation is found in change of the charge transfer energy through a hydrogen bond, the occupancy of the O‒H bond antibonding orbital, the Wiberg indices of the O···H hydrogen bond, and the O‒H covalent bond, as well as the polarization of the O‒H bond, which are the NBO-based descriptors. It was also recognized that the specified descriptors from the spectroscopic, structural, QTAIM-based, and NBO-based categories are functionally related to the values of intramolecular hydrogen bond energy, quantified via the molecular tailoring approach. This allowed one to obtain a system of equations for quantitative estimation of intramolecular hydrogen bond energy based on the spectroscopic, structural, QTAIM, and NBO descriptors, which makes such quantification more dependable and reliable. METHODS To obtain the spectroscopic descriptors, the vibrational spectra and shielding constants were calculated using the GIAO method. Structural descriptors were obtained for the equilibrium geometry of molecules, calculated at the MP2(FC)/6-311 + + (2d,2p) level using the Gaussian 09 program. The QTAIM-based descriptors were calculated using the AIMAll program within the framework of the quantum theory "Atoms in Molecules." The NBO-based descriptors were calculated using the NBO 3.1 program implemented into Gaussian 09. To quantify the energy of intramolecular hydrogen bonds, molecular fragmentation was used within the molecular tailoring approach.
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Affiliation(s)
- Andrei V Afonin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Division of Russian Academy of Sciences, Irkutsk, Russia
| | - Danuta Rusinska-Roszak
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Poznan, Poland.
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Revealing the Reasons for Degeneration of Resonance-Assisted Hydrogen Bond on the Aromatic Platform: Calculations of Ortho-, Meta-, Para-Disubstituted Benzenes, and ( Z)-( E)-Olefins. Molecules 2023; 28:molecules28020536. [PMID: 36677595 PMCID: PMC9860835 DOI: 10.3390/molecules28020536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 01/06/2023] Open
Abstract
The energies of the O-H∙∙∙O=C intramolecular hydrogen bonds were compared quantitatively for the series of ortho-disubstituted benzenes and Z-isomers of olefins via a molecular tailoring approach. It was established that the hydrogen bond energy in the former series is significantly less than that in the latter one. The reason for lowering the hydrogen bond energy in the ortho-disubstituted benzenes compared to the Z-isomers of olefins is the decrease in the π-contribution to the total energy of the complex interaction, in which the hydrogen bond per se is enhanced by the resonance effect. By the example of the para- and meta-disubstituted benzenes, as well as E-isomers of olefins, it was explicitly shown that the aromatic ring is a much poorer conductor of the resonance effect compared to the double bond. The hydrogen bond in the ortho-disubstituted benzenes has a lower energy than a typical resonance-assisted hydrogen bond because the aromatic moiety cannot properly assist the hydrogen bond with a resonance effect. Thus, a hydrogen bond on an aromatic platform should fall into a special category, namely an aromaticity-assisted hydrogen bond, which is closer by nature to a simple hydrogen bond rather than to a resonance-assisted one.
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1-Methylimidazole as an Organic Catalyst for [3+3]-Cyclodimerization of Acylethynylpyrroles to Bis(acylmethylidene)dipyrrolo[1,2-a:1′,2′-d]pyrazines. Catalysts 2022. [DOI: 10.3390/catal12121604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Acylethynylpyrroles, now readily available by the cross-coupling of pyrroles with acylbromoacetylenes in solid Al2O3 media, in the presence of 1-methylimidazole underwent unprecedentedly easy (40–45 °C) cyclodimerization into bis(acylmethylidene)dipyrrolo[1,2-a:1′,2′-d]pyrazines in up to 51% yield. Some other organic and inorganic basic catalysts can also trigger this cyclodimerization, but less efficiently.
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Da Silva HC, Leite TOC, Rodrigues SC, De Carvalho BLC, Martins MT, Fiorot RG, Dias FRF, Campos V, Ferreira VF, Cunha AC, De Almeida WB. Theoretical Investigation of Regiodivergent Addition of Anilines and Phenolates to p-Benzoquinone Ring. ACS OMEGA 2022; 7:40241-40256. [PMID: 36385806 PMCID: PMC9647872 DOI: 10.1021/acsomega.2c04607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Two different products were obtained by the regiodivergent reaction of benzoquinone derivatives with phenolates and anilines: 3-aryloxybenzoquinone and 2-phenylamino-3-bromobenzoquinone. Calculated density functional theory free energies of reaction values corroborate the experimental observation of the formation of the substitution product in the reaction with phenolates in acetonitrile and the product of addition/oxidation for the reaction with aniline in water. Calculated charges and Fukui functions are similar for C2 and C3 atoms, indicating an equal possibility to suffer a nucleophilic attack. The calculated energy barriers for nucleophilic attack steps indicated that the first steps of the substitution with phenolates and addition/oxidation with anilines are faster, which justifies the formation of the respective products. The natural bond order analysis for the transition states revealed that there is a strong interaction between lone pairs of N and O atoms and the πC2C3 * for the O → C2 and N → C3 attacks and a weak interaction for the O → C3 and N → C2 attacks, which also agrees with experimental observations.
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Affiliation(s)
- Haroldo C. Da Silva
- Laboratório
de Química Computacional e Modelagem Molecular, Departamento
de Química Inorgânica, Universidade
Federal Fluminense, Campus do Valonguinho, Outeiro de São João Batista,
s/n, Niterói24020-150, RJ, Brazil
| | - Talita O. C. Leite
- Faculdades
Integradas Maria Thereza, Av. Visconde do Rio Branco, Niterói24020004, RJ, Brazil
| | - Searitha C. Rodrigues
- Departamento
de Química Orgânica, Universidade
Federal Fluminense, Campus
do Valonguinho, Outeiro de São João Batista, s/n, Niterói24020-141, RJ, Brazil
| | - Beatriz L. C. De Carvalho
- Departamento
de Química Orgânica, Universidade
Federal Fluminense, Campus
do Valonguinho, Outeiro de São João Batista, s/n, Niterói24020-141, RJ, Brazil
| | - Maria Tereza Martins
- Departamento
de Química Orgânica, Universidade
Federal Fluminense, Campus
do Valonguinho, Outeiro de São João Batista, s/n, Niterói24020-141, RJ, Brazil
| | - Rodolfo G. Fiorot
- Departamento
de Química Orgânica, Universidade
Federal Fluminense, Campus
do Valonguinho, Outeiro de São João Batista, s/n, Niterói24020-141, RJ, Brazil
| | - Flaviana R. F. Dias
- Departamento
de Química Orgânica, Universidade
Federal Fluminense, Campus
do Valonguinho, Outeiro de São João Batista, s/n, Niterói24020-141, RJ, Brazil
| | - Vinícius
R. Campos
- Departamento
de Química Orgânica, Universidade
Federal Fluminense, Campus
do Valonguinho, Outeiro de São João Batista, s/n, Niterói24020-141, RJ, Brazil
| | - Vitor F. Ferreira
- Faculdade
de Farmácia, Departamento de Tecnologia Farmacêutica,
Programa de Pós-Graduação em Química, Universidade Federal Fluminense, Outeiro de São João Batista, s/n, Niterói24241-000, RJ, Brazil
| | - Anna C. Cunha
- Departamento
de Química Orgânica, Universidade
Federal Fluminense, Campus
do Valonguinho, Outeiro de São João Batista, s/n, Niterói24020-141, RJ, Brazil
| | - Wagner B. De Almeida
- Laboratório
de Química Computacional e Modelagem Molecular, Departamento
de Química Inorgânica, Universidade
Federal Fluminense, Campus do Valonguinho, Outeiro de São João Batista,
s/n, Niterói24020-150, RJ, Brazil
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Krivdin LB. Computational 1 H and 13 C NMR in structural and stereochemical studies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:733-828. [PMID: 35182410 DOI: 10.1002/mrc.5260] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Present review outlines the advances and perspectives of computational 1 H and 13 C NMR applied to the stereochemical studies of inorganic, organic, and bioorganic compounds, involving in particular natural products, carbohydrates, and carbonium ions. The first part of the review briefly outlines theoretical background of the modern computational methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the achievements of the computational 1 H and 13 C NMR in the stereochemical investigation of a variety of inorganic, organic, and bioorganic compounds, providing in an abridged form the material partly discussed by the author in a series of parent reviews. Major attention is focused herewith on the publications of the recent years, which were not reviewed elsewhere.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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Kawada M, Tsuyusaki R, Nakashima K, Akutsu H, Hirashima SI, Matsumoto T, Yanai H, Miura T. Diaminomethylenemalononitrile as a Chiral Single Hydrogen Bond Catalyst: Application to Enantioselective Conjugate Addition of α-Branched Aldehydes. Chem Asian J 2021; 16:2272-2275. [PMID: 34216113 DOI: 10.1002/asia.202100487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/22/2021] [Indexed: 11/09/2022]
Abstract
An improved diaminomethylenemalononitrile organocatalyst, bearing a N,N-disubstituted structure, promoted enantioselective conjugate addition reaction of α-branched aldehydes with vinyl sulfone, affording adducts with excellent enantioselectivities (up to 96% ee). Mechanistic studies revealed that the diaminomethylenemalononitrile motif holds the vinyl sulfone substrate using a single hydrogen bond accompanied by multiple weak interactions, including electrostatic C-H⋅⋅⋅O interactions.
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Affiliation(s)
- Masahiro Kawada
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Ryo Tsuyusaki
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Kosuke Nakashima
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Hiroshi Akutsu
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Shin-Ichi Hirashima
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Takashi Matsumoto
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Hikaru Yanai
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Tsuyoshi Miura
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
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Krivdin LB. Theoretical calculations of carbon-hydrogen spin-spin coupling constants. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 108:17-73. [PMID: 30538048 DOI: 10.1016/j.pnmrs.2018.10.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 06/09/2023]
Abstract
Structural applications of theoretical calculations of carbon-hydrogen spin-spin coupling constants are reviewed covering papers published mainly during the last 10-15 years with a special emphasis on the most notable studies of hybridization, substitution and stereoelectronic effects together with the investigation of hydrogen bonding and intermolecular interactions. The wide scope of different applications of calculated carbon-hydrogen couplings in the structural elucidation of particular classes of organic and bioorganic molecules is reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives, as well as on natural compounds and carbohydrates. The review is dedicated to Professor Emeritus Michael Barfield in view of his invaluable pioneering contribution to this field.
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Affiliation(s)
- Leonid B Krivdin
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia.
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Kondrashov EV, Oznobikhina LP, Aksamentova TN, Chipanina NN, Romanov AR, Rulev AY. Basicity of the polydentate captodative aminoenones. Ab initio
, DFT, and FTIR study. J PHYS ORG CHEM 2016. [DOI: 10.1002/poc.3532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- E. V. Kondrashov
- A. E. Favorsky Institute of Chemistry; Siberian Branch of the Russian Academy of Sciences; 1 Favorsky St. 664033 Irkutsk Russia
| | - L. P. Oznobikhina
- A. E. Favorsky Institute of Chemistry; Siberian Branch of the Russian Academy of Sciences; 1 Favorsky St. 664033 Irkutsk Russia
| | - T. N. Aksamentova
- A. E. Favorsky Institute of Chemistry; Siberian Branch of the Russian Academy of Sciences; 1 Favorsky St. 664033 Irkutsk Russia
| | - N. N. Chipanina
- A. E. Favorsky Institute of Chemistry; Siberian Branch of the Russian Academy of Sciences; 1 Favorsky St. 664033 Irkutsk Russia
| | - A. R. Romanov
- A. E. Favorsky Institute of Chemistry; Siberian Branch of the Russian Academy of Sciences; 1 Favorsky St. 664033 Irkutsk Russia
| | - A. Yu. Rulev
- A. E. Favorsky Institute of Chemistry; Siberian Branch of the Russian Academy of Sciences; 1 Favorsky St. 664033 Irkutsk Russia
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Trofimov BA, Andriyankova LV, Belyaeva KV, Nikitina LP, Afonin AV, Mal'kina AG. Ring-Opening of Pyridines with Acylacetylenes and Water: Straightforward Access to 5-[(Z)-Acylethenyl]amino-2,4-pentadienals. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Vashchenko AV, Afonin AV. A study of intramolecular hydrogen bonds C-H⋯X (X = N, O) within the theory of the electron localization function. J STRUCT CHEM+ 2015. [DOI: 10.1134/s002247661406002x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Lepodise LM, Horvat J, Lewis RA. Terahertz spectroscopy of 2,4-dinitrotoluene over a wide temperature range (7-245 K). J Phys Chem A 2015; 119:263-70. [PMID: 25565292 DOI: 10.1021/jp5052134] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previous THz spectroscopy of the TNT explosive precursor, 2,4-dinitrotoluene (DNT), has been restricted to room temperature (apart from one set of data at 11 K). Here, for the first time, we investigate the spectrum as the temperature is systematically varied, from 7 to 245 K. Many new features appear in the spectrum on cooling below room temperature. As well as the five absorption lines observed previously, we observe five additional lines. In addition, a new room-temperature line at 8.52 THz (281 cm(-1)) is observed. Six of the lines red-shift with temperature and four of them blue-shift. The blue shift is explained by interplay between intramolecular and intermolecular hydrogen bonds. The variation in line width and line intensity with temperature is not systematic, although a conspicuous decrease in line intensity with temperature is observed in all cases. Modeling with hybrid PBE0 and TPSSh functionals helps identify absorption modes.
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Affiliation(s)
- Lucia M Lepodise
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong , Wollongong, New South Wales 2522, Australia
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Vashchenko AV, Afonin AV. Comparative estimation of the energies of intramolecular C-H…O, N-H…O, and O-H…O hydrogen bonds according to the QTAIM analysis and NMR spectroscopy data. J STRUCT CHEM+ 2014. [DOI: 10.1134/s0022476614040076] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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Structural studies of meso-CF3-3(5)-aryl(hetaryl)- and 3,5-diaryl(dihetaryl)-BODIPY dyes by 1H, 13C and 19F NMR spectroscopy and DFT calculations. J Fluor Chem 2013. [DOI: 10.1016/j.jfluchem.2012.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Weinhold F. Natural bond critical point analysis: Quantitative relationships between natural bond orbital-based and QTAIM-based topological descriptors of chemical bonding. J Comput Chem 2012; 33:2440-9. [DOI: 10.1002/jcc.23057] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 05/16/2012] [Accepted: 06/13/2012] [Indexed: 11/09/2022]
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Ramalho TC, Pereira DH, Thiel W. Thermal and solvent effects on NMR indirect spin-spin coupling constants of a prototypical Chagas disease drug. J Phys Chem A 2011; 115:13504-12. [PMID: 21995614 DOI: 10.1021/jp201576u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
NMR J-couplings across hydrogen bonds reflect the static and dynamic character of hydrogen bonding. They are affected by thermal and solvent effects and can therefore be used to probe such effects. We have applied density functional theory (DFT) to compute the NMR (n)J(N,H) scalar couplings of a prototypical Chagas disease drug (metronidazole). The calculations were done for the molecule in vacuo, in microsolvated cluster models with one or few water molecules, in snapshots obtained from molecular dynamics simulations with explicit water solvent, and in a polarizable dielectric continuum. Hyperconjugative and electrostatic effects on spin-spin coupling constants were assessed through DFT calculations using natural bond orbital (NBO) analysis and atoms in molecules (AIM) theory. In the calculations with explicit solvent molecules, special attention was given to the nature of the hydrogen bonds formed with the solvent molecules. The results highlight the importance of properly incorporating thermal and solvent effects into NMR calculations in the condensed phase.
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Affiliation(s)
- Teodorico C Ramalho
- Department of Chemistry, Federal University of Lavras, Lavras, Minas Gerais, Brazil.
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Chizhov DL, Pervova MG, Samorukova MA, Khmara EF, Filyakova VI, Saloutin VI, Charushin VN. Trialkyl borate assisted amination of fluorinated 1,3-diketones for synthesis of N,N′-1,2-phenylen-bis(β-aminoenones) and their Ni(II), Cu(II) and Pd(II) complexes. J Fluor Chem 2011. [DOI: 10.1016/j.jfluchem.2011.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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